Measures Of Genetic Diversity Research Articles

Assessing the suitability of genetic diversity of Chironomus riparius (Meigen) as an indicator of environmental pollution

Reliable and cost-effective indicators are needed to reduce uncertainty in ecological risk assessments of chemicals so that their long-term and evolutionary impacts in the dynamics of stressed biological communities can be accounted for.In the present study we investigate the suitability of genetic diversity as an indicator of ecological disturbance of freshwater ecosystems. For that, we selected three freshwater systems with well-known histories of metal contamination and three nearby reference sites located in Northern Portugal and the effects of metal contamination were assessed both in the levels of genetic diversity of the non-biting midge Chironomus riparius Meigen (at microsatellite markers) and in the diversity and composition of the benthic macroinvertebrate communities.Results showed a remarkable impoverishment in the abundance and diversity of macroinvertebrate communities of metal polluted sites in which most sensitive taxa were eliminated and replaced by more opportunistic ones belonging mainly to Oligochaeta and Diptera. In contrast, no evidence for pollution-induced genetic erosion was found in C. riparius populations in the studied area, with genetic diversity of the species being indeed higher in sites with impoverished macroinvertebrate communities and poor habitat quality.Our findings suggest that there are important limitations to the use of measures of genetic diversity of C. riparius per se to unravel ecological disturbance. Field studies aiming at quantifying pollutant-driven genetic erosion need to carefully consider the ecological and demographic aspects of potential target species.

Genetic diversity of a New Zealand multi-breed sheep population and composite breeds\u2019 history revealed by a high-density SNP chip

BackgroundKnowledge about the genetic diversity of a population is a crucial parameter for the implementation of successful genomic selection and conservation of genetic resources. The aim of this research was to establish the scientific basis for the implementation of genomic selection in a composite Terminal sheep breeding scheme by providing consolidated linkage disequilibrium (LD) measures across SNP markers, estimating consistency of gametic phase between breed-groups, and assessing genetic diversity measures, such as effective population size (Ne), and population structure parameters, using a large number of animals (n = 14,845) genotyped with a high density SNP chip (606,006 markers). Information generated in this research will be useful for optimizing molecular breeding values predictions and managing the available genetic resources.ResultsOverall, as expected, levels of pairwise LD decreased with increasing distance between SNP pairs. The mean LD r2 between adjacent SNP was 0.26 ± 0.10. The most recent effective population size for all animals (687) and separately per breed-groups: Primera (974), Lamb Supreme (380), Texel (227) and Dual-Purpose (125) was quite variable. The genotyped animals were outbred or had an average low level of inbreeding. Consistency of gametic phase was higher than 0.94 for all breed pairs at the average distance between SNP on the chip (~4.74 kb). Moreover, there was not a clear separation between the breed-groups based on principal component analysis, suggesting that a mixed-breed training population for calculation of molecular breeding values would be beneficial.ConclusionsThis study reports, for the first time, estimates of linkage disequilibrium, genetic diversity and population structure parameters from a genome-wide perspective in New Zealand Terminal Sire composite sheep breeds. The levels of linkage disequilibrium indicate that genomic selection could be implemented with the high density SNP panel. The moderate to high consistency of gametic phase between breed-groups and overlapping population structure support the pooling of the animals in a mixed training population for genomic predictions. In addition, the moderate to high Ne highlights the need to genotype and phenotype a large training population in order to capture most of the haplotype diversity and increase accuracies of genomic predictions. The results reported herein are a first step toward understanding the genomic architecture of a Terminal Sire composite sheep population and for the optimal implementation of genomic selection and genome-wide association studies in this sheep population.

Molecular Population Genetics.

Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data.

Genetic diversity and differentiation in reef-building Millepora species, as revealed by cross-species amplification of fifteen novel microsatellite loci.

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coral Millepora platyphylla, an important reef-builder of Indo-Pacific reefs. We tested the cross-species amplification of these loci in five other species of the genus Millepora and analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target species M. platyphylla, among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five other Millepora species revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean species M. complanata due to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species of Millepora. Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoan Millepora species creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

Y-Chromosome Genetic Diversity and Income Inequality

This paper empirically investigates the effect of genetic diversity on income inequality in a large cross-section of countries. Previous studies demonstrated that ethnic, linguistic and religious fractionalization have significant impact on economic performance measures, but the effect will become weaker or disappear once we control for income per capita or latitude as a measure of geographic variation. Other than that, linguistic, ethnic and religious classifications to some extent suffer from the problem of endogeneity and, at best, they capture part of visible diversity. To address these problems, I construct a cross-country genetic fractionalization measure based on the notion of paternal Y-chromosome DNA haplogroups. The resulting genetic diversity measure, which is rooted in long-term history, is less subject to the problem of endogenenity. In addition, the distances among different populations are accounted for in such fractionalization index. Finally, the empirical results show that a higher level of genetic fractionalization is associated with a higher level of income inequality. Also, this paper discusses the main mechanisms through which the genetic fractionalization measure can affect income inequality by presenting empirical evidence. It is presented that the genetic diversity measure is successful in explaining interpersonal trust as an index for individual cooperation and also tax compliance rates, public good output and even the democracy index as measures for social cooperation.

Genetic divergence in two tropical maize composites after four cycles of reciprocal recurrent selection

AbstractTwo tropical maize composites were subjected to four cycles of reciprocal recurrent selection to develop divergent inbred lines with good combining ability. This study was conducted to examine the extent of genetic diversity, changes in allele composition and genetic structure, of 100 randomly selected S1 lines each from the original (C0) and advanced (C4) selection cycles of TZL COMP3 and TZL COMP4, genotyped using single nucleotide polymorphism (SNP) markers. Results revealed that the proportion of alleles at both low and high frequencies decreased from C0 to C4, whereas those at intermediate frequencies increased at C4 in the two composites. More unique and other alleles were lost at C4 in TZL COMP3 relative to those in TZL COMP4. The changes in different measures of genetic diversity were either small or negligible with selection in the two composites. The proportion of markers departing from Hardy–Weinberg equilibrium (HWE) decreased with selection, whereas the total number of pairs of markers in linkage disequilibrium increased with selection in the two composites. Examination of changes in population structures using a model‐based approach as well as cluster and multivariate analyses found a high degree of concordance in stratifying the 400 S1 lines into four non‐overlapping groups corresponding to the two selection cycles each within the reciprocal composites. The observed molecular‐based divergence between cycles within the same composite and the clear differentiation between the complementary composites highlight the importance of reciprocal recurrent selection for preserving genetic diversity for long‐term selection. This increases the potential of the advanced selection cycles to sustain genetic gain in productivity of hybrids adapted to the savannas in West and Central Africa.

Contributions to diversity rather than basic measures of genetic diversity characterise the spreading of donkey throughout the American continent

Donkey was introduced into the Americas soon after its discovery in the 15th century. However, there is no historical consensus on how they spread across the continent. In a previous study, two distinct genetic pools (Clusters A -Southern part - and B -Northern part of South America and Central America) were identified, with likely confluence in Colombia. The aim of this study was to evaluate whether the main genetic diversity parameters, such as gene diversity (GD) and allelic richness (k), or the relative contributions of various breeds to these parameters are useful indicators to give genetic support to historical information on putative routes of the spreading of donkeys across the American continent. In full agreement with historical sources suggesting that Greater Antilles were the first breeding nucleus, both total contributions to gene diversity (gGDT) and to allelic richness (CT(k)) showed a higher ability to identify the "abundant centre" of the species on the Continent. Even though there are historical reports suggesting various entry points of the donkey into the continent (e.g. in Brazil), these parameters suggested that, in our dataset, the Cuban donkey population was the more likely representative of the first breeding nucleus of the species. Central and South American donkey populations in the surroundings of the Caribbean Gulf would more likely be early derivatives of Antillean donkey. The strong North-South genetic structure was confirmed for the American donkey metapopulation. Current analyses suggest that populations classified into Cluster A (South) are essentially a sample of the genetic background of Cluster B (North). The Andean route had the highest importance in the formation of the South American populations. The extinction of either population belonging to Cluster B could lead to a decrease in overall genetic diversity both at the gene diversity level (negative gGDT values) and the allelic richness level (positive CT(k) contributions). The opposite pattern is found for populations belonging to Cluster A. The extinction of the populations belonging to Cluster B would decrease the overall American donkey gene diversity in roughly 8% and would dramatically affect the number of alleles in the metapopulation (19.1%). However, the extinction of the donkey populations classified into Cluster A would increase overall gene diversity by 2.2%. Although, the genetic scenario of each individual population varies substantially, the joint conservation of the donkey populations classified into both Clusters A and B is highly advised.

Contrasting results from molecular and pedigree-based population diversity measures in captive zebra highlight challenges facing genetic management of zoo populations.

Zoo conservation breeding programs manage the retention of population genetic diversity through analysis of pedigree records. The range of demographic and genetic indices determined through pedigree analysis programs allows the conservation of diversity to be monitored relative to the particular founder population for a species. Such approaches are based on a number of well-documented founder assumptions, however without knowledge of actual molecular genetic diversity there is a risk that pedigree-based measures will be misinterpreted and population genetic diversity misunderstood. We examined the genetic diversity of the captive populations of Grevy's zebra, Hartmann's mountain zebra and plains zebra in Japan and the United Kingdom through analysis of mitochondrial DNA sequences. Very low nucleotide variability was observed in Grevy's zebra. The results were evaluated with respect to current and historic diversity in the wild, and indicate that low genetic diversity in the captive population is likely a result of low founder diversity, which in turn suggests relatively low wild genetic diversity prior to recent population declines. Comparison of molecular genetic diversity measures with analogous diversity indices generated from the studbook data for Grevy's zebra and Hartmann's mountain zebra show contrasting patterns, with Grevy's zebra displaying markedly less molecular diversity than mountain zebra, despite studbook analysis indicating that the Grevy's zebra population has substantially more founders, greater effective population size, lower mean kinship, and has suffered less loss of gene diversity. These findings emphasize the need to validate theoretical estimates of genetic diversity in captive breeding programs with empirical molecular genetic data. Zoo Biol. 36:87-94, 2017. © 2016 Wiley Periodicals, Inc.

Clonal structure and high genetic diversity at peripheral populations of Sorbus torminalis (L.) Crantz.

Abstract: Knowing the level of genetic diversity and structure in marginal plant populations is essential for managing their genetic resources. This is particularly important for rare scattered tree species, such as Sorbus torminalis (L.) Crantz. We investigated the genetic diversity and its spatial distribution in peripheral populations of S. torminalis. As the species is known to reproduce vegetatively, we also evaluated clonal structure within populations. Using 13 nuclear microsatellite loci designed in two multiplexes, we genotyped 172 individuals revealing the existence of 100 distinct genotypes. Number of ramets per genotype was variable across populations with an average of 1.72. Examples of somaclonal variation at particular loci were detected. Measures of genetic diversity of the total sample were relatively high (mean allelic richness AR = 10.293; expected heterozygosity He = 0.756), as compared to other S. torminalis populations. We noticed a slightly negative inbreeding coefficient (FIS = -0.029) indicating a small excess of heterozygotes, which is typical for self-incompatible plants. Genetic differentiation among populations was low (FST = 0.048), but Bayesian clustering methods revealed the existence of three distinct genetic clusters only in part related to population structure. Significant spatial genetic structure within populations was also detected (Sp = 0.0125) indicating fine-scale pattern of isolation by distance. Our study demonstrated that peripheral populations of S. torminalis may exhibit relatively high levels of genetic diversity despite the existence of vegetative propagation. Nevertheless, if the studied or similar populations are expected to be utilized as seed sources for ex-situ or in-situ conservation purposes, the existence of clonal structure and spatial genetic structure must be taken into account in order to avoid excessive sampling of the same or closely related genets.

Temporal genetic stability in natural populations of the waterflea Daphnia magna in response to strong selection pressure.

Studies monitoring changes in genetic diversity and composition through time allow a unique understanding of evolutionary dynamics and persistence of natural populations. However, such studies are often limited to species with short generation times that can be propagated in the laboratory or few exceptional cases in the wild. Species that produce dormant stages provide powerful models for the reconstruction of evolutionary dynamics in the natural environment. A remaining open question is to what extent dormant egg banks are an unbiased representation of populations and hence of the species' evolutionary potential, especially in the presence of strong environmental selection. We address this key question using the water flea Daphnia magna, which produces dormant stages that accumulate in biological archives over time. We assess temporal genetic stability in three biological archives, previously used in resurrection ecology studies showing adaptive evolutionary responses to rapid environmental change. We show that neutral genetic diversity does not decline with the age of the population and it is maintained in the presence of strong selection. In addition, by comparing temporal genetic stability in hatched and unhatched populations from the same biological archive, we show that dormant egg banks can be consulted to obtain a reliable measure of genetic diversity over time, at least in the multidecadal time frame studied here. The stability of neutral genetic diversity through time is likely mediated by the buffering effect of the resting egg bank.

An R version of FPTest for testing differences in allelic count

Allelic count is an important measure of genetic diversity. However, it is a function of sample size and its estimation and interpretation can be biased. Previously, we introduced a random permutation method named FPTest to test the differences in allelic count among oat germplasm groups of variable sample size (Fu et al., Crop Sci 43:1989–1995, 2003) and published a SAS routine for it to facilitate its application (Fu, Mol Ecol Resour 10:398–392, 2010). Here we present an R version of FPTest called FPTestR. This R version considers six types of large marker data and generates four to five output files, making the test more accessible and useful in genetic diversity analysis.

A novel hotspot of vertebrate endemism and an evolutionary refugium in tropical Australia

AbstractAimIn lineages or regions that are rife with morphologically cryptic taxa, hotspots of local endemism may remain overlooked when genetic data are unavailable. Here we examine the genetic diversity and evolutionary origins of lizard communities occurring in a relatively restricted, isolated and heretofore poorly surveyed region of limestone karst in northern Australia.LocationThe Devonian Reef System (DRS), an iconic range of exposed weathered limestone at the margin of the Australian Arid Zone (AAZ) and Monsoonal Tropics (AMT) in north‐west Australia, that is widely recognized for its cultural, geological and palaeontological significance.MethodsIn collaboration with local landowners, we sampled four different gecko genera at sites spanning the DRS and adjacent biomes. We then used measures of genetic divergence, neutrality tests, Bayesian dating and hierarchical approximate Bayesian computational (HABC) approaches to identify divergent lineages, test for shared biogeographic history and compare patterns of genetic differentiation in lineages with different ecologies (saxicoline, arboreal and terrestrial).ResultsAmongst saxicoline taxa, we identified 11 genetically divergent lineages that appear to be endemic to the DRS. Generalists and arboreal lineages showed no evidence of endemism in the DRS. Estimated divergence dates and patterns of distribution indicate that endemic lineages have persisted since the Plio‐Pleistocene (or even earlier). Taxa in an old endemic Australian Gondwanan radiation showed evidence of longer persistence and isolation than those in radiations with more recent immigrant origins.Main ConclusionsThe DRS is a heretofore overlooked hotspot of vertebrate endemism and persistence. Areas with distinctive underlying geology that provide microrefugia (such as karst) in tropical regions across the globe are likely important refugia for biodiversity at both ecological and evolutionary scales. They warrant further focused survey efforts (including genetics‐based assessments of diversity) and ongoing conservation attention.

Evaluation of genetic diversity of sweet potato [Ipomoea batatas (L.) Lam.] on different ploidy levels applying two capillary platforms

ABSTRACTThe genetic composition of sweet potato [Ipomoea batatas (L.) Lam.] (2n = 6x = 90) is reflected in different levels of genetic variation. The main objective of the present study was a comparison of genetic diversity parameters of different ploidy levels (2n, 4n, and 6n codominant allele determination), analyzed on two high-resolution capillary platforms. Fragment analysis was performed by applying SSR markers on a 3130XL Genetic Analyzer (ABI 3130) and QIAxcel Advanced System (QX). A high level of expected heterozygosity (He) as a measure of genetic diversity was observed for both ABI3130 (0.731) and QX (0.679). Molecular variance was 17% for ABI3130 and 10% for QX. Comparison between genetic distance matrices based on allele lengths showed a moderate Mantel correlation coefficient (rxy = 0.557) between ABI3130 and QX. Global cluster analysis using the Bayesian approach distributed the observed genotypes into two clusters on both capillary platforms. Our results show that the two high-resolution capillary electrophoreses for codominant data on 2n, 4n, and 6n levels are applicable in genetic diversity studies but their efficiency depends on in-resolution expectations, financial resources, available time, and the equipment of the laboratory.

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection.

The availability of large-scale population genomic sequence data has resulted in an explosion in efforts to infer the demographic histories of natural populations across a broad range of organisms. As demographic events alter coalescent genealogies, they leave detectable signatures in patterns of genetic variation within and between populations. Accordingly, a variety of approaches have been designed to leverage population genetic data to uncover the footprints of demographic change in the genome. The vast majority of these methods make the simplifying assumption that the measures of genetic variation used as their input are unaffected by natural selection. However, natural selection can dramatically skew patterns of variation not only at selected sites, but at linked, neutral loci as well. Here we assess the impact of recent positive selection on demographic inference by characterizing the performance of three popular methods through extensive simulation of data sets with varying numbers of linked selective sweeps. In particular, we examined three different demographic models relevant to a number of species, finding that positive selection can bias parameter estimates of each of these models-often severely. We find that selection can lead to incorrect inferences of population size changes when none have occurred. Moreover, we show that linked selection can lead to incorrect demographic model selection, when multiple demographic scenarios are compared. We argue that natural populations may experience the amount of recent positive selection required to skew inferences. These results suggest that demographic studies conducted in many species to date may have exaggerated the extent and frequency of population size changes.

Mistaken Identity: Another Bias in the Use of Relative Genetic Divergence Measures for Detecting Interspecies Introgression.

Measures of genetic divergence have long been used to identify evolutionary processes operating within and between species. However, recent reviews have described a bias in the use of relative divergence measures towards incorrectly identifying genomic regions that are seemingly immune to introgression. Here, we present a novel and opposite bias of relative divergence measures: misidentifying regions of introgression between sister species. We examine two distinct haplotypes of intermediate frequency within Drosophila pseudoobscura at the DPSX009 locus. One of these haplotypes had lower relative divergence than another to sister species D. persimilis. Although we and others initially presumed one haplotype have spread via introgression between D. pseudoobscura and D. persimilis, absolute divergence measures and individual sequence analysis suggest that haplotype structuring occurred as the result of within-species processes. The potential for this type of misinference may occur with any haplotype that recently spread within a species. We conclude that absolute measures of genetic divergence are necessary for confirming putative regions of introgression.

Adaptation and plasticity in aboveground allometry variation of four pine species along environmental gradients.

Plant species aboveground allometry can be viewed as a functional trait that reflects the evolutionary trade‐off between above‐ and belowground resources. In forest trees, allometry is related to productivity and resilience in different environments, and it is tightly connected with a compromise between efficiency‐safety and competitive ability. A better understanding on how this trait varies within and across species is critical to determine the potential of a species/population to perform along environmental gradients. We followed a hierarchical framework to assess tree height‐diameter allometry variation within and across four common European Pinus species. Tree height‐diameter allometry variation was a function of solely genetic components –approximated by either population effects or clinal geographic responses of the population's site of origin– and differential genetic plastic responses –approximated by the interaction between populations and two climatic variables of the growing sites (temperature and precipitation)–. Our results suggest that, at the species level, climate of the growing sites set the tree height‐diameter allometry of xeric and mesic species (Pinus halepensis, P. pinaster and P. nigra) apart from the boreal species (P. sylvestris), suggesting a weak signal of their phylogenies in the tree height‐diameter allometry variation. Moreover, accounting for interpopulation variability within species for the four pine species aided to: (1) detect genetic differences among populations in allometry variation, which in P. nigra and P. pinaster were linked to gene pools –genetic diversity measurements–; (2) reveal the presence of differential genetic variation in plastic responses along two climatic gradients in tree allometry variation. In P. sylvestris and P. nigra, genetic variation was the result of adaptive patterns to climate, while in P. pinaster and P. halepensis, this signal was either weaker or absent, respectively; and (3) detect local adaptation in the exponent of the tree height‐diameter allometry relationship in two of the four species (P. sylvestris and P. nigra), as it was a function of populations' latitude and altitude variables. Our findings suggest that the four species have been subjected to different historical and climatic constraints that might have driven their aboveground allometry and promoted different life strategies.

Modelling different reintroduction strategies for the critically endangered Floreana mockingbird

AbstractOne of the main recommendations of reintroduction biology for prospective projects is that they should be planned with local species knowledge and with species‐specific quantitative modelling, for example, from population viability analysis (PVA). Here, we apply this approach to the planned reintroduction of the critically endangered Floreana mockingbird Mimus trifasciatus in the Galápagos Archipelago. After its extinction on Floreana Island, the Floreana mockingbird today only persists on two small islets, Champion and Gardner. In the context of a wider island restoration project, there are plans to reintroduce M. trifasciatus back to Floreana to establish a population as large and genetically diverse as possible, while minimizing the impact on the two source populations. To aid the planning of this reintroduction effort, we compared six potential reintroduction strategies that differ in three aspects: (1) use of captive breeding, (2) state‐(in)dependent sourcing of birds, (3) time span for translocations. We assessed the strategies’ performance using a multi‐site count‐based PVA and simulations of coancestry as a measure of genetic diversity. In general, PVA and coancestry results were comparable in terms of the strategies’ performance. Strategies with captive breeding resulted in larger population sizes and higher genetic diversity on Floreana after 20 years. However, the advantages of captive breeding disappeared when the population growth rate in captivity or on Floreana was very low. The reintroductions did not negatively impact the source populations’ viability, provided no more than 2 and 16 birds were taken annually from the two source islets. The approach employed here shows how a count‐based PVA in combination with simulations of genetic diversity can help reintroduction planning.

Range, genetic diversity and future of the threatened butterfly, Pieris virginiensis

Abstract Pieris virginiensis, the West Virginia White butterfly, faces severe potential habitat loss and degradation of existing suitable habitat in the near future from climate change and plant invasion. Increasing isolation and local extinction events resulting from deforestation and climate change have a chance to significantly impact the future of this butterfly. We used genetic analysis and spatial modelling techniques to estimate the current spatial and genetic scope of P. virginiensis. We used linear modelling and machine learning to predict the occurrence of P. virginiensis through space and time using occurrence records between 1879 and 2014 and environmental predictors from a world climate dataset. We predicted the future occurrence of P. virginiensis with climate projections for the year 2070. We sequenced the cytochrome oxidase I, and the internal transcribed spacer region I, in the mitrochondrial and nuclear genomes, respectively, then used a combination of genetic diversity measures and phylogeny construction to evaluate the genetic diversity of P. virginiensis. We found that latitude accounts for nearly one‐fifth of the variation in emergence date. Spatial models predicted that P. virginiensis may lose up to 60% of available habitat in the next 50 years. Genetic data indicated some isolation in an Ohio population's COI gene, and low genetic diversity across the range of P. virginiensis in ITS. These may be indicative of either the last glacial expansion or a more recent disturbance. A large effective population size indicates that P. virginiensis are not yet nearing extinction.

Genetic diversity analyses reveal first insights into breed-specific selection signatures within Swiss goat breeds.

We used genotype data from the caprine 50k Illumina BeadChip for the assessment of genetic diversity within and between 10 local Swiss goat breeds. Three different cluster methods allowed the goat samples to be assigned to the respective breed groups, whilst the samples of Nera Verzasca and Tessin Grey goats could not be differentiated from each other. The results of the different genetic diversity measures show that Appenzell, Toggenburg, Valais and Booted goats should be prioritized in future conservation activities. Furthermore, we examined runs of homozygosity (ROH) and compared genomic inbreeding coefficients based on ROH (FROH ) with pedigree-based inbreeding coefficients (FPED ). The linear relationship between FROH and FPED was confirmed for goats by including samples from the three main breeds (Saanen, Chamois and Toggenburg goats). FROH appears to be a suitable measure for describing levels of inbreeding in goat breeds with missing pedigree information. Finally, we derived selection signatures between the breeds. We report a total of 384 putative selection signals. The 25 most significant windows contained genes known for traits such as: coat color variation (MITF, KIT, ASIP), growth (IGF2, IGF2R, HRAS, FGFR3) and milk composition (PITX2). Several other putative genes involved in the formation of populations, which might have been selected for adaptation to the alpine environment, are highlighted. The results provide a contemporary background for the management of genetic diversity in local Swiss goat breeds.

Population structure and genetic diversity of Populus laurifolia in fragmented riparian gallery forests of the Mongolian Altai Mountains

Riparian forests belong to the most vulnerable ecosystems worldwide and have been severely affected by logging, livestock grazing and altered flooding over the last decades. Several riparian tree species including Populus spp. face a risk of loss in genetic diversity and associated adaptive potential. A model species for such systems in Central Asia is Populus laurifolia, which in Western Mongolia is commonly confined to river floodplains of the Altai Mountains. Populations appear heavily fragmented and show evidence for lack of regeneration. In order to better understand the ecology of these systems and to provide conservation in the study region and beyond, a total of 615 individuals from first and second order water courses of the Bulgan River in Hovd Aimag were mapped, followed by measurements of diameter at breast height, tree height and sampling of leaf material. Five nuclear microsatellites were employed to estimate standard genetic diversity measures and genetic structure within and among populations.Size class distribution showed a clear sign of over-aging, suggesting that establishment of young individuals is hampered by intense grazing/browsing. Genetic diversity tended to increase downstream, though evidence for genetic differentiation and genetic structuring was ambiguous. This pointed to a time lag between demographic and genetic responses to land use, explained by longevity of trees coupled with clonal growth.As hampered regeneration of plant stands may affect future ecosystem stability, controlled grazing strategies should be considered to secure long-term persistence of stands.