{"entity": "researcher", "timestamp": "2026-06-17T04:34:26.443Z", "family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "affiliations": ["Department of Ecology and Genetics Uppsala University Uppsala Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c"}}, "publications": [{"entity": "publication", "iuid": "1b64b2e873f440098c5413b843a1c9cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b64b2e873f440098c5413b843a1c9cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b64b2e873f440098c5413b843a1c9cf"}}, "title": "From high masked to high realized genetic load in inbred Scandinavian wolves.", "authors": [{"family": "Smeds", "given": "Linn\u00e9a", "initials": "L", "orcid": "0000-0002-8415-9259", "researcher": {"href": "https://publications.scilifelab.se/researcher/b46a4a275c954de8bb969ef4cda9e33b.json"}}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2023-04-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "32", "issue": "7", "pages": "1567-1580"}, "abstract": "When new mutations arise at functional sites they are more likely to impair than improve fitness. If not removed by purifying selection, such deleterious mutations will generate a genetic load that can have negative fitness effects in small populations and increase the risk of extinction. This is relevant for the highly inbred Scandinavian wolf (Canis lupus) population, founded by only three wolves in the 1980s and suffering from inbreeding depression. We used functional annotation and evolutionary conservation scores to study deleterious variation in a total of 209 genomes from both the Scandinavian and neighbouring wolf populations in northern Europe. The masked load (deleterious mutations in heterozygote state) was highest in Russia and Finland with deleterious alleles segregating at lower frequency than neutral variation. Genetic drift in the Scandinavian population led to the loss of ancestral alleles, fixation of deleterious variants and a significant increase in the per-individual realized load (deleterious mutations in homozygote state; an increase by 45% in protein-coding genes) over five generations of inbreeding. Arrival of immigrants gave a temporary genetic rescue effect with ancestral alleles re-entering the population and thereby shifting deleterious alleles from homozygous into heterozygote genotypes. However, in the absence of permanent connectivity to Finnish and Russian populations, inbreeding has then again led to the exposure of deleterious mutations. These observations provide genome-wide insight into the magnitude of genetic load and genetic rescue at the molecular level, and in relation to population history. They emphasize the importance of securing gene flow in the management of endangered populations.", "doi": "10.1111/mec.16802", "pmid": "36458895", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "Dryad", "key": "10.5061/dryad.7m0cfxpzj"}], "notes": [], "created": "2023-11-29T09:02:42.251Z", "modified": "2024-01-16T13:48:33.734Z"}, {"entity": "publication", "iuid": "84cea954e35f463d9145c008e1921ca1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84cea954e35f463d9145c008e1921ca1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84cea954e35f463d9145c008e1921ca1"}}, "title": "Genomic inference of contemporary effective population size in a large island population of collared flycatchers (Ficedula albicollis).", "authors": [{"family": "Nadachowska-Brzyska", "given": "Krystyna", "initials": "K", "orcid": "0000-0002-8457-310X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc84301b6f3943058c16d3f644713078.json"}}, {"family": "Dutoit", "given": "Ludovic", "initials": "L", "orcid": "0000-0002-0164-9878", "researcher": {"href": "https://publications.scilifelab.se/researcher/32e987a37c504d9eb3069525bbca54ad.json"}}, {"family": "Smeds", "given": "Linn\u00e9a", "initials": "L", "orcid": "0000-0002-8415-9259", "researcher": {"href": "https://publications.scilifelab.se/researcher/b46a4a275c954de8bb969ef4cda9e33b.json"}}, {"family": "Kardos", "given": "Martin", "initials": "M"}, {"family": "Gustafsson", "given": "Lars", "initials": "L", "orcid": "0000-0001-6566-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04fef54f3f5431f86062e52aaf00748.json"}}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "30", "issue": "16", "pages": "3965-3973", "issn-l": "0962-1083"}, "abstract": "Due to its central importance to many aspects of evolutionary biology and population genetics, the long-term effective population size (Ne ) has been estimated for numerous species and populations. However, estimating contemporary Ne is difficult and in practice this parameter is often unknown. In principle, contemporary Ne can be estimated using either analyses of temporal changes in allele frequencies, or the extent of linkage disequilibrium (LD) between unlinked markers. We applied these approaches to estimate contemporary Ne of a relatively recently founded island population of collared flycatchers (Ficedula albicollis). We sequenced the genomes of 85 birds sampled in 1993 and 2015, and applied several temporal methods to estimate Ne at a few thousand (4000-7000). The approach based on LD provided higher estimates of Ne (20,000-32,000) and was associated with high variance, often resulting in infinite Ne . We conclude that whole-genome sequencing data offers new possibilities to estimate high (>1000) contemporary Ne , but also note that such estimates remain challenging, in particular for LD-based methods for contemporary Ne estimation.", "doi": "10.1111/mec.16025", "pmid": "34145933", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "RefSeq", "key": "GCA_000247815.2"}], "notes": [], "created": "2021-12-07T21:36:36.159Z", "modified": "2024-01-16T13:48:38.980Z"}, {"entity": "publication", "iuid": "623279ebcab34ac7abee4d1296a1fd72", "links": {"self": {"href": "https://publications.scilifelab.se/publication/623279ebcab34ac7abee4d1296a1fd72.json"}, "display": {"href": "https://publications.scilifelab.se/publication/623279ebcab34ac7abee4d1296a1fd72"}}, "title": "Whole-genome analyses provide no evidence for dog introgression in Fennoscandian wolf populations.", "authors": [{"family": "Smeds", "given": "Linn\u00e9a", "initials": "L", "orcid": "0000-0002-8415-9259", "researcher": {"href": "https://publications.scilifelab.se/researcher/b46a4a275c954de8bb969ef4cda9e33b.json"}}, {"family": "Aspi", "given": "Jouni", "initials": "J"}, {"family": "Berglund", "given": "Jonas", "initials": "J"}, {"family": "Kojola", "given": "Ilpo", "initials": "I"}, {"family": "Tirronen", "given": "Konstantin", "initials": "K"}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "14", "issue": "3", "pages": "721-734", "issn-l": "1752-4571"}, "abstract": "Hybridization and admixture can threaten the genetic integrity of populations and be of particular concern to endangered species. Hybridization between grey wolves and dogs has been documented in many wolf populations worldwide and is a prominent example of human-mediated hybridization between a domesticated species and its wild relative. We analysed whole-genome sequences from >200 wolves and >100 dogs to study admixture in Fennoscandian wolf populations. A principal component analysis of genetic variation and admixture showed that wolves and dogs were well-separated, without evidence for introgression. Analyses of local ancestry revealed that wolves had <1% mixed ancestry, levels comparable to the degree of mixed ancestry in many dogs, and likely not resulting from recent wolf-dog hybridization. We also show that the founders of the Scandinavian wolf population were genetically inseparable from Finnish and Russian Karelian wolves, pointing at the geographical origin of contemporary Scandinavian wolves. Moreover, we found Scandinavian-born animals among wolves sampled in Finland, demonstrating bidirectional gene flow between the Scandinavian Peninsula and eastern countries. The low incidence of admixture between wolves and dogs in Fennoscandia may be explained by the fact that feral dogs are rare in this part of Europe and that careful monitoring and management act to remove hybrids before they backcross into wolf populations.", "doi": "10.1111/eva.13151", "pmid": "33767747", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "EVA13151"}, {"db": "pmc", "key": "PMC7980305"}, {"db": "Dryad", "key": "10.5061/dryad.8gtht76n6"}], "notes": [], "created": "2021-06-01T20:53:12.887Z", "modified": "2024-01-16T13:48:40.561Z"}, {"entity": "publication", "iuid": "144f11f34c2647769832d1490ea233c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/144f11f34c2647769832d1490ea233c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/144f11f34c2647769832d1490ea233c6"}}, "title": "Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybrids.", "authors": [{"family": "Mugal", "given": "Carina F", "initials": "CF", "orcid": "0000-0003-4220-4928", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b82f77594994c37b37c72b653e20c28.json"}}, {"family": "Wang", "given": "Mi", "initials": "M"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}, {"family": "Wheatcroft", "given": "David", "initials": "D"}, {"family": "\u00c5lund", "given": "Murielle", "initials": "M"}, {"family": "S\u00e9mon", "given": "Marie", "initials": "M"}, {"family": "McFarlane", "given": "S Eryn", "initials": "SE"}, {"family": "Dutoit", "given": "Ludovic", "initials": "L"}, {"family": "Qvarnstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "30", "issue": "12", "pages": "1727-1739", "issn-l": "1088-9051"}, "abstract": "Changes in interacting cis- and trans-regulatory elements are important candidates for Dobzhansky-Muller hybrid incompatibilities and may contribute to hybrid dysfunction by giving rise to misexpression in hybrids. To gain insight into the molecular mechanisms and determinants of gene expression evolution in natural populations, we analyzed the transcriptome from multiple tissues of two recently diverged Ficedula flycatcher species and their naturally occurring F1 hybrids. Differential gene expression analysis revealed that the extent of differentiation between species and the set of differentially expressed genes varied across tissues. Common to all tissues, a higher proportion of Z-linked genes than autosomal genes showed differential expression, providing evidence for a fast-Z effect. We further found clear signatures of hybrid misexpression in brain, heart, kidney, and liver. However, while testis showed the highest divergence of gene expression among tissues, it showed no clear signature of misexpression in F1 hybrids, even though these hybrids were found to be sterile. It is therefore unlikely that incompatibilities between cis-trans regulatory changes explain the observed sterility. Instead, we found evidence that cis-regulatory changes play a significant role in the evolution of gene expression in testis, which illustrates the tissue-specific nature of cis-regulatory evolution bypassing constraints associated with pleiotropic effects of genes.", "doi": "10.1101/gr.254508.119", "pmid": "33144405", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "gr.254508.119"}, {"db": "pmc", "key": "PMC7706733"}], "notes": [], "created": "2020-12-08T23:45:03.587Z", "modified": "2024-01-16T13:48:41.199Z"}, {"entity": "publication", "iuid": "efc537477cec47219f48e554a101fc12", "links": {"self": {"href": "https://publications.scilifelab.se/publication/efc537477cec47219f48e554a101fc12.json"}, "display": {"href": "https://publications.scilifelab.se/publication/efc537477cec47219f48e554a101fc12"}}, "title": "Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation.", "authors": [{"family": "Ottenburghs", "given": "Jente", "initials": "J", "orcid": "0000-0002-0335-9655", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba165a24313c45a2bb601a47bf851eef.json"}}, {"family": "Honka", "given": "Johanna", "initials": "J"}, {"family": "M\u00fcskens", "given": "Gerard J D M", "initials": "GJDM"}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "125", "issue": "1-2", "pages": "73-84", "issn-l": "0018-067X"}, "abstract": "Several studies have uncovered a highly heterogeneous landscape of genetic differentiation across the genomes of closely related species. Specifically, genetic differentiation is often concentrated in particular genomic regions (\"islands of differentiation\") that might contain barrier loci contributing to reproductive isolation, whereas the rest of the genome is homogenized by introgression. Alternatively, linked selection can produce differentiation islands in allopatry without introgression. We explored the influence of introgression on the landscape of genetic differentiation in two hybridizing goose taxa: the Taiga Bean Goose (Anser fabalis) and the Tundra Bean Goose (A. serrirostris). We re-sequenced the whole genomes of 18 individuals (9 of each taxon) and, using a combination of population genomic summary statistics and demographic modeling, we reconstructed the evolutionary history of these birds. Next, we quantified the impact of introgression on the build-up and maintenance of genetic differentiation. We found evidence for a scenario of allopatric divergence (about 2.5 million years ago) followed by recent secondary contact (about 60,000 years ago). Subsequent introgression events led to high levels of gene flow, mainly from the Tundra Bean Goose into the Taiga Bean Goose. This scenario resulted in a largely undifferentiated genomic landscape (genome-wide FST = 0.033) with a few notable differentiation peaks that were scattered across chromosomes. The summary statistics indicated that some peaks might contain barrier loci while others arose in allopatry through linked selection. Finally, based on the low genetic differentiation, considerable morphological variation and incomplete reproductive isolation, we argue that the Taiga and the Tundra Bean Goose should be treated as subspecies.", "doi": "10.1038/s41437-020-0322-z", "pmid": "32451423", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41437-020-0322-z"}, {"db": "pmc", "key": "PMC7413267"}], "notes": [], "created": "2020-11-16T10:27:10.732Z", "modified": "2024-01-16T13:48:41.989Z"}, {"entity": "publication", "iuid": "c061cfb4e0ac42649fd2c7242bb1f8c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c061cfb4e0ac42649fd2c7242bb1f8c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c061cfb4e0ac42649fd2c7242bb1f8c9"}}, "title": "How Linked Selection Shapes the Diversity Landscape in Ficedula Flycatchers", "authors": [{"family": "Rettelbach", "given": "Agnes", "initials": "A"}, {"family": "Nater", "given": "Alexander", "initials": "A", "orcid": "0000-0002-4805-5575", "researcher": {"href": "https://publications.scilifelab.se/researcher/e92d7e509932438bbfccd2aa94c9c107.json"}}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal-article", "published": "2019-05-01", "journal": {"volume": "212", "issn": "1943-2631", "issue": "1", "pages": "277-285", "title": "Genetics", "issn-l": "0016-6731"}, "abstract": "There is an increasing awareness that selection affecting linked neutral sites strongly influences on how diversity is distributed across the genome. In particular, linked selection is likely involved in the formation of heterogenous landscapes of genetic diversity, including genomic regions with locally reduced effective population sizes that manifest as dips in diversity, and \"islands\" of differentiation between closely related populations or species. Linked selection can be in the form of background selection or selective sweeps, and a long-standing quest in population genetics has been to unveil the relative importance of these processes. Here, we analyzed the theoretically expected reduction of diversity caused by linked selection in the collared flycatcher ( Ficedula albicollis) genome and compared this with population genomic data on the distribution of diversity across the flycatcher genome. By incorporating data on recombination rate variation and the density of target sites for selection (including both protein-coding genes and conserved noncoding elements), we found that background selection can explain most of the observed baseline variation in genetic diversity. However, positive selection was necessary to explain the pronounced local diversity dips in the collared flycatcher genome. We confirmed our analytical findings by comprehensive simulations. Therefore, our study demonstrates that even though both background selection and selective sweeps contribute to the heterogeneous diversity landscape seen in this avian system, they play different roles in shaping it.", "doi": "10.1534/genetics.119.301991", "pmid": "30872320", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "genetics.119.301991"}, {"db": "pmc", "key": "PMC6499528"}], "notes": [], "created": "2019-06-11T15:37:32.132Z", "modified": "2024-01-16T13:48:44.388Z"}, {"entity": "publication", "iuid": "0cf9ba0976a24487bb1a3b38581f125b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0cf9ba0976a24487bb1a3b38581f125b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0cf9ba0976a24487bb1a3b38581f125b"}}, "title": "Genotype-free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data.", "authors": [{"family": "Warmuth", "given": "Vera M", "initials": "VM", "orcid": "0000-0002-0305-5125", "researcher": {"href": "https://publications.scilifelab.se/researcher/fee6013dc4c74608981a293e4bb8016b.json"}}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2019-05-00", "journal": {"volume": "19", "issn": "1755-0998", "issue": "3", "pages": "586-596", "title": "Mol Ecol Resour", "issn-l": "1755-098X"}, "abstract": "Restriction-site associated DNA sequencing (RADSeq) facilitates rapid generation of thousands of genetic markers at relatively low cost; however, several sources of error specific to RADSeq methods often lead to biased estimates of allele frequencies and thereby to erroneous population genetic inference. Estimating the distribution of sample allele frequencies without calling genotypes was shown to improve population inference from whole genome sequencing data, but the ability of this approach to account for RADSeq-specific biases remains unexplored. Here we assess in how far genotype-free methods of allele frequency estimation affect demographic inference from empirical RADSeq data. Using the well-studied pied flycatcher (Ficedula hypoleuca) as a study system, we compare allele frequency estimation and demographic inference from whole genome sequencing data with that from RADSeq data matched for samples using both genotype-based and genotype free methods. The demographic history of pied flycatchers as inferred from RADSeq data was highly congruent with that inferred from whole genome resequencing (WGS) data when allele frequencies were estimated directly from the read data. In contrast, when allele frequencies were derived from called genotypes, RADSeq-based estimates of most model parameters fell outside the 95% confidence interval of estimates derived from WGS data. Notably, more stringent filtering of the genotype calls tended to increase the discrepancy between parameter estimates from WGS and RADSeq data, respectively. The results from this study demonstrate the ability of genotype-free methods to improve allele frequency spectrum- (AFS-) based demographic inference from empirical RADSeq data and highlight the need to account for uncertainty in NGS data regardless of sequencing method.", "doi": "10.1111/1755-0998.12990", "pmid": "30633448", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-04-23T09:56:02.159Z", "modified": "2024-01-16T13:48:44.402Z"}, {"entity": "publication", "iuid": "e96e1b6ccf0f4364a2db800881b5dcf6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e96e1b6ccf0f4364a2db800881b5dcf6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e96e1b6ccf0f4364a2db800881b5dcf6"}}, "title": "Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers.", "authors": [{"family": "Nadachowska-Brzyska", "given": "Krystyna", "initials": "K", "orcid": "0000-0002-8457-310X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc84301b6f3943058c16d3f644713078.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f21e70e2864b42ab9fc532c14c069c.json"}}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2019-05-00", "journal": {"volume": "28", "issn": "1365-294X", "issue": "9", "pages": "2290-2304", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Detecting positive selection using genomic data is critical to understanding the role of adaptive evolution. Of particular interest in this context is sex chromosomes since they are thought to play a special role in local adaptation and speciation. We sought to circumvent the challenges associated with statistical phasing when using haplotype-based statistics in sweep scans by benefitting from that whole chromosome haplotypes of the sex chromosomes can be obtained by resequencing of individuals of the hemizygous sex. We analyzed whole Z chromosome haplotypes from 100 females from several populations of four black and white flycatcher species (in birds, females are ZW and males ZZ). Based on integrated haplotype score (iHS) and number of segregating sites by length (nSL) statistics, we found strong and frequent haplotype structure in several regions of the Z chromosome in each species. Most of these sweep signals were population-specific, with essentially no evidence for regions under selection shared among species. Some completed sweeps were revealed by the cross-population extended haplotype homozygosity (XP-EHH) statistic. Importantly, by using statistically phased Z chromosome data from resequencing of males, we failed to recover the signals of selection detected in analyses based on whole chromosome haplotypes from females; instead, what likely represent false signals of selection were frequently seen. This highlights the power issues in statistical phasing and cautions against conclusions from selection scans using such data. The detection of frequent selective sweeps on the avian Z chromosome supports a large role of sex chromosomes in adaptive evolution.", "doi": "10.1111/mec.15021", "pmid": "30653779", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6852393"}], "notes": [], "created": "2019-12-03T10:21:30.297Z", "modified": "2024-01-16T13:48:44.409Z"}, {"entity": "publication", "iuid": "164404029f4a4a9a9c060ce21f1eb099", "links": {"self": {"href": "https://publications.scilifelab.se/publication/164404029f4a4a9a9c060ce21f1eb099.json"}, "display": {"href": "https://publications.scilifelab.se/publication/164404029f4a4a9a9c060ce21f1eb099"}}, "title": "Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.", "authors": [{"family": "K\u00fcnstner", "given": "Axel", "initials": "A"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JB", "orcid": "0000-0002-2958-5183", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c4445d760a64905a9ea6d8664f6a32d.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}, {"family": "Whitney", "given": "Osceola", "initials": "O"}, {"family": "Balakrishnan", "given": "Christopher N", "initials": "CN", "orcid": "0000-0002-0788-0659", "researcher": {"href": "https://publications.scilifelab.se/researcher/363e6c4a51b647bba7e02e1c8e5464fd.json"}}, {"family": "Day", "given": "Lainy", "initials": "L", "orcid": "0000-0002-9122-3044", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a99dd326b9640629732a9fdbded2662.json"}}, {"family": "Edwards", "given": "Scott V", "initials": "SV"}, {"family": "Janes", "given": "Daniel E", "initials": "DE"}, {"family": "Schlinger", "given": "Barney A", "initials": "BA"}, {"family": "Wilson", "given": "Richard K", "initials": "RK"}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Warren", "given": "Wesley C", "initials": "WC"}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2010-03-00", "journal": {"volume": "19 Suppl 1", "issn": "1365-294X", "issue": "Suppl 1", "pages": "266-276", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Next-generation sequencing technology provides an attractive means to obtain large-scale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across the avian genome, we performed brain transcriptome sequencing using Roche 454 technology of 10 different non-model avian species. Contigs from de novo assemblies were aligned to the two available avian reference genomes, chicken and zebra finch. In total, we identified 6499 different genes across all 10 species, with approximately 1000 genes found in each full run per species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes (male-biased mutation) and a negative correlation between the neutral substitution rate (d(S)) and chromosome size. Analyses of the mean d(N)/d(S) ratio (omega) of genes across chromosomes supported the Hill-Robertson effect (the effect of selection at linked loci) and point at stochastic problems with omega as an independent measure of selection. Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms.", "doi": "10.1111/j.1365-294X.2009.04487.x", "pmid": "20331785", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "mid", "key": "NIHMS216459"}, {"db": "pmc", "key": "PMC2904817"}, {"db": "pii", "key": "MEC4487"}], "notes": [], "created": "2017-05-04T14:57:12.592Z", "modified": "2023-06-19T11:19:36.049Z"}]}