{"entity": "researcher", "timestamp": "2026-07-13T09:23:48.825Z", "family": "Qu", "given": "Yanhua", "initials": "Y", "orcid": "0000-0002-4590-7787", "affiliations": ["Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, 10405, Stockholm, Sweden", "Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China"], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/0443a97c3d564c49bc9361368ea2e20a.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/0443a97c3d564c49bc9361368ea2e20a"}}, "publications": [{"entity": "publication", "iuid": "d4835bd8e2744419b81fc0ab88ed052a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d4835bd8e2744419b81fc0ab88ed052a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d4835bd8e2744419b81fc0ab88ed052a"}}, "title": "Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae).", "authors": [{"family": "Jiang", "given": "Zhiyong", "initials": "Z"}, {"family": "Zang", "given": "Wenqing", "initials": "W"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Song", "given": "Gang", "initials": "G"}, {"family": "Wu", "given": "Shaoyuan", "initials": "S"}, {"family": "Feng", "given": "Shaohong", "initials": "S"}, {"family": "Drovetski", "given": "Sergei V", "initials": "SV"}, {"family": "Liu", "given": "Gang", "initials": "G"}, {"family": "Zhang", "given": "Dezhi", "initials": "D"}, {"family": "Saitoh", "given": "Takema", "initials": "T"}, {"family": "Alstr\u00f6m", "given": "Per", "initials": "P"}, {"family": "Edwards", "given": "Scott V", "initials": "SV"}, {"family": "Lei", "given": "Fumin", "initials": "F"}, {"family": "Qu", "given": "Yanhua", "initials": "Y", "orcid": "0000-0002-4590-7787", "researcher": {"href": "https://publications.scilifelab.se/researcher/0443a97c3d564c49bc9361368ea2e20a.json"}}], "type": "journal article", "published": "2024-02-27", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "22", "issue": "1", "pages": "49", "issn-l": "1741-7007"}, "abstract": "Resolving the phylogeny of rapidly radiating lineages presents a challenge when building the Tree of Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that rapidly diversified at the Pliocene-Pleistocene boundary.\n\nHere we investigate the phylogenetic relationships of all species of Prunellidae using a chromosome-level de novo assembly of Prunella strophiata and 36 high-coverage resequenced genomes. We use homologous alignments of thousands of exonic and intronic loci to build the coalescent and concatenated phylogenies and recover four different species trees. Topology tests show a large degree of gene tree-species tree discordance but only 40-54% of intronic gene trees and 36-75% of exonic genic trees can be explained by incomplete lineage sorting and gene tree estimation errors. Estimated branch lengths for three successive internal branches in the inferred species trees suggest the existence of an empirical anomaly zone. The most common topology recovered for species in this anomaly zone was not similar to any coalescent or concatenated inference phylogenies, suggesting presence of anomalous gene trees. However, this interpretation is complicated by the presence of gene flow because extensive introgression was detected among these species. When exploring tree topology distributions, introgression, and regional variation in recombination rate, we find that many autosomal regions contain signatures of introgression and thus may mislead phylogenetic inference. Conversely, the phylogenetic signal is concentrated to regions with low-recombination rate, such as the Z chromosome, which are also more resistant to interspecific introgression.\n\nCollectively, our results suggest that phylogenomic inference should consider the underlying genomic architecture to maximize the consistency of phylogenomic signal.", "doi": "10.1186/s12915-024-01848-7", "pmid": "38413944", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Other": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10900574"}, {"db": "pii", "key": "10.1186/s12915-024-01848-7"}], "notes": [], "created": "2024-03-14T11:10:52.935Z", "modified": "2024-11-25T10:30:32.973Z"}, {"entity": "publication", "iuid": "301efd49a74e490ea103f7210d81aa56", "links": {"self": {"href": "https://publications.scilifelab.se/publication/301efd49a74e490ea103f7210d81aa56.json"}, "display": {"href": "https://publications.scilifelab.se/publication/301efd49a74e490ea103f7210d81aa56"}}, "title": "A 14,000-year-old genome sheds light on the evolution and extinction of a Pleistocene vulture.", "authors": [{"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Zuccon", "given": "Dario", "initials": "D"}, {"family": "Larsson", "given": "Petter", "initials": "P"}, {"family": "Tison", "given": "Jean-Luc", "initials": "JL"}, {"family": "Emslie", "given": "Steven D", "initials": "SD"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Hume", "given": "Julian P", "initials": "JP"}, {"family": "Werdelin", "given": "Lars", "initials": "L"}, {"family": "Qu", "given": "Yanhua", "initials": "Y", "orcid": "0000-0002-4590-7787", "researcher": {"href": "https://publications.scilifelab.se/researcher/0443a97c3d564c49bc9361368ea2e20a.json"}}], "type": "journal article", "published": "2022-08-23", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "5", "issue": "1", "pages": "857"}, "abstract": "The New World Vulture [Coragyps] occidentalis (L. Miller, 1909) is one of many species that were extinct by the end of the Pleistocene. To understand its evolutionary history we sequenced the genome of a 14,000 year old [Coragyps] occidentalis found associated with megaherbivores in the Peruvian Andes. occidentalis has been viewed as the ancestor, or possibly sister, to the extant Black Vulture Coragyps atratus, but genomic data shows occidentalis to be deeply nested within the South American clade of atratus. Coragyps atratus inhabits lowlands, but the fossil record indicates that occidentalis mostly occupied high elevations. Our results suggest that occidentalis evolved from a population of atratus in southwestern South America that colonized the High Andes 300 to 400 kya. The morphological and morphometric differences between occidentalis and atratus may thus be explained by ecological diversification following from the natural selection imposed by this new and extreme, high elevation environment. The sudden evolution of a population with significantly larger body size and different anatomical proportions than atratus thus constitutes an example of punctuated evolution.", "doi": "10.1038/s42003-022-03811-0", "pmid": "35999361", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9399080"}, {"db": "pii", "key": "10.1038/s42003-022-03811-0"}, {"db": "Dryad", "key": "10.5061/dryad.qz612jmjm"}], "notes": [], "created": "2022-11-09T15:56:49.491Z", "modified": "2024-01-16T13:48:35.118Z"}, {"entity": "publication", "iuid": "8cbc18de608b493d87efccfa5a1ae454", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8cbc18de608b493d87efccfa5a1ae454.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8cbc18de608b493d87efccfa5a1ae454"}}, "title": "Genomic signatures of rapid adaptive divergence in a tropical montane species.", "authors": [{"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "She", "given": "Huishang", "initials": "H"}, {"family": "Qu", "given": "Yanhua", "initials": "Y", "orcid": "0000-0002-4590-7787", "researcher": {"href": "https://publications.scilifelab.se/researcher/0443a97c3d564c49bc9361368ea2e20a.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Biol. Lett.", "issn": "1744-957X", "volume": "17", "issue": "7", "pages": "20210089", "issn-l": "1744-9561"}, "abstract": "Mountain regions contain extraordinary biodiversity. The environmental heterogeneity and glacial cycles often accelerate speciation and adaptation of montane species, but how these processes influence the genomic differentiation of these species is largely unknown. Using a novel chromosome-level genome and population genomic comparisons, we study allopatric divergence and selection in an iconic bird living in a tropical mountain region in New Guinea, Archbold's bowerbird (Amblyornis papuensis). Our results show that the two populations inhabiting the eastern and western Central Range became isolated ca 11 800 years ago, probably because the suitable habitats for this cold-tolerating bird decreased when the climate got warmer. Our genomic scans detect that genes in highly divergent genomic regions are over-represented in developmental processes, which is probably associated with the observed differences in body size between the populations. Overall, our results suggest that environmental differences between the eastern and western Central Range probably drive adaptive divergence between them.", "doi": "10.1098/rsbl.2021.0089", "pmid": "34314643", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8315830"}, {"db": "Dryad", "key": "10.5061/dryad.37pvmcvjr"}], "notes": [], "created": "2021-10-01T09:03:17.400Z", "modified": "2024-01-16T13:48:39.285Z"}, {"entity": "publication", "iuid": "af1d860a40a54aff870af824f6fef807", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af1d860a40a54aff870af824f6fef807.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af1d860a40a54aff870af824f6fef807"}}, "title": "The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau.", "authors": [{"family": "Qu", "given": "Yanhua", "initials": "Y", "orcid": "0000-0002-4590-7787", "researcher": {"href": "https://publications.scilifelab.se/researcher/0443a97c3d564c49bc9361368ea2e20a.json"}}, {"family": "Chen", "given": "Chunhai", "initials": "C", "orcid": "0000-0002-2882-4517", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dd523248fd54ae299c069b960312115.json"}}, {"family": "Chen", "given": "Xiumin", "initials": "X"}, {"family": "Hao", "given": "Yan", "initials": "Y", "orcid": "0000-0002-1415-7610", "researcher": {"href": "https://publications.scilifelab.se/researcher/49c1a42ec6cf4f3f990220e6b4735bec.json"}}, {"family": "She", "given": "Huishang", "initials": "H", "orcid": "0000-0001-6259-7904", "researcher": {"href": "https://publications.scilifelab.se/researcher/a02a8db02a40437a87bd000b995d10c8.json"}}, {"family": "Wang", "given": "Mengxia", "initials": "M"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.json"}}, {"family": "Lin", "given": "Haiyan", "initials": "H", "orcid": "0000-0002-1623-9361", "researcher": {"href": "https://publications.scilifelab.se/researcher/e54d1bf82275458794a989de37b58480.json"}}, {"family": "Cai", "given": "Tianlong", "initials": "T"}, {"family": "Song", "given": "Gang", "initials": "G", "orcid": "0000-0002-0190-8315", "researcher": {"href": "https://publications.scilifelab.se/researcher/f133bb6165494dfaba8173b0e8191765.json"}}, {"family": "Jia", "given": "Chenxi", "initials": "C"}, {"family": "Chen", "given": "Chunyan", "initials": "C", "orcid": "0000-0002-2882-4517", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dd523248fd54ae299c069b960312115.json"}}, {"family": "Zhang", "given": "Hailin", "initials": "H"}, {"family": "Li", "given": "Jiang", "initials": "J", "orcid": "0000-0003-2099-8165", "researcher": {"href": "https://publications.scilifelab.se/researcher/b64bd87a57e0468b879e6361e79e3000.json"}}, {"family": "Liang", "given": "Liping", "initials": "L"}, {"family": "Wu", "given": "Tianyu", "initials": "T"}, {"family": "Zhao", "given": "Jinyang", "initials": "J", "orcid": "0000-0002-8150-044X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d41f239fe612446194498f9e5ed06321.json"}}, {"family": "Gao", "given": "Qiang", "initials": "Q", "orcid": "0000-0001-9880-4944", "researcher": {"href": "https://publications.scilifelab.se/researcher/faf3d20ec8344174a8c001bac7464421.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8.json"}}, {"family": "Zhai", "given": "Weiwei", "initials": "W", "orcid": "0000-0001-7938-0226", "researcher": {"href": "https://publications.scilifelab.se/researcher/e33e2ebb818449b9b95ba2484fccaa86.json"}}, {"family": "Zhang", "given": "Chi", "initials": "C"}, {"family": "Zhang", "given": "Yong E", "initials": "YE", "orcid": "0000-0003-3770-2383", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c91998c67674b75891a4473451916d6.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F", "orcid": "0000-0001-9920-8167", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e9cc44c016c4d099f674d182c08fbaa.json"}}], "type": "journal article", "published": "2021-03-30", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "13", "pages": "e2012398118", "issn-l": "0027-8424"}, "abstract": "Species in a shared environment tend to evolve similar adaptations under the influence of their phylogenetic context. Using snowfinches, a monophyletic group of passerine birds (Passeridae), we study the relative roles of ancestral and species-specific adaptations to an extreme high-elevation environment, the Qinghai-Tibet Plateau. Our ancestral trait reconstruction shows that the ancestral snowfinch occupied high elevations and had a larger body mass than most nonsnowfinches in Passeridae. Subsequently, this phenotypic adaptation diversified in the descendant species. By comparing high-quality genomes from representatives of the three phylogenetic lineages, we find that about 95% of genes under positive selection in the descendant species are different from those in the ancestor. Consistently, the biological functions enriched for these species differ from those of their ancestor to various degrees (semantic similarity values ranging from 0.27 to 0.5), suggesting that the three descendant species have evolved divergently from the initial adaptation in their common ancestor. Using a functional assay to a highly selective gene, DTL, we demonstrate that the nonsynonymous substitutions in the ancestor and descendant species have improved the repair capacity of ultraviolet-induced DNA damage. The repair kinetics of the DTL gene shows a twofold to fourfold variation across the ancestor and the descendants. Collectively, this study reveals an exceptional case of adaptive evolution to high-elevation environments, an evolutionary process with an initial adaptation in the common ancestor followed by adaptive diversification of the descendant species.", "doi": "10.1073/pnas.2012398118", "pmid": "33753478", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "2012398118"}, {"db": "pmc", "key": "PMC8020664"}], "notes": [], "created": "2021-06-09T12:15:45.569Z", "modified": "2024-01-16T13:48:40.345Z"}]}