http://www.mdpi.com/journal/diversity Latest open access articles published in Diversity at http://www.mdpi.com/journal/diversity/ http://www.mdpi.com/1424-2818/4/1/59/ 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. http://www.mdpi.com/1424-2818/4/1/59/ Fri, 10 Feb 2012 00:00:00 CET Diversity 2012-02-10 4 1 Article 59 73 1424-2818 Mosses Like It Rough—Growth Form Specific Responses of Mosses, Herbaceous and Woody Plants to Micro-Relief Heterogeneity 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. http://www.mdpi.com/1424-2818/4/1/33/ Thu, 29 Dec 2011 00:00:00 CET Diversity 2011-12-29 4 1 Article 33 58 1424-2818 Diversity-Carbon Flux Relationships in a Northwest Forest 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. http://www.mdpi.com/1424-2818/4/1/1/ Wed, 21 Dec 2011 00:00:00 CET Diversity 2011-12-21 4 1 Article 1 32 1424-2818 Social Organization of Crop Genetic Diversity. The G × E × S Interaction Model 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. http://www.mdpi.com/1424-2818/3/4/721/ Tue, 20 Dec 2011 00:00:00 CET Diversity 2011-12-20 3 4 Article 721 738 1424-2818 Phyllopshere Bacterial Community Structure of Spinach (Spinacia oleracea) as Affected by Cultivar and Environmental Conditions at Time of Harvest 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. http://www.mdpi.com/1424-2818/3/4/712/ Mon, 28 Nov 2011 00:00:00 CET Diversity 2011-11-28 3 4 Article 712 720 1424-2818 Ecological Impact on Nitrogen and Phosphorus Cycling of a Widespread Fast-growing Leguminous Tropical Forest Plantation Tree Species, Acacia mangium 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. http://www.mdpi.com/1424-2818/3/4/693/ Fri, 18 Nov 2011 00:00:00 CET Diversity 2011-11-18 3 4 Article 693 711 1424-2818 Illustration of the Structure of Arthropod Assemblages (Collembola and Lepidoptera) in Different Forest Types: An Example in the French Pyrenees 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. http://www.mdpi.com/1424-2818/3/4/660/ Wed, 09 Nov 2011 00:00:00 CET Diversity 2011-11-09 3 4 Review 660 692 1424-2818 On the Breeds of Cattle—Historic and Current Classifications 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. http://www.mdpi.com/1424-2818/3/4/641/ Fri, 28 Oct 2011 00:00:00 CEST Diversity 2011-10-28 3 4 Article 641 659 1424-2818 Genetic Diversity in Jatropha curcas Populations in the State of Chiapas, Mexico 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. http://www.mdpi.com/1424-2818/3/4/628/ Mon, 03 Oct 2011 00:00:00 CEST Diversity 2011-10-03 3 4 Article 628 640 1424-2818 Resilience of Florida Keys Coral Communities Following Large-Scale Disturbances 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. http://www.mdpi.com/1424-2818/3/4/611/ Mon, 03 Oct 2011 00:00:00 CEST Diversity 2011-10-03 3 4 Article 611 627 1424-2818 Living More Than Just Enough for the City: Persistence of High-Quality Vegetation in Natural Areas in an Urban Setting 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. http://www.mdpi.com/1424-2818/3/4/592/ Fri, 30 Sep 2011 00:00:00 CEST Diversity 2011-09-30 3 4 Article 592 610 1424-2818 Monitoring Coral Health to Determine Coral Bleaching Response at High Latitude Eastern Australian Reefs: An Applied Model for A Changing Climate 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. http://www.mdpi.com/1424-2818/3/4/581/ Thu, 29 Sep 2011 00:00:00 CEST Diversity 2011-09-29 3 4 Article 581 591 1424-2818 Using DNA Barcoding and Standardized Sampling to Compare Geographic and Habitat Differentiation of Crustaceans: A Hawaiian Islands Example 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. http://www.mdpi.com/1424-2818/3/4/547/ Mon, 26 Sep 2011 00:00:00 CEST Diversity 2011-09-26 3 4 Article 547 580 1424-2818 Diversity of Pharmacological Properties in Chinese and European Medicinal Plants: Cytotoxicity, Antiviral and Antitrypanosomal Screening of 82 Herbal Drugs 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. http://www.mdpi.com/1424-2818/3/3/531/ Wed, 21 Sep 2011 00:00:00 CEST Diversity 2011-09-21 3 3 Article 531 546 1424-2818 Forest Biodiversity Assessment in Relic Ecosystem: Monitoring and Management Practice Implications 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. http://www.mdpi.com/1424-2818/3/3/503/ Thu, 15 Sep 2011 00:00:00 CEST Diversity 2011-09-15 3 3 Review 503 530 1424-2818 Frogs, Fish and Forestry: An Integrated Watershed Network Paradigm Conserves Biodiversity and Ecological Services 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. http://www.mdpi.com/1424-2818/3/3/483/ Wed, 14 Sep 2011 00:00:00 CEST Diversity 2011-09-14 3 3 Article 483 502 1424-2818 Greater Genetic Diversity in Spatially Restricted Coral Reef Fishes Suggests Secondary Contact among Differentiated Lineages 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. http://www.mdpi.com/1424-2818/3/3/466/ Wed, 24 Aug 2011 00:00:00 CEST Diversity 2011-08-24 3 3 Article 466 482 1424-2818 Raiding the Coral Nurseries? 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. http://www.mdpi.com/1424-2818/3/3/453/ Tue, 16 Aug 2011 00:00:00 CEST Diversity 2011-08-16 3 3 Article 453 465 1424-2818 Diversity, Stand Characteristics and Spatial Aggregation of Tree Species in a Bangladesh Forest Ecosystem 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. http://www.mdpi.com/1424-2818/3/3/424/ Fri, 12 Aug 2011 00:00:00 CEST Diversity 2011-08-12 3 3 Review 424 452 1424-2818 Changes in Biodiversity and Functioning of Reef Fish Assemblages following Coral Bleaching and Coral Loss 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. http://www.mdpi.com/1424-2818/3/3/405/ Fri, 12 Aug 2011 00:00:00 CEST Diversity 2011-08-12 3 3 Review 405 423 1424-2818 Novel Genetic Diversity Through Somatic Mutations: Fuel for Adaptation of Reef Corals? 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. http://www.mdpi.com/1424-2818/3/3/390/ Mon, 08 Aug 2011 00:00:00 CEST Diversity 2011-08-08 3 3 Article 390 404 1424-2818 No Evidence for Temporal Variation in a Cryptic Species Community of Freshwater Amphipods of the Hyalella azteca Species Complex 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. http://www.mdpi.com/1424-2818/3/3/375/ Mon, 08 Aug 2011 00:00:00 CEST Diversity 2011-08-08 3 3 Article 375 389 1424-2818 Genetic Risk Assessment of a Threatened Remnant Population of Hairy Prairie-Clover (Dalea villosa var. villosa) in the Canadian Prairie 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. http://www.mdpi.com/1424-2818/3/3/356/ Tue, 19 Jul 2011 00:00:00 CEST Diversity 2011-07-19 3 3 Article 356 374 1424-2818 Infection Dynamics Vary between Symbiodinium Types and Cell Surface Treatments during Establishment of Endosymbiosis with Coral Larvae 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. http://www.mdpi.com/1424-2818/3/3/329/ Tue, 19 Jul 2011 00:00:00 CEST Diversity 2011-07-19 3 3 Article 329 355 1424-2818 Species Richness and Community Structure on a High Latitude Reef: Implications for Conservation and Management 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. http://www.mdpi.com/1424-2818/3/3/308/ Tue, 19 Jul 2011 00:00:00 CEST Diversity 2011-07-19 3 3 Article 308 328 1424-2818 Soil Rhizosphere Microbial Communities and Enzyme Activities under Organic Farming in Alabama 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. http://www.mdpi.com/1424-2818/3/3/296/ Mon, 27 Jun 2011 00:00:00 CEST Diversity 2011-06-27 3 3 Article 296 307 1424-2818 Juvenile Coral Abundance Has Decreased by More Than 50% in Only Three Decades on a Small Caribbean Island 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. http://www.mdpi.com/1424-2818/3/2/275/ Thu, 16 Jun 2011 00:00:00 CEST Diversity 2011-06-16 3 2 Article 275 295 1424-2818 Spatial Identification of Statewide Areas for Conservation Focus in New Mexico: Implications for State Conservation Efforts 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. http://www.mdpi.com/1424-2818/3/2/262/ Mon, 30 May 2011 00:00:00 CEST Diversity 2011-05-30 3 2 Review 262 274 1424-2818 Ocean Acidification and Coral Reefs: An Emerging Big Picture 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. http://www.mdpi.com/1424-2818/3/2/252/ Thu, 26 May 2011 00:00:00 CEST Diversity 2011-05-26 3 2 Article 252 261 1424-2818 Using Maximum Entropy Modeling for Optimal Selection of Sampling Sites for Monitoring Networks 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. http://www.mdpi.com/1424-2818/3/2/235/ Thu, 19 May 2011 00:00:00 CEST Diversity 2011-05-19 3 2 Article 235 251 1424-2818 Invasion Age and Invader Removal Alter Species Cover and Composition at the Suisun Tidal Marsh, California, USA 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. http://www.mdpi.com/1424-2818/3/2/217/ Thu, 28 Apr 2011 00:00:00 CEST Diversity 2011-04-28 3 2 Article 217 234 1424-2818 Mineral Licks as Diversity Hotspots in Lowland Forest of Eastern Ecuador 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. http://www.mdpi.com/1424-2818/3/2/200/ Thu, 14 Apr 2011 00:00:00 CEST Diversity 2011-04-14 3 2 Article 200 216 1424-2818 Relative Influence of Prior Life Stages and Habitat Variables on Dragonfly (Odonata: Gomphidae) Densities among Lake Sites 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. http://www.mdpi.com/1424-2818/3/2/176/ Thu, 14 Apr 2011 00:00:00 CEST Diversity 2011-04-14 3 2 Review 176 199 1424-2818 Diversity Patterns of Benthic Macrofauna Caused by Marine Fish Farming 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. http://www.mdpi.com/1424-2818/3/1/155/ Tue, 15 Mar 2011 00:00:00 CET Diversity 2011-03-15 3 1 Article 155 175 1424-2818 Invasion by Exotic Earthworms Alters Biodiversity and Communities of Litter- and Soil-dwelling Oribatid Mites 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. http://www.mdpi.com/1424-2818/3/1/136/ Mon, 07 Mar 2011 00:00:00 CET Diversity 2011-03-07 3 1 Article 136 154 1424-2818 New Armenian Wood-Associated Coprinoid Mushrooms: Coprinopsis strossmayeri and Coprinellus aff. radians 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. http://www.mdpi.com/1424-2818/3/1/121/ Fri, 04 Mar 2011 00:00:00 CET Diversity 2011-03-04 3 1 Article 121 135 1424-2818 Nucleotide Diversities and Genetic Relationship in the Three Japanese Pine Species; Pinus thunbergii, Pinus densiflora, and Pinus luchuensis 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. http://www.mdpi.com/1424-2818/3/1/112/ Wed, 16 Feb 2011 00:00:00 CET Diversity 2011-02-16 3 1 Article 112 120 1424-2818 rich: An R Package to Analyse Species Richness 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. http://www.mdpi.com/1424-2818/3/1/91/ Fri, 28 Jan 2011 00:00:00 CET Diversity 2011-01-28 3 1 Article 91 111 1424-2818 The Impact of Climate Change on Recent Vegetation Changes on Dovrefjell, Norway 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. http://www.mdpi.com/1424-2818/3/1/8/ Fri, 28 Jan 2011 00:00:00 CET Diversity 2011-01-28 3 1 Review 8 90 1424-2818 Response of Mycorrhizal Diversity to Current Climatic Changes 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. http://www.mdpi.com/1424-2818/3/1/1/ Tue, 18 Jan 2011 00:00:00 CET Diversity 2011-01-18 3 1 Short Note 1 7 1424-2818 Higher-Level Targets for Ecosystem Services and Biodiversity Should Focus on Regional Capacity for Effective Trade-Offs 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. http://www.mdpi.com/1424-2818/2/11/1205/ Mon, 22 Nov 2010 00:00:00 CET Diversity 2010-11-22 2 11 Article 1205 1222 1424-2818 Multilocus Sequence Typing Reveals Relevant Genetic Variation and Different Evolutionary Dynamics among Strains of Xanthomonas arboricola pv. juglandis 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. http://www.mdpi.com/1424-2818/2/11/1181/ Fri, 19 Nov 2010 00:00:00 CET Diversity 2010-11-19 2 11 Article 1181 1204 1424-2818 The CC-Bio Project: Studying the Effects of Climate Change on Quebec Biodiversity 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. http://www.mdpi.com/1424-2818/2/11/1158/ Mon, 15 Nov 2010 00:00:00 CET Diversity 2010-11-15 2 11 Article 1158 1180 1424-2818 Distribution of the Genus Passiflora L. Diversity in Colombia and Its Potential as an Indicator for Biodiversity Management in the Coffee Growing Zone 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. http://www.mdpi.com/1424-2818/2/10/1146/ Tue, 12 Oct 2010 00:00:00 CEST Diversity 2010-10-12 2 10 Article 1146 1157 1424-2818 Responses of Bats to Forest Fragmentation in the Mississippi River Alluvial Valley, Arkansas, USA 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. http://www.mdpi.com/1424-2818/2/9/1130/ Fri, 03 Sep 2010 00:00:00 CEST Diversity 2010-09-03 2 9 Article 1130 1145 1424-2818 Cultural Diversity Issues in Biodiversity Monitoring—Cases of Lithuania, Poland and Denmark 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. http://www.mdpi.com/1424-2818/2/9/1118/ Tue, 31 Aug 2010 00:00:00 CEST Diversity 2010-08-31 2 9 Article 1118 1129 1424-2818 Telomere Length Diversity in Cattle Breeds 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. http://www.mdpi.com/1424-2818/2/9/1097/ Tue, 31 Aug 2010 00:00:00 CEST Diversity 2010-08-31 2 9 Article 1097 1117 1424-2818 Diversity, Conflict and Growth: Theory and Evidence 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. http://www.mdpi.com/1424-2818/2/9/1085/ Fri, 27 Aug 2010 00:00:00 CEST Diversity 2010-08-27 2 9 Review 1085 1096 1424-2818 Understanding the Extent and Sources of Variation in Gut Microbiota Studies; a Prerequisite for Establishing Associations with Disease 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. http://www.mdpi.com/1424-2818/2/8/1059/ Thu, 05 Aug 2010 00:00:00 CEST Diversity 2010-08-05 2 8 Article 1059 1084 1424-2818 Cultural Diversity as a Concept of Global Law: Origins, Evolution and Prospects 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. http://www.mdpi.com/1424-2818/2/8/1048/ Thu, 29 Jul 2010 00:00:00 CEST Diversity 2010-07-29 2 8 Article 1048 1058 1424-2818 The Role of Volunteering in an Era of Cultural Transition: Can It Provide a Role Identity for Older People from Asian Cultures? 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. http://www.mdpi.com/1424-2818/2/7/1026/ Thu, 22 Jul 2010 00:00:00 CEST Diversity 2010-07-22 2 7 Article 1026 1047 1424-2818 Molecular Characterization of the Archaeal Community in an Amazonian Wetland Soil and Culture-Dependent Isolation of Methanogenic Archaea 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. http://www.mdpi.com/1424-2818/2/7/1015/ Wed, 21 Jul 2010 00:00:00 CEST Diversity 2010-07-21 2 7 Article 1015 1025 1424-2818 TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels 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. http://www.mdpi.com/1424-2818/2/7/973/ Fri, 16 Jul 2010 00:00:00 CEST Diversity 2010-07-16 2 7 Review 973 1014 1424-2818 Methods to Estimate the Diversity in the Marine Photosynthetic Protist Community with Illustrations from Case Studies: A Review 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). http://www.mdpi.com/1424-2818/2/7/959/ Thu, 01 Jul 2010 00:00:00 CEST Diversity 2010-07-01 2 7 Article 959 972 1424-2818 Identity Reconfiguration of Immigrants in Portugal 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. http://www.mdpi.com/1424-2818/2/6/946/ Thu, 17 Jun 2010 00:00:00 CEST Diversity 2010-06-17 2 6 Review 946 958 1424-2818 Using Molecular-Assisted Alpha Taxonomy to Better Understand Red Algal Biodiversity in Bermuda 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. http://www.mdpi.com/1424-2818/2/6/932/ Thu, 17 Jun 2010 00:00:00 CEST Diversity 2010-06-17 2 6 Article 932 945 1424-2818 Spatial Trends of Genetic Variation of Domestic Ruminants in Europe 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. http://www.mdpi.com/1424-2818/2/6/910/ Mon, 07 Jun 2010 00:00:00 CEST Diversity 2010-06-07 2 6 Article 910 931 1424-2818 Microbial Community Composition as Affected by Dryland Cropping Systems and Tillage in a Semiarid Sandy Soil 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. http://www.mdpi.com/1424-2818/2/6/897/ Mon, 07 Jun 2010 00:00:00 CEST Diversity 2010-06-07 2 6 Article 897 909 1424-2818 Diversity or Solidarity? Making Sense of the “New” Social Democracy 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. http://www.mdpi.com/1424-2818/2/6/881/ Tue, 01 Jun 2010 00:00:00 CEST Diversity 2010-06-01 2 6 Article 881 896 1424-2818 Coral Ecosystem Resilience, Conservation and Management on the Reefs of Jamaica in the Face of Anthropogenic Activities and Climate Change 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. http://www.mdpi.com/1424-2818/2/6/863/ Fri, 28 May 2010 00:00:00 CEST Diversity 2010-05-28 2 6 Article 863 880 1424-2818 Genome-Wide Loss of Diversity in the Critically Endangered Hawaiian Monk Seal 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. http://www.mdpi.com/1424-2818/2/6/837/ Thu, 27 May 2010 00:00:00 CEST Diversity 2010-05-27 2 6 Review 837 862 1424-2818 Italian Common Bean Landraces: History, Genetic Diversity and Seed Quality 2010-05-27 doi: 10.3390/d2060837 Piergiovanni Lioi http://www.mdpi.com/1424-2818/2/5/810/ Jatropha curcas L. (2n = 2x = 22) is becoming a popular non-food oleaginous crop in several developed countries due to its proposed value in the biopharmaceutical industry. Despite the potentials of its oil-rich seeds as a renewable source of biodiesel and an interest in large-scale cultivation, relatively little is known with respect to plant reproduction strategies and population dynamics. Here, genomic DNA markers and FCSS analyses were performed to gain insights into ploidy variation and heterozygosity levels of multiple accessions, and genomic relationships among commercial varieties of Jatropha grown in different geographical areas. The determination of ploidy and the differentiation of either pseudogamous or autonomous apomixis from sexuality were based on the seed DNA contents of embryo and endosperm. The presence of only a high 2C embryo peak and a smaller 3C endosperm peak (ratio 2:3) is consistent with an obligate sexual reproductive system. Because of the lack of either 4C or 5C endosperm DNA estimates, the occurrence of gametophytic apomixis seems unlikely in this species but adventitious embryony cannot be ruled out. The investigation of genetic variation within and between cultivated populations was carried out using dominant RAPD and Inter-SSR markers, and codominant SSR markers. Nei’s genetic diversity, corresponding to the expected heterozygosity, was equal to He = 0.3491 and the fixation index as low as Fst = 0.2042. The main finding is that seeds commercialized worldwide include a few closely related genotypes, which are not representative of the original Mexican gene pool, revealing high degrees of homozygosity for single varieties and very low genetic diversity between varieties. http://www.mdpi.com/1424-2818/2/5/810/ Tue, 25 May 2010 00:00:00 CEST Diversity 2010-05-25 2 5 Article 810 836 1424-2818 DNA Markers and FCSS Analyses Shed Light on the Genetic Diversity and Reproductive Strategy of Jatropha curcas L. 2010-05-25 doi: 10.3390/d2050810 Ambrosi Galla Purelli Barbi Fabbri Lucretti Sharbel Barcaccia http://www.mdpi.com/1424-2818/2/5/787/ The processes of land conversion and agricultural intensification are a significant cause of biodiversity loss, with consequent negative effects both on the environment and the sustainability of food production.The anthrosols associated with pre-Colombian settlements in the Amazonian region are examples of how anthropogenic activities may sustain the native populations against harsh tropical environments for human establishment, even without a previous intentionality of anthropic soil formation. In a case study (Model I—“Slash-and-Burn”) the community structures detected by automated ribosomal intergenic spacer analysis (ARISA) revealed that soil archaeal, bacterial and fungal communities are heterogeneous and each capable of responding differently to environmental characteristics. ARISA data evidenced considerable difference in structure existing between microbial communities in forest and agricultural soils. In a second study (Model II—“Anthropogenic Soil”), the bacterial community structures revealed by terminal restriction fragment length polymorphism (T-RFLP) differed among an Amazonian Dark Earth (ADE), black carbon (BC) and its adjacent non-anthropogenic oxisoil. The bacterial 16S rRNA gene (OTU) richness estimated by pyrosequencing was higher in ADE than BC. The most abundant bacterial phyla in ADE soils and BC were Proteobacteria—24% ADE, 15% BC; Acidobacteria—10% ADE, 21% BC; Actinobacteria—7% ADE, 12% BC; Verrucomicrobia, 8% ADE; 9% BC; Firmicutes—3% ADE, 8% BC. Overall, unclassified bacteria corresponded to 36% ADE, and 26% BC. Regardless of current land uses, our data suggest that soil microbial community structures may be strongly influenced by the historical soil management and that anthrosols in Amazonia, of anthropogenic origins, in addition to their capacity of enhancing crop yields, may also improve microbial diversity, with the support of the black carbon, which may sustain a particular and unique habitat for the microbes. http://www.mdpi.com/1424-2818/2/5/787/ Wed, 19 May 2010 00:00:00 CEST Diversity 2010-05-19 2 5 Article 787 809 1424-2818 A Molecular Survey of the Diversity of Microbial Communities in Different Amazonian Agricultural Model Systems 2010-05-19 doi: 10.3390/d2050787 Navarrete Cannavan Taketani Tsai http://www.mdpi.com/1424-2818/2/5/768/ Genetic resources of crop plants are essential for crop breeding. They are conserved in gene banks in form of a large numbers of accessions. These accessions harbor allelic variants of agronomically important genes and molecular tools allow a rapid assessment of this allelic diversity. Here, we have screened a collection of 1005 wheat gene bank accessions for powdery mildew resistance and a molecular characterization for functional alleles at the wheat powdery mildew resistance locus Pm3 was carried out mostly on the resistant accessions. The two analyzed sets of accessions consisted of 733 accessions originating from 20 different countries and 272 landraces originating specifically from Afghanistan. The Pm3 haplotype (indicating the presence of a Pm3-type of gene, susceptible or resistant) was found to be abundantly present in both sets. The accessions with a Pm3 haplotype were further screened for the presence of the functional Pm3a to Pm3g alleles using allele-specific molecular markers. Pm3b and Pm3c were the most frequently found alleles while the other five alleles were detected only in few accessions (Pm3d, Pm3e, Pm3f) or not detected at all (Pm3a, Pm3g). The data further showed that Pm3b is the major source of Pm3-mediated powdery mildew resistance in wheat accessions from Afghanistan. Susceptible allelic variants of Pm3 were found to be widespread in the wheat gene pool. The presented molecular analysis of Pm3 alleles in a diverse set of wheat accessions indicates that several alleles have defined geographical origins. Possibly, the widespread Pm3b and Pm3c alleles evolved relatively early in wheat cultivation, allowing their subsequent diffusion into a broad set of wheat lines. http://www.mdpi.com/1424-2818/2/5/768/ Wed, 19 May 2010 00:00:00 CEST Diversity 2010-05-19 2 5 Article 768 786 1424-2818 Genetic Diversity of the Pm3 Powdery Mildew Resistance Alleles in Wheat Gene Bank Accessions as Assessed by Molecular Markers 2010-05-19 doi: 10.3390/d2050768 Bhullar Mackay Keller http://www.mdpi.com/1424-2818/2/5/738/ We used near-term climate scenarios for the continental United States, to model 12 invasive plants species. We created three potential habitat suitability models for each species using maximum entropy modeling: (1) current; (2) 2020; and (3) 2035. Area under the curve values for the models ranged from 0.92 to 0.70, with 10 of the 12 being above 0.83 suggesting strong and predictable species-environment matching. Change in area between the current potential habitat and 2035 ranged from a potential habitat loss of about 217,000 km2, to a potential habitat gain of about 133,000 km2. http://www.mdpi.com/1424-2818/2/5/738/ Wed, 12 May 2010 00:00:00 CEST Diversity 2010-05-12 2 5 Article 738 767 1424-2818 From Points to Forecasts: Predicting Invasive Species Habitat Suitability in the Near Term 2010-05-12 doi: 10.3390/d2050738 Holcombe Stohlgren Jarnevich http://www.mdpi.com/1424-2818/2/5/717/ Top-down controls of complex foodwebs maintain the balance among the critical groups of corals, algae, and herbivores, thus allowing the persistence of corals reefs as three-dimensional, biogenic structures with high biodiversity, heterogeneity, resistance, resilience and connectivity, and the delivery of essential goods and services to societies. On contemporary reefs world-wide, however, top-down controls have been weakened due to reduction in herbivory levels (overfishing or disease outbreak) while bottom-up controls have increased due to water quality degradation (increase in sediment and nutrient load) and climate forcing (seawater warming and acidification) leading to algal-dominated alternate benthic states of coral reefs, which are indicative of a trajectory towards ecological extinction. Management to reverse common trajectories of degradation for coral reefs necessitates a shift from optimization in marine resource use and conservation towards building socio-economic resilience into coral reef systems while attending to the most manageable human impacts (fishing and water quality) and the global-scale causes (climate change). http://www.mdpi.com/1424-2818/2/5/717/ Tue, 11 May 2010 00:00:00 CEST Diversity 2010-05-11 2 5 Review 717 737 1424-2818 Ecological Processes and Contemporary Coral Reef Management 2010-05-11 doi: 10.3390/d2050717 Dikou http://www.mdpi.com/1424-2818/2/5/701/ In this study, we present the morphological and molecular characterization of the ‘Badda’ bean, a landrace of outstanding organoleptic qualities that is diffused in the area of Polizzi in the province of Palermo in Sicily, Italy. This landrace is entitled to be valorized in the local market and therefore needs a thorough description to draw criteria to establish its distinctiveness from landraces with morphological and geographical proximity. Three ‘Badda’ accessions, representing the morphological variability within the landrace, have been evaluated together with suitable references. With the help of morpho-physiological traits, digital scanning of apical leaflets and ISSR molecular markers, we describe a spectrum of descriptors useful to distinguish the ‘Badda’ accessions among themselves and from similar landraces. http://www.mdpi.com/1424-2818/2/5/701/ Wed, 05 May 2010 00:00:00 CEST Diversity 2010-05-05 2 5 Article 701 716 1424-2818 Distinctiveness of Bean Landraces in Italy: the Case Study of the ‘Badda’ Bean 2010-05-05 doi: 10.3390/d2050701 Paniconi Gianfilippi Mosconi Mazzucato http://www.mdpi.com/1424-2818/2/4/679/ This report is a review of some of the results obtained over the course of 20 years spent investigating hemoglobin phenotypes and the related functional effects on hematological patterns in ruminant breeds. Tests included qualitative and quantitative analyses of hemoglobins and qualitative and quantitative analyses of α and β globins, as well as hemochromocytometric analysis. Understanding the adaptive significance of the hemoglobin variants was the goal of most of these investigations. The advances presented in this review and the previously unpublished findings included here provide evidence that Mediterranean breeds exhibit a fair number of positively charged variants, whose possible adaptive significance is discussed. http://www.mdpi.com/1424-2818/2/4/679/ Thu, 22 Apr 2010 00:00:00 CEST Diversity 2010-04-22 2 4 Review 679 700 1424-2818 Insights into Hemoglobin Polymorphism and Related Functional Effects on Hematological Pattern in Mediterranean Cattle, Goat and Sheep 2010-04-22 doi: 10.3390/d2040679 Pieragostini Alloggio Petazzi http://www.mdpi.com/1424-2818/2/4/653/ The chloroplast trnL-F region has been extensively utilized for evolutionary analysis in plants. In the Brassicaceae this fragment contains 1–12 tandemly repeated trnF pseudogene copies in addition to the functional trnF gene. Here we assessed the potential of these highly variable, but complexly evolving duplications, to resolve the population history of the model plant Arabidopsis lyrata. While the region 5’ of the duplications had negligible sequence diversity, extensive variation in pseudogene copy number and nucleotide composition revealed otherwise cryptic population structure in eastern North America. Thus structural changes can be phylogeographically informative when pseudogene evolutionary relationships can be resolved. http://www.mdpi.com/1424-2818/2/4/653/ Thu, 22 Apr 2010 00:00:00 CEST Diversity 2010-04-22 2 4 Article 653 678 1424-2818 Using Chloroplast trnF Pseudogenes for Phylogeography in Arabidopsis Lyrata 2010-04-22 doi: 10.3390/d2040653 Tedder Hoebe Ansell Mable http://www.mdpi.com/1424-2818/2/4/618/ Although the Neotropics are recognized as a region rich in biological diversity, the origin, evolution, and maintenance of this phenomenon continues to be debated. Historical ecologists and landscape archaeologists point out that the Neotropics have a long, complex human history that may have been a key factor in the creation, shaping, and management of present day biodiversity. The construction of monumental earthworks referred to as ring ditches of the Bolivian Amazon and surrounding regions in late prehistory had considerable impact on the fauna, flora, soils, and topography of forest islands. Patterned landscape features, historical documents, energetics, and historical ecology are used to understand the transformation of forest islands into anthropogenic built environments. http://www.mdpi.com/1424-2818/2/4/618/ Mon, 19 Apr 2010 00:00:00 CEST Diversity 2010-04-19 2 4 Article 618 652 1424-2818 The Transformation of Environment into Landscape: The Historical Ecology of Monumental Earthwork Construction in the Bolivian Amazon 2010-04-19 doi: 10.3390/d2040619 Erickson http://www.mdpi.com/1424-2818/2/4/610/ Honey is produced by honeybees from nectar and from secretions of living plants. It reflects the honeybees’ diet and the local plant communities. Honey also shows different plant compositions in different geographical locations. We propose a new method for studying the plant diversity and the geographical origin of honey using a DNA barcoding approach that combines universal primers and massive parallel pyrosequencing. To test this method we use two commercial honeys, one from a regional origin and one composed of a worldwide mix of different honeys. We demonstrate that the method proposed here is fast, simple to implement, more robust than classical methods, and therefore suitable for analyzing plant diversity in honey. http://www.mdpi.com/1424-2818/2/4/610/ Mon, 19 Apr 2010 00:00:00 CEST Diversity 2010-04-19 2 4 Article 610 617 1424-2818 DNA Barcoding for Honey Biodiversity 2010-04-19 doi: 10.3390/d2040610 Valentini Miquel Taberlet http://www.mdpi.com/1424-2818/2/4/586/ While bitter manioc has been one of the most important staple crops in the central Amazon for thousands of years, there have been few studies of its cultivation in the fertile whitewater landscapes of this region. Anthropological research on bitter manioc cultivation in the Amazon has focused almost exclusively on long-fallow shifting cultivation in marginal upland areas of low soil fertility. This has contributed to the persistence of the oversimplified notion that because bitter manioc is well adapted to infertile upland soils; it cannot yield well in alluvial and/or fertile soils. I hypothesized that bitter manioc cultivation would be well adapted to the fertile soils of the whitewater landscapes of the central Amazon because of the centrality of this crop to subsistence in this region. In this article, I examine one such whitewater landscape, the middle Madeira River, Amazonas, Brazil, where smallholders cultivate bitter manioc on fertile Amazonian Dark Earths (ADE) and floodplain soils, and on infertile Oxisols and Ultisols. In this region, cultivation on fertile soils tends to be short-cycled, characterised by short fallowing (0–6 years) and shorter cropping periods (5–12 months) with a predominance of low starch fast maturing “weak” landraces. By contrast, cultivation on infertile soils is normally long-cycled, characterised by longer fallows (>10 years) and longer cropping periods (1–3 years) with a predominance of high starch slow maturing “strong” landraces. This diversity in bitter manioc cultivation systems (landraces, fallow periods, soils) demonstrates that Amazonian farmers have adapted bitter manioc cultivation to the specific characteristics of the landscapes that they inhabit. I conclude that contrary to earlier claims, there are no ecological limitations on growing bitter manioc in fertile soils, and therefore the cultivation of this crop in floodplain and ADE soils would have been possible in the pre-Columbian period. http://www.mdpi.com/1424-2818/2/4/586/ Fri, 16 Apr 2010 00:00:00 CEST Diversity 2010-04-16 2 4 Article 586 609 1424-2818 The Diversity of Bitter Manioc (Manihot Esculenta Crantz) Cultivation in a Whitewater Amazonian Landscape 2010-04-16 doi: 10.3390/d2040586 Fraser http://www.mdpi.com/1424-2818/2/4/572/ There seem to be a certain degree of reluctance in accepting ILP-based methods as part of the range of molecular markers that are classically used for plant genotyping. Indeed, since DNA polymorphism results from difference in length of fragments amplified from specific gene loci, not anonymous sequences, the number of markers that can be generated is sometime inadequate for classical phylogeny studies. Yet, ILP-based markers have many other useful advantages that should not go neglected. We support this statement by presenting a large variety of data we have been collecting for a long while regarding the use of cTBP, an ILP marker based on difference in length of the introns present within the members of the plant beta-tubulin gene family. http://www.mdpi.com/1424-2818/2/4/572/ Thu, 15 Apr 2010 00:00:00 CEST Diversity 2010-04-15 2 4 Article 572 585 1424-2818 cTBP: A Successful Intron Length Polymorphism (ILP)-Based Genotyping Method Targeted to Well Defined Experimental Needs 2010-04-15 doi: 10.3390/d2040572 Braglia Manca Mastromauro Breviario http://www.mdpi.com/1424-2818/2/4/561/ The domestic camel (dromedary) is the most important livestock species in the Canary Islands and the most important autochthonous European camel population. After six centuries of a successful adaptation process to the particular environment of the Canary Islands, the abandonment of traditional agriculture has led this population to a major bottleneck. Along with a lack of foreign genetic interchanges, this could lead the population to the brink of extinction. Genetic analysis using 13 microsatellites showed the closest genetic proximity to the North African (Tindouf, Algeria) camel population and a certain degree of sub-division, with significant genetic differences among breeders. An important level of genetic differentiation among the different populations analyzed was found with a global FST value of 0.116. http://www.mdpi.com/1424-2818/2/4/561/ Wed, 07 Apr 2010 00:00:00 CEST Diversity 2010-04-07 2 4 Article 561 571 1424-2818 The Canarian Camel: A Traditional Dromedary Population 2010-04-07 doi: 10.3390/d2040561 Schulz Tupac-Yupanqui Martínez Méndez Delgado Gómez Dunner Cañón http://www.mdpi.com/1424-2818/2/4/550/ Variation in individual density may explain the unimodal richness-biomass relationship in which species richness peaks at an intermediate level of total biomass. However, it is unclear how individual density is regulated by community thinning (i.e., mortality due to competition with neighbors) as total above-ground biomass increases. We developed a simulation model which demonstrates that the spatial structure of a population can influence the initiation and rate of community thinning and thus the shape of the richness-biomass relationship. Specifically, we found that more clustered populations resulted in a more abrupt initiation and rapid rate of thinning and thus a sharper unimodal richness-biomass relationship. Our simulation also demonstrated that a wide diversity of richness-biomass relationships can be produced by community-thinning. http://www.mdpi.com/1424-2818/2/4/550/ Tue, 06 Apr 2010 00:00:00 CEST Diversity 2010-04-06 2 4 Article 550 560 1424-2818 Spatial Structure Alters the Shape of the Unimodal Species Richness-Biomass Relationship in a Neutral Model 2010-04-06 doi: 10.3390/d2040550 McGlinn Palmer http://www.mdpi.com/1424-2818/2/4/527/ The southwestern highlands forests of Ethiopia are the origin of the coffee plant Coffea arabica. The production of coffee in this area is affected by tracheomycosis caused by a soil-born fungus Gibberella xylarioides. The use of endemic antagonistic strains of mycoparasitic Trichoderma species would be a nature conserving means to combat this disease. We have used molecular methods to reveal that the community of Trichoderma in the rhizosphere of C. arabica in its native forests is highly diverse and includes many putatively endemic species. Among others, the putative new species were particularly efficient to inhibit growth of G. xylarioides. http://www.mdpi.com/1424-2818/2/4/527/ Mon, 05 Apr 2010 00:00:00 CEST Diversity 2010-04-05 2 4 Article 527 549 1424-2818 The Rhizosphere of Coffea Arabica in Its Native Highland Forests of Ethiopia Provides a Niche for a Distinguished Diversity of Trichoderma 2010-04-05 doi: 10.3390/d2040527 Belayneh Mulaw Kubicek Druzhinina http://www.mdpi.com/1424-2818/2/4/505/ Molecular analysis of the bacterial community structure associated with sludge processed by autothermal thermophilic aerobic digestion (ATAD), was performed using a number of extraction and amplification procedures which differed in yield, integrity, ability to amplify extracted templates and specificity in recovering species present. Interference to PCR and qPCR amplification was observed due to chelation, nuclease activity and the presence of thermolabile components derived from the ATAD sludge. Addition of selected adjuvant restored the ability to amplify community DNA, derived from the thermophilic sludge, via a number of primer sets of ecological importance and various DNA polymerases. Resolution of community profiles by molecular techniques was also influenced by the ATAD sludge extraction procedure as demonstrated by PCR-DGGE profiling and comparison of taxonomic affiliations of the most predominant members within 16S rRNA gene libraries constructed from ATAD DNA extracted by different methods. Several modifications have been shown to be necessary to optimize the molecular analysis of the ATAD thermal niche which may have general applicability to diversity recovery from similar environments. http://www.mdpi.com/1424-2818/2/4/505/ Wed, 31 Mar 2010 00:00:00 CEST Diversity 2010-03-31 2 4 Article 505 526 1424-2818 Molecular Analysis of Bacterial Community DNA in Sludge Undergoing Autothermal Thermophilic Aerobic Digestion (ATAD): Pitfalls and Improved Methodology to Enhance Diversity Recovery 2010-03-31 doi: 10.3390/d2040505 Piterina Bartlett Pembroke http://www.mdpi.com/1424-2818/2/4/473/ The emergence of sedentism and agriculture in Amazonia continues to sit uncomfortably within accounts of South American pre-Columbian history. This is partially because deep-seated models were formulated when only ceramic evidence was known, partly because newer data continue to defy simple explanations, and partially because many discussions continue to ignore evidence of pre-Columbian anthropogenic landscape transformations. This paper presents the results of recent geoarchaeological research on Amazonian anthropogenic soils. It advances the argument that properties of two different types of soils, terras pretas and terras mulatas, support their interpretation as correlates of, respectively, past settlement areas and fields where spatially-intensive, organic amendment-reliant cultivation took place. This assessment identifies anthropogenic soil formation as a hallmark of the Amazonian Formative and prompts questions about when similar forms of enrichment first appear in the Amazon basin. The paper reviews evidence for embryonic anthrosol formation to highlight its significance for understanding the domestication of a key Amazonian crop: manioc (Manihot esculenta ssp. esculenta). A model for manioc domestication that incorporates anthropogenic soils outlines some scenarios which link the distribution of its two broader varieties—sweet and bitter manioc—with the widespread appearance of Amazonian anthropogenic dark earths during the first millennium AD. http://www.mdpi.com/1424-2818/2/4/473/ Mon, 29 Mar 2010 00:00:00 CEST Diversity 2010-03-29 2 4 Article 473 504 1424-2818 The Amazonian Formative: Crop Domestication and Anthropogenic Soils 2010-03-29 doi: 10.3390/d2040473 Arroyo-Kalin http://www.mdpi.com/1424-2818/2/4/450/ ‘Biodiversity’ means the variety of life and it can be studied at different levels (genetic, species, ecosystem) and scales (spatial and temporal). Last decades showed that marine biodiversity has been severely underestimated at all levels. In order to investigate diversity patterns and underlying processes, there is a need to know what species live in the marine environment. An emerging tool for species identification, DNA barcoding can reliably assign unknown specimens to known species, also flagging potential cryptic species and genetically distant populations. This paper will review the role of DNA barcoding for the study of marine biodiversity at the species level. http://www.mdpi.com/1424-2818/2/4/450/ Thu, 25 Mar 2010 00:00:00 CET Diversity 2010-03-25 2 4 Review 450 472 1424-2818 DNA Barcodes for Marine Biodiversity: Moving Fast Forward? 2010-03-25 doi: 10.3390/d2040450 Radulovici Archambault Dufresne http://www.mdpi.com/1424-2818/2/4/439/ Tobacco (Nicotiana tabacum L.) is an important agricultural crop plant for the economy of many countries. Assessment of the genetic diversity of cultivated tobacco varieties is of importance for long-term tobacco improvement. Microsatellite markers are currently the marker system of choice for genetic analysis of allopolyploid plants. In this study, we evaluated the use of 30 microsatellite markers for identification of 10 varieties of cultivated tobacco in the Republic of Macedonia. We found 24 of the microsatellite markers to be polymorphic and sufficient for identification of these varieties. Cluster analysis showed that Macedonian tobacco varieties are classifiable into three distinct groups. http://www.mdpi.com/1424-2818/2/4/439/ Wed, 24 Mar 2010 00:00:00 CET Diversity 2010-03-24 2 4 Article 439 449 1424-2818 Genetic Variability of Macedonian Tobacco Varieties Determined by Microsatellite Marker Analysis 2010-03-24 doi: 10.3390/d2040439 Davalieva Maleva Filiposki Spiroski Efremov http://www.mdpi.com/1424-2818/2/3/411/ Neospora caninum is a parasite regarded a major cause of foetal loss in cattle. A key requirement to an understanding of the epidemiology and pathogenicity of N. caninum is knowledge of the biological characteristics of the species and the genetic diversity within it. Due to the broad intermediate host range of the species, worldwide geographical distribution and its capacity for sexual reproduction, significant biological and genetic differences might be expected to exist. N. caninum has now been isolated from a variety of different host species including dogs and cattle. Although isolates of this parasite show only minor differences in ultrastructure, considerable differences have been reported in pathogenicity using mainly mouse models. At the DNA level, marked levels of polymorphism between isolates were detected in mini- and microsatellites found in the genome of N. caninum. Knowledge of what drives the biological differences that have been observed between the various isolates at the molecular level is crucial in aiding our understanding of the epidemiology of this parasite and, in turn, the development of efficacious strategies, such as live vaccines, for controlling its impact. The purpose of this review is to document and discuss for the first time, the nature of the diversity found within the species Neospora caninum. http://www.mdpi.com/1424-2818/2/3/411/ Mon, 22 Mar 2010 00:00:00 CET Diversity 2010-03-22 2 3 Review 411 438 1424-2818 On the Biological and Genetic Diversity in Neospora caninum 2010-03-22 doi: 10.3390/d2030411 Al-Qassab Reichel Ellis http://www.mdpi.com/1424-2818/2/3/395/ Complex systems science has contributed to our understanding of ecology in important areas such as food webs, patch dynamics and population fluctuations. This has been achieved through the use of simple measures that can capture the difference between order and disorder and simple models with local interactions that can generate surprising behaviour at larger scales. However, close examination reveals that commonly applied definitions of complexity fail to accommodate some key features of ecological systems, a fact that will limit the contribution of complex systems science to ecology. We highlight these features of ecological complexity—such as diversity, cross-scale interactions, memory and environmental variability—that continue to challenge classical complex systems science. Further advances in these areas will be necessary before complex systems science can be widely applied to understand the dynamics of ecological systems. http://www.mdpi.com/1424-2818/2/3/395/ Mon, 15 Mar 2010 00:00:00 CET Diversity 2010-03-15 2 3 Article 395 410 1424-2818 Ecological Systems as Complex Systems: Challenges for an Emerging Science 2010-03-15 doi: 10.3390/d2030395 Anand Gonzalez Guichard Kolasa Parrott http://www.mdpi.com/1424-2818/2/3/370/ Generally speaking, the term differentiation refers to differences between collections for the distribution of specified traits of their members, while diversity deals with (effective) numbers of trait states (types). Counting numbers of types implies discrete traits such as alleles and genotypes in population genetics or species and taxa in ecology. Comparisons between the concepts of differentiation and diversity therefore primarily refer to discrete traits. Diversity is related to differentiation through the idea that the total diversity of a subdivided collection should be composed of the diversity within the subcollections and a complement called “diversity between subcollections”. The idea goes back to the perception that the mixing of differentiated collections increases diversity. Several existing concepts of “diversity between subcollections” are based on this idea. Among them, β-diversity and fixation (inadvertently called differentiation) are the most prominent in ecology and in population genetics, respectively. The pertaining measures are shown to quantify the effect of differentiation in terms of diversity components, though from a dual perspective: the classical perspective of differentiation between collections for their type compositions, and the reverse perspective of differentiation between types for their collection affiliations. A series of measures of diversity-oriented differentiation is presented that consider this dual perspective at two levels of diversity partitioning: the overall type or subcollection diversity and the joint type-subcollection diversity. It turns out that, in contrast with common notions, the measures of fixation (such as FST or GST ) refer to the perspective of type rather than subcollection differentiation. This unexpected observation strongly suggests that the popular interpretations of fixation measures must be reconsidered. http://www.mdpi.com/1424-2818/2/3/370/ Wed, 03 Mar 2010 00:00:00 CET Diversity 2010-03-03 2 3 Article 370 394 1424-2818 Linking Diversity and Differentiation 2010-03-03 doi: 10.3390/d2030370 Hans-Rolf Gregorius http://www.mdpi.com/1424-2818/2/3/353/ Several anthropologists of Amazonian societies in Ecuador have claimed that for Achuar [1] and Quichua speaking Runa [2-4] there is no fundamental distinction between humans on the one hand, and plants and animals on the other. A related observation is that Runa and Achuar people share an animistic cosmology whereby animals, plants, and even seemingly inert entities such as rocks and stones are believed to have a life force or essence with a subjectivity that can be expressed. This paper will focus on Quichua speaking Runa to seek linguistic evidence for animacy by examining the sound-symbolic properties of a class of expressions called ideophones. I argue that structural features of ideophones such as canonical length and diversity of sound segments as well as type of sound segments, help express the animism of the Runa lifeworld. Moreover, although these features are not indicative of any essential distinctions between plants and animals, they may be indicative of a scalar view of animacy, along the lines suggested by Descola who first proposed a continuum or ‘ladder of animacy’ for the Achuar [1, pp. 321-326]. Ideophones, then, may be understood as one set of linguistic tools for coming to terms with the diversity of their ecological setting, a setting which spans highly animate humans and animals, through less animate plants, trees, and rocks. http://www.mdpi.com/1424-2818/2/3/353/ Tue, 02 Mar 2010 00:00:00 CET Diversity 2010-03-02 2 3 Article 353 369 1424-2818 The Sound-Symbolic Expression of Animacy in Amazonian Ecuador 2010-03-02 doi: 10.3390/d2030353 Janis B. Nuckolls http://www.mdpi.com/1424-2818/2/3/331/ As in other parts of Amazonia, pre-Columbian Indians have profoundly modified the coast of the Guianas. Between 650 and 1650 AD, Arauquinoid people occupied a territory that was approximately 600 km long and used the raised field technique intensively before the European conquest. They erected thousands of raised fields of various shapes, dug canals, ditches, and pathways, and built artificial mounds to establish their villages. All these earthworks changed forever the face of the coastal flooded savannas and their ecology. Such labor was probably organized under the leadership of a central authority: it seems that Arauquinoid societies were organized in a chiefdom system. Statistical calculations, based on the known surface area of raised fields and on their estimated productivity, suggest a population density of 50 to 100 inhabitants per km2. Pre-Columbian inhabitants of the Guianas coast carefully organized, managed and “anthropisized” their territory following a specific pattern. http://www.mdpi.com/1424-2818/2/3/331/ Tue, 02 Mar 2010 00:00:00 CET Diversity 2010-03-02 2 3 Article 331 352 1424-2818 Pre-Columbian Earthworks in Coastal Amazonia 2010-03-02 doi: 10.3390/d2030331 Stéphen Rostain http://www.mdpi.com/1424-2818/2/3/314/ Infectious diseases caused by ranaviruses (RV, family Iridoviridae) not only affect wild amphibian populations but also agriculture and international animal trade. Although, the prevalence of RV infections and die offs has markedly increased over the last decade, it is still unclear whether these viruses are direct causal agents of extinction or rather are the resulting (secondary) consequences of weakened health of amphibian populations leading to increased susceptibility to viral pathogens. In either case, it is important to understand the critical role of host immune defense in controlling RV infections, pathogenicity, and transmission; this is the focus of this review. http://www.mdpi.com/1424-2818/2/3/314/ Fri, 26 Feb 2010 00:00:00 CET Diversity 2010-02-26 2 3 Review 314 330 1424-2818 Emerging Ranaviral Infectious Diseases and Amphibian Decline 2010-02-26 doi: 10.3390/d2030314 Jacques Robert http://www.mdpi.com/1424-2818/2/2/281/ As part of an overall decline in biodiversity, populations of many organisms are declining and species are being lost at unprecedented rates around the world. This includes many populations and species of amphibians. Although numerous factors are affecting amphibian populations, we show potential direct and indirect effects of climate change on amphibians at the individual, population and community level. Shifts in amphibian ranges are predicted. Changes in climate may affect survival, growth, reproduction and dispersal capabilities. Moreover, climate change can alter amphibian habitats including vegetation, soil, and hydrology. Climate change can influence food availability, predator-prey relationships and competitive interactions which can alter community structure. Climate change can also alter pathogen-host dynamics and greatly influence how diseases are manifested. Changes in climate can interact with other stressors such as UV-B radiation and contaminants. The interactions among all these factors are complex and are probably driving some amphibian population declines and extinctions. http://www.mdpi.com/1424-2818/2/2/281/ Thu, 25 Feb 2010 00:00:00 CET Diversity 2010-02-25 2 2 Article 281 313 1424-2818 Direct and Indirect Effects of Climate Change on Amphibian Populations 2010-02-25 doi: 10.3390/d2020281 Andrew R. Blaustein Susan C. Walls Betsy A. Bancroft Joshua J. Lawler Catherine L. Searle Stephanie S. Gervasi http://www.mdpi.com/1424-2818/2/2/256/ The origin and subsequent proliferation of malarias capable of infecting humans in South America remain unclear, particularly with respect to the role of Neotropical monkeys in the infectious chain. The evidence to date will be reviewed for Pre-Columbian human malaria, introduction with colonization, zoonotic transfer from cebid monkeys, and anthroponotic transfer to monkeys. Cultural behaviors (primate hunting and pet-keeping) and ecological changes favorable to proliferation of mosquito vectors are also addressed. http://www.mdpi.com/1424-2818/2/2/256/ Wed, 24 Feb 2010 00:00:00 CET Diversity 2010-02-24 2 2 Article 256 280 1424-2818 The Historical Ecology of Human and Wild Primate Malarias in the New World 2010-02-24 doi: 10.3390/d2020256 Loretta A. Cormier http://www.mdpi.com/1424-2818/2/2/233/ The area of the Aegean can be described as one of nature’s most active laboratories. The contemporary geomorphology of the Aegean is a result of diverse and still ongoing geological events, which coupled with climate changes, have created mountains and thousands of islands. The Aegean bridges three continents, where human activity has been recorded for at least 10,000 years. Herpetofauna diversity offered early researchers the possibility of describing patterns in the Aegean, especially as the distributional limit for several species and faunal elements. The patterns initially described at a rather coarse scale formed the frame on which the application of new techniques opened new views and permitted finer analyses. Here, we assess recent works on the Aegean’s herpetofauna, outlining the role of sea barriers, especially the Mid Aegean Trench (MAT). We propose four basic patterns (pre-MAT, post-MAT, newcomers, and that of an outlier) and discuss exceptions to these patterns, to interpret the diversity recorded. The interdisciplinary study of taxonomy helps explaining the observed diversity and provides powerful arguments for how exploring diversity can be used to explain more than biological processes. http://www.mdpi.com/1424-2818/2/2/233/ Tue, 16 Feb 2010 00:00:00 CET Diversity 2010-02-16 2 2 Article 233 255 1424-2818 Three Continents Claiming an Archipelago: The Evolution of Aegean’s Herpetofaunal Diversity 2010-02-16 doi: 10.3390/d2020233 Petros Lymberakis Nikos Poulakakis http://www.mdpi.com/1424-2818/2/2/207/ Contrary to common belief, decomposition of diversity into independent richness and evenness components is mathematically impossible. However, richness can be decomposed into independent diversity and evenness or inequality components. The evenness or inequality component derived in this way is connected to most of the common measures of evenness and inequality in ecology and economics. This perspective justifies the derivation of measures of relative evenness, which give the amount of evenness relative to the maximum and minimum possible for a given richness. Pielou’s [1] evenness measure J is shown to be such a measure. http://www.mdpi.com/1424-2818/2/2/207/ Thu, 11 Feb 2010 00:00:00 CET Diversity 2010-02-11 2 2 Article 207 232 1424-2818 The Relation between Evenness and Diversity 2010-02-11 doi: 10.3390/d2020207 Lou Jost http://www.mdpi.com/1424-2818/2/2/182/ Archaeology is a discipline that can offer a long term perspective on the impacts human societies have had on the environment. Landscape studies are critical for understanding these impacts, because they embrace a dialectical view regarding the relationship between humans and their immediate surroundings. Such studies are well suited to the Amazon basin, a region that has driven much media attention due to astonishing rates of deforestation in certain areas, with likely consequences on the planet’s climate, posing challenges to the survival of the human species for the coming decades. In fact, although much has been said about the impacts of contemporary societies on tropical forest environments, ancient landscape management practices have not yet been considered part of the equation. Thus far, we know that Amerindian societies have been actively transforming their surroundings for millennia. On the eve of European contact, large, complex societies were bringing about long-lasting transformations of landscapes throughout the basin. Conquest and colonization resulted in epidemics, enslavement, and changes to the indigenous economies that managed to survive the genocide. Afterwards, as colonizers would exploit traditional resources leading, in many instances, to their exhaustion, a huge quantity of information on sustainable ways of dealing with certain environments became lost. Traditional knowledge, however, still survives among certain indigenous, peasant (caboclo), and African-Brazilian populations. Documentation of surviving management practices together with the study of the archaeological record could provide valuable information for policy makers. This article examines historical transformations that took place on Marajó Island during the last two millennia and advocates the importance of archaeological research for understanding the historical ecology of landscape change. It is argued that ancient economic strategies, some still being practiced today, could be re-created in the present, since these may constitute opportunities for sustainable sources of income to local communities. http://www.mdpi.com/1424-2818/2/2/182/ Mon, 01 Feb 2010 00:00:00 CET Diversity 2010-02-01 2 2 Article 182 206 1424-2818 Long-Term Human Induced Impacts on Marajó Island Landscapes, Amazon Estuary 2010-02-01 doi: 10.3390/d2020182 Denise Schaan http://www.mdpi.com/1424-2818/2/2/163/ Behaviorally modern human beings have lived in Amazonia for thousands of years. Significant dynamics in species turnovers due to human-mediated disturbance were associated with the ultimate emergence and expansion of agrarian technologies in prehistory. Such disturbances initiated primary and secondary landscape transformations in various locales of the Amazon region. Diversity in these locales can be understood by accepting the initial premise of contingency, expressed as unprecedented human agency and human history. These effects can be accessed through the archaeological record and in the study of living languages. In addition, landscape transformation can be demonstrated in the study of traditional knowledge (TK). One way of elucidating TK distinctions between anthropic and nonanthropic landscapes concerns elicitation of differential labeling of these landscapes and more significantly, elicitation of the specific contents, such as trees, occurring in these landscapes. Freelisting is a method which can be used to distinguish the differential species compositions of landscapes resulting from human-mediated disturbance vs. those which do not evince records of human agency and history. The TK of the Ka’apor Indians of Amazonian Brazil as revealed in freelisting exercises shows differentiation of anthropogenic from high forests as well as a recognition of diversity in the anthropogenic forests. This suggests that the agents of human-mediated disturbance and landscape transformation in traditional Amazonia encode diversity and contingency into their TK, which encoding reflects past cultural influence on landscape and society over time. http://www.mdpi.com/1424-2818/2/2/163/ Mon, 01 Feb 2010 00:00:00 CET Diversity 2010-02-01 2 2 Article 163 181 1424-2818 Contingent Diversity on Anthropic Landscapes 2010-02-01 doi: 10.3390/d2020163 William Balée http://www.mdpi.com/1424-2818/2/2/142/ Rapid, global declines among amphibians are partly alarming because many occur for apparently unknown or enigmatic reasons. Moreover, the relationship between phylogeny and enigmatic declines in higher clades of the amphibian phylogeny appears at first to be an intractable problem. I present a working solution by assessing threatening processes potentially underlying enigmatic declines in the family, Hylidae. Applying comparative methods that account for various evolutionary scenarios, I find extreme concentrations of threatening processes, including pollution and habitat loss, in the clade Hylini, potentially influenced by traits under selection. The analysis highlights hotspots of declines under phylogenetic influence in the genera Isthmohyla, Plectrohyla and Ptychohyla, and geographically in Mexico and Guatemala. The conservation implications of concentrated phylogenetic influence across multiple threatening processes are twofold: Data Deficient species of threatened clades should be prioritized in future surveys and, perhaps, a greater vulnerability should be assigned to such clades for further consideration of clade-level conservation priorities. http://www.mdpi.com/1424-2818/2/2/142/ Wed, 27 Jan 2010 00:00:00 CET Diversity 2010-01-27 2 2 Article 142 162 1424-2818 Phylogenetic Signal of Threatening Processes among Hylids: The Need for Clade-Level Conservation Planning 2010-01-27 doi: 10.3390/d2020142 Sarah J. Corey http://www.mdpi.com/1424-2818/2/1/127/ In recent years, diversity, whether it be ecological, biological, cultural, or linguistic diversity, has emerged as a major cultural value. This paper analyzes whether a single concept of diversity can underwrite discussions of diversity in different disciplines. More importantly, it analyzes the normative justification for the endorsement of diversity as a goal in all contexts. It concludes that no more than a relatively trivial concept of diversity as richness is common to all contexts. Moreover, there is no universal justification for the endorsement of diversity. Arguments to justify the protection of diversity must be tailored to individual contexts. http://www.mdpi.com/1424-2818/2/1/127/ Tue, 26 Jan 2010 00:00:00 CET Diversity 2010-01-26 2 1 Article 127 141 1424-2818 Diversity: A Philosophical Perspective 2010-01-26 doi: 10.3390/d2010127 Sahotra Sarkar http://www.mdpi.com/1424-2818/2/1/115/ Research policies ensuing from the Convention on Biological Diversity made huge funds available to study biodiversity. These were mostly dedicated to projects aimed at providing services to taxonomy via information and technology, or to develop “modern”, i.e., molecular, approaches to taxonomy. Traditional taxonomy was overly neglected and is in serious distress all over the world. It is argued that both novel and traditional ways to study biodiversity are essential and that the demise of traditional taxonomy (based on phenotypes) in the era of biodiversity is the result of an unwise policy, mainly fostered by portions of the scientific community that aim at taking total advantage of the funds dedicated to the study of biodiversity. http://www.mdpi.com/1424-2818/2/1/115/ Fri, 22 Jan 2010 00:00:00 CET Diversity 2010-01-22 2 1 Communication 115 126 1424-2818 The Study of Species in the Era of Biodiversity: A Tale of Stupidity 2010-01-22 doi: 10.3390/d2010115 Ferdinando Boero http://www.mdpi.com/1424-2818/2/1/107/ The genetic diversity among Tunisian pomegranate cultivars has been investigated. Using universal primers, the random amplified polymorphic DNA (RAPD) method was used to generate banding profiles from a set of twelve cultivars. Data was then computed with appropriate programs to construct a dendrogram illustrating the relationships between the studied cultivars. Our data proved the efficiency of the designed method to examine the DNA polymorphism in this crop since the tested primers are characterized by a collective resolving power of 12.83. In addition, the cluster analysis has exhibited a parsimonious tree branching independent from the geographic origin of the cultivars. In spite of the relatively low number of primers and cultivars, RAPD constitutes an appropriate procedure to assess the genetic diversity and to survey the phylogenetic relationships in this crop. http://www.mdpi.com/1424-2818/2/1/107/ Mon, 18 Jan 2010 00:00:00 CET Diversity 2010-01-18 2 1 Communication 107 114 1424-2818 Molecular Polymorphisms in Tunisian Pomegranate (Punica granatum L.) as Revealed by RAPD Fingerprints 2010-01-18 doi: 10.3390/d2010107 Néjib Hasnaoui Messaoud Mars Jemni Chibani Mokhtar Trifi http://www.mdpi.com/1424-2818/2/1/72/ Molecular analyses are providing new elements to decipher the origin, domestication and dispersal of native Amazonian crops in an expanding archaeological context. Solid molecular data are available for manioc (Manihot esculenta), cacao (Theobroma cacao), pineapple (Ananas comosus), peach palm (Bactris gasipaes) and guaraná (Paullinia cupana), while hot peppers (Capsicum spp.), inga (Inga edulis), Brazil nut (Bertholletia excelsa) and cupuassu (Theobroma grandiflorum) are being studied. Emergent patterns include the relationships among domestication, antiquity (terminal Pleistocene to early Holocene), origin in the periphery, ample pre-Columbian dispersal and clear phylogeographic population structure for manioc, pineapple, peach palm and, perhaps, Capsicum peppers. Cacao represents the special case of an Amazonian species possibly brought into domestication in Mesoamerica, but close scrutiny of molecular data suggests that it may also have some incipiently domesticated populations in Amazonia. Another pattern includes the relationships among species with incipiently domesticated populations or very recently domesticated populations, rapid pre- or post-conquest dispersal and lack of phylogeographic population structure, e.g., Brazil nut, cupuassu and guaraná. These patterns contrast the peripheral origin of most species with domesticated populations with the subsequent concentration of their genetic resources in the center of the basin, along the major white water rivers where high pre-conquest population densities developed. Additional molecular genetic analyses on these and other species will allow better examination of these processes and will enable us to relate them to other historical ecological patterns in Amazonia. http://www.mdpi.com/1424-2818/2/1/72/ Wed, 06 Jan 2010 00:00:00 CET Diversity 2010-01-06 2 1 Review 72 106 1424-2818 Origin and Domestication of Native Amazonian Crops 2010-01-06 doi: 10.3390/d2010072 Charles R. Clement Michelly De Cristo-Araújo Geo Coppens D’Eeckenbrugge Alessandro Alves Pereira Doriane Picanço-Rodrigues http://www.mdpi.com/1424-2818/2/1/47/ It is well established that a decrease in genetic variation can lead to reduced fitness and lack of adaptability to a changing environment. Amphibians are declining on a global scale, and we present a four-point argument as to why this taxonomic group seems especially prone to such genetic processes. We elaborate on the extent of recent fragmentation of amphibian gene pools and we propose the term dissociated populations to describe the residual population structure. To put their well-documented loss of genetic diversity into context, we provide an overview of 34 studies (covering 17 amphibian species) that address a link between genetic variation and >20 different fitness traits in amphibians. Although not all results are unequivocal, clear genetic-fitness-correlations (GFCs) are documented in the majority of the published investigations. In light of the threats faced by amphibians, it is of particular concern that the negative effects of various pollutants, pathogens and increased UV-B radiation are magnified in individuals with little genetic variability. Indeed, ongoing loss of genetic variation might be an important underlying factor in global amphibian declines. http://www.mdpi.com/1424-2818/2/1/47/ Tue, 05 Jan 2010 00:00:00 CET Diversity 2010-01-05 2 1 Review 47 71 1424-2818 Global Amphibian Declines, Loss of Genetic Diversity and Fitness: A Review 2010-01-05 doi: 10.3390/d2010047 Morten E. Allentoft John O’Brien http://www.mdpi.com/1424-2818/2/1/28/ We have studied the population genetic structure of slightly admixed populations of crested newts (Triturus cristatus and T. carnifex) in a continuously fragmented landscape, located in northern Salzburg (Austria) and neighbouring Bavaria (Germany). Crested newts are listed as Critically Endangered in the provincial Red List of Salzburg and strictly protected by the EU Habitats Directive. We used seven polymorphic microsatellite loci to evaluate genetic diversity and processes that may determine the genetic architecture of populations. Genetic diversity was moderate, pairwise FST-values were comparatively high showing significant genetic differentiation and limited gene flow. Isolation by distance was significant for the whole data set, but not significant when calculated for T. cristatus- and T. carnifex-like populations separately. Bayesian analyses of population structure, using three different programs showed similar results. Spatial statistics reveal that the geographical isolation of populations is very high. http://www.mdpi.com/1424-2818/2/1/28/ Thu, 31 Dec 2009 00:00:00 CET Diversity 2009-12-31 2 1 Article 28 46 1424-2818 Conservation Genetics of Crested Newt Species Triturus cristatus and T. carnifex within a Contact Zone in Central Europe: Impact of Interspecific Introgression and Gene Flow 2009-12-31 doi: 10.3390/d2010028 Andreas Maletzky Roland Kaiser Peter Mikulíček http://www.mdpi.com/1424-2818/2/1/17/ Single Nucelotide Polymorphisms (SNPs) have become the most widely used markers in many current genetic applications. Here we report the discovery of nine new SNPs in olives by direct partial sequencing of two genes (OEX and OEW) in sixteen Tunisian cultivars. The SNP markers were then used to genotype 24 olive cultivars and assess the level of genetic diversity. Power of discrimination of SNP markers was then compared to that of microsatellites (SSRs). A combination of SSR and SNP markers was finally proposed that can be used for cultivars identification in juvenile step or for oil traceability. http://www.mdpi.com/1424-2818/2/1/17/ Wed, 30 Dec 2009 00:00:00 CET Diversity 2009-12-30 2 1 Article 17 27 1424-2818 Discovery and Potential of SNP Markers in Characterization of Tunisian Olive Germplasm 2009-12-30 doi: 10.3390/d2010017 Imen Rekik Hakim Naziha Grati Kammoun Emna Makhloufi Ahmed Rebaï