Comparative Transcriptomics Reveals Patterns of Adaptive Evolution Associated with Depth and Age Within Marine Rockfishes (Sebastes)

Parallel amino acid replacements in the rhodopsins of the rockfishes (Sebastes spp.) associated with shifts in habitat depth.

Among various groups of fishes, a shift in peak wavelength sensitivity has been correlated with changes in their photic environments. The genus Sebastes is a radiation of marine fish species that inhabit a wide range of depths from intertidal to over 600 m. We examined 32 species of Sebastes for evidence of adaptive amino acid substitution at the rhodopsin gene. Fourteen amino acid positions we...

Evolutionary analysis of life span, competition, and adaptive radiation, motivated by the Pacific rockfishes (Sebastes).

The Pacific rockfishes (Sebastes spp) are remarkable for both their diversity (on the order of 100 species) and range of maximum life span ( approximately 10 years for Calico rockfish to approximately 200 years for Rougheye rockfish). We describe the natural history and patterns of diversity and life span in these species and then use independent contrasts to explore correlates of these. When p...

Tests for Ancient Species Flocks Based on Molecular Phylogenetic Appraisals of Sebastes Rockfishes and Other Marine Fishes.

The concept of species flocks has been central to previous interpretations of patterns and processes of explosive species radiations within several groups of freshwater fishes. Here, molecular phytogenies of species-rich Sebastes rockfishes from the northeastern Pacific Ocean were used to test predictions of null theoretical models that assume random temporal placements of phylogenetic nodes. S...

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato.

Although applied over extremely short timescales, artificial selection has dramatically altered the form, physiology, and life history of cultivated plants. We have used RNAseq to define both gene sequence and expression divergence between cultivated tomato and five related wild species. Based on sequence differences, we detect footprints of positive selection in over 50 genes. We also document...

Comparative transcriptomics reveals candidate genes involved in the adaptation to non-marine habitats in panpulmonate mollusks