Estimates Of Effective Population Size Research Articles

Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

Key messageBrazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation.Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity ({H}_{o}), effective population size estimate widehat{{(N}_{e}}) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

The Pan social brain: An evolutionary history of neurochemical receptor genes and their potential impact on sociocognitive differences

Humans have unique cognitive capacities that, compared with apes, are not only simply expressed as a higher level of general intelligence, but also as a quantitative difference in sociocognitive skills. Humans’ closest living relatives, bonobos (Pan paniscus), and chimpanzees (Pan troglodytes), show key between-species differences in social cognition despite their close phylogenetic relatedness, with bonobos arguably showing greater similarities to humans. To better understand the evolution of these traits, we investigate the neurochemical mechanisms underlying sociocognitive skills by focusing on variation in genes encoding proteins with well-documented roles in mammalian social cognition: the receptors for vasopressin (AVPR1A), oxytocin (OXTR), serotonin (HTR1A), and dopamine (DRD2). Although these genes have been well studied in humans, little is known about variation in these genes that may underlie differences in social behavior and cognition in apes. We comparatively analyzed sequence data for 33 bonobos and 57 chimpanzees, together with orthologous sequence data for other apes. In all four genes, we describe genetic variants that alter the amino acid sequence of the respective receptors, raising the possibility that ligand binding or signal transduction may be impacted. Overall, bonobos show 57% more fixed substitutions than chimpanzees compared with the ancestral Pan lineage. Chimpanzees, show 31% more polymorphic coding variation, in line with their larger historical effective population size estimates and current wider distribution. An extensive literature review comparing allelic changes in Pan with known human behavioral variants revealed evidence of homologous evolution in bonobos and humans (OXTR rs4686301(T) and rs237897(A)), while humans and chimpanzees shared OXTR rs2228485(A), DRD2 rs6277(A), and DRD2 rs11214613(A) to the exclusion of bonobos. Our results offer the first in-depth comparison of neurochemical receptor gene variation in Pan and put forward new variants for future behavior–genotype association studies in apes, which can increase our understanding of the evolution of social cognition in modern humans.

Subspecies hybridization as a potential conservation tool in species reintroductions.

Reintroductions are a powerful tool for the recovery of endangered species. However, their long‐term success is strongly influenced by the genetic diversity of the reintroduced population. The chances of population persistence can be improved by enhancing the population's adaptive ability through the mixing of individuals from different sources. However, where source populations are too diverse the reintroduced population could also suffer from outbreeding depression or unsuccessful admixture due to behavioural or genetic barriers. For the reintroduction of Asiatic wild ass Equus hemionus ssp. in Israel, a breeding core was created from individuals of two different subspecies (E. h. onager & E. h. kulan). Today the population comprises approximately 300 individuals and displays no signs of outbreeding depression. The aim of this study was a population genomic evaluation of this conservation reintroduction protocol. We used maximum likelihood methods and genetic clustering analyses to investigate subspecies admixture and test for spatial autocorrelation based on subspecies ancestry. Further, we analysed heterozygosity and effective population sizes in the breeding core prior to release and the current wild population. We discovered high levels of subspecies admixture in the breeding core and wild population, consistent with a significant heterozygote excess in the breeding core. Furthermore, we found no signs of spatial autocorrelation associated with subspecies ancestry in the wild population. Inbreeding and variance effective population size estimates were low. Our results indicate no genetic or behavioural barriers to admixture between the subspecies and suggest that their hybridization has led to greater genetic diversity in the reintroduced population. The study provides rare empirical evidence of the successful application of subspecies hybridization in a reintroduction. It supports use of intraspecific hybridization as a tool to increase genetic diversity in conservation translocations.

Can effective population size estimates be used to monitor population trends of woodland bats? A case study of Myotis bechsteinii.

Molecular approaches to calculate effective population size estimates (Ne) are increasingly used as an alternative to long‐term demographic monitoring of wildlife populations. However, the complex ecology of most long‐lived species and the consequent uncertainties in model assumptions means that effective population size estimates are often imprecise. Although methods exist to incorporate age structure into Ne estimations for long‐lived species with overlapping generations, they are rarely used owing to the lack of relevant information for most wild populations. Here, we performed a case study on an elusive woodland bat, Myotis bechsteinii, to compare the use of the parentage assignment Ne estimator (EPA) with the more commonly used linkage disequilibrium (LD) Ne estimator in detecting long‐term population trends, and assessed the impacts of deploying different overall sample sizes. We used genotypic data from a previously published study, and simulated 48 contrasting demographic scenarios over 150 years using the life history characteristics of this species The LD method strongly outperformed the EPA method. As expected, smaller sample sizes resulted in a reduced ability to detect population trends. Nevertheless, even the smallest sample size tested (n = 30) could detect important changes (60%–80% decline) with the LD method. These results demonstrate that genetic approaches can be an effective way to monitor long‐lived species, such as bats, provided that they are undertaken over multiple decades.

Spatial Genetic Structure and Demographic History of the Wild Boar in the Qinling Mountains, China.

Simple SummaryThe wild boar is native to the temperate region of Eurasia, which is now one of the most widely distributed mammals worldwide. The recent expansion in the wild boar population has attracted a lot of attention, which may cause great damage to ecosystems. Elucidating the patterns of the population structure, genetic diversity, population origin, and colonization route of wild boar is very helpful in the conservation and management of wild populations. Phylogeographic analysis has proven to be a powerful tool. Here, 82 samples of wild boars in 16 sampling locations were collected in Qinling Mountains (QM). Genetic analysis was conducted based on the mitochondrial control region and nuclear genes. The level of genetic diversity of wild boars in QM was lower than the total population in East Asia, but higher than European population. No obvious phylogeographic pattern were found. The effective population size was under demographic equilibrium in the past.Species dispersal patterns and population genetic structure can be influenced by geographical features. Qinling Mountains (QM) provide an excellent area for phylogeographic study. The phylogeography of Asian-wide wild boars revealed the colonization route. However, the impact of the QM on genetic diversity, genetic structure and population origin is still poorly understood. In this study, genetic analysis of wild boar in the QM was conducted based on the mitochondrial control region (943 bp) and twelve microsatellite loci of 82 individuals in 16 sampling locations. Overall genetic haplotype diversity was 0.86, and the nucleotide diversity was 0.0079. A total of 17 new haplotypes were detected. The level of genetic diversity of wild boars in QM was lower than in East Asia, but higher than in Europe. Phylogenetic analysis showed the weak genetic divergence in QM. Mismatch analysis, neutrality tests, and Bayesian Skyline Plot (BSP) results revealed that the estimates of effective population size were under demographic equilibrium in the past. Spatial analysis of molecular variance indicated no obvious phylogeographic structure.

Genomic evidence of past and future climate-linked loss in a migratory Arctic fish

Despite widespread biodiversity losses, an understanding of how most taxa will respond to future climate change is lacking. Here we integrate genomics and environmental modelling to assess climate change responses in an ecologically and economically important Arctic species. Environmentally associated genomic diversity and machine learning are used to identify highly vulnerable populations of anadromous (migratory) Arctic charr, and we reconstruct estimates of effective population size spanning the twentieth century to identify past climate-associated declines. We uncover past region-wide declines in effective population size that correspond to decreases in temperature and community biomass in the Northwest Atlantic. We find vulnerable populations near the southern range limit, indicating northward shifts and a possible loss of commercially important life-history variation in response to climate change. The genomic approach used here to investigate climate change response identifies past and future declines that impact species persistence, ecosystem stability and food security in the Arctic. Genomics and environmental modelling are integrated to assess past and future changes in Arctic charr populations in response to changing climate. Southern population vulnerability suggests climate change may lead to northward shifts and the loss of important life-history variation.

Conservation Genomics of the Threatened Western Spadefoot, Spea hammondii, in Urbanized Southern California.

Populations of the western spadefoot (Spea hammondii) in southern California occur in one of the most urbanized and fragmented landscapes on the planet and have lost up to 80% of their native habitat. Orange County is one of the last strongholds for this pond-breeding amphibian in the region, and ongoing restoration efforts targeting S. hammondii have involved habitat protection and the construction of artificial breeding ponds. These efforts have successfully increased breeding activity, but genetic characterization of the populations, including estimates of effective population size and admixture between the gene pools of constructed artificial and natural ponds, has never been undertaken. Using thousands of genome-wide single-nucleotide polymorphisms, we characterized the population structure, genetic diversity, and genetic connectivity of spadefoots in Orange County to guide ongoing and future management efforts. We identified at least 2, and possibly 3 major genetic clusters, with additional substructure within clusters indicating that individual ponds are often genetically distinct. Estimates of landscape resistance suggest that ponds on either side of the Los Angeles Basin were likely interconnected historically, but intense urban development has rendered them essentially isolated, and the resulting risk of interruption to natural metapopulation dynamics appears to be high. Resistance surfaces show that the existing artificial ponds were well-placed and connected to natural populations by low-resistance corridors. Toad samples from all ponds (natural and artificial) returned extremely low estimates of effective population size, possibly due to a bottleneck caused by a recent multi-year drought. Management efforts should focus on maintaining gene flow among natural and artificial ponds by both assisted migration and construction of new ponds to bolster the existing pond network in the region.

High genetic drift in endangered northern peripheral populations of the Behr's hairstreak butterfly (Satyrium behrii)

Abstract The persistence and adaptation of leading‐edge peripheral populations may be critical for allowing species to shift their range limits under climate change. However, peripheral populations are potentially vulnerable to genetic, demographic, and environmental stochasticity. Here, we characterise genetic variation across space and among years in northern peripheral populations of the Behr's hairstreak butterfly in British Columbia, Canada. This butterfly is dependent on antelope‐brush ecosystems that are threatened in this part of the world and is federally listed as Endangered in Canada. Using a large panel of amplified fragment length polymorphism (AFLP) genetic markers, we found low diversity in these populations. We also detected a high degree of year‐to‐year variation in allele frequencies, resulting in low effective population size estimates. Our findings suggest that Canadian populations of the Behr's hairstreak experience high genetic drift and may be vulnerable to genetic stochasticity. Unstable demography, low effective population size, and low genetic diversity in these populations could impede their adaptation to rapidly changing environmental conditions and contribute to a contraction of the species' range under climate change.

Contrasting Trends of Population Size Change for Two Eurasian Owlet Species—Athene brama and Glaucidium radiatum From South Asia Over the Late Quaternary

Climatic oscillations over the Quaternary have had a lasting impact on species’ distribution, evolutionary history, and genetic composition. Many species show dramatic population size changes coinciding with the last glacial period. However, the extent and direction of change vary across biogeographic regions, species-habitat associations, and species traits. Here we use genomic data to assess population size changes over the late Quaternary using the Pairwise Sequential Markovian Coalescent (PSMC) approach in two Eurasian Owlet species—the Spotted Owlet, Athene brama, and the Jungle Owlet, Glaucidium radiatum. While Spotted Owlets are typically associated with open habitats, Jungle Owlets are found in deciduous forests and scrublands. We find that the effective population size for the Spotted Owlet increased after the Interglacial period till the Last Glacial Maxima and subsequently declined toward the Mid-Holocene. On the other hand, effective population size estimates for the Jungle Owlet increased gradually throughout this period. These observations are in line with climatic niche model-based predictions for range size change for both species from a previous study and suggest that habitat associations at the local scale are important in determining responses to past climatic and vegetational changes. The Spotted Owlet result also aligns well with the expectation of open habitat expansion during the arid Glacial Maxima, whereas for the Jungle Owlet the contrasting expectation does not hold. Therefore, assessing the impacts of glacial history on population trajectories of multiple species with different habitat associations is necessary to understand the impacts of past climate on South Asian taxa.

The scales of coevolution: comparative phylogeography and genetic demography of a locally adapted venomous predator and its prey

AbstractCoevolutionary theory predicts that differences in the genetic demography of interacting species can influence patterns of local adaptation by affecting the potential of local populations to respond to selection. We conducted a comparative phylogeographical study of venomous rattlesnakes and their venom-resistant ground squirrel prey across California, and assessed how effective population size (Ne) estimates correspond with a previously documented pattern of rattlesnake local adaptation. Using RAD sequencing markers, we detected lineage relationships among both the rattlesnakes (Crotalus oreganus ssp.) and ground squirrels (Otospermophilus sp.) that are incongruent with previous phylogenetic hypotheses. Both rattlesnakes and squirrels share a deep divergence at the Sacramento–San Joaquin River Delta. At this broad phylogeographical scale, we found that the locally adapted rattlesnakes had higher Ne than squirrels. At the population scale, snakes also had larger Ne accompanied by larger values of several metrics of population genetic diversity. However, the specific magnitude of local adaptation of venom activity to ground squirrel venom resistance was not significantly correlated with local differences in Ne or other diversity statistics between predator and prey populations, suggesting that other factors in the geographic mosaic of coevolution contribute to the specific local-scale outcomes of this interaction. These results suggest an evolutionary mechanism that may explain some (but clearly not all) of rattlesnake local adaptation in this coevolutionary interaction – larger population sizes raise the adaptive potential of rattlesnakes compared to ground squirrels.

Fine-scale analysis of six beef cattle breeds revealed patterns of their genomic diversity

There has been a significant decrease in genetic diversity on a global scale for several livestock species, including beef cattle. Therefore, the aim of this study was to deliver fine-scale analysis of the genomic structure and to describe the diversity status of six beef cattle breeds, with a specific focus on genomic inbreeding and the trend of effective population size. The genome-wide data of 639 animals belonging to cosmopolitan (Aberdeen Angus, Charolais, Hereford and Limousin) and local (Piedmontese and Romagnola) cattle breeds were included due to their importance for the local and global beef industry in Europe. In addition, the local dual-purpose Slovak Pinzgau was used to extend the study due to increasing interest from beef cattle breeders in Slovakia. The results showed that more than 3% of the Aberdeen Angus, Hereford and Romagnola genomes, less than 1% of the Limousin, Charolais and Slovak Pinzgau genomes and 0.38% of the Piedmontese genome could have been significantly affected by the mating of relatives over the last three generations. The estimates of effective population size indicated a linear decline within each of the analysed populations. The decrease was mainly evident in populations of the Slovak Pinzgau (7.39 animals per generation), Limousin, Piedmontese and Charolais cattle (average 5 animals per generation). Due to the fact that the decrease in effective population size may be accompanied by a decrease in breed competitiveness with regard to a changing production environment, genetic diversity should be continuously monitored to preserve the long-term potential of the analysed breeds. Highlights Decreased diversity across beef breeds is evident Monitoring genetic diversity is needed to prevent inbreeding depression Use of genomic data can increase the accuracy of breeding schemes

Comparison of three techniques for genetic estimation of effective population size in a critically endangered parrot

AbstractUnderstanding the current population size of small, spatially aggregating populations of species is essential for their conservation. Reliable estimates of the effective population size (Ne) can be used to provide an early warning for conservation managers of the risks to genetic viability of small populations. Critically endangered, migratory swift parrots Lathamus discolor exist in a single panmictic population in Australia. In their Tasmanian breeding range, they are at severe risk of predation by introduced sugar gliders, exacerbated by deforestation. We used three genetic approaches to estimate Ne using DNA samples genotyped by microsatellite markers and existing life‐history data of swift parrots. Based on all samples, we revealed small contemporary Ne estimates across methods (range: 44–140), supporting the need to urgently address threatening processes. Using the 0.5 Ne/N ratio calculated from demographic data suggests that the minimum potential contemporary population size is below 300 individual swift parrots. This is considerably lower than the published estimates derived from expert elicitation, and accords with modeled estimates of extinction risk in this species. Our study has important implications for other threatened species with unknown population sizes and demonstrates that by utilizing available genetic data, reasonable estimates of Ne can be derived.

Genetic variability and connectivity of the Mexican long-nosed bat between two distant roosts

AbstractGenetic variability generally is associated with adaptive potential of species and can be assessed using microsatellite markers. Mexican long-nosed bats (Leptonycteris nivalis) are endangered, migratory nectarivores thought to be experiencing population declines. Despite historical and current tracking efforts, migratory connections among roost sites remain elusive. Our objective was to assess the genetic variability and connectivity of two of the most geographically separated populations of L. nivalis currently known—a mating roost in central Mexico used from September to March, and a maternity roost in western Texas used by adult females and their young from June to August. Twelve loci developed for L. yerbabuenae and four for Glossophaga soricina amplified L. nivalis DNA; of those 16 loci, seven (all from L. yerbabuenae) were useful in genetic analyses of 113 individuals. High levels of genetic variation in L. nivalis from the two sites were not significantly different and no substructure was detected between these two roost sites separated by more than 1,200 km. Further, we recovered evidence of close relationship (parent–offspring) in nine pairs of juveniles captured at the northern roost and adults from the southern roost, confirming a connection between the two locations. For this endangered species, the level of variation detected, the lack of a recent bottleneck, and estimates of effective population size, are encouraging for future recovery. Management plans aimed at conserving Mexican long-nosed bats should recognize the need for managing these bats as a single population and conserving foraging and roosting habitat along migratory routes to reduce population fragmentation.

Population Genetics of a Common Freshwater Mussel, Amblema plicata, in a Southern U.S. River

Myriad anthropogenic factors have led to substantial declines in North America's freshwater mussel populations over the last century. A greater understanding of mussel dispersal abilities, genetic structure, and effective population sizes is imperative to improve conservation strategies. This study used microsatellites to investigate genetic structure among mussel beds and estimate effective population sizes of a common North American mussel species, Amblema plicata, in the Little River, Oklahoma. We used five microsatellite loci to genotype 270 individuals from nine mussel beds distributed throughout the river and one of its tributaries, the Glover River. Our results indicate that subpopulations of A. plicata in the Little River are genetically similar. Upstream subpopulations had less genetic diversity than sites located downstream of the confluence of the Glover and Little rivers. Downstream subpopulations were primarily assigned to the same genetic group as upstream subpopulations, but they were admixed with a second genetic group. Low flows during droughts likely influenced the observed genetic structuring in A. plicata populations in the Little River. Additionally, downstream subpopulations may be admixed with a genetically distinct population of A. plicata, which may account for the increased genetic diversity. Estimates of effective population sizes (Ne) of large mussel beds were low compared to the total abundance (N) of A. plicata. While our data have limitations, they provide important information on the spatial scale at which conservation plans should focus and the population sizes that should be sustained through relocation and restocking programs.

A globally threatened shark, Carcharias taurus, shows no population decline in South Africa

Knowledge about the demographic histories of natural populations helps to evaluate their conservation status, and potential impacts of natural and anthropogenic pressures. In particular, estimates of effective population size obtained through molecular data can provide useful information to guide management decisions for vulnerable populations. The spotted ragged-tooth shark, Carcharias taurus (also known as the sandtiger or grey nurse shark), is widely distributed in warm-temperate and subtropical waters, but has suffered severe population declines across much of its range as a result of overexploitation. Here, we used multilocus genotype data to investigate the demographic history of the South African C. taurus population. Using approximate Bayesian computation and likelihood-based importance sampling, we found that the population underwent a historical range expansion that may have been linked to climatic changes during the late Pleistocene. There was no evidence for a recent anthropogenic decline. Together with census data suggesting a stable population, these results support the idea that fishing pressure and other threats have so far not been detrimental to the local C. taurus population. The results reported here indicate that South Africa could possibly harbour the last remaining, relatively pristine population of this widespread but vulnerable top predator.

Population genetic structure analysis of Shall sheep using pedigree information and effect of inbreeding on growth traits

The objective of this study was to use pedigree analysis to describe the population structure, genetic variability and inbreeding to quantify their effects on growth traits in Shall sheep. The analysis was based on the pedigree information of 64,964 animals. Data and pedigree information used in this study were collected from 1982 to 2012 by the Animal Breeding Centre of Iran. Growth traits included were birth weight (n = 12,786), 3-month weight (n = 9521), 6-month weight (n = 5106), average daily gain from birth to three- (n = 8543) and 6-month of age (n = 4,303) and their corresponding Kleiber ratios (n = 8543; n = 4,303, respectively). The CFC program was applied to calculate pedigree statistics and the population genetic structure of the Shall sheep. Also, the INBUPGF90 program was used for calculating inbreeding coefficients for individuals. The pedigree analysis indicated that the inbreeding coefficient ranged from 0 to 38% with an average of 1.62%. The average coancestry was 0.0072% and the generation interval was 3.755 years. Inbreeding depression was observed for all growth traits in this population of sheep. Based on the estimate of effective population size (910.25), it is expected to have enough genetic variability in the understudy population. On the other hand, the ratio of the effective number of founders to the effective number of ancestors (1.001) indicated no genetic bottleneck in Shall sheep. Breeders must do their best to prevent the mating between closely related animals and use this as an appropriate strategy to maintain the inbreeding under control in this sheep breed. HIGHLIGHTS The average coefficients of inbreeding and coancestry were low in Shall sheep. Enough genetic variability was available in Shall sheep and no genetic bottleneck occurred in this population. Inbreeding depression was observed for growth traits in this population of sheep.

Relationship of Effective Size to Hatchery Supplementation and Habitat Connectivity in a Simulated Population of Rio Grande Silvery Minnow

Simultaneous management actions often are used to improve the status of imperiled species, yet the effects of these actions can be difficult to determine. The endangered Rio Grande Silvery Minnow Hybognathus amarus is a short‐lived fish with a dispersive life history and thus requires—but does not occupy—unfragmented habitat for recruitment and survival. We used Rio Grande Silvery Minnow as a model system for an individual‐based simulation study to evaluate responses of genetic effective size to hatchery supplementation and fish passage in a managed population. Simulations were designed to test effects of fish passage on the relationship between estimates of inbreeding (NeI) and variance (NeV) effective sizes, which differ consistently (NeI >> NeV) in long‐term genetic‐monitoring data from hatchery‐supplemented Rio Grande Silvery Minnow populations. Values of different effective population size measures should be identical in a demographically stable and connected (admixed) population but can differ substantially under nonequilibrium conditions. When a barrier prevented upstream dispersal, NeI was associated negatively with rate of downstream dispersal and positively with supplementation rate, whereas NeV was associated negatively with both. This mirrored observations from Rio Grande Silvery Minnow. Individual effects of dispersal and supplementation, however, were difficult to discern due to significant interaction between these factors. When connectivity was restored, NeI and NeV depended on supplementation rate, with positive association between NeI and supplementation rate versus a negative association for NeV and interaction terms, and effects of dispersal were nonsignificant. Although fish passage did not alter the difference between NeI and NeV, our study suggests that for Rio Grande Silvery Minnow, and potentially other intensively managed species in regulated rivers, fish passage may help to distinguish effects of management actions, such as supplementation, from effects of other demographic influences. More generally, explicit analytical consideration of differences in effective population size estimates can provide important details of genetic responses to management.

Evolutionary history of a Scottish harbour seal population.

Efforts to conserve marine mammals are often constrained by uncertainty over their population history. Here, we examine the evolutionary history of a harbour seal (Phoca vitulina) population in the Moray Firth, northeast Scotland using genetic tools and microsatellite markers to explore population change. Previous fine-scale analysis of UK harbour seal populations revealed three clusters in the UK, with a northeastern cluster that included our Moray Firth study population. Our analysis revealed that the Moray Firth cluster is an independent genetic group, with similar levels of genetic diversity across each of the localities sampled. These samples were used to assess historic abundance and demographic events in the Moray Firth population. Estimates of current genetic diversity and effective population size were low, but the results indicated that this population has remained at broadly similar levels following the population bottleneck that occurred after post-glacial recolonization of the area.

Drift, selection and adaptive variation in small populations of a threatened rattlesnake.

An important goal of conservation genetics is to determine if the viability of small populations is reduced by a loss of adaptive variation due to genetic drift. Here, we assessed the impact of drift and selection on direct measures of adaptive variation (toxin loci encoding venom proteins) in the eastern massasauga rattlesnake (Sistrurus catenatus), a threatened reptile that exists in small isolated populations. We estimated levels of individual polymorphism in 46 toxin loci and 1,467 control loci across 12 populations of this species, and compared the results with patterns of selection on the same loci following speciation of S.catenatus and its closest relative, the western massasauga (S.tergeminus). Multiple lines of evidence suggest that both drift and selection have had observable impacts on standing adaptive variation. In support of drift effects, we found little evidence for selection on toxin variation within populations and a significant positive relationship between current levels of adaptive variation and long- and short-term estimates of effective population size. However, we also observed levels of directional selection on toxin loci among populations that are broadly similar to patterns predicted from interspecific selection analyses that pre-date the effects of recent drift, and that functional variation in these loci persists despite small short-term effective sizes. This suggests that much of the adaptive variation present in populations may represent an example of "drift debt," a nonequilibrium state where present-day levels of variation overestimate the amount of functional genetic diversity present in future populations.

Estimation of Linkage Disequilibrium and Effective Population Size in Three Italian Autochthonous Beef Breeds.

Simple SummaryLinkage disequilibrium (LD) of genomic markers is related to various evolutionary forces, such as inbreeding, nonrandom mating, population bottleneck, drift, recombination, and mutations, and hence is an essential parameter to examine population history. In this analysis, we examined the LD pattern of three Italian local beef breeds (Calvana, Mucca Pisana, and Pontremolese) facing the risk of extinction, using the commercial Limousin beef breed as a control. Our results provide important information on the population history and the current status of the breeds and they can be further used for conservation and breeding purposes.The objective was to investigate the pattern of linkage disequilibrium (LD) in three local beef breeds, namely, Calvana (n = 174), Mucca Pisana (n = 270), and Pontremolese (n = 44). As a control group, samples of the Italian Limousin breed (n = 100) were used. All cattle were genotyped with the GeneSeek GGP-LDv4 33k SNP chip containing 30,111 SNPs. The genotype quality control for each breed was conducted separately, and SNPs with call rate < 0.95 and minor allele frequency (MAF) > 1% were used for the analysis. LD extent was estimated in PLINK v1.9 using the squared correlation between pairs of loci (r2) across autosomes. Moreover, r2 values were used to calculate historical and contemporary effective population size (Ne) in each breed. Average r2 was similar in Calvana and Mucca Pisana (~0.14) and higher in Pontremolese (0.17); Limousin presented the lowest LD extent (0.07). LD up to 0.11–0.15 was persistent in the local breeds up to 0.75 Mbp, while in Limousin, it showed a more rapid decay. Variation of different LD levels across autosomes was observed in all the breeds. The results demonstrated a rapid decrease in Ne across generations for local breeds, and the contemporary population size observed in the local breeds, ranging from 41.7 in Calvana to 17 in Pontremolese, underlined the demographic alarming situation.