| 51. |
- Broseth, Henrik, et al.
(författare)
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Large-scale noninvasive genetic monitoring of wolverines using scats reveals density dependent adult survival
- 2010
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Ingår i: Biological Conservation. - : Elsevier BV. - 0006-3207 .- 1873-2917. ; 143:1, s. 113-120
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Tidskriftsartikel (refereegranskat)abstract
- Noninvasive genetic monitoring has the potential to estimate vital rates essential for conservation and management of many species. In a long-term genetic capture-mark-recapture study using scats we evaluated temporal variation in adult survival in a wolverine (Gulo gulo) population in southern Norway. In contrast to most previous studies of large mammals we found evidence for negative density dependence in adult survival in this large carnivore. Both sexes showed the same pattern of density dependence, with higher annual survival rates in adult females than males. In addition, we also found an additive mortality effect of harvesting in the population, resulting in the lowest adult survival rates at a combination of high population density and high harvest rate. The additive effects of density and harvest on adult survival of wolverines have relevance to the conservation and management of solitary carnivores with strong intrasexual territoriality, especially for species where combats among conspecifics can cause serious injury or even mortality.
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| 52. |
- Burri, Reto, et al.
(författare)
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Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
- 2015
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 25:11, s. 1656-1665
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 53. |
- Chase, Madeline A., et al.
(författare)
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Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs
- 2021
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Ingår i: Evolution. - : John Wiley & Sons. - 0014-3820 .- 1558-5646. ; 75:9, s. 2179-2196
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Tidskriftsartikel (refereegranskat)abstract
- 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 regions often coincide with high gene density and/or low recombination, leading to the hypothesis that the genomic differentiation landscape mostly reflects a history of background selection, and reveals little about adaptation or speciation. A comparative genomics approach with multiple independent species pairs at a timescale where gene flow and ILS are negligible permits investigating whether different evolutionary processes are responsible for generating lineage-specific versus shared patterns of species differentiation. We use whole-genome resequencing data of 195 individuals from four Ficedula flycatcher species comprising two independent species pairs: collared and pied flycatchers, and red-breasted and taiga flycatchers. We found that both shared and lineage-specific FST peaks could partially be explained by selective sweeps, with recurrent selection likely to underlie shared signatures of selection, whereas indirect evidence supports a role of recombination landscape evolution in driving lineage-specific signatures of selection. This work therefore provides evidence for an interplay of positive selection and recombination to genomic landscape evolution.
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| 54. |
- Corl, Ammon, et al.
(författare)
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Sampling strategies for species trees : The effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal
- 2013
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 67:2, s. 358-366
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Tidskriftsartikel (refereegranskat)abstract
- Systematists can now use multi-locus data to construct species trees that take into account the stochastic nature of gene tree divergence among populations. There is a need to evaluate the new methods for species tree reconstruction in order to determine what kinds of loci to use and the most effective sampling schemes in terms of numbers of genes and numbers of individuals per species. Here we study sampling strategies with an empirical data set for six shorebird species in which we sequenced I mitochondrial, 12 autosomal, and 12 Z-linked loci for >8 individuals/species. We found that sampling greater numbers of genes resulted in substantial improvements to the resolution of the species tree, but sampling greater numbers of individuals had minor effects. We found that Z-linked loci significantly outperformed autosomal loci at all levels of sampling, which likely resulted from the lower effective population size of the Z-linked loci. Therefore, sex-linked loci are likely to be a powerful tool for multi-locus phylogenetic studies. We found that adding a mitochondria] gene to a set of Z-linked or autosomal loci substantially improved the resolution of the tree. Overall, our results help evaluate how best to maximize phylogenetic resolution while minimizing the costs of sequencing and computation when performing species tree analyses.
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| 55. |
- Corl, Ammon, et al.
(författare)
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The genomic signature of sexual selection in the genetic diversity of the sex chromosomes and autosomes
- 2012
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Ingår i: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 66:7, s. 2138-2149
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Tidskriftsartikel (refereegranskat)abstract
- Genomic levels of variation can help reveal the selective and demographic forces that have affected a species during its history. The relative amount of genetic diversity observed on the sex chromosomes as compared to the autosomes is predicted to differ among monogamous and polygynous species. Many species show departures from the expectation for monogamy, but it can be difficult to conclude that this pattern results from variation in mating system because forces other than sexual selection can act upon sex chromosome genetic diversity. As a critical test of the role of mating system, we compared levels of genetic diversity on the Z chromosome and autosomes of phylogenetically independent pairs of shorebirds that differed in their mating systems. We found general support for sexual selection shaping sex chromosome diversity because most polygynous species showed relatively reduced genetic variation on their Z chromosomes as compared to monogamous species. Differences in levels of genetic diversity between the sex chromosomes and autosomes may therefore contribute to understanding the long-term history of sexual selection experienced by a species.
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| 56. |
- Craig, Rory J., et al.
(författare)
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Natural selection beyond genes : Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis)
- 2018
-
Ingår i: Molecular Ecology. - : WILEY. - 0962-1083 .- 1365-294X. ; 27:2, s. 476-492
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Tidskriftsartikel (refereegranskat)abstract
- 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 functional, sequence is poorly understood in most species. Moreover, identification and analysis of the full suite of functional sequence are particularly important for the understanding of the genetic basis of trait loci identified in genome scans or quantitative trait locus mapping efforts. We report that similar to 6.6% of the collared flycatcher genome (74.0Mb) is spanned by similar to 1.28 million CEs, a higher proportion of the genome but a lower total amount of conserved sequence than has been reported in mammals. We identified >200,000 CEs specific to either the archosaur, avian, neoavian or passeridan lineages, constituting candidates for lineage-specific adaptations. Importantly, no less than similar to 71% of CE sites were nonexonic (52.6Mb), and conserved nonexonic sequence density was negatively correlated with functional exonic density at local genomic scales. Additionally, nucleotide diversity was strongly reduced at nonexonic conserved sites (0.00153) relative to intergenic nonconserved sites (0.00427). By integrating deep transcriptome sequencing and additional genome annotation, we identified novel protein-coding genes, long noncoding RNA genes and transposon-derived (exapted) CEs. The approach taken here based on the use of a progressive cactus whole-genome alignment to identify CEs should be readily applicable to nonmodel organisms in general and help to reveal the rich repertoire of putatively functional noncoding sequence as targets for selection.
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| 57. |
- Dutoit, Ludovic, et al.
(författare)
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Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting
- 2017
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : ROYAL SOC. - 0962-8452 .- 1471-2954. ; 284:1849
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 58. |
- Dutoit, Ludovic
(författare)
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Determinants of genomic diversity in the collared flycatcher (Ficedula albicollis)
- 2017
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Individuals vary from each other in their genetic content. Genetic diversity is at the core of the evolutionary theory. Rooted in a solid theoretical framework developed as early as the 1930s, current empirical observations of genomic diversity became possible due to technological advances. These measurements, originally based on a few gene sequences from several individuals, are becoming possible at the genome scale for entire populations. We can now explore how evolutionary forces shape diversity levels along different parts of the genome. In this thesis, I focus on the variation in levels of diversity within genomes using avian systems and in particular that of the collared flycatcher (Ficedula albicollis). First, I describe the variation in genetic diversity along the genome of the collared flycatcher and compare it to the amount of variation in diversity across individuals within the population. I provide guidelines on how a small number of makers can capture the extent of variability in a population. Second, I investigate the stability of the local levels of diversity in the genome across evolutionary time scales by comparing collared flycatcher to the hooded crow (Corvus (corone) corone). Third, I study how selection can maintain variation through pervasive evolutionary conflict between sexes. Lastly, I explore how shifts in genome-wide variant frequencies across few generations can be utilised to estimate the effective size of population.
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| 59. |
- Dutoit, Ludovic, et al.
(författare)
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Estimation of contemporary effect population size in an island population of the collared flycatcher (Ficedula albicollis) using large-scale genome data
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Due to its central importance to many aspects of evolutionary biology and population genetics, the long-term effective population size (Ne) has been estimated for numerous species and populations. However, estimating contemporary Ne is difficult and in practice this parameter is often not known. In principle, contemporary Ne can be estimated using either analyses of temporal changes in allele frequencies or the extent of linkage disequilibrium (LD) between unlinked markers. We applied these approaches for contemporary Ne estimation of a relatively recently founded island population of collared flycatchers (Ficedula albicollis). We sequenced the genomes of 85 birds sampled in 1993 and 2015, and used a method of Jorde & Ryman (2007) to estimate Ne to ≈5,000 based on the amount of genetic drift observed between the two cohorts. This corresponds to an effective size/census size (Ne/Nc) ratio of ≈0.5. An approach based on LD applied to each cohort could not separate from Ne infinity. When individuals from the two cohorts were pooled, Ne was estimated to 10,000-25,000, but these estimates may be sensitive to biases. We conclude that whole-genome sequence data offer new possibilities for estimation of contemporary Ne, but also note that such estimation remains difficult.
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| 60. |
- Dutoit, Ludovic, et al.
(författare)
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Genomic distribution and estimation of nucleotide diversity in natural populations : perspectives from the collared flycatcher (Ficedula albicollis) genome
- 2017
-
Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 17:4, s. 586-597
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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