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Diversity, Volume 6, Issue 4 (December 2014) , Pages 633-854

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Open AccessArticle
Why Did the Bear Cross the Road? Comparing the Performance of Multiple Resistance Surfaces and Connectivity Modeling Methods
Diversity 2014, 6(4), 844-854; https://doi.org/10.3390/d6040844 - 18 Dec 2014
Cited by 28 | Viewed by 2889
Abstract
There have been few assessments of the performance of alternative resistance surfaces, and little is known about how connectivity modeling approaches differ in their ability to predict organism movements. In this paper, we evaluate the performance of four connectivity modeling approaches applied to [...] Read more.
There have been few assessments of the performance of alternative resistance surfaces, and little is known about how connectivity modeling approaches differ in their ability to predict organism movements. In this paper, we evaluate the performance of four connectivity modeling approaches applied to two resistance surfaces in predicting the locations of highway crossings by American black bears in the northern Rocky Mountains, USA. We found that a resistance surface derived directly from movement data greatly outperformed a resistance surface produced from analysis of genetic differentiation, despite their heuristic similarities. Our analysis also suggested differences in the performance of different connectivity modeling approaches. Factorial least cost paths appeared to slightly outperform other methods on the movement-derived resistance surface, but had very poor performance on the resistance surface obtained from multi-model landscape genetic analysis. Cumulative resistant kernels appeared to offer the best combination of high predictive performance and sensitivity to differences in resistance surface parameterization. Our analysis highlights that even when two resistance surfaces include the same variables and have a high spatial correlation of resistance values, they may perform very differently in predicting animal movement and population connectivity. Full article
(This article belongs to the Special Issue Biodiversity Loss & Habitat Fragmentation)
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Open AccessArticle
Variations of Bacterial Community Structure and Composition in Mangrove Sediment at Different Depths in Southeastern Brazil
Diversity 2014, 6(4), 827-843; https://doi.org/10.3390/d6040827 - 11 Dec 2014
Cited by 12 | Viewed by 3109
Abstract
Tropical mangroves are considered one of the most productive ecosystems of the world, being characterized as nurseries and food sources for fish and other animals. Microorganisms play important roles in these environments, and the study of bacterial communities is of paramount importance for [...] Read more.
Tropical mangroves are considered one of the most productive ecosystems of the world, being characterized as nurseries and food sources for fish and other animals. Microorganisms play important roles in these environments, and the study of bacterial communities is of paramount importance for a better comprehension of mangrove dynamics. This study focused on the structure and composition of bacterial communities in mangrove sediments at different depths and points, located in Southeastern Brazil. Terminal Restriction Fragment Length Polymorphism (T-RFLP) was used to determine the community structure, and 16S rRNA gene pyrosequencing was used to characterize the community composition. Redundancy analysis of T-RFLP patterns revealed differences in bacterial community structure according to soil attributes and depth. The parameters K and depth presented significant correlation with general community structure. Most sequences were classified into the phylum Proteobacteria (88%), which presented differences according to the depth, where the classes Betaproteobacteria (21%) and Deltaproteobacteria (16%) were abundant at 10 cm and Epsilonproteobacteria (35%) was abundant at 40 cm depth. Clear differences were observed in community composition as shown by the differential distribution of the phyla Firmicutes (1.13% and 3.8%, for 10 cm and 40 cm respectively), Chloroflexi (2.8% and 0.75%), and Acidobacteria (2.75% and 0.57%) according to the depth. Bacterial diversity measurements indicated higher diversity in shallow samples. Taken together, our findings indicate that mangrove holds a diverse bacterial community, which is shaped by the variations found in the ecosystem, such as sediment properties and depth. Full article
(This article belongs to the Special Issue Mangrove Conservation)
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Open AccessArticle
Differences in Manioc Diversity Among Five Ethnic Groups of the Colombian Amazon
Diversity 2014, 6(4), 792-826; https://doi.org/10.3390/d6040792 - 09 Dec 2014
Cited by 12 | Viewed by 4294
Abstract
Manioc is an important root crop in the tropics and the most important staple food in the Amazon. Manioc is diverse but its diversity has not yet been clearly associated with environmental or social factors. Our study evaluates how variation in edaphic environments [...] Read more.
Manioc is an important root crop in the tropics and the most important staple food in the Amazon. Manioc is diverse but its diversity has not yet been clearly associated with environmental or social factors. Our study evaluates how variation in edaphic environments and in social factors influences manioc diversity among five ethnic groups of the Amazon region of Colombia. Inventories of landraces, genetic analysis of manioc diversity, visits to farmers’ swiddens and interviews with farmers were carried out during two years of field work. Morphotypic and genotypic diversity of manioc were large. The different ethnic groups of our study cultivate different sweet and bitter manioc landraces which they select and maintain in accordance with their ancestral rules and norms. Differences in available environments among indigenous communities (such as the presence of different soils) did not markedly affect manioc morphotypic or genotypic diversity, while social factors considerably influenced observed manioc diversity. Manioc diversity was explained by two parallel processes of manioc diversification: volunteer seedling selection and manioc seed exchange. We argue that, for a full understanding of manioc diversity, indigenous knowledge, as well as morphological and genetic variation should be taken into account. Full article
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Open AccessArticle
Dynamics of Invertebrate Diversity in a Tropical Stream
Diversity 2014, 6(4), 771-791; https://doi.org/10.3390/d6040771 - 05 Dec 2014
Cited by 12 | Viewed by 2670
Abstract
Regional studies of biotic communities are important for characterising their normal spatial and temporal variation, but there are few such studies of tropical streams. This paper describes changes in invertebrate communities in Yuccabine Creek, a seasonal upland rainforest stream in tropical Australia, over [...] Read more.
Regional studies of biotic communities are important for characterising their normal spatial and temporal variation, but there are few such studies of tropical streams. This paper describes changes in invertebrate communities in Yuccabine Creek, a seasonal upland rainforest stream in tropical Australia, over three-year and decadal periods. Invertebrate abundance, richness and evenness were temporally stable, except after major drying or wet-season flows, from which they recovered quickly; however, three wet seasons contrasted in abundance patterns. Species’ responses to flood or drought varied depending on life-histories and habitat dynamics. Communities showed contrasts between wet, early-dry and late-dry seasons, with different characteristic species. Current velocity, leaf litter and substratum particle size were the main environmental correlates with species abundances and multivariate scores. Between-decade contrasts were due to antecedent rainfall and loss of canopy cover. Trophic composition varied seasonally, driven by abundances of predators and detritivores. Yuccabine Creek differs from comparable temperate streams in its high diversity of invertebrates, continual recruitment and spring-dominated continual leaf fall; and from some other tropical streams in its seasonal flow regime. Interpretation of invertebrate metrics in these streams needs to account for historical, antecedent and current conditions, but biannual samples would adequately characterise the fauna. Full article
(This article belongs to the Special Issue Global Freshwater Biodiversity)
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Open AccessArticle
Grazer Functional Roles, Induced Defenses, and Indirect Interactions: Implications for Eelgrass Restoration in San Francisco Bay
Diversity 2014, 6(4), 751-770; https://doi.org/10.3390/d6040751 - 26 Nov 2014
Cited by 6 | Viewed by 2814
Abstract
Understanding the individual and interactive roles of consumer species is more than academic when the host plant is a subject of intense conservation interest. In a mesocosm experiment, we compared effects of common invertebrate grazers in San Francisco Bay seagrass (Zostera marina [...] Read more.
Understanding the individual and interactive roles of consumer species is more than academic when the host plant is a subject of intense conservation interest. In a mesocosm experiment, we compared effects of common invertebrate grazers in San Francisco Bay seagrass (Zostera marina, eelgrass) beds, finding that some species (a native opisthobranch, Phyllaplysia taylori; a native isopod, Idotea resecata; and an introduced gastropod, Ilyanassa obsoleta) enhanced eelgrass growth through removal of epiphytic algae, as is often predicted for small invertebrate grazers on seagrasses, while one (an introduced caprellid amphipod, Caprella cf. drepanochir) had neutral effects. In contrast, the putatively-introduced gammaridean amphipod, Ampithoe valida, had strong negative effects on eelgrass (in addition to epiphytes) through consumption, as we had previously observed in the field during restoration programs. We tested whether other common grazer species could influence the effects of the eelgrass-grazing Ampithoe, and found that Idotea induced production of phenolic compounds and limited eelgrass damage by Ampithoe, without affecting Ampithoe abundance. These results have implications for restoration strategies, and contribute to a growing awareness of the importance of trait-mediated indirect grazer interactions through grazer-induced changes in plant traits, providing the first example in a seagrass system. Full article
(This article belongs to the Special Issue Biological Invasions)
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Open AccessReview
On the History of Cattle Genetic Resources
Diversity 2014, 6(4), 705-750; https://doi.org/10.3390/d6040705 - 12 Nov 2014
Cited by 35 | Viewed by 7515
Abstract
Cattle are our most important livestock species because of their production and role in human culture. Many breeds that differ in appearance, performance and environmental adaptation are kept on all inhabited continents, but the historic origin of the diverse phenotypes is not always [...] Read more.
Cattle are our most important livestock species because of their production and role in human culture. Many breeds that differ in appearance, performance and environmental adaptation are kept on all inhabited continents, but the historic origin of the diverse phenotypes is not always clear. We give an account of the history of cattle by integrating archaeological record and pictorial or written sources, scarce until 300 years ago, with the recent contributions of DNA analysis. We describe the domestication of their wild ancestor, migrations to eventually all inhabited continents, the developments during prehistory, the antiquity and the Middle Ages, the relatively recent breed formation, the industrial cattle husbandry in the Old and New World and the current efforts to preserve the cattle genetic resources. Surveying the available information, we propose three main and overlapping phases during the development of the present genetic diversity: (i) domestication and subsequent wild introgression; (ii) natural adaptation to a diverse agricultural habitat; and (iii) breed development. Full article
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Open AccessArticle
Phytoplankton Communities in Green Bay, Lake Michigan after Invasion by Dreissenid Mussels: Increased Dominance by Cyanobacteria
Diversity 2014, 6(4), 681-704; https://doi.org/10.3390/d6040681 - 06 Nov 2014
Cited by 13 | Viewed by 3129
Abstract
Biological invasions of aquatic systems disrupt ecological communities, and cause major changes in diversity and ecosystem function. The Laurentian Great Lakes of North America have been dramatically altered by such invasions, especially zebra (Dreissena polymorpha) and quagga (D. rostriformis bugensis [...] Read more.
Biological invasions of aquatic systems disrupt ecological communities, and cause major changes in diversity and ecosystem function. The Laurentian Great Lakes of North America have been dramatically altered by such invasions, especially zebra (Dreissena polymorpha) and quagga (D. rostriformis bugensis) mussels. Responses to mussel invasions have included increased water clarity, and decreased chlorophyll and phytoplankton abundance. Although not all systems have responded similarly, in general, mussels have changed nutrient dynamics and physical habitat conditions. Therefore examination of different impacts can help us further understand mechanisms that underlie ecosystem responses to biological invasions. To aid our understanding of ecosystem impacts, we sampled established locations along a well-studied trophic gradient in Green Bay, Lake Michigan, after the 1993 zebra mussel invasion. A strong trophic gradient remained during the period sampled after the mussel invasion (2000–2012). However, mean summer chlorophyll increased and other measures of phytoplankton biomass (microscope and electronic cell counting) did not change significantly. Multivariate analyses of phytoplankton community structure demonstrate a significant community shift after the invasion. Cyanobacteria increased in dominance, with Microcystis becoming the major summer taxon in lower Green Bay. Diatom diversity and abundance also increased and Chlorophyta became rare. Phytoplankton responses along the trophic gradient of Green Bay to zebra mussel invasion highlight the importance of mussel effects on nutrient dynamics and phytoplankton diversity and function. Full article
(This article belongs to the Special Issue Biological Invasions)
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Open AccessArticle
Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping
Diversity 2014, 6(4), 665-680; https://doi.org/10.3390/d6040665 - 20 Oct 2014
Cited by 24 | Viewed by 7951
Abstract
Genotyping-by-sequencing (GBS) has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and [...] Read more.
Genotyping-by-sequencing (GBS) has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and use for plant genetic diversity analysis. It uses two restriction enzymes to reduce genome complexity, applies Illumina multiplexing indexes for barcoding and has a custom bioinformatics pipeline for genotyping. This genetic diversity-focused GBS (gd-GBS) protocol can serve as an easy-to-follow lab guide to assist a researcher through every step of a GBS application with five main components: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. Specifically, in this presentation, we provide a brief overview of the GBS approach, describe the gd-GBS procedures, illustrate it with an application to analyze genetic diversity in 20 flax (Linum usitatissimum L.) accessions and discuss related issues in GBS application. Following these lab bench procedures and using the custom bioinformatics pipeline, one could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a non-model plant species. Full article
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)
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Open AccessArticle
Invasion of Eastern Texas Forestlands by Chinese Privet: Efficacy of Alternative Management Strategies
Diversity 2014, 6(4), 652-664; https://doi.org/10.3390/d6040652 - 15 Oct 2014
Cited by 3 | Viewed by 2757
Abstract
Chinese privet (Ligustrum sinense) was the most prevalent invasive shrub in the forestlands of Eastern Texas in 2006. We analyzed extensive field data collected by the Forest Inventory and Analysis Program of the U.S. Forest Service to quantify the range expansion [...] Read more.
Chinese privet (Ligustrum sinense) was the most prevalent invasive shrub in the forestlands of Eastern Texas in 2006. We analyzed extensive field data collected by the Forest Inventory and Analysis Program of the U.S. Forest Service to quantify the range expansion of Chinese privet from 2006 to 2011. Our results indicated the presence of Chinese privet on sampled plots increased during this period. Chinese privet spread extensively in the north. Results of logistic regression, which classified 73% of the field plots correctly with regard to species presence and absence, indicated probability of invasion was correlated positively with elevation, adjacency (within 300 m) to water bodies, and site productivity, and was correlated negatively with stand age, site preparation (including clearing, slash burning, chopping, disking, bedding, and other practices clearly intended to prepare a site for regeneration), artificial regeneration (which refers to planting or direct seeding that results in at least 50% of the stand being comprised of stocked trees), and distance to the nearest road. Habitats most at risk to further invasion (likelihood of invasion > 40%) under current conditions occurred primarily in Northeast Texas. Practicing site preparation and artificial regeneration reduced the estimated probabilities of further invasion. Full article
(This article belongs to the Special Issue Biological Invasions)
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Open AccessArticle
Genetic Segregation and Genomic Hybridization Patterns Support an Allotetraploid Structure and Disomic Inheritance for Salix Species
Diversity 2014, 6(4), 633-651; https://doi.org/10.3390/d6040633 - 29 Sep 2014
Cited by 5 | Viewed by 2742
Abstract
The Salix alba L. (white willow)—Salix fragilis L. (crack willow) complex includes closely related polyploid species, mainly tetraploid (2n = 4x = 76), which are dioecious and hence obligate allogamous. Because little is known about the genome constitution and chromosome [...] Read more.
The Salix alba L. (white willow)—Salix fragilis L. (crack willow) complex includes closely related polyploid species, mainly tetraploid (2n = 4x = 76), which are dioecious and hence obligate allogamous. Because little is known about the genome constitution and chromosome behavior of these pure willow trees, genetic analysis of their naturally occurring interspecific polyploid hybrids is still very difficult. A two-way pseudo-testcross strategy was exploited using single-dose AFLP markers in order to assess the main inheritance patterns of tetraploid biotypes (disomy vs. tetrasomy) in segregating populations stemmed from S. alba × S. fragilis crosses and reciprocals. In addition, a genomic in situ hybridization (GISH) technology was implemented in willow to shed some light on the genome structure of S. alba and S. fragilis species, and their hybrids (allopolyploidy vs. autopolyploidy). The frequency of S. alba-specific molecular markers was almost double compared to that of S. fragilis-specific ones, suggesting the phylogenetic hypothesis of S. fragilis as derivative species from S. alba-like progenitors. Cytogenetic observations at pro-metaphase revealed about half of the chromosome complements being less contracted than the remaining ones, supporting an allopolyploid origin of both S. alba and S. fragilis. Both genetic segregation and genomic hybridization data are consistent with an allotetraploid nature of the Salix species. In particular, the vast majority of the AFLP markers were inherited according to disomic patterns in S. alba × S. fragilis populations and reciprocals. Moreover, in all S. alba against S. fragilis hybridizations and reciprocals, GISH signals were observed only on the contracted chromosomes whereas the non-contracted chromosomes were never hybridized. In conclusion, half of the chromosomes of the pure species S. alba and S. fragilis are closely related and they could share a common diploid ancestor, while the rest of chromosomes are morphologically differentiated in either S. alba or S. fragilis and they should derive from distinct diploid ancestors. Full article
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)
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