uu.seUppsala University Publications
Change search
Link to record
Permanent link

Direct link
BETA
Alternative names
Publications (10 of 171) Show all publications
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
Bolivar, P., Gueguen, L., Duret, L., Ellegren, H. & Mugal, C. (2019). GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes. Genome Biology, 20, Article ID 5.
Open this publication in new window or tab >>GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes
Show others...
2019 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 20, article id 5Article in journal (Refereed) Published
Abstract [en]

Background: The nearly neutral theory of molecular evolution predicts that the efficacy of natural selection increases with the effective population size. This prediction has been verified by independent observations in diverse taxa, which show that life-history traits are strongly correlated with measures of the efficacy of selection, such as the d(N)/d(S) ratio. Surprisingly, avian taxa are an exception to this theory because correlations between life-history traits and d(N)/d(S) are apparently absent. Here we explore the role of GC-biased gene conversion on estimates of substitution rates as a potential driver of these unexpected observations.

Results: We analyze the relationship between d(N)/d(S) estimated from alignments of 47 avian genomes and several proxies for effective population size. To distinguish the impact of GC-biased gene conversion from selection, we use an approach that accounts for non-stationary base composition and estimate d(N)/d(S) separately for changes affected or unaffected by GC-biased gene conversion. This analysis shows that the impact of GC-biased gene conversion on substitution rates can explain the lack of correlations between life-history traits and d(N)/d(S). Strong correlations between life-history traits and d(N)/d(S) are recovered after accounting for GC-biased gene conversion. The correlations are robust to variation in base composition and genomic location.

Conclusions: Our study shows that gene sequence evolution across a wide range of avian lineages meets the prediction of the nearly neutral theory,the efficacy of selection increases with effective population size. Moreover, our study illustrates that accounting for GC-biased gene conversion is important to correctly estimate the strength of selection.

Place, publisher, year, edition, pages
BMC, 2019
Keywords
Nearly neutral theory, Life-history traits, d(N), d(S), GC-biased gene conversion, Base composition, Avian genomes
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-375222 (URN)10.1186/s13059-018-1613-z (DOI)000455139400002 ()30616647 (PubMedID)
Funder
Swedish Research Council, 2013-8271Knut and Alice Wallenberg Foundation, 2014/0044
Available from: 2019-01-30 Created: 2019-01-30 Last updated: 2019-04-09Bibliographically approved
Warmuth, V. & Ellegren, H. (2019). Genotype-free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data. Molecular Ecology Resources, 19(3), 586-596
Open this publication in new window or tab >>Genotype-free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data
2019 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 19, no 3, p. 586-596Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
WILEY, 2019
Keywords
allele frequencies, angsd, demographic inference, genotyping error, RADSeq
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-383154 (URN)10.1111/1755-0998.12990 (DOI)000465220100003 ()30633448 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 2013-8271
Available from: 2019-05-10 Created: 2019-05-10 Last updated: 2019-05-10Bibliographically approved
Rettelbach, A., Nater, A. & Ellegren, H. (2019). How Linked Selection Shapes the Diversity Landscape in Ficedula Flycatchers. Genetics, 212(1), 277-285
Open this publication in new window or tab >>How Linked Selection Shapes the Diversity Landscape in Ficedula Flycatchers
2019 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 212, no 1, p. 277-285Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
GENETICS SOCIETY AMERICA, 2019
Keywords
diversity, background selection, selective sweeps, flycatcher
National Category
Genetics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-383847 (URN)10.1534/genetics.119.301991 (DOI)000466802000018 ()30872320 (PubMedID)
Funder
Swedish Research Council, 2013-8271Knut and Alice Wallenberg Foundation
Available from: 2019-05-24 Created: 2019-05-24 Last updated: 2019-05-24Bibliographically approved
Ellegren, H. (2019). Hvad nytt och nyttigt: Tillkomsten av Sveriges första lärda sällskap: Kungl. Vetenskaps-Societeten i Uppsala. Uppsala: Acta Universitatis Upsaliensis
Open this publication in new window or tab >>Hvad nytt och nyttigt: Tillkomsten av Sveriges första lärda sällskap: Kungl. Vetenskaps-Societeten i Uppsala
2019 (Swedish)Book (Other academic)
Abstract [sv]

Kungl. Vetenskaps-Societeten i Uppsala är Sveriges äldsta lärda sällskap, vår första vetenskapsakademi. Den har sitt ursprung i det Collegium Curiosorum som den framsynte bibliotekarien Erik Benzelius d.y. samlade 1710. Det var i en tid då teologin och humaniora ännu dominerade i lärdomsstaden. Men den vetenskapliga revolutionen drog fram genom Europa och på kontinenten hade vetenskapare börjat organisera sig i akademier. Inspiration hämtades därifrån.

Sällskapet korresponderar med Christopher Polhem kring den nya naturvetenskapen. De skickar ut den unge Emanuel Swedenborg för att bevaka den internationella forskningsfronten. Verksamheten utvecklas och man börjar ger ut landets första vetenskapstidskrift, Acta Literaria Sveciæ. Genom förarbete av Arvid Horn beslutar så Fredrik I 1728 om inrättandet av Kungl. Vetenskaps--Societeten. Under nära 20 år är det Anders Celsius som leder organisationen.

Societetens inledande stadgar utgjorde ett patriotiskt forskningsprogram. Att lyfta fram landets naturtillgångar och unika resurser var viktigt. Ett tecken på detta är att man använder nästan hela sin kassa för att finansiera Linnés lappländska resa 1732. 

Röster höjs dock för att frångå latinet till förmån för publicering på svenska, för att nå ut med nyttiga rön i samhället snarare än att söka internationell spridning. Dessutom föreslås att verksamheten ska flytta till Stockholm. I Hvad nytt och nyttigt beskriver Hans Ellegren händelser under 1700-talets första del, då vetenskapen började bedrivas på ett sätt som känns igen än idag. I arbetet kommer författaren i kontakt med kollegor från en annan tid, och lär känna deras personligheter och egenheter. 

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. p. 306
Series
Nova acta Regiae Societatis scientiarum Upsaliensis. Ser. 5, volumen extra ordinem editum ; 3
National Category
Other Humanities not elsewhere specified
Research subject
History of Sciences and Ideas
Identifiers
urn:nbn:se:uu:diva-383651 (URN)978-91-513-0679-7 (ISBN)
Available from: 2019-08-21 Created: 2019-05-21 Last updated: 2019-08-22
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
Yazdi, H. P. & Ellegren, H. (2018). A Genetic Map of Ostrich Z Chromosome and the Role of Inversions in Avian Sex Chromosome Evolution. Genome Biology and Evolution, 10(8), 2049-2060
Open this publication in new window or tab >>A Genetic Map of Ostrich Z Chromosome and the Role of Inversions in Avian Sex Chromosome Evolution
2018 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 10, no 8, p. 2049-2060Article in journal (Refereed) Published
Abstract [en]

Recombination arrest is a necessary step for the evolution of distinct sex chromosomes. Structural changes, such as inversions, may represent the mechanistic basis for recombination suppression and comparisons of the structural organization of chromosomes as given by chromosome-level assemblies offer the possibility to infer inversions across species at some detail. In birds, deduction of the process of sex chromosome evolution has been hampered by the lack of a validated chromosome-level assembly from a representative of one of the two basal clades of modern birds, Paleognathae. We therefore developed a high-density genetic linkage map of the ostrich Z chromosome and used this to correct an existing assembly, including correction of a large chimeric superscaffold and the order and orientation of other superscaffolds. We identified the pseudoautosomal region as a 52 Mb segment (approximate to 60% of the Z chromosome) where recombination occurred in both sexes. By comparing the order and location of genes on the ostrich Z chromosome with that of six bird species from the other major Glade of birds (Neognathae), and of reptilian outgroup species, 25 Z-linked inversions were inferred in the avian lineages. We defined Z chromosome organization in an early avian ancestor and identified inversions spanning the candidate sex-determining DMRT1 gene in this ancestor, which could potentially have triggered the onset of avian sex chromosome evolution. We conclude that avian sex chromosome evolution has been characterized by a complex process of probably both Z-linked and W-linked inversions (and/or other processes). This study illustrates the need for validated chromosome-level assemblies for inference of genome evolution.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2018
Keywords
sex chromosomes, inversions, assembly correction, linkage analysis
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-365830 (URN)10.1093/gbe/evy163 (DOI)000444553900017 ()30099482 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Available from: 2018-11-26 Created: 2018-11-26 Last updated: 2019-03-25Bibliographically 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
Bolivar, P., Mugal, C., Sebastiano, M. R., Nater, A., Wang, M., Dutoit, L. & Ellegren, H. (2018). Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It. Molecular biology and evolution, 35(10), 2475-2486
Open this publication in new window or tab >>Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It
Show others...
2018 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 35, no 10, p. 2475-2486Article in journal (Refereed) Published
Abstract [en]

The rate of recombination impacts on rates of protein evolution for at least two reasons: it affects the efficacy of selection due to linkage and influences sequence evolution through the process of GC-biased gene conversion (gBGC). We studied how recombination, via gBGC, affects inferences of selection in gene sequences using comparative genomic and population genomic data from the collared flycatcher (Ficedula albicollis). We separately analyzed different mutation categories ("strong"-to-"weak" "weak-to-strong," and GC-conservative changes) and found that gBGC impacts on the distribution of fitness effects of new mutations, and leads to that the rate of adaptive evolution and the proportion of adaptive mutations among nonsynonymous substitutions are underestimated by 22-33%. It also biases inferences of demographic history based on the site frequency spectrum. In light of this impact, we suggest that inferences of selection (and demography) in lineages with pronounced gBGC should be based on GC-conservative changes only. Doing so, we estimate that 10% of nonsynonymous mutations are effectively neutral and that 27% of nonsynonymous substitutions have been fixed by positive selection in the flycatcher lineage. We also find that gene expression level, sex-bias in expression, and the number of protein-protein interactions, but not Hill-Robertson interference (HRI), are strong determinants of selective constraint and rate of adaptation of collared flycatcher genes. This study therefore illustrates the importance of disentangling the effects of different evolutionary forces and genetic factors in interpretation of sequence data, and from that infer the role of natural selection in DNA sequence evolution.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2018
Keywords
d(N)/d(S), distribution of fitness effects, GC-biased gene conversion, gene expression, Hill-Robertson interference
National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-372675 (URN)10.1093/molbev/msy149 (DOI)000452566800011 ()30085180 (PubMedID)
Available from: 2019-01-09 Created: 2019-01-09 Last updated: 2019-04-09Bibliographically 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
Show others...
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
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-5035-1736

Search in DiVA

Show all publications