{"entity": "researcher", "timestamp": "2026-08-09T07:29:21.240Z", "family": "Liu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4580-5518", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/abd2de623f33467b89b1cf800db4b3f5.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/abd2de623f33467b89b1cf800db4b3f5"}}, "publications": [{"entity": "publication", "iuid": "eaf9b454889b42e98966f350d0a69e84", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eaf9b454889b42e98966f350d0a69e84.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eaf9b454889b42e98966f350d0a69e84"}}, "title": "A mosaic of modular variation at a single gene underpins convergent plumage coloration.", "authors": [{"family": "Lutgen", "given": "Dave", "initials": "D", "orcid": "0000-0003-0793-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/68173a10b32e4dca953933b92e0cec4e.json"}}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Chase", "given": "Madeline A", "initials": "MA", "orcid": "0000-0002-7916-3560", "researcher": {"href": "https://publications.scilifelab.se/researcher/3053121df4b64418bc1dcc2d7e50d87c.json"}}, {"family": "Kakhki", "given": "Niloofar Alaei", "initials": "NA"}, {"family": "Lammers", "given": "Fritjof", "initials": "F", "orcid": "0000-0002-3110-8220", "researcher": {"href": "https://publications.scilifelab.se/researcher/40a13a19d3594543a30c5146011aaa3a.json"}}, {"family": "de Souza", "given": "Stacey G", "initials": "SG", "orcid": "0000-0001-6596-5522", "researcher": {"href": "https://publications.scilifelab.se/researcher/63b19ded18de4742b8b0e63408500bc7.json"}}, {"family": "Ducrest", "given": "Anne-Lyse", "initials": "AL", "orcid": "0000-0001-6412-2769", "researcher": {"href": "https://publications.scilifelab.se/researcher/020a4c63ac834ff1a09234094ff552d2.json"}}, {"family": "Burri", "given": "Marta", "initials": "M"}, {"family": "Andriopoulos", "given": "Pavlos", "initials": "P", "orcid": "0000-0002-5377-2974", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef8407f9cb79440d80f580cef8536175.json"}}, {"family": "Lukhele", "given": "Sifiso M", "initials": "SM", "orcid": "0000-0003-0638-0641", "researcher": {"href": "https://publications.scilifelab.se/researcher/67a4a265644e452898bd89600ca081d8.json"}}, {"family": "Moysi", "given": "Michaella", "initials": "M"}, {"family": "Yohannes", "given": "Elizabeth", "initials": "E"}, {"family": "Abbasov", "given": "Abdin", "initials": "A", "orcid": "0009-0002-6370-9167", "researcher": {"href": "https://publications.scilifelab.se/researcher/de8b1ae2193849cc956e9750bfc47ead.json"}}, {"family": "Albayrak", "given": "Tamer", "initials": "T", "orcid": "0000-0003-4115-3946", "researcher": {"href": "https://publications.scilifelab.se/researcher/36f1ec59f0da42d89af256efda6c7db5.json"}}, {"family": "Aliabadian", "given": "Mansour", "initials": "M", "orcid": "0000-0002-3200-4853", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf133d36d2ec42bba680538cd5e69151.json"}}, {"family": "Auchli", "given": "Nicolas", "initials": "N"}, {"family": "Bontzorlos", "given": "Vasileios", "initials": "V", "orcid": "0000-0002-1276-3385", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebafa22103ec46ab87ce2b5fa878519d.json"}}, {"family": "Christoforou", "given": "Ioulios", "initials": "I"}, {"family": "Copete", "given": "Jos\u00e9 Luis", "initials": "JL", "orcid": "0000-0001-8542-0351", "researcher": {"href": "https://publications.scilifelab.se/researcher/e18b36757e804e0fb00a2f13015e79b6.json"}}, {"family": "Fulco", "given": "Egidio", "initials": "E"}, {"family": "Garcia", "given": "Jesus T", "initials": "JT"}, {"family": "Javakhishvili", "given": "Zura", "initials": "Z", "orcid": "0000-0001-7587-4974", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15c16f36f8d407d8b3c69723f6470e2.json"}}, {"family": "Kazazou", "given": "Anna", "initials": "A", "orcid": "0009-0003-6518-8833", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcdef2602fe44fd98f1b36f83acde23a.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F", "orcid": "0000-0001-9920-8167", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e9cc44c016c4d099f674d182c08fbaa.json"}}, {"family": "Liu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4580-5518", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd2de623f33467b89b1cf800db4b3f5.json"}}, {"family": "Paposhvili", "given": "Nika", "initials": "N"}, {"family": "Patchett", "given": "Robert", "initials": "R", "orcid": "0000-0003-4105-3136", "researcher": {"href": "https://publications.scilifelab.se/researcher/787404ed66114f6ca1df945d9110ca8a.json"}}, {"family": "P\u00e9ter", "given": "\u00c1ron", "initials": "\u00c1", "orcid": "0000-0003-3219-9344", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b840805e45a4e0e95ade7ce7d0bdb99.json"}}, {"family": "Ritter", "given": "Raphael", "initials": "R", "orcid": "0009-0000-3060-1622", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b0db805e7214250b7df8d01e0803641.json"}}, {"family": "S\u00e1ndor", "given": "Attila D", "initials": "AD", "orcid": "0000-0001-8852-8341", "researcher": {"href": "https://publications.scilifelab.se/researcher/6db813f6be6943cc93dfbb9222bd112f.json"}}, {"family": "Schneider", "given": "Fabian", "initials": "F"}, {"family": "Shurulinkov", "given": "Petar", "initials": "P"}, {"family": "Sklyarenko", "given": "Sergey", "initials": "S", "orcid": "0000-0002-7443-347X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0de4c8591f1b4929ae73d3ea81ca2c17.json"}}, {"family": "Stumberger", "given": "Borut", "initials": "B"}, {"family": "Tagiyev", "given": "Abulfaz", "initials": "A"}, {"family": "Uboldi", "given": "Alessia", "initials": "A", "orcid": "0009-0001-3940-3697", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c73538105e441eb6a5402ad0883799.json"}}, {"family": "Vogiatzis", "given": "Nikitas", "initials": "N", "orcid": "0009-0008-9592-923X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9be0f74759fd4d429c3cb891c51d6e83.json"}}, {"family": "Taborsak-Lines", "given": "Fanny", "initials": "F"}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Yao", "given": "Liqun", "initials": "L"}, {"family": "Peichel", "given": "Catherine L", "initials": "CL", "orcid": "0000-0002-7731-8944", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b4d7c680f69458dbde56257ff4820c5.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Gagnaire", "given": "Pierre-Alexandre", "initials": "PA", "orcid": "0000-0002-1908-3235", "researcher": {"href": "https://publications.scilifelab.se/researcher/10f9487cea1d40938b3f9f00f72e6433.json"}}, {"family": "Kirschel", "given": "Alexander N G", "initials": "ANG", "orcid": "0000-0003-4379-7956", "researcher": {"href": "https://publications.scilifelab.se/researcher/d533e6378c094ef7bf44e570bcbb1145.json"}}, {"family": "Schweizer", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7555-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a043d6f016b46709ace7f181d8cd3b8.json"}}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d7e24b36a24560bafa92f08848ac46.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f21e70e2864b42ab9fc532c14c069c.json"}}], "type": "journal article", "published": "2025-10-16", "journal": {"title": "Science", "issn": "1095-9203", "volume": "390", "issue": "6770", "pages": "eado8005", "issn-l": "0036-8075"}, "abstract": "The reshuffling of genomic variation from multiple origins is an important contributor to phenotypic diversification, yet insights into the evolutionary trajectories of this combinatorial process and their interplay with genetic architecture remain scarce. We show that convergent plumage color evolution in wheatears involves a monogenic architecture with modular variation introgressed at the agouti signaling protein (ASIP) locus. Introgression of a new transposable element insertion and linked protein-coding variation underpin a transspecific throat color polymorphism, which stable isotopes suggest is associated with alternative foraging niches. Cointrogression of linked regulatory ASIP variation resulted in mantle color convergence in one species, whereas convergent color evolution at the genus level required new variation. Our results demonstrate evolutionary trajectories from introgressed variation realized within the constraints of a monogenic architecture.", "doi": "10.1126/science.ado8005", "pmid": "41100596", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Short read": "Service", "NGI Other": "Service"}, "xrefs": [], "notes": [], "created": "2026-01-26T14:53:27.788Z", "modified": "2026-01-26T14:53:31.469Z"}, {"entity": "publication", "iuid": "57d336fde81e4a409b232134a6c24a50", "links": {"self": {"href": "https://publications.scilifelab.se/publication/57d336fde81e4a409b232134a6c24a50.json"}, "display": {"href": "https://publications.scilifelab.se/publication/57d336fde81e4a409b232134a6c24a50"}}, "title": "Low mutation load in a supergene underpinning alternative male mating strategies in ruff (Calidris pugnax).", "authors": [{"family": "Hill", "given": "Jason", "initials": "J", "orcid": "0000-0002-0151-8931", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2cb6f3cce5f4919959e18074d51256d.json"}}, {"family": "Enbody", "given": "Erik D", "initials": "ED", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Bi", "given": "Huijuan", "initials": "H"}, {"family": "Lamichhaney", "given": "Sangeet", "initials": "S"}, {"family": "Lei", "given": "Weipan", "initials": "W"}, {"family": "Chen", "given": "Juexin", "initials": "J"}, {"family": "Wei", "given": "Chentao", "initials": "C"}, {"family": "Liu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4580-5518", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd2de623f33467b89b1cf800db4b3f5.json"}}, {"family": "Schwochow", "given": "Doreen", "initials": "D"}, {"family": "Younis", "given": "Shady", "initials": "S"}, {"family": "Widemo", "given": "Fredrik", "initials": "F"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2023-10-06", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "40", "issue": "12", "pages": "msad224"}, "abstract": "A paradox in evolutionary biology is how supergenes can maintain high fitness despite reduced effective population size, the suppression of recombination, and the expected accumulation of mutational load. The ruff supergene involves two rare inversion haplotypes (Satellite and Faeder). These are recessive lethals but with dominant effects on male mating strategies, plumage, and body size. Sequence divergence to the wild-type (Independent) haplotype indicates that the inversion could be as old as 4 million years. Here we have constructed a highly contiguous genome assembly of the inversion region for both the Independent and Satellite haplotypes. Based on the new data we estimate that the recombination event(s) creating the Satellite haplotype occurred only about 70,000 years ago. Contrary to expectations for supergenes, we find no substantial expansion of repeats and only a modest mutation load on the Satellite and Faeder haplotypes despite high sequence divergence to the non-inverted haplotype (1.46%). The essential centromere protein N gene CENPN is disrupted by the inversion, and is as well conserved on the inversion haplotypes as on the noninversion haplotype. These results suggest that the inversion may be much younger than previously thought. The low mutation load, despite recessive lethality, may be explained by the introgression of the inversion from a now extinct lineage.", "doi": "10.1093/molbev/msad224", "pmid": "37804117", "labels": {"NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7296052"}], "notes": [], "created": "2023-10-10T08:45:20.886Z", "modified": "2024-01-16T13:48:31.996Z"}, {"entity": "publication", "iuid": "838e0b3db3344e009deafc5bec93347c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/838e0b3db3344e009deafc5bec93347c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/838e0b3db3344e009deafc5bec93347c"}}, "title": "Introgression underlies phylogenetic uncertainty but not parallel plumage evolution in a recent songbird radiation.", "authors": [{"family": "Rancilhac", "given": "Lo\u00efs", "initials": "L", "orcid": "0000-0002-9859-1448", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3a53ef0421c4c0990fbf9ef20f6bd3b.json"}}, {"family": "Enbody", "given": "Erik D", "initials": "ED"}, {"family": "Harris", "given": "Rebecca", "initials": "R"}, {"family": "Saitoh", "given": "Takema", "initials": "T"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Liu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4580-5518", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd2de623f33467b89b1cf800db4b3f5.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Alstr\u00f6m", "given": "Per", "initials": "P", "orcid": "0000-0001-7182-2763", "researcher": {"href": "https://publications.scilifelab.se/researcher/f426ea7151c546939b707d5ed71e7d04.json"}}], "type": "journal article", "published": "2023-10-06", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "issn-l": "1063-5157", "volume": null, "issue": null, "pages": null}, "abstract": "Instances of parallel phenotypic evolution offer great opportunities to understand the evolutionary processes underlying phenotypic changes. However, confirming parallel phenotypic evolution and studying its causes requires a robust phylogenetic framework. One such example is the \"black-and-white wagtails\", a group of five species in the songbird genus Motacilla: one species, Motacilla alba, shows wide intra-specific plumage variation, while the four others form two pairs of very similar-looking species (M. aguimp + M. samveasnae and M. grandis + M. maderaspatensis, respectively). However, the two species in each of these pairs were not recovered as sisters in previous phylogenetic inferences. Their relationships varied depending on the markers used, suggesting that gene tree heterogeneity might have hampered accurate phylogenetic inference. Here, we use whole genome resequencing data to explore the phylogenetic relationships within this group, with a special emphasis on characterizing the extent of gene tree heterogeneity and its underlying causes. We first used multispecies coalescent methods to generate a \"complete evidence\" phylogenetic hypothesis based on genome-wide variants, while accounting for incomplete lineage sorting (ILS) and introgression. We then investigated the variation in phylogenetic signal across the genome, to quantify the extent of discordance across genomic regions, and test its underlying causes. We found that wagtail genomes are mosaics of regions supporting variable genealogies, because of ILS and inter-specific introgression. The most common topology across the genome, supporting M. alba and M. aguimp as sister species, appears to be influenced by ancient introgression. Additionally, we inferred another ancient introgression event, between M. alba and M. grandis. By combining results from multiple analyses, we propose a phylogenetic network for the black-and-white wagtails that confirms that similar phenotypes evolved in non-sister lineages, supporting parallel plumage evolution. Furthermore, the inferred reticulations do not connect species with similar plumage coloration, suggesting that introgression does not underlie parallel plumage evolution in this group. Our results demonstrate the importance of investigation of genome-wide patterns of gene tree heterogeneity to help understanding the mechanisms underlying phenotypic evolution.", "doi": "10.1093/sysbio/syad062", "pmid": "37801684", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7294611"}], "notes": [], "created": "2023-10-19T13:54:24.722Z", "modified": "2024-01-16T13:48:32.004Z"}, {"entity": "publication", "iuid": "74edcc5b9fba41868b68c733c017e739", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74edcc5b9fba41868b68c733c017e739.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74edcc5b9fba41868b68c733c017e739"}}, "title": "Seasonal migration patterns and the maintenance of evolutionary diversity in a cryptic bird radiation.", "authors": [{"family": "Tang", "given": "Qindong", "initials": "Q"}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f21e70e2864b42ab9fc532c14c069c.json"}}, {"family": "Liu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4580-5518", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd2de623f33467b89b1cf800db4b3f5.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Sundev", "given": "Gombobaatar", "initials": "G"}, {"family": "Heckel", "given": "Gerald", "initials": "G", "orcid": "0000-0002-0162-323X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7865cb9352f5436da669b49f251a0430.json"}}, {"family": "Schweizer", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7555-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a043d6f016b46709ace7f181d8cd3b8.json"}}], "type": "journal article", "published": "2021-10-21", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083"}, "abstract": "Morphological differentiation associated with evolutionary diversification is often explained with adaptive benefits but the processes and mechanisms maintaining cryptic diversity are still poorly understood. Using genome-wide data, we show here that the pale sand martin Riparia diluta in Central and East Asia consists of three genetically deeply differentiated lineages which vary only gradually in morphology but broadly reflect traditional taxonomy. We detected no signs of gene flow along the eastern edge of the Qinghai-Tibetan plateau between lowland south-eastern Chinese R. d. fohkienensis and high-altitude R. d. tibetana. Largely different breeding and migration timing between these low and high altitude populations as indicated by phenology data suggests that allochrony might act as prezygotic isolation mechanism in the area where their ranges abut. Mongolian populations of R. d. tibetana, however, displayed signs of limited mixed ancestries with Central Asian R. d. diluta. Their ranges meet in the area of a well-known avian migratory divide, where western lineages take a western migration route around the Qinghai-Tibetan plateau to winter quarters in South Asia, and eastern lineages take an eastern route to Southeast Asia. This might also be the case between western R. d. diluta and eastern R. d. tibetana as indicated by differing wintering grounds. We hypothesize that hybrids might have nonoptimal intermediate migration routes and selection against them might restrict gene flow. Although further potential isolation mechanisms might exist in the pale sand martin, our study points towards contrasting migration behaviour as an important factor in maintaining evolutionary diversity under morphological stasis.", "doi": "10.1111/mec.16241", "pmid": "34674334", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-12-06T13:49:42.335Z", "modified": "2024-01-16T13:48:38.214Z"}, {"entity": "publication", "iuid": "0cd1833de8764e41812f14260f5961b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0cd1833de8764e41812f14260f5961b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0cd1833de8764e41812f14260f5961b5"}}, "title": "Dense sampling of bird diversity increases power of comparative genomics.", "authors": 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"researcher": {"href": "https://publications.scilifelab.se/researcher/8c77b745d8b044d4aed9478d056be226.json"}}, {"family": "Haussler", "given": "David", "initials": "D", "orcid": "0000-0003-1533-4575", "researcher": {"href": "https://publications.scilifelab.se/researcher/de140026a4f24291be768e713e4881bb.json"}}, {"family": "Li", "given": "Qiye", "initials": "Q", "orcid": "0000-0002-5993-0312", "researcher": {"href": "https://publications.scilifelab.se/researcher/d807a3a13669425c9b00e4a2b7db672a.json"}}, {"family": "Yang", "given": "Huanming", "initials": "H"}, {"family": "Wang", "given": "Jian", "initials": "J"}, {"family": "Lei", "given": "Fumin", "initials": "F"}, {"family": "Rahbek", "given": "Carsten", "initials": "C"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/873e2383b99a43d7848bf387264cf0e8.json"}}, {"family": "Graves", "given": "Gary R", "initials": "GR", "orcid": "0000-0003-1406-5246", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc3b9edee185456d971f5b596c3086fe.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications.scilifelab.se/researcher/956ebe9c0b6e43d7ac2a568519f43431.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8.json"}}], "type": "journal article", "published": "2020-11-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "587", "issue": "7833", "pages": "252-257", "issn-l": "0028-0836"}, "abstract": "Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.", "doi": "10.1038/s41586-020-2873-9", "pmid": "33177665", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-020-2873-9"}, {"db": "pmc", "key": "PMC7759463"}], "notes": [], "created": "2020-12-07T16:36:44.079Z", "modified": "2021-11-10T12:45:51.851Z"}]}