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Assessment of phylogenetic approaches to study the timing of recombination cessation on sex chromosomes

Zhang, Hongkai LU ; Sigeman, Hanna LU and Hansson, Bengt LU orcid (2022) In Journal of evolutionary biology 35(12). p.1721-1733
Abstract

The evolution of sex chromosomes is hypothesized to be punctuated by consecutive recombination cessation events, forming “evolutionary strata” that ceased to recombine at different time points. The demarcation of evolutionary strata is often assessed by estimates of the timing of recombination cessation (tRC) along the sex chromosomes, commonly inferred from the level of synonymous divergence or with species phylogenies at gametologous (X-Y or Z-W) sequence data. However, drift and selection affect sequences unpredictably and introduce uncertainty when inferring tRC. Here, we assess two alternative phylogenetic approaches to estimate tRC; (i) the expected likelihood weight (ELW) approach that finds the... (More)

The evolution of sex chromosomes is hypothesized to be punctuated by consecutive recombination cessation events, forming “evolutionary strata” that ceased to recombine at different time points. The demarcation of evolutionary strata is often assessed by estimates of the timing of recombination cessation (tRC) along the sex chromosomes, commonly inferred from the level of synonymous divergence or with species phylogenies at gametologous (X-Y or Z-W) sequence data. However, drift and selection affect sequences unpredictably and introduce uncertainty when inferring tRC. Here, we assess two alternative phylogenetic approaches to estimate tRC; (i) the expected likelihood weight (ELW) approach that finds the most likely topology among a set of hypothetical topologies and (ii) the BEAST approach that estimates tRC with specified calibration priors on a reference species topology. By using Z and W gametologs of an old and a young evolutionary stratum on the neo-sex chromosome of Sylvioidea songbirds, we show that the ELW and BEAST approaches yield similar tRC estimates, and that both outperform two frequently applied approaches utilizing synonymous substitution rates (dS) and maximum likelihood (ML) trees, respectively. Moreover, we demonstrate that both ELW and BEAST provide more precise tRC estimates when sequences of multiple species are included in the analyses.

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author
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type
Contribution to journal
publication status
published
subject
keywords
evolutionary strata, phylogenetic approaches, sex chromosome, timing of recombination cessation
in
Journal of evolutionary biology
volume
35
issue
12
pages
1721 - 1733
publisher
John Wiley & Sons Inc.
external identifiers
  • scopus:85134936272
  • pmid:35895083
ISSN
1010-061X
DOI
10.1111/jeb.14068
language
English
LU publication?
yes
id
7e799f30-2349-4e8a-9b47-6fd80571463f
date added to LUP
2022-09-09 15:33:43
date last changed
2025-02-06 07:45:48
@article{7e799f30-2349-4e8a-9b47-6fd80571463f,
  abstract     = {{<p>The evolution of sex chromosomes is hypothesized to be punctuated by consecutive recombination cessation events, forming “evolutionary strata” that ceased to recombine at different time points. The demarcation of evolutionary strata is often assessed by estimates of the timing of recombination cessation (t<sub>RC</sub>) along the sex chromosomes, commonly inferred from the level of synonymous divergence or with species phylogenies at gametologous (X-Y or Z-W) sequence data. However, drift and selection affect sequences unpredictably and introduce uncertainty when inferring t<sub>RC</sub>. Here, we assess two alternative phylogenetic approaches to estimate t<sub>RC</sub>; (i) the expected likelihood weight (ELW) approach that finds the most likely topology among a set of hypothetical topologies and (ii) the BEAST approach that estimates t<sub>RC</sub> with specified calibration priors on a reference species topology. By using Z and W gametologs of an old and a young evolutionary stratum on the neo-sex chromosome of Sylvioidea songbirds, we show that the ELW and BEAST approaches yield similar t<sub>RC</sub> estimates, and that both outperform two frequently applied approaches utilizing synonymous substitution rates (dS) and maximum likelihood (ML) trees, respectively. Moreover, we demonstrate that both ELW and BEAST provide more precise t<sub>RC</sub> estimates when sequences of multiple species are included in the analyses.</p>}},
  author       = {{Zhang, Hongkai and Sigeman, Hanna and Hansson, Bengt}},
  issn         = {{1010-061X}},
  keywords     = {{evolutionary strata; phylogenetic approaches; sex chromosome; timing of recombination cessation}},
  language     = {{eng}},
  number       = {{12}},
  pages        = {{1721--1733}},
  publisher    = {{John Wiley & Sons Inc.}},
  series       = {{Journal of evolutionary biology}},
  title        = {{Assessment of phylogenetic approaches to study the timing of recombination cessation on sex chromosomes}},
  url          = {{http://dx.doi.org/10.1111/jeb.14068}},
  doi          = {{10.1111/jeb.14068}},
  volume       = {{35}},
  year         = {{2022}},
}