title: Transcriptome-wide patterns of divergence during allopatric evolution.
abstract: Recent studies have revealed repeated patterns of genomic divergence associated with species formation. Such patterns suggest that natural selection tends to target a set of available genes, but is also indicative that closely related taxa share evolutionary constraints that limit genetic variability. Studying patterns of genomic divergence among populations within the same species may shed light on the underlying evolutionary processes. Here, we examine transcriptome-wide divergence and polymorphism in the marine copepod Tigriopus californicus, a species where allopatric evolution has led to replicate sets of populations with varying degrees of divergence and hybrid incompatibility. Our analyses suggest that relatively small effective population sizes have resulted in an exponential decline of shared polymorphisms during population divergence and also facilitated the fixation of slightly deleterious mutations within allopatric populations. Five interpopulation comparisons at three different stages of divergence show that nonsynonymous mutations tend to accumulate in a specific set of proteins. These include proteins with central roles in cellular metabolism, such as those encoded in mtDNA, but also include an additional set of proteins that repeatedly show signatures of positive selection during allopatric divergence. Although our results are consistent with a contribution of nonadaptive processes, such as genetic drift and gene expression levels, generating repeatable patterns of genomic divergence in closely related taxa, they also indicate that adaptive evolution targeting a specific set of genes contributes to this pattern. Our results yield insights into the predictability of evolution at the gene level.
authors: Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093-0202, USA.|Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.
authors: Ricardo J
authors: RJ
authors: Pereira
authors: Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093-0202, USA.|Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA.
authors: Felipe S
authors: FS
authors: Barreto
authors: Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093-0202, USA.
authors: N Tessa
authors: NT
authors: Pierce
authors: CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
authors: Miguel
authors: M
authors: Carneiro
authors: Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093-0202, USA.
authors: Ronald S
authors: RS
authors: Burton
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D000818:Animals; D033342:Copepoda / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D040961:Genetic Drift; D005828:Genetics, Population; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011156:Population Density; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D004272:DNA, Mitochondrial
keywords: comparative transcriptomics; copepod; genetic drift; positive selection; protein evolution; speciation