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Evolutionary genomics in Corvids: – From single nucleotides to structural variants
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. (Jochen Wolf)ORCID iD: 0000-0001-9302-798X
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Heritable genetic variation is the raw material of evolution and can occur in many different forms, from altering single nucleotides to rearranging stretches of millions at once. DNA mutations that result in phenotypic differences are the basis upon which natural selection can act, leading to a shift of the frequency of those mutations.

In this thesis I aim to comprehensively characterize and quantify genetic variation in a natural system, the songbird genus Corvus.

First, we expand on previous work from a hybrid zone of different populations of Eurasian crows. All black carrion crows and black-and-grey hooded crows meet in a narrow hybrid zone in central Europe, and also in central and Southeast Asia. Comparing population genetic data acquired from these three hybrid zones yielded no single genetic region as a candidate responsible for phenotypic divergence, yet a parallelism in sets of genes and gene networks was evident.

Second, we capitalize on varying evolutionary timescales to investigate the driver of the heterogeneous genetic differentiation landscape observed in multiple avian species. Genetic diversity, and thus differentiation, seems to be correlated both between populations within single species and between species which diverged 50 million years ago. This pattern is best explained by conserved broad-scale recombination rate variation, which is in turn likely associated with chromosomal features such as centromeres and telomeres.

Third, we introduce a de-novo assembly of the hooded crow based on long-read sequencing and optical mapping. The use of this technology allowed a glimpse into previously hidden regions of the genome, and uncovered large-scale tandem repeat arrays consisting of a 14-kbp satellite repeat or its 1.2-kpb subunit. Furthermore, these tandem repeat arrays are associated with regions of reduced recombination rate.

Lastly, we extend the population genetic analysis to structural genomic variation, such as insertions and deletions. A large-scale population re-sequencing data set based on short-read and long-read technologies, spread across the entire genus is the foundation of a fine-scale genome-wide map of structural variation. A differentiation outlier approach between all-black carrion and black-and-grey hooded crows identified a 2.25-kilobase LTR retrotransposon inserted 20-kb upstream of the NDP gene. The element, which is fixed in the hooded crow population, is associated with decreased expression of NDP and may be responsible for differences in plumage color.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. , p. 42
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1762
Keywords [en]
evolutionary genetics, genomics, population genetics, selection, recombination, chromosomal features, colouration, insertion, deletion, inversion, crow, tandem repeat, transposable element, gene expression
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-369878ISBN: 978-91-513-0550-9 (print)OAI: oai:DiVA.org:uu-369878DiVA, id: diva2:1275838
Public defence
2019-02-25, Ekmansalen, Norbyvägen 14 A, Uppsala, 13:00 (English)
Opponent
Supervisors
Available from: 2019-02-04 Created: 2019-01-07 Last updated: 2019-02-18
List of papers
1. Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex
Open this publication in new window or tab >>Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex
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2016 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 13195Article in journal (Refereed) Published
Abstract [en]

Uncovering the genetic basis of species diversification is a central goal in evolutionary biology. Yet, the link between the accumulation of genomic changes during population divergence and the evolutionary forces promoting reproductive isolation is poorly understood. Here, we analysed 124 genomes of crow populations with various degrees of genome-wide differentiation, with parallelism of a sexually selected plumage phenotype, and ongoing hybridization. Overall, heterogeneity in genetic differentiation along the genome was best explained by linked selection exposed on a shared genome architecture. Superimposed on this common background, we identified genomic regions with signatures of selection specific to independent phenotypic contact zones. Candidate pigmentation genes with evidence for divergent selection were only partly shared, suggesting context-dependent selection on a multigenic trait architecture and parallelism by pathway rather than by repeated single-gene effects. This study provides insight into how various forms of selection shape genome-wide patterns of genomic differentiation as populations diverge.

National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-308915 (URN)10.1038/ncomms13195 (DOI)000386500600001 ()27796282 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 621-2010-5553EU, European Research Council, ERCStG-336536
Available from: 2016-12-01 Created: 2016-12-01 Last updated: 2019-01-07Bibliographically approved
2. Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa
Open this publication in new window or tab >>Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa
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2017 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 16, p. 4284-4295Article in journal (Refereed) Published
Abstract [en]

Genomewide 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 (N-e) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage-specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in N-e. Utilizing population-level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in N-e would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population-scaled recombination rate (rho), nucleotide diversity (pi) and measures of genetic differentiation between populations (F-ST, PBS, d(xy)) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.

Place, publisher, year, edition, pages
WILEY, 2017
Keywords
background selection, genetic diversity, genetic draft, genetic hitchhiking, linked selection, recombination rate, speciation genetics
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-333716 (URN)10.1111/mec.14195 (DOI)000407255100013 ()28570015 (PubMedID)
Funder
Swedish Research Council, 621-2010-5553, 2014-6325, 2013-08721EU, European Research Council, ERCStG-336536Knut and Alice Wallenberg FoundationSwedish National Infrastructure for Computing (SNIC)
Available from: 2017-11-16 Created: 2017-11-16 Last updated: 2019-01-07Bibliographically approved
3. Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
Open this publication in new window or tab >>Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
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2017 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 27, no 5, p. 697-708Article in journal (Refereed) Published
Abstract [en]

Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality genome references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [ OM]). A three-way comparison including the published short-read assembly (SR) constructed for the same individual allowed assessing assembly properties and pinpointing misassemblies. By combining information from all three assemblies, we characterized 36 previously unidentified large repetitive regions in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole-genome population resequencing data, we estimated the population-scaled recombination rate (rho) and found it to be significantly reduced in these regions. These findings are consistent with an effect of low recombination in regions adjacent to centromeric or subtelomeric heterochromatin and add to our understanding of the processes generating widespread heterogeneity in genetic diversity and differentiation along the genome. By combining three different technologies, our results highlight the importance of adding a layer of information on genome structure that is inaccessible to each approach independently.

Place, publisher, year, edition, pages
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2017
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-323040 (URN)10.1101/gr.215095.116 (DOI)000400392400005 ()28360231 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish National Infrastructure for Computing (SNIC)Swedish Research Council, 621-2010-5553EU, European Research Council, ERCStG-336536
Available from: 2017-06-01 Created: 2017-06-01 Last updated: 2019-01-07Bibliographically approved
4. Fine-scale analysis of Structural Genomic Variation in Natural Populations
Open this publication in new window or tab >>Fine-scale analysis of Structural Genomic Variation in Natural Populations
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(English)Manuscript (preprint) (Other (popular science, discussion, etc.))
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-369880 (URN)
Available from: 2019-01-07 Created: 2019-01-07 Last updated: 2019-01-07

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