{"entity": "researcher", "timestamp": "2026-09-23T14:43:41.164Z", "family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "affiliations": ["Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.", "Department of Population Ecology, Friedrich Schiller University Jena, Jena, Germany."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8b109ad7c724c3f9db1732c2f93b175.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8b109ad7c724c3f9db1732c2f93b175"}}, "publications": [{"entity": "publication", "iuid": "25097aaa734742df92306b857ccf68bb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/25097aaa734742df92306b857ccf68bb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/25097aaa734742df92306b857ccf68bb"}}, "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-affiliated.scilifelab.se/researcher/8fccaeeed5bd43e98eb49003c72f050b.json"}}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/12d645d316a64a54ad02fb915cf9b2d6.json"}}, {"family": "Chase", "given": "Madeline A", "initials": "MA", "orcid": "0000-0002-7916-3560", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd10d49062ab4e7696ea41ff79500a14.json"}}, {"family": "Kakhki", "given": "Niloofar Alaei", "initials": "NA"}, {"family": "Lammers", "given": "Fritjof", "initials": "F", "orcid": "0000-0002-3110-8220", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d9cd55239514b758ada7b2c809d5a5b.json"}}, {"family": "de Souza", "given": "Stacey G", "initials": "SG", "orcid": "0000-0001-6596-5522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0243a657beb549bb8daf2f67bfd6496a.json"}}, {"family": "Ducrest", "given": "Anne-Lyse", "initials": "AL", "orcid": "0000-0001-6412-2769", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe6b67ccb5b44c3aa4dc0218c26ae27b.json"}}, {"family": "Burri", "given": "Marta", "initials": "M"}, {"family": "Andriopoulos", "given": "Pavlos", "initials": "P", "orcid": "0000-0002-5377-2974", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8607ae348d9e43b18809e9c95c5fe8be.json"}}, {"family": "Lukhele", "given": "Sifiso M", "initials": "SM", "orcid": "0000-0003-0638-0641", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/00429502f5164468bf880f2ce6c2b485.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-affiliated.scilifelab.se/researcher/b07318dd31384727a04590f9402f8eaa.json"}}, {"family": "Albayrak", "given": "Tamer", "initials": "T", "orcid": "0000-0003-4115-3946", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94b52fe4ef834bd5853d582c6903b762.json"}}, {"family": "Aliabadian", "given": "Mansour", "initials": "M", "orcid": "0000-0002-3200-4853", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d0494e25a1e142528554ac6fcfa06855.json"}}, {"family": "Auchli", "given": "Nicolas", "initials": "N"}, {"family": "Bontzorlos", "given": "Vasileios", "initials": "V", "orcid": "0000-0002-1276-3385", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4eaf573973047ecb18f4557675bf800.json"}}, {"family": "Christoforou", "given": "Ioulios", "initials": "I"}, {"family": "Copete", "given": "Jos\u00e9 Luis", "initials": "JL", "orcid": "0000-0001-8542-0351", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2483f3edbe054010b980d3c8acd0c02e.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-affiliated.scilifelab.se/researcher/bdbbd63fe30e4ebc81f704592e084e5a.json"}}, {"family": "Kazazou", "given": "Anna", "initials": "A", "orcid": "0009-0003-6518-8833", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/79d15591c2c446a0840ecd7a3ec0e1f0.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F", "orcid": "0000-0001-9920-8167", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/46aae162df774593b6335191a12c69e7.json"}}, {"family": "Liu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4580-5518", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2362e303577e40039c09346ba068709b.json"}}, {"family": "Paposhvili", "given": "Nika", "initials": "N"}, {"family": "Patchett", "given": "Robert", "initials": "R", "orcid": "0000-0003-4105-3136", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c99ed506c696487c96ceb87a030954a1.json"}}, {"family": "P\u00e9ter", "given": "\u00c1ron", "initials": "\u00c1", "orcid": "0000-0003-3219-9344", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/709d976f0b3c4c01bfeb589fee5f61bf.json"}}, {"family": "Ritter", "given": "Raphael", "initials": "R", "orcid": "0009-0000-3060-1622", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3289e68bc0434c90aa2976facb146c69.json"}}, {"family": "S\u00e1ndor", "given": "Attila D", "initials": "AD", "orcid": "0000-0001-8852-8341", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe71fb4d700246b1b0f490bdae1a4a6e.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-affiliated.scilifelab.se/researcher/5ff5d529d0bc4cc681cbe7d438450906.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-affiliated.scilifelab.se/researcher/5b3ff358957746a89d626af7ece53733.json"}}, {"family": "Vogiatzis", "given": "Nikitas", "initials": "N", "orcid": "0009-0008-9592-923X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aaadacfe4c63492f96f991b0ae2989f6.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-affiliated.scilifelab.se/researcher/87211ef79f5d470c8616a4edc8e0fed8.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1790a31477c4376957d8c328299db1c.json"}}, {"family": "Gagnaire", "given": "Pierre-Alexandre", "initials": "PA", "orcid": "0000-0002-1908-3235", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/62a8f583e4be4ba1a61fe574a046e9f8.json"}}, {"family": "Kirschel", "given": "Alexander N G", "initials": "ANG", "orcid": "0000-0003-4379-7956", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c85e353537614548acad02b53809a14c.json"}}, {"family": "Schweizer", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7555-8450", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/127271f95a954d1da12d2ae4d393d90f.json"}}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/185297e474cc4e09b1f2087fb7d902a1.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8b109ad7c724c3f9db1732c2f93b175.json"}}], "type": "journal article", "published": "2025-10-16", "journal": {"title": "Science (New York, N.Y.)", "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": [], "xrefs": [], "notes": [], "created": "2026-09-23T09:12:07.397Z", "modified": "2026-09-23T09:12:08.529Z"}, {"entity": "publication", "iuid": "49d66041d7f143fda8d8dbfa7dc1bbdd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/49d66041d7f143fda8d8dbfa7dc1bbdd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/49d66041d7f143fda8d8dbfa7dc1bbdd"}}, "title": "An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca).", "authors": [{"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/12d645d316a64a54ad02fb915cf9b2d6.json"}}, {"family": "Palacios-Gimenez", "given": "Octavio Manuel", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4d3d53ea54b4ec293da675c9c63a0de.json"}}, {"family": "Lutgen", "given": "Dave", "initials": "D", "orcid": "0000-0003-0793-3930", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8fccaeeed5bd43e98eb49003c72f050b.json"}}, {"family": "Olsen", "given": "Remi Andr\u00e9", "initials": "RA"}, {"family": "Alaei Kakhki", "given": "Niloofar", "initials": "N"}, {"family": "Andriopoulos", "given": "Pavlos", "initials": "P", "orcid": "0000-0002-5377-2974", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8607ae348d9e43b18809e9c95c5fe8be.json"}}, {"family": "Bontzorlos", "given": "Vasileios", "initials": "V", "orcid": "0000-0002-1276-3385", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4eaf573973047ecb18f4557675bf800.json"}}, {"family": "Schweizer", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7555-8450", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/127271f95a954d1da12d2ae4d393d90f.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1790a31477c4376957d8c328299db1c.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8b109ad7c724c3f9db1732c2f93b175.json"}}], "type": "journal article", "published": "2023-06-01", "journal": {"title": "G3", "issn": "2160-1836", "volume": "13", "issue": "6", "issn-l": "2160-1836"}, "abstract": "Pervasive convergent evolution and in part high incidences of hybridization distinguish wheatears (songbirds of the genus Oenanthe) as a versatile system to address questions at the forefront of research on the molecular bases of phenotypic and species diversification. To prepare the genomic resources for this venture, we here generated and annotated a chromosome-scale assembly of the Eastern black-eared wheatear (Oenanthe melanoleuca). This species is part of the Oenanthe hispanica complex that is characterized by convergent evolution of plumage coloration and high rates of hybridization. The long-read-based male nuclear genome assembly comprises 1.04 Gb in 32 autosomes, the Z chromosome, and the mitogenome. The assembly is highly contiguous (contig N50, 12.6 Mb; scaffold N50, 70 Mb), with 96% of the genome assembled at the chromosome level and 95.5% benchmarking universal single-copy orthologs (BUSCO) completeness. The nuclear genome was annotated with 18,143 protein-coding genes and 31,333 mRNAs (annotation BUSCO completeness, 98.0%), and about 10% of the genome consists of repetitive DNA. The annotated chromosome-scale reference genome of Eastern black-eared wheatear provides a crucial resource for research into the genomics of adaptation and speciation in an intriguing group of passerines.", "doi": "10.1093/g3journal/jkad088", "pmid": "37097035", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10234393"}, {"db": "pii", "key": "7141353"}], "notes": [], "created": "2026-09-23T11:21:58.575Z", "modified": "2026-09-23T11:21:58.676Z"}, {"entity": "publication", "iuid": "ad246699989a49989f9895b01812d11b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ad246699989a49989f9895b01812d11b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ad246699989a49989f9895b01812d11b"}}, "title": "A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats.", "authors": [{"family": "Alaei Kakhki", "given": "Niloofar", "initials": "N"}, {"family": "Schweizer", "given": "Manuel", "initials": "M"}, {"family": "Lutgen", "given": "Dave", "initials": "D"}, {"family": "Bowie", "given": "Rauri C K", "initials": "RCK"}, {"family": "Shirihai", "given": "Hadoram", "initials": "H"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/185297e474cc4e09b1f2087fb7d902a1.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8b109ad7c724c3f9db1732c2f93b175.json"}}], "type": "journal article", "published": "2023-01-04", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "40", "issue": "1", "issn-l": "0737-4038"}, "abstract": "Insights into the processes underpinning convergent evolution advance our understanding of the contributions of ancestral, introgressed, and novel genetic variation to phenotypic evolution. Phylogenomic analyses characterizing genome-wide gene tree heterogeneity can provide first clues about the extent of ILS and of introgression and thereby into the potential of these processes or (in their absence) the need to invoke novel mutations to underpin convergent evolution. Here, we were interested in understanding the processes involved in convergent evolution in open-habitat chats (wheatears of the genus Oenanthe and their relatives). To this end, based on whole-genome resequencing data from 50 taxa of 44 species, we established the species tree, characterized gene tree heterogeneity, and investigated the footprints of ILS and introgression within the latter. The species tree corroborates the pattern of abundant convergent evolution, especially in wheatears. The high levels of gene tree heterogeneity in wheatears are explained by ILS alone only for 30% of internal branches. For multiple branches with high gene tree heterogeneity, D-statistics and phylogenetic networks identified footprints of introgression. Finally, long branches without extensive ILS between clades sporting similar phenotypes provide suggestive evidence for the role of novel mutations in the evolution of these phenotypes. Together, our results suggest that convergent evolution in open-habitat chats involved diverse processes and highlight that phenotypic diversification is often complex and best depicted as a network of interacting lineages.", "doi": "10.1093/molbev/msac278", "pmid": "36578177", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10161543"}, {"db": "pii", "key": "6964684"}], "notes": [], "created": "2026-09-23T11:13:45.057Z", "modified": "2026-09-23T11:13:45.084Z"}, {"entity": "publication", "iuid": "92e5751ccb764c80aaad3eda1d65a060", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/92e5751ccb764c80aaad3eda1d65a060.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/92e5751ccb764c80aaad3eda1d65a060"}}, "title": "Linked-read sequencing enables haplotype-resolved resequencing at population scale.", "authors": [{"family": "Lutgen", "given": "Dave", "initials": "D", "orcid": "0000-0003-0793-3930", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8fccaeeed5bd43e98eb49003c72f050b.json"}}, {"family": "Ritter", "given": "Raphael", "initials": "R"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/185297e474cc4e09b1f2087fb7d902a1.json"}}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Ewels", "given": "Philip", "initials": "P", "orcid": "0000-0003-4101-2502", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fcec263f8dde4e788d6bd4702483c7f4.json"}}, {"family": "Garc\u00eda", "given": "Jes\u00fas T", "initials": "JT", "orcid": "0000-0003-4126-9658", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7611bf7a3894ce89af20a2d3b69c462.json"}}, {"family": "Shirihai", "given": "Hadoram", "initials": "H"}, {"family": "Schweizer", "given": "Manuel", "initials": "M"}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1790a31477c4376957d8c328299db1c.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8b109ad7c724c3f9db1732c2f93b175.json"}}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "volume": "20", "issue": "5", "pages": "1311-1322", "issn-l": "1755-098X"}, "abstract": "The feasibility to sequence entire genomes of virtually any organism provides unprecedented insights into the evolutionary history of populations and species. Nevertheless, many population genomic inferences - including the quantification and dating of admixture, introgression and demographic events, and inference of selective sweeps - are still limited by the lack of high-quality haplotype information. The newest generation of sequencing technology now promises significant progress. To establish the feasibility of haplotype-resolved genome resequencing at population scale, we investigated properties of linked-read sequencing data of songbirds of the genus Oenanthe across a range of sequencing depths. Our results based on the comparison of downsampled (25\u00d7, 20\u00d7, 15\u00d7, 10\u00d7, 7\u00d7, and 5\u00d7) with high-coverage data (46-68\u00d7) of seven bird genomes mapped to a reference suggest that phasing contiguities and accuracies adequate for most population genomic analyses can be reached already with moderate sequencing effort. At 15\u00d7 coverage, phased haplotypes span about 90% of the genome assembly, with 50% and 90% of phased sequences located in phase blocks longer than 1.25-4.6 Mb (N50) and 0.27-0.72 Mb (N90). Phasing accuracy reaches beyond 99% starting from 15\u00d7 coverage. Higher coverages yielded higher contiguities (up to about 7 Mb/1 Mb [N50/N90] at 25\u00d7 coverage), but only marginally improved phasing accuracy. Phase block contiguity improved with input DNA molecule length; thus, higher-quality DNA may help keeping sequencing costs at bay. In conclusion, even for organisms with gigabase-sized genomes like birds, linked-read sequencing at moderate depth opens an affordable avenue towards haplotype-resolved genome resequencing at population scale.", "doi": "10.1111/1755-0998.13192", "pmid": "32419391", "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T10:14:00.932Z", "modified": "2026-09-23T10:52:26.121Z"}, {"entity": "publication", "iuid": "6038235617bf49ffa614f7f6417531bc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6038235617bf49ffa614f7f6417531bc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6038235617bf49ffa614f7f6417531bc"}}, "title": "Linked-read sequencing enables haplotype-resolved resequencing at population scale", "authors": [{"family": "Lutgen", "given": "Dave", "initials": "D", "orcid": "0000-0003-0793-3930", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8fccaeeed5bd43e98eb49003c72f050b.json"}}, {"family": "Ritter", "given": "Raphael", "initials": "R"}, {"family": "Olsen", "given": "Remi Andr\u00e9", "initials": "RA"}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/185297e474cc4e09b1f2087fb7d902a1.json"}}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Ewels", "given": "Phil", "initials": "P", "orcid": "0000-0003-4101-2502", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fcec263f8dde4e788d6bd4702483c7f4.json"}}, {"family": "Garc\u00eda", "given": "Jes\u00fas T", "initials": "JT"}, {"family": "Shirihai", "given": "Hadoram", "initials": "H"}, {"family": "Schweizer", "given": "Manuel", "initials": "M"}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1790a31477c4376957d8c328299db1c.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8b109ad7c724c3f9db1732c2f93b175.json"}}], "type": "posted-content", "published": "2020-01-15", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.01.15.907261", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T14:15:49.379Z", "modified": "2026-09-23T14:15:49.460Z"}, {"entity": "publication", "iuid": "c342a446ad91426884ec9609899722c1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c342a446ad91426884ec9609899722c1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c342a446ad91426884ec9609899722c1"}}, "title": "Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa.", "authors": [{"family": "Vijay", "given": "Nagarjun", "initials": "N", "orcid": "0000-0003-3955-3369", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed1ce78266fe4f6489f9fb88969eb18b.json"}}, {"family": "Weissensteiner", "given": "Matthias", "initials": "M"}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8b109ad7c724c3f9db1732c2f93b175.json"}}, {"family": "Kawakami", "given": "Takeshi", "initials": "T"}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f93e2a7be9704a38ba01e49e1b8e8a56.json"}}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW"}], "type": "journal article", "published": "2017-08-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "26", "issue": "16", "pages": "4284-4295", "issn-l": "0962-1083"}, "abstract": "Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (Ne ) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage-specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in Ne . Utilizing population-level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in Ne would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population-scaled recombination rate (\u03c1), nucleotide diversity (\u03c0) and measures of genetic differentiation between populations (FST , PBS, dxy ) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.", "doi": "10.1111/mec.14195", "pmid": "28570015", "labels": [], "xrefs": [{"db": "GENBANK", "key": "GCA_000247815"}, {"db": "GENBANK", "key": "GCA_000738735"}, {"db": "GENBANK", "key": "GCA_000277835"}], "notes": [], "created": "2018-12-05T11:25:37.752Z", "modified": "2026-09-23T07:44:48.037Z"}]}