A Direct Assessment of the Role of Genetic Drift in Determining Allele Frequency Variation in Populations of EUPHYDRYAS EDITHA

Estimates of allele frequencies at six polymorphic loci were collected over eight generations in two populations of Euphydryas editha. We have estimated, in addition, the effective population size for each generation for both populations with results from mark-recapture and other field data. The variation in allele frequencies generated by random genetic drift was then studied using computer simulations and our direct estimates of effective population size. Substantial differences between observed values and computer-generated expected values assuming drift alone were found for three loci (Got, Hk, Pgi) in one population. These observations are consistent with natural selection in a variable environment.     

Genetic evidence for long-term population decline in a savannah-dwelling primate: inferences from a hierarchical bayesian model

The purpose of this study was to test for evidence that savannah baboons (Papio cynocephalus) underwent a population expansion in concert with a hypothesized expansion of African human and chimpanzee populations during the late Pleistocene. The rationale is that any type of environmental event sufficient to cause simultaneous population expansions in African humans and chimpanzees would also be expected to affect other codistributed mammals. To test for genetic evidence of population expansion or contraction, we performed a coalescent analysis of multilocus microsatellite data using a hierarchical Bayesian model. Markov chain Monte Carlo (MCMC) simulations were used to estimate the posterior probability density of demographic and genealogical parameters. The model was designed to allow interlocus variation in mutational and demographic parameters, which made it possible to detect aberrant patterns of variation at individual loci that could result from heterogeneity in mutational dynamics or from the effects of selection at linked sites. Results of the MCMC simulations were consistent with zero variance in demographic parameters among loci, but there was evidence for a 10- to 20-fold difference in mutation rate between the most slowly and most rapidly evolving loci. Results of the model provided strong evidence that savannah baboons have undergone a long-term historical decline in population size. The mode of the highest posterior density for the joint distribution of current and ancestral population size indicated a roughly eightfold contraction over the past 1,000 to 250,000 years. These results indicate that savannah baboons apparently did not share a common demographic history with other codistributed primate species.     

Origin and number of founders in an introduced insular primate: estimation from nuclear genetic data

Cynomolgus macaques (Macaca fascicularis) were introduced on the island of Mauritius between 400 and 500 years ago and underwent a strong population expansion after a probable initial founding event. However, in practice, little is known of the geographical origin of the individuals that colonized the island, on how many individuals were introduced, and of whether the following demographic expansion erased any signal of this putative bottleneck. In this study, we asked whether the current nuclear genome of the Mauritius population retained a signature that would allow us to answer these questions. Altogether, 21 polymorphic autosomal and sex-linked microsatellites were surveyed from 81 unrelated Mauritius individuals and 173 individuals from putative geographical sources in Southeast Asia: Java, the Philippines islands and the Indochinese peninsula. We found that (i) the Mauritius population was closer to different populations depending on the markers we used, which suggests a possible mixed origin with Java playing most probably a major role; and (ii) the level of diversity was lower than the other populations but there was no clear and consistent bottleneck signal using either summary statistics or full-likelihood methods. However, summary statistics strongly suggest that Mauritius is not at mutation-drift equilibrium and favours an expansion rather than a bottleneck. This suggests that on a short time scale, population decline followed by growth can be difficult to deduce from genetic data based on mutation-drift theory. We then used a simple Bayesian rejection algorithm to estimate the number of founders under different demographic models (exponential, logistic and logistic with lag) and pure genetic drift. This new method uses current population size estimates and expected heterozygosity of Mauritius and source population(s). Our results indicate that a simple exponential growth is unlikely and that, under the logistic models, the population may have expanded from an initial effective number of individuals of 10-15. The data are also consistent with a logistic growth with different lag values, indicating that we cannot exclude past population fluctuation.     

Heterosis and inbreeding depression in bottlenecked populations: a test in the hermaphroditic freshwater snail Lymnaea stagnalis

Small population size is expected to induce heterosis, due to the random fixation and accumulation of mildly deleterious mutations, whereas within‐population inbreeding depression should decrease due to increased homozygosity. Population bottlenecks, although less effective, may have similar consequences. We tested this hypothesis in the self‐fertile freshwater snail Lymnaea stagnalis, by subjecting experimental populations to a single bottleneck of varied magnitude. Although patterns were not strong, heterosis was significant in the most severely bottlenecked populations, under stressful conditions. This was mainly due to hatching rate, suggesting that early acting and highly deleterious alleles were involved. Although L. stagnalis is a preferential outcrosser, inbreeding depression was very low and showed no clear relationship with bottleneck size. In the less reduced populations, inbreeding depression for hatching success increased under high inbreeding. This may be consistent with the occurence of synergistic epistasis between fitness loci, which may contribute to favour outcrossing in L. stagnalis.     

Temporal dynamics of linkage disequilibrium in two populations of bighorn sheep

Linkage disequilibrium (LD) is the nonrandom association of alleles at two markers. Patterns of LD have biological implications as well as practical ones when designing association studies or conservation programs aimed at identifying the genetic basis of fitness differences within and among populations. However, the temporal dynamics of LD in wild populations has received little empirical attention. In this study, we examined the overall extent of LD, the effect of sample size on the accuracy and precision of LD estimates, and the temporal dynamics of LD in two populations of bighorn sheep (Ovis canadensis) with different demographic histories. Using over 200 microsatellite loci, we assessed two metrics of multi‐allelic LD, D′, and χ^′2. We found that both populations exhibited high levels of LD, although the extent was much shorter in a native population than one that was founded via translocation, experienced a prolonged bottleneck post founding, followed by recent admixture. In addition, we observed significant variation in LD in relation to the sample size used, with small sample sizes leading to depressed estimates of the extent of LD but inflated estimates of background levels of LD. In contrast, there was not much variation in LD among yearly cross‐sections within either population once sample size was accounted for. Lack of pronounced interannual variability suggests that researchers may not have to worry about interannual variation when estimating LD in a population and can instead focus on obtaining the largest sample size possible.     

Selection versus demography: a multilocus investigation of the domestication process in maize

The domestication of maize (Zea mays ssp. mays) from its wild ancestor (Zea mays ssp. parviglumis) led to a loss of genetic diversity both through a population bottleneck and through directional selection at agronomically important genes. In order to discriminate between those effects and to investigate the nature of the domestication bottleneck, we analyzed nucleotide diversity data from 12 chromosome 1 loci in parviglumis. We found an average loss of nucleotide diversity of 38% across genes, but this average was skewed downward by four putatively selected loci (tb1, d8, ts2, and zagl1). To better understand the domestication process, we used the coalescent with recombination to simulate bottlenecks under various lengths and population sizes. For each locus, we determine the likelihood of the observed data using three summary statistics: the number of segregating sites, an estimate of the population recombination parameter, and Tajima's D. Based on the eight neutrally evolving loci, a model with a bottleneck had a significantly higher likelihood than a model without one. The four putatively selected loci had significantly different likelihood optimums than the neutral loci, and this approach confirmed that ts2 and d8 were selected either during domestication or breeding. Overall, the best-fitting models had a bottleneck in which the population size and the bottleneck duration had a ratio of approximately 4- to approximately 5; for example, if the initial domestication event occurred over a 500-year period, the population size was roughly 2,000 to 2,500 individuals. However, this range did vary with the summary statistic used to assess the fit of simulations to data. In this context, Tajima's D performed poorly as a goodness-of-fit statistic, probably because Z. mays ssp. parviglumis has a frequency spectrum that is significantly skewed toward low-frequency variants. Finally, we found that demography is unlikely to account for the previously observed positive correlation between nucleotide diversity and the population-recombination parameter in maize, leaving this observation difficult to interpret.     

Testing models of selection and demography in Drosophila simulans

We analyze patterns of nucleotide variability at 15 X-linked loci and 14 autosomal loci from a North American population of Drosophila simulans. We show that there is significantly more linkage disequilibrium on the X chromosome than on chromosome arm 3R and much more linkage disequilibrium on both chromosomes than expected from estimates of recombination rates, mutation rates, and levels of diversity. To explore what types of evolutionary models might explain this observation, we examine a model of recurrent, nonoverlapping selective sweeps and a model of a recent drastic bottleneck (e.g., founder event) in the demographic history of North American populations of D. simulans. The simple sweep model is not consistent with the observed patterns of linkage disequilibrium nor with the observed frequencies of segregating mutations. Under a restricted range of parameter values, a simple bottleneck model is consistent with multiple facets of the data. While our results do not exclude some influence of selection on X vs. autosome variability levels, they suggest that demography alone may account for patterns of linkage disequilibrium and the frequency spectrum of segregating mutations in this population of D. simulans.     

Reduced Mtdna Diversity in the Ngobe Amerinds of Panama

Mitochondrial DNA (mtDNA) haplotype diversity was determined for 46 Ngobe Amerinds sampled widely across their geographic range in western Panama. The Ngobe data were compared with mtDNA control region I sequences from two additional Amerind groups located at the northern and southern extremes of Amerind distribution, the Nuu-Chah-Nulth of the Pacific Northwest and the Chilean Mapuche and from one Na-Dene group, the Haida of the Pacific Northwest. The Ngobe exhibit the lowest mtDNA control region sequence diversity yet reported for an Amerind group. Moreover, they carry only two of the four Amerind founding lineages first described by Wallace and coworkers. We posit that the Ngobe passed through a population bottleneck caused by ethnogenesis from a small founding population and/or European conquest and colonization. Dating of the Ngobe population expansion using the HARPENDING et al. approach to the analysis of pairwise genetic differences indicates a Ngobe expansion at roughly 6800 years before present (range: 1850-14,000 years before present), a date more consistent with a bottleneck at Chibcha ethnogenesis than a conquest-based event.     

独龙牛遗传多样性及其种群遗传结构的等位酶分析

采用水平片淀粉凝胶电泳技术,进行３０头独牛牛４１种蛋白质共计４４个遗传座位的等位酶分析,只在Ｔｒ,Ｈｐ,Ａｍｙ,Ｅｓｔ等４个座位发现多态性。每个座位等基因的平均数、多态座位百分比和平均杂合度值分别为Ａ＝１．０９０９、Ｐ＝０．０６８２和Ｈ＝０．０２６２。贡山县和福贡县独龙牛群体从酶基因的角度上看遗传多样性贫乏,可能是分别由小种群引种而来,受到瓶颈效应的作用,并伴随着创立者事件的发生。我们结合独龙牛在     

Bottlenecks and rescue effects in a fluctuating population of golden-mantled ground squirrels (Spermophilus lateralis)

Mammal species characterized by highly fluctuating populations often maintain genetic diversity in response to frequent demographic bottlenecks, suggesting the ameliorating influence of life history and behavioral factors. Immigration in particular is expected to promote genetic recovery and is hypothesized to be the most likely process maintaining genetic diversity in fluctuating mammal populations. Most demographic bottlenecks have been inferred retrospectively, and direct analysis of a natural population before, during, and after a bottleneck is rare. Using a continuous 10-year dataset detailing the complete demographic and genetic history of a fluctuating population of golden-mantled ground squirrels (Spermophilus lateralis), we analyzed the genetic consequences of a 4-year demographic bottleneck that reduced the population to seven adult squirrels, and we evaluated the potential “rescue effect” of immigration. Analysis of six microsatellite loci revealed that, while a decline in allelic richness was observed during the bottleneck, there was no observed excess of heterozygosity, a characteristic bottleneck signature, and no evidence for heterozygote deficiency during the recovery phase. In addition, we found no evidence for inbreeding depression during or after the bottleneck. By identifying immigrants and analyzing their demographic and genetic contributions, we found that immigration promoted demographic recovery and countered the genetic effects of the bottleneck, especially the loss of allelic richness. Within 3 years both population size and genetic variation had recovered to pre-bottleneck levels, supporting the role of immigration in maintaining genetic variation during bottleneck events in fluctuating populations. Our analyses revealed considerable variation among analytical techniques in their ability to detect genetic bottlenecks, suggesting that caution is warranted when evaluating bottleneck events based on one technique.     

Impact of insecticide-treated bed nets implementation on the genetic structure of Anopheles arabiensis in an area of irrigated rice fields in the Sahelian region of Cameroon

Variation at 12 microsatellite loci was investigated to assess the impact of the implementation of insecticide-treated bed nets (ITNs) on the genetic structure of Anopheles arabiensis in Simatou, a village surrounded by irrigated rice fields in the Sahelian area of Cameroon. The An. arabiensis population of Simatou was sampled twice before ITN implementation, and twice after. Effective population size estimates (N(e)) were similar across each time point, except for the period closely following ITN introduction where a nonsignificant reduction was recorded. Hence, we believe that ITN implementation resulted in a temporary bottleneck, rapidly followed by a demographic expansion. The genetic diversity of the population was not significantly affected since different genetic parameters (allele number, observed and expected heterozygosities) remained stable. Low estimates of genetic differentiation between the populations from Simatou and Lagdo, separated by 300 km, suggested extensive gene flow among populations of An. arabiensis in the Sahelian region of Cameroon. A decrease in the susceptibility to deltamethrin was observed following ITN introduction, but no kdr mutation was detected and a metabolic resistance mechanism is probably involved. The temporary effect of ITNs on the genetic structure of An. arabiensis population suggests that, to optimize the success of any control programme of this species based on ITNs, the control area should be very large and the programme should be implemented for a long period of time.     

Human population expansion and microsatellite variation

Polymorphisms at di-, tri-, and tetranucleotide microsatellite loci have been analyzed in 14 worldwide populations. A statistical index of population expansion, denoted S(k), is introduced to detect historical changes in population size using the variation at the microsatellites. The index takes the value 0 at equilibrium with constant population size and is positive or negative according to whether the population is expanding or contracting, respectively. The use of S(k) requires estimation of properties of the mutation distribution for which we use both family data of Dib et al. for dinucleotide loci and our population data on tri- and tetranucleotide loci. Statistical estimates of the expansion index, as well as their confidence intervals from bootstrap resampling, are provided. In addition, a dynamical analysis of S(k) is presented under various assumptions on population growth or decline. The studied populations are classified as having high, intermediate, or low values of S(k) and genetic variation, and we use these to interpret the data in terms of possible population dynamics. Observed values of S(k) for samples of di-, tri-, and tetranucleotide data are compatible with population expansion earlier than 60,000 years ago in Africa, Asia, and Europe if the initial population size before the expansion was on the order of 500. Larger initial population sizes force the lower bound for the time since expansion to be much earlier. We find it unlikely that bottlenecks occurred in Central African, East Asian, or European populations, and the estimated expansion times are rather similar for all of these populations. This analysis presented here suggests that modern human populations departed from Africa long before they began to expand in size. Subsequently, the major groups (the African, East Asian, and European groups) started to grow at approximately same time. Populations of South America and Oceania show almost no growth. The Mbuti population from Zaire appears to have experienced a bottleneck during its expansion.     

Genetic characterization and management of the endangered Mohave tui chub

The Mohave tui chub (Siphateles bicolor mohavensis) is the only fish native to the Mojave River, California. The fish were displaced by introduced arroyo chubs (Gila orcutti) throughout most of their range, starting in the 1930s. Two potentially relictual populations and two transplanted populations were genetically characterized using 12 microsatellite DNA loci, along with contemporary cyprinid populations in the Mojave River. We found only un-hybridized Mohave tui chubs in the refuge populations, and only un-hybridized arroyo chubs in the Mojave River. The two largest Mohave tui chub populations (Lake Tuendae and China Lake) exhibit similar, comparatively high genetic variation. Another large population (Camp Cady) with low genetic diversity shows the effect of a bottleneck of ten individuals during the historic founding event. The fourth population (MC Spring) has the fewest alleles, lowest heterozygosity, and is the most divergent, suggesting that genetic drift from a persistently low effective population size has reduced genetic diversity since its apparent isolation in 1934. We recommend instituting artificial gene flow to rebuild genetic variation in Camp Cady from both Lake Tuendae and China Lake, and the establishment of new populations with founders from both Lake Tuendae and China Lake. Additionally, we comment on the infeasibility of restoring populations of Mohave tui chub in their historic habitats.     

No apparent genetic bottleneck in the demographically declining European eel using molecular genetics and forward-time simulations

The stock of the European eel is considered to be outside safe biological limits, following a dramatic demographic decline in recent decades (90–99% drop) that involves a large number of factors including overfishing, contaminants and environmental fluctuations. The aim of the present study is to estimate the effective population size of the European eel and the possible existence of a genetic bottleneck, which is expected during or after a severe demographic crash. Using a panel of 22 EST-derived microsatellite loci, we found no evidence for a genetic bottleneck in the European eel as our data showed moderate to high levels of genetic diversity, no loss of allele size range or rare alleles, and a stationary population with growth values not statistically different from zero, which is confirmed by finding comparable value of short-term and long-term effective population size. Our results suggest that the observed demographic decline in the European eel did not entail a genetic decline of the same magnitude. Forward-time simulations confirmed that large exploited marine fish populations can undergo genetic bottleneck episodes and experience a loss of genetic variability. Simulations indicated that the failure to pick up the signal of a genetic bottleneck in the European eel is not due to lack of power. Although anthropogenic factors lowered the continental stock biomass, the observation of a stable genetic effective population size suggests that the eel crash was not due to a reduction in spawning stock abundance. Alternatively, we propose that overfishing, pollution and/or parasites might have affected individual fitness and fecundity, leading to an impoverished spawning stock that may fail to produce enough good quality eggs. A reduced reproduction success due to poor quality of the spawners may be exacerbated by oceanic processes inducing changes in primary production in the Sargasso Sea and/or pathway of transport across the Atlantic Ocean leading to a higher larval mortality.     

Genetic diversity and effective size of the Atlantic salmon Salmo salar L. inhabiting the River Eo (Spain) following a stock collapse

Historic angling records suggest the occurrence of a drastic decline in the River Eo (Spain) Atlantic salmon population size during the past two decades, as a result of overexploitation and habitat deterioration. In recent years, the population has been apparently recovering, and the present study is aimed to report information on the level of genetic diversity and the effective size of the current population as these may have immediate consequences for its conservation. Eighty-six salmon from two temporal groups (1998–1999 and 2004–2006), representing three generations, were genotyped using a panel of eight microsatellites. Inspite of the recent decline in census numbers and the detection of the signs of a population bottleneck, the population exhibits a high level of genetic diversity, similar to that from other populations, and almost unchanged during the period of study [average allelic richness ( A ) = 14·0 and 13·9, and average heterozygosity ( H _e) = 0·843 and 0·851 in 1998–1999 and 2004–2006, respectively]. The effective population size ( N _e) estimated by two different temporal methods showed a consistent value around 80 salmon, whereas the estimates from the linkage disequilibrium (LD) method provided a value around 165 individuals for either sample. The recent growing number of salmon, as indicated by fisheries records, the relatively large estimates of the ratio N _e/ N (with range 0·23–0·44 for the temporal estimates and 0·31–0·59 for the LD estimates) and the high levels of diversity found suggest that the population has not been greatly affected by the historical census declines and can be expected to recover in the future.     

Admixture and patterns of linkage disequilibrium in a free-living vertebrate population

Linkage disequilibrium (LD), a measure of nonrandom association of alleles at different loci, is of great interest to evolutionary geneticists as it can be used to help identify loci that explain phenotypic variation. Surveys of the extent of LD across genomes have been carried out in a number of systems, most notably humans and model organisms. However, studies of natural populations of vertebrates have rarely been performed. Here, we describe an investigation of LD in a free-living island population of red deer Cervus elaphus. Relatively high levels of LD extended several tens of centimorgans, and significant LD was frequently detected between unlinked markers. The magnitude of LD varied depending on how the population was sampled. It also varied across different chromosomes, and was shown to be a function of sample size, intermarker distance and marker heterozygosity. A recent admixture event in the population led to an ephemeral increase in LD. Association mapping may be possible in this population, although a high 'baseline' level of LD could lead to false positive associations between marker loci and a trait of interest.     

Statistical properties of the variation at linked microsatellite loci: implications for the history of human Y chromosomes [published erratum appears in Mol Biol Evol 1997 Mar;14(3):354]

It has recently been suggested that observed levels of variation at microsatellite loci can be used to infer patterns of selection in genomes and to assess demographic history. In order to evaluate the feasibility of these suggestions it is necessary to know something about how levels of variation at microsatellite loci are expected to fluctuate due simply to stochasticity in the processes of mutation and inheritance (genetic sampling). Here we use recently derived properties of the stepwise mutation model to place confidence intervals around the variance in repeat score that is expected at mutation-drift equilibrium and outline a statistical test for whether an observed value differs significantly from expectation. We also develop confidence intervals for the time course of the buildup of variation following a complete elimination of variation, such as might be caused by a selective sweep or an extreme population bottleneck. We apply these methods to the variation observed at human Y-specific microsatellites. Although a number of authors have suggested the possibility of a very recent sweep, our analyses suggest that a sweep or extreme bottleneck is unlikely to have occurred anytime during the last approximately 74,000 years. To generate this result we use a recently estimated mutation rate for microsatellite loci of 5.6 x 10(-4) along with the variation observed at autosomal microsatellite loci to estimate the human effective population size. This estimate is 18,000, implying an effective number of 4,500 Y chromosomes. One important general conclusion to emerge from this study is that in order to reject mutation-drift equilibrium at a set of linked microsatellite loci it is necessary to have an unreasonably large number of loci unless the observed variance is far below that expected at mutation-drift equilibrium.      

Evaluating outlier loci and their effect on the identification of pedigree errors

Homozygosity outlier loci, which show patterns of variation that are extremely divergent from the rest of the genome, can be evaluated by comparison of the homozygosity under Hardy-Weinberg proportions (the sum of the squares of allele frequencies) with the expected homozygosity under neutrality. Such outlier loci are potentially under selection (balancing selection or directional selection) when genome-wide effects (such as bottleneck and rapid population growth) are excluded. Outlier loci show skewed allele frequencies with respect to neutrality and may therefore affect the identification of pedigree errors. However, choosing neutral markers (excluding outlier loci) for the identification of pedigree errors has been neglected thus far. Our results showed that 4.1%, 5.5%, and 1.5% of the microsatellite markers, Illumina single-nucleotide polymorphisms (SNPs), and Affymetrix SNPs, respectively, on the autosomes appear to be under balancing selection (p or=40%) appear to be under balancing selection. Pedigree structure errors in 15 of 143 pedigrees were detected using microsatellite markers from the autosomes and/or selected SNPs from chromosomes 1 to 18 of the Illumina and/or selected SNPs from chromosomes 1 to 16 of the Affymetrix. Outlier loci did not make a major difference to the identification of pedigree errors. The Collaborative Study on the Genetics of Alcoholism data has pedigree errors and some of them may be due to sample mix up.     

Linkage disequilibrium,SNP frequency change due to selection,and association mapping in popcorn chromosome regions containing QTLs for quality traits

The objectives of this study were to assess linkage disequilibrium (LD) and selection-induced changes in single nucleotide polymorphism (SNP) frequency, and to perform association mapping in popcorn chromosome regions containing quantitative trait loci (QTLs) for quality traits. Seven tropical and two temperate popcorn populations were genotyped for 96 SNPs chosen in chromosome regions containing QTLs for quality traits. The populations were phenotyped for expansion volume, 100-kernel weight, kernel sphericity, and kernel density. The LD statistics were the difference between the observed and expected haplotype frequencies (D), the proportion of D relative to the expected maximum value in the population, and the square of the correlation between the values of alleles at two loci. Association mapping was based on least squares and Bayesian approaches. In the tropical populations, D-values greater than 0.10 were observed for SNPs separated by 100-150 Mb, while most of the D-values in the temperate populations were less than 0.05. Selection for expansion volume indirectly led to increase in LD values, population differentiation, and significant changes in SNP frequency. Some associations were observed for expansion volume and the other quality traits. The candidate genes are involved with starch, storage protein, lipid, and cell wall polysaccharides synthesis.     

Estimations of linkage disequilibrium,effective population size and ROH‐based inbreeding coefficients in Spanish Churra sheep using imputed high‐density SNP genotypes

In this study, the availability of the Ovine HD SNP BeadChip (HD‐chip) and the development of an imputation strategy provided an opportunity to further investigate the extent of linkage disequilibrium (LD) at short distances in the genome of the Spanish Churra dairy sheep breed. A population of 1686 animals, including 16 rams and their half‐sib daughters, previously genotyped for the 50K‐chip, was imputed to the HD‐chip density based on a reference population of 335 individuals. After assessing the imputation accuracy for beagle v4.0 (0.922) and fimpute v2.2 (0.921) using a cross‐validation approach, the imputed HD‐chip genotypes obtained with beagle were used to update the estimates of LD and effective population size for the studied population. The imputed genotypes were also used to assess the degree of homozygosity by calculating runs of homozygosity and to obtain genomic‐based inbreeding coefficients. The updated LD estimations provided evidence that the extent of LD in Churra sheep is even shorter than that reported based on the 50K‐chip and is one of the shortest extents compared with other sheep breeds. Through different comparisons we have also assessed the impact of imputation on LD and effective population size estimates. The inbreeding coefficient, considering the total length of the run of homozygosity, showed an average estimate (0.0404) lower than the critical level. Overall, the improved accuracy of the updated LD estimates suggests that the HD‐chip, combined with an imputation strategy, offers a powerful tool that will increase the opportunities to identify genuine marker‐phenotype associations and to successfully implement genomic selection in Churra sheep.