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At least 19 recordsLinked to original sources
PubMed2026

Population history rather than tree age contributes to the evolutionary importance of ancient trees in an endangered conifer.

Ancient trees are in global decline and face increasing conservation challenges. Their exceptional longevity has fostered the view that they are genetic reservoirs, yet whether old age is synonymous with unique genetic variation remains unclear. Here we assembled a ~8-Gb chromosome-level reference genome for the critically endangered conifer Glyptostrobus pensilis, now largely restricted to southern China with scattered populations in Vietnam and Laos, and resequenced 147 individuals, including 64 ancient (>100 years old and persisting in human-dominated landscapes), 33 wild and 50 recently cultivated individuals. Ancient individuals comprised both likely natural relics and historically introduced individuals and formed two deeply divergent lineages and one ancestral-admixed group, each with distinct demographic histories of prolonged contraction and genomic erosion. Lineage identity explained more variation in genome-wide diversity, inbreeding and genetic load than the three conservation types, despite broad differences in age structure. Rare-allele analyses revealed pronounced heterogeneity among ancient trees: only relic and ancestral-origin individuals from high-diversity lineages contributed substantial unique variation, much of which is poorly represented in wild and cultivated populations. Together, our findings suggest that ancient trees are not uniformly genetically irreplaceable and that, at least in this conifer, evolutionary importance is shaped more strongly by population history than by age alone.

Endangered Species↗
PubMed2025

Genomic insights into the population history of fat-tailed sheep and identification of two mutations that contribute to fat tail adipogenesis.

INTRODUCTION: Since their domestication, domestic sheep (Ovis aries) have been culturally and economically significant farming animals worldwide. Fat-tailed sheep serve as a unique genetic resource for understanding adipogenesis and adaptive evolution in livestock. OBJECTIVES: Several genomic analyses have been conducted on various sheep breeds to elucidate the genome and regulation mechanism of the fat tail trait, prior genomic studies have failed to reconcile conflicting evidence about the genetic basis of tail morphology, particularly regarding the roles of PDGFD and BMP2. METHODS: Here, we conducted whole-genome resequencing of 283 sheep, encompassing 66 domestic breeds and 5 wild ovine species, to investigate the domestication history and selection signatures of fat-tailed sheep. Additionally, we performed transcriptome sequencing on adipose tissue to identify differentially expressed genes and cellular assays to validate these results. RESULTS: Demographic analysis revealed that domestic sheep descended from Asiatic mouflon and fat-tailed sheep began to diverge from thin-tailed sheep approximately 4.4-7.5 thousand years ago in East Asia. Chinese indigenous sheep were classified into Mongolian, Kazakh, Tibetan, and Yunnan populations. The Yunnan population may have experienced more recent genetic introgression from wild species, rather than an independent domestication event. Moreover, many potential regions associated with the fat-tailed phenotype (DDI1, PDGFD, and BMP2) were identified by selective sweep and genome-wide association analyses. Additionally, a fine-scale analysis of fat-tailed and thin-tailed sheep revealed two novel mutations: a G/A missense variant of PDGFD (Chr15: 3900312) and a C/T missense variant of BMP2 (Chr13: 48462350), both of which were significantly associated with tail adiposity. Functional validation demonstrated that mutant A-PDGFD significantly activated PFGFD expression and reduced fat deposition compared to wildtype. The C-BMP2 mutant activated BMP2 expression and promoted preadipocyte fat deposition. CONCLUSION: Our study provides the first evidence that these genes jointly regulate fat tail development through complementary mechanisms: PDGFD promotes adipose expansion, whereas BMP2 modulates energy partitioning. These findings offer new insights into the evolutionary history of fat-tailed sheep and identify potential targets for precision breeding in small ruminants.

Animals↗
PubMed2019

Identifying loci under positive selection in complex population histories.

Detailed modeling of a species' history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method-called graph-aware retrieval of selective sweeps (GRoSS)-has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish, and human population genomic data containing panels of multiple populations related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in understudied human populations, as well as muscle mass, milk production, and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation owing to inversions in the history of Atlantic codfish.

Animals↗
PubMed2024

Next-generation phylogeography reveals unanticipated population history and climate and human impacts on the endangered floodplain bitterling (Acheilognathus longipinnis).

BACKGROUND: Floodplains harbor highly biodiverse ecosystems, which have been strongly affected by both past climate change and by recent human activities, resulting in a high prevalence of many endangered species in these habitats. Understanding the history of floodplain species over a wide range of timescales can contribute to effective conservation planning. We reconstructed the population formation history of the Itasenpara bitterling Acheilognathus longipinnis, an endangered floodplain fish species in Japan, over a broad timescale based on phylogenetic analysis, demographic modeling, and historical demographic analysis using mitogenome and whole-genome sequences. A genome sequence was newly assembled as a reference for the resequencing analysis. This bitterling is distributed in three plains separated by high mountain ranges and exhibits ecological characteristics well adapted to floodplain environments. RESULTS: Our analyses revealed an unexpected population branching pattern, gene flow, and timing of the differentiation that occurred within a few hundred thousand years, i.e., long after the mountain uplift that was assumed to be the primary geological cause of the population differentiation. The analyses also showed that all local populations experienced a severe decline during the last glacial and post-glacial periods. CONCLUSIONS: Our results suggest that the floodplain bitterling was able to disperse through unknown routes after mountain uplift and that its populations were strongly influenced by climatic and geographic changes in glacial-interglacial cycles and subsequent human activities, probably related to its floodplain-dependent ecology. The genomic data highlight the unanticipated distribution process of this species and the magnitude of the impact of human activities, with important implications for its conservation.

Endangered Species↗
PubMed2026

Mitogenomic Insights Into the Population Structure and Demographic History of Tree Shrews (Tupaia belangeri) in China.

The northern tree shrew (Tupaia belangeri) exhibits significant morphological and geographical variations, but its evolutionary history and subspecies boundaries remain controversial. Here, we analyzed the complete mitochondrial genomes of 63 individuals, representing 12 populations in China to study phylogenetic relationships, genetic diversity, and population history. Phylogenetic analysis consistently restored four mitochondrial branches with strong geographic structures and significant differences. The three lineages correspond to geographically restricted subspecies (T. b. tonquinia, T. b. modesta, and T. b. gaoligongensis), while individuals assigned to several traditional subspecies cluster in a broad mainland lineage (T. b. chinensis, T. b. yunalis, and T. b. yaoshanensis). The divergence time estimate places the origin of the main lineage in the Miocene, consistent with major tectonic and geomorphological events. Demographic analysis revealed different population histories, including varying degrees of expansion in recent continental and island lineages, as well as the long-term stability of T. b. gaoligongensis. Genetic diversity varied markedly among lineages, with the highest diversity observed in the T. b. gaoligongensis and the lowest diversity observed in the T. b. modesta. These findings demonstrate that landscape complexity and demographic history are key drivers of evolutionary diversification in T. belangeri, challenging classical morphology-based subspecies classifications and underscoring the need for comprehensive sampling across both domestic and international ranges.

Tupaia belangeri↗
PubMed2026

Inferring the demographic history of Chinese and Indian rhesus macaque (Macaca mulatta) populations from PacBio HiFi long-read sequencing data.

The rhesus macaque (Macaca mulatta) is one of the most widely used animal models in biomedical research, both as it resembles humans in key biological aspects and as it is characterized by a broad geographic range. Most of the individuals housed in U.S. research colonies have been sampled from either China or India, though notably the source population of these animals has significantly shifted over time. Given the substantial genetic and immunological differences between these populations, a deeper understanding of the underlying population structure is critically important for biomedical interpretation. Despite this, the demographic histories of these two populations remain poorly resolved. Here, we present an analysis of whole-genome, PacBio HiFi long-read sequencing data from ten unrelated individuals of each population, applying four related model- and non-model based demographic inference approaches, in order to reconstruct their ancestral history. We evaluated the fit of the subsequently estimated models against the empirical data, and incorporated underlying uncertainty in the mutation rates used for scaling. We inferred a well-fitting population history characterized by substantial structure between Chinese and Indian populations, with a split time ∼140,000 generations ago from an ancestral population of ∼65,000 individuals. We additionally inferred the subsequent history of size change within, and gene flow between, these populations, reaching the current estimated sizes of ∼220,000 individuals in the Chinese population and ∼14,000 individuals in the Indian population. The robust baseline demographic model established in this study will serve as a valuable resource for future research on this species, including for improved fine-scale recombination mapping, selection inference, and association studies.

Cercopithecidae↗
PubMed2025

Landscape genomics analysis reveals the genetic basis underlying cashmere goats and dairy goats adaptation to frigid environments.

Understanding the genetic mechanism of cold adaptation in cashmere goats and dairy goats is very important to improve their production performance. The purpose of this study was to comprehensively analyze the genetic basis of goat adaptation to cold environments, clarify the impact of environmental factors on genome diversity, and lay the foundation for breeding goat breeds to adapt to climate change. A total of 240 dairy goats were subjected to genome resequencing, and the whole genome sequencing data of 57 individuals from 6 published breeds were incorporated. By integrating multiple approaches such as phylogenetic analysis, population structure analysis, gene flow and population history exploration, selection signal analysis, and genome-environment association analysis, an in-depth investigation was carried out. Phylogenetic analysis unraveled the genetic relationships and differentiation patterns among dairy goats and other goat breeds. Through signal analysis (θπ, FST, XP-CLR), we identified numerous candidate genes associated with cold adaptation in dairy goats (STRIP1, ALX3, HTR4, NTRK2, MRPL11, PELI3, DPP3, BBS1) and cashmere goats (MED12L, MARC2, MARC1, DSG3, C6H4orf22, CHD7, MYPN, KIAA0825, MITF). Genome-environment association (GEA) analysis confirmed the link between these genes and environmental factors. Moreover, a detailed analysis of the critical genes C6H4orf22 and STRIP1 demonstrated their significant roles in the geographical variations of cold adaptation and allele frequency differences among different breeds. This study contributes to understanding the genetic basis of cold adaptation, providing crucial theoretical support for precision breeding programs aimed at improving production performance in cold regions by leveraging adaptive alleles, thereby ensuring sustainable animal husbandry.

Environmental adaptation↗
PubMed2025

A genealogy-based approach for revealing ancestry-specific structures in admixed populations.

Elucidating ancestry-specific structures in admixed populations is crucial for comprehending population history and mitigating confounding effects in genome-wide association studies. Existing methods to reveal the ancestry-specific structures generally rely on frequency-based estimates of genetic relationship matrix (GRM) among admixed individuals after masking segments from ancestry components not being targeted for investigation. However, these approaches disregard linkage information between markers, potentially limiting their resolution in revealing structure within an ancestry component. We introduce ancestry-specific expected GRM (as-eGRM), a novel framework for estimating the relatedness within ancestry components between admixed individuals. The key design of as-eGRM consists of defining ancestry-specific pairwise relatedness between individuals based on genealogical trees encoded in the ancestral recombination graph (ARG) and local ancestry calls and then computing the expectation of the ancestry-specific relatedness across the genome. Comprehensive evaluations using both simulated stepping-stone models of population structure and empirical datasets based on three-way admixed Latino cohorts showed that analysis based on as-eGRM robustly outperforms existing methods in revealing the structure in admixed populations with diverse demographic histories, which in turn improves the robustness against confounding due to population structure in association testing.

Humans↗
PubMed2026

Ten millennia of purifying selection on HLA-B27 reveals an ancient epidemic-scale burden of spondyloarthritis in West Eurasia.

HLA-B27 exemplifies an evolutionary trade-off between protection against infection and susceptibility to inflammatory disease. To investigate its long-term population history, this study examined three HLA-B27-tagging variants-rs116488202, rs4349859, and rs116666910-in present-day populations from UK biobank and 1000 Genomes Project, and in 15,836 ancient West Eurasian individuals. The estimated frequency of HLA-B27 reached 49.0% approximately 8500 years before present, then declined progressively to 3.9% in the present-day reference population. Comparison with genome-wide association study (GWAS) data for ankylosing spondylitis (AS) showed that HLA-B27-linked alleles conferring increased disease risk had negative selection coefficients, indicating sustained selection against HLA-B27 over the past 10,000 years. The decline coincided with major Holocene changes in settlement and subsistence patterns, microbial exposure, and enteric infection, which may have increased the inflammatory costs of HLA-B27. Because previous paleopathological studies have largely been limited to identifying advanced skeletal manifestations of AS, this ancient genetic study may provide currently the most sensitive population-level record of an otherwise largely undetectable, epidemic-scale disease burden in antiquity. These findings support the hypothesis that HLA-B27-associated spondyloarthritis was sufficiently prevalent and severe to influence human evolution in prehistoric West Eurasia.

Humans↗
PubMed2026

Ancient Mongolian aurochs and cattle genomes reveal population shifts associated with the expansion of herding.

Humans hunted aurochs (Bos primigenius) for millennia in Mongolia prior to the introduction of domestic cattle sometime after ca. 5,000 years ago. Here, we present genomic data from Mongolian aurochs and domestic cattle at key points in Mongolia's prehistory to understand changes in population history associated with the adoption of domestic taurine cattle (B. taurus). We compare these low-coverage genomes with other cattle genomes worldwide and make comparisons about the nature of bovine populations before and after the adoption of domestic cattle. Individuals dating to before the introduction of taurine cattle have shared ancestry with North Asian aurochs, and individuals dating after the introduction of taurine cattle are related to other ancient East Asian cattle from archaeological sites such as Shimao in the Ordos region. We identify unique connections between ancient Mongolian aurochs and cattle and modern cattle breeds from Central China and Tibet.

Bos primigenius↗
PubMed2026

First insights into the role of evolutionary history in shaping venom composition of Vipera ammodytes.

Understanding intraspecific venom variation requires distinguishing the contributions of neutral population history from natural selection. This study aims to determine whether venom variation in Vipera ammodytes species complex is structured across eight phylogenetic groups. Despite a complex evolutionary history, venom composition did not differ among phylogenetic groups within the analytical framework used, suggesting that shared ancestry alone does not explain venom variation. Whether local adaptation to environmental conditions explains the observed variation remains an open question for future studies.

Animals↗
PubMed2026

Genomic insights into natural selection in recent human history.

For over a century, scientists have debated the extent to which genetic and phenotypic variation among present-day humans is the result of natural selection - in which heritable traits influence survival or reproduction - versus neutral processes such as genetic drift or population history. The initial sequencing of the human genome and subsequent population resequencing studies enabled genome-scale searches for signatures of selection in present-day genomes. This first generation of genome-wide selection scans identified many targets but left open questions about the timing and nature of selection, making it challenging to identify environmental and biological drivers. Recent methodological advances based on reconstructing ancestral recombination graphs have increased the potential power and resolution of selection scans based on present-day genomes, while the availability of new data on ancient DNA has facilitated the direct reconstruction of genetic change through time. However, there is little consensus on how to use these data to detect and interpret signatures of selection, while avoiding confounders. Here, we review the current state of knowledge about the impact of selection on human genomic diversity and highlight conceptual advances in our understanding of human evolution over the past 10,000 years.

Journal Article↗
PubMed2026

Interactive exploration of biobank-scale ancestral recombination graphs with Lorax.

MOTIVATION: Ancestral Recombination Graphs (ARGs) provide a comprehensive representation of genetic ancestry and underpin analyses of natural selection, disease association, and population history. However, existing visualization tools are limited in scalability and interactivity, making ARGs difficult to explore at biobank scale. RESULTS: We introduce Lorax, a GPU-accelerated, web-native platform for real-time visualization of population-scale ARGs. Lorax integrates genomic position, coalescent time, local genealogy, and metadata, enabling interactive exploration of ancestry and variant inheritance in biobank-scale datasets. AVAILABILITY AND IMPLEMENTATION: Lorax is freely available as a live demo at https://lorax.ucsc.edu/ and as a Python package "lorax-arg" on PyPI. The source code and documentation are available on GitHub at https://github.com/pratikkatte/lorax.

Software↗
PubMed2026

Reference genomes of Japanese raccoon dog (Nyctereutes viverrinus) and a Japanese red fox (Vulpes vulpes japonica).

We established primary fibroblast cultures from a Japanese raccoon dog (Nyctereutes viverrinus) and a Japanese red fox (Vulpes vulpes japonica) and generated highly contiguous reference genome assemblies using Oxford Nanopore Technologies PromethION long-read sequencing. The Japanese raccoon dog assembly spanned 2.69 Gb in 813 scaffolds, with a scaffold N50 of 52 Mb and a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 98.2%. The Japanese red fox assembly spanned 2.47 Gb in 903 scaffolds, with a scaffold N50 of 139 Mb and a BUSCO completeness score of 97.5%. Phylogenomic analysis placed the Japanese raccoon dog in a lineage distinct from the continental raccoon dog, supporting its evolutionary differentiation within Nyctereutes. The Japanese red fox formed a distinct lineage within the red fox clade, consistent with its recognized regional differentiation. These genome assemblies and associated fibroblast cultures provide resources for studies of canid systematics, population history, local adaptation, comparative genome evolution, and conservation genetics.

Canidae↗
PubMed2025

Comparative Analysis of Mammalian Adaptive Immune Loci Revealed Spectacular Divergence and Common Genetic Patterns.

Adaptive immune responses are mediated by the production of adaptive immune receptors, antibodies, and T-cell receptors, which bind antigens, thus causing their neutralization. Unlike other proteins, adaptive immune receptors are not fully encoded in the germline genome and result from a complex of somatic processes collectively called V(D)J recombination affecting germline immunoglobulin (IG) and T-cell receptor (TR) loci consisting of template genes. While various existing studies report extreme diversity of antibodies and T-cell receptors, little is known about the diversity of germline IG and TR loci. To overcome this gap, the first comparative analysis of full-length sequences of IG/TR loci across 46 mammalian species from 13 taxonomic orders was performed. First, germline gene counts were shown to correlate in immunoglobulin heavy chain immunoglobulin heavy chain (IGH)/immunoglobulin lambda (IGL) loci and T-cell receptor alpha (TRA)/T-cell receptor beta (TRB) and anticorrelate in immunoglobulin kappa (IGK)/IGL, possibly indicating coevolution between corresponding chains. Second, structures of IG/TR loci were analyzed, and it was shown that IG/TR loci formed by long arrays of high multiplicity repeats are more common for species that have experienced population bottlenecks. Finally, haplotypes of IG/TR loci with little or no sequence similarity within a species were found, suggesting that they may have a limited potential for homologous recombination. These results demonstrate that IG/TR loci are rapidly evolving genomic regions whose structural variation is shaped by the population history of the species and open new perspectives for immunogenomics studies.

Animals↗
PubMed2025

Largest-Scale Genomic Resource Reconstructing the Genetic Origin, Population Structure, and Biological Adaptations of the Hui People.

Historical and archaeological records indicate that the Maritime and Land Silk Roads played a pivotal role in facilitating Trans-Eurasian migrations and cultural exchanges. However, the extent to which population movements or the spread of ideas shape Chinese Hui populations remains debated. We present the largest genomic resource to date, including 2,280 Hui individuals sequenced or genotyped from 30 diverse regions, to examine the genetic origins, population structure, and biological adaptations of this underrepresented group in global human genome research. We identified a detailed population structure characterized by five distinct genetic lineages of the Hui, influenced by geography and varying gene flow. The admixture history and demographic events suggest that the northwestern and northern Hui lineages emerged from demic diffusion during the Tang and Yuan Dynasties via the Land Silk Road. In contrast, the southern and island Hui lineages reflect cultural diffusion along the Maritime Silk Road, while the mixed southern-northern lineage likely developed through a combination of demic and cultural diffusion. Our findings support a hybrid model for Hui formation, indicating that both demographic processes and sociocultural transmissions contributed to their population history. We identified east-west highly differentiated variants and pre- and post-admixture adaptations in Hui genomes, demonstrating that admixture-driven adaptive or neutral variants impacted susceptibility to cardiovascular diseases and immune- and diet-related traits. These adaptive signatures include post-admixture signals of SLC24A5 and ECHDC1 in the Hui, as well as pre-admixture signals of the HLA region, BCL2A1, and KCNH8 in the East Asian source. Overall, our study suggests that Han-related genetic components helped the Hui population rapidly adapt to new local environments. Additionally, the frequency spectrum of clinically essential variants differed significantly between Hui and Han individuals, emphasizing the importance of including underrepresented populations in genomic research to promote health equity.

Humans↗
PubMed2026

Ancient DNA unveils distinctive ancestries in the Bronze and Iron Ages of East Tianshan.

The East Tianshan Mountains occupy a key corridor between Central and East Asia, but their population history remains poorly understood. Here we report genome-wide data from 135 ancient individuals from 11 archaeological sites. We identify a previously unrecognized Bronze Age admixture between populations related to Yellow River millet farmers and steppe pastoralists associated with the Chemurchek culture. In contrast, we find little genetic contribution from contemporaneous middle-to-late Bronze Age steppe pastoralists, despite their eastward expansion across the Eurasian Steppe. By the Iron Age, regional populations had become more heterogeneous, incorporating additional eastern and steppe-related sources while retaining variable contributions from Early Bronze Age groups. These results reveal sustained demographic interactions in eastern Central Asia nearly 1800 years preceding the establishment of the historic Silk Road.

DNA, Ancient↗
PubMed2025

Divergent and stabilizing selection shape the phenotypic space of Arabidopsis thaliana.

Why do we observe some plant phenotypes but not others? The multivariate phenotypic space occupied by individuals or species often reveals both limits and phenotypes strikingly deviating from main syndromes. These observations are usually thought to indicate, respectively, inviable trait combinations and unique phenotypes adapted to specific environments. However, the evolutionary drivers underlying trait covariations often remain unclear. Here, we characterized the phenotypic space of Arabidopsis thaliana by comparing 713 wild accessions collected across the globe with 2,544 artificially-created recombinant individuals. This, combined with the detection of adaptive processes operating within species, allowed us to elucidate the roles of natural selection as a driver of phenotypic (co)variations within A. thaliana. We found that the phenotypic space of this species is constrained and driven by varying levels of divergent and stabilizing selection across different traits. Moreover, at the margins of the European geographic range, strong directional selection favored outlier phenotypes characterized by very late flowering and variation in a WRKY transcription factor gene. Genome analyses revealed that these extreme phenotypes may be explained by hybridization between ancestral and modern lineages of A. thaliana. Our findings demonstrate how interplays between population history and natural selection shape phenotypic diversity in a plant species.

Arabidopsis↗