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Nadachowska-Brzyska, K., Burri, R. & Ellegren, H. (2019). Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers. Molecular Ecology, 28(9), 2290-2304
Open this publication in new window or tab >>Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers
2019 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 9, p. 2290-2304Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
John Wiley & Sons, 2019
Keywords
Ficedula flycatchers, haplotype-based statistics, ongoing selection, sex chromosomes
National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-389875 (URN)10.1111/mec.15021 (DOI)000471073000012 ()30653779 (PubMedID)
Funder
Swedish Research Council, 2013-8271Knut and Alice Wallenberg Foundation
Available from: 2019-07-31 Created: 2019-07-31 Last updated: 2019-07-31Bibliographically approved
Schweizer, M., Warmuth, V., Kakhki, N. A., Aliabadian, M., Foerschler, M., Shirihai, H., . . . Burri, R. (2019). Parallel plumage colour evolution and introgressive hybridization in wheatears. Journal of Evolutionary Biology, 32(1), 100-110
Open this publication in new window or tab >>Parallel plumage colour evolution and introgressive hybridization in wheatears
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2019 (English)In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 32, no 1, p. 100-110Article in journal (Refereed) Published
Abstract [en]

Genetic and phenotypic mosaics, in which various phenotypes and different genomic regions show discordant patterns of species or population divergence, offer unique opportunities to study the role of ancestral and introgressed genetic variation in phenotypic evolution. Here, we investigated the evolution of discordant phenotypic and genetic divergence in a monophyletic clade of four songbird taxa-pied wheatear (O. pleschanka), Cyprus wheatear (Oenanthe cypriaca), and western and eastern subspecies of black-eared wheatear (O. h. hispanica and O. h. melanoleuca). Phenotypically, black back and neck sides distinguish pied and Cyprus wheatears from the white-backed/necked black-eared wheatears. Meanwhile, mitochondrial variation only distinguishes western black-eared wheatear. In the absence of nuclear genetic data, and given frequent hybridization among eastern black-eared and pied wheatear, it remains unclear whether introgression is responsible for discordance between mitochondrial divergence patterns and phenotypic similarities, or whether plumage coloration evolved in parallel. Multispecies coalescent analyses of about 20,000 SNPs obtained from RAD data mapped to a draft genome assembly resolve the species tree, provide evidence for the parallel evolution of colour phenotypes and establish western and eastern black-eared wheatears as independent taxa that should be recognized as full species. The presence of the entire admixture spectrum in the Iranian hybrid zone and the detection of footprints of introgression from pied into eastern black-eared wheatear beyond the hybrid zone despite strong geographic structure of ancestry proportions furthermore suggest a potential role for introgression in parallel plumage colour evolution. Our results support the importance of standing heterospecific and/or ancestral variation in phenotypic evolution.

Keywords
incomplete lineage sorting, introgression, melanin-based coloration, standing genetic variation
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-375851 (URN)10.1111/jeb.13401 (DOI)000455543700009 ()30421480 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Available from: 2019-02-01 Created: 2019-02-01 Last updated: 2019-02-01Bibliographically approved
Dutoit, L., Vijay, N., Mugal, C. F., Bossu, C. M., Burri, R., Wolf, J. & Ellegren, H. (2017). Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting. Proceedings of the Royal Society of London. Biological Sciences, 284(1849), Article ID 20162756.
Open this publication in new window or tab >>Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting
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2017 (English)In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1849, article id 20162756Article in journal (Refereed) Published
Abstract [en]

Closely related species may show similar levels of genetic diversity in homologous regions of the genome owing to shared ancestral variation still segregating in the extant species. However, after completion of lineage sorting, such covariation is not necessarily expected. On the other hand, if the processes that govern genetic diversity are conserved, diversity may potentially covary even among distantly related species. We mapped regions of conserved synteny between the genomes of two divergent bird speciescollared flycatcher and hooded crow-and identified more than 600 Mb of homologous regions (66% of the genome). From analyses of whole-genome resequencing data in large population samples of both species we found nucleotide diversity in 200 kb windows to be well correlated (Spearman's rho = 0.407). The correlation remained highly similar after excluding coding sequences. To explain this covariation, we suggest that a stable avian karyotype and a conserved landscape of recombination rate variation render the diversity-reducing effects of linked selection similar in divergent bird lineages. Principal component regression analysis of several potential explanatory variables driving heterogeneity in flycatcher diversity levels revealed the strongest effects from recombination rate variation and density of coding sequence targets for selection, consistent with linked selection. It is also possible that a stable karyotype is associated with a conserved genomic mutation environment contributing to covariation in diversity levels between lineages. Our observations imply that genetic diversity is to some extent predictable.

Place, publisher, year, edition, pages
ROYAL SOC, 2017
Keywords
nucleotide diversity, linked selection, recombination rate, birds
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-320453 (URN)10.1098/rspb.2016.2756 (DOI)000395893200017 ()
Available from: 2017-04-26 Created: 2017-04-26 Last updated: 2018-02-22Bibliographically approved
Dutoit, L., Burri, R., Nater, A., Mugal, C. F. & Hans, E. (2017). Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome. Molecular Ecology Resources, 17(4), 586-597
Open this publication in new window or tab >>Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome
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2017 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, no 4, p. 586-597Article in journal (Refereed) Published
Abstract [en]

Properly estimating genetic diversity in populations of nonmodel species requires a basic understanding of how diversity is distributed across the genome and among individuals. To this end, we analysed whole-genome resequencing data from 20 collared flycatchers (genome size approximate to 1.1 Gb; 10.13 million single nucleotide polymorphisms detected). Genomewide nucleotide diversity was almost identical among individuals (mean = 0.00394, range = 0.00384-0.00401), but diversity levels varied extensively across the genome (95% confidence interval for 200-kb windows = 0.0013-0.0053). Diversity was related to selective constraint such that in comparison with intergenic DNA, diversity at fourfold degenerate sites was reduced to 85%, 3' UTRs to 82%, 5' UTRs to 70% and nondegenerate sites to 12%. There was a strong positive correlation between diversity and chromosome size, probably driven by a higher density of targets for selection on smaller chromosomes increasing the diversity-reducing effect of linked selection. Simulations exploring the ability of sequence data from a small number of genetic markers to capture the observed diversity clearly demonstrated that diversity estimation from finite sampling of such data is bound to be associated with large confidence intervals. Nevertheless, we show that precision in diversity estimation in large out-bred population benefits from increasing the number of loci rather than the number of individuals. Simulations mimicking RAD sequencing showed that this approach gives accurate estimates of genomewide diversity. Based on the patterns of observed diversity and the performed simulations, we provide broad recommendations for how genetic diversity should be estimated in natural populations.

Keywords
genetic markers, nucleotide diversity, population genomics, recombination
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-327358 (URN)10.1111/1755-0998.12602 (DOI)000403258900002 ()
Available from: 2017-08-22 Created: 2017-08-22 Last updated: 2018-02-22Bibliographically approved
Promerová, M., Alavioon, G., Tusso, S., Burri, R. & Immler, S. (2017). No evidence for MHC class II-based non-random mating at the gametic haplotype in Atlantic salmon. Heredity, 118(6), 563-567
Open this publication in new window or tab >>No evidence for MHC class II-based non-random mating at the gametic haplotype in Atlantic salmon
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2017 (English)In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 118, no 6, p. 563-567Article in journal (Refereed) Published
Abstract [en]

Genes of the major histocompatibility complex (MHC) are a likely target of mate choice because of their role in inbreeding avoidance and potential benefits for offspring immunocompetence. Evidence for female choice for complementary MHC alleles among competing males exists both for the pre- and the postmating stages. However, it remains unclear whether the latter may involve non-random fusion of gametes depending on gametic haplotypes resulting in transmission ratio distortion or non-random sequence divergence among fused gametes. We tested whether non-random gametic fusion of MHC-II haplotypes occurs in Atlantic salmon Salmo salar. We performed in vitro fertilizations that excluded interindividual sperm competition using a split family design with large clutch sample sizes to test for a possible role of the gametic haplotype in mate choice. We sequenced two MHC-II loci in 50 embryos per clutch to assess allelic frequencies and sequence divergence. We found no evidence for transmission ratio distortion at two linked MHC-II loci, nor for non-random gamete fusion with respect to MHC-II alleles. Our findings suggest that the gametic MHC-II haplotypes play no role in gamete association in Atlantic salmon and that earlier findings of MHC-based mate choice most likely reflect choice among diploid genotypes. We discuss possible explanations for these findings and how they differ from findings in mammals.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-390738 (URN)10.1038/hdy.2016.129 (DOI)000401023700007 ()28098849 (PubMedID)
Funder
Swedish Research CouncilEU, European Research Council
Available from: 2019-08-14 Created: 2019-08-14 Last updated: 2019-12-16Bibliographically approved
Gaigher, A., Burri, R., Gharib, W. H., Taberlet, P., Roulin, A. & Fumagalli, L. (2016). Family-assisted inference of the genetic architecture of major histocompatibility complex variation. Molecular Ecology Resources, 16(6), 1353-1364
Open this publication in new window or tab >>Family-assisted inference of the genetic architecture of major histocompatibility complex variation
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2016 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 16, no 6, p. 1353-1364Article in journal (Refereed) Published
Abstract [en]

With their direct link to individual fitness, genes of the major histocompatibility complex (MHC) are a popular system to study the evolution of adaptive genetic diversity. However, owing to the highly dynamic evolution of the MHC region, the isolation, characterization and genotyping of MHC genes remain a major challenge. While high-throughput sequencing technologies now provide unprecedented resolution of the high allelic diversity observed at the MHC, in many species, it remains unclear (i) how alleles are distributed among MHC loci, (ii) whether MHC loci are linked or segregate independently and (iii) how much copy number variation (CNV) can be observed for MHC genes in natural populations. Here, we show that the study of allele segregation patterns within families can provide significant insights in this context. We sequenced two MHC class I (MHC-I) loci in 1267 European barn owls (Tyto alba), including 590 offspring from 130 families using Illumina MiSeq technology. Coupled with a high per-individual sequencing coverage (similar to 3000x), the study of allele segregation patterns within families provided information on three aspects of the architecture of MHC-I variation in barn owls: (i) extensive sharing of alleles among loci, (ii) strong linkage of MHC-I loci indicating tandem architecture and (iii) the presence of CNV in the barn owl MHC-I. We conclude that the additional information that can be gained from high-coverage amplicon sequencing by investigating allele segregation patterns in families not only helps improving the accuracy of MHC genotyping, but also contributes towards enhanced analyses in the context of MHC evolutionary ecology.

Keywords
adaptive genetic diversity, birds, copy number variation, gene duplication, immunogenetics, major histocompatibility complex
National Category
Biochemistry and Molecular Biology Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-308630 (URN)10.1111/1755-0998.12537 (DOI)000385941500007 ()27176619 (PubMedID)
Available from: 2016-11-30 Created: 2016-11-29 Last updated: 2017-11-29Bibliographically approved
Burri, R., Antoniazza, S., Gaigher, A., Ducrest, A.-L., Simon, C., Fumagalli, L., . . . Roulin, A. (2016). The genetic basis of color-related local adaptation in a ring-like colonization around the Mediterranean. Evolution, 70(1), 140-153
Open this publication in new window or tab >>The genetic basis of color-related local adaptation in a ring-like colonization around the Mediterranean
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2016 (English)In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 70, no 1, p. 140-153Article in journal (Refereed) Published
Abstract [en]

Uncovering the genetic basis of phenotypic variation and the population history under which it established is key to understand the trajectories along which local adaptation evolves. Here, we investigated the genetic basis and evolutionary history of a clinal plumage color polymorphism in European barn owls (Tyto alba). Our results suggest that barn owls colonized the Western Palearctic in a ring-like manner around the Mediterranean and meet in secondary contact in Greece. Rufous coloration appears to be linked to a recently evolved nonsynonymous-derived variant of the melanocortin 1 receptor (MC1R) gene, which according to quantitative genetic analyses evolved under local adaptation during or following the colonization of Central Europe. Admixture patterns and linkage disequilibrium between the neutral genetic background and color found exclusively within the secondary contact zone suggest limited introgression at secondary contact. These results from a system reminiscent of ring species provide a striking example of how local adaptation can evolve from derived genetic variation.

Keywords
Barn owl, clines, local adaptation, melanin-based coloration, ring species
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-276834 (URN)10.1111/evo.12824 (DOI)000368249200012 ()26773815 (PubMedID)
Available from: 2016-02-16 Created: 2016-02-16 Last updated: 2017-11-30Bibliographically approved
Smeds, L., Warmuth, V., Bolivar, P., Uebbing, S., Burri, R., Suh, A., . . . Ellegren, H. (2015). Evolutionary analysis of the female-specific avian W chromosome. Nature Communications, 6, Article ID 7330.
Open this publication in new window or tab >>Evolutionary analysis of the female-specific avian W chromosome
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2015 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 7330Article in journal (Refereed) Published
Abstract [en]

The typically repetitive nature of the sex-limited chromosome means that it is often excluded from or poorly covered in genome assemblies, hindering studies of evolutionary and population genomic processes in non-recombining chromosomes. Here, we present a draft assembly of the non-recombining region of the collared flycatcher W chromosome, containing 46 genes without evidence of female-specific functional differentiation. Survival of genes during W chromosome degeneration has been highly non-random and expression data suggest that this can be attributed to selection for maintaining gene dose and ancestral expression levels of essential genes. Re-sequencing of large population samples revealed dramatically reduced levels of within-species diversity and elevated rates of between-species differentiation (lineage sorting), consistent with low effective population size. Concordance between W chromosome and mitochondrial DNA phylogenetic trees demonstrates evolutionary stable matrilineal inheritance of this nuclear-cytonuclear pair of chromosomes. Our results show both commonalities and differences between W chromosome and Y chromosome evolution.

National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-259122 (URN)10.1038/ncomms8330 (DOI)000357172100013 ()26040272 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 2007-8731, 2010-5650, 2013-8271
Available from: 2015-07-28 Created: 2015-07-27 Last updated: 2018-02-22Bibliographically approved
Burri, R., Nater, A., Kawakami, T., Mugal, C. F., Ólason, P. I., Smeds, L., . . . Ellegren, H. (2015). Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers. Genome Research, 25(11), 1656-1665
Open this publication in new window or tab >>Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
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2015 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 25, no 11, p. 1656-1665Article in journal (Refereed) Published
Abstract [en]

Speciation is a continuous process during which genetic changes gradually accumulate in the genomes of diverging species. Recent studies have documented highly heterogeneous differentiation landscapes, with distinct regions of elevated differentiation ("differentiation islands") widespread across genomes. However, it remains unclear which processes drive the evolution of differentiation islands; how the differentiation landscape evolves as speciation advances; and ultimately, how differentiation islands are related to speciation. Here, we addressed these questions based on population genetic analyses of 200 resequenced genomes from 10 populations of four Ficedula flycatcher sister species. We show that a heterogeneous differentiation landscape starts emerging among populations within species, and differentiation islands evolve recurrently in the very same genomic regions among independent lineages. Contrary to expectations from models that interpret differentiation islands as genomic regions involved in reproductive isolation that are shielded from gene flow, patterns of sequence divergence (d(XY) relative node depth) do not support a major role of gene flow in the evolution of the differentiation landscape in these species. Instead, as predicted by models of linked selection, genome-wide variation in diversity and differentiation can be explained by variation in recombination rate and the density of targets for selection. We thus conclude that the heterogeneous landscape of differentiation in Ficedula flycatchers evolves mainly as the result of background selection and selective sweeps in genomic regions of low recombination. Our results emphasize the necessity of incorporating linked selection as a null model to identify genome regions involved in adaptation and speciation.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-268800 (URN)10.1101/gr.196485.115 (DOI)000364355600007 ()26355005 (PubMedID)
Funder
EU, European Research Council, AdG 249976Knut and Alice Wallenberg FoundationSwedish Research Council, 2010-5650Swedish Research Council, 80576801Swedish Research Council, 70374401Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Available from: 2015-12-09 Created: 2015-12-09 Last updated: 2018-02-22Bibliographically approved
Nater, A., Burri, R., Kawakami, T., Smeds, L. & Ellegren, H. (2015). Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data. Systematic Biology, 64(6), 1000-1017
Open this publication in new window or tab >>Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data
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2015 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 6, p. 1000-1017Article in journal (Refereed) Published
Abstract [en]

Using genetic data to resolve the evolutionary relationships of species is of major interest in evolutionary and systematic biology. However, reconstructing the sequence of speciation events, the so-called species tree, in closely related and potentially hybridizing species is very challenging. Processes such as incomplete lineage sorting and interspecific gene flow result in local gene genealogies that differ in their topology from the species tree, and analyses of few loci with a single sequence per species are likely to produce conflicting or even misleading results. To study these phenomena on a full phylogenomic scale, we use whole-genome sequence data from 200 individuals of four black-and-white flycatcher species with so far unresolved phylogenetic relationships to infer gene tree topologies and visualize genome-wide patterns of gene tree incongruence. Using phylogenetic analysis in nonoverlapping 10-kb windows, we show that gene tree topologies are extremely diverse and change on a very small physical scale. Moreover, we find strong evidence for gene flow among flycatcher species, with distinct patterns of reduced introgression on the Z chromosome. To resolve species relationships on the background of widespread gene tree incongruence, we used four complementary coalescent-based methods for species tree reconstruction, including complex modeling approaches that incorporate post-divergence gene flow among species. This allowed us to infer the most likely species tree with high confidence. Based on this finding, we show that regions of reduced effective population size, which have been suggested as particularly useful for species tree inference, can produce positively misleading species tree topologies. Our findings disclose the pitfalls of using loci potentially under selection as phylogenetic markers and highlight the potential of modeling approaches to disentangle species relationships in systems with large effective population sizes and post-divergence gene flow.

Keywords
Approximate Bayesian computation, demographic modeling, gene flow, gene tree, incomplete lineage sorting, introgression, phylogenomics, species tree
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-267189 (URN)10.1093/sysbio/syv045 (DOI)000363168100009 ()26187295 (PubMedID)
Funder
EU, European Research CouncilKnut and Alice Wallenberg FoundationSwedish Research Council, 2007-8731Swedish Research Council, 2010-5650Swedish Research Council, 2013-8271
Available from: 2015-11-20 Created: 2015-11-19 Last updated: 2018-02-22Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0002-1813-0079

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