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Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Michigan, Dept Ecol & Evolutionary Biol, Lab Mol & Genom Evolut, Ann Arbor, MI USA..
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Stockholm Univ, Dept Zool, S-10691 Stockholm, Sweden.
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2017 (English)In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1849, article id 20162756Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
ROYAL SOC , 2017. Vol. 284, no 1849, article id 20162756
Keywords [en]
nucleotide diversity, linked selection, recombination rate, birds
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-320453DOI: 10.1098/rspb.2016.2756ISI: 000395893200017OAI: oai:DiVA.org:uu-320453DiVA, id: diva2:1091475
Available from: 2017-04-26 Created: 2017-04-26 Last updated: 2018-02-22Bibliographically approved
In thesis
1. Determinants of genomic diversity in the collared flycatcher (Ficedula albicollis)
Open this publication in new window or tab >>Determinants of genomic diversity in the collared flycatcher (Ficedula albicollis)
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

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.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2017. p. 43
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1582
Keywords
collared flycatcher, Ficedula albicollis, enetic diversity, sexual conflict, effective population size, nucleotide diversity, linked selection
National Category
Evolutionary Biology
Research subject
Biology with specialization in Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-331919 (URN)978-91-513-0120-4 (ISBN)
Public defence
2017-12-08, Ekmansalen, Norbyvägen 14 A, Uppsala, 10:00 (English)
Opponent
Supervisors
Available from: 2017-11-14 Created: 2017-10-19 Last updated: 2018-03-07

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Dutoit, LudovicVijay, NagarjunMugal, Carina F.Bossu, Christen M.Burri, RetoWolf, JochenEllegren, Hans

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