GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes
(2019) In Genome Biology 20(1).- Abstract
BACKGROUND: The nearly neutral theory of molecular evolution predicts that the efficacy of natural selection increases with the effective population size. This prediction has been verified by independent observations in diverse taxa, which show that life-history traits are strongly correlated with measures of the efficacy of selection, such as the dN/dS ratio. Surprisingly, avian taxa are an exception to this theory because correlations between life-history traits and dN/dS are apparently absent. Here we explore the role of GC-biased gene conversion on estimates of substitution rates as a potential driver of these unexpected observations.
RESULTS: We analyze the relationship between dN/dS estimated from alignments of 47 avian... (More)
BACKGROUND: The nearly neutral theory of molecular evolution predicts that the efficacy of natural selection increases with the effective population size. This prediction has been verified by independent observations in diverse taxa, which show that life-history traits are strongly correlated with measures of the efficacy of selection, such as the dN/dS ratio. Surprisingly, avian taxa are an exception to this theory because correlations between life-history traits and dN/dS are apparently absent. Here we explore the role of GC-biased gene conversion on estimates of substitution rates as a potential driver of these unexpected observations.
RESULTS: We analyze the relationship between dN/dS estimated from alignments of 47 avian genomes and several proxies for effective population size. To distinguish the impact of GC-biased gene conversion from selection, we use an approach that accounts for non-stationary base composition and estimate dN/dS separately for changes affected or unaffected by GC-biased gene conversion. This analysis shows that the impact of GC-biased gene conversion on substitution rates can explain the lack of correlations between life-history traits and dN/dS. Strong correlations between life-history traits and dN/dS are recovered after accounting for GC-biased gene conversion. The correlations are robust to variation in base composition and genomic location.
CONCLUSIONS: Our study shows that gene sequence evolution across a wide range of avian lineages meets the prediction of the nearly neutral theory, the efficacy of selection increases with effective population size. Moreover, our study illustrates that accounting for GC-biased gene conversion is important to correctly estimate the strength of selection.
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- author
- Bolívar, Paulina LU ; Guéguen, Laurent ; Duret, Laurent ; Ellegren, Hans and Mugal, Carina F
- publishing date
- 2019-01-07
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Molecular Evolution, Base Composition, Birds/genetics, Chromosomes, Gene Conversion, Genetic Drift, Natural Selection
- in
- Genome Biology
- volume
- 20
- issue
- 1
- article number
- 5
- publisher
- BioMed Central (BMC)
- external identifiers
-
- pmid:30616647
- scopus:85059704184
- ISSN
- 1474-7596
- DOI
- 10.1186/s13059-018-1613-z
- language
- English
- LU publication?
- no
- id
- 7e626a7c-3ed1-498f-a20f-66d952c57fb4
- date added to LUP
- 2024-05-14 11:10:47
- date last changed
- 2024-05-15 04:00:35
@article{7e626a7c-3ed1-498f-a20f-66d952c57fb4,
abstract = {{<p>BACKGROUND: The nearly neutral theory of molecular evolution predicts that the efficacy of natural selection increases with the effective population size. This prediction has been verified by independent observations in diverse taxa, which show that life-history traits are strongly correlated with measures of the efficacy of selection, such as the dN/dS ratio. Surprisingly, avian taxa are an exception to this theory because correlations between life-history traits and dN/dS are apparently absent. Here we explore the role of GC-biased gene conversion on estimates of substitution rates as a potential driver of these unexpected observations.</p><p>RESULTS: We analyze the relationship between dN/dS estimated from alignments of 47 avian genomes and several proxies for effective population size. To distinguish the impact of GC-biased gene conversion from selection, we use an approach that accounts for non-stationary base composition and estimate dN/dS separately for changes affected or unaffected by GC-biased gene conversion. This analysis shows that the impact of GC-biased gene conversion on substitution rates can explain the lack of correlations between life-history traits and dN/dS. Strong correlations between life-history traits and dN/dS are recovered after accounting for GC-biased gene conversion. The correlations are robust to variation in base composition and genomic location.</p><p>CONCLUSIONS: Our study shows that gene sequence evolution across a wide range of avian lineages meets the prediction of the nearly neutral theory, the efficacy of selection increases with effective population size. Moreover, our study illustrates that accounting for GC-biased gene conversion is important to correctly estimate the strength of selection.</p>}},
author = {{Bolívar, Paulina and Guéguen, Laurent and Duret, Laurent and Ellegren, Hans and Mugal, Carina F}},
issn = {{1474-7596}},
keywords = {{Molecular Evolution; Base Composition; Birds/genetics; Chromosomes; Gene Conversion; Genetic Drift; Natural Selection}},
language = {{eng}},
month = {{01}},
number = {{1}},
publisher = {{BioMed Central (BMC)}},
series = {{Genome Biology}},
title = {{GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes}},
url = {{http://dx.doi.org/10.1186/s13059-018-1613-z}},
doi = {{10.1186/s13059-018-1613-z}},
volume = {{20}},
year = {{2019}},
}