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1,598 results for “genetic diversity”
Data from: No consistent effects of humans on animal genetic diversity worldwide
Human impacts on genetic diversity are poorly understood yet critical to biodiversity conservation. We used 175,247 COI sequences collected between 1980 and 2016 to assess the global effects of land use and human density on the intraspecific genetic diversity of 17,082 species of birds, fishes, insects, and mammals. Human impacts on mtDNA diversity were taxon and scale-dependent, and were generally weak or non-significant. Spatial analyses identified weak latitudinal diversity gradients as well as negative effects of human density on insect diversity, and negative effects of intensive land use on fish diversity. The observed effects were predominantly associated with species turnover. Time series analyses found nearly an equal number of positive and negative temporal trends in diversity, resulting in no net monotonic trend in diversity over this time period. Our analyses reveal critical data and theory gaps and call for increased efforts to monitor global genetic diversity.
Drivers of within-host genetic diversity in acute infections of viruses
<p>Mutations frequencies of HIV, RSV and CMV samples taken from acute infections.</p>
Data from: Genetic diversity and conservation status of Helianthus verticillatus, an endangered sunflower of the Southern United States
<p>Evaluating species diversity and patterns of population genetic variation is an essential aspect of conservation biology to determine appropriate management strategies and preserve the biodiversity of native plants. Habitat fragmentation and potential habitat loss are often an outcome of a reduction in naturally occurring wildfires and controlled prescribed burning, as seen in <i>Helianthus verticillatus</i> (whorled sunflower). This endangered, wild relative of the common sunflower, <i>Helianthus annuus</i>, is endemic to four locations in Alabama, Georgia, and Tennessee, United States. Despite its endangered status, there is no recovery plan for <i>H. verticillatus</i>, and knowledge related to its basic plant biology and importance in ecosystem services is mostly unknown. In this study, we utilized 14 microsatellite loci to investigate fine-scale population structure and genetic diversity of <i>H. verticillatus</i> individuals found on two sampling sites within the Georgia population. Our results indicated moderate genetic diversity and the presence of two distinct genetic clusters. Analyses of molecular variance indicated that the majority of variance was individually based, thus confirming high genetic differentiation and limited gene flow between <i>H. verticillatus</i> collection sites. The evidence of a population bottleneck in these sites suggests a recent reduction in population size that could be explained by habitat loss and population fragmentation. Also, high levels of linkage disequilibrium were detected, putatively suggesting clonal reproduction among these individuals. Our study provides a better understanding of fine-scale genetic diversity and spatial distribution of <i>H. verticillatus</i> populations in Georgia. Our results can underpin an original recovery plan for <i>H. verticillatus</i> that could be utilized for the conservation of this endangered species and to promote its persistence in the wild.</p>
Predicting amphibian intraspecific diversity with machine learning: Challenges and prospects for integrating traits, geography, and genetic data
<p>The growing availability of genetic datasets, in combination with machine learning frameworks, offer great potential to answer long-standing questions in ecology and evolution. One such question has intrigued population geneticists, biogeographers, and conservation biologists: What factors determine intraspecific genetic diversity? This question is challenging to answer because many factors may influence genetic variation, including life history traits, historical influences, and geography, and the relative importance of these factors varies across taxonomic and geographic scales. Furthermore, interpreting the influence of numerous, potentially correlated variables is difficult with traditional statistical approaches. To address these challenges, we analyzed repurposed data using machine learning and investigated predictors of genetic diversity, focusing on Nearctic amphibians as a case study. We aggregated species traits, range characteristics, and >42,000 genetic sequences for 299 species using open-access scripts and various databases. After identifying important predictors of nucleotide diversity with random forest regression, we conducted follow-up analyses to examine the roles of phylogenetic history, geography, and demographic processes on intraspecific diversity. Although life history traits were not important predictors for this dataset, we found significant phylogenetic signal in genetic diversity within amphibians. We also found that salamander species at northern latitudes contain lower genetic diversity. Data repurposing and machine learning provide valuable tools for detecting patterns with relevance for conservation, but concerted efforts are needed to compile meaningful datasets with greater utility for understanding global biodiversity.</p>
Does genetic diversity protect host populations from parasites? A meta-analysis across natural and agricultural systems
<p>If parasites transmit more readily between closely related hosts, then parasite burdens should decrease with increased genetic diversity of host populations. This important hypothesis is often accepted at face value - notorious epidemics of crop monocultures testify to the vulnerability of host populations that have been purged of diversity. Yet the relationship between genetic diversity and parasitism likely varies across contexts, differing between crop and non-crop hosts and between experimental and natural host populations. Here, we used a meta-analytic approach to ask if host diversity confers protection against parasites over the range of contexts in which it has been tested.</p> <p>We synthesized the results of 102 studies, comprising 2,004 effect sizes representing a diversity of approaches and host-parasite systems. Our results validate a protective effect of genetic diversity, while revealing significant variation in its strength across biological and empirical contexts. In experimental host populations, genetic diversity reduces parasitism by ~20% for non-crop hosts and by ~50% for crop hosts. In contrast, observational studies of natural host populations show no consistent relationship between genetic diversity and parasitism, with both strong negative and positive correlations reported. This result supports the idea that, if parasites preferentially attack close relatives, the correlation of genetic diversity with parasitism could be positive or negative depending upon the potential for host populations to evolve in response to parasite selection. Taken together, these results reinforce genetic diversity as a priority for both conservation and agriculture and emphasize the challenges inherent to drawing comparisons between controlled experimental populations and dynamic natural populations.</p>
Reconstructing hotspots of genetic diversity from glacial refugia and subsequent dispersal in Italian common toads (Bufo bufo)
<p>Genetic diversity feeds the evolutionary process and allows populations to adapt to environmental changes. However, we still lack a thorough understanding of why hotspots of genetic diversity are so 'hot'. Here, we analysed the relative contribution of bioclimatic stability and genetic admixture between divergent lineages in shaping spatial patterns of genetic diversity in the common toad <i>Bufo bufo</i> along the Italian peninsula. We combined population genetic, phylogeographic and species distribution modelling (SDM) approaches to map ancestral areas, glacial refugia, and secondary contact zones. We consistently identified three phylogeographic lineages, distributed in northern, central and southern Italy. These lineages expanded from their ancestral areas and established secondary contact zones, before the last interglacial. SDM identified widespread glacial refugia in peninsular Italy, sometimes located under the present-day sea-level. Generalized linear models indicated genetic admixture as the only significant predictor of the levels of population genetic diversity. Our results show that glacial refugia contributed to preserving both levels and patterns of genetic diversity across glacial-interglacial cycles, but not to their formation, and highlight a general principle emerging in Mediterranean species: higher levels of genetic diversity mark populations with substantial contributions from multiple genetic lineages, irrespective of the location of glacial refugia.</p>
Genetic diversity in two insular populations of bobcats (Lynx rufus)
<p>We documented changes in genetic diversity in an isolated, reintroduced population of bobcats on Cumberland Island (CUIS), Georgia, USA, compared to another bobcat population on Kiawah Island, South Carolina, USA, that was naturally established and experiences limited immigration from the mainland. We compared the predictions of a novel population viability analysis (PVA) to empirical estimates of abundance and genetic diversity on CUIS and used our PVA to identify management actions that are likely to support long-term viability.</p>
Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers
<p>Hosting unique and important plant germplasms, the Qinghai-Tibet Plateau (QTP), as the third pole of the world, and Xinjiang, located in the centre of the Eurasian continent, are major distribution areas of perennial Triticeae grasses, especially the widespread <i>Elymus</i> species. <i>Elymus excelsus</i> Turcz. ex Griseb, a perennial forage grass with strong tolerance to environmental stresses, such as drought, cold and soil impoverishment, can be appropriately used for grassland establishment due to its high seed production. To provide basic information for collection, breeding strategies and utilization of <i>E. excelsus</i> germplasm, microsatellite markers (SSR) were employed in the present study to determine the genetic variation and population structure of 25 wild accessions of <i>E. excelsus</i> from Xinjiang (XJC) and the QTP, including Sichuan (SCC) and Gansu (GSC) of western China. Based on the 159 polymorphic bands amplified by 35 primer pairs developed from three related species, the average values of the polymorphic information content (PIC), marker index (MI), resolving power (Rp), Nei's genetic diversity (H) and Shannon's diversity index (I) of each pair of primers were 0.289, 1.348, 1.897, 0.301 and 0.459, respectively, validating that these SSR markers can also be used for the evaluation of genetic diversity of <i>E. excelsus</i> germplasms, and demonstrating the superior versatility of EST-SSR vs. G-SSR. We found a relatively moderate differentiation (<i>F</i><sub><i>st</i></sub> = 0.151) among the XJC, SCC and GSC geo-groups, and it is worth noting that, the intra-group genetic diversity of the SCC group (<i>H</i><sub><i>e</i></sub> = 0.197) was greater than that of the GSC (<i>H</i><sub><i>e</i></sub> = 0.176) and XJC (<i>H</i><sub><i>e</i></sub> = 0.148) groups. Both the Unweighted Pair Group Method with Arithmetic (UPGMA) clustering and principal coordinates analysis (PCoA) divided the 25 accessions into three groups, whereas the Bayesian STRUCTURE analysis suggested that <i>E. excelsus</i> accessions fell into four main clusters. Besides, this study suggested that geographical distance and environmental variables (annual mean precipitation and average precipitation in growing seasons), especially for QTP accessions, should be combined to explain the population genetic differentiation among the divergent geographical regions. These data provided comprehensive information about these valuable <i>E. excelsus</i> germplasm resources for the protection and collection of germplasms and for breeding strategies in areas of Xinjiang and QTP in western China.</p>
Data from: Genetic diversity, infection prevalence, and possible transmission routes of Bartonella spp. in vampire bats
Bartonella spp. are globally distributed bacteria that cause endocarditis in humans and domestic animals. Recent work has suggested bats as zoonotic reservoirs of some human Bartonella infections; however, the ecological and spatiotemporal patterns of infection in bats remain largely unknown. Here we studied the genetic diversity, prevalence of infection across seasons and years, individual risk factors, and possible transmission routes of Bartonella in populations of common vampire bats (Desmodus rotundus) in Peru and Belize, for which high infection prevalence has previously been reported. Phylogenetic analysis of the gltA gene for a subset of PCR-positive blood samples revealed sequences that were related to Bartonella described from vampire bats from Mexico, other Neotropical bat species, and streblid bat flies. Sequences associated with vampire bats clustered significantly by country but commonly spanned Central and South America, implying limited spatial structure. Stable and nonzero Bartonella prevalence between years supported endemic transmission in all sites. The odds of Bartonella infection for individual bats was unrelated to the intensity of bat flies ectoparasitism, but nearly all infected bats were infested, which precluded conclusive assessment of support for vector-borne transmission. While metagenomic sequencing found no strong evidence of Bartonella DNA in pooled bat saliva and fecal samples, we detected PCR positivity in individual saliva and feces, suggesting the potential for bacterial transmission through both direct contact (i.e., biting) and environmental (i.e., fecal) exposures. Further investigating the relative contributions of direct contact, environmental, and vector-borne transmission for bat Bartonella is an important next step to predict infection dynamics within bats and the risks of human and livestock exposures.
Data from: Patterns of intra- and inter-population genetic diversity in Alaskan coho salmon: implications for conservation
Little is known about the genetic diversity of coho salmon in Alaska, although this area represents half of the species' North American range. In this study, nine microsatellite loci were used to genotype 32 putative coho salmon populations from seven regions of Alaska. The primary objectives were to estimate and evaluate the degree and spatial distribution of neutral genetic diversity within and among populations of Alaskan coho salmon. Genetic analysis yielded four results that provide insight into forces influencing genetic diversity in Alaskan coho salmon and have important conservation implications: 1) significant population differentiation was found within each region; 2) the degree of differentiation (FST = 0.099) among populations was as large or larger than that reported for other Pacific salmon species in Alaska; 3) phenetic clustering of populations showed weak geographic concordance; 4) strong genetic isolation by distance was only apparent at the finest geographic scale (within a drainage). These results suggest that coho salmon populations are small relative to populations of other Pacific salmon, and the genetic diversity within and among coho salmon populations is influenced primarily by genetic drift, and not gene flow. Resource management and conservation actions affecting coho salmon in Alaska must recognize that the populations are generally small, isolated, and probably exhibit local adaptation to different spawning and freshwater rearing habitats. These factors justify managing and conserving Alaskan coho salmon at a fine geographic scale.
Data from: Genetic structure and diversity of the blueface darter Etheostoma cyanoprosopum, a microendemic freshwater fish in the southeastern United States
Darters represent one of the most diverse groups of freshwater fishes in North America, but approximately 33% of the 215 recognized species are considered imperiled on the IUCN Red List. Discovery and description of new darter species continues at a relatively rapid pace, with many exhibiting microendemic geographic distributions and little baseline data for conservation decisions. The Blueface Darter Etheostoma cyanoprosopum is a newly described species that occupies < 20 km of stream reaches in the Bear Creek system of the Tennessee River drainage and the Hubbard Creek system of the Black Warrior River drainage in the Mobile Basin (Alabama, USA). In addition to restricted distribution, the species is threatened by habitat degradation and several natural and man-made barriers that putatively fragment connectivity among populations. This study used microsatellite and mitochondrial (mt) DNA data with comparisons to the relatively broadly distributed sister species (Bandfin Darter E. zonistium) to evaluate multiple objectives about genetic connectivity and diversity among Blueface Darter populations. Analysis of mtDNA data indicated a lack of historical structuring across the Tennessee-Black Warrior river drainage divide and within the Bear Creek system. However, microsatellite-based Bayesian cluster analyses and F-statistics suggested contemporary isolation across the drainage divide and evidence for reservoir-induced fragmentation within the Bear Creek system. Compared to the sister Bandfin Darter, Blueface Darter populations exhibited reduced levels of genetic diversity, rendering them more susceptible to local extirpation and reduced fitness. Continued monitoring and quantitative ecological studies are recommended to understand population-specific measures of occurrence and abundance.
Data from: Genetics-based interactions of foundation species affect community diversity, stability, and network structure
We examined the hypothesis that genetics-based interactions between strongly interacting foundation species, the tree Populus angustifolia and the aphid Pemphigus betae, affect arthropod community diversity, stability and species interaction networks of which little is known. In a 2-year experimental manipulation of the tree and its aphid herbivore four major findings emerged: (i) the interactions of these two species determined the composition of an arthropod community of 139 species; (ii) both tree genotype and aphid presence significantly predicted community diversity; (iii) the presence of aphids on genetically susceptible trees increased the stability of arthropod communities across years; and (iv) the experimental removal of aphids affected community network structure (network degree, modularity and tree genotype contribution to modularity). These findings demonstrate that the interactions of foundation species are genetically based, which in turn significantly contributes to community diversity, stability and species interaction networks. These experiments provide an important step in understanding the evolution of Darwin's 'entangled bank', a metaphor that characterizes the complexity and interconnectedness of communities in the wild.
Data from: Is MHC diversity a better marker for conservation than neutral genetic diversity? a case study of two contrasting dolphin populations
Genetic diversity is essential for populations to adapt to changing environments. Measures of genetic diversity are often based on selectively neutral markers, such as microsatellites. Genetic diversity to guide conservation management, however, is better reflected by adaptive markers, including genes of the major histocompatibility complex (MHC). Our aim was to assess MHC and neutral genetic diversity in two contrasting bottlenose dolphin (Tursiops aduncus) populations in Western Australia—one apparently viable population with high reproductive output (Shark Bay) and one with lower reproductive output that was forecast to decline (Bunbury). We assessed genetic variation in the two populations by sequencing the MHC class II DQB, which encompasses the functionally important peptide binding regions (PBR). Neutral genetic diversity was assessed by genotyping twenty‐three microsatellite loci. We confirmed that MHC is an adaptive marker in both populations. Overall, the Shark Bay population exhibited greater MHC diversity than the Bunbury population—for example, it displayed greater MHC nucleotide diversity. In contrast, the difference in microsatellite diversity between the two populations was comparatively low. Our findings are consistent with the hypothesis that viable populations typically display greater genetic diversity than less viable populations. The results also suggest that MHC variation is more closely associated with population viability than neutral genetic variation. Although the inferences from our findings are limited, because we only compared two populations, our results add to a growing number of studies that highlight the usefulness of MHC as a potentially suitable genetic marker for animal conservation. The Shark Bay population, which carries greater adaptive genetic diversity than the Bunbury population, is thus likely more robust to natural or human‐induced changes to the coastal ecosystem it inhabits.
Data from: Archipelago-wide survey of Philippine forest dragons (Agamidae: Gonocephalus): multilocus phylogeny uncovers unprecedented levels of genetic diversity in a biodiversity hotspot
We utilize robust geographical genetic sampling, a multilocus dataset, and coalescent-based species delimitation statistics to provide the first phylogenetic inferences of relationships of Philippine Gonocephalus, combined with estimates of putative species diversity in this virtually unknown island radiation. Our results reveal startling levels of undocumented diversity, genetically partitioned at a number of geographic levels across the archipelago. In this paper we present the first survey of genetic lineage diversity, coupled with an archipelago-wide elucidation of geographic structure in a unique archipelago-endemic radiation. Philippine Gonocephalus have previously escaped the attention of biogeographers, due to taxonomic confusion associated with low numbers of preserved specimens in museum collections. With new vouchered material and genetic sampling from a comprehensive, archipelago-wide vertebrate biodiversity inventory, our findings join many recent studies highlighting the unprecedented faunal diversity in one of the world's most unique biodiversity conservation hotspots.
Genetic diversity and thermal performance in invasive and native populations of African fig flies
<p>During biological invasions, invasive populations can suffer losses of genetic diversity that are predicted to negatively impact their fitness/performance. Despite examples of invasive populations harboring lower diversity than conspecific populations in their native range, few studies have linked this lower diversity to a decrease in fitness. Using genome sequences, we show that invasive populations of the African fig fly, <i>Zaprionus indianus</i>, have less genetic diversity than conspecific populations in their native range and that diversity is proportionally lower in regions of the genome experiencing low recombination rates. This result suggests that selection may have played a role in lowering diversity in the invasive populations. We next use interspecific comparisons to show that genetic diversity remains relatively high in invasive populations of <i>Z. indianus</i> when compared to other closely related species. By comparing genetic diversity in orthologous gene regions, we also show that the genome-wide landscape of genetic diversity differs between invasive and native populations of <i>Z. indianus</i>, indicating that invasion not only affects amounts of genetic diversity, but also how that diversity is distributed across the genome. Finally, we use parameter estimates from thermal performance curves measured for 13 species of <i>Zaprionus</i> to show that <i>Z. indianus</i> has the broadest thermal niche of measured species, and that performance does not differ between invasive and native populations. These results illustrate how aspects of genetic diversity in invasive species can be decoupled from measures of fitness, and that a broad thermal niche may have helped facilitate <i>Z. indianus's</i> range expansion.</p>
Data from: Propagule pressure and genetic diversity enhance colonization by a ruderal species: a multi-generation field experiment
Colonization is a critical filter, setting the stage for short-term and long-term population success. Increased propagule pressure (e.g., more founding individuals) usually enhances colonization; however, this pattern may be driven by purely numeric effects, population genetic diversity effects, or both. To determine the independent and interactive effects of propagule pressure and genetic diversity, we conducted a seed addition experiment in the field using the ruderal annual Arabidopsis thaliana. Propagule pressure treatments spanned five levels, from 32 to 960 seeds per 0.25-m2 plot. Founder populations were composed of one, four or eight genotypes and exposed to ambient or reduced levels of interspecific competition. Genotype monocultures were included to quantify additive versus non-additive effects. Populations were followed for three generations, with abundance, population persistence and genotype retention (the proportion of introduced genotypes persisting over time) as the major response variables. Increased propagule pressure enhanced abundance immediately following introduction, particularly where nutrient availability was high and competition reduced. Greater propagule pressure also increased the likelihood of population persistence and genotype retention through three generations. However, most populations experienced rapid abundance declines over time, yielding no relationship between propagule pressure and third-generation abundance across persisting populations. Under reduced competition, increased genetic diversity led to a marginal increase in persistence through the third generation that was more pronounced, and statistically significant, in low nutrient conditions. Genetic diversity did not affect persistence through the first generation, thus indicating that genetic diversity effects strengthened over time. Nevertheless, genotypic mixture populations fell short of expectations based on performance in monocultures (negative non-additive effects). Increased genetic diversity was also associated with abundance declines, largely due to one particularly high-performing genotype in the lowest diversity treatments (i.e, genotypic identity effects). Overall, our results indicate that increases in both propagule pressure and genetic diversity can enhance colonization success but are highly context-dependent. They also highlight novel ways in which both factors can impact the retention of introduced genetic diversity over time. Our findings pinpoint the determinants of a fundamental population process and have key implications for applications where enhanced or suppressed colonization is desired, including ecological restoration and invasive species management.
Ultra-deep sequencing of HIV-1 near full-length and partial proviral genomes reveals high genetic diversity among Brazilian blood donors
<p>Here, we aimed to gain a comprehensive picture of the HIV-1 diversity in the northeast and southeast part of Brazil. To this end, a high-throughput sequencing-by-synthesis protocol and instrument were used to characterize the near full length (NFLG) and partial HIV-1 proviral genome in 259 HIV-1 infected blood donors at four major blood centers in Brazil: Pro-Sangue foundation (São Paulo state (SP), n 51), Hemominas foundation (Minas Gerais state (MG), n 41), Hemope foundation (Recife state (PE), n 96) and Hemorio blood bank (Rio de Janeiro (RJ), n 70).</p>
Figure 11. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 11. - The neighbour-joining tree of available COI sequences. Numbers associated with nodes represent bootstrap values. Length of each sequence is listed in Table 1.
Figure 12. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 12. - The neighbour-joining tree of available 12S sequences. Numbers associated with nodes represent bootstrap values. Length of each sequence is listed in Table 1.
Figure 10b. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 10b. - Habitat of Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan.Figure 10a.small pond where the present leeches were found. Photo taken by Dr Atsushi Tominaga.Figure 10b.landscape of the Suygaty Valley (Ili River Depression). Photo taken by KN. <br> landscape of the Suygaty Valley (Ili River Depression). Photo taken by KN.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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