Genomic analysis reveals a polygenic architecture of antler morphology in wild red deer (Cervus elaphus).

Sexually selected traits show large variation and rapid evolution across the animal kingdom, yet genetic variation often persists within populations despite apparent directional selection. A key step in solving this long-standing paradox is to determine the genetic architecture of sexually selected traits to understand evolutionary drivers and constraints at the genomic level. Antlers are a form of sexual weaponry in male red deer (Cervus elaphus).

Increased genetic marker density reveals high levels of admixture between red deer and introduced Japanese sika in Kintyre, Scotland.

Hybridization is a natural process at species range boundaries, but increasing numbers of species are hybridizing due to direct or indirect human activities. In such cases of anthropogenic hybridization, subsequent introgression can threaten the survival of native species. To date, many such systems have been studied with too few genetic markers to assess the level of threat resulting from advanced backcrossing.

Estimating selection on the act of inbreeding in a population with strong inbreeding depression.

Inbreeding depression is widely regarded as a driving force in the evolution of dispersal, mate choice and sperm selection. However, due to likely costs of inbreeding avoidance, which are poorly understood, it is unclear to what extent selection to avoid inbreeding is expected in nature. Moreover, there are currently very few empirical estimates of the strength of selection against the act of inbreeding (mating with a relative), as opposed to the fitness costs of being inbred.

A Genomic Region Containing and Is Associated with Individual Recombination Rate Variation in a Wild Population of Red Deer ().

Recombination is a fundamental feature of sexual reproduction, ensuring proper disjunction, preventing mutation accumulation and generating new allelic combinations upon which selection can act. However it is also mutagenic, and breaks up favorable allelic combinations previously built up by selection. Identifying the genetic drivers of recombination rate variation is a key step in understanding the causes and consequences of this variation, how loci associated with recombination are evolving and how they affect the potential of a population to respond to selection.

A High-Density Linkage Map Reveals Sexual Dimorphism in Recombination Landscapes in Red Deer ().

High-density linkage maps are an important tool to gain insight into the genetic architecture of traits of evolutionary and economic interest, and provide a resource to characterize variation in recombination landscapes. Here, we used information from the cattle genome and the 50 K Cervine Illumina BeadChip to inform and refine a high-density linkage map in a wild population of red deer (). We constructed a predicted linkage map of 38,038 SNPs and a skeleton map of 10,835 SNPs across 34 linkage groups.

Pedigree reconstruction from SNP data: parentage assignment, sibship clustering and beyond.

Data on hundreds or thousands of single nucleotide polymorphisms (SNPs) provide detailed information about the relationships between individuals, but currently few tools can turn this information into a multigenerational pedigree. I present the r package sequoia, which assigns parents, clusters half-siblings sharing an unsampled parent and assigns grandparents to half-sibships. Assignments are made after consideration of the likelihoods of all possible first-, second- and third-degree relationships between the focal individuals, as well as the traditional alternative of being unrelated.

Inbreeding depression across the lifespan in a wild mammal population.

Inbreeding depression is of major concern for the conservation of threatened species, and inbreeding avoidance is thought to be a key driver in the evolution of mating systems. However, the estimation of individual inbreeding coefficients in natural populations has been challenging, and, consequently, the full effect of inbreeding on fitness remains unclear. Genomic inbreeding coefficients may resolve the long-standing paucity of data on inbreeding depression in adult traits and total fitness.

Modelling wild-domestic interbreeding: how selection on a quantitative trait affects gene flow at a neutral locus.

Interbreeding between domesticated individuals and their wild conspecifics occurs in a range of species. The rate of gene flow into the wild population, estimated using genetic markers, is often smaller than the fraction of immigrants, as immigrants and their descendants generally have lower relative fitness. Here the difference between one-way migration rate and gene flow (effective migration rate) is explored using quantitative genetic simulations.

Comparison of non-Gaussian quantitative genetic models for migration and stabilizing selection.

The balance between stabilizing selection and migration of maladapted individuals has formerly been modeled using a variety of quantitative genetic models of increasing complexity, including models based on a constant expressed genetic variance and models based on normality. The infinitesimal model can accommodate nonnormality and a nonconstant genetic variance as a result of linkage disequilibrium. It can be seen as a parsimonious one-parameter model that approximates the underlying genetic details well when a large number of loci are involved.

Varying disease-mediated selection at different life-history stages of Atlantic salmon in fresh water.

Laboratory studies on associations between disease resistance and susceptibility and major histocompatibility (MH) genes in Atlantic salmon Salmo salar have shown the importance of immunogenetics in understanding the capacity of populations to fight specific diseases. However, the occurrence and virulence of pathogens may vary spatially and temporally in the wild, making it more complicated to predict the overall effect that MH genes exert on fitness of natural populations and over several life-history stages. Here we show that MH variability is a significant determinant of salmon survival in fresh water, by comparing observed and expected genotype frequencies at MH and control microsatellite loci at parr and migrant stages in the wild.