{"entity": "researcher", "timestamp": "2026-06-17T04:09:14.365Z", "family": "J\u00f8nsson", "given": "Knud Andreas", "initials": "KA", "orcid": "0000-0002-1875-9504", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02"}}, "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 \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"}, {"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"}, {"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"}, {"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"}, {"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", "initials": "R", "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": "2026-05-09", "journal": {"title": "Gigascience", "issn": "2047-217X", "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 (B10K) 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 QV 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"}], "notes": [], "created": "2026-06-08T17:18:43.899Z", "modified": "2026-06-08T17:18:48.101Z"}, {"entity": "publication", "iuid": "0577c5369a1d4893bc7f6fb121420f6f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0577c5369a1d4893bc7f6fb121420f6f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0577c5369a1d4893bc7f6fb121420f6f"}}, "title": "Ephemeral Speciation in a New Guinean Honeyeater Complex (Aves: Melidectes).", "authors": [{"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}}, {"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "Rajan", "given": "Samyuktha", "initials": "S"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "R"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.json"}}, {"family": "Peona", "given": "Valentina", "initials": "V"}, {"family": "Smith", "given": "Brian Tilston", "initials": "BT"}, {"family": "Maiah", "given": "Gibson", "initials": "G"}, {"family": "Koane", "given": "Bonny", "initials": "B"}, {"family": "Iova", "given": "Bulisa", "initials": "B"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "34", "issue": "21", "pages": "e17760"}, "abstract": "Speciation is a fundamental concept in evolutionary biology, and understanding the mechanisms driving speciation remains the foremost research topic within this field. Hybridisation is often involved in speciation and can influence its rates, potentially accelerating, decelerating or even reversing the process. This study investigates the evolutionary history of the New Guinean bird genus Melidectes, consisting of six species that inhabit various montane regions at different elevations. While most Melidectes species have allopatric distributions, two species overlap in the central mountain range and hybridise. However, plumage differences and elevational adaptations are assumed to maintain the species' boundaries. Utilising specimens from natural history collections and comprehensive genomic analyses, including a de novo genome assembly, we characterise allopatric speciation patterns within the genus and highlight how future speciation could potentially be driven by climate change. Contrary to previous hypotheses, our findings suggest that in the two distributionally overlapping species, phenotypic differences do not prevent gene flow. We find limited acoustic differentiation and extensive admixture across most of their distributions. Divergence and admixture levels conform poorly to the current taxonomy and follow a geographical pattern in which the most isolated populations at the ends of the distributions are most divergent and show least admixture. However, in contrast, their mitochondrial genomes do group in accordance with species identity, namely, into two deeply divergent lineages. We propose that this system demonstrates the ephemeral nature of speciation, in which two incipient species have started mixing extensively as they came into secondary contact, resulting in nearly complete fusion into a single lineage.", "doi": "10.1111/mec.17760", "pmid": "40219608", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Other": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12573753"}], "notes": [], "created": "2025-11-19T08:27:00.806Z", "modified": "2025-11-19T09:18:52.732Z"}, {"entity": "publication", "iuid": "fdfce138b5554e72a4f6cf82097b08e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fdfce138b5554e72a4f6cf82097b08e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fdfce138b5554e72a4f6cf82097b08e2"}}, "title": "Reticulate and Hybrid Speciation is Promoted by Environmental Instability in an Indo-Pacific Species Complex of Whistlers (Aves: Pachycephala).", "authors": [{"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}}, {"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "Joseph", "given": "Leo", "initials": "L", "orcid": "0000-0001-7564-1978", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a0b6c400914ba9aaca4a51587d1893.json"}}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA"}, {"family": "Guinet", "given": "Benjamin", "initials": "B"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"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": "2025-11-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "34", "issue": "21", "pages": "e70018", "issn-l": "0962-1083"}, "abstract": "Genomic studies have revealed introgressive hybridisation as a common phenomenon across the tree of life, particularly among young radiations. As incipient speciation tends to be induced by vicariance events, it is assumed that introgressive hybridisation is more frequent in young radiations in which allopatrically distributed species have a high probability of coming into secondary contact. In this study, we use whole genomic data to investigate spatio-temporal introgression patterns in a songbird radiation that has colonised a highly dynamic island region in the Indo-Pacific. Some taxa within this radiation have colonised remote oceanic islands whereas others occur on landmasses and islands in the Sahul region that were periodically connected during Pleistocene periods of lower sea levels. Our results show that introgressive hybridisation has been pervasive within this young radiation, despite prominent plumage differences between taxa. Geographical proximity has been an important factor for hybridisation and we further find that species occupying islands in the environmentally unstable Sahul region exhibit particularly high signatures of introgressive hybridisation. Yet, one species appears to have been shielded from hybridisation, perhaps due to specific ecological specialisations. Finally, we identify a hybrid species on an island where two oceanic radiations meet. Our results also caution against relying solely on analyses that only detect asymmetric introgression when examining systems with complex introgression histories. Collectively, our results support a growing body of literature that suggests that reticulate speciation is more common than previously thought. This has implications for our understanding of species formation and their persistence through time.", "doi": "10.1111/mec.70018", "pmid": "40650490", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12573736"}], "notes": [], "created": "2025-11-19T08:33:24.398Z", "modified": "2025-11-19T08:33:24.490Z"}, {"entity": "publication", "iuid": "3e287d397db04ea4a121c1a2cbd8a106", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e287d397db04ea4a121c1a2cbd8a106.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e287d397db04ea4a121c1a2cbd8a106"}}, "title": "Museomics unravels cryptic diversity in an endemic group of New Guinean songbirds.", "authors": [{"family": "Blom", "given": "Mozes Pil Kyu", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Bloom-Quinn", "given": "Saphira", "initials": "S", "orcid": "0009-0000-6457-8264", "researcher": {"href": "https://publications.scilifelab.se/researcher/766f9c58f99a4263a464c1138001ab83.json"}}, {"family": "Marki", "given": "Petter Zahl", "initials": "PZ", "orcid": "0000-0001-6990-9915", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ac768b5d0d540988dfeca8f83cf41cf.json"}}, {"family": "Koane", "given": "Bonny", "initials": "B", "orcid": "0000-0001-6770-5126", "researcher": {"href": "https://publications.scilifelab.se/researcher/966dc22dd4ca456294f7f2ed0a853c87.json"}}, {"family": "Joseph", "given": "Leo", "initials": "L", "orcid": "0000-0001-7564-1978", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a0b6c400914ba9aaca4a51587d1893.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.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": "2025-07-00", "journal": {"title": "Biol. Lett.", "issn": "1744-957X", "volume": "21", "issue": "7", "pages": "20240611", "issn-l": "1744-9561"}, "abstract": "Deciphering cryptic diversity can have substantial implications for our understanding of evolutionary processes and species conservation. Birds are arguably among the best studied organismal groups, but even in avian clades there are some genera that have not been thoroughly surveyed. This is particularly true for taxa that occur in hyperdiverse biogeographic regions. In this study, we focus on an endemic group of New Guinean birds, the jewel-babblers (genus: Ptilorrhoa), and study the diversification history of all known taxa. We assemble a de novo genome using linked-read sequencing and genomic data for 40 historical specimens. Both phylogenomic and population-genomic analyses strongly support the recovery of a cryptic species and shed new light on the diversification history of this group. The blue jewel-babbler (Ptilorrhoa caerulescens) is a paraphyletic species complex and P. c. nigricrissus is more closely related to the phenotypically distinct and sexually dimorphic P. geislerorum, than to other P. caerulescens subspecies. These findings demonstrate that even in well-studied groups such as birds, cryptic diversity can still be a prevalent reality. Moreover, by deciphering cryptic diversity, we shed new light on the processes driving speciation within Ptilorrhoa and the need to potentially revise the taxonomic status of all subspecies.", "doi": "10.1098/rsbl.2024.0611", "pmid": "40664242", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2025-07-18T10:24:09.986Z", "modified": "2025-07-18T10:24:10.511Z"}, {"entity": "publication", "iuid": "dbbacfc5e2734fc19c98ec14dd081705", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dbbacfc5e2734fc19c98ec14dd081705.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dbbacfc5e2734fc19c98ec14dd081705"}}, "title": "Frequent Hybridisation Between Parapatric Lekking Bird-of-Paradise Species.", "authors": [{"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}}, {"family": "Soares", "given": "Andr\u00e9 E R", "initials": "AER"}, {"family": "Nagombi", "given": "Elizah", "initials": "E"}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "34", "issue": "11", "pages": "e17780", "issn-l": "0962-1083"}, "abstract": "Hybridisation is known to occur between a wide range of taxa, including species for which strong sexual selection has led to markedly different sexual phenotypes and lek-mating behaviours. To what extent occasional hybridisation can overcome the reproductive barriers in such systems and, for example, lead to the establishment of hybrid zones is poorly known. In this study, we address this question by focusing on one of the most well-known avian radiations in which sexual selection has resulted in an extraordinary assemblage of phenotypic diversity and lek-mating behaviours: the birds-of-paradise (Paradisaeidae). We quantify the genome-wide distribution of introgression and find multiple signals of recent and historical gene flow between and within two genera of birds-of-paradise, Astrapia and Paradigalla. In addition, we present the first empirical genomic indication of a putative hybrid zone between two lekking bird-of-paradise species that differ substantially in their sexually selected traits and behaviours. Our findings are consistent with the idea that behavioural and phenotypic traits may constitute weaker pre- and post-zygotic barriers to gene flow than generally thought in lek-mating species.", "doi": "10.1111/mec.17780", "pmid": "40298045", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12100584"}], "notes": [], "created": "2025-05-26T07:50:33.961Z", "modified": "2025-11-28T10:51:32.111Z"}, {"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": "92f07130682a4fa283e3b89d3d9a1249", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92f07130682a4fa283e3b89d3d9a1249.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92f07130682a4fa283e3b89d3d9a1249"}}, "title": "The formation of avian montane diversity across barriers and along elevational gradients.", "authors": [{"family": "Pujolar", "given": "Jos\u00e9 Mart\u00edn", "initials": "JM"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Reeve", "given": "Andrew Hart", "initials": "AH"}, {"family": "Kennedy", "given": "Jonathan D", "initials": "JD", "orcid": "0000-0002-2843-122X", "researcher": {"href": "https://publications.scilifelab.se/researcher/efdccdbf3f5a44b39a66d7ece5f174f7.json"}}, {"family": "Marki", "given": "Petter Zahl", "initials": "PZ"}, {"family": "Korneliussen", "given": "Thorfinn S", "initials": "TS"}, {"family": "Freeman", "given": "Benjamin G", "initials": "BG", "orcid": "0000-0001-6131-6832", "researcher": {"href": "https://publications.scilifelab.se/researcher/e05aaf37772b4f50a12b20db5d2db3c8.json"}}, {"family": "Sam", "given": "Katerina", "initials": "K"}, {"family": "Linck", "given": "Ethan", "initials": "E"}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e409936447e49ef9cb6fe1c75417fb0.json"}}, {"family": "Iova", "given": "Bulisa", "initials": "B"}, {"family": "Koane", "given": "Bonny", "initials": "B"}, {"family": "Maiah", "given": "Gibson", "initials": "G"}, {"family": "Paul", "given": "Luda", "initials": "L"}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.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": "2022-01-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "268"}, "abstract": "Tropical mountains harbor exceptional concentrations of Earth's biodiversity. In topographically complex landscapes, montane species typically inhabit multiple mountainous regions, but are absent in intervening lowland environments. Here we report a comparative analysis of genome-wide DNA polymorphism data for population pairs from eighteen Indo-Pacific bird species from the Moluccan islands of Buru and Seram and from across the island of New Guinea. We test how barrier strength and relative elevational distribution predict population differentiation, rates of historical gene flow, and changes in effective population sizes through time. We find population differentiation to be consistently and positively correlated with barrier strength and a species' altitudinal floor. Additionally, we find that Pleistocene climate oscillations have had a dramatic influence on the demographics of all species but were most pronounced in regions of smaller geographic area. Surprisingly, even the most divergent taxon pairs at the highest elevations experience gene flow across barriers, implying that dispersal between montane regions is important for the formation of montane assemblages.", "doi": "10.1038/s41467-021-27858-5", "pmid": "35022441", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-27858-5"}, {"db": "pmc", "key": "PMC8755808"}], "notes": [], "created": "2022-03-29T13:48:03.888Z", "modified": "2024-01-16T13:48:37.739Z"}, {"entity": "publication", "iuid": "6f70e1a8af3e47a5a3fa4fba74483b35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f70e1a8af3e47a5a3fa4fba74483b35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f70e1a8af3e47a5a3fa4fba74483b35"}}, "title": "The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities.", "authors": [{"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Palacios-Gimenez", "given": "Octavio M", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90e29ecd5724ff19509983e65891915.json"}}, {"family": "Blommaert", "given": "Julie", "initials": "J", "orcid": "0000-0003-1411-2313", "researcher": {"href": "https://publications.scilifelab.se/researcher/761067515ad240c9b82f0ea7625b1320.json"}}, {"family": "Liu", "given": "Jing", "initials": "J"}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e409936447e49ef9cb6fe1c75417fb0.json"}}, {"family": "J\u00f8nsson", "given": "Knud A", "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": "Zhou", "given": "Qi", "initials": "Q", "orcid": "0000-0002-7419-2047", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69266aa587d4126a23aa91c5bedfff8.json"}}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}], "type": "journal article", "published": "2021-09-13", "journal": {"title": "Philos. Trans. R. Soc. Lond., B, Biol. Sci.", "issn": "1471-2970", "issn-l": "0962-8436", "volume": "376", "issue": "1833", "pages": "20200186"}, "abstract": "It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the 'toxic-Y' effect in Drosophila males. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.", "doi": "10.1098/rstb.2020.0186", "pmid": "34304594", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8310711"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.5450746"}], "notes": [], "created": "2021-10-01T09:03:22.481Z", "modified": "2024-01-16T13:48:38.503Z"}, {"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": "https://publications.scilifelab.se/researcher/62045d9b6dc443be936d3346daa4e1b1.json"}}, {"family": "Wang", "given": "Zongji", "initials": "Z", "orcid": "0000-0002-5107-6246", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a18bde0ee684560ae3217db4b30a920.json"}}, {"family": "Zhou", "given": "Qi", "initials": "Q", "orcid": "0000-0002-7419-2047", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69266aa587d4126a23aa91c5bedfff8.json"}}, {"family": "Diekhans", "given": "Mark", "initials": "M", "orcid": "0000-0002-0430-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/da3441938f7b437b81cc92068bea158c.json"}}, {"family": "Chen", "given": "Wanjun", "initials": "W", "orcid": "0000-0002-4418-7650", "researcher": {"href": "https://publications.scilifelab.se/researcher/992e7029a2704d039ce578df2806f57f.json"}}, {"family": "Andreu-S\u00e1nchez", "given": "Sergio", "initials": "S"}, {"family": "Margaryan", "given": "Ashot", "initials": "A", "orcid": "0000-0002-2576-2429", "researcher": {"href": "https://publications.scilifelab.se/researcher/487f29e4a666414a8437f964e2052be7.json"}}, {"family": "Howard", "given": "Jason Travis", "initials": "JT"}, {"family": "Parent", "given": "Carole", "initials": "C"}, {"family": "Pacheco", "given": "George", "initials": "G", "orcid": "0000-0002-9367-6813", "researcher": {"href": "https://publications.scilifelab.se/researcher/449f532c61df4157b9bd1dc15deab965.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Puetz", "given": "Lara", "initials": "L", "orcid": "0000-0002-0323-799X", "researcher": {"href": "https://publications.scilifelab.se/researcher/986da811e11341379e73f5382b0f69ad.json"}}, {"family": "Cavill", "given": "Emily", "initials": "E", "orcid": "0000-0003-2198-8102", "researcher": {"href": "https://publications.scilifelab.se/researcher/eacd61b411f046d88c1e8942eb46cfff.json"}}, {"family": "Ribeiro", "given": "\u00c2ngela M", "initials": "\u00c2M"}, {"family": "Eckhart", "given": "Leopold", "initials": "L", "orcid": "0000-0002-5645-2036", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a24adae52741698457e9a733f36f6c.json"}}, {"family": "Fjelds\u00e5", "given": "Jon", "initials": "J", "orcid": "0000-0003-0790-3600", "researcher": {"href": "https://publications.scilifelab.se/researcher/f280ada51dfb41b2a3d035676a27ffb6.json"}}, {"family": "Hosner", "given": "Peter A", "initials": "PA", "orcid": "0000-0001-7499-6224", "researcher": {"href": "https://publications.scilifelab.se/researcher/87a4c8cd6229436d9a39761aa77eeec2.json"}}, {"family": "Brumfield", "given": "Robb T", "initials": "RT", "orcid": "0000-0003-2307-0688", "researcher": {"href": "https://publications.scilifelab.se/researcher/71a3a36f83154d3dbe14e1a5290f425f.json"}}, {"family": "Christidis", "given": "Les", "initials": "L", "orcid": "0000-0002-3345-6034", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd916cfab85848b683744b92f994bd74.json"}}, {"family": "Bertelsen", "given": "Mads F", "initials": "MF"}, {"family": "Sicheritz-Ponten", "given": "Thomas", "initials": "T", "orcid": "0000-0001-6615-1141", "researcher": {"href": "https://publications.scilifelab.se/researcher/0da5029f417945a790fbb57b5120dceb.json"}}, {"family": "Tietze", "given": "Dieter Thomas", "initials": "DT", "orcid": "0000-0001-6868-227X", "researcher": {"href": "https://publications.scilifelab.se/researcher/820c40b8230d46fca4c8f6d6af483f71.json"}}, {"family": "Robertson", "given": "Bruce C", "initials": "BC", "orcid": "0000-0002-5348-2731", "researcher": {"href": "https://publications.scilifelab.se/researcher/765ee347a5f04b29b28a17f14f707231.json"}}, {"family": "Song", "given": "Gang", "initials": "G", "orcid": "0000-0002-0190-8315", "researcher": {"href": "https://publications.scilifelab.se/researcher/f133bb6165494dfaba8173b0e8191765.json"}}, {"family": "Borgia", "given": "Gerald", "initials": "G"}, {"family": "Claramunt", "given": "Santiago", "initials": "S", "orcid": "0000-0002-8926-5974", "researcher": {"href": "https://publications.scilifelab.se/researcher/24bba44e15a14f3fa2798de2f0f86f55.json"}}, {"family": "Lovette", "given": "Irby J", "initials": "IJ", "orcid": "0000-0003-0268-4875", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f3e74e4c49e4a7f8ce6109e255cbb1c.json"}}, {"family": "Cowen", "given": "Saul J", "initials": "SJ", "orcid": "0000-0002-1045-5637", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9565f0452e343c89113e611942e3285.json"}}, {"family": "Njoroge", "given": "Peter", "initials": "P", "orcid": "0000-0003-1165-3579", "researcher": {"href": "https://publications.scilifelab.se/researcher/99cda46acb47431eb59b7a4a25b103f0.json"}}, {"family": "Dumbacher", "given": "John Philip", "initials": "JP", "orcid": "0000-0001-8942-1554", "researcher": {"href": "https://publications.scilifelab.se/researcher/6221be035944462989353d66f126a5c5.json"}}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a55f8ea442f4168a8426ae4a2c43a46.json"}}, {"family": "Fuchs", "given": "J\u00e9r\u00f4me", "initials": "J", "orcid": "0000-0003-1972-0078", "researcher": {"href": "https://publications.scilifelab.se/researcher/2976574cfb9b423cb487dcf840619c94.json"}}, {"family": "Bunce", "given": "Michael", "initials": "M", "orcid": "0000-0002-0302-4206", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a6cb7d93e7c4785a0334adaf12aca6b.json"}}, {"family": "Burt", "given": "David W", "initials": "DW", "orcid": "0000-0002-9991-1028", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb2c7a18d5b64136b08fa00cf65624e5.json"}}, {"family": "Cracraft", "given": "Joel", "initials": "J", "orcid": "0000-0001-7587-8342", "researcher": {"href": "https://publications.scilifelab.se/researcher/99c4c500419d491c96654e37210dee27.json"}}, {"family": "Meng", "given": "Guanliang", "initials": "G", "orcid": "0000-0002-6488-1527", "researcher": {"href": "https://publications.scilifelab.se/researcher/7191d467d9b3497f80212ff402c8f9cd.json"}}, {"family": "Hackett", "given": "Shannon J", "initials": "SJ", "orcid": "0000-0002-1404-0332", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac60e949323442e39e2e53b03610f99f.json"}}, {"family": "Ryan", "given": "Peter G", "initials": "PG"}, {"family": "J\u00f8nsson", "given": "Knud Andreas", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}, {"family": "Jamieson", "given": "Ian G", "initials": "IG"}, {"family": "da Fonseca", "given": "Rute R", "initials": "RR", "orcid": 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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"}]}