Single nucleotide polymorphisms (SNPs) have gained wide use in humans and model species and are becoming the marker of choice for applications in other species. Technology that was developed for work in model species may provide useful tools for SNP discovery and genotyping in non-model organisms. However, SNP discovery can be expensive, labour intensive, and introduce ascertainment bias. In addition, the most efficient approaches to SNP discovery will depend on the research questions that the markers are to resolve as well as the focal species. We discuss advantages and disadvantages of several past and recent technologies for SNP discovery and genotyping and summarize a variety of SNP discovery and genotyping studies in ecology and evolution.

To predict how climate change will influence populations, it is necessary to understand the mechanisms, particularly microevolution and phenotypic plasticity, that 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 a genetic change towards earlier migration timing in a population of pink salmon that shows phenotypic change; average migration time occurs nearly two 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 more than 30% to less than 10% of the total abundance). From 1983 to 2011, there was a significant decrease-over threefold-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 that 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 to 2009.

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Variation in mitochondrial DNA is often assumed to be neutral and is used to construct the genealogical relationships among populations and species. However, if extant variation is the result of episodes of positive selection, these genealogies may be incorrect, although this information itself may provide biologically and evolutionary meaningful information. In fact, positive Darwinian selection has been detected in the mitochondrial‐encoded subunits that comprise complex I from diverse taxa with seemingly dissimilar bioenergetic life histories, but the functional implications of the selected sites are unknown. Complex I produces roughly 40% of the proton flux that is used to synthesize ATP from ADP, and a functional model based on the high‐resolution structure of complex I described a unique biomechanical apparatus for proton translocation. We reported positive selection at sites in this apparatus during the evolution of Pacific salmon, and it appeared this was also the case in published reports from other taxa, but a comparison among studies was difficult because different statistical tests were used to detect selection and oftentimes, specific sites were not reported. Here we review the literature of positive selection in mitochondrial genomes, the statistical tests used to detect selection, and the structural and functional models that are currently available to study the physiological implications of selection. We then search for signatures of positive selection among the coding mitochondrial genomes of 237 species with a common set of tests and verify that the ND5 subunit of complex I is a repeated target of positive Darwinian selection in diverse taxa. We propose a novel hypothesis to explain the results based on their bioenergetic life histories and provide a guide for laboratory and field studies to test this hypothesis.

Hybridization between distinct populations of salmon can cause fitness loss (outbreeding depression), and may result in reduced survival. The erosion of fitness-related traits such as homing ability and change in family size distribution may underlie reduced survival. Outbreeding depression was investigated in two independent experiments that made hybrids between geographically separated and genetically divergent pink salmon populations. Control crosses were made from male and female Auke Creek (Southeast Alaska) pink salmon and hybrid crosses were between Auke Creek females and Pillar Creek (Kodiak Island, about 1000km away) males. Parentage assignment from microsatellite analysis improved estimates of survival and straying, and was used to examine variation in family size. The return rates of even-broodyear Fi control and hybrid fish were similar, but the odd-broodyear Fj control returns exceeded hybrid returns. The F2 control returns exceeded hybrid returns in both the even-and oddbroodyears. Hybridization did not impair homing ability; weekly surveys in nearby (~ 1km) Waydelich Creek revealed similar straying rates from Auke Creek by both hybrid and control fish in all years. Family data were available only for even-broodyear returns; hybridization did not increase the index of variability (ratio of variance to mean) in family size in these years. Outbreeding depression in hybrids of geographically separated populations demonstrates the potential for introgression of normative fish to erode natural production.

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.

Quantitative genetic variation of development rate was evident among 20 half-sib and 40 full-sib families within each of two seasonally separate components of a population of pink salmon (Oncorhynchus gorbuscha) (H o : no sire effect on temperature units at hatch, P < 0.02). Differences between averages of families spawned 3 weeks apart may have had genetic or environmental sources (e.g., in constant 8°C, early embryos hatched at 606 temperature units, and late embryos, at 625). Statistical interactions between paternal effects and environment (embryos were cultured in four temperature regimes, two simulated natural regimes and two constant temperatures; H o : no sire by regime interaction effect on temperature units at hatch, P < 0.09) were weak evidence that genotype by environment interactions contributed to variation. Paternal effects in analysis of variance (evidence of additive genetic variation) were detected only at later stages. Evidences of genetic variation and of interactions between genotypes and environments are pertinent to resource conservation because they suggest that harvest management or hatchery practice have the potential to reduce genetic variation in salmon populations.Résumé : Une variation génétique quantitative du taux de développement était apparente chez 20 familles de demifrères et 40 familles de plein-frères au sein de deux composantes saisonnières distinctes d'une population de saumon rose, Oncorhynchus gorbuscha. (H o : aucun effet du père sur le nombre d'unités de température au moment de l'éclosion, P < 0,02). Les écarts notés entre les moyennes des familles dont la fécondation présentait trois semaines d'intervalle peuvent s'expliquer par des facteurs génétiques ou environnementaux (p. ex. : à une température constante de 8°C l'éclosion des embryons se produisait à 606 unités de température pour les plus hâtifs et à 625 pour les plus tardifs). Les interactions statistiques entre les effets paternels et l'environnement (embryons élevés sous quatre régimes de température, deux régimes naturels simulés et deux à température constante; H o : aucune interaction père-régime sur les unités de température à l'éclosion, P < 0,09) constituaient un indice faible du faible apport à la variation des effets de l'environnement sur le génotype. Une analyse de variance des effets paternels (évidence d'une variation génétique additive) n'a permis de mettre ces derniers en évidence qu'aux stades ultérieurs. L'existence de signes de variation génétique et d'interactions entre les génotypes et les environnements s'avère pertinente pour la conservation des ressources car elle indique que la gestion de la récolte ou les pratiques des piscicultures pourraient influer sur la variation génétique des populations de saumon.[Traduit par la Rédaction]

Anthropogenic-induced change is forcing organisms to shift their distributions and colonize novel habitats at an increasing rate, which leads to complex interactions among evolutionary processes. Coastrange sculpin (Cottus aleuticus) have colonized recently deglaciated streams of Glacier Bay in Alaska within the last 220 years. We examined divergence among populations in background matching coloration and tested the hypothesis that observed variation is due to morphological color plasticity. To examine how color-change plasticity has interacted with other evolutionary processes, we also determined the influence of colonization on neutral genetic diversity. We observed clinal variation in substrate-matching fish color along the chronological continuum of streams. Microsatellites provided little evidence of genetic subdivision among sculpin populations. Fish color was significantly correlated to substrate color, but was not correlated to neutral population genetic structure. Furthermore, a laboratory experiment revealed that morphological color plasticity could explain much, but not all, of the observed fish color divergence. Our study demonstrates that sculpin in Glacier Bay have colonized and adapted to recently deglaciated habitat and suggests that color change plasticity has aided in this process. This research, therefore, highlights the important role phenotypic plasticity may play in the adaptation of species to rapid climate change.