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Variation in the Z Chromosome to Autosomes Ratio of Genetic Diversity across Birds and its Relationship to the Fast-Z effect
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
(English)Manuscript (preprint) (Other academic)
Keywords [en]
sex chromosomes, genetic diversity, Fast-Z evolution, genetic drift, selection
National Category
Evolutionary Biology
Research subject
Biology with specialization in Evolutionary Genetics
Identifiers
URN: urn:nbn:se:uu:diva-380263OAI: oai:DiVA.org:uu-380263DiVA, id: diva2:1298906
Available from: 2019-03-25 Created: 2019-03-25 Last updated: 2019-04-09
In thesis
1. The evolution of sex chromosomes and sex-linked sequences in birds
Open this publication in new window or tab >>The evolution of sex chromosomes and sex-linked sequences in birds
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Identifying the processes involved in the evolution of suppressed recombination between sex chromosomes and understanding their consequences for the evolutionary dynamics of sex-linked loci have been major topics of research during the last century. In this thesis, I used the avian ZW system, where females are the heterogametic sex, to investigate the underlying processes in sex chromosome evolution in birds. I identified the gametologous genes between the largely recombining Z and W chromosomes of ostrich and dated the timing of the cessation of recombination to prior to the split of modern birds. I then constructed a genetic map of the ostrich Z chromosome and corrected its assembly in order to obtain the ancestral organization of the Z chromosome in a basal clade of birds. By analyzing the inversion events across the avian phylogeny, I concluded that a combination of Z- and possibly W-linked inversions might have been responsible for the evolution of suppressed recombination in avian sex chromosomes. To understand the determinants of levels of genetic diversity on Z chromosome compared to autosomes, I calculated Z to autosome (Z:A) genetic diversity across 32 avian species. This revealed a broad range of Z:A genetic diversity, between 0.278 – 1.27. Lineage-specific estimates of the nonsynonymous to synonymous substitution rate ratio (dN:dS) for autosomal and Z-linked genes further revealed a Fast-Z effect in the majority of birds. The lack of a significant correlation between Z:A dN:dS and Z:A genetic diversity indicated that genetic drift might not be sufficient to explain faster evolution of Z-linked genes, suggesting that positive selection might also contribute to the observed values. Finally, I calculated genetic diversity and linkage disequilibrium (LD) along the pseudoautosomal region (PAR) of the Z chromosome using population genomics data of ostrich. In contrast to theoretical expectation, levels of diversity on the PAR were not significantly higher close to the sex-determining region (SDR) compared to autosomal values. Additionally, I observed a lower level of LD on the PAR compared to the average for the Z chromosome and no significant level of LD across the PAR boundary was detected, indicating recombination allows the boundary-proximal region of PAR to behave independently of SDR. Considered together with a higher level of recombination rate in females in the proximity of the SDR, this observation might help explain the maintenance of a long PAR in ostriches and other ratites. Altogether, the results of this thesis make a modest contribution to our understanding of sex chromosome evolution in birds.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. p. 51
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1788
Keywords
sex chromosomes, female heterogamety, recombination suppression, genetic map, inversions, genetic diversity, pseudoautosomal region
National Category
Evolutionary Biology Genetics
Research subject
Biology with specialization in Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-379665 (URN)978-91-513-0612-4 (ISBN)
Public defence
2019-05-20, Lindahlsalen, Evolutionsbiologiskt centrum, Norbyvägen 18A, Uppsala, 13:00 (English)
Opponent
Supervisors
Available from: 2019-04-23 Created: 2019-03-25 Last updated: 2019-06-18
2. Rates and patterns of molecular evolution in avian genomes
Open this publication in new window or tab >>Rates and patterns of molecular evolution in avian genomes
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Evolution is the change in inherited characteristics of a population through subsequent generations. The interplay of several evolutionary mechanisms determines the rate at which this change occurs. In short, genetic variation is generated though mutation, and the fate of these mutations in a population is determined mainly by the combined effect of genetic drift, natural selection and recombination. Elucidating the relative impact of these mechanisms is complex; making it a long-standing question in evolutionary biology. In this thesis, I focus on disentangling the relative roles of these evolutionary mechanisms and genetic factors in determining rates and patterns of evolution at the molecular level, by studying variation in the DNA sequence of multiple avian species, and in particular the collared flycatcher (Ficedula albicollis). Specifically, I aim to further our understanding regarding the impact of recombination rate on genome evolution, through its interaction with the efficacy of selection and through the process of GC-biased gene conversion (gBGC), which has been poorly characterized in birds. I demonstrate that gBGC has a pervasive effect on the genome of the collared flycatcher and other avian species, as it increases the substitution rate and affects interpretations of the impact of natural selection and adaptation. Interestingly, its effect is even stronger in neutrally evolving sites compared to sites evolving under selection. After accounting for gBGC, I disentangle the true impact of natural selection versus non-adaptive processes in determining rates of molecular evolution in the collared flycatcher genome, shedding light on the process of adaptation. Finally, I demonstrate the significant role of recombination through its impact on linked selection, along with mutation rate differences, in determining relative levels of genetic diversity and their relationship to the fast-Z effect across the avian phylogeny. This thesis urges future studies to account for the effect of recombination before interpreting patterns of selection in sequence evolution.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. p. 51
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1800
Keywords
Molecular evolution, recombination, GC-biased gene conversion, Hill-Robertson interference, effective population size, dN/dS, distribution of fitness effects, avian genomes, collared flycatcher, sex chromosomes
National Category
Evolutionary Biology Genetics
Research subject
Biology with specialization in Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-381373 (URN)978-91-513-0637-7 (ISBN)
Public defence
2019-06-11, Evolutionary Biology Center, Norbyvägen 14, Uppsala, 13:00 (English)
Opponent
Supervisors
Available from: 2019-05-20 Created: 2019-04-09 Last updated: 2019-06-17

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