Adaptation and Conservation throughout the Drosophila melanogaster Life-Cycle
Coronado-Zamora, Marta (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Salvador-Martínez, Irepan (University College London. Department of Genetics, Evolution and Environment)
Castellano Esteve, David (Aarhus University. Bioinformatics Research Center)
Barbadilla Prados, Antonio (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Salazar Ciudad, Isaac (Centre de Recerca Matemàtica)

Data:	2019
Resum:	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 (α) and then α is discomposed into the ratio of adaptive (ω ) and nonadaptive (ω ) 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 ω ), whereas in postembryonic stages it is due, instead, to high rates of adaptive substitutions (high ω ). 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.
Ajuts:	Ministerio de Economía y Competitividad CGL2017-89160-P Agència de Gestió d'Ajuts Universitaris i de Recerca 2017/SGR-1379
Nota:	Altres ajuts: FI-DGR-2015
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Adaptation ; Conservation ; Natural selection ; Evo-devo ; DFE-alpha ; Hourglass hypothesis
Publicat a:	Genome biology and evolution, Vol. 11, Num. 5 (May 2019) , p. 1463-1482, ISSN 1759-6653

DOI: 10.1093/gbe/evz086
PMID: 31028390

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