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Genome Biol Evol. 2018 Feb 1;10(2):507-520. doi: 10.1093/gbe/evy015.

Disentangling the Causes for Faster-X Evolution in Aphids.

Author information

1
INRA UMR IGEPP Domaine de la Motte, Le Rheu, France.
2
CNRS UMR 6553 ECOBIO, Université de Rennes 1, France.
3
CNRS UMR 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, France.
4
INRIA Centre Rennes - Bretagne Atlantique, GenOuest, Rennes, France.
5
Institute of Population Genetics, Vetmeduni Vienna, Vienna, Austria.
6
Department of Biology, University of Rochester.
7
Multidisciplinary Center for Advance Research and Studies (MCARS), Jamia Millia Islamia, New Delhi, India.
8
Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France.
9
Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Centre National de Génotypage (CNG), Evry, France.
10
BIOEPAR, INRA, ONIRIS, La Chantrerie, Nantes, France.

Abstract

The faster evolution of X chromosomes has been documented in several species, and results from the increased efficiency of selection on recessive alleles in hemizygous males and/or from increased drift due to the smaller effective population size of X chromosomes. Aphids are excellent models for evaluating the importance of selection in faster-X evolution because their peculiar life cycle and unusual inheritance of sex chromosomes should generally lead to equivalent effective population sizes for X and autosomes. Because we lack a high-density genetic map for the pea aphid, whose complete genome has been sequenced, we first assigned its entire genome to the X or autosomes based on ratios of sequencing depth in males (X0) to females (XX). Then, we computed nonsynonymous to synonymous substitutions ratios (dN/dS) for the pea aphid gene set and found faster evolution of X-linked genes. Our analyses of substitution rates, together with polymorphism and expression data, showed that relaxed selection is likely to be the greatest contributor to faster-X because a large fraction of X-linked genes are expressed at low rates and thus escape selection. Yet, a minor role for positive selection is also suggested by the difference between substitution rates for X and autosomes for male-biased genes (but not for asexual female-biased genes) and by lower Tajima's D for X-linked compared with autosomal genes with highly male-biased expression patterns. This study highlights the relevance of organisms displaying alternative chromosomal inheritance to the understanding of forces shaping genome evolution.

KEYWORDS:

drift; evolutionary rates; hemizygosity; selection; sex chromosome; sex-biased expression

PMID:
29360959
PMCID:
PMC5798017
DOI:
10.1093/gbe/evy015
[Indexed for MEDLINE]
Free PMC Article

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