Local adaptation with high gene flow: temperature parameters drive adaptation to altitude in the common frog (Rana temporaria)

Both environmental and genetic influences can result in phenotypic variation. Quantifying the relative contributions of local adaptation and phenotypic plasticity to phenotypes is key to understanding the effect of environmental variation on populations. Identifying the selective pressures that drive divergence is an important, but often lacking, next step. High gene flow between high- and low-altitude common frog (Rana temporaria) breeding sites has previously been demonstrated in Scotland. The aim of this study was to assess whether local adaptation occurs in the face of high gene flow and to identify potential environmental selection pressures that drive adaptation. Phenotypic variation in larval traits was quantified in R. temporaria from paired high- and low-altitude sites using three common temperature treatments. Local adaptation was assessed using QST–FST analyses, and quantitative phenotypic divergence was related to environmental parameters using Mantel tests. Although evidence of local adaptation was found for all traits measured, only variation in larval period and growth rate was consistent with adaptation to altitude. Moreover, this was only evident in the three mountains with the highest high-altitude sites. This variation was correlated with mean summer and winter temperatures, suggesting that temperature parameters are potentially strong selective pressures maintaining local adaptation, despite high gene flow

Patterns of genetic diversity in outcrossing and selfing populations of Arabidopsis lyrata

Arabidopsis lyrata is normally considered an obligately outcrossing species with a strong self-incompatibility system, but a shift in mating system towards inbreeding has been found in some North American populations (subspecies A. lyrata ssp. lyrata). This study provides a survey of the Great Lakes region of Canada to determine the extent of this mating system variation and how outcrossing rates are related to current population density, geographical distribution, and genetic diversity. Based on variation at microsatellite markers (progeny arrays to estimate multilocus outcrossing rates and population samples to estimate diversity measures) and controlled greenhouse pollinations, populations can be divided into two groups: (i) group A, consisting of individuals capable of setting selfed seed (including autogamous fruit set in the absence of pollinators), showing depressed outcrossing rates (T<sub>m</sub> = 0.2–0.6), heterozygosity (H<sub>O</sub> = 0.02–0.06) and genetic diversity (H<sub>E</sub> = 0.08–0.10); and (ii) group B, consisting of individuals that are predominantly self-incompatible (T<sub>m</sub> > 0.8), require pollinators for seeds set, and showing higher levels of heterozygosity (H<sub>O</sub> = 0.13–0.31) and diversity (H<sub>E</sub> = 0.19–0.410). Current population density is not related to the shift in mating system but does vary with latitude. Restricted gene flow among populations was evident among all but two populations (F<sub>ST</sub> = 0.11–0.8). Group A populations were more differentiated from one another (F<sub>ST</sub> = 0.78) than they were from group B populations (F<sub>ST</sub> = 0.59), with 41% of the variation partitioned within populations, 47% between populations, and 12% between groups. No significant relationship was found between genetic and geographical distance. Results are discussed in the context of possible postglacial expansion scenarios in relation to loss of self-incompatibility

Inferring the ancestry of African wild dogs that returned to the Serengeti-Mara

An endangered population of African wild dogs (Lycaon pictus) disappeared from the Serengeti-Mara area in 1991. The reasons for the extinction are not well understood, but disease was implicated in the disappearance. In 2001, wild dogs naturally re-established themselves in the region. We conducted genetic profiling on samples collected prior and subsequent to this event, as well as samples from three geographically close populations, to determine the potential source of colonisers. Contrary to expectations, we found no evidence of re-colonisation from these nearby wild dog populations. Rather, our analyses suggest that the re-established animals are primarily derived from the same genetic population as the pre-extinction animals, indicating that wild dogs are likely to have persisted in the Serengeti-Mara after 1991. We also detected some migrants that could be derived from genetically distinct populations outside the recovery area. Overall, we did not detect a decline in genetic diversity at either neutral microsatellites or major histocompatibility complex loci, indicating that the supposed disappearance of wild dogs in the Serengeti-Mara did not substantially impact genetic variation of the population

Kin recognition via phenotype matching in a cooperatively breeding cichlid, Neolamprologus pulcher

Cooperatively breeding groups are often made up of a mixture of related and unrelated individuals. In such groups, being able to identify and differentially cooperate with relatives can bring indirect fitness benefits to helpers. We investigated the kin recognition abilities of the cooperatively breeding African cichlid Neolamprologus pulcher, while controlling for familiarity between individuals. When given a choice of associating with unfamiliar kin or unfamiliar nonkin, juvenile N. pulcher spent significantly longer associating with kin. Although both chemical and visual cues were required to stimulate the fish, chemical cues were more important than visual cues in kin recognition in this species. As all stimulus fish were reared separately from the focal fish, we can also conclude that N. pulcher used phenotype matching rather than familiarity to assess relatedness to other individuals. Furthermore, when given the choice of associating with familiar over unfamiliar kin, N. pulcher showed no significant preference. Hence, relatedness rather than familiarity appears to be more important in the association preferences of N. pulcher. This is advantageous, particularly if familiar individuals within the cooperatively breeding group are not necessarily relatives. In highly social species such as N. pulcher, being able to recognize kin can bring fitness advantages through kin selection and inbreeding avoidanc

Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools

Despite the importance of polyploidy and the increasing availability of new genomic data, there remain important gaps in our knowledge of polyploid population genetics. These gaps arise from the complex nature of polyploid data (e.g. multiple alleles and loci, mixed inheritance patterns, association between ploidy and mating system variation). Furthermore, many of the standard tools for population genetics that have been developed for diploids are often not feasible for polyploids. This review aims to provide an overview of the state-of-the-art in polyploid population genetics and to identify the main areas where further development of molecular techniques and statistical theory is required. We review commonly used molecular tools (amplified fragment length polymorphism, microsatellites, Sanger sequencing, next-generation sequencing and derived technologies) and their challenges associated with their use in polyploid populations: that is, allele dosage determination, null alleles, difficulty of distinguishing orthologues from paralogues and copy number variation. In addition, we review the approaches that have been used for population genetic analysis in polyploids and their specific problems. These problems are in most cases directly associated with dosage uncertainty and the problem of inferring allele frequencies and assumptions regarding inheritance. This leads us to conclude that for advancing the field of polyploid population genetics, most priority should be given to development of new molecular approaches that allow efficient dosage determination, and to further development of analytical approaches to circumvent dosage uncertainty and to accommodate ‘flexible’ modes of inheritance. In addition, there is a need for more simulation-based studies that test what kinds of biases could result from both existing and novel approaches

Macrogeographic population structure in a parasitic nematode with avian hosts

Much remains to be discovered about the population genetic structure of parasites, despite the importance of such knowledge to understanding the processes involved in the spread of drug resistance through populations. Here we present a study of population genetic diversity in <i>Trichostrongylus</i> tenuis, an avian parasitic nematode infecting both poultry and game birds, where anthelmintic use is common. We examined diversity of nicotinamide dehydrogenase subunit 4 (<i>nad4</i>) mtDNA sequences within and between seven locations: five in the UK (red grouse hosts), one in Iceland (domestic goose) and one in Norway (willow grouse). Within-UK comparisons showed high nucleotide diversity (π = 0.015, n = 23) but no structure between locations (ΦST = 0.022, P = 0.27), with over 97% of variation distributed within-hosts. The highest diversity was found in Iceland (π = 0.043, n = 4), and the lowest in Norway (π = 0.003, n = 4). Differentiation between countries was considerable (ΦCT = 0.44, P < 0.05), in spite of the potential mixing effects of gene flow via migrating wild hosts and the poultry trade. However, significant pairwise FST values were found only between Norway and the other locations. Phylogenetic analysis provided statistical support for a separate clade for Norwegian samples only, with unresolved diversity leading to a star-shaped relationship between Icelandic and UK haplotypes. These results suggest that Norwegian T. tenuis are isolated, but that there is some connectivity between UK and Icelandic populations. Although anthelmintic resistance has not yet been reported for <i>T. tenuis</i>, the population structure is such that emerging resistance has the potential to spread by gene flow over a large geographic scale