T Brock Wooldridge, Merly Escalona, Blair W Perry, Alexis N Enstrom, Dalya Salih, William E Seligmann, Samuel Sacco, Katherine L Moon, Ruta Sahasrabudhe, Noravit Chumchim, Oanh Nguyen, Joanna L Kelley, Ross D E MacPhee, Beth Shapiro
{"title":"染色体尺度的基因组显示了熊类物种之间的快速多样化和古老的基因流动。","authors":"T Brock Wooldridge, Merly Escalona, Blair W Perry, Alexis N Enstrom, Dalya Salih, William E Seligmann, Samuel Sacco, Katherine L Moon, Ruta Sahasrabudhe, Noravit Chumchim, Oanh Nguyen, Joanna L Kelley, Ross D E MacPhee, Beth Shapiro","doi":"10.1093/gbe/evaf188","DOIUrl":null,"url":null,"abstract":"<p><p>Reconstructions of evolutionary history can be restricted by a lack of high quality reference genomes. To-date, only four of the eight species of bears (family Ursidae) have chromosome-level genome assemblies. Here, we present assemblies for three additional species - the sun, sloth, and spectacled bears - and use a whole-genome alignment of all bear species and other carnivores to reconstruct the evolution of Ursidae. Divergence dating based on patterns of coalescence indicates a more rapid diversification than previously reported, with a ∼19 Ma origin for all bears but a ∼3.3 Ma origin for the six species of the subfamily Ursinae. Surprisingly, we observe that nearly 50% of gene tree topologies conflict with our highly supported species tree, a pattern driven by a significant early hybridization event within Ursinae. We also find that the ancestral karyotype of Ursinae has remained largely conserved with the ancestral karyotype of all bears over roughly fifteen million years. In contrast to this stability, dozens of chromosomal fissions and fusions associated with LINE/L1 retrotransposons dramatically restructured the genomes of the giant panda and spectacled bear. Finally, we leverage these genomes to identify species-specific evidence for positive selection on genes associated with color, diet, and metabolism. One of these genes, TCPN2, has a role in pigmentation and shows a series of amino acid mutations in the polar bear over the last 0.5 Ma. Collectively, these new genomic resources enable improved reconstruction of the complex evolutionary history of bears and clarify how this enigmatic group diversified.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8000,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Chromosome-scale genomes show rapid diversification and ancient gene flow among bear species.\",\"authors\":\"T Brock Wooldridge, Merly Escalona, Blair W Perry, Alexis N Enstrom, Dalya Salih, William E Seligmann, Samuel Sacco, Katherine L Moon, Ruta Sahasrabudhe, Noravit Chumchim, Oanh Nguyen, Joanna L Kelley, Ross D E MacPhee, Beth Shapiro\",\"doi\":\"10.1093/gbe/evaf188\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Reconstructions of evolutionary history can be restricted by a lack of high quality reference genomes. To-date, only four of the eight species of bears (family Ursidae) have chromosome-level genome assemblies. Here, we present assemblies for three additional species - the sun, sloth, and spectacled bears - and use a whole-genome alignment of all bear species and other carnivores to reconstruct the evolution of Ursidae. Divergence dating based on patterns of coalescence indicates a more rapid diversification than previously reported, with a ∼19 Ma origin for all bears but a ∼3.3 Ma origin for the six species of the subfamily Ursinae. Surprisingly, we observe that nearly 50% of gene tree topologies conflict with our highly supported species tree, a pattern driven by a significant early hybridization event within Ursinae. We also find that the ancestral karyotype of Ursinae has remained largely conserved with the ancestral karyotype of all bears over roughly fifteen million years. In contrast to this stability, dozens of chromosomal fissions and fusions associated with LINE/L1 retrotransposons dramatically restructured the genomes of the giant panda and spectacled bear. Finally, we leverage these genomes to identify species-specific evidence for positive selection on genes associated with color, diet, and metabolism. One of these genes, TCPN2, has a role in pigmentation and shows a series of amino acid mutations in the polar bear over the last 0.5 Ma. Collectively, these new genomic resources enable improved reconstruction of the complex evolutionary history of bears and clarify how this enigmatic group diversified.</p>\",\"PeriodicalId\":12779,\"journal\":{\"name\":\"Genome Biology and Evolution\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":2.8000,\"publicationDate\":\"2025-10-06\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genome Biology and Evolution\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/gbe/evaf188\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"EVOLUTIONARY BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome Biology and Evolution","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/gbe/evaf188","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"EVOLUTIONARY BIOLOGY","Score":null,"Total":0}
Chromosome-scale genomes show rapid diversification and ancient gene flow among bear species.
Reconstructions of evolutionary history can be restricted by a lack of high quality reference genomes. To-date, only four of the eight species of bears (family Ursidae) have chromosome-level genome assemblies. Here, we present assemblies for three additional species - the sun, sloth, and spectacled bears - and use a whole-genome alignment of all bear species and other carnivores to reconstruct the evolution of Ursidae. Divergence dating based on patterns of coalescence indicates a more rapid diversification than previously reported, with a ∼19 Ma origin for all bears but a ∼3.3 Ma origin for the six species of the subfamily Ursinae. Surprisingly, we observe that nearly 50% of gene tree topologies conflict with our highly supported species tree, a pattern driven by a significant early hybridization event within Ursinae. We also find that the ancestral karyotype of Ursinae has remained largely conserved with the ancestral karyotype of all bears over roughly fifteen million years. In contrast to this stability, dozens of chromosomal fissions and fusions associated with LINE/L1 retrotransposons dramatically restructured the genomes of the giant panda and spectacled bear. Finally, we leverage these genomes to identify species-specific evidence for positive selection on genes associated with color, diet, and metabolism. One of these genes, TCPN2, has a role in pigmentation and shows a series of amino acid mutations in the polar bear over the last 0.5 Ma. Collectively, these new genomic resources enable improved reconstruction of the complex evolutionary history of bears and clarify how this enigmatic group diversified.
期刊介绍:
About the journal
Genome Biology and Evolution (GBE) publishes leading original research at the interface between evolutionary biology and genomics. Papers considered for publication report novel evolutionary findings that concern natural genome diversity, population genomics, the structure, function, organisation and expression of genomes, comparative genomics, proteomics, and environmental genomic interactions. Major evolutionary insights from the fields of computational biology, structural biology, developmental biology, and cell biology are also considered, as are theoretical advances in the field of genome evolution. GBE’s scope embraces genome-wide evolutionary investigations at all taxonomic levels and for all forms of life — within populations or across domains. Its aims are to further the understanding of genomes in their evolutionary context and further the understanding of evolution from a genome-wide perspective.