Angus cattle, originally from Scotland, have been selectively bred for over 400 years, making them one of the most prominent beef breeds globally. Known for their adaptability, natural polled traits, and high-quality beef, Angus cattle have been intensively selected for growth, body size, and feed efficiency. This study investigates the genetic diversity, selection history, and key genomic regions across five Angus populations from the USA, Canada, Australia, Brazil, and Red Angus of America. Genomic data from 71,283 animals born between 1961 and 2024 were analyzed using Principal Component Analysis (PCA), phylogenetic tree construction, and Runs of Homozygosity (ROH), with the Generation Proxy Selection Mapping (GPSM) approach used to assess selection history. Functional annotation identified candidate genes and pathways related to selection. Our analysis revealed both similarities and differences across populations. The PCA and FST metrics showed minimal differentiation between the American, Canadian, Australian, and Brazilian populations, with greater differentiation observed in the Red Angus population. The ROH analysis revealed that the Brazilian population had the highest number of ROHs. The ROH islands identified on BTA8 and BTA13 in the American and Australian populations were linked to traits like body weight, marbling, and tenderness. The GPSM identified significant markers associated with body weight and growth in all populations, reflecting ongoing selection pressures. This study highlights the potential of genomics to improve our understanding of Angus cattle’s genetic architecture and selection history. It underscores the feasibility of integrating global populations for more accurate genomic evaluations, enhancing genetic predictions, and supporting sustainable beef production worldwide.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00335-025-10188-y.

Runs of homozygosity (ROH) are contiguous genomic regions where all sites are homozygous, inherited from identical haplotypes due to shared ancestry. The number and length of ROH in individuals varies based on population history and sociocultural behaviors. Although often discussed in the context of inbreeding, ROH are ubiquitous in putatively outbred human populations, and their prevalence are associated with multiple complex traits, including height and measures of lung function. Importantly, ROH have been shown to be enriched for deleterious alleles, suggesting a mechanism by which ROH prevalence can influence traits. Here we employ realistic forward-in-time population genetic simulations and a flexible quantitative model of a generic complex phenotype to explore how population history and genetic architecture influence ROH associations with a generic quantitative phenotype. We show that ROH are important for all simulated demographic histories and genetic architectures but especially when phenotypes have a recessive component. This is even more prominent when the rare-allele contribution to the phenotype is upweighted and in high-diversity populations (e.g. African). For a fully recessive phenotype, ROH can account for 25–45% of an individual’s total phenotype score, depending on demographic history and rare-allele weight. Our results emphasize the utility of ROH in helping to explain phenotype variation across different population histories and genetic architectures.

Parameter optimization for runs of homozygosity (ROH) detection in the pig genome

BackgroundDuroc is one of the most popular terminal sire pig breeds worldwide due to its greater growth rate, meat quality, feed efficiency, and carcass characteristics compared to other breeds. Despite the breed’s popularity, its developmental history, genetic diversity, and genetic relationships with other pig breeds remain largely unknown. Therefore, the primary objective of this study was to investigate population structure and genetic diversity of Duroc subpopulations from Europe, North America, and Australia, and of other pig breeds.ResultsThe studied pig populations were differentiated into five subgroups(European and North American Durocs, Australian Durocs, Asian-Pacific pig breeds, and two other breed groups [OBP1 and OBP2]), consistent with their geographical origins, as revealed by population structure analyses. The estimated effective population size (Ne) of Duroc subpopulations ranged from 17 to 47, while the Ne for the combined Duroc subpopulations was 172. A total of 140,713 runs of homozygosity (ROHs) were identified across all individuals, with 98,039 ROHs in Durocs and 42,674 in other pig breeds. Durocs had a greater number and proportion of longer ROHs (> 8 Mb) compared to other pig breeds. The ROH-based inbreeding (FROH) values were significantly greater in Durocs than in most of the other breeds, indicating the need for better management of genetic diversity in the breed. We observed strong correlations (> 0.65) between different inbreeding metrics in all the studied pig populations. A total of 43, 18, 27, 37, and 20 candidate genes were identified in the ROH islands for European and North American Durocs, Australian Durocs, Asian-Pacific pigs, OBP1, and OBP2 pigs, respectively. The significant KEGG pathways were mainly related to growth, metabolism, immune system, cellular processes, and signal transduction.ConclusionsSignificant differences exist in genetic diversity, population structure, and ancestry within Duroc subpopulations and between Duroc and other pig breeds. The observed inbreeding levels in Duroc subpopulations indicate the need for better management of genetic diversity within the breed. Functional enrichment analyses of shared ROH islands provide new insights into biological pathways shaped by selection decisions in the past decades, especially those related to the immune system and energy metabolism.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12711-025-01017-6.

In autochthonous livestock breeds with small populations, such as the Rubia Galega from Galicia (Spain), mating between relatives is common and can lead to inbreeding depression. Genomic inbreeding coefficients were estimated for 4984 animals using ~63,000 SNPs to assess inbreeding depression in four key traits: age at first calving (AFC) with 3503 records, calving interval (CI) with 3315 records, birth weight (BW) with 4878 records and weight at 210 days (W210) with 3285 records. Runs of homozygosity were sorted by length ([1,2], (2,4], (4,8], (8,16], > 16 Mb), and the corresponding inbreeding coefficients (FROH>1, FROH>2, FROH>4, FROH>8, FROH>16) were calculated using the consecutiveRUNs R package. A Genomic BLUP (GBLUP) was conducted for each FROH estimate using the BLUPF90+ programs. The results revealed significant inbreeding depression for AFC and CI, whereas W210 and BW exhibited similar inbreeding trends, but the effects of inbreeding on these traits were not statistically significant. To further explore the genetic basis of inbreeding depression, SNPs located within ROHs were tested, though a t-test, for their association with phenotypic traits. Genes located in significant regions (-log(p-value) > 3 from t-test) were annotated using Ensembl BioMart within a ± 0.5 Mb window. Recent inbreeding (ROH > 8 Mb) showed significant negative effects on reproductive traits, and key genomic regions-particularly on chromosome 2 involving MSTN, NAB1, and COL5A2-were linked to increased AFC and reduced BW and W210; ROH-based inbreeding estimates proved effective in detecting inbreeding depression in this native breed. Overall, ROH-based analyses revealed genomic regions and candidate genes, notably MSTN, contributing to inbreeding depression and key production traits in Rubia Galega cattle.

Bovine respiratory disease (BRD) poses a significant health and economic challenge in cattle farming, particularly affecting young calves. Although previous SNP-based genome-wide association studies (GWAS) have identified candidate loci linked to BRD susceptibility, they only explain a fraction of the trait’s heritability. Using genotypes from a previous study that employed a selective genotyping approach, we analyzed Holstein calves classified as BRD-resistant or BRD-susceptible, based on thoracic ultrasonography and clinical scoring. In particular, structural variations, specifically copy number variants (CNVs) and runs of homozygosity (ROH), were investigated due to their emerging role as complementary genomic features that may be involved in disease resistance. A total of 2,666 CNVs were identified, and the CNV-GWAS revealed 10 significant CNV regions (CNVRs), encompassing or near 15 candidate genes. While the ROH analysis identified 8,226 segments, we further applied a fixed-window approach to compare ROH frequencies between groups, revealing 19 regions with significantly different ROH frequencies. Gene annotation of both CNVRs and differential ROH windows uncovered genes linked to immune response, lung development, and known BRD-associated pathways. Functional enrichment analyses using DAVID and Cytoscape-GeneMANIA indicated involvement of antiviral responses, GPCR signaling, calcium signaling, and estrogen receptor pathway in disease resistance. Notably, 37% of the genes identified in this study overlapped with those reported in previous BRD-related studies. This integrative genomic analysis highlights the relevance of structural variation in shaping BRD resistance and susceptibility in dairy calves. By integrating CNV mapping, ROH analysis, and functional annotation approaches, we identified novel and previously reported candidate genes potentially involved in innate immune processes. These findings support the implementation of precision breeding strategies aimed at improving disease resilience in cattle.

BackgroundSingle nucleotide polymorphism (SNP) arrays are commonly used for studying the genomic structure and diversity of livestock breeds, but whole-genome sequencing (WGS) provides higher-resolution genomic data. Genotype imputation has become a standard practice for increasing the genomic resolution of association studies. This work aimed to extend imputation to biodiversity analyses, comparing SNP array data before and after imputation. A 40 k SNP dataset of 281 horses from 12 breeds (DSSNP) was imputed to sequence-level using a reference panel of 327 sequenced individuals, generating approximately 9 million markers after filtering (DSIMP). Both datasets were used to study genetic variability, population structure and runs of homozygosity (ROH).ResultsGenetic indices and relationships showed similar trends for both datasets, with high Pearson correlations and Mantel test values (> 0.8) indicating that the imputed data are a reliable alternative to SNP array data for genetic studies. Multidimensional scaling and admixture analyses highlighted how the genetic proximity between breeds observed for the DSSNP was amplified by the imputation process in cases of those breeds with a few sequences included in the WGS reference panel. ROH investigation showed overlapping homozygosity regions between the two datasets, highlighting the benefits of having more markers for gene and QTL annotation. Of the 141 ROH islands identified in the DSSNP, 79 overlapped perfectly with those found in the imputed data. Validation with the reference panel of 327 sequenced horses revealed a single ROH island on ECA11 shared across all three datasets, containing genes associated with morphology and behavioral traits.ConclusionsHigh correlations between SNP array and imputed data indicate that imputed genotypes provide a reliable alternative for assessing population structure and genetic diversity in horse breeds. Specifically, imputation can enhance the detection of ROH and the annotation of genes within ROH islands, with the reliability of these results depending on the quality of the reference panel and its representation of the studied breeds, among others.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-025-12256-8.

Fengjing pigs are a Chinese native breed known for their high reproductive ability. Runs of homozygosity (ROHs) have emerged as an effective tool for evaluating inbreeding levels and identifying relevant genes in selection. However, the declining population of Fengjing pigs in recent years has raised concerns about inbreeding. Therefore, this study aimed to investigate the ROH patterns, estimate genomic inbreeding levels, and identify candidate genes associated with economic traits using whole-genome resequencing data from 105 Fengjing pigs. A total of 2448 ROHs were identified, with an average of 23.31 ROHs per individual and an average length of 9.50 Mb. The inbreeding coefficient, based on ROHs, was 0.098. Additionally, three genomic regions with a high frequency of ROHs were identified. These regions contained 64 unique genes, including 14 genes associated with important economic traits. Moreover, six overlapping quantitative trait loci (QTLs) and four candidate genes (HSPG2, CDC42, EPHB2, and GRHL3) were identified on Sus scrofa chromosome (SSC) 6. These QTLs are associated with birth traits (health and reproductive efficiency) and meat development traits (meat quality and growth). This study identified many candidate genes and QTLs that overlapped with ROHs and are associated with economically significant traits. These findings can be used in future breeding, conservation, and utilization of specific Chinese native pig breeds.

ABSTRACTInbreeding and inbreeding depression pose a critical challenge to the persistence of small and isolated populations, driving the need for precise assessment of genomic metrics. Genome‐wide runs of homozygosity (ROH) have been widely used for evaluating contemporary inbreeding levels and tracing historical events, circumventing the limitations of methods based on pedigree records. However, the reliability of ROH detection is contingent upon the quality of both the reference genome and resequencing data. Here, we employed a simulation‐based approach, generating an inbred population with individuals exhibiting varying inbreeding coefficients and 13 reference genomes with differing levels of contiguity. This framework enabled us to systematically investigate the effects of sequencing depth, read length, reference genome continuity and the phylogenetic divergence of reference genomes on detecting genome‐wide ROH segments. We found that a sequencing depth of ≥ 15× and a reference genome with a contig N50 > 4 Mb enabled discrimination of both the recent and historical inbreeding events, and a reference genome of congeneric subspecies is an optimal choice for ROH detection if a species‐specific reference genome is not available. Furthermore, we performed parameter optimisation for PLINK to enhance ROH detection accuracy under low‐coverage sequencing data and imperfect reference genomes. Our findings established methodological guidance for improving ROH‐based inbreeding assessments, providing critical insights for conservation genomics and breeding programmes where accurate characterisation of genomic homozygosity is paramount.

Inbreeding is caused by mating between related individuals and is associated with reduced fitness and performance. Generally, in the horse population, inbreeding is caused by geographically restricted areas and intensive natural or artificial selection. For this reason, assessing accurate inbreeding is essential for developing and implementing effective breeding strategies aimed at preserving genetic diversity and reducing the harmful consequences of inbreeding. One of the most accurate approaches for assessing genomic inbreeding and autozygosity is through the analysis of runs of homozygosity (ROH), which are long stretches of homozygous genotypes inherited from common ancestors and provide valuable insights into population diversity, demographic history, and selection. In this study, we analyzed the distribution of ROH, estimated genomic inbreeding coefficients, and mapped ROH islands across 14 diverse horse breeds. We used 670K and MNEc2M SNP array datasets, comprising 279,040 SNPs from 424 horses and 1,083,942 SNPs from 438 horses, respectively. A total of 35,396 and 17,382 ROHs were detected in all breeds for the 670K and MNEc2M SNP array datasets, respectively. The majority of the detected ROHs were < 16Mb (only 2.23% and 1.38% were greater than 16Mb in for the 670K and MNEc2M SNP array datasets, respectively) and the average total number of ROHs per individual were 81.36 ± 33.38 and 38.71 ± 22.73 for the 670K and MNEc2M SNP array datasets, respectively. The mean ROH length per individual was 248.57Mb for the 670K SNP array and 89.56Mb for the MNEc2M SNP array. Genomic inbreeding based on ROH (FROH) was relatively higher than homozygosity-based inbreeding (FHOM) and ranged from 0.0364 ± 0.0049 to 0.2357 ± 0.0584 and from 0.004 ± 0.0044 to 0.1102 ± 0.0779 for 670K and MNEc2M SNP array datasets, respectively. We identified genomic regions with high ROH coverage so called ROH islands that may reflect recent selection events. Several chromosomes, including ECA7 and ECA11, contained large ROH islands that include genes associated with important traits such as pigmentation, fertility, and performance. These ROH islands represent genomic footprints of past selection events and serve as candidate regions for future functional and association studies.

ObjectiveYantai Black pig (YT), as a native population of the eastern China’s Jiaodong Peninsula of Shandong province, characterized by coarse feeding tolerance, strong disease resistance, early sexual maturity, high litter size, and superior meat quality. However, the genetic characteristics and variations underlying its crucial economic traits remain poorly understood.MethodsIn this study, we resequenced the whole genome of 17 YT individuals from distinctly different lineages breeding in three conservation farms to detect single nucleotide polymorphism (SNP) density, pairwise fixation index (FST), nucleotide diversity (π), runs of homozygosity (ROHs).ResultsOur findings revealed that YT has higher genomic diversity compared to Chinese partial indigenous pig populations and Western commercial pig populations, but lower diversity than Asian wild boars (AWB). Based on FST and values (top 1%), we identified 321 selected regions, encompassing 156 genes, between YT and AWB. Functional annotation analysis suggested that these genes are potentially responsible for growth, reproduction, and immune responses. The RBFOX3 and WDR27 genes were confirmed to be strong positively selected in YT’s breeding. Combining the results of selection sweeps and ROH islands of YT, three overlapping regions were detected. Furthermore, we found that the quantitative trait loci (QTLs) with the most overlapping regions were related to teat number, body weight, and mean corpuscular hemoglobin concentration.ConclusionWe characterized the genomic features and population structure and identified selection signals in genomic regions linked to important germplasm characteristics of YT. The insights gained from this study provide valuable references and a solid foundation for the preservation, breeding, and utilization of YT and its valuable genetic resources.

The multi-millennia-long history between dogs and humans has placed them at the forefront of archaeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding the evolutionary processes that led to the diversity of breeds today. Although ancient genome sequences provide valuable information about these processes, their utility is hindered by low depths of coverage and postmortem damage, which inhibits confident genotype calling. In the present study, we assess how genotype imputation of ancient dog and wolf genomes, using a large reference panel, can increase the amount of information provided by ancient datasets. We evaluated imputation accuracy by down-sampling high-coverage dog and wolf genomes to 0.05 to 2× coverage and compared concordance between imputed and high-coverage genotypes. We measured the impact of imputation on principal component analyses and runs of homozygosity (ROH). Our findings show high (R2 > 0.9) imputation accuracy for dogs with coverage as low as 0.5× and for wolves as low as 1.0×. We then imputed a dataset of 90 ancient dog and wolf genomes to assess changes in inbreeding during the last 10,000 y of dog evolution. Ancient dog and wolf populations generally exhibit lower inbreeding levels than present-day individuals. Regions with low ROH density maintained across ancient and present-day dogs were significantly associated with genes related to immunity and chemosensory receptors. Our study indicates that imputing ancient canine genomes is a viable strategy that allows for the use of analytical methods previously limited to high-quality genetic data.

Genomic regions affecting perinatal and early life survival in dairy calves.

ABSTRACTHumans have relied on animal fur for centuries, yet fur farming only began recently during the mid‐19th Century. Little is known about this incipient domestication or the genomic processes involved. Domestication may involve founder effects, population bottlenecks and low population size, which, when combined with intense artificial selection, lead to inbreeding, a limited gene pool and reduced fitness. The arctic fox (Vulpes lagopus) has been farmed intensively since the early 1900s and has been artificially selected for economic phenotypes. We investigated the origin of these lineages and the genomic consequences of intensive farming by comparing the genomes of farmed and wild arctic foxes from across their range. Our research indicates recent inbreeding through long Runs of Homozygosity and reduced genomic variation in farmed foxes relative to their respective wild populations. We identified a coastal ecotype origin for all Fennoscandian farmed arctic foxes, aligning them phylogenetically with the wild Icelandic population, a geographically isolated and phenotypically distinct coastal lineage. The depleted genome‐wide heterozygosity and increased recent inbreeding in farmed fox lineages is consistent with a heavy consequence of domestication, shedding light on the demographic history and genomic consequences of human manipulation. We highlight the need for increased genomic investigations into fur farm populations to understand the incipient domestication process and uncover the cost of intense farming. The genomic consequences of domestication must be considered in the management of fur farms, with actionable steps needed to prevent descendants of escaped farmed foxes from polluting the gene pool in the wild through introgression.

Background: The Siberian Husky has evolved as a versatile dog capable of traversing over 1600 km in extreme Arctic conditions, being a competitive show dog in the American Kennel Club, or a favorite pet for companionship. Modern genomics provides an opportunity to explore the biological implications of selection within the Siberian Husky breed for the purpose of sledding, show, or pet. Methods: We identified regions of genetic selection associated with sledding, show, or pet purposes using a whole-genome panel of 234 K SNPs from 237 Siberian Huskies. We assessed allelic variation using Wright’s FST and selective sweeps with runs of homozygosity (ROH). Results: Genomic and morphometric measurement principal component analyses identified population structure aligning with breeding purpose. In total, 118 SNPs demonstrated significant allelic variation (FST ≥ 0.6) and 22,598 ROH segments were identified within the Siberian Husky breed. ROH islands (n = 91) highlighted selective sweeps, whereas homozygosity association tests characterized regions of the genome under differential selection between populations. Genes within regions were assessed using GO and KEGG pathway analysis for biological insight. Pet dogs showed selection for olfactory performance genes, whereas show dogs were selected for immune function, tissue and nervous system development, and cytoskeletal motor activity. Sledding Siberian Huskies were selected for the development of muscle organs, lung vasculature, limbs, bones, eye structure, and pigmentation, plus genes influencing lipid metabolism and glucose transport. Conclusions: In all, this provides the first evidence of the biological impact of genetic selection within a breed for the distinct sledding, show, and pet purposes while simultaneously maintaining overall population uniformity to meet breed standards.

Insights into pedigree- and genome-based inbreeding patterns in Martina Franca donkey breed.

Goats were among the earliest managed animals, making them a natural model to explore the genetic consequences of domestication. However, a challenge in ancient genomic analysis is the relatively low genome coverage for most samples, limiting analysis to pseudohaploid genotypes. Genotype imputation offers potential to alleviate this limitation by improving information content and accuracy in low coverage genomes. To test this, we used published high coverage (>8✕) goat palaeogenomes, imputing downsampled genomes using the VarGoats dataset (1,372 individuals) as a reference panel. Measuring concordance between imputed and high coverage genotypes, we find high concordance after filtering for common (>5%), high confidence variants, with 0.5✕ genomes reaching >0.97 concordance. There is a trade-off between coverage, genotype probability (GP) thresholds, and genotype recovery, where higher coverage and more lenient GP thresholds result in higher recovery, and a reduction in heterozygous false-positive rates with stricter thresholds. We then imputed 36 goat palaeogenomes with ≥0.5✕ coverage to examine runs-of-homozygosity (ROH) and identity-by-descent (IBD) patterns. Using a novel approach combining ROH profiles across tools, we find that among Neolithic goats, ROH increases with distance from the Zagros Mountains, suggesting a large effect of the initial dispersal of managed herds. Inbreeding levels decrease across Southwest Asia in more recent periods. IBD mirrored this pattern, with less relatedness in the early herding site of Ganj Dareh compared to higher relatedness in goats from later in the dispersal process. These findings provide insights into the genetic consequences of early goat management on demography, and confirm the utility of imputation in leveraging low coverage palaeogenomes.

IntroductionKele pig (KLP) is a valuable Chinese indigenous pig breed, renowned for its strong adaptability, high intramuscular fat content, and excellent meat quality. However, the genomic characteristics of KLPs are still unknown. This study aims to investigate the genetic diversity, population structure, and trait-related selection signatures of KLPs based on whole-genome resequencing.MethodsThe genomes of 30 KLPs were resequenced and analyzed alongside genomic data from 90 pigs of three commercial breeds, comprising 30 Duroc (DUPs), 30 Landrace (LRPs), and 30 Yorkshire pigs (YRPs). To evaluate their genetic diversity, we calculated the expected heterozygosity, observed heterozygosity, polymorphic marker ratio, minor allele frequency, nucleotide diversity (π), runs of homozygosity (ROH), and inbreeding coefficient (FROH). Meanwhile, a neighbor-joining tree, principal component analysis, ADMIXTURE analysis, linkage disequilibrium (LD) analysis, genetic distance and relationship matrices were constructed to analyze the population structure. In addition, selection signatures between KLPs and DUPs, LRPs, and YRPs were detected using fixation index (Fst) and π ratio methods.Results and DiscussionA total of 66,204,339 autosomal single nucleotide polymorphisms (SNPs) were detected in the 120 pigs, and 21,738,497 SNPs were retained for further analysis after filtering. The results showed that KLPs had higher genetic diversity, along with the smallest FROH value compared to DUPs, LRPs, and YRPs. Moreover, KLPs displayed a relatively unique genetic structure with a higher LD decay, and the majority of individuals within the KLPs exhibited distant genetic distances and relationships. Totals of 688 selected regions were identified, including 723 published QTLs. Within the selected regions, 192 candidate genes were annotated, and seven genes were found to be functionally involved in coat color (KIT), immune response (JAK2 and SOCS1), heart development (NTRK3 and SRF), muscle growth and development (VDR), and fat deposition (KDR). These findings will provide valuable insights for the future conservation, breeding, and utilization of KLPs.

BackgroundThe species Capra hircus encompasses numerous breeds that exhibit a high level of phenotypic and genetic variability, resulting from environmental adaptation and artificial selection for meat, milk, and fiber production. Today, the global domestic goat population is steadily increasing, primarily due to their ability to adapt to harsh environments. Their worldwide distribution offers the opportunity to study how different environmental conditions and farming systems have shaped the goat genome. In this work, 194 whole-genome sequencing data sets from wild, feral, and domestic goats have been used to detect Runs of Homozygosity (ROH) and study Extended Haplotype Homozygosity (EHH) to identify the so-called 'Signatures of Selection' that uniquely characterize each goat population.ResultsCommon signals of selection have been identified in CCSER1 and ADAMTSL3, two genes associated with body development, which were under selection in feral and wild goats, and in Angora and Boer breeds, respectively. Similarly, both feral and cashmere breeds exhibited selection signals in PCDH15, a gene linked to environmental adaptation. Selection in wild and feral goats was primarily observed at loci related to environmental adaptation and immune response. Moreover, selection signals related to productive traits such as milk and meat production were still detectable in feral populations. The Angora goat genome showed selective pressure mainly targeting efficient reproduction and body development, with relatively low pressure related to environmental adaptation. The four cashmere breeds studied displayed selection signals predominantly in genes involved in environmental adaptation, immune response, and hair follicle biology. Several signatures of selection related to environmental adaptation were also observed in both meat- and milk-producing goats, as well as in genes associated with reproduction, milk, and meat production.ConclusionThese findings suggest that, despite long-term domestication, natural and environmental selection have shaped the goat genome more than artificial selection. Identifying genes linked to adaptation and fitness is vital for future livestock production amid climate change. Our study highlights genetic loci related to environmental adaptation and disease resistance, offering a foundation for targeted breeding and conservation strategies to enhance resilience and sustainability in goat populations.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-025-12133-4.

Pollinator declines globally threaten ecosystem stability and agricultural productivity. Reconstructing pollinator historic demographies provides an evolutionary perspective to understand contemporary population declines. The Franklin bumble bee (Bombus franklini), once endemic to Oregon and California and last observed alive in 2006, is emblematic of this phenomenon. We collected whole-genome sequence data from museum specimens spanning four decades to elucidate the genetic and demographic history of this potentially extinct species. Heterozygosity estimates of 25 individuals were remarkably low, and runs of homozygosity (ROH) patterns identified short segments suggestive of historical inbreeding, with some individuals having almost entire chromosomes in ROH. Demographic reconstructions revealed a marked decline in effective population size beginning in the late Pleistocene, with further declines in the last 400 y, which may have been influenced by fire and drought stressors. We found little to no genomic evidence implicating pathogens in the species' decline and used coalescent simulations to show that we would be able to detect recently reduced heterozygosity only when colony-level survival rates are 15 to 30%. We conclude that a combination of historically low effective population size and genetic diversity along with environmental stochasticity heightened this species' extinction vulnerability prior to recent anthropogenic stressors. This study demonstrates the utility of museum collections for clarifying genetic and demographic dynamics of rare species and suggests that B. franklini may have already been on a trajectory of decline prior to human impacts.