http://www.mdpi.com/journal/diversity Latest open access articles published in Diversity at http://www.mdpi.com/journal/diversity http://www.mdpi.com/1424-2818/5/2/352 While multifaceted, a chief aim when designating parks and protected areas is to support the preservation of biological diversity, in part, through representing and conserving the full range of landscape conditions observed throughout a representative area. Parks and protected areas are, however, typically developed using a static interpretation of current biodiversity and landscape conditions. The observed and potential climate change impacts to biodiversity have created a need to also contemplate how parks and protected areas will respond to climate change and how these areas will represent the future range of landscape conditions. To assess change in biodiversity, broad-scale ecosystem information can be sourced from indirect remotely sensed indicators. Quantifying biodiversity through indirect indicators allows characterization of inter-relationships between climate and biodiversity. Such characterizations support the assessment of possible implications of climatic change, as the indicators can be generated using modeled forecasts of future climatic conditions. In this paper we model and map impacts of climate change on British Columbia’s parks and protected areas by quantifying change in a number of remotely sensed indicators of biodiversity. These indicators are based on the measured amount of incoming solar energy used by vegetation and map the overall annual energy utilization, variability (seasonality), and latent or baseline energy. We compare current conditions represented by parks and protected areas, to those forecasted in the year 2065. Our results indicate that parks and protected areas are forecasted to become more productive and less seasonal, due to increased vegetation productivity in higher elevation environments. While increased vegetation productivity may be beneficial for biodiversity overall, these changes will be particularly problematic for sensitive and specialist species. Future gaps in vegetation conditions protected by parks and protected areas are observed in the eastern edge of the Rocky Mountains and the central interior region of British Columbia. Protected areas along the Coast Mountains, Vancouver Island highlands, and the Rocky Mountains show the greatest levels of change in the biodiversity indicators, including decreasing seasonality, with the Mountain Hemlock ecozone most at risk. Examples of large parks that are predicted to experience rapid change in vegetation characteristics include Strathcona, Garabaldi, and Kitlope. Our maps of future spatial distributions of indirect biodiversity indicators fill a gap in information products available for adaptive parks management and provide an opportunity for dialogue and further research on the use of future scenarios of landscape conditions in conservation planning. Diversity 2013-05-16 5 2 Article 10.3390/d5020352 352 373 1424-2818 2013-05-16 doi: 10.3390/d5020352 Keith Holmes Trisalyn Nelson Nicholas Coops Michael Wulder http://www.mdpi.com/1424-2818/5/2/335 Land cover change has been one of the major drivers of change leading to an alteration of critical habitats for many of the threatened species worldwide. Species with a narrow range and specialized habitats such as wetland ecosystems are at higher risk. The present paper describes spatial and temporal land use and cover change over the period of last 34 years (1976–2010) in the Koshi Tappu Wildlife Reserve (KTWR), Nepal. High spatial resolution Indian Remote-Sensing Satellite (IRS) Linear Imaging and Self Scanning Sensor (LISS-4) from 2005 and medium spatial resolution Landsat Multispectral Scanner (MSS) from 1976; Thematic Mapper (TM) from 1989; Enhanced Thematic Mapper Plus (ETM+) from 1999 and TM from 2010 were used to generate a land use/land cover map and change analysis. Acquired IRS LISS-4 and Landsat image was orthorectified into Universal Transverse Mercator (UTM), Zone 45 based on generated digital terrain model (DTM) from a topographic map and Ground Control Point (GCP) from the field. After rectifying all the images, eCognition developer software was used for object-based image analysis (OBIA). The change in the land cover and land use types were compared with the potential habitat of twenty globally significant species present in the reserve. The habitat information was collected from the literature and a map was prepared based on ‘presence’ data, habits and habitats used to identify their distribution pattern. The analysis revealed that the KTWR has gone through significant changes in land cover and ecosystems over the last 34 years due to the change in river course and anthropogenic pressure leading to direct change in habitats of the species. Forests have been reduced by 94% from their original state whereas the grassland has increased by 79% from its original state. On the basis of total land cover, forests, river and stream, swamp and marshes decreased by 16%, 14% and 3% respectively over the last 34 years whereas the grassland has increased by 45%. These ecosystems are also an important habitat for the majority of the species, which is resulting in habitat loss. Notably, the wetland ecosystems (marshes/swamps and river/streams), being one of the most important habitat for many globally threatened species, have changed by more than 30% from their original state in 1976. Based on the analysis, recommendations for management interventions were made. Diversity 2013-05-02 5 2 Article 10.3390/d5020335 335 351 1424-2818 2013-05-02 doi: 10.3390/d5020335 Nakul Chettri Kabir Uddin Sunita Chaudhary Eklabya Sharma http://www.mdpi.com/1424-2818/5/2/320 The northern Ethiopian landscape is dotted with small patches of church forests that are religious centers for the Ethiopian Orthodox Tewahido Church (EOTC). These sacred groves are what remain of the once vast tropical Afromontane dry forest. Herein we review the landscape pattern of sacred groves in the Amhara region of Ethiopia, and their local scale nutrient status at two sites, Zahara and Debresena. A total of 1,488 sacred groves were inventoried within the study area, yielding an overall density of one sacred grove for every twenty square kilometers. Sacred groves averaged a little over five hectares and were separated from one another by more than two kilometers. At the local scale we found that soil carbon and nitrogen stocks have decreased significantly between the forest interior and the clearing indicating decreased soil fertility. Together our data indicate that these sacred groves are vulnerable to loss because of their small average size, isolation from seed sources, and decreasing soil status. Diversity 2013-04-19 5 2 Article 10.3390/d5020320 320 334 1424-2818 2013-04-19 doi: 10.3390/d5020320 Catherine Cardelús Peter Scull Joshua Hair Maria Baimas-George Margaret Lowman Alemaheyu Eshete http://www.mdpi.com/1424-2818/5/2/293 Genetic diversity within species provides the raw material for adaptation and evolution. Just as regions of high species diversity are conservation targets, identifying regions containing high genetic diversity and divergence within and among populations may be important to protect future evolutionary potential. When multiple co-distributed species show spatial overlap in high genetic diversity and divergence, these regions can be considered evolutionary hotspots. We mapped spatial population genetic structure for 17 animal species across the Mojave Desert, USA. We analyzed these in concurrence and located 10 regions of high genetic diversity, divergence or both among species. These were mainly concentrated along the western and southern boundaries where ecotones between mountain, grassland and desert habitat are prevalent, and along the Colorado River. We evaluated the extent to which these hotspots overlapped protected lands and utility-scale renewable energy development projects of the Bureau of Land Management. While 30–40% of the total hotspot area was categorized as protected, between 3–7% overlapped with proposed renewable energy project footprints, and up to 17% overlapped with project footprints combined with transmission corridors. Overlap of evolutionary hotspots with renewable energy development mainly occurred in 6 of the 10 identified hotspots. Resulting GIS-based maps can be incorporated into ongoing landscape planning efforts and highlight specific regions where further investigation of impacts to population persistence and genetic connectivity may be warranted. Diversity 2013-04-15 5 2 Article 10.3390/d5020293 293 319 1424-2818 2013-04-15 doi: 10.3390/d5020293 Amy Vandergast Richard Inman Kelly Barr Kenneth Nussear Todd Esque Stacie Hathaway Dustin Wood Philip Medica Jesse Breinholt Catherine Stephen Andrew Gottscho Sharyn Marks W. Jennings Robert Fisher http://www.mdpi.com/1424-2818/5/2/276 Although changes in habitat area, driven by changes in sea level, have long been considered as a possible cause of marine diversity change in the Phanerozoic, the lack of Pleistocene extinction in the Californian Province has raised doubts, given the large and rapid sea-level changes during the Pleistocene. Neutral models of metacommunities presented here suggest that diversity responds rapidly to changes in habitat area, with relaxation times of a few hundred to a few thousand years. Relaxation time is controlled partly by metacommunity size, implying that different provinces or trophic levels might have measurably different responses to changes in habitable area. Geologically short relaxation times imply that metacommunities should be able to stay nearly in equilibrium with all but the most rapid changes in area. A simulation of the Californian Province during the Pleistocene confirms this, with the longest lags in diversity approaching 20 kyr. The apparent lack of Pleistocene extinction in the Californian Province likely results from the difficulty of sampling rare species, coupled with repopulation from adjacent deep-water or warm-water regions. Diversity 2013-04-15 5 2 Article 10.3390/d5020276 276 292 1424-2818 2013-04-15 doi: 10.3390/d5020276 Steven Holland http://www.mdpi.com/1424-2818/5/2/263 As marine environments change, the greatest ecological shifts—including resource usage and species interactions—are likely to take place in or near regions of biogeographic and phylogeographic transition. However, our understanding of where these transitional regions exist depends on the defining criteria. Here we evaluate phylogeographic transitions using a bootstrapping procedure that allows us to focus on either the strongest genetic transitions between a pair of contiguous populations, versus evaluation of transitions inclusive of the entire overlap between two intraspecific genetic lineages. We compiled data for the Atlantic coast of the United States, and evaluate taxa with short- and long-dispersing larval phases separately. Our results are largely concordant with previous biogeographic and phylogeographic analyses, indicating strong biotic change associated with the regions near Cape Cod, the Delmarva Peninsula, and eastern Florida. However, inclusive analysis of the entire range of sympatry for intraspecific lineages suggests that broad regions—the Mid-Atlantic Bight and eastern Florida–already harbor divergent intraspecific lineages, suggesting the potential for ecological evaluation of resource use between these lineages. This study establishes baseline information for tracking how such patterns change as predicted environmental changes take place. Diversity 2013-04-11 5 2 Article 10.3390/d5020263 263 275 1424-2818 2013-04-11 doi: 10.3390/d5020263 Safra Altman John Robinson James Pringle James Byers John Wares http://www.mdpi.com/1424-2818/5/2/240 The fundamental biodiversity number, θ, as proposed by Hubbell, should be positively correlated with province area. Because θ can be calculated from preserved relative abundance distributions, this correlation can be tested in the fossil record for regions with known provinces. Late Ordovician (443–458 Ma) strata of Laurentia are divided into four geochemically and biologically distinct regions that reflect provinces in the epicontinental sea. We use existing and newly obtained bed-level census data to test whether Hubbell’s θ is positively correlated with the area of these four regions, corresponding roughly to the Appalachian Basin, Cincinnati Arch, Upper Mississippi Valley, and western United States and Canada. Results indicate a positive relationship between province area and θ that suggests the influence of provincial area, among other factors, on diversity. This correlation highlights the inherent link between diversity and abundance structure at local and regional scales, such that changes at one scale will necessarily affect the other. Since diversity at these smaller spatial scales is an important component of global biodiversity, determining the nature of this relationship in the fossil record has implications for understanding how diversity is assembled globally throughout the Phanerozoic. Diversity 2013-04-10 5 2 Article 10.3390/d5020240 240 262 1424-2818 2013-04-10 doi: 10.3390/d5020240 Judith Sclafani Steven Holland http://www.mdpi.com/1424-2818/5/2/166 We describe and illustrate the biogeography of the cicadas inhabiting continental North America, north of Mexico. Species distributions were determined through our collecting efforts as well as label data from more than 110 institutional collections. The status of subspecies is discussed with respect to their distributions. As we have shown over limited geographic areas, the distribution of individual species is related to the habitat in which they are found. We discuss the biogeography of the genera with respect to their phylogenetic relationships. California is the state with the greatest alpha diversity (89 species, 46.6% of taxa) and unique species (35 species, 18.3% of taxa). Texas, Arizona, Colorado and Utah are the states with the next greatest alpha diversity with Texas, Arizona and Utah being next for unique species diversity. Maine, New Hampshire and Rhode Island are the states with the least amount of cicada diversity. Diversity is greatest in states and areas where there is a diversity of plant communities and habitats within these communities. Mountainous terrain also coincides with increases in diversity. Several regions of the focus area require additional collection efforts to fill in the distributions of several species. Diversity 2013-04-09 5 2 Article 10.3390/d5020166 166 239 1424-2818 2013-04-09 doi: 10.3390/d5020166 Allen Sanborn Polly Phillips http://www.mdpi.com/1424-2818/5/2/149 Defining units of conservation below the species level is a widely accepted conservation priority, but is especially challenging for widespread taxa that have experienced diverse geographic histories and exist across heterogenous environments. The lake chub (Pisces: Couesius plumbeus) is a widespread freshwater fish in North America and occurs from the southcentral USA to northwestern Alaska and Canada. We used mtDNA sequence analysis to test for divergent lineages predicted to occur as a result of survival of lake chub in distinct glacial refugia. Lake chub consisted of two major mtDNA lineages separated by 3.8% sequence divergence which are probably late to pre-Pleistocene in origin. We combined these data with those consistent with thermal adaptation in fish living in thermal springs versus those living in a lake with wide seasonal temperature variation, and with data on distribution of lake chub in major watershed units. We assessed these data against objective criteria developed to identify conservation units under Canadian endangered species legislation. Our analysis identified twelve major units of conservation within C. plumbeus that could be assessed under Canada’s Species-at-Risk Act. Our study illustrates how different character traits manifested at very different spatial scales can be used to define conservation units within widely-distributed taxa. Diversity 2013-04-02 5 2 Article 10.3390/d5020149 149 165 1424-2818 2013-04-02 doi: 10.3390/d5020149 Eric Taylor Charles-A. Darveau Patricia Schulte http://www.mdpi.com/1424-2818/5/1/139 The Wallacean island of Timor is of particular biological interest due to its relatively large size and transitional location between the Indo-Malayan and Australasian biogeographic realms. However, the origins and levels of endemism of its invertebrate fauna are poorly known. A recent study of Timorese ants revealed a diverse fauna with predominantly Indo-Malayan affinities, but species-level taxonomy was considered to be too poorly understood for an analysis of levels of endemism. The highly diverse Old World tropical genus Polyrhachis represents a notable exception, and here we analyse levels of endemism in the Polyrhachis fauna of Timor and surrounding islands. We supplement the species listed in the previous study with additional collections to record a total of 35 species of Polyrhachis from Timor and surrounding islands. Only 14 (40%) of the 35 species could be named (P. constricta, P. costulata, P. gab, P. sokolova, P. hera, P. illaudata, P. rixosa, P. acantha chrysophanes, P. saevissima, P. bicolor, P. cryptoceroides, P. dives, P. longipes and P. olybria), and the large majority of the remaining species have not previously been collected. These are very likely to be endemic to Timor and surrounding islands, and point to remarkably high levels (>50%) of endemism in the regional ant fauna. Diversity 2013-03-21 5 1 Article 10.3390/d5010139 139 148 1424-2818 2013-03-21 doi: 10.3390/d5010139 Alan Andersen Rudolf Kohout Colin Trainor http://www.mdpi.com/1424-2818/5/1/124 Here we investigate the interaction between ecology and climate concerning the distribution of rainforest species differentially distributed along altitudinal gradients of eastern Australia. The potential distributions of the two species closely associated with different rainforest types were modelled to infer the potential contribution of post-glacial warming on spatial distribution and altitudinal range shift. Nothofagus moorei is an integral element of cool temperate rainforest, including cloud forests at high elevation. This distinct climatic envelope is at increased risk with future global warming. Elaeocarpus grandis on the other hand is a lowland species and typical element of subtropical rainforest occupying a climatic envelope that may shift upwards into areas currently occupied by N. moorei. Climate envelope models were used to infer range shift differences between the two species in the past (21 thousand years ago), current and future (2050) scenarios, and to provide a framework to explain observed genetic diversity/structure of both species. The models suggest continuing contraction of the highland cool temperate climatic envelope and expansion of the lowland warm subtropical envelope, with both showing a core average increase in elevation in response to post-glacial warming. Spatial and altitudinal overlap between the species climatic envelopes was at a maximum during the last glacial maximum and is predicted to be a minimum at 2050. Diversity 2013-03-20 5 1 Article 10.3390/d5010124 124 138 1424-2818 2013-03-20 doi: 10.3390/d5010124 Rohan Mellick Peter Wilson Maurizio Rossetto http://www.mdpi.com/1424-2818/5/1/114 Climate change has created potential major threats to global biodiversity. The multiple components of climate change are projected to affect all pillars of biodiversity, from genes over species to biome level. Of particular concerns are “tipping points” where the exceedance of ecosystem thresholds will possibly lead to irreversible shifts of ecosystems and their functioning. As biodiversity underlies all goods and services provided by ecosystems that are crucial for human survival and wellbeing, this paper presents potential effects of climate change on biodiversity, its plausible impacts on human society as well as the setting in addressing a global crisis. Species affected by climate change may respond in three ways: change, move or die. Local species extinctions or a rapidly affected ecosystem as a whole respectively might move toward its particular “tipping point”, thereby probably depriving its services to human society and ending up in a global crisis. Urgent and appropriate actions within various scenarios of climate change impacts on biodiversity, especially in tropical regions, are needed to be considered. Foremost a multisectoral approach on biodiversity issues with broader policies, stringent strategies and programs at international, national and local levels is essential to meet the challenges of climate change impacts on biodiversity. Diversity 2013-03-07 5 1 Brief Report 10.3390/d5010114 114 123 1424-2818 2013-03-07 doi: 10.3390/d5010114 Fitria Rinawati Katharina Stein André Lindner http://www.mdpi.com/1424-2818/5/1/99 The accuracy of ten methods of scaling (Smalian, Huber, Newton, Neloïd, paraboloid, cone, paracone, cylinder, truncated cone and truncated Neloïd) was evaluated on logs of 0.5, 1, 2 and 3 m cut to different heights of 27 teak trees. For this purpose, the volumes estimated by the ten formulas were compared with real volumes obtained by the technique of xylometer. The results obtained showed that the method of Huber was more efficient to calculate the volume of logs throughout the stem when the length was 0.5 m. For the other length logs, it was also the best formula when the logs came from the base of the stem. The formulas of Newton and Smalian gave in the center and top of the stem, in the case of 1 m and 2 m logs, relatively similar results and were better than other methods of scaling. As might be expected, the dendrometric method (cylinder, paraboloid, Neloïd, cone) gave worse results regardless of the length of logs considered. With logs of 0.5, 1, 2 and 3 m long, truncated forms of cone and Neloïd could also be used without significant errors in estimating the volume of teak logs. The model scaling obtained for the entire tree expresses the logarithm of the volume against the logarithm of the diameter and the logarithm of height. Diversity 2013-03-05 5 1 Article 10.3390/d5010099 99 113 1424-2818 2013-03-05 doi: 10.3390/d5010099 Arcadius Akossou Soufianou Arzouma Eloi Attakpa Noël Fonton Kouami Kokou http://www.mdpi.com/1424-2818/5/1/73 Identifying a soil core microbiome is crucial to appreciate the established microbial consortium, which is not usually subjected to change and, hence, possibly resistant/resilient to disturbances and a varying soil context. Fungi are a major part of soil biodiversity, yet the mechanisms driving their large-scale ecological ranges and distribution are poorly understood. The degree of fungal community overlap among 16 soil samples from distinct ecosystems and distant geographic localities (truffle grounds, a Mediterranean agro-silvo-pastoral system, serpentine substrates and a contaminated industrial area) was assessed by examining the distribution of fungal ITS1 and ITS2 sequences in a dataset of 454 libraries. ITS1 and ITS2 sequences were assigned to 1,660 and 1,393 Operational Taxonomic Units (OTUs; as defined by 97% sequence similarity), respectively. Fungal beta-diversity was found to be spatially autocorrelated. At the level of individual OTUs, eight ITS1 and seven ITS2 OTUs were found in all soil sample groups. These ubiquitous taxa comprised generalist fungi with oligotrophic and chitinolytic abilities, suggesting that a stable core of fungi across the complex soil fungal assemblages is either endowed with the capacity of sustained development in the nutrient-poor soil conditions or with the ability to exploit organic resources (such as chitin) universally distributed in soils. Diversity 2013-02-21 5 1 Article 10.3390/d5010073 73 98 1424-2818 2013-02-21 doi: 10.3390/d5010073 Alberto Orgiazzi Valeria Bianciotto Paola Bonfante Stefania Daghino Stefano Ghignone Alexandra Lazzari Erica Lumini Antonietta Mello Chiara Napoli Silvia Perotto Alfredo Vizzini Simonetta Bagella Claude Murat Mariangela Girlanda http://www.mdpi.com/1424-2818/5/1/51 The predominant analytical approach to associate landscape patterns with gene flow processes is based on the association of cost distances with genetic distances between individuals. Mantel and partial Mantel tests have been the dominant statistical tools used to correlate cost distances and genetic distances in landscape genetics. However, the inherent high correlation among alternative resistance models results in a high risk of spurious correlations using simple Mantel tests. Several refinements, including causal modeling, have been developed to reduce the risk of affirming spurious correlations and to assist model selection. However, the evaluation of these approaches has been incomplete in several respects. To demonstrate the general reliability of the causal modeling approach with Mantel tests, it must be shown to be able to correctly identify a wide range of landscape resistance models as the correct drivers relative to alternative hypotheses. The objectives of this study were to (1) evaluate the effectiveness of the originally published causal modeling framework to support the correct model and reject alternative hypotheses of isolation by distance and isolation by barriers and to (2) evaluate the effectiveness of causal modeling involving direct competition of all hypotheses to support the correct model and reject all alternative landscape resistance models. We found that partial Mantel tests have very low Type II error rates, but elevated Type I error rates. This leads to frequent identification of support for spurious correlations between alternative resistance hypotheses and genetic distance, independent of the true resistance model. The frequency in which this occurs is directly related to the degree of correlation between true and alternative resistance models. We propose an improvement based on the relative support of the causal modeling diagnostic tests. Diversity 2013-02-18 5 1 Article 10.3390/d5010051 51 72 1424-2818 2013-02-18 doi: 10.3390/d5010051 Samuel Cushman Tzeidle Wasserman Erin Landguth Andrew Shirk http://www.mdpi.com/1424-2818/5/1/39 In the terrestrial environment, endemic species and isolated populations of widespread species have the highest rates of extinction partly due to their low genetic diversity. To determine if this pattern holds in the marine environment, we examined genetic diversity in endemic coral reef angelfishes and isolated populations of widespread species. Specifically, this study tested the prediction that angelfish (genus: Centropyge) populations at Christmas and Cocos Islands have low genetic diversity. Analyses of a 436 base pair fragment of the mtDNA control region revealed that the endemic C. joculator exhibited high haplotype (h > 0.98 at both locations) and nucleotide (Christmas p% = 3.63, Cocos p% = 9.99) diversity. Similarly, isolated populations of widespread angelfishes (C. bispinosa and C. flavicauda) had high haplotype (h > 0.98) and nucleotide (p% = 2.81 and p% = 5.78%, respectively) diversity. Therefore, in contrast to terrestrial patterns, endemic and isolated populations of widespread angelfishes do not have low genetic diversity, rather their haplotype and nucleotide diversities were among the highest reported for marine fishes. High genetic diversity should reduce extinction risk in these species as it could provide the evolutionary potential to adapt to the rapidly changing environmental conditions forecast for coral reefs. Diversity 2013-02-04 5 1 Article 10.3390/d5010039 39 50 1424-2818 2013-02-04 doi: 10.3390/d5010039 Jean-Paul Hobbs Lynne van Herwerden Dean Jerry Geoffrey Jones Philip Munday http://www.mdpi.com/1424-2818/5/1/26 Land-use degradation and climate change are well-known drivers of biodiversity loss, but little information is available about their potential interaction. Here, we focus on the effects of land-use and precipitation on ant diversity in cacao agroforestry. In Central Sulawesi, Indonesia, we selected 16 cacao agroforestry plots with a shaded vs. unshaded plot in each of eight villages differing in precipitation (1032–2051 mm annual rainfall). On each plot, 10 cacao trees with similar size and age (7–10 years) were selected for hand collection of ants on each cacao tree and the soil surface. In total, we found 80 ant species belonging to five subfamilies. Land-use intensification (removal of shade trees) and precipitation had no effect on species richness of ants per cacao tree (alpha diversity) and, in an additive partitioning approach, within-plot beta diversity. However, higher precipitation (but not shade) significantly increased ant species dissimilarity across cacao trees within a plot, with ant species showing contrasting responses to precipitation. Reduced precipitation causing drought stress appeared to contribute to convergence of ant community structure, presumably via reduced heterogeneity in cacao tree growth. In conclusion, reduced precipitation greatly influenced ant community dissimilarity and appeared to be more important for ant community structure than land-use intensification. Diversity 2013-01-31 5 1 Article 10.3390/d5010026 26 38 1424-2818 2013-01-31 doi: 10.3390/d5010026 Akhmad Rizali Yann Clough Damayanti Buchori Teja Tscharntke http://www.mdpi.com/1424-2818/5/1/15 One goal of the LIFE project “Del.Ta.” (NAT/IT/000163) was the preparation of an Action Plan to protect the bottlenose dolphin community in the Pelagie Archipelago (Sicily, Italy). It stressed the importance of regular monitoring of the spatial and temporal distribution of dolphins in order to evaluate the impact of local activities. This study assesses whether land-based surveys could be an effective alternative to vessel-based surveys. During the summer of 2006, both surveys’ methodologies were used at Lampedusa, with 35 sightings recorded from land and 31 from a boat. Comparison was based on the assessment of the type of information they provided in relation to the presence of the animals and their behavior. Both methodologies were applicable, but there were differences in their requirements, potential information generated, costs, and sensitivity to weather conditions. Vessel-based surveys require well trained observers and enable photo-identification and observation of social interaction and morphology. Animal movements, interactions with anthropogenic elements and group dynamics are better collected from land but spatial data can be documented up to 1 nautical mile from the coast. Weather conditions have a significant platform specific effect on sighting frequencies. The high sighting frequency during land surveys provides support for the development of zero-impact land-based dolphins watching activity. Diversity 2013-01-10 5 1 Article 10.3390/d5010015 15 25 1424-2818 2013-01-10 doi: 10.3390/d5010015 Cristina Giacoma Elena Papale Marta Azzolin http://www.mdpi.com/1424-2818/5/1/1 Mountain forest ecosystems in the Andes are threatened by deforestation. Increasing fire frequencies lead to fire-degraded habitats that are often characterized by a persistent fern-dominated vegetation. Little is known about the consequences of these drastic changes in habitat conditions for pollinator communities. In a rapid diversity assessment, we collected individuals of two major groups of insect pollinators (bees and butterflies/moths) with pan traps and compared pollinator diversities in a spatial block design between forest interior, forest edge and adjacent fire-degraded habitats at eight sites in the Bolivian Andes. We found that bee species richness and abundance were significantly higher in fire-degraded habitats than in forest habitats, whereas species richness and abundance of butterflies/moths increased towards the forests interior. Species turnover between forest and fire-degraded habitats was very high for both pollinator groups and was reflected by an increase in the body size of bee species and a decrease in the body size of butterfly/moth species in fire-degraded habitats. We conclude that deforestation by frequent fires has profound impacts on the diversity and composition of pollinator communities. Our tentative findings suggest shifts towards bee-dominated pollinator communities in fire-degraded habitats that may have important feedbacks on the regenerating communities of insect-pollinated plant species. Diversity 2012-12-27 5 1 Article 10.3390/d5010001 1 14 1424-2818 2012-12-27 doi: 10.3390/d5010001 Stephan Kambach Fernando Guerra Stephan Beck Isabell Hensen Matthias Schleuning http://www.mdpi.com/1424-2818/4/4/475 The practice of adding organic amendments to crop soils is undergoing resurgence as an efficient way to restore soil organic matter content and to improve soil quality. The quantity and quality of the organic matter inputs affect soil physicochemical properties and soil microbiota, influencing different parameters such as microbial biomass and diversity, community structure and microbial activities or functions. The influence of organic amendments on soil quality has also effects on crop production and plant health. The enhancement of soil suppressiveness using organic amendments has been widely described, especially for soil-borne diseases. However, there is great variability in the effectiveness of suppression depending on the nature of the amendment, the crop, the pathogen, and the environmental conditions. Although the effects of organic amendments on soil properties have been widely studied, relationships between these properties and soil suppressiveness are not still well understood. Changes in soil physicochemical parameters may modulate the efficacy of suppression. However, the parameters more frequently associated to disease suppression appear to be related to soil microbiota, such as microbial biomass and activity, the abundance of specific microbial groups and some hydrolytic activities. This review focuses on the effect of organic amendments on soil microbial populations, diversity and activities; their ability to enhance plant health through disease suppression; and which of the parameters affected by the organic amendments are potentially involved in soil suppressiveness. Diversity 2012-12-14 4 4 Review 10.3390/d4040475 475 491 1424-2818 2012-12-14 doi: 10.3390/d4040475 Nuria Bonilla José Gutiérrez-Barranquero Antonio Vicente Francisco Cazorla http://www.mdpi.com/1424-2818/4/4/453 Unicellular saprobic fungi (yeasts) inhabit soils worldwide. Although yeast species typically occupy defined areas on the biome scale, their distribution patterns within a single type of vegetation, such as forests, are more complex. In order to understand factors that shape soil yeast communities, soils collected underneath decaying wood logs and under forest litter were analyzed. We isolated and identified molecularly a total of 25 yeast species, including three new species. Occurrence and distribution of yeasts isolated from these soils provide new insights into ecology and niche specialization of several soil-borne species. Although abundance of typical soil yeast species varied among experimental plots, the analysis of species abundance and community composition revealed a strong influence of wood log deposition and leakage of organic carbon. Unlike soils underneath logs, yeast communities in adjacent areas harbored a considerable number of transient (phylloplane-related) yeasts reaching 30% of the total yeast quantity. We showed that distinguishing autochthonous community members and species transient in soils is essential to estimate appropriate effects of environmental factors on soil fungi. Furthermore, a better understanding of species niches is crucial for analyses of culture-independent data, and may hint to the discovery of unifying patterns of microbial species distribution. Diversity 2012-12-10 4 4 Article 10.3390/d4040453 453 474 1424-2818 2012-12-10 doi: 10.3390/d4040453 Andrey Yurkov Thorsten Wehde Tiemo Kahl Dominik Begerow http://www.mdpi.com/1424-2818/4/4/419 An approach to the management of marine biodiversity was developed based on two levels of environmental diagnostics: (1) the characterization (to identify types), and (2) the evaluation (to define status and values). Both levels involve the production of maps, namely: (i) morphobathymetry and sedimentology; (ii) habitats; (iii) natural emergencies; (iv) degradation and risk; (v) weighted vulnerability; (vi) environmental quality; and, (vii) susceptibility to use. A general methodological aspect that must be stated first is the need of dividing the mapped area in territorial units corresponding to submultiples of the UTM grid and having different sizes according to the scale adopted. Territorial units (grid cells) are assigned to one of five classes of evaluation, ranging from high necessity of conservation or protection to non-problematic, unimportant or already compromised (according to the specific map) situations. Depending on the scale, these maps are suited for territorial planning (small scales, allowing for a synoptic view) or for administration and decision making (large scales, providing detail on local situations and problems). Mapping should be periodically repeated (diachronic cartography) to assure an efficient tool for integrated coastal zone management. Diversity 2012-11-23 4 4 Abstract 10.3390/d4040419 419 452 1424-2818 2012-11-23 doi: 10.3390/d4040419 Carlo Bianchi Valeriano Parravicini Monica Montefalcone Alessio Rovere Carla Morri http://www.mdpi.com/1424-2818/4/4/396 The Wetlands Reserve Program (WRP) is one of several programs implemented by the United States Department of Agriculture to facilitate natural resource management on private lands. Since the WRP’s inception approximately 29,000 ha in California’s Central Valley (CCV) have been restored. However until now, actual benefits of the program to wildlife have never been evaluated. Hydrology in the CCV has been heavily modified and WRP wetlands are managed primarily to support wintering waterfowl. We surveyed over 60 WRP easements in 2008 and 2009 to quantify avian use and categorized bird species into 11 foraging guilds. We detected over 200 bird species in 2008 and 119 species in 2009, which is similar to or higher than numbers observed on other managed sites in the same area. We found that actively managed WRP wetlands support more waterfowl than sites under low or intermediate management, which is consistent with intended goals. Despite reported water shortages, greater upland and un-restored acreage in the southern CCV, WRP wetlands support large numbers of waterfowl and shorebirds, particularly in the early fall months. This is probably due to the severe lack of alternative habitat such as wildlife friendly crops at appropriate stages of the migration cycle. Improved access to water resources for hydrological management would greatly enhance waterfowl use in the southern CCV. Diversity 2012-11-23 4 4 Article 10.3390/d4040396 396 418 1424-2818 2012-11-23 doi: 10.3390/d4040396 Sharon Kahara Walter Duffy Ryan DiGaudio Rosemary Records http://www.mdpi.com/1424-2818/4/4/375 Agricultural management alters physical and chemical soil properties, which directly affects microbial life strategies and community composition. The microbial community drives important nutrient cycling processes that can influence soil quality, cropping productivity and environmental sustainability. In this research, a long-term agricultural experiment in a subtropical Acrisol was studied in south Brazil. The plots at this site represent two tillage systems, two nitrogen fertilization regimes and three crop rotation systems. Using Illumina high-throughput sequencing of the 16S rRNA gene, the archaeal and bacterial composition was determined from phylum to species level in the different plot treatments. The relative abundance of these taxes was correlated with measured soil properties. The P, Mg, total organic carbon, total N and mineral N were significantly higher in the no-tillage system. The microbial diversity was higher in the no-tillage system at order, family, genus and species level. In addition, overall microbial composition changed significantly between conventional tillage and no-tillage systems. Anaerobic bacteria, such as clostridia, dominate in no-tilled soil as well as anaerobic methanogenic archaea, which were detected only in the no-tillage system. Microbial diversity was higher in plots in which only cereals (oat and maize) were grown. Soil management influenced soil biodiversity on Acrisol by change of composition and abundance of individual species. Diversity 2012-10-31 4 4 Article 10.3390/d4040375 375 395 1424-2818 2012-10-31 doi: 10.3390/d4040375 Patricia Dorr de Quadros Kateryna Zhalnina Austin Davis-Richardson Jennie R. Fagen Jennifer Drew Cimelio Bayer Flavio A.O. Camargo Eric W. Triplett http://www.mdpi.com/1424-2818/4/4/363 We characterized soil communities in the Mojave Desert across an elevation gradient. Our goal was to test the hypothesis that as soil quality improved with increasing elevation (due to increased productivity), the diversity of soil prokaryotes and nematodes would also increase. Soil organic matter and soil moisture content increased with elevation as predicted. Soil salinity did not correlate to elevation, but was highest at a mid-gradient, alluvial site. Soil nematode density, community trophic structure, and diversity did not show patterns related to elevation. Similar results were obtained for diversity of bacteria and archaea. Relationships between soil properties, nematode communities, and prokaryotic diversity were site-specific. For example, at the lowest elevation site, nematode communities contained a high proportion of fungal-feeding species and diversity of bacteria was lowest. At a high-salinity site, nematode density was highest, and overall, nematode density showed an unexpected, positive correlation to salinity. At the highest elevation site, nematode density and species richness were attenuated, despite relatively high moisture and organic matter content for the soils. Our results support emerging evidence for the lack of a relationship between productivity and the diversity of soil nematodes and prokaryotes. Diversity 2012-10-15 4 4 Article 10.3390/d4040363 363 374 1424-2818 2012-10-15 doi: 10.3390/d4040363 Amy Treonis Kelsey Sutton Brendan Kavanaugh Archana Narla Timothy McLlarky Jasmine Felder Cecilia O’Leary Megan Riley Alyxandra Pikus Sarah Thomas http://www.mdpi.com/1424-2818/4/3/334 We compared forest floor depth, soil organic matter, soil moisture, anaerobic mineralizable nitrogen (a measure of microbial biomass), denitrification potential, and soil/litter arthropod communities among old growth, unthinned mature stands, and thinned mature stands at nine sites (each with all three stand types) distributed among three regions of Oregon. Mineral soil measurements were restricted to the top 10 cm. Data were analyzed with both multivariate and univariate analyses of variance. Multivariate analyses were conducted with and without soil mesofauna or forest floor mesofauna, as data for those taxa were not collected on some sites. In multivariate analysis with soil mesofauna, the model giving the strongest separation among stand types (P = 0.019) included abundance and richness of soil mesofauna and anaerobic mineralizable nitrogen. The best model with forest floor mesofauna (P = 0.010) included anaerobic mineralizable nitrogen, soil moisture content, and richness of forest floor mesofauna. Old growth had the highest mean values for all variables, and in both models differed significantly from mature stands, while the latter did not differ. Old growth also averaged higher percent soil organic matter, and analysis including that variable was significant but not as strong as without it. Results of the multivariate analyses were mostly supported by univariate analyses, but there were some differences. In univariate analysis, the difference in percent soil organic matter between old growth and thinned mature was due to a single site in which the old growth had exceptionally high soil organic matter; without that site, percent soil organic matter did not differ between old growth and thinned mature, and a multivariate model containing soil organic matter was not statistically significant. In univariate analyses soil mesofauna had to be compared nonparametrically (because of heavy left-tails) and differed only in the Siskiyou Mountains, where they were most abundant and species rich in old growth forests. Species richness of mineral soil mesofauna correlated significantly (+) with percent soil organic matter and soil moisture, while richness of forest floor mesofauna correlated (+) with depth of the forest floor. Composition of forest floor and soil mesofauna suggest the two groups represent a single community. Soil moisture correlated highly with percent soil organic matter, with no evidence for drying in sites that were sampled relatively late in the summer drought, suggesting losses of surface soil moisture were at least partially replaced by hydraulic lift (which has been demonstrated in other forests of the region). Diversity 2012-09-20 4 3 Article 10.3390/d4030334 334 362 1424-2818 2012-09-20 doi: 10.3390/d4030334 David A. Perry Robert P. Griffiths Andrew R. Moldenke Stephanie L. Madson http://www.mdpi.com/1424-2818/4/3/318 The distribution and species assembly of Japanese Protura collected from forest soils were examined using published databases and statistical analysis. We used records from 3110 sites where 71 taxa were found. The species richness of Protura ranged from one to 16 species, and TWINSPAN analysis of regional populations indicated that the northern and southern regions could be separated into distinct groups. Three major species assemblages were identified by cluster analysis from points containing more than six species. Three groups reflected historical migration from northern and western linkages to the Asian continent. The northern assemblage showed a negative correlation to winter minimum temperature and the other two assemblages exhibited relationships to precipitation and temperature. Vegetation was not responsible for proturan distribution. These results suggest that the history of Protura invasion explains the biogeography of these soil-based, small arthropods and also that climate change will induce a shift in the distribution of species irrespective of changes in vegetation type. Diversity 2012-08-31 4 3 Article 10.3390/d4030318 318 333 1424-2818 2012-08-31 doi: 10.3390/d4030318 Nobuhiro Kaneko Yukio Minamiya Osami Nakamura Masayuki Saito Minori Hashimoto http://www.mdpi.com/1424-2818/4/3/301 The Himalaya region of Nepal encompasses significant habitats for several endangered species, among them the brown bear (Ursus arctos pruinosus). However, owing to the remoteness of the region and a dearth of research, knowledge on the conservation status, habitat and population size of this species is lacking. Our aim in this paper is to report a habitat survey designed to assess the distribution and habitat characteristics of the brown bear in the Nepalese Himalaya, and to summarize a conservation action plan for the species devised at a pair of recent workshops held in Nepal. Results of our survey showed that brown bear were potentially distributed between 3800 m and 5500 m in the high mountainous region of Nepal, across an area of 4037 km2 between the eastern border of Shey Phoksundo National Park (SPNP) and the Manasalu Conservation Area (MCA). Of that area, 2066 km2 lie inside the protected area (350 km2 in the MCA; 1716 km2 in the Annapurna Conservation Area) and 48% (1917 km2) lies outside the protected area in the Dolpa district. Furthermore, 37% of brown bear habitat also forms a potential habitat for blue sheep (or bharal, Pseudois nayaur), and 17% of these habitats is used by livestock, suggesting a significant potential for resource competition. Several plant species continue to be uprooted by local people for fuel wood. Based on the results of our field survey combined with consultations with local communities and scientists, we propose that government and non-government organizations should implement a three-stage program of conservation activities for the brown bear. This program should: (a) Detail research activities in and outside the protected area of Nepal; (b) support livelihood and conservation awareness at local and national levels; and (c) strengthen local capacity and reduce human-wildlife conflict in the region. Diversity 2012-08-10 4 3 Article 10.3390/d4030301 301 317 1424-2818 2012-08-10 doi: 10.3390/d4030301 Achyut Aryal David Raubenheimer Sambandam Sathyakumar Buddi Sagar Poudel Weihong Ji Kamal Jung Kunwar Jose Kok Shiro Kohshima Dianne Brunton http://www.mdpi.com/1424-2818/4/3/258 Species migrating across boundaries represent the classic case for international cooperation in biodiversity conservation. Climate change is adding fresh challenges to such cooperation, on account of the shifting ranges and particular vulnerabilities to climate change of migratory wildlife. In view of the need to help migratory species adapt to climate change with minimal losses, this article performs an in-depth analysis of the present and potential future role in respect of climate adaptation of the main intergovernmental regime for migratory species conservation, the 1979 Bonn Convention on the Conservation of Migratory Species of Wild Animals (CMS) and its various daughter instruments. Diversity 2012-06-25 4 3 Article 10.3390/d4030258 258 300 1424-2818 2012-06-25 doi: 10.3390/d4030258 Arie Trouwborst http://www.mdpi.com/1424-2818/4/2/239 Wild barley [Hordeum vulgare ssp. spontaneum (C. Koch) Thell.] is a part of the primary gene pool with valuable sources of beneficial genes for barley improvement. This study attempted to develop a core subset of 269 accessions representing 16 countries from the Plant Gene Resources of Canada (PGRC) collection of 3,782 accessions, and to characterize them using barley simple sequence repeat (SSR) markers. Twenty-five informative primer pairs were applied to screen all samples and 359 alleles were detected over seven barley chromosomes. Analyses of the SSR data showed the effectiveness of the stratified sampling applied in capturing country-wise SSR variation. The frequencies of polymorphic alleles ranged from 0.004 to 0.708 and averaged 0.072. More than 24% or 7% SSR variation resided among accessions of 16 countries or two regions, respectively. Accessions from Israel and Jordan were genetically most diverse, while accessions from Lebanon and Greece were most differentiated. Four and five optimal clusters of accessions were obtained using STRUCTURE and BAPS programs and partitioned 16.3% and 20.3% SSR variations, respectively. The five optimal clusters varied in size from 15 to 104 and two clusters had only country-specific accessions. A genetic separation was detected between the accessions east and west of the Zagros Mountains only at the country, not the individual, level. These SSR patterns enhance our understanding of the wild barley gene pool, and are significant for conserving wild barley germplasm and exploring new sources of useful genes for barley improvement. Diversity 2012-06-14 4 2 Article 10.3390/d4020239 239 257 1424-2818 2012-06-14 doi: 10.3390/d4020239 Yong-Bi Fu Carolee Horbach http://www.mdpi.com/1424-2818/4/2/224 Governance of marine biodiversity has long suffered from lack of adequate information about the ocean’s many species and ecosystems. Nevertheless, even as we are learning much more about the ocean’s biodiversity and the impacts to it from stressors such as overfishing, habitat destruction, and marine pollution, climate change is imposing new threats and exacerbating existing threats to marine species and ecosystems. Coastal nations could vastly improve their fragmented approaches to ocean governance in order to increase the protections for marine biodiversity in the climate change era. Specifically, three key governance improvements would include: (1) incorporation of marine spatial planning as a key organizing principle of marine governance; (2) working to increase the resilience of marine ecosystems be reducing or eliminating existing stressors on those ecosystems; and (3) anticipation of climate change’s future impacts on marine biodiversity through the use of anticipatory zoning and more precautionary regulation. Diversity 2012-05-18 4 2 Article 10.3390/d4020224 224 238 1424-2818 2012-05-18 doi: 10.3390/d4020224 Robin Kundis Craig http://www.mdpi.com/1424-2818/4/2/196 In forest ecosystems, fungal mats are functionally important in nutrient and water uptake in litter and wood decomposition processes, in carbon resource allocation, soil weathering and in cycling of soil resources. Fungal mats can occur abundantly in forests and are widely distributed globally. We sampled ponderosa pine/white fir and mountain hemlock/noble fir communities at Crater Lake National Park for mat-forming soil fungi. Fungus collections were identified by DNA sequencing. Thirty-eight mat-forming genotypes were identified; members of the five most common genera (Gautieria, Lepiota, Piloderma, Ramaria, and Rhizopogon) comprised 67% of all collections. The mycorrhizal genera Alpova and Lactarius are newly identified as ectomycorrhizal mat-forming taxa, as are the saprotrophic genera Flavoscypha, Gastropila, Lepiota and Xenasmatella. Twelve typical mat forms are illustrated, representing both ectomycorrhizal and saprotrophic fungi that were found. Abundance of fungal mats was correlated with higher soil carbon to nitrogen ratios, fine woody debris and needle litter mass in both forest ecotypes. Definitions of fungal mats are discussed, along with some of the challenges in defining what comprises a fungal “mat”. Diversity 2012-04-24 4 2 Article 10.3390/d4020196 196 223 1424-2818 2012-04-24 doi: 10.3390/d4020196 Matthew J. Trappe Kermit Cromack Bruce A. Caldwell Robert P. Griffiths James M. Trappe http://www.mdpi.com/1424-2818/4/2/194 Written for anyone interested in green development—including policy makers, architects, developers, builders, and homeowners—this practical guide focuses on the central question of how to conserve biodiversity in neighborhoods and to minimize development impacts on surrounding habitats. The Green Leap specifically helps move green development beyond the design stage by thoroughly addressing construction and post-construction issues. [...] Diversity 2012-04-20 4 2 New Book Received 10.3390/d4020194 194 195 1424-2818 2012-04-20 doi: 10.3390/d4020194 Shu-Kun Lin http://www.mdpi.com/1424-2818/4/2/179 Our aim was to investigate species co-occurrence patterns in a large number of published biotic communities, in order to document to what extent species associations can be found in presence-absence matrices. We also aim to compare and evaluate two metrics that focus on species pairs (the ‘natural’ and the ‘checkerboard’ metric) using also artificial matrices. We applied the two metrics to many data sets from a huge variety of insular systems around the world. Both metrics reliably recover deviating species pairs and provide similar, albeit not identical, results. Nevertheless, only a few matrices exhibit significant deviations from random patterns, mostly vertebrates and higher plants. The benchmark cases cited in literature in favor of such assembly rules are indeed included in these exceptional cases. In conclusion, competitive or cooperative species interactions shaping communities cannot be inferred from patterns exhibited by presence-absence matrices. When such an analysis is attempted though, both the ‘natural’ and the ‘checkerboard’ metric should be set in a proper framework in order to provide useful insights regarding species associations. A large part of the discussion on species co-occurrence had originally been based on a few exceptional data sets that are not indicative of general patterns. Diversity 2012-04-17 4 2 Article 10.3390/d4020179 179 193 1424-2818 2012-04-17 doi: 10.3390/d4020179 Eva Pitta Sinos Giokas Spyros Sfenthourakis http://www.mdpi.com/1424-2818/4/2/164 Although flawed, the most powerful tool for protecting biodiversity in the United States is the Endangered Species Act, which requires the use of the best available science to ensure that endangered and threatened species are not put in jeopardy of extinction. Unfortunately, the best available science mandate is virtually meaningless and imposes no additional scientific rigor in agency decision making beyond what is normally required of administrative procedures. In this paper, we propose to define best available science in a way that shifts from a way of using science to a way of doing science, and a sound method of doing science for wildlife management and climate change is via the principles of adaptive management [1]. Adaptive management, as a means of data accumulation and continuous learning, can fulfill and give teeth to the best available science mandate while increasing the adaptive capacity of wildlife management agencies to protect biodiversity in an unpredictably dynamic environment. Diversity 2012-03-30 4 2 Article 10.3390/d4020164 164 178 1424-2818 2012-03-30 doi: 10.3390/d4020164 Olivia Odom Green Ahjond S. Garmestani http://www.mdpi.com/1424-2818/4/1/161 In the original version of our article [1], insufficient acknowledgement was given for the source of some of the DNA samples used. We apologize for the original error. To correct this oversight, Yvonne Willi has been added as an author, a recent paper by Willi, Y. et al. (2010) has been added, the acknowledgements have been altered to more appropriately recognize support and funding, and the sources of samples collected have been corrected in Table 1. [...] Diversity 2012-03-21 4 1 Correction 10.3390/d4010161 161 163 1424-2818 2012-03-21 doi: 10.3390/d4010161 Andrew Tedder Peter N. Hoebe Yvonne Willi Stephen W. Ansell Barbara K. Mable http://www.mdpi.com/1424-2818/4/1/105 Widespread coral reef decline has included the decline of reef fish populations, and the subsistence and artisanal fisheries that depend on them. Overfishing and destructive fishing have been identified as the greatest local threats to coral reefs, but the greatest future threats are acidification and increases in mass coral bleaching caused by global warming. Some reefs have shifted from dominance by corals to macroalgae, in what are called “phase shifts”. Depletion of herbivores including fishes has been identified as a contributor to such phase shifts, though nutrients are also involved in complex interactions with herbivory and competition. The depletion of herbivorous fishes implies a reduction of the resilience of coral reefs to the looming threat of mass coral mortality from bleaching, since mass coral deaths are likely to be followed by mass macroalgal blooms on the newly exposed dead substrates. Conventional stock assessment of each fish species would be the preferred option for understanding the status of the reef fishes, but this is far too expensive to be practical because of the high diversity of the fishery and poverty where most reefs are located. In addition, stock assessment models and fisheries in general assume density dependent populations, but a key prediction that stocks recover from fishing is not always confirmed. Catch Per Unit Effort (CPUE) has far too many weaknesses to be a useful method. The ratio of catch to stock and the proportion of catch that is mature depend on fish catch data, and are heavily biased toward stocks that are in good condition and incapable of finding species that are in the worst condition. Near-pristine reefs give us a reality check about just how much we have lost. Common fisheries management tools that control effort or catch are often prohibitively difficult to enforce for most coral reefs except in developed countries. Ecosystem-based management requires management of impacts of fishing on the ecosystem, but also vice versa. Marine Protected Areas (MPAs) have been a favorite management tool, since they require little information. MPAs are excellent conservation and precautionary tools, but address only fishing threats, and may be modest fisheries management tools, which are often chosen because they appear to be the only feasible alternative. “Dataless management” is based on qualitative information from traditional ecological knowledge and/or science, is sufficient for successful reef fisheries management, and is very inexpensive and practical, but requires either customary marine tenure or strong governmental leadership. Customary marine tenure has high social acceptance and compliance and may work fairly well for fisheries management and conservation where it is still strong. Diversity 2012-03-13 4 1 Review 10.3390/d4010105 105 160 1424-2818 2012-03-13 doi: 10.3390/d4010105 Douglas Fenner http://www.mdpi.com/1424-2818/4/1/94 Coral reefs are declining worldwide as a result of many anthropogenic disturbances. This trend is alarming because coral reefs are hotspots of marine biodiversity and considered the ‘rainforests of the sea. As in the rainforest, much of the diversity on a coral reef is cryptic, remaining hidden among the cracks and crevices of structural taxa. Although the cryptofauna make up the majority of a reef’s metazoan biodiversity, we know little about their basic ecology or how these communities respond to reef degradation. Emerging research shows that the species richness of the motile cryptofauna is higher among dead (framework) vs. live coral substrates and, surprisingly, increases within successively more eroded reef framework structures, ultimately reaching a maximum in dead coral rubble. Consequently, the paradigm that abundant live coral is the apex of reef diversity needs to be clarified. This provides guarded optimism amidst alarming reports of declines in live coral cover and the impending doom of coral reefs, as motile cryptic biodiversity should persist independent of live coral cover. Granted, the maintenance of this high species richness is contingent on the presence of reef rubble, which will eventually be lost due to physical, chemical, and biological erosion if not replenished by live coral calcification and mortality. The trophic potential of a reef, as inferred from the abundance of cryptic organisms, is highest on live coral. Among dead framework substrates, however, the density of cryptofauna reaches a peak at intermediate levels of degradation. In summary, the response of the motile cryptofauna, and thus a large fraction of the reef’s biodiversity, to reef degradation is more complex and nuanced than currently thought; such that species richness may be less sensitive than overall trophic function. Diversity 2012-02-15 4 1 Review 10.3390/d4010094 94 104 1424-2818 2012-02-15 doi: 10.3390/d4010094 Ian C. Enochs Derek P. Manzello http://www.mdpi.com/1424-2818/4/1/74 We summarize the factors that shaped the biodiversity of Chicago and its hinterland and point out the conservation significance of these ecological systems, addressing why conservation of Chicago’s biodiversity has importance locally and beyond. We highlight Chicago Wilderness (CW), a regional biodiversity conservation alliance committed to protecting nature and enriching the lives of the region’s residents. Chicago Wilderness, with over 250 institutional members, has for over a decade coordinated the efforts of diverse institutions, including federal, state, and local agencies, public land-management agencies, conservation organizations, and scientific and cultural institutions. Chicago Wilderness is committed to using science and emerging knowledge as a foundation for its conservation work. CW has several specialist teams that promote an interdisciplinary approach to conservation; we focus on the work of the CW Science Team, the one team with a research mission. The scientific investigations that are undertaken to provide a knowledge base for the work of Chicago Wilderness have drawn upon a wide variety of conservation paradigms, including that of resilience thinking, which we illustrate in a series of case studies. Diversity 2012-02-15 4 1 Review 10.3390/d4010074 74 93 1424-2818 2012-02-15 doi: 10.3390/d4010074 Liam Heneghan Christopher Mulvaney Kristen Ross Lauren Umek Cristy Watkins Lynne M. Westphal David H. Wise http://www.mdpi.com/1424-2818/4/1/59 Micro-relief heterogeneity can lead to substantial variability in microclimate and hence niche opportunities on a small scale. We explored the relationship between plant species richness and small-scale heterogeneity of micro-relief on the subtropical island of La Palma, Canary Islands. Overall, we sampled 40 plots in laurel and pine forests at four altitudinal bands. Species richness was recorded separately for various growth forms (i.e., mosses, herbaceous and woody plants). Site conditions such as altitude, slope, aspect, and tree density were measured. Micro-relief heterogeneity was characterized by surface structure and a subsequently derived surface heterogeneity index. The effect of micro-relief heterogeneity on species richness was analysed by means of linear mixed effect models and variance partitioning. Effects of micro-relief heterogeneity on species richness varied considerably between growth forms. While moss richness was affected significantly by micro-relief heterogeneity, herbaceous and woody plants richness responded mainly to larger-scale site conditions such as aspect and tree density. Our results stress the importance of small-scale relief heterogeneity for the explanation of spatial patterns of species richness. This poses new challenges as small-scale heterogeneity is largely underrepresented, e.g. with regard to its application in species distribution models. Diversity 2012-02-10 4 1 Article 10.3390/d4010059 59 73 1424-2818 2012-02-10 doi: 10.3390/d4010059 Benjamin F. Leutner Manuel J. Steinbauer Carina M. Müller Andrea J. Früh Severin Irl Anke Jentsch Carl Beierkuhnlein http://www.mdpi.com/1424-2818/4/1/33 While aboveground biomass and forest productivity can vary over abiotic gradients (e.g., temperature and moisture gradients), biotic factors such as biodiversity and tree species stand dominance can also strongly influence biomass accumulation. In this study we use a permanent plot network to assess variability in aboveground carbon (C) flux in forest tree annual aboveground biomass increment (ABI), tree aboveground net primary productivity (ANPPtree), and net soil CO2 efflux in relation to diversity of coniferous, deciduous, and a nitrogen (N)-fixing tree species (Alnus rubra). Four major findings arose: (1) overstory species richness and indices of diversity explained between one third and half of all variation in measured aboveground C flux, and diversity indices were the most robust models predicting measured aboveground C flux; (2) trends suggested decreases in annual tree biomass increment C with increasing stand dominance for four of the five most abundant tree species; (3) the presence of an N-fixing tree species (A. rubra) was not related to changes in aboveground C flux, was negatively related to soil CO2 efflux, and showed only a weak negative relationship with aboveground C pools; and (4) stands with higher overstory richness and diversity typically had higher soil CO2 efflux. Interestingly, presence of the N-fixing species was not correlated with soil inorganic N pools, and inorganic N pools were not correlated with any C flux or pool measure. We also did not detect any strong patterns between forest tree diversity and C pools, suggesting potential balancing of increased C flux both into and out of diverse forest stands. These data highlight variability in second-growth forests that may have implications for overstory community drivers of C dynamics. Diversity 2011-12-29 4 1 Article 10.3390/d4010033 33 58 1424-2818 2011-12-29 doi: 10.3390/d4010033 Justin L. Kirsch Dylan G. Fischer Alexandra N. Kazakova Abir Biswas Rachael E. Kelm David W. Carlson Carri J. LeRoy http://www.mdpi.com/1424-2818/4/1/1 A better knowledge of factors organizing crop genetic diversity in situ increases the efficiency of diversity analyses and conservation strategies, and requires collaboration between social and biological disciplines. Four areas of anthropology may contribute to our understanding of the impact of social factors on crop diversity: ethnobotany, cultural, cognitive and social anthropology. So far, most collaborative studies have been based on ethnobotanical methods, focusing on farmers’ individual motivations and actions, and overlooking the effects of farmer’s social organization per se. After reviewing common shortcomings in studies on sorghum and maize, this article analyzes how social anthropology, through the analysis of intermarriage, residence and seed inheritance practices, can contribute to studies on crop genetic diversity in situ. Crop varieties are thus considered social objects and socially based sampling strategies can be developed. Such an approach is justified because seed exchange is built upon trust and as such seed systems are embedded in a pre-existing social structure and centripetally oriented as a function of farmers’ social identity. The strong analogy between farmers’ cultural differentiation and crop genetic differentiation, both submitted to the same vertical transmission processes, allows proposing a common methodological framework for social anthropology and crop population genetics, where the classical interaction between genetic and environmental factors, G × E, is replaced by a three-way interaction G × E × S, where “S” stands for the social differentiation factors. Diversity 2011-12-21 4 1 Article 10.3390/d4010001 1 32 1424-2818 2011-12-21 doi: 10.3390/d4010001 Christian Leclerc Geo Coppens d’Eeckenbrugge http://www.mdpi.com/1424-2818/3/4/721 Modern molecular ecology techniques were used to demonstrate the effects of plant genotype and environmental conditions prior to harvest on the spinach epiphytic bacterial community. Three cultivars of spinach with different leaf topographies were collected at three different periods during the fall growing season. Leaf surface topography had an effect on diversity and number of culturable bacteria on the phylloepiphtyic community of spinach. Savoy cultivars, which had larger surface area and more stomata and glandular trichomes, where bacterial aggregates were observed, featured more diverse communities with increased richness and larger bacterial populations compared to flat-leaved cultivars. Bacterial community richness was compared using denaturant gradient gel electrophoresis (DGGE), while abundance was quantified using 16s rRNA primers for major phyla. The most diverse communities, both in richness and abundance, were observed during the first sampling period, immediately following a period of rapid spinach growth. Exposure to lower air and soil temperatures and decreased precipitation resulted in significantly reduced bacterial population size and bacterial community richness in November and December. This study describes the effect of the plant characteristics and environmental conditions that affect spinach microbiota population size and diversity, which might have implications in the survival of food and plant bacterial pathogens. Diversity 2011-12-20 3 4 Article 10.3390/d3040721 721 738 1424-2818 2011-12-20 doi: 10.3390/d3040721 Gabriela Lopez-Velasco Gregory E. Welbaum Joseph O. Falkinham III Monica A. Ponder http://www.mdpi.com/1424-2818/3/4/712 Symbiotic nitrogen fixation is one of the major pathways of N input to forest ecosystems, enriching N availability, particularly in lowland tropics. Recently there is growing concern regarding the wide areas of fast-growing leguminous plantations that could alter global N2O emissions. Here, we highlight substantially different N and phosphorus utilization and cycling at a plantation of Acacia mangium, which is N2-fixing and one of the major plantation species in tropical/subtropical Asia. The litterfall, fresh leaf quality and fine-root ingrowth of A. mangium were compared to those of non-N2-fixing Swietenia macrophylla and coniferous Araucaria cunninghamii in wet tropical climates in Borneo, Malaysia. The N and P concentrations of the A. mangium fresh leaves were higher than those of the other two species, whereas the P concentration in the leaf-litterfall of A. mangium was less than half that of the others; in contrast the N concentration was higher. The N:P ratio in the A. mangium leaf was markedly increased from fresh-leaf (29) to leaf-litterfall (81). Although the N flux in the total litterfall at the A. mangium plantation was large, the fine-root ingrowth of A. mangium significantly increased by applying both N and P. In conclusion, large quantities of N were accumulated and returned to the forest floor in A. mangium plantation, while its P resorption capacity was efficient. Such large N cycling and restricted P cycling in wide areas of monoculture A. mangium plantations may alter N and P cycling and their balance in the organic layer and soil on a stand level. Diversity 2011-11-28 3 4 Article 10.3390/d3040712 712 720 1424-2818 2011-11-28 doi: 10.3390/d3040712 Masahiro Inagaki Shigehiro Ishizuka http://www.mdpi.com/1424-2818/3/4/693 To analyze the impact of management choices on diversity in Pyrenean forests, we selected two ecological indicators: springtails; indicators of long-term responses to perturbation, and moths; which respond quickly to changes in their environment. Our data show that monoculture has a short-term impact on overall diversity and richness of species but with a relative resilience capacity of the forest ecosystem. More precisely, real impacts are visible on dynamics and abundances of certain species, depending on the vertical distribution of the biota and on the composition of soil and forest floor. Diversity 2011-11-18 3 4 Article 10.3390/d3040693 693 711 1424-2818 2011-11-18 doi: 10.3390/d3040693 Carine Luque Luc Legal Peter Winterton Nestor A. Mariano Charles Gers http://www.mdpi.com/1424-2818/3/4/660 Classification of cattle breeds contributes to our understanding of the history of cattle and is essential for an effective conservation of genetic diversity. Here we review the various classifications over the last two centuries and compare the most recent classifications with genetic data. The classifications devised during the 19th to the late 20th century were in line with the Linnaean taxonomy and emphasized cranial or horn morphology. Subsequent classifications were based on coat color, geographic origin or molecular markers. Several theories were developed that linked breed characteristics either to a supposed ancestral aurochs subspecies or to a presumed ethnic origin. Most of the older classifications have now been discarded, but have introduced several Latin terms that are still in use. The most consistent classification was proposed in 1995 by Felius and emphasizes the geographic origin of breeds. This is largely in agreement with the breed clusters indicated by a biochemical and molecular genetic analysis, which reflect either groups of breeds with a common geographic origin or single breeds that have expanded by export and/or crossbreeding. We propose that this information is also relevant for managing the genetic diversity of cattle. Diversity 2011-11-09 3 4 Review 10.3390/d3040660 660 692 1424-2818 2011-11-09 doi: 10.3390/d3040660 Marleen Felius Peter A. Koolmees Bert Theunissen European Cattle Genetic Diversity Consortium Johannes A. Lenstra http://www.mdpi.com/1424-2818/3/4/641 Jatropha curcas L. has become an important source of oil production for biodiesel fuel. Most genetic studies of this plant have been conducted with Asian and African accessions, where low diversity was encountered. There are no studies of this kind focusing in the postulated region of origin. Therefore, five populations of J. curcas were studied in the state of Chiapas, Mexico, using amplified fragment length polymorphism (AFLP) markers. One hundred and fifty-two useful markers were obtained: overall polymorphism = 81.18% and overall Nei’s genetic diversity (He) = 0.192. The most diverse population was the Border population [He: 0.245, Shanon’s information index (I): 0.378]. A cluster analysis revealed the highest dissimilarity coefficient (0.893) yet to be reported among accessions. An analysis of molecular variance (AMOVA) revealed that the greatest variation is within populations (87.8%), followed by the variation among populations (7.88%). The PhiST value (0.121) indicated moderate differentiation between populations. However, a spatial AMOVA (SAMOVA) detected a stronger genetic structure of populations, with a PhiST value of 0.176. To understand the fine structure of populations, an analysis of data with Bayesian statistics was conducted with software Structure©. The number of genetic populations (K) was five, with mixed ancestry in most individuals (genetic migrants), except in the Soconusco, where there was a tiny fraction of fragments from other populations. In contrast, SAMOVA grouped populations in four units. To corroborate the above findings, we searched for possible genetic barriers, determining as the main barrier that separating the Border from the rest of the populations. The results are discussed based on the possible ancestry of populations. Diversity 2011-10-28 3 4 Article 10.3390/d3040641 641 659 1424-2818 2011-10-28 doi: 10.3390/d3040641 Isidro Ovando-Medina Adriana Sánchez-Gutiérrez Lourdes Adriano-Anaya Francisco Espinosa-García Juan Núñez-Farfán Miguel Salvador-Figueroa http://www.mdpi.com/1424-2818/3/4/628 The decline of coral reefs in the Caribbean over the last 40 years has been attributed to multiple chronic stressors and episodic large-scale disturbances. This study assessed the resilience of coral communities in two different regions of the Florida Keys reef system between 1998 and 2002 following hurricane impacts and coral bleaching in 1998. Resilience was assessed from changes in coral abundance, diversity, disease, and bleaching prevalence in reefs near the remote off-shore islands of the Dry Tortugas compared to reefs near Key West, a center of high population density and anthropogenic influences. During the first assessment in spring 1998, Key West and Dry Tortugas coral communities had similar abundance, species diversity, and disease prevalence. Bleaching and disease significantly increased in all reef areas during the summer 1998 El Niño event, with Key West reefs exhibiting higher bleaching and disease prevalence and severity compared to Dry Tortugas. Acroporids and total coral abundance significantly declined in both regions during 1998 following mass-coral bleaching and hurricane impact, but remained reduced only on Key West reefs during the 5-year assessment. These results provide additional evidence that coral reef systems distant from anthropogenic influences may have greater resilience to large-scale disturbances. Diversity 2011-10-03 3 4 Article 10.3390/d3040628 628 640 1424-2818 2011-10-03 doi: 10.3390/d3040628 Deborah L. Santavy Erich M. Mueller Lauri MacLaughlin Esther C. Peters Robert L. Quarles Mace G. Barron http://www.mdpi.com/1424-2818/3/4/611 Urban environments pose special challenges to flora, including altered disturbance regimes, habitat fragmentation, and increased opportunity for invasion by non-native species. In addition, urban natural area represents most people’s contact with nature, given the majority of the world’s population currently live in cities. We used coefficients of conservatism (C-values), a system that ranks species based on perceived fidelity to remnant native plant communities that retain ecological integrity, to quantify habitat quality of 14 sites covering 850 ha within the city of Indianapolis, Indiana, in the Midwestern United States. All sites contained significant natural area and were inventoried via intensive complete censuses throughout one or two growing seasons within the last 15 years. Mean C-values for five sites were high, especially when compared to values reported for the highest quality preserves in central Indiana. However, for most sites the difference in mean C-value with and without non-natives was rather high, meaning that natural quality is likely to have been compromised by the presence of non-natives. Sites receiving the highest levels of stewardship and those with the least public access via trails had the highest mean native C-values. A total of 34 invasive non-native species were found across all 14 sites. Most were woody species. Mean C-value over all sites was significantly negatively correlated with the number of non-natives present, especially those considered invasive. These results demonstrate for the Indianapolis area, and likely other urbanized Midwestern cities, remnant natural areas can retain high ecological value, especially if they receive regular environmental stewardship. Diversity 2011-10-03 3 4 Article 10.3390/d3040611 611 627 1424-2818 2011-10-03 doi: 10.3390/d3040611 Rebecca W. Dolan Jessica D. Stephens Marcia E. Moore http://www.mdpi.com/1424-2818/3/4/592 Limited information is available on the bleaching susceptibility of coral species that dominate high latitude reefs along the eastern seaboard of Australia. The main aims of this study were to: (i) monitor coral health and spatial patterns of coral bleaching response at the Solitary Islands Marine Park (SIMP) and Lord Howe Island Marine Park (LHIMP), to determine variability of bleaching susceptibility among coral taxa; (ii) predict coral bleaching thresholds at 30 °S and 31.5 °S, extrapolated from published bleaching threshold data; and (iii) propose a subtropical northern New South Wales coral bleaching model from biological and physical data. Between 2005 and 2007 minor bleaching was observed in dominant coral families including Pocilloporidae, Poritidae and Dendrophylliidae in the SIMP and Pocilloporidae, Poritidae and Acroporidae (Isopora and Montipora spp.) in the LHIMP, with a clear difference in bleaching susceptibility found between sites, both within and between locations. Bleaching susceptibility was highest in Porites spp. at the most offshore island site within the SIMP during summer 2005. Patterns of subtropical family bleaching susceptibility within the SIMP and LHIMP differed to those previously reported for the central Great Barrier Reef (GBR). These differences may be due to a number of factors, including temperature history and/or the coral hosts association with different zooxanthellae clades, which may have lower thermal tolerances. An analysis of published estimates of coral bleaching thresholds from the Caribbean, South Africa, GBR and central and northern Pacific regions suggests that the bleaching threshold at 30–31.5 °S ranges between 26.5–26.8 °C. This predicted threshold was confirmed by an extensive coral bleaching event on the world’s southernmost coral reef at Lord Howe Island, during the 2010 austral summer season. These results imply that dominant coral taxa at subtropical reefs along the eastern Australian seaboard are highly susceptible to thermal stress; which, in turn, could lead to a future decline in total live coral cover if predicted rising seawater temperatures lead to more frequent coral bleaching events in future. Diversity 2011-09-30 3 4 Article 10.3390/d3040592 592 610 1424-2818 2011-09-30 doi: 10.3390/d3040592 Steven J. Dalton Andrew G. Carroll http://www.mdpi.com/1424-2818/3/4/581 Recently, the Census of Marine Life has explored methods to assess coral reef diversity by combining standardized sampling (to permit comparison across sites) with molecular techniques (to make rapid counts of species possible). To date, this approach has been applied across geographically broad scales (seven sites spanning the Indian, Pacific and Atlantic Oceans), focusing on similar habitats at all sites (10–12 m forereef). Here we examine crustacean spatial diversity patterns for a single atoll, comparing results for four sites (comprising forereef, backreef, and lagoon habitats) at French Frigate Shoals (FFS), Northwestern Hawaiian Islands, Hawaii, USA, within the Papahanaumokuakea Marine National Monument. The Bray-Curtis index of similarity across these habitats at FFS was the same or greater than the similarity between similar habitats on Heron Island and Lizard Island in the Great Barrier Reef and much greater than similarity between more widely separated localities in the Indo-Pacific Ocean (e.g., Ningaloo, Moorea, French Polynesia or the Line Islands). These results imply that, at least for shallow reefs, sampling multiple locations versus sampling multiple habitats within a site maximizes the rate at which we can converge on the best global estimate of coral reef biodiversity. Diversity 2011-09-29 3 4 Article 10.3390/d3040581 581 591 1424-2818 2011-09-29 doi: 10.3390/d3040581 Laetitia Plaisance Russell Brainard M. Julian Caley Nancy Knowlton http://www.mdpi.com/1424-2818/3/4/547 In an extensive screening, the antiviral, antitrypanosomal and anticancer properties of extracts from 82 plants used in traditional Chinese medicine and European phytomedicine were determined. Several promising plants that were highly effective against hepatitis B virus (HBV), bovine viral diarrhoea virus (BVDV)—a flavivirus used here as a surrogate in vitro model of hepatitis C virus, trypanosomes (Trypanosoma brucei brucei) and several cancer cell lines were identified. Six aqueous extracts from Celosia cristata, Ophioglossum vulgatum, Houttuynia cordata, Selaginella tamariscina, Alpinia galanga and Alpinia oxyphylla showed significant antiviral effects against BVDV without toxic effects on host embryonic bovine trachea (EBTr) cells, while Evodia lepta, Hedyotis diffusa and Glycyrrhiza spp. demonstrated promising activities against the HBV without toxic effects on host human hepatoblastoma cells transfected with HBV-DNA (HepG2 2.2.15) cells. Seven organic extracts from Alpinia oxyphylla, Coptis chinensis, Kadsura longipedunculata, Arctium lappa, Panax ginseng, Panax notoginseng and Saposhnikovia divaricata inhibited T. b. brucei. Moreover, among fifteen water extracts that combined high antiproliferative activity (IC50 0.5–20 µg/mL) and low acute in vitro toxicity (0–10% reduction in cell viability at IC50), Coptis chinensis presented the best beneficial characteristics. In conclusion, traditional herbal medicine from Europe and China still has a potential for new therapeutic targets and therapeutic applications. Diversity 2011-09-26 3 4 Article 10.3390/d3040547 547 580 1424-2818 2011-09-26 doi: 10.3390/d3040547 Florian Herrmann Marta R. Romero Alba G. Blazquez Dorothea Kaufmann Mohamed L. Ashour Stefan Kahl Jose J.G. Marin Thomas Efferth Michael Wink http://www.mdpi.com/1424-2818/3/3/531 The remnants of old-growth cedar forests in Lebanon are currently protected since they are taken to represent relic ecosystems sheltering many endemic, rare and endangered species. However, it is not always obvious how “natural” these forest relics are, and how the past use, conservation and management history have affected their current structural properties and species community composition. Even though Integrated Monitoring Programs have been initiated and developed, they are not being implemented effectively. The present research studied the effect of forest stand structure and the impacts of the anthropogenic activities effects on forest composition and floristic richness in four cedar forests in Lebanon. Horizontal and vertical structure was assessed by relying on the measurement of the physical characteristics and status of cedar trees including diversity and similarity indices. Two hundred and seventeen flora species were identified, among which 51 species were found to have biogeographical specificity and peculiar traits. The species composition seems not to be correlated with stand age structure; however, the occurrence of multiple age cedar stands favors floristic richness and variability in species composition as observed in one of the stands where the variation in diversity indices was high. In conclusion; to conserve biodiversity across landscapes, it is necessary to maintain a collection of stands of different vertical structure; an effect produced both by natural and anthropogenic disturbances since they both create a mosaic of different aged succession stands. Diversity 2011-09-21 3 3 Article 10.3390/d3030531 531 546 1424-2818 2011-09-21 doi: 10.3390/d3030531 Elsa Sattout Peter D. S. Caligari http://www.mdpi.com/1424-2818/3/3/503 Successfully addressing the multitude of stresses influencing forest catchments, their native biota, and the vital ecological services they provide humanity will require adapting an integrated view that incorporates the full range of natural and anthropogenic disturbances acting on these landscapes and their embedded fluvial networks. The concepts of dendritic networks, disturbance domains, the stream continuum, and hydrologic connectivity can facilitate this integration. Managing catchments based on these combined concepts would better maintain all the components of watersheds and the interacting processes that comprise their ecological integrity. To examine these ideas, I review riparian protection regulations in the Pacific Northwest of the United States, regulations considered by many to be among the best available, and evaluate their ability to protect headwater amphibians. I present evidence for the inadequacy of these rules to maintain robust populations of these amphibians, and discuss the implications of these shortcomings for downstream-dwelling coho salmon. Emphasizing headwaters (1st to 3rd-order channels), I discuss disturbance regimes and how differences in their fluvial and geomorphic processes determine the structuring of channels, their internal environments, and the composition of the resident biota. I examine amphibian dependence on specific channel attributes, and discuss links between their abundances, altered attribute states, and natural and anthropogenic disturbances. Using these examples, I discuss the limitations of current protections to maintain key attributes necessary to support robust populations of headwater amphibians, and via hydrologic connectivity, many downstream organisms. I propose that the goal of maintaining whole catchment biodiversity and ecological services could be improved by managing watersheds based on integrating science-based network organizing concepts and evaluating and adjusting outcomes with a suite of responsive bio-indicators. Diversity 2011-09-15 3 3 Review 10.3390/d3030503 503 530 1424-2818 2011-09-15 doi: 10.3390/d3030503 Hartwell H. Welsh Jr. http://www.mdpi.com/1424-2818/3/3/483 The maintenance of genetic diversity is a central goal of conservation. It is the raw material for evolutionary change and if lost, can accelerate extinction of species. According to theory, total genetic diversity should be less in species with restricted ranges and in populations on the margins of distributional ranges, making such species or populations more vulnerable to environmental perturbations. Using mtDNA and nuclear Inter Simple Sequence Repeat (ISSR) data we investigated how the genetic diversity and structure of three con-generic species pairs of coral reef fishes (Pomacentridae) was related to species’ range size and position of populations within these ranges. Estimates of genetic structure did not differ significantly among species, but mtDNA and nucDNA genetic diversities were up to 10 times greater in spatially restricted species compared to their widespread congeners. In two of the three species pairs, the distribution of genetic variation indicated secondary contact among differentiated lineages in the spatially restricted species. In contrast, the widespread species displayed a typical signature of population expansion suggesting recent genetic bottlenecks, possibly associated with the (re) colonization of the Great Barrier Reef. These results indicate that historical processes, involving hybridization and founder effects, possibly associated with Pleistocene sea level fluctuations, have differentially influenced the widespread and spatially restricted coral reef damselfish species studied here. Diversity 2011-09-14 3 3 Article 10.3390/d3030483 483 502 1424-2818 2011-09-14 doi: 10.3390/d3030483 Line K. Bay M. Julian Caley http://www.mdpi.com/1424-2818/3/3/466 A recent shift in the pattern of commercial harvest in the Keppel Island region of the southern inshore Great Barrier Reef raises concern about the depletion of a number of relatively rare restricted range taxa. The shift appears to be driven by demand from the United States (US) for corals for domestic aquaria. Data from the annual status reports from the Queensland Coral Fishery were compared with export trade data to the US from the Convention on International Trade in Endangered Species (CITES). Evidence was found of recent increases in the harvest of species from the Mussidae family (Acanthastrea spp.) which appears to be largely driven by demand from the US. On present trends, the industry runs the risk of localized depletion of Blastomussa and Scolymia; evidenced by an increase in the harvest of small specimens and the trend of decreasing harvest despite a concurrent increase in demand. Considering their relatively high sediment tolerance compared to other reef-building species, and the current lack of information about their functional role in reef stability, the trend raises concerns about the impact of the harvest on local coral communities. The recent shift in harvest patterns could have impacts on slow-growing species by allowing harvest beyond the rate of population regeneration. In light of these factors, combined with the value of such species to local tourism, a commercial coral fishery based on uncommon but highly sought-after species may not be ecologically sustainable or economically viable in the Keppels. Diversity 2011-08-24 3 3 Article 10.3390/d3030466 466 482 1424-2818 2011-08-24 doi: 10.3390/d3030466 Alison M. Jones http://www.mdpi.com/1424-2818/3/3/453 Assessing biodiversity and the spatial structures of forest ecosystems are important for forestry and nature conservation. However, tropical forests of Bangladesh are only sparsely investigated. Here we determined biodiversity (alpha, beta and gamma), spatial species turnover and stand characteristics of one of the few remnant tropical forests in Bangladesh. Two differently protected areas of Satchari forest were compared. We recorded tree species composition, in a systematic plot design, measured diameter at breast height for each individual tree (to assess basal area), and calculated decay in similarity of tree species composition with geographical distance. The distance-decay was assessed separately for the whole study area and for two subsamples from Satchari National Park and Satchari Reserve Forest. Satchari National Park (strictly protected) had, despite its smaller area, a higher Alpha and Gamma diversity, but a lower Beta diversity than Satchari Reserve Forest. Variation in species composition was not significant between the two differently protected areas. Basal area increased significantly with protection status although tree individuals were of equal size in both areas. Plots in the Reserve Forest were associated with higher species turnover than in the National Park. We suggest anthropogenic disturbance, which occurs in the less strictly protected Reserve Forest, is the main driver for the detected spatial heterogeneity in species composition. Diversity 2011-08-16 3 3 Article 10.3390/d3030453 453 465 1424-2818 2011-08-16 doi: 10.3390/d3030453 Mohammad B. Uddin Manuel J. Steinbauer Carl Beierkuhnlein http://www.mdpi.com/1424-2818/3/3/424 Coral reef ecosystems are increasingly subject to severe, large-scale disturbances caused by climate change (e.g., coral bleaching) and other more direct anthropogenic impacts. Many of these disturbances cause coral loss and corresponding changes in habitat structure, which has further important effects on abundance and diversity of coral reef fishes. Declines in the abundance and diversity of coral reef fishes are of considerable concern, given the potential loss of ecosystem function. This study explored the effects of coral loss, recorded in studies conducted throughout the world, on the diversity of fishes and also on individual responses of fishes within different functional groups. Extensive (>60%) coral loss almost invariably led to declines in fish diversity. Moreover, most fishes declined in abundance following acute disturbances that caused >10% declines in local coral cover. Response diversity, which is considered critical in maintaining ecosystem function and promoting resilience, was very low for corallivores, but was much higher for herbivores, omnivores and carnivores. Sustained and ongoing climate change thus poses a significant threat to coral reef ecosystems and diversity hotspots are no less susceptible to projected changes in diversity and function. Diversity 2011-08-12 3 3 Review 10.3390/d3030424 424 452 1424-2818 2011-08-12 doi: 10.3390/d3030424 Morgan S. Pratchett Andrew S. Hoey Shaun K. Wilson Vanessa Messmer Nicholas A.J. Graham http://www.mdpi.com/1424-2818/3/3/405 Adaptation of reef corals to climate change is an issue of much debate, and often viewed as too slow a process to be of relevance over decadal time scales. This notion is based on the long sexual generation times typical for some coral species. However, the importance of somatic mutations during asexual reproduction and growth on evolution and adaptation (i.e., cell lineage selection) is rarely considered. Here we review the existing literature on cell lineage selection and show that the scope for somatic mutations to arise in the coral animal and associated Symbiodinium is large. For example, we estimate that ~100 million somatic mutations can arise within a branching Acropora coral colony of average size. Similarly, the large population sizes and rapid turn-over times of in hospite Symbiodinium likely result in considerable numbers of somatic mutations. While the fate of new mutations depends on many factors, including ploidy level and force and direction of selection, we argue that they likely play a key role in the evolution of reef corals. Diversity 2011-08-12 3 3 Review 10.3390/d3030405 405 423 1424-2818 2011-08-12 doi: 10.3390/d3030405 Madeleine J. H. Van Oppen Petra Souter Emily J. Howells Andrew Heyward Ray Berkelmans http://www.mdpi.com/1424-2818/3/3/390 The co-occurrence of cryptic species of Hyalella amphipods is a challenge to our traditional views of how species assemble. Since these species have similar morphologies, it is not evident that they have developed phenotypic differences that would allow them to occupy different ecological niches. We examined the structure of a community of Hyalella amphipods in the littoral zone of a boreal lake to verify if temporal variation was present in relative abundances. Morphological and molecular analyses using the mitochondrial cytochrome c oxidase I (COI) gene enabled us to detect three cryptic species at the study site. No temporal variation was observed in the community, as one cryptic species was always more abundant than the two others. The relative abundances of each species in the community appeared constant at least for the open-water season, both for adult and juvenile amphipods. Niche differences are still to be found among these species, but it is suggested that migration from nearby sites may be an important factor explaining the species co-occurrence. Diversity 2011-08-08 3 3 Article 10.3390/d3030390 390 404 1424-2818 2011-08-08 doi: 10.3390/d3030390 Kaven Dionne Roland Vergilino France Dufresne François Charles Christian Nozais http://www.mdpi.com/1424-2818/3/3/375 Hairy prairie-clover [Dalea villosa (Nutt.) Spreng. var. villosa] is a threatened Canadian wildflower. To facilitate the efforts of conserving this threatened plant, amplified fragment length polymorphism (AFLP) technique was applied to assess genetic diversity in a remnant hairy prairie-clover population in the Canadian Prairie. Three AFLP primer pairs were employed to genotype 610 individual plants from the population and 15 plants from a North Dakota composite population, and 100 polymorphic AFLP bands were analyzed. The assayed plants displayed 23% AFLP variation present between the remnant population and the North Dakota composite population, but maintained a high level (91%) of AFLP variation within patches of the remnant population. The individual genetic distinctiveness measured by average AFLP dissimilarity was positively associated with latitude and negatively with elevation. The among-patch AFLP variation was significantly related to inter-patch distance, indicating local genetic differentiation within the remnant population. However, the proportions of within-patch AFLP variation were not associated with any patch characteristics assessed (i.e., patch size, perimeter, nearest neighbor distance, mean inter-patch distance). No fine-scale genetic structure was found within three large patches, suggesting little genetic correlations present for plants five meters apart. Some genetically distinctive and diverse patches were also identified. These findings indicate that the genetic risk of the remnant hairy prairie-clover population in the Canadian Prairie is low. Diversity 2011-08-08 3 3 Article 10.3390/d3030375 375 389 1424-2818 2011-08-08 doi: 10.3390/d3030375 Yong-Bi Fu Gregory W. Peterson Ken W. Richards http://www.mdpi.com/1424-2818/3/3/356 Symbioses between microbes and higher organisms underpin high diversity in many ecosystems, including coral reefs, however mechanisms underlying the early establishment of symbioses remain unclear. Here we examine the roles of Symbiodinium type and cell surface recognition in the establishment of algal endosymbiosis in the reef-building coral, Acropora tenuis. We found 20–70% higher infection success (proportion of larvae infected) and five-fold higher Symbiodinium abundance in larvae exposed to ITS-1 type C1 compared to ITS-1 type D in the first 96 h following exposure. The highest abundance of Symbiodinium within larvae occurred when C1-type cells were treated with enzymes that modified the 40–100 kD glycome, including glycoproteins and long chain starch residues. Our finding of declining densities of Symbiodinium C1 through time in the presence of intact cell surface molecules supports a role for cell surface recognition molecules in controlling post-phagocytosis processes, leading to rejection of some Symbiodinium types in early ontogeny. Reductions in the densities of unmodified C1 symbionts after 96 h, in contrast to increases in D symbionts may suggest the early initiation of a winnowing process contributing to the establishment of Symbiodinium D as the dominant type in one-month old juveniles of A. tenuis. Diversity 2011-07-19 3 3 Article 10.3390/d3030356 356 374 1424-2818 2011-07-19 doi: 10.3390/d3030356 Line Kolind Bay Vivian Ruth Cumbo David Abrego Johnathan Travis Kool Tracy Danielle Ainsworth Bette Lynn Willis http://www.mdpi.com/1424-2818/3/3/329 In spite of the wealth of research on the Great Barrier Reef, few detailed biodiversity assessments of its inshore coral communities have been conducted. Effective conservation and management of marine ecosystems begins with fine-scale biophysical assessments focused on diversity and the architectural species that build the structural framework of the reef. In this study, we investigate key coral diversity and environmental attributes of an inshore reef system surrounding the Keppel Bay Islands near Rockhampton in Central Queensland, Australia, and assess their implications for conservation and management. The Keppels has much higher coral diversity than previously found. The average species richness for the 19 study sites was ~40 with representatives from 68% of the ~244 species previously described for the southern Great Barrier Reef. Using scleractinian coral species richness, taxonomic distinctiveness and coral cover as the main criteria, we found that five out of 19 sites had particularly high conservation value. A further site was also considered to be of relatively high value. Corals at this site were taxonomically distinct from the others (representatives of two families were found here but not at other sites) and a wide range of functionally diverse taxa were present. This site was associated with more stressful conditions such as high temperatures and turbidity. Highly diverse coral communities or biodiversity ‘hotspots’ and taxonomically distinct reefs may act as insurance policies for climatic disturbance, much like Noah’s Arks for reefs. While improving water quality and limiting anthropogenic impacts are clearly important management initiatives to improve the long-term outlook for inshore reefs, identifying, mapping and protecting these coastal ‘refugia’ may be the key for ensuring their regeneration against catastrophic climatic disturbance in the meantime. Diversity 2011-07-19 3 3 Article 10.3390/d3030329 329 355 1424-2818 2011-07-19 doi: 10.3390/d3030329 Alison M. Jones Ray Berkelmans Wayne Houston http://www.mdpi.com/1424-2818/3/3/308 Evaluation of the soil rhizosphere has been limited by the lack of robust assessments that can explore the vast complex structure and diversity of soil microbial communities. Our objective was to combine fatty acid methyl ester (FAME) and pyrosequencing techniques to evaluate soil microbial community structure and diversity. In addition, we evaluated biogeochemical functionality of the microbial communities via enzymatic activities of nutrient cycling. Samples were taken from a silt loam at 0–10 and 10–20 cm in an organic farm under lettuce (Lactuca sativa), potato (Solanum tuberosum), onion (Allium cepa L), broccoli (Brassica oleracea var. botrytis) and Tall fescue pasture grass (Festuca arundinacea). Several FAMEs (a15:0, i15:0, i15:1, i16:0, a17:0, i17:0, 10Me17:0, cy17:0, 16:1ω5c and 18:1ω9c) varied among the crop rhizospheres. FAME profiles of the soil microbial community under pasture showed a higher fungal:bacterial ratio compared to the soil under lettuce, potato, onion, and broccoli. Soil under potato showed higher sum of fungal FAME indicators compared to broccoli, onion and lettuce. Microbial biomass C and enzyme activities associated with pasture and potato were higher than the other rhizospheres. The lowest soil microbial biomass C and enzyme activities were found under onion. Pyrosequencing revealed significant differences regarding the maximum operational taxonomic units (OTU) at 3% dissimilarity level (roughly corresponding to the bacterial species level) at 0–10 cm (581.7–770.0) compared to 10–20 cm (563.3–727.7) soil depths. The lowest OTUs detected at 0–10 cm were under broccoli (581.7); whereas the lowest OTUs found at 10–20 cm were under potato (563.3). The predominant phyla (85%) in this soil at both depths were Bacteroidetes (i.e., Flavobacteria, Sphingobacteria), and Proteobacteria. Flavobacteriaceae and Xanthomonadaceae were predominant under broccoli. Rhizobiaceae, Hyphomicrobiaceae, and Acidobacteriaceae were more abundant under pasture compared to the cultivated soils under broccoli, potato, onion and lettuce. This study found significant differences in microbial community structure and diversity, and enzyme activities of nutrient cycling in this organic farming system under different rhizospheres, which can have implications in soil health and metabolic functioning, and the yield and nutritional value of each crop. Diversity 2011-07-19 3 3 Article 10.3390/d3030308 308 328 1424-2818 2011-07-19 doi: 10.3390/d3030308 Terrence Gardner V. Acosta-Martinez Zachary Senwo Scot E. Dowd http://www.mdpi.com/1424-2818/3/3/296 A comparison of the community structure of juvenile hermatypic corals of 2 to 37 m depth at the fringing reefs of Curaçao between 1975 and 2005 shows a decline of 54.7% in juvenile coral abundance and a shift in species composition. Agaricia species and Helioseris cucullata, the most common juveniles in 1975, showed the largest decline in juvenile abundance (a 9 and 120 fold decrease in density respectively) with Helioseris cucullata being nearly extirpated locally. In 2005, Porites astreoides contributed most colonies to the juvenile coral community, increasing from 8.2% (in 1975) to 19.9% of the total juvenile community. Between 1975 and 2005, juveniles of brooding species decreased in relative abundance while the abundance of juveniles of broadcast spawning species increased or remained the same. These data illustrate the magnitude of the changes that have occurred in only three decades in the composition of juvenile coral communities. Diversity 2011-06-27 3 3 Article 10.3390/d3030296 296 307 1424-2818 2011-06-27 doi: 10.3390/d3030296 Mark J.A. Vermeij Judith Bakker Noam van der Hal Rolf P.M. Bak http://www.mdpi.com/1424-2818/3/2/275 Landscape scale conservation planning efforts have been in place for the past several decades to maintain biodiversity. Objectives of past efforts have been to identify areas to create reserves based on species diversity, land ownership, and landscape context. Risk analysis has not often been included in these spatial analyses. Datasets such as the Southwest Regional Gap Analysis (SWReGAP) are now available as are processes that allow risk analysis to be viewed in a spatial context in relations to factors that affect habitats over broad scales. We describe a method to include four spatial datasets to provide coarse scale delineation on areas to focus conservation including species numbers, key habitats, land management and factors that influence habitats. We used the SWReGAP management status dataset to identify management categories for long-term intent of management for biodiversity. The New Mexico Department of Game and Fish identified a set of 290 Species of Greatest Conservation Need (SGCN). Species occurrences for these species were associated with hydrologic unit codes from the National Hydrography Dataset (NHD). Key habitats were identified by using the SWReGAP land cover dataset and NHD derivatives. Factors that influence habitats were identified and scored for 89 land cover types and 23 aquatic habitats identified by the NMDGF. Our final model prioritizes landscapes that are within key habitats, have high numbers of terrestrial and aquatic Species of Greatest Conservation Need taxa, may be potentially altered by multiple effects that influence habitats, and lack long-term legally-binding management plans protecting them from anthropogenic degradation. Similar to other efforts, riparian and aquatic habitats were identified as the most important for conservation. This information may be displayed spatially, allowing land managers and decision makers to understand the ecological context where multiple effects of potential factors may influence some habitats greater than others, and repeat process with CWCS revisions. Diversity 2011-06-16 3 2 Article 10.3390/d3020275 275 295 1424-2818 2011-06-16 doi: 10.3390/d3020275 Kenneth G. Boykin Kendal E. Young Rachel K. Guy http://www.mdpi.com/1424-2818/3/2/262 This article summarises the sometimes controversial contributions made by the different sciences to predict the path of ocean acidification impacts on the diversity of coral reefs during the present century. Although the seawater carbonate system has been known for a long time, the understanding of acidification impacts on marine biota is in its infancy. Most publications about ocean acidification are less than a decade old and over half are about coral reefs. Contributions from physiological studies, particularly of coral calcification, have covered such a wide spectrum of variables that no cohesive picture of the mechanisms involved has yet emerged. To date, these studies show that coral calcification varies with carbonate ion availability which, in turn controls aragonite saturation. They also reveal synergies between acidification and the better understood role of elevated temperature. Ecological studies are unlikely to reveal much detail except for the observations of the effects of carbon dioxide springs in reefs. Although ocean acidification events are not well constrained in the geological record, recent studies show that they are clearly linked to extinction events including four of the five greatest crises in the history of coral reefs. However, as ocean acidification is now occurring faster than at any know time in the past, future predictions based on past events are in unchartered waters. Pooled evidence to date indicates that ocean acidification will be severely affecting reefs by mid century and will have reduced them to ecologically collapsed carbonate platforms by the century’s end. This review concludes that most impacts will be synergistic and that the primary outcome will be a progressive reduction of species diversity correlated with habitat loss and widespread extinctions in most metazoan phyla. Diversity 2011-05-30 3 2 Review 10.3390/d3020262 262 274 1424-2818 2011-05-30 doi: 10.3390/d3020262 John E.N. Veron http://www.mdpi.com/1424-2818/3/2/252 Environmental monitoring programs must efficiently describe state shifts. We propose using maximum entropy modeling to select dissimilar sampling sites to capture environmental variability at low cost, and demonstrate a specific application: sample site selection for the Central Plains domain (453,490 km2) of the National Ecological Observatory Network (NEON). We relied on four environmental factors: mean annual temperature and precipitation, elevation, and vegetation type. A “sample site” was defined as a 20 km × 20 km area (equal to NEON’s airborne observation platform [AOP] footprint), within which each 1 km2 cell was evaluated for each environmental factor. After each model run, the most environmentally dissimilar site was selected from all potential sample sites. The iterative selection of eight sites captured approximately 80% of the environmental envelope of the domain, an improvement over stratified random sampling and simple random designs for sample site selection. This approach can be widely used for cost-efficient selection of survey and monitoring sites. Diversity 2011-05-26 3 2 Article 10.3390/d3020252 252 261 1424-2818 2011-05-26 doi: 10.3390/d3020252 Thomas J. Stohlgren Sunil Kumar David T. Barnett Paul H. Evangelista http://www.mdpi.com/1424-2818/3/2/235 Wetland ecosystems are vulnerable to plant species invasions, which can greatly alter species composition and ecosystem functioning. The response of these communities to restoration can vary following invader removal, but few studies have evaluated how recent and long-term invasions can affect the plant community’s restoration potential. Perennial pepperweed (Lepidium latifolium) has invaded thousands of hectares of marshland in the San Francisco Estuary, California, United States of America, while the effects of invasion and removal of this weed remain poorly studied. In this study, perennial pepperweed was removed along a gradient of invasion age in brackish tidal marshes of Suisun Marsh, within the Estuary. In removal plots, resident plant cover significantly increased during the 2-year study period, particularly in the densest and oldest parts of the perennial pepperweed colonies, while species richness did not change significantly. In bare areas created by removal of perennial pepperweed, recolonization was dominated by three-square bulrush (Schoenoplectus americanus). Ultimately, removal of invasive perennial pepperweed led to reinvasion of the resident plant community within two years. This study illustrates that it is important to consider invasion age, along with exotic species removal, when developing a restoration strategy in wetland ecosystems. Diversity 2011-05-19 3 2 Article 10.3390/d3020235 235 251 1424-2818 2011-05-19 doi: 10.3390/d3020235 Sarah Estrella Jamie M. Kneitel http://www.mdpi.com/1424-2818/3/2/217 Mineral licks are sites where a diverse array of mammals and birds consume soil (geophagy) or drink water, likely for mineral supplementation. The diversity of species that visit such sites makes them important for conservation, particularly given that hunters often target animals at licks. Use of mineral licks varies among species, with frugivores among the most common visitors but there is considerable temporal and spatial variation in lick use both within and among species. Camera traps triggered by heat and motion were used to document use of mineral licks by birds and non-volant mammals over a four-year period at a lowland forest site in eastern Ecuador. We obtained 7,889 photographs representing 23 mammal species and 888 photographs representing 15 bird species. Activity (photographs/100 trap-days) at the four licks varied from 89 to 292 for mammals and from six to 43 for birds. Tapirs (Tapirus terrestris), peccaries (Pecari tajacu, Tayassu pecari), deer (Mazama americana), and pacas (Cuniculus paca) were the most frequent mammal visitors; guans (Pipile pipile) and pigeons (Columba plumbea) were the most common birds. Use of licks varied diurnally and seasonally but patterns of use varied among species and sites. Mineral licks provide an important resource for many species but further studies are needed to determine the precise benefit(s) obtained and how benefits may vary with diet and other factors, such as rainfall. Diversity 2011-04-28 3 2 Article 10.3390/d3020217 217 234 1424-2818 2011-04-28 doi: 10.3390/d3020217 John G. Blake Diego Mosquera Jaime Guerra Bette A. Loiselle David Romo Kelly Swing http://www.mdpi.com/1424-2818/3/2/200 Many aquatic species have discrete life stages, making it important to understand relative influences of the different habitats occupied within those populations. Although population demographics in one stage can carry over to spatially separated life stages, most studies of habitat associations have been restricted to a single life stage. Among Gomphidae dragonflies (Odonata: Anisoptera), recruitment via adult oviposition establishes initial population sizes of the aquatic larvae. However, spatial variability in larval survivorship could obscure the relationship between adult and larval densities. This study uses surveys conducted during 2005 and 2006 of Gomphidae larval, emergence, and adult stages from 22 lake sites in northern Wisconsin, USA, to investigate (1) whether the Gomphidae density of each life stage correlated spatially with that of the preceding life stage and (2) what habitat factors help explain variation in densities at each life stage. Results indicated that adult densities from the previous season helped predict densities of early-instar larvae. This finding suggests that oviposition site selection controlled the local larval distribution more than larval survivorship or movement. Late-instar larval densities helped predict densities of emerging Gomphidae later the same season, suggesting that variation in survivorship of final-instar larvae among sites is small relative to the variation in larval recruitment. This study demonstrates that locations with higher densities of odonates in the water also have higher densities of odonates on land. In addition to the densities of Gomphidae in previous life stages, water clarity helped predict larval densities, and riparian wetland vegetation helped predict emergent dragonfly densities. Diversity 2011-04-14 3 2 Article 10.3390/d3020200 200 216 1424-2818 2011-04-14 doi: 10.3390/d3020200 Alysa Remsburg http://www.mdpi.com/1424-2818/3/2/176 This paper reviews the patterns observed in the diversity and structure of the macrofauna benthic community under the influence of fish farming. First, we explain the effects of organic enrichment on the sediment and the consequences for the inhabiting communities. We describe the diversity trends in spatial and temporal gradients affected by fish farming and compare them with those described by the Pearson and Rosenberg model. We found that in general terms, the trends of diversity and other community parameters followed the Pearson and Rosenberg model but they can vary to some extent due to sediment local characteristics or to secondary disturbances. We also show the different mechanisms by which wild fish can affect macrofauna diversity patterns under fish farming influence. In addition, we comment the importance of the macrofauna diversity in the ecosystem functions and propose some guidelines to measure functional diversity related to relevant processes at ecosystem level. We propose more research efforts in the main topics commented in this review to improve management strategies to guarantee a good status of the diversity and ecosystem functioning of sediments influenced by fish farming. Diversity 2011-04-14 3 2 Review 10.3390/d3020176 176 199 1424-2818 2011-04-14 doi: 10.3390/d3020176 Carlos Sanz-Lázaro Arnaldo Marín http://www.mdpi.com/1424-2818/3/1/155 Exotic earthworms are drivers of biotic communities in invaded North American forest stands. Here we used ecologically important oribatid mite (Arachnida: Acari) communities, as model organisms to study the responses of litter- and soil-dwelling microarthropod communities to exotic earthworm invasion in a northern temperate forest. Litter- and soil-dwelling mites were sampled in 2008–2009 from forest areas: (1) with no earthworms; (2) those with epigeic and endogeic species, including Lumbricus rubellus Hoffmeister; and (3) those with epigeic, endogeic, and anecic earthworms including L. terrestris L. Species richness and diversity of litter- and soil-dwelling (0–2 cm soil depth) oribatid mites was 1–2 times higher in sites without earthworms than in sites with worms. Similarly, litter-dwelling oribatid mites were between 72 and 1,210 times more abundant in earthworm-free sites than in sites with worms. Among earthworm invaded sites, abundance of litter-dwelling oribatid mites in sites without the anecic L. terrestris was twice as high in May and 28 times higher in October, compared to sites with L. terrestris. Species richness, diversity, and abundance of oribatid mites were greater in litter-layers than in the soil-layers that showed a varied response to earthworm invasion. Species compositions of both litter- and soil-dwelling oribatid mite communities of forests with no earthworms were markedly different from those with earthworms. We conclude that exotic earthworm invasions are associated with significant declines of species diversity, numbers, and compositional shifts in litter- and soil-inhabiting communities. These faunal shifts may contribute to earthworm effects on soil processes and food web dynamics in historically earthworm-free, northern temperate forests. Diversity 2011-03-15 3 1 Article 10.3390/d3010155 155 175 1424-2818 2011-03-15 doi: 10.3390/d3010155 Jordan L. Burke John C. Maerz Joseph R. Milanovich Melany C. Fisk Kamal J.K. Gandhi http://www.mdpi.com/1424-2818/3/1/136 Coprinoid mushrooms grown on wood of broad-leaf species were collected for the first time in Armenia and dikaryotic mycelial cultures were established. ITS (internal transcribed spacer) sequences identified one species as Coprinopsis strossmayeri and the other as a species closely related to Coprinellus radians. Mycelial growth and morphological features on different media are described. The pearl-white-silky colonies of C. strossmayeri are characterized by mycelial strands and by a light-yellow agar colorization. The species forms chlamydospores intercalary in its hyphae. Some hyphal ends form hyphal loops. Colonies of C. aff. radians have a characteristic yellow pigmentation and stain the agar yellowish. Hyphae are mostly clampless but at some septa, pseudoclamps are seen from which side-branches develop growing along the parental hyphae. In the mycelium of C. aff. radians, hyphal loops, hyphal swellings, cystidia and typical allocysts were observed. Both new species from Armenia show growth optima at temperatures of 25 to 30 °C and pHs of 6.0 to 7.0. Both grow in alkaline conditions up to pH 12.0 but not at pHs 3.0 and 4.0, classifying them with other coprinoid mushrooms as “ammonia fungi”. Both species grew on a variety of lignocellulosic substrates and both show polyphenol oxidase activities. Diversity 2011-03-07 3 1 Article 10.3390/d3010136 136 154 1424-2818 2011-03-07 doi: 10.3390/d3010136 Susanna M. Badalyan Karol Szafranski Patrik J. Hoegger Monica Navarro-González Andrzej Majcherczyk Ursula Kües http://www.mdpi.com/1424-2818/3/1/121 The nucleotide diversities and genetic relationship in the three Japanese pine species, P. thunbergii, P. densiflora, and P. luchuensis, were measured using low-copy anchor loci in Pinaceae. The average nucleotide diversity among these three Japanese pines revealed that P. thunbergii was the highest (6.05 × 10−3), followed by P. densiflora (5.27 × 10−3) and P. luchuensis (5.02 × 10−3). In comparison to other conifer species, it was concluded that the pines possessed an intermediate level of nucleotide diversity. The Heat shock protein (HSP) gene in P. thunbergii, Phenylalanine tRNA synthetase, RuBP carboxylase, and Disease resistance response protein 206 genes in P. densiflora were significantly deviated from standard neutral models. Some of these genes were related to stress or pathogen/defense response. As the samples used in this study were collected from natural populations that showed specific characteristics of being resistant to pine wilt nematode, it was hypothesized that the initial selection was an important factor in discriminating the deviation from neutrality models. Phylogenetic reconstruction revealed that the three Japanese pines were split into two lineages corresponding to P. densiflora and P. thunbergii–P. luchuensis. The latter lineage was differentiated further into two clades; P. thunbergii and P. luchuensis. The result concludes that the three Japanese pines are closely related and P. thunbergii is genetically closer to P. luchuensis, than P. densiflora. Diversity 2011-03-04 3 1 Article 10.3390/d3010121 121 135 1424-2818 2011-03-04 doi: 10.3390/d3010121 Suharyanto Susumu Shiraishi http://www.mdpi.com/1424-2818/3/1/112 The paper describes rich, a new R package to perform species richness estimation and comparison. Species richness is the simplest surrogate for the more complex concept of species biodiversity. It is relatively easy to assess although estimations strongly depend on sampling intensity with the consequence that richness estimations should be standardized to perform valid comparisons. The R package rich allows such corrections as well as the computation of various statistics and implements different randomization tests to compare cumulative and average species richness of two communities. These tests are useful for ranking sites or communities which is a classical goal in restoration ecology and conservation biology. Diversity 2011-02-16 3 1 Article 10.3390/d3010112 112 120 1424-2818 2011-02-16 doi: 10.3390/d3010112 Jean-Pierre Rossi http://www.mdpi.com/1424-2818/3/1/91 The ongoing climate warming has been reported to affect a broad range of organisms, and mountain ecosystems are considered to be particularly sensitive because they are limited by low temperatures. Meteorological data show an increased temperature for the alpine areas at Dovrefjell, Norway, causing a prolonged growing season and increased temperature sum. As part of the worldwide project Global Observation Research Initiative in Alpine Environments (GLORIA), the short-term changes in vascular plant species richness, species composition of lichen and vascular plant communities, and abundance of single species were studied at four summits representing an altitudinal gradient from the low alpine to the high alpine zone. During the period from 2001 to 2008, an increase in species richness at the lowest summit, as well as a change in the composition of vascular plant communities, was found at the two lowest summits. The results also indicate an increase in abundance of some shrubs and graminoids and a decline in the cover of some species of lichens at the lowest summit. These changes are in accordance with climate induced changes reported in other studies, but other causes for the observed vegetation changes, in particular changes in grazing and trampling pressure, cannot be ruled out. Diversity 2011-01-28 3 1 Article 10.3390/d3010091 91 111 1424-2818 2011-01-28 doi: 10.3390/d3010091 Ottar Michelsen Anne Olga Syverhuset Bård Pedersen Jarle Inge Holten http://www.mdpi.com/1424-2818/3/1/8 Form and function of mycorrhizas as well as tracing the presence of the mycorrhizal fungi through the geological time scale are herein first addressed. Then mycorrhizas and plant fitness, succession, mycorrhizas and ecosystem function, and mycorrhizal resiliency are introduced. From this, four hypotheses are drawn: (1) mycorrhizal diversity evolved in response to changes in Global Climate Change (GCC) environmental drivers, (2) mycorrhizal diversity will be modified by present changes in GCC environmental drivers, (3) mycorrhizal changes in response to ecological drivers of GCC will in turn modify plant, community, and ecosystem responses to the same, and (4) Mycorrhizas will continue to evolve in response to present and future changes in GCC factors. The drivers of climate change examined here are: CO2 enrichment, temperature rise, altered precipitation, increased N-deposition, habitat fragmentation, and biotic invasion increase. These impact the soil-rhizosphere, plant and fungal physiology and/or ecosystem(s) directly and indirectly. Direct effects include changes in resource availability and change in distribution of mycorrhizas. Indirect effects include changes in below ground allocation of C to roots and changes in plant species distribution. GCC ecological drivers have been partitioned into four putative time frames: (1) Immediate (1–2 years) impacts, associated with ecosystem fragmentation and habitat loss realized through loss of plant-hosts and disturbance of the soil; (2) Short-term (3–10 year) impacts, resultant of biotic invasions of exotic mycorrhizal fungi, plants and pests, diseases and other abiotic perturbations; (3) Intermediate-term (11–20 year) impacts, of cumulative and additive effects of increased N (and S) deposition, soil acidification and other pollutants; and (4) Long-term (21–50+ year) impacts, where increased temperatures and CO2 will destabilize global rainfall patterns, soil properties and plant ecosystem resilience. Due to dependence on their host for C-supply, orchid mycorrhizas and all heterotrophic mycorrhizal groups will be immediately impacted through loss of habitat and plant-hosts. Ectomycorrhizal (ECM) associations will be the principal group subject to short-term impacts, along with Ericoid mycorrhizas occurring in high altitude or high latitude ecosystems. This is due to susceptibility (low buffer capacity of soils) of many of the ECM systems and that GCC is accentuated at high latitudes and altitudes. Vulnerable mycorrhizal types subject to intermediate-term GCC changes include highly specialized ECM species associated with forest ecosystems and finally arbuscular mycorrhizas (AM) associated with grassland ecosystems. Although the soils of grasslands are generally well buffered, the soils of arid lands are highly buffered and will resist even fairly long term GCC impacts, and thus these arid, largely AM systems will be the least affect by GCC. Once there are major perturbations to the global hydrological cycle that change rainfall patterns and seasonal distributions, no aspect of the global mycorrhizal diversity will remain unaffected. Diversity 2011-01-28 3 1 Review 10.3390/d3010008 8 90 1424-2818 2011-01-28 doi: 10.3390/d3010008 Stanley E. Bellgard Stephen E. Williams http://www.mdpi.com/1424-2818/3/1/1 The Convention on Biological Diversity has adopted 20 targets as part of its new Strategic Plan. Perrings et al. have proposed that such targets should focus solely on critical ecosystem services. Such a strategy may neglect the need to conserve overall biodiversity and corresponding option values. It also may neglect the important role of ecosystem services in systematic conservation planning strategies that seek effective regional trade-offs and synergies among different needs of society. Parties to the Convention have an opportunity to address not only conventional lists of individual targets for ecosystem services and overall biodiversity, but also higher-level targets that focus directly on how well the country achieves—and maintains its capacity to achieve—effective trade-offs among different needs of society. Diversity 2011-01-18 3 1 Short Note 10.3390/d3010001 1 7 1424-2818 2011-01-18 doi: 10.3390/d3010001 Daniel P. Faith http://www.mdpi.com/1424-2818/2/11/1205 Forty-five Xanthomonas arboricola pv. juglandis (Xaj) strains originating from Juglans regia cultivation in different countries were molecularly typed by means of MultiLocus Sequence Typing (MLST), using acnB, gapA, gyrB and rpoD gene fragments. A total of 2.5 kilobases was used to infer the phylogenetic relationship among the strains and possible recombination events. Haplotype diversity, linkage disequilibrium analysis, selection tests, gene flow estimates and codon adaptation index were also assessed. The dendrograms built by maximum likelihood with concatenated nucleotide and amino acid sequences revealed two major and two minor phylotypes. The same haplotype was found in strains originating from different continents, and different haplotypes were found in strains isolated in the same year from the same location. A recombination breakpoint was detected within the rpoD gene fragment. At the pathovar level, the Xaj populations studied here are clonal and under neutral selection. However, four Xaj strains isolated from walnut fruits with apical necrosis are under diversifying selection, suggesting a possible new adaptation. Gene flow estimates do not support the hypothesis of geographic isolation of the strains, even though the genetic diversity between the strains increases as the geographic distance between them increases. A triplet deletion, causing the absence of valine, was found in the rpoD fragment of all 45 Xaj strains when compared with X. axonopodis pv. citri strain 306. The codon adaptation index was high in all four genes studied, indicating a relevant metabolic activity. Diversity 2010-11-22 2 11 Article 10.3390/d2111205 1205 1222 1424-2818 2010-11-22 doi: 10.3390/d2111205 Simone Marcelletti Patrizia Ferrante Marco Scortichini http://www.mdpi.com/1424-2818/2/11/1181 Anticipating the effects of climate change on biodiversity is now critical for managing wild species and ecosystems. Climate change is a global driver and thus affects biodiversity globally. However, land-use planners and natural resource managers need regional or even local predictions. This provides scientists with formidable challenges given the poor documentation of biodiversity and its complex relationships with climate. We are approaching this problem in Quebec, Canada, through the CC-Bio Project (http://cc‑bio.uqar.ca/), using a boundary organization as a catalyst for team work involving climate modelers, biologists, naturalists, and biodiversity managers. In this paper we present the CC-Bio Project and its general approach, some preliminary results, the emerging hypothesis of the northern biodiversity paradox (a potential increase of biodiversity in northern ecosystems due to climate change), and an early assessment of the conservation implications generated by our team work. Diversity 2010-11-19 2 11 Article 10.3390/d2111181 1181 1204 1424-2818 2010-11-19 doi: 10.3390/d2111181 Dominique Berteaux Sylvie de Blois Jean-François Angers Joël Bonin Nicolas Casajus Marcel Darveau François Fournier Murray M. Humphries Brian McGill Jacques Larivée Travis Logan Patrick Nantel Catherine Périé Frédéric Poisson David Rodrigue Sébastien Rouleau Robert Siron Wilfried Thuiller Luc Vescovi http://www.mdpi.com/1424-2818/2/11/1158 Analysis was made of 3,923 records of 162 wild Passiflora specimens to assess the distribution of their diversity in Colombia, identify collection gaps, and explore their potential as indicator species. Despite variable collecting density among and within biogeographic regions, the Andean region clearly presents a higher species richness, particularly in the central coffee growing zone and the departments of Antioquia, Cundinamarca and Valle del Cauca. The elevational distribution of diversity shows a small peak below 500 m, and two higher ones between 1,000–2,000 and 2,500–3,000 m. This pattern corresponds to divergent adaptive trends among infrageneric divisions. The analysis on 19 climatic variables showed that the two principal variance components, explaining 77 percent of the total, are respectively associated with temperature and precipitation, without influence of seasonality. Distribution parameters allow recognizing more than 36 narrow endemics. Prediction of species distribution showed nine areas with very high richness (predicted sympatry of 41 to 54 species) in the Andean region, three of which correspond to collection gaps. Endemics were not particularly frequent there, so a prioritization of protected areas based on species richness would not favor their conservation. The sites with high Passiflora diversity are poorly represented in the current system of protected areas. Instead, their striking correspondence with ecotopes of the coffee growing zone imposes a conservation strategy integrating agricultural and environmental management at the landscape level. Reciprocally, several traits of Passiflora species make them particularly suited as indicators for any effort of conservation or restoration in this region of importance for the country. Diversity 2010-11-15 2 11 Article 10.3390/d2111158 1158 1180 1424-2818 2010-11-15 doi: 10.3390/d2111158 John Ocampo Geo Coppens D’Eeckenbrugge Andy Jarvis http://www.mdpi.com/1424-2818/2/10/1146 Intense conversion of bottomland hardwood forests to rice and soybeans in the Mississippi River Valley of Arkansas has restricted the remaining forest to isolated fragments. Habitat fragmentation has proven to be detrimental to population sustainability of several species, and is the subject of intense study with often species and latitude specific responses. We compared both coarse land area classes and landscape fragmentation metrics from six 30 km × 30 km subsets centered on publicly owned management areas to bat captures obtained from a 2005 population study. Patch density was the strongest predictor of total captures (R2 = 0.801, p = 0.016) and of Myotis austroriparius captures (R2 = 0.856, p = 0.008). Our findings indicate that patch density and area are important predictors of bottomland bat captures. Diversity 2010-10-12 2 10 Article 10.3390/d2101146 1146 1157 1424-2818 2010-10-12 doi: 10.3390/d2101146 Rex E. Medlin Matthew B. Connior Karen F. Gaines Thomas S. Risch http://www.mdpi.com/1424-2818/2/9/1130 Public participation is a key element in nature conservation in Europe and a necessity for collecting broad scale data on biodiversity and its dynamics. However, vast societal differences exist between eastern and western European countries, resulting in problems for public participation in post-communist states as compared to western countries. Here, we compare diversity in monitoring practices and public participation in countries with different political histories. Drawing on in-depth ethnographic studies conducted in Lithuania and Poland, as well as a rapid assessment in Denmark, we have focused on the historical, cultural and social determinants of the volunteers’ participation in biodiversity monitoring. Our results indicate the reasons why volunteer involvement—as an expression of a participatory approach—has a lower incidence in the post-communist countries, compared to voluntarism common in occidental democracies. We discuss our results in the context of the main social factors considered to be a legacy of the Soviet regime. Diversity 2010-09-03 2 9 Article 10.3390/d2091130 1130 1145 1424-2818 2010-09-03 doi: 10.3390/d2091130 Deivida Vandzinskaite Hanna Kobierska Dirk S. Schmeller Małgorzata Grodzińska-Jurczak http://www.mdpi.com/1424-2818/2/9/1118 Telomeres are specialized nucleoprotein structures that have two important functions: (i) protection of the chromosomal ends from deleterious events such as chromosome fusion and degradation; (ii) counteraction of the “end replication problem” by allowing telomerase-dependent or, more rarely, telomerase-independent telomere elongation. The DNA sequences underlying these activities are short simple tandem repeats, which in vertebrate consist of a variable number of TTAGGG. Telomeres dysfunction may be caused either by the absence of telomerase activity or by mutations in telomeric proteins involved in telomere length and structure regulation. Additionally, increasing experimental evidence suggests that telomeres take part in the complex network regulating cell proliferation. Accordingly, telomeres are involved in biological process such as aging and tumor progression. In this study we determined the telomere length in two bovine Italian cattle breeds, Chianina and Maremmana, which are characterized by high longevity and range breeding. In order to account for possible variation among different tissues, we have determined telomere length in different organs such as spleen, lung and liver. Overall, the median telomere length was significant lower in Chianina (11 ± 0.69 kb) than in Maremmana (12.05 ± 1.57 kb). Moreover, telomere length variation among individuals was very low in Chianina but rather high in Maremmana. These data suggest that telomere length is influenced by the breeds. This hypothesis is confirmed by the different history of these Italian breeds. Indeed, Chianina has a long history and its size was maintained by the Breeders Association without necessity to crossbreed with other breeds, whereas the population of Maremmana underwent a dramatic shrinkage in the recent past. Therefore, breeders have crossed Maremmana with other breeds, like Charolais, and have relaxed the rules for the inclusion in the herd book. Diversity 2010-08-31 2 9 Article 10.3390/d2091118 1118 1129 1424-2818 2010-08-31 doi: 10.3390/d2091118 Francesca Tilesi Enea Gino Di Domenico Lorraine Pariset Luigi Bosco Daniela Willems Alessio Valentini Fiorentina Ascenzioni http://www.mdpi.com/1424-2818/2/9/1097 This article re-examines recent studies that link different forms of social diversity—ethnic polarization and fractionalization—to underdevelopment and an increased risk of civil war. We review theoretical arguments in favor of a connection between diversity and these social outcomes and discuss the inter-linkage between economic growth and internal conflict in situations of extreme diversity. Our analysis confirms that the relationship between ethnic polarization and civil war is ambiguous and depends on the use of civil war incidence or civil war onset as an outcome variable. Furthermore, fractionalization rather than polarization seems to be negatively related to economic growth. Diversity 2010-08-31 2 9 Article 10.3390/d2091097 1097 1117 1424-2818 2010-08-31 doi: 10.3390/d2091097 Gerald Schneider Nina Wiesehomeier http://www.mdpi.com/1424-2818/2/9/1085 Humans harbor distinct commensal microbiota at various anatomic sites. There has been renewed interest in the contributions of microbiota activities to human health and disease. The microbiota of the gut is the most complex of all anatomic sites in terms of total numbers of bacteria that interact closely with the mucosal immune system and contribute various functions to host physiology. Especially in the proximal large intestine a diverse microbiota ferments complex substrates such as dietary fiber and host mucins, but also metabolizes bile acids and phytoestrogens that reach the large intestine. It is now well established that microbiota composition differs between but over time also within individuals. However, a thorough understanding of the sources of variations in microbiota composition, which is an important requirement for large population based microbiota studies is lacking. Microbiota composition varies depending on what kind of sample is collected, most commonly stool samples, stool swabs or superficial rectal or intestinal biopsies, and the time of collection. Microbiota dynamics are affected by life style factors including diet and exercise that determine what nutrients reach the proximal colon and how fast these nutrients pass through (transit time). Here we review sample collection issues in gut microbiota studies and recent findings about dynamics in microbiota composition. We recommend standardizing human microbiota analysis methods to facilitate comparison and pooling between studies. Finally, we outline a need for prospective microbiota studies in large human cohorts. Diversity 2010-08-27 2 9 Review 10.3390/d2091085 1085 1096 1424-2818 2010-08-27 doi: 10.3390/d2091085 Volker Mai Maria Ukhanova David J. Baer http://www.mdpi.com/1424-2818/2/8/1059 “Cultural diversity” has become one of the latest buzzwords on the international policymaking scene. It is employed in various contexts—sometimes as a term close to “biological diversity”, at other times as correlated to the “exception culturelle” and most often, as a generic concept that is mobilised to counter the perceived negative effects of economic globalisation. While no one has yet provided a precise definition of what cultural diversity is, what we can observe is the emergence of the notion of cultural diversity as incorporating a distinct set of policy objectives and choices at the global level. These decisions are not confined, as one might have expected, to cultural policymaking, but rather spill over to multiple governance domains because of the complex linkages inherent to the simultaneous pursuit of economic and other societal goals that cultural diversity encompasses and has effects on. Accounting for these intricate interdependencies, the present article clarifies the origins of the concept of cultural diversity as understood in global law and traces its evolution over time. Observing the dynamics of the concept and the surrounding political and legal developments in particular in the context of trade and culture, the article explores its justification and overall impact on the global legal regime, as well as its discrete effects on different domains of policymaking, such as media and intellectual property. While the analysis is legal in essence, the article is also meant to speak to a broader transdisciplinary public. Diversity 2010-08-05 2 8 Article 10.3390/d2081059 1059 1084 1424-2818 2010-08-05 doi: 10.3390/d2081059 Mira Burri http://www.mdpi.com/1424-2818/2/8/1048 In western countries, one of the challenges facing ageing populations is an absence of social roles. One response to this is to volunteer, with evidence suggesting that this assigns meaning to the lives of older people and enhances health and well-being. This holds potential significance for older people from diverse cultural and linguistic backgrounds, and particularly those from Asian cultures, where there is evidence that cultural erosion is diminishing older people’s traditional roles. However, while volunteering can create role identities for older people, it may also further challenge existing cultural values. This paper debates these issues, drawing on a growing body of evidence relating to volunteering within Asian cultures. Diversity 2010-07-29 2 8 Article 10.3390/d2081048 1048 1058 1424-2818 2010-07-29 doi: 10.3390/d2081048 Jeni Warburton Rachel Winterton http://www.mdpi.com/1424-2818/2/7/1026 Tropical wetlands are the major natural source of methane released into the atmosphere, producing about 60% of all natural emissions. The great wetland areas of the Amazon basin are the largest source of methane in this region, contributing an estimated 5% of the total emissions from the world’s flooded areas. However, despite the important role that methanogenic archaea play in these environments, there have been few studies on the composition of their archaeal communities. In this survey, four 16S rRNA archaeal clone libraries from different depths were constructed to examine the archaeal community in an Amazon wetland soil. A total of 599 clones were used to perform diversity and phylogenetic analyses. A broad, diverse archaeal community was found at the site, with the diversity decreasing as the depth increased (Shannon index range: 2.40–1.94). Phylogenetic analysis revealed sequences belonging to two archaeal phyla, with 65% classified as Crenarchaeota and 35% classified as Euryarchaeota. Within the Euryarchaeota group, most sequences were clustered into the Methanococci and Methanomicrobia classes, two groups of methanogens. Based on the abundance of methanogenic organisms, culture–dependent isolation was used to isolate these organisms. To enhance the growth of methanogenic archaea, a modified atmosphere (H2:CO2 = 80:20) was established combined with an anoxic environment for 18 months. Among the isolates, the genera Methanosarcina and Methanobacterium were detected throughout the anaerobic in vitro cultivation, indicating a possible role for these organisms in methane production. In conclusion, these exploratory molecular and culture–dependent approaches enhance our understanding of the archaeal community and methanogenic archaea living in wetland soils of the eastern Amazon and their role in methane production. Diversity 2010-07-22 2 7 Article 10.3390/d2071026 1026 1047 1424-2818 2010-07-22 doi: 10.3390/d2071026 Jeanedy M. Pazinato Ezio N. Paulo Lucas W. Mendes Rosana F. Vazoller Siu M. Tsai http://www.mdpi.com/1424-2818/2/7/1015 The high level of conservation of 16S ribosomal RNA gene (16S rRNA) in all Prokaryotes makes this gene an ideal tool for the rapid identification and classification of these microorganisms. Databases such as the Ribosomal Database Project II (RDP-II) and the Greengenes Project offer access to sets of ribosomal RNA sequence databases useful in identification of microbes in a culture-independent analysis of microbial communities. However, these databases do not contain all of the taxonomic levels attached to the published names of the bacterial and archaeal sequences. TaxCollector is a set of scripts developed in Python language that attaches taxonomic information to all 16S rRNA sequences in the RDP-II and Greengenes databases. These modified databases are referred to as TaxCollector databases, which when used in conjunction with BLAST allow for rapid classification of sequences from any environmental or clinical source at six different taxonomic levels, from domain to species. The TaxCollector database prepared from the RDP-II database is an important component of a new 16S rRNA pipeline called PANGEA. The usefulness of TaxCollector databases is demonstrated with two very different datasets obtained using samples from a clinical setting and an agricultural soil. The six TaxCollector scripts are freely available on http://taxcollector.sourceforge.net and on http://www.microgator.org. Diversity 2010-07-21 2 7 Article 10.3390/d2071015 1015 1025 1424-2818 2010-07-21 doi: 10.3390/d2071015 Adriana Giongo Austin G. Davis-Richardson David B. Crabb Eric W. Triplett http://www.mdpi.com/1424-2818/2/7/973 We review the application of molecular methods to estimate biodiversity in the marine environment. All of the methods reviewed here, which are at the forefront of molecular research, can be applied to all organisms in all habitats, but the case studies used to illustrate the points are derived from marine photosynthetic eukaryotic protists. It has been accepted that we know less than 10% of the identified diversity in the marine microbial world and the marine micro- and pico-eukaryotes are no exception. Even the species that we think we can easily recognize are often poorly described, and even less is known of their life histories and spatial and temporal trends in their abundance and distribution. With new molecular and analytical techniques, we can advance our knowledge of marine biodiversity at the species level to understand how marine biodiversity supports ecosystem structure, dynamics and resilience. Biogeochemical reactions performed by marine photosynthetic microbial organisms constitute a major sustaining component of ecosystem functioning, and therefore, affect climate changes. New interpretations of how environmental, ecological and evolutionary processes control and structure marine ecosystem biodiversity can be made so that we can augment our understanding of biodiversity and ecosystem dynamics in especially the pico- and nano-fractions of the plankton as well as in the deep sea benthos, both of which are very difficult to study without good analytical methods. Diversity 2010-07-16 2 7 Review 10.3390/d2070973 973 1014 1424-2818 2010-07-16 doi: 10.3390/d2070973 Medlin Kooistra http://www.mdpi.com/1424-2818/2/7/959 The starting point is the principle that there is no immigrant culture, but rather, different ways of living, coexisting and identifying oneself within the cultural worlds that each subject crosses on his or her social path. Here we study Brazilian immigrants in Portugal, working with the first wave (starting at the end of the 1980s) and the second wave (at the turn of the 20th to 21st century). We intend, firstly, to show how identity is reconstructed between two banks: the departure culture and the arrival culture. Secondly, we intend to give a voice to the most silent in the understanding of immigrants: the process of identity reconstruction of Brazilian immigrants is presented, resulting from ethno-biographic interviews. We will consider the cultural transfusion theory and observe the heterogeneous ways of living between cultures, whether by rejecting the departure culture (the Oblato‘s case), refusing the arrival one at a given moment (the mono-cultural subject according to the source culture), living in an ambivalent manner between the two (the multicultural self), or, finally, inventing a third bank, as the poets say, which corresponds to an attitude of including the cultural differences through which one crosses during his or her life history in an intercultural self (the Intercultural Transfuga). Diversity 2010-07-01 2 7 Article 10.3390/d2070959 959 972 1424-2818 2010-07-01 doi: 10.3390/d2070959 Vieira Mendes http://www.mdpi.com/1424-2818/2/6/946 Molecular-assisted alpha taxonomy has recently become an effective practice in reassessing biodiversity and floristics for a variety of different organisms. This paper presents a series of examples that have been drawn from biodiversity work being carried out on the marine red algae of Bermuda. Molecular sequencing of DNA from Bermuda samples has already begun to greatly alter the makeup of the flora as it was known just decades ago, and will help set a new database for future comparison as climate change affects species composition in the islands. Diversity 2010-06-17 2 6 Review 10.3390/d2060946 946 958 1424-2818 2010-06-17 doi: 10.3390/d2060946 Cianciola Popolizio Schneider Lane http://www.mdpi.com/1424-2818/2/6/932 The introduction of livestock species in Europe has been followed by various genetic events, which created a complex spatial pattern of genetic differentiation. Spatial principal component (sPCA) analysis and spatial metric multidimensional scaling (sMDS) incorporate geography in multivariate analysis. This method was applied to three microsatellite data sets for 45 goat breeds, 46 sheep breeds, and 101 cattle breeds from Europe, Southwest Asia, and India. The first two sPCA coordinates for goat and cattle, and the first sPCA coordinate of sheep, correspond to the coordinates of ordinary PCA analysis. However, higher sPCA coordinates suggest, for all three species, additional spatial structuring. The goat is the most geographically structured species, followed by cattle. For all three species, the main genetic cline is from southeast to northwest, but other geographic patterns depend on the species. We propose sPCA and sMDS to be useful tools for describing the correlation of genetic variation with geography. Diversity 2010-06-17 2 6 Article 10.3390/d2060932 932 945 1424-2818 2010-06-17 doi: 10.3390/d2060932 Denis Laloë Katayoun Moazami-Goudarzi Johannes A. Lenstra Paolo Ajmone Marsan Pedro Azor Roswitha Baumung Daniel G. Bradley Michael W. Bruford Javier Cañón Gaudenz Dolf Susana Dunner Georg Erhardt Godfrey Hewitt Juha Kantanen Gabriela Obexer-Ruff Ingrid Olsaker Clemen Rodellar Alessio Valentini Pamela Wiener European Cattle Genetic Diversity Consortium and Econogene Consortium http://www.mdpi.com/1424-2818/2/6/910 This study evaluated microbial communities of soil (0–10 cm) as affected by dryland cropping systems under different tillage practices after 5 years. The soil type was an Olton sandy loam with an average of 16.4% clay, 67.6% sand and 0.65 g kg−1 of organic matter (OM). The cropping systems evaluated were grain sorghum (Sorghum bicolor L.)—cotton (Gossypium hirsutum) (Srg-Ct), cotton-winter rye (Secale cereale)-grain sorghum (Ct-Rye-Srg), and a rotation of forage (f) sorghum (Sorghum bicolor L. and Sorghum sudanense) with winter rye (Srf-Rye), which were under no-tillage (nt) and conventional tillage (ct) practices. Soil microbial communities under cotton based cropping systems (Srg-Ct and Ct-Rye-Srg) showed lower fungal:bacterial ratios compared to the soil under Srf-Rye. Soil under Srf-Rye showed higher population densities of Bacteroidetes and Proteobacteria while lower Actinobacteria compared to Srg-Ct and Ct-Rye-Srg. Chloroflexi, Gemmatimonadetes and Verrucomicrobiae were higher in tilled soil compared to the no-tilled plots. Regardless the limited irrigation available to sustain agricultural production within these dryland cropping systems, this study demonstrated that differences in microbial communities are more affected by crop rotation than tillage management history. Although soil fungal diversity was not analyzed in this study, pyrosequencing suggests that tillage practices can affect bacterial phyla distribution in this sandy soil. Diversity 2010-06-07 2 6 Article 10.3390/d2060910 910 931 1424-2818 2010-06-07 doi: 10.3390/d2060910 Acosta-Martínez Dowd Bell Lascano Booker Zobeck Upchurch http://www.mdpi.com/1424-2818/2/6/897 One of the key discussions emerging from within the centre and centre-left of British politics is the means of combining a commitment to diversity with the aim of achieving social solidarity. While there has been a populist strand to this debate recently with the contribution of writers such as Goodhart who has argued that diversity specifically undermines the willingness of the majority (white Anglo-Saxons) to pay for collective welfare provision, there has also been recognition of the difficulty of promoting difference and unity from within even the more sympathetic elements of the academic literature. The purpose of this paper is to consider the nature of this dilemma and to propose a tentative solution. In essence we suggest that the problem lies not in creating a fit between the two elements for the sake of making the ‘new’ social democracy work but in rebuilding traditional social democracy. Diversity 2010-06-07 2 6 Article 10.3390/d2060897 897 909 1424-2818 2010-06-07 doi: 10.3390/d2060897 Nick Johns Mark Hyde Adrian Barton http://www.mdpi.com/1424-2818/2/6/881 Knowledge of factors that are important in reef resilience and integrity help us understand how reef ecosystems react following major anthropogenic and environmental disturbances. The North Jamaican fringing reefs have shown some recent resilience to acute disturbances from hurricanes and bleaching, in addition to the recurring chronic stressors of over-fishing and land development. Factors that can improve coral reef resilience are reviewed, and reef rugosity is shown to correlate with coral cover and growth, particularly for branching Acropora species. The biodiversity index for the Jamaican reefs was lowered after the 2005 mass bleaching event, as were the numbers of coral colonies, but both had recovered by 2009. The importance of coastal zone reef management strategies and the economic value of reefs are discussed, and a protocol is suggested for future management of Jamaican reefs. Diversity 2010-06-01 2 6 Article 10.3390/d2060881 881 896 1424-2818 2010-06-01 doi: 10.3390/d2060881 Crabbe http://www.mdpi.com/1424-2818/2/6/863 Threatened species often exhibit low genetic diversity as a result of selective sweeps, historical bottlenecks, or persistent small population size. Whereas selective sweeps create localized reduction of variation at a chromosome, population bottlenecks result in the loss of rare alleles throughout the genome. Heterozygosity is lost more slowly and is severely impacted only when populations are small for an extended period of time. We test the hypotheses of selective sweep, historical bottleneck and persistently small population size to explain extremely low genetic diversity in the critically endangered Hawaiian monk seal (Monachus schauinslandi). Of 163 microsatellite loci isolated from the species’ genome, only 17 are polymorphic. Mapping 98 monomorphic and 12 polymorphic loci to 35 chromosomes throughout the dog genome, we reject the selective sweep hypothesis. Genotyping 2,423 Hawaiian monk seals at the 17 polymorphic loci plus a locus previously isolated from another pinniped species, we find evidence for a recent bottleneck (P = 0.04). This is consistent with historical records describing intense hunting in the 19th century; however, the bottleneck was not of sufficient severity and duration to explain the genome-wide depletion of genetic diversity (HO = 0.05; A = 1.1). Long-term population size restriction is a more likely explanation. Though at least two of the polymorphic loci appear to be candidates for selection, the low genetic diversity of the species may further threaten chances for survival of this critically endangered species in a changing world. Diversity 2010-05-28 2 6 Article 10.3390/d2060863 863 880 1424-2818 2010-05-28 doi: 10.3390/d2060863 Schultz Marshall Pfunder http://www.mdpi.com/1424-2818/2/6/837 The long tradition of common bean cultivation in Italy has allowed the evolution of many landraces adapted to restricted areas. Nowadays, in response to market demands, old landraces are gradually being replaced by improved cultivars. However, landraces still survive in marginal areas of several Italian regions. Most of them appear severely endangered with risk of extinction due to the advanced age of the farmers and the socio-cultural context where they are cultivated. The present contribution is an overview of the state of the art about the knowledge of Italian common bean germplasm, describing the most important and recent progresses made in its characterization, including genetic diversity and nutritional aspects. Diversity 2010-05-27 2 6 Review 10.3390/d2060837 837 862 1424-2818 2010-05-27 doi: 10.3390/d2060837 Piergiovanni Lioi