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Old but Not (So) Degenerated-Slow Evolution of Largely Homomorphic Sex Chromosomes in Ratites
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.ORCID iD: 0000-0002-5035-1736
2014 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 31, no 6, p. 1444-1453Article in journal (Refereed) Published
Abstract [en]

Degeneration of the nonrecombining chromosome is a common feature of sex chromosome evolution, readily evident by the presence of a pair of largely heteromorphic chromosomes, like in eutherian mammals and birds. However, in ratites (order Palaeognathae, including, e.g., ostrich), the Z and W chromosomes are similar in size and largely undifferentiated, despite avian sex chromosome evolution was initiated > 130 Ma. To better understand what may limit sex chromosome evolution, we performed ostrich transcriptome sequencing and studied genes from the nonrecombining region of the W chromosome. Fourteen gametologous gene pairs present on the W chromosome and Z chromosome were identified, with synonymous sequence divergence of 0.027-0.177. The location of these genes on the Z chromosome was consistent with a sequential increase in divergence, starting 110-157 and ending 24-30 Ma. On the basis of the occurrence of Z-linked genes hemizygous in females, we estimate that about one-third of the Z chromosome does not recombine with the W chromosome in female meiosis. Pairwise d(N)/d(S) between gametologs decreased with age, suggesting strong evolutionary constraint in old gametologs. Lineage-specific d(N)/d(S) was consistently higher in W-linked genes, in accordance with the lower efficacy of selection expected in nonrecombining chromosomes. A higher ratio of GC > AT:AT > GC substitutions in W-linked genes supports a role for GC-biased gene conversion in differentially driving base composition on the two sex chromosomes. A male-to-female (M:F) expression ratio of close to one for recombining genes and close to two for Z-linked genes lacking a W copy show that dosage compensation is essentially absent. Some gametologous genes have retained active expression of the W copy in females (giving a M:F ratio of 1 for the gametologous gene pair), whereas for others W expression has become severely reduced resulting in a M:F ratio of close to 2. These observations resemble the patterns of sex chromosome evolution seen in other avian and mammalian lineages, suggesting similar underlying evolutionary processes, although the rate of sex chromosome differentiation has been atypically low. Lack of dosage compensation may be a factor hindering sex chromosome evolution in this lineage.

Place, publisher, year, edition, pages
2014. Vol. 31, no 6, p. 1444-1453
Keywords [en]
Z chromosome, W chromosome, evolutionary strata, gametologs, nonrecombining chromosome, biased gene conversion
National Category
Biochemistry and Molecular Biology Evolutionary Biology Genetics
Identifiers
URN: urn:nbn:se:uu:diva-228463DOI: 10.1093/molbev/msu101ISI: 000337067400013OAI: oai:DiVA.org:uu-228463DiVA, id: diva2:734285
Available from: 2014-07-16 Created: 2014-07-15 Last updated: 2019-03-25Bibliographically approved
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

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