Adaptation and Conservation throughout the Drosophila melanogaster Life-Cycle

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Coronado-Zamora , M , Salvador-Martinez , I , Castellano , D , Barbadilla , A & Salazar-Ciudad , I 2019 , ' Adaptation and Conservation throughout the Drosophila melanogaster Life-Cycle ' , Genome Biology and Evolution , vol. 11 , no. 5 , pp. 1463-1482 . https://doi.org/10.1093/gbe/evz086

Title: Adaptation and Conservation throughout the Drosophila melanogaster Life-Cycle
Author: Coronado-Zamora, Marta; Salvador-Martinez, Irepan; Castellano, David; Barbadilla, Antonio; Salazar-Ciudad, Isaac
Contributor: University of Helsinki, Institute of Biotechnology
University of Helsinki, Institute of Biotechnology
Date: 2019-05
Language: eng
Number of pages: 20
Belongs to series: Genome Biology and Evolution
ISSN: 1759-6653
URI: http://hdl.handle.net/10138/310230
Abstract: Previous studies of the evolution of genes expressed at different life-cycle stages of Drosophila melanogaster have not been able to disentangle adaptive from nonadaptive substitutions when using nonsynonymous sites. Here, we overcome this limitation by combining whole-genome polymorphism data from D. melanogaster and divergence data between D. melanogaster and Drosophila yakuba. For the set of genes expressed at different life-cycle stages of D. melanogaster, as reported in modENCODE, we estimate the ratio of substitutions relative to polymorphism between nonsynonymous and synonymous sites (alpha) and then alpha is discomposed into the ratio of adaptive (omega(a)) and nonadaptive (omega(na)) substitutions to synonymous substitutions. We find that the genes expressed in mid- and late-embryonic development are the most conserved, whereas those expressed in early development and postembryonic stages are the least conserved. Importantly, we found that low conservation in early development is due to high rates of nonadaptive substitutions (high omega(na)), whereas in postembryonic stages it is due, instead, to high rates of adaptive substitutions (high omega(a)). By using estimates of different genomic features (codon bias, average intron length, exon number, recombination rate, among others), we also find that genes expressed in mid- and late-embryonic development show the most complex architecture: they are larger, have more exons, more transcripts, and longer introns. In addition, these genes are broadly expressed among all stages. We suggest that all these genomic features are related to the conservation of mid- and late-embryonic development. Globally, our study supports the hourglass pattern of conservation and adaptation over the life-cycle.
Subject: adaptation
conservation
natural selection
evo-devo
DFE-alpha
hourglass hypothesis
ADAPTIVE MOLECULAR EVOLUTION
PROTEIN-PROTEIN INTERFACES
EFFECTIVE POPULATION-SIZE
NATURAL-SELECTION
DEVELOPMENTAL HOURGLASS
DELETERIOUS MUTATIONS
POSITIVE SELECTION
EXPRESSED GENES
CODING GENES
GENOMIC RATE
1181 Ecology, evolutionary biology
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