Current Effective Population Size Research Articles

Disentangling genetic diversity of Myotis septentrionalis: population structure, demographic history, and effective population size

Abstract Myotis septentrionalis (Northern Long-eared Bat) has recently suffered a >90% decline in population size in North America due to white-nose syndrome (WNS). We assessed genetic diversity, population structure, current effective population size, and demographic history of M. septentrionalis distributed across the United States to determine baseline levels pre-WNS. We analyzed RADseq data from 81 individuals from Kentucky, Louisiana, Michigan, Minnesota, North Carolina, Oklahoma, and Wisconsin. Additionally, we examined population genetic structure using discriminant analysis of principal components, fastStructure, and STRUCTURE. We then estimated effective population size and demographic history using fastsimcoal2. Similar levels of genetic diversity were found across all samples. We found no population genetic structure in the varied analyses from these contemporary samples. The best model for demographic history estimated a rapid population expansion followed by a slower expansion approximately 340,000 years ago. The vagility of M. septentrionalis, along with male dispersal and random mating, may provide a buffer against serious bottleneck effects stemming from rapid population declines due to WNS. This research provides a baseline for tracking and monitoring the influence of WNS on genetic diversity such as potential reduced diversity or increased population structuring in the future.

Living on the edge—Genomic and ecological delineation of cryptic lineages in the high‐elevation specialist Erebia nivalis

Abstract Cold‐adapted species at high elevations may be especially impacted by global warming since they may be limited in their capacity to adapt to changing conditions or may be prevented from shifting their distributions upwards if no suitable habitats are available. The latter may be true for Erebia nivalis, a high‐elevation specialist that mainly occurs in the Austrian Alps and on few mountaintops in Switzerland, where its taxonomic and conservation status remains unclear. We aimed to clarify the relationships among geographically isolated populations of E. nivalis using whole‐genome resequencing data to reconstruct population connectivity and phylogenetic relationships. We inferred current and historical effective population sizes and combined these with tests for ecological differentiation based on available occurrence data to re‐evaluate the conservation status of E. nivalis. Our results confirm that Swiss and Austrian E. nivalis should be considered different evolutionarily significant units for conservation purposes, as they are marked by moderate genomic differentiation, distinct demographic histories and a difference in the abiotic conditions of their habitats. In both Austria and Switzerland, we found rapid uphill range shifts over the last decades, little population connectivity, low current effective population sizes and low genetic diversity. The above, combined with the low dispersal capacity of this 2‐year lifecycle species and its need to overwinter under snow, which is rapidly retreating from several regions of the Alps, leads us to suggest that the status of E. nivalis should be updated to ‘Vulnerable’ or ‘Endangered’ in the European, Swiss and Austrian Red Lists.

Using recent genetic history to inform conservation options of two Lesser Caymans iguana (Cyclura nubila caymanensis) populations

The Sister Islands rock iguana (Cyclura nubila caymanensis) is critically endangered and endemic to the Caribbean islands Little Cayman and Cayman Brac. The Cayman Brac population and indeed the entire species is under threat from habitat destruction, invasive species, and anthropogenic impacts on the island. We assessed the genetic diversity, estimated effective population sizes, and tested for differentiation of populations between these two islands to inform potential future translocation should this be needed for the Cayman Brac population. Two mitochondrial DNA markers (cytochrome b and NADH subunit 4) and seven DNA microsatellite markers were used to assess the genetic diversity, genetic structure, demographic history, and effective population size of the two iguana populations. Mitochondrial DNA showed no genetic differentiation between populations; however, we found little to moderate divergence with microsatellites. We compared multiple demographic scenarios and revealed that ongoing gene flow is likely. The demographic history implied a significant genetic bottleneck around 10,000 years ago, coinciding with the sea level rise at the close of the last glacial period, and the start of the Holocene. Estimates of current effective population sizes indicate a small-scale number of breeders on each island of similar magnitude to the census mature population size (between 100 and 800 individuals). The relatively low differentiation between populations supports the possible development of active genetic management plans to manage the declining populations of the Sister Islands rock iguana.

Estimating current effective sizes of large populations from a single sample of genomic marker data: A comparison of estimators by simulations

AbstractGenome‐wide single nucleotide polymorphisms (SNPs) data are increasingly used in estimating the current effective population sizes (Ne) for informing the conservation of endangered species and guiding the management of exploited species. Previous assessments of sibship frequency (SF) and linkage disequilibrium (LD) estimators of Ne focused on small populations where genetic drift is strong and thus Ne is easy to estimate. Genomic single nucleotide polymorphism (SNP) data provide ample information and hold the potential for application of these estimators to large populations where genetic drift is rather weak and thus Ne is difficult to estimate. In this study, I simulated very large populations and sampled a widely variable number of individuals (genotyped at 10,000 SNPs) for estimating Ne by both SF and LD methods. I also considered the more realistic situation where a population experiences a bottleneck, and where marker data suffer from genotyping errors. The simulations show that both SF and LD methods can yield accurate Ne estimates of very large populations when sampled individuals are sufficiently numerous. When n is much smaller than Ne, however, Ne estimates are in a bimodal distribution with a substantial proportion of the estimates being infinitely large. For a population with a bottleneck, LD estimator overestimates and underestimates the Ne of the parental population from samples taken at and after the bottleneck, respectively. LD estimator also overestimates Ne substantially when applied to data suffering from allelic dropouts and false alleles. In contrast, SF estimator is unbiased and accurate when populations are changing in size or markers suffer from genotyping errors.

Long‐term population decline of a genetically homogeneous continental‐wide top Arctic predator

Genetic analysis can provide valuable information for conservation programmes by unravelling the demographic trajectory of populations, estimating effective population size or inferring genetic differentiation between populations. Here, we investigated the genetic differentiation within Snowy Owls Bubo scandiacus in North America, a species identified as vulnerable by the IUCN, to (1) quantify connectivity among wintering areas, (2) evaluate current genetic diversity and effective population size, and (3) infer changes in the historical effective population size changes from the last millennia to the recent past. The Snowy Owl, a highly mobile top predator, breeds across the Arctic tundra, a region especially sensitive to current climate change. Using single‐nucleotide polymorphism (SNP)‐based analyses on Snowy Owls sampled across the North American non‐breeding range, we found an absence of genetic differentiation among individuals located up to 4650 km apart. Our results suggest high genetic intermixing and effective dispersal at the continental scale despite documented philopatry to non‐breeding sites in winter. Reconstructing the population demographic indicated that North American Snowy Owls have been steadily declining since the Last Glacial Maximum c. 20 000 years ago, and concurrently with global increases in temperature. Conservation programmes should now consider North American Snowy Owls a single, genetically homogeneous continental‐wide population which is probably sensitive to the long‐term global warming occurring since the Last Glacial Maximum.

Current sika deer effective population size is near to reaching its historically highest level in the Japanese archipelago by release from hunting rather than climate change and top predator extinction

Deer species were repeatedly overexploited and protected for their meat and fur and they had strong impacts on ecosystems and human society by damaging crops and planted trees, altering vegetation, deer vehicle collision, and increasing ticks that vector zoonosis. To accomplish appropriate population management, the historical demography and its main driver need to be clarified. In this study, we estimated the historical demography of effective population size ( Ne) of sika deer ( Cervus nippon Temminck) in Hokkaido and Hyogo Prefectures of the Japanese archipelago. We estimated Ne of >100 generations from present (2020) by folded single nucleotide polymorphisms (SNP) frequency spectra and, within 100 generations from present, by linkage disequilibrium between SNP. In Hokkaido, Ne drastically increased around 3.0 ky BP and decreased around 100–150 years ago with the assumption of their generation length as 4 or 9 years. The Ne decreased by a 10th before the recent bottleneck. In Hyogo, Ne increased around 80 and 1 ky BP and decreased around 100–250 years ago. Ne decreased by a 100th before the recent bottleneck. After these recent bottlenecks, Ne of both regions recovered and the current Ne has nearly reaches the highest level of the last 100 ky BP. Literature survey and paleoclimate indicates that the decrease and increase of Ne of sika deer in Japanese archipelago may be caused by variations in the hunting activity of humans rather than climate change or the top predator extinction.

Conservation genomics reveals fine-scale population structuring and recent declines in the Critically Endangered Australian Kuranda Treefrog

The Kuranda Treefrog occurs in tropical north-east Australia and is listed as Critically Endangered due to its small distribution and population size, with observed declines due to drought and human-associated impacts to habitat. Field surveys identified marked population declines in the mid-2000s, culminating in very low abundance at most sites in 2005 and 2006, followed by limited recovery. Here, samples from before (2001–2004) and after (2007–2009) this decline were analysed using 7132 neutral genome-wide SNPs to assess genetic connectivity among breeding sites, genetic erosion, and effective population size. We found a high level of genetic connectivity among breeding sites, but also structuring between the population at the eastern end of the distribution (Jumrum Creek) versus all other sites. Despite finding no detectable sign of genetic erosion between the two times periods, we observed a marked decrease in effective population size (Ne), from 1720 individuals pre-decline to 818 post-decline. This mirrors the decline detected in the field census data, but the magnitude of the decline suggested by the genetic data is greater. We conclude that the current effective population size for the Kuranda Treefrog remains around 800 adults, split equally between Jumrum Creek and all other sites combined. The Jumrum Creek habitat requires formal protection. Connectivity among all other sites must be maintained and improved through continued replanting of rainforest, and it is imperative that impacts to stream flow and water quality are carefully managed to maintain or increase population sizes and prevent genetic erosion.

Joint estimation of selection intensity and mutation rate under balancing selection with applications to HLA.

A composite likelihood method is introduced for jointly estimating the intensity of selection and the rate of mutation, both scaled by the effective population size, when there is balancing selection at a single multi-allelic locus in an isolated population at demographic equilibrium. The performance of the method is tested using simulated data. Average estimated mutation rates and selection intensities are close to the true values but there is considerable variation about the averages. Allowing for both population growth and population subdivision does not result in qualitative differences but the estimated mutation rates and selection intensities do not in general reflect the current effective population size. The method is applied to 3 class I (HLA-A, HLA-B, and HLA-C) and 2 class II loci (HLA-DRB1 and HLA-DQA1) in the 1000 Genomes populations. Allowing for asymmetric balancing selection has only a slight effect on the results from the symmetric model. Mutations that restore symmetry of the selection model are preferentially retained because of the tendency of natural selection to maximize average fitness. However, slight differences in selective effects result in much longer persistence time of some alleles. Trans-species polymorphism, which is characteristic of major-histocompatibility loci in vertebrates, is more likely when there are small differences in allelic fitness than when complete symmetry is assumed. Therefore, variation in allelic fitness expands the range of parameter values consistent with observations of trans-species polymorphism.

The evaluation of genomic diversity and selection signals in the autochthonous Slovak Spotted cattle

The aim of this study was to evaluate the effective population size based on linkage disequilibrium and the trend of inbreeding derived from runs of homozygosity (ROH) in the Slovak Spotted cattle. The ROH segments longer than 4 Mb were then analysed to identify selection signals. Eighty-five individuals were genotyped using the ICBF International Dairy and Beef chip (dams of sires) and Illumina BovineSNP50 BeadChip (sires). The ROH segments > 1 Mb occurred most often in the autosomal genome with an average number of 16.75 ± 7.23. The ROH segments > 16 Mb covering 0.41% of the genome pointed to the long-term effort of breeders to reduce inbreeding in the population of Slovak Spotted cattle. However, the average observed heterozygosity indicated a decrease in overall diversity in the current population. The decrease of heterozygosity per generation also confirmed the estimates of historical and recent effective population size (a decrease of 6.88 animals per generation). The predicted current effective population size was 58 animals. Twenty-one regions across 12 different autosomes were fixed due to the high selection pressure. Within these genomic regions were identified various genes associated with reproduction (SLC9C1, PTPN12), milk production (IGF1, ABCG2), beef production (IFRD1, PTPN4), developmental processes (FMNL2, GLI2), immune system (CD96, CSK) and coat colour (KIT). These selection signals detected in the genome of Slovak Spotted cattle confirm the constant effort of breeders to preserve the dual-purpose nature of this breed.

Effective population size of broad-snouted caiman (Caiman latirostris) in Brazil: A historical and spatial perspective

Caiman latirostris has a large geographic distribution, that includes Argentina, Bolivia, Brazil, Paraguay, and Uruguay. In Brazil illegal hunting and land use change have caused population decline, relatively well documented in the last three decades. Due to such circumstances, the estimate of species effective population size might help analyze its viability. Single-sample estimator was used to estimate current effective population size (Ne) of broad-snouted caiman populations in representative areas of the species range in Brazil. For the analyzes, genotypes previously obtained were used for subpopulations of the captive colony of the University of São Paulo (USP) and for wild subpopulations. The microsatellites used were Amiμ8, Amiμ11, Amiμ13, Amiμ20, Claμ2, Claμ5, Claμ6, Claμ7, Claμ8, Claμ9 and Claμ10. The 11 loci analyzed produced 18.27 alleles on average. Wild populations showed significant genic and genotypic differentiation among them (p < 0.01). Population structure analyses (Rho-statistics) at Genepop for all loci was 0.376. The effective number of population sizes (Ɵ, the Ne estimator of Migrate-n software) of Caiman latirostris populations from the captive colony at the USP was 117.1 (N = 7) for NRF, 115.2 (N = 4) for Fm1, and 107.5 (N = 4) for Fm5, on the oposite side, the mean value of theta (Ɵ) was 7.7 (N = 51) for the Atlantic SE basin wild population, 9.4 (N = 42) for the Atlantic N/NE basin wild population and 9.6 (N = 91) for the Paraná basin wild population. The mean number of migrants (M of Migrate-n software) varied from 1.7 to 1.9 estimated by migrate-n are comparable to 1.3 estimated by Genepop. It is observed that in most wild population only few adults effectively contribute to genetic variation. The following guidlines are proposed as management actions: (1) an update of population sampling; (2) redefinition, delimitation and conservation of natural habitats; and (3) new conservation genetic studies with special attention to genetic diversity recovery.

A chromosome-level genome assembly for the tertiary relict plant Tetracentron sinense oliv. (trochodendraceae).

Tetracentron sinense and Trochodendron aralioides are two Tertiary relict species of large trees in the family Trochodendraceae with narrow distributions on the mainland and islands of eastern Asia. They belong to the order Trochodendrales, which is one of the four early-diverged eudicot lineages. These two relict species provide a good system in which to examine genomic changes that occurred as they survived during repeated climatic oscillations in the Quaternary. We sequenced the genome of Te. sinense and compared it with that of Tr. aralioides. We found that Te. sinense has a smaller genome size (986.3Mb) than that of Tr. aralioides (1610Mb). Repetitive elements made the major contribution to the contrasting genome sizes in the two species, with most bursts of repeats occurring within the past four million years when the climate oscillated greatly. These species share two rounds of whole-genome duplications. The mainland species Te. sinense had a larger effective population size than the island species Tr. aralioides after the largest glaciation during the Quaternary climatic oscillation. However, soon after this recovery stage, the effective population sizes of both species continued to decrease, although the current effective population size of Te. sinense is still larger than that of Tr. aralioides. We recovered three distinctly diverged clades through resequencing the genomes of 50 individuals across the distributional range of Te. sinense in China. Our results provide an important genomic resource with which to examine early trait evolution in the core eudicots and assist efforts to conserve this relict tree species.

Dammed river: Short‐ and long‐term consequences for fish species inhabiting a river in a Mediterranean climate in central Chile

AbstractThe presence of a dam disturbs river flow, which in turn directly affects the communities and evolutionary potential of riverine species. To detect the ecological effects of a dam on genetic diversity, genetic structure, and their progress in time, two riverine fishes living upstream and downstream of an irrigation reservoir were studied at two periods after its construction in 2004 in central Chile.Samples of the Neotropical silversideBasilichthys microlepidotusand the pencil catfishTrichomycterus areolatuswere obtained 2 and 7 years after the Corrales Dam was built. The microsatellite DNA variability of both species upstream and downstream of the dam was analysed.Fish analysed 2 years after dam construction did not show genetic differences between upstream and downstream populations; however, fish obtained 7 years after dam construction showed differences between populations above and below the dam and differences from individuals collected 5 years earlier.The current effective population sizes of both species were smaller in samples obtained upstream than in samples obtained downstream. Simulations showed a migration equal to zero as most probable after reservoir construction, suggesting that the dam is an impermeable barrier to the movement of individuals of these species. These results showed that population fragmentation in time could be related to the barrier imposed by the dam.In a scenario of no new contact between populations located upstream and downstream of the dam, the simulation predicts a reduction of genetic diversity ranging from 3.98 to 8.09% over the next 60 years.Analyses suggest that the Corrales Reservoir may be affecting the evolutionary potential of the populations upstream and downstream from the dam.

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.

The Limits to Estimating Population-Genetic Parameters with Temporal Data.

The ability to obtain genome-wide sequences of very large numbers of individuals from natural populations raises questions about optimal sampling designs and the limits to extracting information on key population-genetic parameters from temporal-survey data. Methods are introduced for evaluating whether observed temporal fluctuations in allele frequencies are consistent with the hypothesis of random genetic drift, and expressions for the expected sampling variances for the relevant statistics are given in terms of sample sizes and numbers. Estimation methods and aspects of statistical reliability are also presented for the mean and temporal variance of selection coefficients. For nucleotide sites that pass the test of neutrality, the current effective population size can be estimated by a method of moments, and expressions for its sampling variance provide insight into the degree to which such methodology can yield meaningful results under alternative sampling schemes. Finally, some caveats are raised regarding the use of the temporal covariance of allele-frequency change to infer selection. Taken together, these results provide a statistical view of the limits to population-genetic inference in even the simplest case of a closed population.

Reduced genetic diversity and low effective size in peripheral northern European catfish Silurus glanis populations.

Using 10 polymorphic microsatellites and 1251 individual samples (some dating back to the early 1980s), genetic structure and effective population size in all native and introduced Swedish populations of the European wels catfish or Silurus glanis were studied. Levels of genetic variability and phylogeographic relationships were compared with data from a previous study of populations in other parts of Europe. The genetically distinct Swedish populations displayed comparably low levels of genetic variability and according to one-sample estimates based on linkage disequilibrium and sib ship-reconstruction, current local effective population sizes were lower than minimum levels recommended for short-term genetic conservation. In line with a previous suggestion of postglacial colonisation from a single refugium, all Swedish populations were assembled on a common branch in a star-shaped dendrogram together with other European populations. Two distinct subpopulations were detected in upper and lower habitats of River Emån, indicating that even minor dispersal barriers may restrict gene flow for wels in running waters. Genetic assignment of specimens encountered in the brackish Baltic Sea and in lakes where the species does not occur naturally indicated presence of long-distance sea dispersal and confirmed unauthorised translocations, respectively.

Evaluation of Linkage Disequilibrium, Effective Population Size and Haplotype Block Structure in Chinese Cattle.

Simple SummaryEvaluation of the population structure and linkage disequilibrium can offer important insights to fully understand the genetic diversity and population history of cattle, which can enable us to appropriately design and implement GWAS and GS in cattle. In this study, we characterized the extent of genome-wide LD and the haplotype block structure, and estimated the persistence of phase of Chinese indigenous cattle with Illumina BovineHD BeadChip. According to our study, 58K, 87K, 95K, 52K, and 52K markers would be necessary for SCHC, NCC, SWC, SIM, and WAG, respectively, in the implementation of GWAS and GS and combining a multipopulation with high persistence of phase is feasible for the implication of genomic selection for Chinese beef cattle.Understanding the linkage disequilibrium (LD) across the genome, haplotype structure, and persistence of phase between breeds can enable us to appropriately design and implement the genome-wide association (GWAS) and genomic selection (GS) in beef cattle. We estimated the extent of genome-wide LD, haplotype block structure, and the persistence of phase in 10 Chinese cattle population using high density BovinHD BeadChip. The overall LD measured by r2 between adjacent SNPs were 0.60, 0.67, 0.58, 0.73, and 0.71 for South Chinese cattle (SCHC), North Chinese cattle (NCC), Southwest Chinese cattle (SWC), Simmental (SIM), and Wagyu (WAG). The highest correlation (0.53) for persistence of phase across groups was observed for SCHC vs. SWC at distances of 0–50 kb, while the lowest correlation was 0.13 for SIM vs. SCHC at the same distances. In addition, the estimated current effective population sizes were 27, 14, 31, 34, and 43 for SCHC, NCC, SWC, SIM, and WAG, respectively. Our result showed that 58K, 87K, 95K, 52K, and 52K markers were required for implementation of GWAS and GS in SCHC, NCC, SWC, SIM, and WAG, respectively. Also, our findings suggested that the implication of genomic selection for multipopulation with high persistence of phase is feasible for Chinese cattle.

Historical demography and genetic differentiation of the giant freshwater prawn Macrobrachium rosenbergii in Bangladesh based on mitochondrial and ddRAD sequence variation.

Macrobrachium rosenbergii, the giant freshwater prawn, is an important source of high quality protein and occurs naturally in rivers as well as commercial farms in South and South‐East Asia, including Bangladesh. This study investigated the genetic variation and population structure of M. rosenbergii sampled from four rivers in Bangladesh (sample size ranged from 19 to 20), assessing sequence variation, both in the mitochondrial cytochrome oxidase subunit 1 (CO1) gene and in 106 single nucleotide polymorphisms (SNPs) sampled randomly from the genome with double digest RAD sequencing (ddRADseq). The mitochondrial variation presented a shallow genealogy with high haplotype diversity (h = 0.95), reflecting an expansion in population size for the last ~82 kyr. Based on the CO1 variation the current effective population size (N e) was 9.7 × 106 (CI: 1.33 × 106 – 35.84 × 106) individuals. A significant population differentiation was observed with the mitochondrial CO1 sequence variation and based on the ddRADseq variation, which could be traced to the divergence of the population in the Naf River in the South‐East border with Myanmar from the other populations. A differentiation in mtDNA haplotype frequencies was also observed between the Biskhali River and the Karnaphuli Rivers in eastern Bangladesh. This study demonstrated the use of high‐throughput genotyping based on the ddRADseq method to reveal population structure at a small geographical scale for an important freshwater prawn. The information from this study can be utilized for management and conservation of this species in Bangladesh.

Genetic diversity, extent of linkage disequilibrium and persistence of gametic phase in Canadian pigs

BackgroundKnowledge on the levels of linkage disequilibrium (LD) across the genome, persistence of gametic phase between breed pairs, genetic diversity and population structure are important parameters for the successful implementation of genomic selection. Therefore, the objectives of this study were to investigate these parameters in order to assess the feasibility of a multi-herd and multi-breed training population for genomic selection in important purebred and crossbred pig populations in Canada. A total of 3,057 animals, representative of the national populations, were genotyped with the Illumina Porcine SNP60 BeadChip (62,163 markers).ResultsThe overall LD (r2) between adjacent SNPs was 0.49, 0.38, 0.40 and 0.31 for Duroc, Landrace, Yorkshire and Crossbred (Landrace x Yorkshire) populations, respectively. The highest correlation of phase (r) across breeds was observed between Crossbred animals and either Landrace or Yorkshire breeds, in which r was approximately 0.80 at 1 Mbp of distance. Landrace and Yorkshire breeds presented r ≥ 0.80 in distances up to 0.1 Mbp, while Duroc breed showed r ≥ 0.80 for distances up to 0.03 Mbp with all other populations. The persistence of phase across herds were strong for all breeds, with r ≥ 0.80 up to 1.81 Mbp for Yorkshire, 1.20 Mbp for Duroc, and 0.70 Mbp for Landrace. The first two principal components clearly discriminate all the breeds. Similar levels of genetic diversity were observed among all breed groups. The current effective population size was equal to 75 for Duroc and 92 for both Landrace and Yorkshire.ConclusionsAn overview of population structure, LD decay, demographic history and inbreeding of important pig breeds in Canada was presented. The rate of LD decay for the three Canadian pig breeds indicates that genomic selection can be successfully implemented within breeds with the current 60 K SNP panel. The use of a multi-breed training population involving Landrace and Yorkshire to estimate the genomic breeding values of crossbred animals (Landrace × Yorkshire) should be further evaluated. The lower correlation of phase at short distances between Duroc and the other breeds indicates that a denser panel may be required for the use of a multi-breed training population including Duroc.

Genome-wide population structure and evolutionary history of the Frizarta dairy sheep

In the present study, we used genomic data, generated with a medium density single nucleotide polymorphisms (SNP) array, to acquire more information on the population structure and evolutionary history of the synthetic Frizarta dairy sheep. First, two typical measures of linkage disequilibrium (LD) were estimated at various physical distances that were then used to make inferences on the effective population size at key past time points. Population structure was also assessed by both multidimensional scaling analysis and k-means clustering on the distance matrix obtained from the animals’ genomic relationships. The Wright’s fixation FST index was also employed to assess herds’ genetic homogeneity and to indirectly estimate past migration rates. The Wright’s fixation FIS index and genomic inbreeding coefficients based on the genomic relationship matrix as well as on runs of homozygosity were also estimated. The Frizarta breed displays relatively low LD levels with r2 and |Dʹ| equal to 0.18 and 0.50, respectively, at an average inter-marker distance of 31 kb. Linkage disequilibrium decayed rapidly by distance and persisted over just a few thousand base pairs. Rate of LD decay (β) varied widely among the 26 autosomes with larger values estimated for shorter chromosomes (e.g. β=0.057, for OAR6) and smaller values for longer ones (e.g. β=0.022, for OAR2). The inferred effective population size at the beginning of the breed’s formation was as high as 549, was then reduced to 463 in 1981 (end of the breed’s formation) and further declined to 187, one generation ago. Multidimensional scaling analysis and k-means clustering suggested a genetically homogenous population, FST estimates indicated relatively low genetic differentiation between herds, whereas a heat map of the animals’ genomic kinship relationships revealed a stratified population, at a herd level. Estimates of genomic inbreeding coefficients suggested that most recent parental relatedness may have been a major determinant of the current effective population size. A denser than the 50k SNP panel may be more beneficial when performing genome wide association studies in the breed.

Nationwide Genomic Study in Denmark Reveals Remarkable Population Homogeneity.

Denmark has played a substantial role in the history of Northern Europe. Through a nationwide scientific outreach initiative, we collected genetic and anthropometrical data from ∼800 high school students and used them to elucidate the genetic makeup of the Danish population, as well as to assess polygenic predictions of phenotypic traits in adolescents. We observed remarkable homogeneity across different geographic regions, although we could still detect weak signals of genetic structure reflecting the history of the country. Denmark presented genomic affinity with primarily neighboring countries with overall resemblance of decreasing weight from Britain, Sweden, Norway, Germany, and France. A Polish admixture signal was detected in Zealand and Funen, and our date estimates coincided with historical evidence of Wend settlements in the south of Denmark. We also observed considerably diverse demographic histories among Scandinavian countries, with Denmark having the smallest current effective population size compared to Norway and Sweden. Finally, we found that polygenic prediction of self-reported adolescent height in the population was remarkably accurate (R2 = 0.639 ± 0.015). The high homogeneity of the Danish population could render population structure a lesser concern for the upcoming large-scale gene-mapping studies in the country.