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Smeds, L., Kojola, I. & Ellegren, H. (2019). The evolutionary history of grey wolf Y chromosomes. Molecular Ecology, 28(9), 2173-2191
Open this publication in new window or tab >>The evolutionary history of grey wolf Y chromosomes
2019 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 9, p. 2173-2191Article in journal (Refereed) Published
Abstract [en]

Analyses of Y chromosome haplotypes uniquely provide a paternal picture of evolutionary histories and offer a very useful contrast to studies based on maternally inherited mitochondrial DNA (mtDNA). Here we used a bioinformatic approach based on comparison of male and female sequence coverage to identify 4.7 Mb from the grey wolf (Canis lupis) Y chromosome, probably representing most of the male-specific, nonampliconic sequence from the euchromatic part of the chromosome. We characterized this sequence and then identified approximate to 1,500 Y-linked single nucleotide polymorphisms in a sample of 145 resequenced male wolves, including 75 Finnish wolf genomes newly sequenced in this study, and in 24 dogs and eight other canids. We found 53 Y chromosome haplotypes, of which 26 were seen in grey wolves, that clustered in four major haplogroups. All four haplogroups were represented in samples of Finnish wolves, showing that haplogroup lineages were not partitioned on a continental scale. However, regional population structure was indicated because individual haplotypes were never shared between geographically distant areas, and genetically similar haplotypes were only found within the same geographical region. The deepest split between grey wolf haplogroups was estimated to have occurred 125,000 years ago, which is considerably older than recent estimates of the time of divergence of wolf populations. The distribution of dogs in a phylogenetic tree of Y chromosome haplotypes supports multiple domestication events, or wolf paternal introgression, starting 29,000 years ago. We also addressed the disputed origin of a recently founded population of Scandinavian wolves and observed that founding as well as most recent immigrant haplotypes were present in the neighbouring Finnish population, but not in sequenced wolves from elsewhere in the world, or in dogs.

Place, publisher, year, edition, pages
John Wiley & Sons, 2019
Keywords
bioinfomatics, phyloinfomatics, conservation genetics, haplotypes, population genomics, Y chromosome
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-389874 (URN)10.1111/mec.15054 (DOI)000471073000005 ()30788868 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Available from: 2019-07-31 Created: 2019-07-31 Last updated: 2019-07-31Bibliographically approved
Suh, A., Smeds, L. & Ellegren, H. (2018). Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes. Molecular Ecology, 27(1), 99-111
Open this publication in new window or tab >>Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes
2018 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 1, p. 99-111Article in journal (Refereed) Published
Abstract [en]

Transposable elements (TEs) are genomic parasites capable of inserting virtually anywhere in the host genome, with manifold consequences for gene expression, DNA methylation and genomic stability. Notably, they can contribute to phenotypic variation and hence be associated with, for example, local adaptation and speciation. However, some organisms such as birds have been widely noted for the low densities of TEs in their genomes and this has been attributed to a potential dearth in transposition during their evolution. Here, we show that avian evolution witnessed diverse and abundant transposition on very recent timescales. First, we made an in-depth repeat annotation of the collared flycatcher genome, including identification of 23 new, retrovirus-like LTR retrotransposon families. Then, using whole-genome resequencing data from 200 Ficedula flycatchers, we detected 11,888 polymorphic TE insertions (TE presence/absence variations, TEVs) that segregated within and among species. The density of TEVs was one every 1.5-2.5Mb per individual, with heterozygosities of 0.12-0.16. The majority of TEVs belonged to some 10 different LTR families, most of which are specific to the flycatcher lineage. TEVs were validated by tracing the segregation of hundreds of TEVs across a three-generation pedigree of collared flycatchers and also by their utility as markers recapitulating the phylogenetic relationships among flycatcher species. Our results suggest frequent germline invasions of songbird genomes by novel retroviruses as a rich source of structural variation, which may have had underappreciated phenotypic consequences for the diversification of this species-rich group of birds.

Place, publisher, year, edition, pages
John Wiley & Sons, 2018
Keywords
bird, insertion polymorphism, pedigree, retrotransposon, retrovirus, structural variation, transposon
National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-346898 (URN)10.1111/mec.14439 (DOI)000424111400008 ()29171119 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Available from: 2018-04-04 Created: 2018-04-04 Last updated: 2018-04-04Bibliographically approved
Ekblom, R., Brechlin, B., Persson, J., Smeds, L., Johansson, M., Magnusson, J., . . . Ellegren, H. (2018). Genome sequencing and conservation genomics in the Scandinavian wolverine population. Conservation Biology, 32(6), 1301-1312
Open this publication in new window or tab >>Genome sequencing and conservation genomics in the Scandinavian wolverine population
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2018 (English)In: Conservation Biology, ISSN 0888-8892, E-ISSN 1523-1739, Vol. 32, no 6, p. 1301-1312Article in journal (Refereed) Published
Abstract [en]

Genetic approaches have proved valuable to the study and conservation of endangered populations, especially for monitoring programs, and there is potential for further developments in this direction by extending analyses to the genomic level. We assembled the genome of the wolverine (Gulo gulo), a mustelid that in Scandinavia has recently recovered from a significant population decline, and obtained a 2.42 Gb draft sequence representing >85% of the genome and including >21,000 protein-coding genes. We then performed whole-genome resequencing of 10 Scandinavian wolverines for population genomic and demographic analyses. Genetic diversity was among the lowest detected in a red-listed population (mean genome-wide nucleotide diversity of 0.05%). Results of the demographic analyses indicated a long-term decline of the effective population size (N-e) from 10,000 well before the last glaciation to N-e appeared even lower. The genome-wide F-IS level was 0.089 (possibly signaling inbreeding), but this effect was not observed when analyzing a set of highly variable SNP markers, illustrating that such markers can give a biased picture of the overall character of genetic diversity. We found significant population structure, which has implications for population connectivity and conservation. We used an integrated microfluidic circuit chip technology to develop an SNP-array consisting of 96 highly informative markers that, together with a multiplex pre-amplification step, was successfully applied to low-quality DNA from scat samples. Our findings will inform management, conservation, and genetic monitoring of wolverines and serve as a genomic roadmap that can be applied to other endangered species. The approach used here can be generally utilized in other systems, but we acknowledge the trade-off between investing in genomic resources and direct conservation actions.

Place, publisher, year, edition, pages
WILEY, 2018
Keywords
genome assembly, non-invasive sampling, population genetics, single nucleotide polymorphisms
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-387248 (URN)10.1111/cobi.13157 (DOI)000449856900008 ()29935028 (PubMedID)
Funder
Swedish Research CouncilSwedish Research CouncilKnut and Alice Wallenberg Foundation
Available from: 2019-06-27 Created: 2019-06-27 Last updated: 2019-06-27Bibliographically approved
Dutoit, L., Mugal, C., Bolivar, P., Wang, M., Nadachowska-Brzyska, K., Smeds, L., . . . Ellegren, H. (2018). Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome. Molecular Ecology, 27(18), 3572-3581
Open this publication in new window or tab >>Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome
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2018 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 18, p. 3572-3581Article in journal (Other academic) Published
Abstract [en]

Theoretical work suggests that sexual conflict should promote the maintenance of genetic diversity by the opposing directions of selection on sexually antagonistic mutations in males and females. This prediction, so far not been empirically tested on a genome-wide scale, could potentially contribute towards genomic heterogeneity in levels of genetic diversity. We used large-scale population genomic and transcriptomic data from the collared flycatcher (Ficedula albicollis) to analyse how sex-biased gene expression – one outcome of sexual conflict – relates to genetic variability. Here, we demonstrate that the extent of sex-biased gene expression of both male-biased and female-biased genes is significantly correlated with levels of nucleotide diversity in gene sequences and that this correlation extends to the overall levels of genomic diversity. We find evidence for balancing selection in sex-biased genes, suggesting that sex-biased gene expression could be seen as a component counteracting the diversity-reducing effects of linked positive and purifying selection. The observation of significant genetic differentiation between males and females for male-biased genes indicates ongoing sexual conflict and sex-specific viability selection, potentially driven by sexual selection. Our results thus provide a new perspective on the long-standing question in evolutionary biology of how genomes can remain so genetically variable in face of strong natural and sexual selection.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-331832 (URN)10.1111/mec.14789 (DOI)000444577100002 ()30055065 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council
Available from: 2017-10-18 Created: 2017-10-18 Last updated: 2018-11-15Bibliographically approved
Kawakami, T., Mugal, C., Suh, A., Nater, A., Burri, R., Smeds, L. & Ellegren, H. (2017). Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds. Molecular Ecology, 26(16), 4158-4172
Open this publication in new window or tab >>Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds
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2017 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 16, p. 4158-4172Article in journal (Refereed) Published
Abstract [en]

Recombination rate is heterogeneous across the genome of various species and so are genetic diversity and differentiation as a consequence of linked selection. However, we still lack a clear picture of the underlying mechanisms for regulating recombination. Here we estimated fine-scale population recombination rate based on the patterns of linkage disequilibrium across the genomes of multiple populations of two closely related flycatcher species (Ficedula albicollis and F. hypoleuca). This revealed an overall conservation of the recombination landscape between these species at the scale of 200 kb, but we also identified differences in the local rate of recombination despite their recent divergence (<1 million years). Genetic diversity and differentiation were associated with recombination rate in a lineage-specific manner, indicating differences in the extent of linked selection between species. We detected 400-3,085 recombination hotspots per population. Location of hotspots was conserved between species, but the intensity of hotspot activity varied between species. Recombination hotspots were primarily associated with CpG islands (CGIs), regardless of whether CGIs were at promoter regions or away from genes. Recombination hotspots were also associated with specific transposable elements (TEs), but this association appears indirect due to shared preferences of the transposition machinery and the recombination machinery for accessible open chromatin regions. Our results suggest that CGIs are a major determinant of the localization of recombination hotspots, and we propose that both the distribution of TEs and fine-scale variation in recombination rate may be associated with the evolution of the epigenetic landscape.

Place, publisher, year, edition, pages
WILEY, 2017
Keywords
CpG island, GC-biased gene conversion, linked selection, population genomics, recombination, transposon
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-333715 (URN)10.1111/mec.14197 (DOI)000407255100005 ()28597534 (PubMedID)
Funder
Swedish Research Council, 2007-8731, 2010-5650, 2013-8271, 2014-6325Knut and Alice Wallenberg Foundation
Available from: 2017-11-21 Created: 2017-11-21 Last updated: 2018-02-22Bibliographically approved
Smeds, L., Mugal, C. F., Qvarnström, A. & Ellegren, H. (2016). High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree. PLoS Genetics, 12(5), Article ID e1006044.
Open this publication in new window or tab >>High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree
2016 (English)In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 12, no 5, article id e1006044Article in journal (Refereed) Published
Abstract [en]

Recombination is an engine of genetic diversity and therefore constitutes a key process in evolutionary biology and genetics. While the outcome of crossover recombination can readily be detected as shuffled alleles by following the inheritance of markers in pedigreed families, the more precise location of both crossover and non-crossover recombination events has been difficult to pinpoint. As a consequence, we lack a detailed portrait of the recombination landscape for most organisms and knowledge on how this landscape impacts on sequence evolution at a local scale. To localize recombination events with high resolution in an avian system, we performed whole-genome re-sequencing at high coverage of a complete three-generation collared flycatcher pedigree. We identified 325 crossovers at a median resolution of 1.4 kb, with 86% of the events localized to <10 kb intervals. Observed crossover rates were in excellent agreement with data from linkage mapping, were 52% higher in male (3.56 cM/Mb) than in female meiosis (2.28 cM/Mb), and increased towards chromosome ends in male but not female meiosis. Crossover events were non-randomly distributed in the genome with several distinct hot-spots and a concentration to genic regions, with the highest density in promoters and CpG islands. We further identified 267 non-crossovers, whose location was significantly associated with crossover locations. We detected a significant transmission bias (0.18) in favour of 'strong' (G, C) over 'weak' (A, T) alleles at non-crossover events, providing direct evidence for the process of GC-biased gene conversion in an avian system. The approach taken in this study should be applicable to any species and would thereby help to provide a more comprehensive portray of the recombination landscape across organism groups.

National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-296467 (URN)10.1371/journal.pgen.1006044 (DOI)000377197100044 ()27219623 (PubMedID)
Funder
Swedish Research Council, 2010-5650; 2013-8271EU, European Research Council, AdG 24997Knut and Alice Wallenberg Foundation
Available from: 2016-06-16 Created: 2016-06-16 Last updated: 2018-02-22Bibliographically approved
Nadachowska-Brzyska, K., Burri, R., Smeds, L. & Ellegren, H. (2016). PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers. Molecular Ecology, 25(5), 1058-1072
Open this publication in new window or tab >>PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers
2016 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 5, p. 1058-1072Article, review/survey (Refereed) Published
Abstract [en]

Climatic fluctuations during the Quaternary period governed the demography of species and contributed to population differentiation and ultimately speciation. Studies of these past processes have previously been hindered by a lack of means and genetic data to model changes in effective population size (N-e) through time. However, based on diploid genome sequences of high quality, the recently developed pairwise sequentially Markovian coalescent (PSMC) can estimate trajectories of changes in N-e over considerable time periods. We applied this approach to resequencing data from nearly 200 genomes of four species and several populations of the Ficedula species complex of black-and-white flycatchers. N-e curves of Atlas, collared, pied and semicollared flycatcher converged 1-2million years ago (Ma) at an N-e of approximate to 200000, likely reflecting the time when all four species last shared a common ancestor. Subsequent separate N-e trajectories are consistent with lineage splitting and speciation. All species showed evidence of population growth up until 100-200thousand years ago (kya), followed by decline and then start of a new phase of population expansion. However, timing and amplitude of changes in N-e differed among species, and for pied flycatcher, the temporal dynamics of N-e differed between Spanish birds and central/northern European populations. This cautions against extrapolation of demographic inference between lineages and calls for adequate sampling to provide representative pictures of the coalescence process in different species or populations. We also empirically evaluate criteria for proper inference of demographic histories using PSMC and arrive at recommendations of using sequencing data with a mean genome coverage of 18X, a per-site filter of 10 reads and no more than 25% of missing data.

Keywords
Atlas flycatcher, collared flycatcher, coverage, effective population size, pied flycatcher, PSMC, semicollared flycatcher, whole-genome sequencing
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-294812 (URN)10.1111/mec.13540 (DOI)000371433400004 ()26797914 (PubMedID)
Funder
Swedish Research Council, 2007-8731 2010-5650 2013-8271Knut and Alice Wallenberg FoundationEU, European Research Council, AdG 249976
Available from: 2016-08-19 Created: 2016-05-27 Last updated: 2018-02-22Bibliographically approved
Lamatsch, D. K., Adolfsson, S., Senior, A. M., Christiansen, G., Pichler, M., Ozaki, Y., . . . Nakagawa, S. (2015). A Transcriptome Derived Female-Specific Marker from the Invasive Western Mosquitofish (Gambusia affinis). PLoS ONE, 10(2), Article ID e0118214.
Open this publication in new window or tab >>A Transcriptome Derived Female-Specific Marker from the Invasive Western Mosquitofish (Gambusia affinis)
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2015 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 2, article id e0118214Article in journal (Refereed) Published
Abstract [en]

Sex-specific markers are a prerequisite for understanding reproductive biology, genetic factors involved in sex differences, mechanisms of sex determination, and ultimately the evolution of sex chromosomes. The Western mosquitofish, Gambusia affinis, may be considered a model species for sex-chromosome evolution, as it displays female heterogamety (ZW/ZZ), and is also ecologically interesting as a worldwide invasive species. Here, de novo RNA-sequencing on the gonads of sexually mature G. affinis was used to identify contigs that were highly transcribed in females but not in males (i.e., transcripts with ovary-specific expression). Subsequently, 129 primer pairs spanning 79 contigs were tested by PCR to identify sex-specific transcripts. Of those primer pairs, one female-specific DNA marker was identified, Sanger sequenced and subsequently validated in 115 fish. Sequence analyses revealed a high similarity between the identified sex-specific marker and the 3' UTR of the aminomethyl transferase (amt) gene of the closely related platyfish (Xiphophorus maculatus). This is the first time that RNA-seq has been used to successfully characterize a sex-specific marker in a fish species in the absence of a genome map. Additionally, the identified sex-specific marker represents one of only a handful of such markers in fishes.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-251841 (URN)10.1371/journal.pone.0118214 (DOI)000350662100154 ()25707007 (PubMedID)
Available from: 2015-04-27 Created: 2015-04-24 Last updated: 2017-12-04Bibliographically 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
Husby, A., Kawakami, T., Ronnegard, L., Smeds, L., Ellegren, H. & Qvarnström, A. (2015). Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait. Proceedings of the Royal Society of London. Biological Sciences, 282(1806)
Open this publication in new window or tab >>Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait
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2015 (English)In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 282, no 1806Article in journal (Refereed) Published
Abstract [en]

Understanding the genetic basis of traits involved in adaptation is a major challenge in evolutionary biology but remains poorly understood. Here, we use genome-wide association mapping using a custom 50 k single nucleotide polymorphism (SNP) array in a natural population of collared flycatchers to examine the genetic basis of clutch size, an important life-history trait in many animal species. We found evidence for an association on chromosome 18 where one SNP significant at the genome-wide level explained 3.9% of the phenotypic variance. We also detected two suggestive quantitative trait loci (QTLs) on chromosomes 9 and 26. Fitness differences among genotypes were generally weak and not significant, although there was some indication of a sex-by-genotype interaction for lifetime reproductive success at the suggestive QTL on chromosome 26. This implies that sexual antagonism may play a role in maintaining genetic variation at this QTL. Our findings provide candidate regions for a classic avian life-history trait that will be useful for future studies examining the molecular and cellular function of, as well as evolutionary mechanisms operating at, these loci.

Keywords
clutch size, egg production, Ficedula albicollis, fitness trait, GWAS, QTL
National Category
Evolutionary Biology Ecology
Identifiers
urn:nbn:se:uu:diva-252968 (URN)10.1098/rspb.2015.0156 (DOI)000353351000019 ()
Available from: 2015-05-20 Created: 2015-05-18 Last updated: 2018-02-22Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0002-8415-9259

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