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Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents.

ABSTRACT: The contribution of regulatory versus protein change to adaptive evolution has long been controversial. In principle, the rate and strength of adaptation within functional genetic elements can be quantified on the basis of an excess of nucleotide substitutions between species compared to the neutral expectation or from effects of recent substitutions on nucleotide diversity at linked sites. Here, we infer the nature of selective forces acting in proteins, their UTRs and conserved noncoding elements (CNEs) using genome-wide patterns of diversity in wild house mice and divergence to related species. By applying an extension of the McDonald-Kreitman test, we infer that adaptive substitutions are widespread in protein-coding genes, UTRs and CNEs, and we estimate that there are at least four times as many adaptive substitutions in CNEs and UTRs as in proteins. We observe pronounced reductions in mean diversity around nonsynonymous sites (whether or not they have experienced a recent substitution). This can be explained by selection on multiple, linked CNEs and exons. We also observe substantial dips in mean diversity (after controlling for divergence) around protein-coding exons and CNEs, which can also be explained by the combined effects of many linked exons and CNEs. A model of background selection (BGS) can adequately explain the reduction in mean diversity observed around CNEs. However, BGS fails to explain the wide reductions in mean diversity surrounding exons (encompassing ~100 Kb, on average), implying that there is a substantial role for adaptation within exons or closely linked sites. The wide dips in diversity around exons, which are hard to explain by BGS, suggest that the fitness effects of adaptive amino acid substitutions could be substantially larger than substitutions in CNEs. We conclude that although there appear to be many more adaptive noncoding changes, substitutions in proteins may dominate phenotypic evolution.

SUBMITTER: Halligan DL

PROVIDER: S-EPMC3854965 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents.

Halligan Daniel L DL Kousathanas Athanasios A Ness Rob W RW Harr Bettina B Eöry Lél L Keane Thomas M TM Adams David J DJ Keightley Peter D PD

PLoS genetics 20131205 12

The contribution of regulatory versus protein change to adaptive evolution has long been controversial. In principle, the rate and strength of adaptation within functional genetic elements can be quantified on the basis of an excess of nucleotide substitutions between species compared to the neutral expectation or from effects of recent substitutions on nucleotide diversity at linked sites. Here, we infer the nature of selective forces acting in proteins, their UTRs and conserved noncoding eleme ...[more]

PMID: 24339797

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Project description:BackgroundIn the Canary Islands there are no previous data about tapeworms (Cestoda) of rodents. In order to identify the hymenolepidid species present in these hosts, a survey of 1,017 murine (349 Rattus rattus, 13 Rattus norvegicus and 655 Mus musculus domesticus) was carried out in the whole Archipelago. Molecular studies based on nuclear ITS1 and mitochondrial COI loci were performed to confirm the identifications and to analyse the levels of genetic variation and differentiation.ResultsThree species of hymenolepidids were identified: Hymenolepis diminuta, Rodentolepis microstoma and Rodentolepis fraterna. Hymenolepis diminuta (in rats) and R. microstoma (in mice) showed a widespread distribution in the Archipelago, and R. fraterna was the least spread species, appearing only on five of the islands. The hymenolepidids found on Fuerteventura, Lanzarote and La Graciosa were restricted to one area. The COI network of H. diminuta showed that the haplotypes from Lanzarote and Fuerteventura are the most distant with respect to the other islands, but clearly related among them.ConclusionsFounder effects and biotic and abiotic factors could have played important role in the presence/absence of the hymenolepidid species in determined locations. The haplotypes from the eastern islands (Fuerteventura and Lanzarote) seem to have shared an ancestral haplotype very distant from the most frequent one that was found in the rest of the islands. Two colonization events or a single event with subsequent isolation and reduced gene flow between western-central and eastern islands, have taken place in the Archipelago. The three tapeworms detected are zoonotic species, and their presence among rodents from this Archipelago suggests a potential health risk to human via environmental contamination in high risk areas. However, the relatively low prevalence of infestations detected and the focal distribution of some of these species on certain islands reduce the general transmission risk to human.

Dataset Information

Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents.

Publications

Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents.

Similar Datasets

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