A fundamental question in evolutionary genetics concerns the extent to which adaptive phenotypic convergence is attributable to convergent or parallel changes at the molecular sequence level. Here we report a comparative analysis of hemoglobin (Hb) function in eight phylogenetically replicated pairs of high- and low-altitude waterfowl taxa to test for convergence in the oxygenation properties of Hb, and to assess the extent to which convergence in biochemical phenotype is attributable to repeated amino acid replacements. Functional experiments on native Hb variants and protein engineering experiments based on site-directed mutagenesis revealed the phenotypic effects of specific amino acid replacements that were responsible for convergent increases in Hb-O2 affinity in multiple high-altitude taxa. In six of the eight taxon pairs, high-altitude taxa evolved derived increases in Hb-O2 affinity that were caused by a combination of unique replacements, parallel replacements (involving identical-by-state variants with independent mutational origins in different lineages), and collateral replacements (involving shared, identical-by-descent variants derived via introgressive hybridization). In genome scans of nucleotide differentiation involving high- and low-altitude populations of three separate species, function-altering amino acid polymorphisms in the globin genes emerged as highly significant outliers, providing independent evidence for adaptive divergence in Hb function. The experimental results demonstrate that convergent changes in protein function can occur through multiple historical paths, and can involve multiple possible mutations. Most cases of convergence in Hb function did not involve parallel substitutions and most parallel substitutions did not affect Hb-O2 affinity, indicating that the repeatability of phenotypic evolution does not require parallelism at the molecular level.

Aim  Limited population structure is predicted for vagile, generalist species, such as the grey wolf (Canis lupus L.). Our aims were to study how genetic variability of grey wolves was distributed in an area comprising different habitats that lay within the potential dispersal range of an individual and to make inferences about the impact of ecology on population structure. Location  British Columbia, Canada – which is characterized by a continuum of biogeoclimatic zones across which grey wolves are distributed – and adjacent areas in both Canada and Alaska, United States. Methods  We obtained mitochondrial DNA control region sequences from grey wolves from across the province and integrated our genetic results with data on phenotype, behaviour and ecology (distance, habitat and prey composition). We also compared the genetic diversity and differentiation of British Columbia grey wolves with those of other North American wolf populations. Results  We found strong genetic differentiation between adjacent populations of grey wolves from coastal and inland British Columbia. We show that the most likely factor explaining this differentiation is habitat discontinuity between the coastal and interior regions of British Columbia, as opposed to geographic distance or physical barriers to dispersal. We hypothesize that dispersing grey wolves select habitats similar to the one in which they were reared, and that this differentiation is maintained largely through behavioural mechanisms. Main conclusions  The identification of strong genetic structure on a scale within the dispersing capabilities of an individual suggests that ecological factors are driving wolf differentiation in British Columbia. Coastal wolves are highly distinct and representative of a unique ecosystem, whereas inland British Columbia grey wolves are more similar to adjacent populations of wolves located in Alaska, Alberta and Northwest Territories. Given their unique ecological, morphological, behavioural and genetic characteristics, grey wolves of coastal British Columbia should be considered an Evolutionary Significant Unit (ESU) and, consequently, warrant special conservation status. If ecology can drive differentiation in a highly mobile generalist such as the grey wolf, ecology probably drives differentiation in many other species as well.

The International Mouse Phenotyping Consortium (IMPC) is building a catalogue of mammalian gene function by producing and phenotyping a knockout mouse line for every protein-coding gene. To date, the IMPC has generated and characterised 5186 mutant lines. One-third of the lines have been found to be non-viable and over 300 new mouse models of human disease have been identified thus far. While current bioinformatics efforts are focused on translating results to better understand human disease processes, IMPC data also aids understanding genetic function and processes in other species. Here we show, using gorilla genomic data, how genes essential to development in mice can be used to help assess the potentially deleterious impact of gene variants in other species. This type of analyses could be used to select optimal breeders in endangered species to maintain or increase fitness and avoid variants associated to impaired-health phenotypes or loss-of-function mutations in genes of critical importance. We also show, using selected examples from various mammal species, how IMPC data can aid in the identification of candidate genes for studying a condition of interest, deliver information about the mechanisms involved, or support predictions for the function of genes that may play a role in adaptation. With genotyping costs decreasing and the continued improvements of bioinformatics tools, the analyses we demonstrate can be routinely applied.Electronic supplementary materialThe online version of this article (10.1007/s10592-018-1072-9) contains supplementary material, which is available to authorized users.

The ruddy duck, Oxyura jamaicensis, was introduced to Great Britain in the mid-20th century and has recently spread to other Western European countries. In Spain, ruddy ducks hybridize with the globally endangered white-headed duck, Oxyura leucocephala. We assessed the effects of hybridization on the Spanish white-headed ducks, which constitute 25% of the global population of this species, using a panel of eight nuclear intron markers, 10 microsatellite loci, and mtDNA control region sequences. These data allowed parental individuals, F(1) hybrids, and the progeny of backcrossing to be reliably distinguished. We show that hybrids between the two species are fertile and produce viable offspring in backcrosses with both parental species. To date, however, we found no extensive introgression of ruddy duck genes into the Spanish white-headed duck population, probably due to the early implementation of an effective ruddy duck and hybrid control programme. We also show that genetic diversity in the expanding European ruddy duck population, which was founded by just seven individuals, exceeds that of the native Spanish white-headed duck population, which recently recovered from a severe bottleneck. Unless effective control of ruddy ducks is continued, genetic introgression will compromise the unique behavioural and ecological adaptations of white-headed ducks and consequently their survival as a genetically and evolutionary distinct species.