SEARCH · PubMed Health

Results for “Adaptive evolution”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4Linked to original sources

PubMed2025

The chromosome-level genome of Stylosanthes guianensis provides insights into genome evolution and environmental adaptation.

Stylosanthes guianensis is a leguminous forage crop of significant economic importance, primarily distributed in tropical and subtropical regions. It exhibits strong adaptability to various stresses, yet the genetic basis underlying this trait remains unclear. In this study, we constructed the first chromosome-scale reference genome of S. guianensis using a combination of Nanopore and Hi-C sequencing technologies. The assembled genome size is 1254 Mb, with 10 pseudochromosomes. Using Nanopore full-length transcriptome data, we generated high-quality transcript-level gene annotations, identifying 36 585 gene models and 110 601 transcripts. The repetitive sequences in S. guianensis account for 79.16% of the genome, with the extensive expansion of Gypsy elements in long terminal repeats contributing to its genome size enlargement. Comparative genomic and transcriptomic analyses revealed that flavonoid metabolism plays a pivotal role in stress adaptation, providing new insights into the genetic basis of stress tolerance. Additionally, we generated whole-genome methylation profiles under cold treatment and control conditions, offering valuable data for future epigenomic research. These findings provide essential molecular resources for understanding stress resilience in S. guianensis and advancing its molecular breeding.

Genome, Plant↗

PubMed2025

Multiomic Analyses Reveal the Molecular Mechanisms of Arid Adaptation in a Desert Rodent Species.

Organisms living in desert habitats face multiple simultaneous pressures, such as high temperatures and arid, and the population dynamics and community diversity of small rodents are strongly affected by climate extremes. However, the potential mechanisms by which desert rodents adapt to arid remain largely unexplored. Here, we assembled a 3.18 Gb genome, including 25,812 protein-encoding genes, for Orientallactaga sibirica, which is widely distributed across both arid and semihumid environments in Eurasia. Orientallactaga sibirica has longer ears and hind limbs to enhance heat dissipation, which may be related to the positively selected genes, such as Fgf10, Fgf11, Hoxc4, Hoxd1, and Bmp4. The renal transcriptome revealed increased fat and carbohydrate metabolism for metabolic water production in O. sibirica residing in arid habitats. Pathways such as material metabolism, oxidative stress response, osmoregulation, and water and salt reabsorption were enriched in candidate genes, such as Avp, Ang, and Ace, under positive selection in O. sibirica. Moreover, amino acid replacement was observed in the protein sequences of seven candidate genes, including Aldh7a1, Lnpep, Wnk4, C1qc, and Awat2, and these specific amino acid replacements of genes such as Umod and Scnn1a were related to unique osmoregulation, osmotic protection, and water retention compensation mechanisms. Water deprivation under laboratory conditions induced the upregulation of Umod and Aldh7a1 expression, further supporting the results observed in the wild population. These findings demonstrate that the positively selected genes related to limb development and specific amino acid replacements in the genes Umod and Scnn1a for unique osmoregulation in the renal vascular system may contribute to arid adaptation in the desert rodent species O. sibirica. This study provides novel insights into the adaptive evolution of desert small mammals and can serve as a reference for future research on renal damage-related diseases, such as human kidney stones and salt-sensitive hypertension.

Animals↗

PubMed2025

Exploring genetic adaptation and microbial dynamics in engineered anaerobic ecosystems via strain-level metagenomics.

Genetic heterogeneity exists within all microbial populations, with sympatric cells of the same species often exhibiting single-nucleotide variations that influence phenotypic traits, including metabolic efficiency. However, the evolutionary dynamics of these strain-level differences in response to environmental stress remain poorly understood. Here, we present a first-of-its-kind study tracking the adaptive evolution of an anaerobic, carbon-fixing microbiota under a controlled engineered ecosystem focused on carbon dioxide bioconversion into methane. Leveraging strain-resolved metagenomics with an ad hoc variant calling and phasing approach, we mapped mutation trajectories and observed that the two dominant Methanothermobacter species maintained distinct sweeping haplotypes over time, most likely due to niche-specific metabolic roles. By combining population genetic statistics and peptide reconstruction, mer and mcrB genes emerged as potential drivers of archaeal strain-level competition. These findings pave the way for targeted engineering of microbial communities to enhance bioconversion efficiency, with significant implications for sustainable energy and carbon management in anaerobic systems.

Metagenomics↗

PubMed1992

Adaptedness, evolution and a hierarchical concept of fitness.

Fitness is a consequence of the adaptedness of an entity to its environment. The fitness of an evolutionary entity, when the entity is defined by a set of attributes determining how it interacts with its environment, is manifested as persistence of those attributes. Two measures of fitness are presented to explicate this concept: (1) an extensive measure of the persistence of the original set of attributes in the individual entity and its descendants, but corrected for evolution; this includes as a special case fitness as used in population genetics; and, (2) an intensive measure that is independent of the abundance of descendant exemplars. Fitness as conceived here is a function of survival time, degree of evolution, and when applicable, reproductive contribution. The rate of fitness increase of an entity will vary inversely with the degree of evolutionary change experienced by the entity, its descendants, or both through time. Adaptive evolution can increase the length of time that fitness accumulates by increasing the survival of descendants possessing all or some of the ancestral attributes. Reproduction, where possible, can increase the number of descendants. This concept of fitness is simple, unambiguous, coherent, and applicable to entities at any hierarchical level of interest to ecologists and evolutionary biologists.

Adaptation, Physiological↗

PubMed1987

Towards a general theory of adaptive walks on rugged landscapes.

Adaptive evolution, to a large extent, is a complex combinatorial optimization process. In this article we take beginning steps towards developing a general theory of adaptive "walks" via fitter variants in such optimization processes. We introduce the basic idea of a space of entities, each a 1-mutant neighbor of many other entities in the space, and the idea of a fitness ascribed to each entity. Adaptive walks proceed from an initial entity, via fitter neighbors, to locally or globally optimal entities that are fitter than their neighbors. We develop a general theory for the number of local optima, lengths of adaptive walks, and the number of alternative local optima accessible from any given initial entity, for the baseline case of an uncorrelated fitness landscape. Most fitness landscapes are correlated, however. Therefore we develop parts of a universal theory of adaptation on correlated landscapes by adaptive processes that have sufficient numbers of mutations per individual to "jump beyond" the correlation lengths in the underlying landscape. In addition, we explore the statistical character of adaptive walks in two independent complex combinatorial optimization problems, that of evolving a specific cell type in model genetic networks, and that of finding good solutions to the traveling salesman problem. Surprisingly, both show similar statistical features, encouraging the hope that a general theory for adaptive walks on correlated and uncorrelated landscapes can be found. In the final section we explore two limits to the efficacy of selection. The first is new, and surprising: for a wide class of systems, as the complexity of the entities under selection increases, the local optima that are attainable fall progressively closer to the mean properties of the underlying space of entities. This may imply that complex biological systems, such as genetic regulatory systems, are "close" to the mean properties of the ensemble of genomic regulatory systems explored by evolution. The second limit shows that with increasing complexity and a fixed mutation rate, selection often becomes unable to pull an adapting population to those local optima to which connected adaptive walks via fitter variants exist. These beginning steps in theory development are applied to maturation of the immune response, and to the problem of radiation and stasis. Despite the limitations of the adaptive landscape metaphor, we believe that further development along the lines begun here will prove useful.

Adaptation, Biological↗

PubMed1989

Selection, adaptation, and bacterial operons.

Bacteria are especially useful as systems to study the molecular basis of adaptive evolution. Selection for novel metabolic capabilities has allowed us to study the evolutionary potential of organisms and has shown that there are three major "strategies" for the evolution of new metabolic functions. (i) Regulatory mutations may allow a gene to be expressed under unusual conditions. If the product of that gene is already active toward a novel resource, then a regulatory mutation alone may confer a new metabolic capability. (ii) Structural gene mutations may alter the catalytic properties of enzymes so that they can act on novel substrates. These structural gene mutations may dramatically improve catalytic capabilities, and in some cases they can confer entirely new capabilities upon enzymes. In most cases both regulatory and structural gene mutations are required for the effective evolution of new metabolic functions. (iii) Operons that are normally silent, or cryptic, may be activated by either point mutations or by the action of mobile genetic elements. When activated, these operons can provide entirely new pathways for the metabolism of novel resources. Selection can also play a role in modulating the probability that a particular adaptive mutation will occur. In this paper I present evidence that a specific adaptive mutation, reversion of the metB1 mutation, occurs 60 to 80 times more frequently during prolonged selection on plates under conditions where the members of the population are not growing than it does in growing cells under nonselective conditions. This selective condition, methionine starvation, does not increase the frequency of other mutations unrelated to methionine biosynthesis.(ABSTRACT TRUNCATED AT 250 WORDS)

Adaptation, Biological↗

PubMed2026

The Adaptive Roles of Active Transposable Elements in Insect Hosts.

Active transposable elements (TEs) are capable of generating new insertions in genomes and have historically been viewed as genomic parasites due to their largely detrimental or neutral effects. However, emerging evidence suggests that these elements also play a crucial role in driving adaptive evolution in insects. This mini-review synthesizes recent findings on how active TEs contribute to insect adaptation through various mechanisms, including regulation of gene expression, structural variation, and epigenetic effects. Notable examples of adaptation driven by active TEs include their roles in insecticide resistance, morphological adaptations, tolerance to harsh climates, and antiviral immune responses. We argue that while host silencing mechanisms, such as the piRNA pathway, tightly regulate TE activity to minimize harmful effects, the context-dependent activation of active TEs can generate beneficial genetic variation that enhances insect adaptations to anthropogenic and climatic pressures. Future research that integrates long-read sequencing, single-cell omics, and gene editing techniques will provide a robust mechanistic foundation for understanding the adaptive significance of active TEs in insects, with important implications for pest management, pollinator protection, and evolutionary biology.

Journal Article↗

PubMed2025

Distinct evolutionary trajectories of subgenomic centromeres in polyploid wheat.

BACKGROUND: Centromeres are crucial for precise chromosome segregation and maintaining genome stability during cell division. However, their evolutionary dynamics, particularly in polyploid organisms with complex genomic architectures, remain largely enigmatic. Allopolyploid wheat, with its well-defined hierarchical ploidy series and recent polyploidization history, serves as an excellent model to explore centromere evolution. RESULTS: In this study, we perform a systematic comparative analysis of centromeres in common wheat and its corresponding ancestral species, utilizing the latest comprehensive reference genome assembly available. Our findings reveal that wheat centromeres predominantly consist of five types of centromeric-specific retrotransposon elements (CRWs), with CRW1 and CRW2 being the most prevalent. We identify distinct evolutionary trajectories in the functional centromeres of each subgenome, characterized by variations in copy number, insertion age, and CRW composition. By utilizing CENH3-ChIP data across various ploidy levels, we uncover a series of CRW invasion events that have shaped the evolution of AA subgenome centromeres. Conversely, the evolutionary process of the DD subgenome centromeres involves their expansion from diploid to hexaploid wheat, facilitating adaptation to a larger genomic context. Integration of complete einkorn centromere assemblies and Aegilops tauschii pan-genomes further revealed subgenome-specific centromere evolutionary trajectories. By inclusion of synthetic hexaploid from S2-S3 generations, alongside 2x/6 × natural accessions, we demonstrate that DD subgenome centromere expansion represents a gradual evolutionary process rather than an immediate response to polyploidization. CONCLUSIONS: Our study provides a comprehensive landscape of centromere adaptation, evolution, and maturation, along with insights into how retrotransposon invasions drive centromere evolution in polyploid wheat.

Centromere↗

PubMed2025

Host-Associated Genetic Differentiation in the Face of Ongoing Gene Flow: Ecological Speciation in a Pathogenic Parasite of Freshwater Fish.

Adaptive evolution in response to varying environments, leading to population divergence, is among the most intriguing processes of speciation. However, the extent to which these adaptive processes effectively drive population divergence amidst ongoing gene flow remains controversial. Our study addresses this by analyzing population genetic structure, gene flow, and genomic divergence between lineages of a tapeworm parasite (Ligula intestinalis) isolated from sympatric fish hosts. This parasite, which must overcome host immunological defenses for successful infection, significantly impacts host health. Utilizing genome-wide Single Nucleotide Polymorphisms (SNPs) and transcriptome data, we investigated whether host species impose distinct selection pressures on parasite populations. Genetic clustering analyses revealed clear divergence, with parasites from bream (Abramis brama) forming a distinct genetic cluster separate from those infecting roach (Rutilus rutilus), rudd (Scardinius erythrophthalmus), and bleak (Alburnus alburnus). Demographic modeling indicated isolation with continuous gene flow as the most plausible scenario for this divergence. Selection analyses identified 896 SNPs under selection, displaying low to moderate nucleotide diversity and genetic divergence compared with neutral loci. Transcriptome profiling supported these findings, revealing distinct gene expression profiles between parasite populations. Examination of selected SNPs and differentially expressed genes identified candidate genes linked to immune evasion mechanisms, potentially driving ecological speciation. This research highlights the interplay of host specificity, population demography, and disruptive selection in ecological speciation. By dissecting genomic factors, our study improves the understanding of mechanisms facilitating population divergence despite ongoing gene flow.

Animals↗

PubMed2026

Haplotype-resolved genome of Forsythia suspensa reveals the reticulate evolution in Oleaceae and a novel gene cluster regulating stamen development.

The olive family (Oleaceae) comprises numerous species of economic, horticultural, and medicinal importance. Despite its significance, the evolutionary history of this complex family remains enigmatic. Here, we generated a high-quality haplotype-resolved genome of Forsythia suspensa, a distylous species that occupies a key phylogenetic position in Oleaceae. The 2 haplotypes exhibit significant allelic divergence with potential allele-specific regulation. We reconstructed the polyploidization history of Oleaceae by confirming and precisely dating a shared whole-genome triplication and an independent whole-genome duplication event. We revealed a complex reticulate evolution that gave rise to the tribe Oleeae: an initial hybridization between Forsythieae (♂) and Jasmineae (♀), a subsequent backcrossing event, and a final whole-genome duplication. We identified a novel tandemly duplicated pectin methylesterase inhibitor gene cluster that regulates filament length and pollen size via restricting cell elongation in the long-styled morph. Dosage augmentation via stepwise cluster formation (0.99 to 3.83 Mya) may contribute to maintaining stamen traits of the long-styled morph. These FsPMEIs are co-expressed with many cell wall-related genes, suggesting a functional link in cell wall modification. Our study reveals the reticulate evolution in Oleaceae and a novel gene cluster controlling stamen development in F. suspensa and provides valuable haplotype-resolved genomic resources for heterostylous species, offering novel framework and molecular pathways to understand plant adaptive evolution.

Forsythia↗

PubMed1991

Influence of tension reduction and peripheral dissection on histologic, biochemical and bioenergetic profiles, and kinetics of skeletal muscle fast-to-slow transformation.

Seven goat latissimus dorsi muscles were submitted to a progressive electrostimulation program through intramuscular electrodes (Medtronic SP5528). Group 1 (n = 3) consisted of muscles stimulated in situ, and group 2 (n = 4), of muscles dissected distally and reinserted on the chest wall with a reduced tension. In group 1, complete fiber switch from type II to I occurred within 60-100 days after the beginning of stimulation, as demonstrated by myosin isoforms and lactate dehydrogenase (LDH) isozymes pattern. Respiratory chain oxidases first increased within 30-70 days after stimulation, then progressively decreased to stabilized values, higher than the basal ones. Total LDH activity showed progressive decrease to one-fifth of the initial value. Morphological analysis confirmed the structural integrity and physical reinforcement of the muscles. In group 2, respiratory chain oxidases showed initial increase followed first by a fast reduction to values less than the starting ones, and then by a slow secondary increase between day 40 and 90. LDH activity displayed a sharp decrease between day 15 and 36. Myosin as well as LDH isoforms showed progressive conversion. This kinetic study suggests a three-phase adaptative evolution of the goat latissimus dorsi submitted to increased workload (group 1): a fast increase (phase I) in oxidative capacities is followed by the development of an efficient contractile machinery (phase II), with subsequent adaptation (phase III) of the terminal chemosmotic enzymes involved in energy production.+2

Adaptation, Physiological↗

PubMed2026

Spatially resolved single-cell atlas reveals the macroevolutionary trajectory of animal hearts.

Animal hearts display diverse anatomical structures during adaptive evolution. Here, we present a multiomics atlas of adult hearts from 27 species across chordates, arthropods, and mollusks. Joint analysis indicates that Bilateria hearts share a core gene repertoire, taking a stepwise "add-on" approach as a universal evolutionary strategy. The "proto-heart" is populated by key cell types, including cardiomyocytes, fibroblasts, endothelial cells, and neural cells, which maintained core signatures while evolving with shifts in living environments and corresponding adaptations in the cardiovascular system. Additionally, we reveal an evolutionarily conserved cardiomyocyte state dynamic potentially linked to cardiac development and stress responses. Finally, we identify a common molecular program underpinning chamber evolution from a ventricular foundation. This work establishes a resource for understanding the intrinsic mechanisms of heart evolution.

Animals↗

PubMed2026

Chromosome-Level Genome Assembly and Annotation of the Chinese Lizard Gudgeon (Saurogobio dabryi).

The Chinese lizard gudgeon (Saurogobio dabryi) is an economically important freshwater species within the Cyprinidae family, abundant in the middle and lower reaches of the Yangtze River and its adjacent basins. As a promising species suitable for aquaculture in China, the lack of genomic resources has rendered the genetic breeding and conservation research. Here, we present the first chromosome-level genome assembly of S. dabryi using PacBio HiFi long reads, short reads, and Hi-C sequencing data. The final assembly reaches a total size of 1.09 Gb and Hi-C scaffolding anchors 99.55% of the assembled contigs onto 25 chromosomes, with a scaffold N50 reaching 43.15 Mb. The final genome assembly shows a BUSCO completeness of 98.39%. We annotated 659.55 Mb repetitive sequences and 26,036 protein-coding genes, 99.47% of which are functionally annotated. Comparative phylogenomic analysis clarifies the phylogenetic position of Saurogobio within Gobioninae. This high-quality genome provides a critical genetic basis for exploring cyprinid phylogeny, benthic adaptive evolution, genetic improvement, and conservation efforts of S. dabryi.

Saurogobio dabryi↗

PubMed1992

Transgenic animal studies on the evolution of genetic regulatory circuitries.

The ability to transfer genes from one species to another provides a powerful method to study genetic regulatory differences between species in a homogeneous genetic background. A survey of several transgenic animal experiments indicates that the vast majority of regulatory differences observed between species are due to differences in the cis-acting elements associated with the genes under study. A corollary is that in almost all cases the host species provides the necessary regulatory proteins for expression of the transgenes in specific tissues in which the endogenous homolog is not expressed. Although the details of the cis-acting differences are unknown for most cases, it appears that these differences may consist of the acquisition or loss of unique elements or subtle variation of conserved elements. It is unknown whether much of this variation is directly related to adaptive evolution. The identification of the promoter/enhancer elements responsible for these differences is an important first step in examining the functional significance of this variation.

Animals↗

PubMed2025

Chromosome-level genome assembly of an Arctic fish species pale eelpout (Lycodes pallidus).

Eelpouts (Zoarcidae) are known for their bipolar distributions and distinctive biogeographic histories. However, limited genomic data have hindered our understanding of their adaptive evolution. In this study, we present a thoroughly annotated chromosome-level genome assembly of pale eelpout (Lycodes pallidus) generated through the integration of Illumina, PacBio circular consensus, and Hi-C sequencing techniques. The final assembly spans 753.4 Mb, with its high quality confirmed by a scaffold N50 of 28.6 Mb and a Benchmarking Universal Single-Copy Ortholog (BUSCO) completeness of 99.3%. In comparison to other eelpouts and related fishes, the L. pallidus genome is larger and exhibits greater repetitive element content, accounting for approximately 45% of its total length. We annotated 21,419 protein-coding genes, a significant proportion of which are involved in signal transduction mechanisms and transcription. These findings provide valuable genetic resources for elucidating the evolutionary mechanisms underlying polar fish adaptation.

Animals↗

PubMed1989

The NK model of rugged fitness landscapes and its application to maturation of the immune response.

Adaptive evolution is, to a large extent, a complex combinatorial optimization process. Such processes can be characterized as "uphill walks on rugged fitness landscapes". Concrete examples of fitness landscapes include the distribution of any specific functional property such as the capacity to catalyze a specific reaction, or bind a specific ligand, in "protein space". In particular, the property might be the affinity of all possible antibody molecules for a specific antigenic determinant. That affinity landscape presumably plays a critical role in maturation of the immune response. In this process, hypermutation and clonal selection act to select antibody V region mutant variants with successively higher affinity for the immunizing antigen. The actual statistical structure of affinity landscapes, although knowable, is currently unknown. Here, we analyze a class of mathematical models we call NK models. We show that these models capture significant features of the maturation of the immune response, which is currently thought to share features with general protein evolution. The NK models have the important property that, as the parameter K increases, the "ruggedness" of the NK landscape varies from a single peaked "Fujiyama" landscape to a multi-peaked "badlands" landscape. Walks to local optima on such landscapes become shorter as K increases. This fact allows us to choose a value of K that corresponds to the experimentally observed number of mutational "steps", 6-8, taken as an antibody sequence matures. If the mature antibody is taken to correspond to a local optimum in the model, tuning the model requires that K be about 40, implying that the functional contribution of each amino acid in the V region is affected by about 40 others. Given this value of K, the model then predicts several features of "antibody space" that are in qualitative agreement with experiment: (1) The fraction of fitter variants of an initial "roughed in" germ line antibody amplified by clonal selection is about 1-2%. (2) Mutations at some sites of the mature antibody hardly affect antibody function at all, but mutations at other sites dramatically decrease function. (3) The same "roughed in" antibody sequence can "walk" to many mature antibody sequences. (4) Many adaptive walks can end on the same local optimum. (5) Comparison of different mature sequences derived from the same initial V region shows evolutionary hot spots and parallel mutations. All these predictions are open to detailed testing by obtaining monoclonal antibodies early in the immune response and carrying out in vitro mutagenesis and adaptive hill climbing with respect to affinity for the immunizing antigen.

Amino Acid Sequence↗

PubMed2026

A horizontally transferred bacterial gene for pantothenic acid biosynthesis regulates diapause and reproduction in the spider mite Amphitetranychus viennensis.

Horizontal gene transfer (HGT) has contributed substantially to the evolution of arthropod genomes, yet the functional significance of many horizontally acquired genes remains poorly understood. The hawthorn spider mite, Amphitetranychus viennensis, is a devastating agricultural pest whose high fecundity and overwintering diapause afford its exceptional ecological resilience. Through a genome-wide screen, we identified 37 high-confidence horizontally transferred genes (HTGs) in A. viennensis. Among these candidates, we prioritized AvPBL, a gene encoding pantothenate-β-alanine ligase, for functional characterization because it controls the rate-limiting step of a distinctly non-metazoan pantothenic acid (vitamin B5) biosynthesis pathway. RNAi-mediated suppression of AvPBL significantly reduced transcript abundance and endogenous pantothenic acid levels, triggering a 23.7% reduction in cumulative fecundity and severely compromising the mites' ability to enter winter diapause. Importantly, exogenous pantothenic acid supplementation rescued these reproductive and diapause defects, directly linking the observed phenotypes to the disruption of pantothenic acid biosynthesis. Our results demonstrate that the horizontally transferred bacterial gene AvPBL has been functionally integrated into the endogenous metabolic network of A. viennensis, playing a critical role in vitamin B5 biosynthesis, reproduction, and diapause regulation. These findings provide direct evidence that horizontally acquired metabolic genes can shape key life-history traits and drive adaptive evolution in arthropods.

Amphitetranychus viennensis↗

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↗