{"entity": "researcher", "timestamp": "2026-08-14T13:14:17.705Z", "family": "Reeve", "given": "Andrew Hart", "initials": "AH", "orcid": "0000-0001-5233-6030", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/c9c0cc8c4ff44848960ec2d43dce41d7.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/c9c0cc8c4ff44848960ec2d43dce41d7"}}, "publications": [{"entity": "publication", "iuid": "f74db641b67b4485b01bf07e453d5dd0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f74db641b67b4485b01bf07e453d5dd0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f74db641b67b4485b01bf07e453d5dd0"}}, "title": "Draft assemblies for 177 bird species enhance genus-level coverage", "authors": [{"family": "Chen", "given": "Guangji", "initials": "G", "orcid": "0000-0002-9441-1155", "researcher": {"href": "https://publications.scilifelab.se/researcher/19514f67b1504dc6b4b7d393e97f8cc0.json"}}, {"family": "Wang", "given": "Shuang", "initials": "S", "orcid": "0009-0008-9451-5684", "researcher": {"href": "https://publications.scilifelab.se/researcher/186a6001c26a403e8b0640a3cb516a1a.json"}}, {"family": "Bilyeli\u00a0\u00d8ksnebjerg", "given": "Daniel", "initials": "D"}, {"family": "Nielsen", "given": "Sascha Dreyer", "initials": "SD", "orcid": "0000-0003-2485-9314", "researcher": {"href": "https://publications.scilifelab.se/researcher/70ff8708bff74ea4b0c80c5f434329a8.json"}}, {"family": "Dai", "given": "Wei", "initials": "W", "orcid": "0000-0001-9286-759X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7c48f0de21d478ab23bc18b439472e0.json"}}, {"family": "Jiang", "given": "Wei", "initials": "W", "orcid": "0000-0003-1570-1208", "researcher": {"href": "https://publications.scilifelab.se/researcher/9908e45f950149e2963961d88783dabb.json"}}, {"family": "Liang", "given": "Jing", "initials": "J"}, {"family": "Han", "given": "Wei", "initials": "W"}, {"family": "Zhou", "given": "Chengran", "initials": "C", "orcid": "0000-0002-9468-5973", "researcher": {"href": "https://publications.scilifelab.se/researcher/49d36e1d73bb440184212119bf82858c.json"}}, {"family": "Li", "given": "Qiye", "initials": "Q", "orcid": "0000-0002-5993-0312", "researcher": {"href": "https://publications.scilifelab.se/researcher/d807a3a13669425c9b00e4a2b7db672a.json"}}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": "https://publications.scilifelab.se/researcher/62045d9b6dc443be936d3346daa4e1b1.json"}}, {"family": "Monadjem", "given": "Ara", "initials": "A", "orcid": "0000-0003-1906-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/94671b1f708d49f5b9eebc0e6b78b82e.json"}}, {"family": "Bhembe", "given": "Zamekile D", "initials": "ZD", "orcid": "0009-0006-5354-5751", "researcher": {"href": "https://publications.scilifelab.se/researcher/d276b65085fa48bdb17d12ecb8b014ac.json"}}, {"family": "Maphalala", "given": "Machawe", "initials": "M", "orcid": "0000-0002-9304-1391", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eebd8acec5a4084b64c3be4a3627b67.json"}}, {"family": "Ocampo", "given": "Diego", "initials": "D"}, {"family": "Sandoval", "given": "Luis", "initials": "L", "orcid": "0000-0002-0793-6747", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8f560d617c2432aa26f9700d2311ac1.json"}}, {"family": "Fickel", "given": "J\u00f6rns", "initials": "J", "orcid": "0000-0002-0593-5820", "researcher": {"href": "https://publications.scilifelab.se/researcher/40018134351a481ab2d00b4113404c47.json"}}, {"family": "Greenwood", "given": "Alex D", "initials": "AD", "orcid": "0000-0002-8249-1565", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab62cca19d7641918b6dd9adbff919c5.json"}}, {"family": "Szentiks", "given": "Claudia A", "initials": "CA"}, {"family": "Roller", "given": "Marco", "initials": "M"}, {"family": "Birks", "given": "Sharon M", "initials": "SM"}, {"family": "Leach\u00e9", "given": "Adam D", "initials": "AD", "orcid": "0000-0001-8929-6300", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c9502316d344a1282bec0f444638222.json"}}, {"family": "Rico-Guevara", "given": "Alejandro", "initials": "A", "orcid": "0000-0003-4067-5312", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe305adf4d234dce94a9c74ca873169d.json"}}, {"family": "Fuchs", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Vy", "given": "Nguyen Tran", "initials": "NT"}, {"family": "Hvilsom", "given": "Christina", "initials": "C", "orcid": "0000-0001-7870-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/19e68386a9414dad9162026abafad7ce.json"}}, {"family": "Berner", "given": "Juliana Andrea", "initials": "JA"}, {"family": "Lifjeld", "given": "Jan Terje", "initials": "JT"}, {"family": "Johnsen", "given": "Arild", "initials": "A", "orcid": "0000-0003-4864-6284", "researcher": {"href": "https://publications.scilifelab.se/researcher/d610052c8e134f9a9ddff3eee7ed864d.json"}}, {"family": "Johannessen", "given": "Lars Erik", "initials": "LE", "orcid": "0000-0001-5981-9190", "researcher": {"href": "https://publications.scilifelab.se/researcher/838c1d1eb4bb4861a2408a5d83b616cb.json"}}, {"family": "Labuschagne", "given": "Kim", "initials": "K", "orcid": "0000-0003-2784-4767", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfa0e1dbf2194c5bbcfb36769d1b2cf4.json"}}, {"family": "J\u00f8nsson", "given": "Knud Andreas", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Reeve", "given": "Andrew Hart", "initials": "AH", "orcid": "0000-0001-5233-6030", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9c0cc8c4ff44848960ec2d43dce41d7.json"}}, {"family": "Joseph", "given": "Leo", "initials": "L", "orcid": "0000-0001-7564-1978", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a0b6c400914ba9aaca4a51587d1893.json"}}, {"family": "Hellgren", "given": "Olof", "initials": "O", "orcid": "0000-0002-4062-7276", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bca3b673a2447ecbc55eaf9edf56a02.json"}}, {"family": "Brumfield", "given": "Robb T", "initials": "RT", "orcid": "0000-0003-2307-0688", "researcher": {"href": "https://publications.scilifelab.se/researcher/71a3a36f83154d3dbe14e1a5290f425f.json"}}, {"family": "Burg", "given": "Theresa M", "initials": "TM", "orcid": "0000-0001-5096-3479", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab837fec0ea64df5bd66001038f505c5.json"}}, {"family": "Illera", "given": "Juan Carlos", "initials": "JC", "orcid": "0000-0002-4389-0264", "researcher": {"href": "https://publications.scilifelab.se/researcher/d137c193d3cd4f8c8b9fe09a6443033c.json"}}, {"family": "Aleixo", "given": "Alexandre", "initials": "A", "orcid": "0000-0002-7816-9725", "researcher": {"href": "https://publications.scilifelab.se/researcher/b397ed6da07246caa50a438c233820ab.json"}}, {"family": "Smit", "given": "Ben", "initials": "B"}, {"family": "Rheindt", "given": "Frank E", "initials": "FE", "orcid": "0000-0001-8946-7085", "researcher": {"href": "https://publications.scilifelab.se/researcher/744276ae56e24e7295f672854fbaf3d9.json"}}, {"family": "Lee", "given": "Jessica", "initials": "J", "orcid": "0000-0003-0757-4237", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ec08a3cbe214f22b05c730bf94613aa.json"}}, {"family": "Nishiumi", "given": "Isao", "initials": "I"}, {"family": "Quesada", "given": "Javier", "initials": "J", "orcid": "0000-0002-6010-8473", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c4e889bf2fd424c915c6487038f7950.json"}}, {"family": "Dumbacher", "given": "John P", "initials": "JP", "orcid": "0000-0001-8942-1554", "researcher": {"href": "https://publications.scilifelab.se/researcher/6221be035944462989353d66f126a5c5.json"}}, {"family": "Schweizer", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7555-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a043d6f016b46709ace7f181d8cd3b8.json"}}, {"family": "Andersen", "given": "Michael J", "initials": "MJ", "orcid": "0000-0002-7220-5588", "researcher": {"href": "https://publications.scilifelab.se/researcher/15d3b310f2f34fc4969520d431a14f6d.json"}}, {"family": "Witt", "given": "Christopher C", "initials": "CC", "orcid": "0000-0003-2781-1543", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a6a535b32f94e59acf1398df72a8cd1.json"}}, {"family": "Phillips", "given": "Richard A", "initials": "RA", "orcid": "0000-0002-0208-1444", "researcher": {"href": "https://publications.scilifelab.se/researcher/f35746710d7c4ae6a86d1b12e805ea14.json"}}, {"family": "Prum", "given": "Richard O", "initials": "RO", "orcid": "0000-0002-4741-7132", "researcher": {"href": "https://publications.scilifelab.se/researcher/28d15772cf924924b7e5630bfbdb5b89.json"}}, {"family": "Zyskowski", "given": "Kristof", "initials": "K", "orcid": "0000-0002-5680-6412", "researcher": {"href": "https://publications.scilifelab.se/researcher/49aadb5fab7b4fbebf1c65c9f3a04217.json"}}, {"family": "Goodman", "given": "Steven M", "initials": "SM"}, {"family": "Raherilalao", "given": "Marie Jeanne", "initials": "MJ", "orcid": "0000-0002-8618-7157", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5653450df494d96b15d77a12d77e932.json"}}, {"family": "Ottosson", "given": "Ulf", "initials": "U", "orcid": "0000-0001-7914-0484", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b035efe180248eaa188b0e1d23f2007.json"}}, {"family": "Barshep", "given": "Yahkat", "initials": "Y"}, {"family": "Ivande", "given": "Sam", "initials": "S", "orcid": "0000-0003-4949-1376", "researcher": {"href": "https://publications.scilifelab.se/researcher/181e4fbbf6ae40d1bebe504c5c24f797.json"}}, {"family": "Brl\u00edk", "given": "Vojt\u011bch", "initials": "V", "orcid": "0000-0002-7902-8123", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ed62d45f978413d9c983e53b07b7ad8.json"}}, {"family": "Okposio", "given": "Emmanuel", "initials": "E"}, {"family": "Koane", "given": "Bonny", "initials": "B", "orcid": "0000-0001-6770-5126", "researcher": {"href": "https://publications.scilifelab.se/researcher/966dc22dd4ca456294f7f2ed0a853c87.json"}}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e409936447e49ef9cb6fe1c75417fb0.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Rahbek", "given": "Carsten", "initials": "C", "orcid": "0000-0003-4585-0300", "researcher": {"href": "https://publications.scilifelab.se/researcher/341ee33c55904249b6e70a9b55b5509a.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F", "orcid": "0000-0001-9920-8167", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e9cc44c016c4d099f674d182c08fbaa.json"}}, {"family": "Graves", "given": "Gary R", "initials": "GR", "orcid": "0000-0003-1406-5246", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc3b9edee185456d971f5b596c3086fe.json"}}, {"family": "Feng", "given": "Shaohong", "initials": "S", "orcid": "0000-0002-2462-7348", "researcher": {"href": "https://publications.scilifelab.se/researcher/92ad360b09004877aee9cfde491c76a3.json"}}, {"family": "Hosner", "given": "Peter A", "initials": "PA", "orcid": "0000-0001-7499-6224", "researcher": {"href": "https://publications.scilifelab.se/researcher/87a4c8cd6229436d9a39761aa77eeec2.json"}}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/873e2383b99a43d7848bf387264cf0e8.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": "2026-01-21", "journal": {"title": "Gigascience", "issn": "2047-217X", "volume": "15", "issn-l": "2047-217X"}, "abstract": "With over 10,000 recognized species, birds constitute one of the most diverse and widely distributed vertebrate groups. Although avian genomics has advanced rapidly over the past decade, substantial gaps remain across the global avifauna. Filling these gaps is essential for understanding macroevolutionary patterns, population structure, and the molecular basis of ecological and behavioral diversity. Worldwide museum collections represent invaluable resources for filling these gaps, yet the typically degraded DNA and limited quantities from historical specimens have posed significant challenges for generating high-quality genome assemblies.\n\nHere, the Bird Genome 10 K Project adopted low-input sequencing strategies that reduce costs while improving assembly quality compared with earlier order- and family-level genomes. Using mainly stLFR, complemented by 10X Genomics and standard next-generation sequencing, we assembled 177 avian genomes from museum specimens and tissue collections representing 161 genera, including 102 newly sequenced at the genomic level. The assemblies average \u223c1.2 Gb in size, with scaffold N50 = 8.03 Mb, contig N50 = 120 kb, 93% BUSCO completeness, and Merqury Quality Value score of 56.\n\nThese genomes greatly expand avian taxonomic coverage and demonstrate the efficiency of low-input sequencing for generating high-quality assemblies from limited and often degraded material sourced from museum specimens. This resource provides a foundation for comparative genomics, conservation genetics, and evolutionary studies across the avian tree of life.", "doi": "10.1093/gigascience/giag045", "pmid": "42104960", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "8675036"}, {"db": "pmc", "key": "PMC13274736"}], "notes": [], "created": "2026-06-08T17:18:43.899Z", "modified": "2026-06-29T07:41:18.996Z"}, {"entity": "publication", "iuid": "a6edd515f3214f8594dc78220571aa36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a6edd515f3214f8594dc78220571aa36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a6edd515f3214f8594dc78220571aa36"}}, "title": "The formation of the Indo-Pacific montane avifauna.", "authors": [{"family": "Reeve", "given": "Andrew Hart", "initials": "AH", "orcid": "0000-0001-5233-6030", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9c0cc8c4ff44848960ec2d43dce41d7.json"}}, {"family": "Kennedy", "given": "Jonathan David", "initials": "JD"}, {"family": "Pujolar", "given": "Jos\u00e9 Mart\u00edn", "initials": "JM"}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": "https://publications.scilifelab.se/researcher/62045d9b6dc443be936d3346daa4e1b1.json"}}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK"}, {"family": "Alstr\u00f6m", "given": "Per", "initials": "P", "orcid": "0000-0001-7182-2763", "researcher": {"href": "https://publications.scilifelab.se/researcher/f426ea7151c546939b707d5ed71e7d04.json"}}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e409936447e49ef9cb6fe1c75417fb0.json"}}, {"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", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA", "orcid": "0000-0001-8940-456X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f54d4c39cdd74208ad03500bd22b7609.json"}}, {"family": "J\u00f8nsson", "given": "Knud Andreas", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}], "type": "journal article", "published": "2023-12-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "8215", "issn-l": "2041-1723"}, "abstract": "The processes generating the earth's montane biodiversity remain a matter of debate. Two contrasting hypotheses have been advanced to explain how montane populations form: via direct colonization from other mountains, or, alternatively, via upslope range shifts from adjacent lowland areas. We seek to reconcile these apparently conflicting hypotheses by asking whether a species' ancestral geographic origin determines its mode of mountain colonization. Island-dwelling passerine birds at the faunal crossroads between Eurasia and Australo-Papua provide an ideal study system. We recover the phylogenetic relationships of the region's montane species and reconstruct their ancestral geographic ranges, elevational ranges, and migratory behavior. We also perform genomic population studies of three super-dispersive montane species/clades with broad island distributions. Eurasian-origin species populated archipelagos via direct colonization between mountains. This mode of colonization appears related to ancestral adaptations to cold and seasonal climates, specifically short-distance migration. Australo-Papuan-origin mountain populations, by contrast, evolved from lowland ancestors, and highland distribution mostly precludes their further colonization of island mountains. Our study explains much of the distributional variation within a complex biological system, and provides a synthesis of two seemingly discordant hypotheses for montane community formation.", "doi": "10.1038/s41467-023-43964-y", "pmid": "38081809", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10713610"}, {"db": "pii", "key": "10.1038/s41467-023-43964-y"}], "notes": [], "created": "2024-01-02T13:39:08.815Z", "modified": "2024-11-25T10:16:06.008Z"}, {"entity": "publication", "iuid": "f7f0a2b696f74c7c97f50e51dcbc32d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f7f0a2b696f74c7c97f50e51dcbc32d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f7f0a2b696f74c7c97f50e51dcbc32d8"}}, "title": "Population genomics of the island thrush elucidates one of earth's great archipelagic radiations.", "authors": [{"family": "Reeve", "given": "Andrew Hart", "initials": "AH", "orcid": "0000-0001-5233-6030", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9c0cc8c4ff44848960ec2d43dce41d7.json"}}, {"family": "Gower", "given": "Graham", "initials": "G", "orcid": "0000-0002-6197-3872", "researcher": {"href": "https://publications.scilifelab.se/researcher/6734ceea85184d94bf6f35eaf593f05e.json"}}, {"family": "Pujolar", "given": "Jos\u00e9 Mart\u00edn", "initials": "JM"}, {"family": "Smith", "given": "Brian Tilston", "initials": "BT"}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": "https://publications.scilifelab.se/researcher/62045d9b6dc443be936d3346daa4e1b1.json"}}, {"family": "Olsson", "given": "Urban", "initials": "U", "orcid": "0000-0003-1435-5411", "researcher": {"href": "https://publications.scilifelab.se/researcher/f16c5531607c4f5190f68a35b15cbd0e.json"}}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e409936447e49ef9cb6fe1c75417fb0.json"}}, {"family": "Koane", "given": "Bonny", "initials": "B"}, {"family": "Maiah", "given": "Gibson", "initials": "G"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Racimo", "given": "Fernando", "initials": "F", "orcid": "0000-0002-5025-2607", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcd12137b4184a72a81c48d2926c5280.json"}}, {"family": "J\u00f8nsson", "given": "Knud Andreas", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}], "type": "journal article", "published": "2023-02-01", "journal": {"title": "Evolution Letters", "issn": "2056-3744", "volume": "7", "issue": "1", "pages": "24-36", "issn-l": "2056-3744"}, "abstract": "Tropical islands are renowned as natural laboratories for evolutionary study. Lineage radiations across tropical archipelagos are ideal systems for investigating how colonization, speciation, and extinction processes shape biodiversity patterns. The expansion of the island thrush across the Indo-Pacific represents one of the largest yet most perplexing island radiations of any songbird species. The island thrush exhibits a complex mosaic of pronounced plumage variation across its range and is arguably the world's most polytypic bird. It is a sedentary species largely restricted to mountain forests, yet it has colonized a vast island region spanning a quarter of the globe. We conducted a comprehensive sampling of island thrush populations and obtained genome-wide SNP data, which we used to reconstruct its phylogeny, population structure, gene flow, and demographic history. The island thrush evolved from migratory Palearctic ancestors and radiated explosively across the Indo-Pacific during the Pleistocene, with numerous instances of gene flow between populations. Its bewildering plumage variation masks a biogeographically intuitive stepping stone colonization path from the Philippines through the Greater Sundas, Wallacea, and New Guinea to Polynesia. The island thrush's success in colonizing Indo-Pacific mountains can be understood in light of its ancestral mobility and adaptation to cool climates; however, shifts in elevational range, degree of plumage variation and apparent dispersal rates in the eastern part of its range raise further intriguing questions about its biology.", "doi": "10.1093/evlett/qrac006", "pmid": "37065434", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10091502"}, {"db": "pii", "key": "qrac006"}], "notes": [], "created": "2023-10-04T12:42:09.643Z", "modified": "2023-10-19T11:58:02.781Z"}, {"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": [{"family": "Feng", "given": "Shaohong", "initials": "S", "orcid": "0000-0002-2462-7348", "researcher": {"href": "https://publications.scilifelab.se/researcher/92ad360b09004877aee9cfde491c76a3.json"}}, {"family": "Stiller", "given": "Josefin", "initials": "J", "orcid": "0000-0001-6009-9581", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e54e7b719bb422aa18ccd99d6c2edf6.json"}}, {"family": "Deng", "given": "Yuan", "initials": "Y"}, {"family": "Armstrong", "given": "Joel", "initials": "J", "orcid": "0000-0003-2077-4671", "researcher": {"href": "https://publications.scilifelab.se/researcher/63cfeea6ae9942b8a48e6e13ecf4bf0d.json"}}, {"family": "Fang", "given": "Qi", "initials": "Q", "orcid": "0000-0002-9181-8689", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9ff76a9a8bb42c8973d968c7e39a216.json"}}, {"family": "Reeve", "given": "Andrew Hart", "initials": "AH", "orcid": "0000-0001-5233-6030", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9c0cc8c4ff44848960ec2d43dce41d7.json"}}, {"family": "Xie", "given": "Duo", "initials": "D", "orcid": "0000-0001-7010-3601", "researcher": {"href": "https://publications.scilifelab.se/researcher/9258a952a3c54596add7d930e1432ebe.json"}}, {"family": "Chen", "given": "Guangji", "initials": "G", "orcid": "0000-0002-9441-1155", "researcher": {"href": "https://publications.scilifelab.se/researcher/19514f67b1504dc6b4b7d393e97f8cc0.json"}}, {"family": "Guo", "given": "Chunxue", "initials": "C"}, {"family": "Faircloth", "given": "Brant C", "initials": "BC", "orcid": "0000-0002-1943-0217", "researcher": {"href": "https://publications.scilifelab.se/researcher/6df01b37d97a44ffb6f4d069085d7b64.json"}}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": 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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"}]}