Hans Ellegren's research while affiliated with Uppsala University and other places

Publications (687)

Article
Information on genetic population structure provides important knowledge for species conservation. Yet, few studies combine extensive genetic data to evaluate the structure and population dynamics of transboundary populations. Here we used single nucleotide polymorphisms (SNPs), microsatellites and mitochondrial haplotypes to analyze the genetic po...
Preprint
Any random genetic change is more likely to impair than improve fitness, a situation that owes to the fact that contemporary genotypes bear a history of having been shaped by natural selection for a very long time. Most mutations are thus deleterious and generate a genetic load that can be difficult to handle in small populations and increase the r...
Article
Genetic drift can dramatically change allele frequencies in small populations and lead to reduced levels of genetic diversity, including loss of segregating variants. However, there is a shortage of quantitative studies of how genetic diversity changes over time in natural populations, especially on genome-wide scales. Here, we analyzed whole-genom...
Article
Climate change influences population demography by altering patterns of gene flow and reproductive isolation. Direct mutation rates offer the possibility for accurate dating on the within-species level but are currently only available for a handful of vertebrate species. Here, we use the first directly estimated mutation rate in birds to study the...
Article
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 not known. In principle, contemporary Ne can be estimated using...
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A current debate within population genomics surrounds the relevance of patterns of genomic differentiation between closely related species for our understanding of adaptation and speciation. Mounting evidence across many taxa suggests that the same genomic regions repeatedly develop elevated differentiation in independent species pairs. These regio...
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Hybridisation and admixture can threaten the genetic integrity of populations and be of particular concern to endangered species. Hybridisation between grey wolves and dogs has been documented in many wolf populations worldwide and is a prominent example of human‐mediated hybridisation between a domesticated species and its wild relative. We analys...
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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 tran...
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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...
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The effect of selection on linked neutral sites is widely used to detect selected loci. While existing models provide a good description of the patterns expected from background selection or sweeps on a small... There is an increasing awareness that selection affecting linked neutral sites strongly influences on how diversity is distributed across...
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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. Here we used a bioinformatic approach based on comparison of male and female sequence coverage to identify 4.7 Mb from the grey wolf Y chromosome, likely repre...
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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...
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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...
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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...
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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 speci...
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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 a...
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Theoretical work suggests that sexual conflict should promote the maintenance of genetic diversity by the opposing directions of selection on males and females. If such conflict is pervasive, it could potentially lead to genomic heterogeneity in levels of genetic diversity an idea that so far has not been empirically tested on a genome‐wide scale....
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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...
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It is becoming increasingly clear that a significant proportion of the functional sequence within eukaryotic genomes is noncoding. However, since the identification of conserved elements (CEs) has been restricted to a limited number of model organisms, the dynamics and evolutionary character of the genomic landscape of conserved, and hence likely f...
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Inbreeding (mating between relatives) is a major concern for conservation as it decreases individual fitness and can increase the risk of population extinction. We used whole-genome resequencing of 97 grey wolves (Canis lupus) from the highly inbred Scandinavian wolf population to identify 'identical-by-descent' (IBD) chromosome segments as runs of...
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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...
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Knowledge about the underlying genetic architecture of phenotypic traits is needed to understand and predict evolutionary dynamics. The number of causal loci, magnitude of the effects and location in the genome are, however, still largely unknown. Here, we use genome-wide single-nucleotide polymorphism (SNP) data from two large-scale data sets on h...
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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...
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Genome-wide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (Ne ) are candidates for barrier loci contributing to population divergen...
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Polymorphism in cis-regulatory sequences can lead to different levels of expression for the two alleles of a gene, providing a starting point for the evolution of gene expression. Little is known about the genome-wide abundance of genetic variation in gene regulation in natural populations but analysis of allele-specific expression (ASE) provides a...
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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 conser...
Preprint
Genome-wide screens of genetic variation can reveal signatures of population-specific selection implicated in adaptation and speciation. Yet, unrelated processes such as linked selection arising as a consequence of genome architecture can generate comparable signatures across taxa. To investigate prevalence and phylogenetic stability of linked sele...
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Identifying causal genetic variants underlying heritable phenotypic variation is a longstanding goal in evolutionary genetics. We previously identified several quantitative trait loci (QTL) for five morphological traits in a captive population of zebra finches (Taeniopygia guttata) by whole-genome linkage mapping. We here follow up on these studies...
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Individual inbreeding and historical demography can be estimated by analyzing runs of homozygosity (ROH), which are indicative of chromosomal segments... Individual inbreeding and historical demography can be estimated by analyzing runs of homozygosity (ROH), which are indicative of chromosomal segments of identity by descent (IBD). Such analyses h...
Article
As populations diverge, genetic differences accumulate across the genome. Spurred by rapid developments in sequencing technology, genome-wide population surveys of natural populations promise insights into the evolutionary processes and the genetic basis underlying speciation. Although genomic regions of elevated differentiation are the focus of se...
Article
Properly estimating genetic diversity in populations of non-model species requires a basic understanding of how diversity is distributed across the genome and among individuals. To this end we analysed whole-genome re-sequencing data from 20 collared flycatchers (genome size ?1.1 Gb; 10.13 million single nucleotide polymorphisms detected). Genome-w...
Article
Inbreeding depression (reduced fitness of individuals with related parents) has long been a major focus of ecology, evolution, and conservation biology. Despite decades of research, we still have a limited understanding of the strength, underlying genetic mechanisms, and demographic consequences of inbreeding depression in the wild. Studying inbree...
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The fidelity of DNA replication together with repair mechanisms ensure that the genetic material is properly copied from one generation to another. However, at the extremely rare occasions when damages to DNA or replication errors are not repaired, germline mutations can be transmitted to the next generation. Because of the rarity of these events,...
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Genomewide association studies (GWAS) enable detailed dissections of the genetic basis for organisms' ability to adapt to a changing environment. In long‐term studies of natural populations, individuals are often marked at one point in their life and then repeatedly recaptured. It is therefore essential that a method for GWAS includes the process o...
Data
Appendix S1. Transforming underlying effects to observed effects for binary traits.
Article
Genetic polymorphism varies among species and within genomes, and has important implications for the evolution and conservation of species. The determinants of this variation have been poorly understood, but population genomic data from a wide range of organisms now make it possible to delineate the underlying evolutionary processes, notably how va...
Data
The distribution of transmission of recombinant versus non-recombinant chromosomes for the whole data set, separate for females and males. (PDF)
Data
Genomic distribution of CO events on flycatcher chromosomes 4A-12, and Z. Maternal events are shown to the left of each chromosomes in red and paternal events are shown to the right in blue. Each symbol (diamond, triangle, box, cross, plus) represents one of the five F2 offspring in which CO events were observed. (PDF)
Data
Relationship between genetic distance and physical length. Cumulative, sex-average genetic distance along chromosomes obtained from the distribution of CO events are shown for the six largest chromosomes. (PDF)
Data
Details of phasing. Phasing of haplotypes originating from the paternal (left) and maternal (right) grandparents. Genotypes are shown only for the five individuals that need to be considered for the line in question, and are given as 0 (reference allele) and 1 (alternative allele). In the paternal example, the first and third SNPs in the F2 are inf...
Data
Mean autosomal sequence coverage for each of the 11 birds included in the study. (DOCX)
Article
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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 recombinat...
Data
Genomic distribution of CO events on flycatcher chromosomes 1–4. Maternal events are shown to the left of each chromosomes in red and paternal events are shown to the right in blue. Each symbol (diamond, triangle, box, cross, plus) represents one of the five F2 offspring in which CO events were observed. (PDF)
Data
Distribution of the number of non-crossover events in relation to distance to nearest chromosome end. (a) chromosomes >100 Mb (males, black; female, white) and chromosomes 50–100 Mb (males, grey; females dotted) for 10 Mb intervals, and (b) the terminal 10 Mb of all chromosomes in 1 Mb intervals (males, black; female, white). (PDF)
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Summary statistics for recombination events detected in F2 offspring. (DOCX)
Data
Genomic distribution of CO events on flycatcher chromosomes 13–28. Maternal events are shown to the left of each chromosomes in red and paternal events are shown to the right in blue. Each symbol (diamond, triangle, box, cross, plus) represents one of the five F2 offspring in which CO events were observed. (PDF)
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Distribution of the length (kb) of identified CO intervals. Only regions shorter than 20 kb are shown; there are 24 additional intervals larger than 20 kb. (PDF)
Data
Appendix S1 Genome annotation methods. Figure S1. Expression variance (a), divergence (calculated as difference in log2 means) (b), and divergence/variance (c) compared for the different analyzed organs. Figure S2. Outlier genes show both within‐ (σw) and between‐species (σb) variance components which spread over their whole respective genome‐wid...
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The nearly neutral theory of molecular evolution predicts that small populations should accumulate deleterious mutations at a faster rate than large populations. The analysis of non-synonymous (dN) vs. synonymous (dS) substitution rates in birds vs. mammals, however, has provided contradictory results, questioning the generality of the nearly neutr...
Data
Table S1 Number of individuals per population with a mean genome coverage of ≥18X, and meeting the criteria of a per‐site filter of ≥10 reads and with no more than 25% of missing data. Fig. S1 PSMC results for a test population of collared flycatchers for different per‐site filtering regimes: no filtering (A), read depth ≥1/3 of the average read d...