Positive Darwinian Selection in the Piston That Powers Proton Pumps in Complex I of the Mitochondria of Pacific Salmon

The mechanism of oxidative phosphorylation is well understood, but evolution of the proteins involved is not. We combined phylogenetic, genomic, and structural biology analyses to examine the evolution of twelve mitochondrial encoded proteins of closely related, yet phenotypically diverse, Pacific salmon. Two separate analyses identified the same seven positively selected sites in ND5. A strong signal was also detected at three sites of ND2. An energetic coupling analysis revealed several structures in the ND5 protein that may have co-evolved with the selected sites. These data implicate Complex I, specifically the piston arm of ND5 where it connects the proton pumps, as important in the evolution of Pacific salmon. Lastly, the lineage to Chinook experienced rapid evolution at the piston arm

Data_For_Kovachetal2013_EvolApps

This file contains the data used in "Temporal patterns of genetic variation in a salmon population undergoing rapid change in migration timing". The data are organized based on the methods used to analyze them and year. The first three sheets are the data used for estimating the effective population size - the files are in ONeSAMP format. The next three files are the data sets used to test for autocorrelation (GENALEX) and population structure (STRUCTURE) - the files are in GENALEX format. The next sheet "Allozymes" contains the raw allele frequency data that were used to calculate G"st between early and late migrating fish in 1979-1983. Each row is a different locus, the first column is the number of genotypes for each locus, and the next several columns are the observed allele frequencies at that locus. The next three sheets are the data files used to calculate G"st for the microsatellite data from 1993, 2001, 2009. The final file contain the data that were used to test for genetic homogeneity between the different quartiles of the migration timing distribution

Data from: Genetic change for earlier migration timing in a population of pink salmon

To predict how climate change will influence populations it is necessary to understand the mechanisms, particularly microevolution and phenotypic plasticity, which allow populations to persist in novel environmental conditions. Although evidence for climate-induced phenotypic change in populations is widespread, evidence documenting that these phenotypic changes are due to microevolution is exceedingly rare. In this study we use 32 years of genetic data (17 complete generations) to determine whether there has been genetic change toward earlier migration timing in a population of pink salmon that shows phenotypic change; average migration time occurs nearly 2 weeks earlier than it did 40 years ago. Experimental genetic data support the hypothesis that there has been directional selection for earlier migration timing, resulting in a substantial decrease in the late migrating phenotype (from >30% to <10% of the total abundance). From 1983-2011 there was a significant decrease – over three fold – in the frequency of a genetic marker for late migration timing, but there were minimal changes in allele frequencies at other neutral loci. These results demonstrate there has been rapid microevolution for earlier migration timing in this population. Circadian rhythm genes, however, did not show any evidence for selective changes from 1993-2009

Kovach_geneticdata

These data were used in various combinations for the analyses in "Genetic change for earlier migration timing in a pink salmon population." The first sheet includes the microsatellite data, which are in GENEPOP format. The next 8 sheets are the data for the experimental genetic allozyme marker MdH. The last sheet are the daily allele counts for the "control" allozyme locus AGP. See additional details within the data