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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
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.
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, Animal ecology.
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

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. 

National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-331916OAI: oai:DiVA.org:uu-331916DiVA: diva2:1150659
Note

Dutoit L and Nadachowska-Brzyska K contributed equally.

Available from: 2017-10-19 Created: 2017-10-19 Last updated: 2017-10-19
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. 43 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1582
Keyword
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)
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Available from: 2017-11-14 Created: 2017-10-19 Last updated: 2017-11-14

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