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opencc-by-4.0Sep 2019View details →

T a b l e 2 in Genetic Diversity And Place In The General Phylogeographic Structure Of Capercaillie,Tetrao Urogallus (Galliformes, Phasianidae), From Belarus

T a b l e 2. The number of the capercaillie in Belarus

opencc-zeroAug 2022View details →

Determinants of genetic diversity and species richness of North American amphibians

Aim: Ecological limits on population sizes and the number of species a region can sustain are thought to simultaneously produce spatial patterns in population genetic diversity and species richness due to the effects of random drift operating in parallel across population and community levels. Here, we test the extent to which resource-based environmental limits jointly determine these patterns of biodiversity in amphibians. Location: North America. Taxon: Amphibians. Methods: We repurposed open, raw microsatellite data from 19 species sampled at 554 sites in North America and mapped nuclear genetic diversity at the continental scale. We then tested whether ecological limits defined by resource availability and environmental heterogeneity could simultaneously shape biogeographic patterns in genetic diversity and species richness with structural equation modeling. Results: Spatial patterns of population genetic diversity run opposite patterns of species richness and genetic differentiation. However, while measures of resource availability and niche heterogeneity predict 89% of the variation in species richness, these landscape metrics were poor predictors of genetic diversity. Main conclusions: Although heterogeneity appears to be an important driver of genetic and species biodiversity patterns in amphibians, variation in genetic diversity both within and across species makes it difficult to infer general processes producing spatial patterns of amphibian genetic diversity. This result differs from those found in endotherms and may be due to the considerable life history variation found across amphibians.

opencc-zeroAug 2022View details →

Population dynamics of Amazonian floodplain forest species support spatial variation on genetic diversity but not range expansions through time

Aim: We tested if historical demographic changes of populations occurring on the floodplains of a major Amazon Basin tributary could be associated with range expansions from upper and middle sections of the river, following the establishment of widespread river-created environments during the Late Pleistocene and Holocene. Location: Solimões River, Western Amazon, South America. Taxon: Myrmoborus lugubris, Thamnophilus cryptoleucus and Myrmotherula assimilis. Methods: We explored spatial patterns of genetic diversity and connectivity among sampled localities using thousands of Ultra-Conserved Elements. Range expansions were tested with alternative methods. We quantified habitat preference for the analyzed species to test whether the occupation of dynamic habitats could predict spatial patterns of genetic diversity. Results: Our study did not support shared population range expansions related to historical regionalized changes in habitat availability. We found considerable variation in the spatial distribution of the genetic diversity between studied taxa, and that species with higher levels of specialization to dynamic environments have a more heterogeneous distribution of genetic diversity and reduced levels of gene flow across space. Main conclusions: Our results suggest that demographic expansions along the Solimões River might be linked to spatially homogeneous oscillation in the distribution of floodplain environments, promoting effective population size changes but not range expansion. We found that habitat specificity might be a good predictor of population connectivity along the Amazonian floodplains.

opencc-zeroSep 2022View details →

Pollinator data from: Pollinator movement activity influences genetic diversity and differentiation of spatially isolated populations of clonal forest herbs

In agricultural landscapes, forest herbs live in small, spatially isolated forest patches. For their long-term survival, their populations depend on animals as genetic linkers that provide pollen- or seed-mediated gene flow among different forest patches. However, whether insect pollinators serve as genetic linkers among spatially isolated forest herb populations in agricultural landscapes remains to be shown. Here, we used population genetic methods to analyze: (A) the genetic diversity and genetic differentiation of populations of two common, slow-colonizing temperate forest herb species (Polygonatum multiflorum (L.) All. and Anemone nemorosa L.) in spatially isolated populations within three agricultural landscapes in Germany and Sweden and (B) the movement activity of their most relevant associated pollinator species, i.e., the bumblebee Bombus pascuorum (Scopoli, 1763) and the hoverfly Melanostoma scalare (Fabricus, 1794), respectively, which differ in their mobility. We tested whether the indicated pollinator movement activity affected the genetic diversity and genetic differentiation of the forest herb populations. Bumblebee movement indicators that solely indicated movement activity between the forest patches affected both genetic diversity and genetic differentiation of the associated forest herb P. multiflorum in a way that can be explained by pollen-mediated gene flow among the forest herb populations. In contrast, movement indicators reflecting the total movement activity at a forest patch (including within-forest patch movement activity) showed unexpected effects for both plant-pollinator pairs that might be explained by accelerated genetic drift due to enhanced sexual reproduction. Our integrated approach revealed that bumblebees serve as genetic linkers of associated forest herb populations, even if they are more than 2 km apart from each other. No such evidence was found for the forest-associated hoverfly species which showed significant genetic differentiation among forest patches itself. Our approach also indicated that a higher within-forest patch movement activity of both pollinator species might enhance sexual recruitment and thus diminishes the temporal buffer that clonal growth provides against habitat fragmentation effects.

opencc-zeroSep 2022View details →

Data from: Linking environmental stability with genetic diversity and population structure in two Atlantic Forest palm trees

Spatial patterns of biodiversity in the Atlantic Forest of Brazil are well characterized. However, there is no consensus on the biological processes underlying these patterns, and multiple competing hypotheses have been proposed, several of which center on climatic stability. Here, we ask if Late Quaternary climatic stability predicts contemporary population structure and genomic-level diversity in two palm species: Syagrus botryophora and S. pseudococos (Arecaceae) We first use species occurrence data to model the distribution of suitable environments in 62 time-slice climate projections over the last 120 thousand years, and summarize stability over that period. We then use >25,000 RADseq-generated SNPs to i) describe the spatial patterns of genomic variation in both species, ii) test how well genomic variation is explained by isolation by distance and by the environmental resistance imposed by historical instability (isolation by resistance) and iii) test for a correlation between genetic diversity and historical stability. The contemporary range of S. botryophora has been relatively stable over the last 30 thousand years and there are two isolated regions of high stability for S. pseudococos. The genomic data recovers a clear pattern of isolation by distance in S. botryophora and two structured populations in S. pseudococos. Consequently, the contribution of isolation by resistance to overall genetic structure is much higher in S. pseudococos. Genetic diversity is not significantly correlated with historical stability in either species. Based on the concordance between historical stability and genetic structure, Late Quaternary climate stability may have maintained population connectivity within S. botryophora and promoted intraspecific divergence in S. pseudococos. Conversely, historical stability does not seem to be driving spatial patterns of genetic diversity. This study supports the primary role of climatic stability in determining spatial population structure, but not genetic diversity, in the Atlantic Forest.

opencc-zeroOct 2022View details →

Data from: Extra-pair paternity correlates with genetic diversity, but not breeding density, in a Neotropical passerine, the Black Catbird

The frequency of extra-pair paternity (EPP) varies widely across socially monogamous birds, but the proximate mechanisms driving this variation remain unclear. In this study, we tested two major factors hypothesized to influence extra-pair mating—breeding density and genetic diversity—by comparing genetic mating patterns in two populations of black catbirds Melanoptila glabrirostris. This Neotropical songbird is endemic to the Yucatán Peninsula, including eastern Mexico, and its offshore islands. We sampled one mainland (Sian Ka'an Biosphere Reserve) and one island (Isla Cozumel) population and used single-nucleotide polymorphisms (SNPs) to quantify heterozygosity and genetic parentage over two breeding seasons. Moderate levels of EPP occurred in both populations (9.5 – 35% of offspring and 17 – 45% of nests). Contrary to predictions, breeding density did not affect EPP: although breeding densities were much higher on the mainland than on the island, EPP rates did not differ between populations, and local breeding density was not correlated with EPP at individual nests. In contrast, partial support emerged for the hypothesis that genetic diversity influences EPP: extra-pair offspring were more heterozygous than within-pair offspring. However, the two populations did not differ in genetic diversity, and neither the heterozygosity of social fathers nor within-pair relatedness predicted EPP. These results are consistent with recent comparative studies suggesting that breeding density is not a critical driver of EPP rates, and that not all tropical songbirds exhibit low rates of EPP.

opencc-by-4.0Dec 2021View details →

Dataset for "Genetic diversity and population structure of a wide Pisum spp. core collection."

Silico-DArT and SNP datasets of the IAS pea core collection. Each file contain key information of the molecular markers used to establish the population structure and genetic diversity of the IAs pea core collection.

opencc-zeroApr 2024View details →

Data from: Genetic diversity in tempo determines foraging range in ants

The foraging behavior of a colony arises from the activity of individual workers. In this paper we explore the phenotypic differences among the workers of the western harvester ant, Pogonomyrmex occidentalis in order to understand the temporal pattern of foraging in colonies. We know that the genetic diversity of colonies influences the temporal pattern of foraging: with greater genetic diversity colonies begin foraging earlier and forage for greater duration. We test two mechanisms to account for this pattern. The Temperature Hypothesis predicts that early foragers will be more active at lower temperatures than late foragers and will be the first workers to initiate foraging. Late foragers will be more active at high temperatures. The Tempo Hypothesis predicts that early foragers will be the first to forage because they have the higher overall tempo of activity at all temperatures. We measure the movement activity of samples of early and late foragers from 32 colonies over a range of temperatures from 9-37̊C. We find that early workers are more active at all temperatures than late workers, supporting the Tempo Hypothesis. Early and late foragers tend to belong to different patrilines, suggesting that there is a genetic basis for the difference in the tempo of behavior. We also find that colonies that have greater number of patrilines, due to greater mating frequency by the queen, have a greater range temporal range of foraging.

opencc-zeroMay 2024View details →

Data from: Small but connected islands can maintain populations and genetic diversity under climate change

In response to the striking effects of environmental change, conservation strategies often include the identification of conservation areas that can effectively maintain vulnerable species. Consequently, identifying system-specific conditions that maintain the demographic and genetic viability of species of conservation concern is essential. Connectivity plays a critical role in the persistence of populations. Islands have been model systems to understand connectivity and metapopulation processes and have emerged as particularly favorable targets for conservation. While islands can be isolated from mainland disturbances, it is unknown what degree of isolation is necessary to avoid unfavorable changes but remain sufficiently connected to maintain population viability. To test this question, we explored connectivity within the Apostle Islands, an archipelago of 22 islands within Lake Superior, by comparing historical and contemporary trends in ice bridge connectivity and by simulating the effect of reduced connectivity within this system. We developed a demographically informed individual-based model to explicitly test the role of connectivity to influence the persistence and genetic diversity of American marten (Martes americana), a forest carnivore at risk across its southern range boundary. We found that genetic diversity was resilient to moderate changes in ice cover, but a complete loss of connectivity resulted in rapid genetic erosion. Despite genetic erosion, populations persisted as long as nominal connectivity occurred between islands. Our work suggests that connectivity will decline, but martens would be resilient to moderate changes, and, in the short term, the Apostle Islands can act as a refuge along this species' southern range boundary. Identifying thresholds in connectivity that maintain populations but allow for isolation from disturbance will be necessary to identify suitable areas for species conservation across space and time.

opencc-zeroMay 2024View details →

Genome-wide single nucleotide polymorphisms reveal the genetic diversity and population structure of Creole goats from northern Peru

Goat farming constitutes a significant source of income for farmers in northern Peru. There is currently an absence of information about the genetics of Peruvian Creole goats that would enable us to understand their origins and genetic spread. The objective of this study was to estimate the genetic diversity of Creole goats from northern Peru using SNP markers. This study involved the collection of 192 male Creole goats from three key goat production regions in northern Peru. These goat samples were genotyped using the GGPGoat70k SNP panel. To explore the genetic influence of other breeds on Peruvian Creole goats, our dataset was combined with previously published SNP genotypes. External data set includes multiple breeds genotypes sampled from Argentina, Brazil, Spain, and Alpine breed from Italy, France, and Switzerland. After quality control 52,832 autosomal SNPs were used to assess genetic diversity in the Peruvian goats. For the population structure analysis of the merged data 20,513 common SNPs were used. Estimations for expected heterozygosity (He), observed heterozygosity (Ho), and inbreeding coefficient (FIS) were computed for the Peruvian groups. AMOVA, principal component analysis and ADMIXTURE were conducted to evaluate the population structure in the two data sets, Peru and merged. The results revealed a considerable genetic diversity, with Ho values ranging from 0.40 to 0.41 for the Peruvian sampling groups, and inbreeding coefficient was notably low for Peruvian goat. The population structure analysis demonstrated a distinction (p< 0.05) from other breeds. These findings suggest a level of genetic differentiation of the Peruvian goat population among other breeds, although further research is needed considering samples from other Peruvian areas. We expect this study will contribute to define genetic management strategies to prevent the loss of genetic diversity in Peruvian goat populations and for upcoming advancements in this field.

opencc-by-4.0Mar 2019View details →

Fig. 1 in Genetic diversity of Egyptian populations of the African Common Toad (Sclerophrys regularis, Reuss 1833)

Fig. 1. Map of the sampled localities.

opencc-zeroMay 2024View details →

Data from: Analysis of genotyping data reveals the unique genetic diversity represented by the breeds of sheep native to the United Kingdom

Background: Sheep breeds native to the United Kingdom are noted for high breed variability and exhibit a striking diversity of different traits in phenotypes and genetic diversity. Some of these traits are highly sustainable, such as seasonal wool shedding in the Wiltshire Horn, are likely to become more important as pressures on sheep production increase in coming decades. Despite their clear importance to the future of sheep farming, the genetic diversity of native UK sheep breeds is poorly characterised. This increases the risk of losing the ability to select for breed-specific traits from native breeds that might be important to the UK sheep sector in the future. Here, we use 50K genotyping to perform preliminary analysis of breed relationships and genetic diversity within native UK sheep breeds, as a first step towards a comprehensive characterisation. This study generates novel data for thirteen native UK breeds, including 6 on the UK Breeds at Risk (BAR) list, and utilises existing data from the publicly available Sheep HapMap dataset to investigate population structure, heterozygosity and admixture. Results: In this study the commercial breeds exhibited high levels of admixture, weaker population structure and had higher heterozygosity compared to the other native breeds, which generally tend to be more distinct, less admixed, and have lower genetic diversity and higher kinship coefficients. Some breeds including the Wiltshire Horn, Lincoln Longwool and Ryeland showed very little admixture at all, indicating a high level of breed integrity but potentially low genetic diversity. Population structure and admixture were strongly influenced by sample size and sample provenance – highlighting the need for equal sample sizes, sufficient numbers of individuals per breed, and sampling across multiple flocks. The genetic profiles both within and between breeds were highly complex for UK sheep, reflecting the complexity in the demographic history of these breeds. Conclusion: Our results highlight the utility of genotyping data for investigating breed diversity and genetic structure. They also suggest that routine generation of genotyping data would be very useful in informing conservation strategies for rare and declining breeds with small populations sizes. We conclude that generating genetic resources for the sheep breeds that are native to the UK will help preserve the considerable genetic diversity represented by these breeds, and safe guard this diversity as a valuable resource for the UK sheep sector to utilise in the face of future challenges.

opencc-zeroJun 2024View details →

Polyandry and non-random fertilisation maintain long-term genetic diversity in an isolated island population of adders (Vipera berus)

Conservation genetic theory suggests that small and isolated populations should be subjected to reduced genetic diversity i.e., heterozygosity and allelic diversity. Our 34 years study of an isolated island population of adders (Vipera berus) in southern Sweden challenges this notion. Despite a lack of gene flow and a yearly mean estimated reproductive adult population size of only 65 adult adders (range 12 to 171), the population has been able to maintain high levels of heterozygosity and allelic diversity similar to that observed in two mainland populations. Even a 14-year major "bottleneck" i.e., a reduction in adult adder numbers, encompassing at least four adder generations, did not result in any reduction in the island adders' heterozygosity and allelic diversity. Female adders are polyandrous, and fertilisation is non-random, which our empirical data and modelling suggest underpinning the island adders' ability to maintain a high level of heterozygosity. Our empirical results and subsequent modelling suggest that the positive genetic effects of polyandry in combination with non-random fertilisation, often overlooked in conservation genetic analyses, deserve greater consideration when predicting long-term survival of small and isolated populations.

opencc-zeroJul 2024View details →

An assemblage-level comparison of genetic diversity and population genetic structure between island and mainland ant populations

Island biotas provide unparalleled opportunities to examine evolutionary processes. Founder effects and bottlenecks, for example, typically decrease genetic diversity in island populations, while selection for reduced dispersal can increase population structure. Given that support for these generalities mostly comes from single-species analyses, assemblage-level comparisons are needed to clarify how (i) colonization affects the gene pools of interacting insular organisms, and (ii) patterns of genetic differentiation vary within assemblages of organisms. Here, we use genome-wide sequence data from ultraconserved elements (UCEs) to compare genetic diversity and population structure of mainland and island populations of nine ant species in coastal southern California with respect to genetic diversity and population structure. As expected, island populations (from Santa Cruz Island) had lower than expected heterozygosity and Watterson's theta compared to mainland populations (from the Lompoc Valley). Island populations, however, exhibited smaller genetic distances among samples, indicating less population subdivision and a higher capacity for dispersal compared to mainland populations. Within the focal assemblage, pairwise Fst values revealed pronounced interspecific variation in mainland-island differentiation, which increases with gyne body size. Our results reveal differences in genetic diversity and population genetic structure across an assemblage of interacting species, and illuminate general patterns of insularization in ants. Compared to single-species studies, our analysis of nine species pairs from the same island-mainland system offers a powerful approach to studying fundamental evolutionary processes.

opencc-by-4.0Dec 2020View details →

Fig.1 in Testing The Microsatellites-Pcr Markers For Genetic Diversity Research Of Alien Ponto-Caspian Amphipod Pontogammarus Robustoides G. O. Sars, 1894

Fig.1. Localities of sampling sities in the Latvian reservoirs.

opencc-by-4.0Dec 2009View details →

Fig.4 in Genetic Diversity Of (Brassica Napus L.) Spring Oilseed Rape

Fig.4. Analysis of Molecular Variance among cultivars and within cultivars

Figure 1 in Unveiling the genetic diversity of bicolored-spined porcupines (Rodentia: Erethizontidae): a novel karyotype, population structuring, and evolutionary insights

Figure 1. Map of part of South America with collecting localities of C. bicolor specimens with sequences on the GenBank (Black circles), generated in the present study (triangle), others register of occurrences (white circles), and type locality (star). Gray area represents the Amazon Biome. ARG = Argentina, BOL = Bolivia, BRA = Brazil, PER = Peru.

Figure 4 in Unveiling the genetic diversity of bicolored-spined porcupines (Rodentia: Erethizontidae): a novel karyotype, population structuring, and evolutionary insights

Figure 4. Topology of median joining on top of the map showing the current separation of C. bicolor populations by the rivers Ucayali and Beni/Madre de Dios. Circles are haplotypes and its dimension are proportional to the number of shared sequences. Numbers in the segments connecting the circles are nucleotide substitutions and black circle is the median vector. For haplotypes localities see figure 2. BOL = Bolivia, BRA = Brazil, PER = Peru.

Figure 3 in Unveiling the genetic diversity of bicolored-spined porcupines (Rodentia: Erethizontidae): a novel karyotype, population structuring, and evolutionary insights

Figure 3. Maximum likelihood phylogenetic tree. Symbols near nodes represent Bootstrap values: black circles (90-100%), white circles (80-89%), white squares (70-79%), black square (66%). BOL = Bolivia, BRA = Brazil, COL = Colombia, ECU = Ecuador, GUF = French Guiana, MEX = Mexico, PAR = Paraguay, PER = Peru.

Figure 2 in Unveiling the genetic diversity of bicolored-spined porcupines (Rodentia: Erethizontidae): a novel karyotype, population structuring, and evolutionary insights

Figure 2. Conventional stained karyotypes of Coendou (Sphiggurus) bicolor male LBCE21287 (above) and female LBCE21289 (below) from Brazilian Acre state with 2n = 52 and FN = 82. The X and Y are sexual chromosomes.