Multilocus heterozygosity, parental relatedness and individual fitness components in a wild mountain goat,Oreamnos americanuspopulation

Effect of MHC and inbreeding on disassortative reproduction: A data revisit, extension and inclusion of fertilization in sand lizards

The harmful effects of close inbreeding have been recognized for centuries and, with the rise of Mendelian genetics, was realized to be an effect of homozygosis. This historical background led to great interest in ways to quantify inbreeding, its depression effects on the phenotype and flow‐on effects on mate choice and other aspects of behavioral ecology. The mechanisms and cues used to avoid inbreeding are varied and include major histocompatibility complex (MHC) molecules and the peptides they transport as predictors of the degree of genetic relatedness. Here, we revisit and complement data from a Swedish population of sand lizards (Lacerta agilis) showing signs of inbreeding depression to assess the effects of genetic relatedness on pair formation in the wild. Parental pairs were less similar at the MHC than expected under random mating but mated at random with respect to microsatellite relatedness. MHC clustered in groups of RFLP bands but no partner preference was observed with respect to partner MHC cluster genotype. Male MHC band patterns were unrelated to their fertilization success in clutches selected for analysis on the basis of showing mixed paternity. Thus, our data suggest that MHC plays a role in pre‐copulatory, but not post‐copulatory partner association, suggesting that MHC is not the driver of fertilization bias and gamete recognition in sand lizards.

Genome Assembly and Analysis of the North American Mountain Goat (Oreamnos americanus) Reveals Species-Level Responses to Extreme Environments

The North American mountain goat (Oreamnos americanus) is an iconic alpine species that faces stressors from climate change, industrial development, and recreational activities. This species’ phylogenetic position within the Caprinae lineage has not been resolved and their phylogeographic history is dynamic and controversial. Genomic data could be used to address these questions and provide valuable insights to conservation and management initiatives. We sequenced short-read genomic libraries constructed from a DNA sample of a 2.5-year-old female mountain goat at 80X coverage. We improved the short-read assembly by generating Chicago library data and scaffolding using the HiRise approach. The final assembly was 2,506 Mbp in length with an N50 of 66.6 Mbp, which is within the length range and in the upper quartile for N50 published ungulate genome assemblies. Comparative analysis identified 84 gene families unique to the mountain goat. The species demographic history in terms of effective population size generally mirrored climatic trends over the past one hundred thousand years and showed a sharp decline during the last glacial maximum. This genome assembly will provide a reference basis for future population and comparative genomic analyses.

Reproductive senescence: new perspectives in the wild

According to recent empirical studies, reproductive senescence, the decline in reproductive success with increasing age, seems to be nearly ubiquitous in the wild. However, a clear understanding of the evolutionary causes and consequences of reproductive senescence is still lacking and requires new and integrative approaches. After identifying the sequential and complex nature of female reproductive senescence, we show that the relative contributions of physiological decline and alterations in the efficiency of parental care to reproductive senescence remain unknown and need to be assessed in the light of current evolutionary theories of ageing. We demonstrate that, although reproductive senescence is generally studied only from the female viewpoint, age-specific female reproductive success strongly depends on male-female interactions. Thus, a reduction in male fertilization efficiency with increasing age has detrimental consequences for female fitness. Lastly, we call for investigations of the role of environmental conditions on reproductive senescence, which could provide salient insights into the underlying sex-specific mechanisms of reproductive success. We suggest that embracing such directions should allow building new bridges between reproductive senescence and the study of sperm competition, parental care, mate choice and environmental conditions.

Isolation of Clostridium perfringens type A from wild bharals (Pseudois nayaur) following sudden death in Tibet, China

Dozens of wild bharals died suddenly in Tibet. Necropsy showed severe congestion and hemorrhage in multiple organs, with large numbers of Gram-positive bacilli. Strains of Clostridium perfringens type A were isolated from the different organs and the intestinal contents. The other possible pathogens were ruled out by PCR.

Candidate gene-environment interactions and their relationships with timing of breeding in a wild bird population

Monitoring and predicting evolutionary changes underlying current environmental modifications are complex challenges. Recent approaches to achieve these objectives include assessing the genetic variation and effects of candidate genes on traits indicating adaptive potential. In birds, for example, short tandem repeat polymorphism at four candidate genes (CLOCK, NPAS2, ADCYAP1, and CREB1) has been linked to variation in phenological traits such as laying date and timing of migration. However, our understanding of their importance as evolutionary predictors is still limited, mainly because the extent of genotype–environment interactions (GxE) related to these genes has yet to be assessed. Here, we studied a population of Tree swallow (Tachycineta bicolor) over 4 years in southern Québec (Canada) to assess the relationships between those four candidate genes and two phenological traits related to reproduction (laying date and incubation duration) and also determine the importance of GxE in this system. Our results showed that NPAS2 female genotypes were nonrandomly distributed across the study system and formed a longitudinal cline with longer genotypes located to the east. We observed relationships between length polymorphism at all candidate genes and laying date and/or incubation duration, and most of these relationships were affected by environmental variables (breeding density, latitude, or temperature). In particular, the positive relationships detected between laying date and both CLOCK and NPAS2 female genotypes were variable depending on breeding density. Our results suggest that all four candidate genes potentially affect timing of breeding in birds and that GxE are more prevalent and important than previously reported in this context.

Reduced microsatellite heterozygosity does not affect natal dispersal in three contrasting roe deer populations

Although theoretical studies have predicted a link between individual multilocus heterozygosity and dispersal, few empirical studies have investigated the effect of individual heterozygosity on dispersal propensity or distance. We investigated this link using measures of heterozygosity at 12 putatively neutral microsatellite markers and natal dispersal behaviour in three contrasting populations of European roe deer (Capreolus capreolus), a species displaying pre-saturation condition-dependent natal dispersal. We found no effect of individual heterozygosity on either dispersal propensity or dispersal distance. Average heterozygosity was similar across the three studied populations, but dispersal propensity and distance differed markedly among them. In Aurignac, dispersal propensity and distance were positively related to individual body mass, whereas there was no detectable effect of body mass on dispersal behaviour in Chizé and Trois Fontaines. We suggest that we should expect both dispersal propensity and distance to be greater when heterozygosity is lower only in those species where dispersal behaviour is driven by density-dependent competition for resources.

Neighbouring-group composition and within-group relatedness drive extra-group paternity rate in the European badger (Meles meles)

Extra-group paternity (EGP) occurs commonly among group-living mammals and plays an important role in mating systems and the dynamics of sexual selection; however, socio-ecological and genetic correlates of EGP have been underexplored. We use 23 years of demographic and genetic data from a high-density European badger (Meles meles) population, to investigate the relationship between the rate of EGP in litters and mate availability, mate incompatibility and mate quality (heterozygosity). Relatedness between within-group assigned mothers and candidate fathers had a negative quadratic effect on EGP, whereas the number of neighbouring-group candidate fathers had a linear positive effect. We detected no effect of mean or maximum heterozygosity of within-group candidate fathers on EGP. Consequently, EGP was associated primarily with mate availability, subject to within-group genetic effects, potentially to mitigate mate incompatibility and inbreeding. In badgers, cryptic female choice, facilitated by superfecundation, superfoetation and delayed implantation, prevents males from monopolizing within-group females. This resonates with a meta-analysis in group-living mammals, which proposed that higher rates of EGP occur when within-group males cannot monopolize within-group females. In contrast to the positive meta-analytic association, however, we found that EGP associated negatively with the number of within-group assigned mothers and the number of within-group candidate fathers; potentially a strategy to counter within-group males committing infanticide. The relationship between the rate of EGP and socio-ecological or genetic factors can therefore be intricate, and the potential for cryptic female choice must be accounted for in comparative studies.

Modelling the dispersal of the two main hosts of the raccoon rabies variant in heterogeneous environments with landscape genetics

Predicting the geographic spread of wildlife epidemics requires knowledge about the movement patterns of disease hosts or vectors. The field of landscape genetics provides valuable approaches to study dispersal indirectly, which in turn may be used to understand patterns of disease spread. Here, we applied landscape genetic analyses and spatially explicit models to identify the potential path of raccoon rabies spread in a mesocarnivore community. We used relatedness estimates derived from microsatellite genotypes of raccoons and striped skunks to investigate their dispersal patterns in a heterogeneous landscape composed predominantly of agricultural, forested and residential areas. Samples were collected in an area covering 22 000 km² in southern Québec, where the raccoon rabies variant (RRV) was first detected in 2006. Multiple regressions on distance matrices revealed that genetic distance among male raccoons was strictly a function of geographic distance, while dispersal in female raccoons was significantly reduced by the presence of agricultural fields. In skunks, our results suggested that dispersal is increased in edge habitats between fields and forest fragments in both males and females. Resistance modelling allowed us to identify likely dispersal corridors used by these two rabies hosts, which may prove especially helpful for surveillance and control (e.g. oral vaccination) activities.

Sex-biased inbreeding effects on reproductive success and home range size of the critically endangered black rhinoceros

A central premise of conservation biology is that small populations suffer reduced viability through loss of genetic diversity and inbreeding. However, there is little evidence that variation in inbreeding impacts individual reproductive success within remnant populations of threatened taxa, largely due to problems associated with obtaining comprehensive pedigree information to estimate inbreeding. In the critically endangered black rhinoceros, a species that experienced severe demographic reductions, we used model selection to identify factors associated with variation in reproductive success (number of offspring). Factors examined as predictors of reproductive success were age, home range size, number of nearby mates, reserve location, and multilocus heterozygosity (a proxy for inbreeding). Multilocus heterozygosity predicted male reproductive success (p< 0.001, explained deviance >58%) and correlated with male home range size (p < 0.01, r(2) > 44%). Such effects were not apparent in females, where reproductive success was determined by age (p < 0.01, explained deviance 34%) as females raise calves alone and choose between, rather than compete for, mates. This first report of a 3-way association between an individual male's heterozygosity, reproductive output, and territory size in a large vertebrate is consistent with an asymmetry in the level of intrasexual competition and highlights the relevance of sex-biased inbreeding for the management of many conservation-priority species. Our results contrast with the idea that wild populations of threatened taxa may possess some inherent difference from most nonthreatened populations that necessitates the use of detailed pedigrees to study inbreeding effects. Despite substantial variance in male reproductive success, the increased fitness of more heterozygous males limits the loss of heterozygosity. Understanding how individual differences in genetic diversity mediate the outcome of intrasexual competition will be essential for effective management, particularly in enclosed populations, where individuals have restricted choice about home range location and where the reproductive impact of translocated animals will depend upon the background distribution in individual heterozygosity.

No correlation between multi-locus heterozygosity and fitness in the common buzzard despite heterozygote advantage for plumage colour

Correlations between heterozygosity and fitness are frequently found but rarely well understood. Fitness can be affected by single loci of large effect which correlate with neutral markers via linkage disequilibrium, or as a result of variation in genome-wide heterozygosity following inbreeding. We explored these alternatives in the common buzzard, a raptor species in which three colour morphs differ in their lifetime reproductive success. Using 18 polymorphic microsatellite loci, we evaluated potential genetic differences among the morphs which may lead to subpopulation structuring and tested for correlations between three fitness-related traits and heterozygosity, both genome wide and at each locus separately. Despite their assortative mating pattern, the buzzard morphs were found to be genetically undifferentiated. Multilocus heterozygosity was only found to be correlated with a single fitness-related trait, infection with the blood parasite, Leucocytozoon buteonis, and this was via interactions with vole abundance and age. One locus also showed a significant relationship with blood parasite infection and ectoparasite infestation. The vicinity of this locus contains two genes, one of which is potentially implicated in the immune system of birds. We conclude that genome-wide heterozygosity is unlikely to be a major determinant of parasite burden and body condition in the polymorphic common buzzard.

Heterozygosity-fitness correlations in adult and juvenile Zenaida Dove, Zenaida aurita

Understanding how fitness is related to genetic variation is of crucial importance in both evolutionary ecology and conservation biology. We report a study of heterozygosity-fitness correlations in a wild, noninbred population of Zenaida Doves, Zenaida aurita, based on a sample comprising 489 individuals (382 adults and 107 juveniles) typed at 13 microsatellite loci, resulting in a data set comprising 5793 genotypes. In both adults and juveniles, and irrespective of sex, no evidence was found for an effect of either multilocus or single-locus heterozygosity on traits potentially related to fitness such as foraging tactic, competitive ability, and fluctuating asymmetry. In contrast, a significant negative correlation between body condition and multilocus heterozygosity, indicative of outbreeding depression, was found in juveniles, whereas no such trend was observed in adults. However, the frequency distribution of heterozygosity did not differ between the two age classes, suggesting compensatory growth by heterozygous juveniles. We discuss our results in relation to some practical limitations associated with studies of heterozygosity-fitness correlations, and suggest that tropical bird species with allopatric divergence between island populations may provide a good biological model for the detection of outbreeding depression.

Translating effects of inbreeding depression on component vital rates to overall population growth in endangered bighorn sheep

Evidence of inbreeding depression is commonly detected from the fitness traits of animals, yet its effects on population growth rates of endangered species are rarely assessed. We examined whether inbreeding depression was affecting Sierra Nevada bighorn sheep (Ovis canadensis sierrae), a subspecies listed as endangered under the U.S. Endangered Species Act. Our objectives were to characterize genetic variation in this subspecies; test whether inbreeding depression affects bighorn sheep vital rates (adult survival and female fecundity); evaluate whether inbreeding depression may limit subspecies recovery; and examine the potential for genetic management to increase population growth rates. Genetic variation in 4 populations of Sierra Nevada bighorn sheep was among the lowest reported for any wild bighorn sheep population, and our results suggest that inbreeding depression has reduced adult female fecundity. Despite this population sizes and growth rates predicted from matrix-based projection models demonstrated that inbreeding depression would not substantially inhibit the recovery of Sierra Nevada bighorn sheep populations in the next approximately 8 bighorn sheep generations (48 years). Furthermore, simulations of genetic rescue within the subspecies did not suggest that such activities would appreciably increase population sizes or growth rates during the period we modeled (10 bighorn sheep generations, 60 years). Only simulations that augmented the Mono Basin population with genetic variation from other subspecies, which is not currently a management option, predicted significant increases in population size. Although we recommend that recovery activities should minimize future losses of genetic variation, genetic effects within these endangered populations-either negative (inbreeding depression) or positive (within subspecies genetic rescue)-appear unlikely to dramatically compromise or stimulate short-term conservation efforts. The distinction between detecting the effects of inbreeding depression on a component vital rate (e.g., fecundity) and the effects of inbreeding depression on population growth underscores the importance of quantifying inbreeding costs relative to population dynamics to effectively manage endangered populations.

sGD: software for estimating spatially explicit indices of genetic diversity

Anthropogenic landscape changes have greatly reduced the population size, range and migration rates of many terrestrial species. The small local effective population size of remnant populations favours loss of genetic diversity leading to reduced fitness and adaptive potential, and thus ultimately greater extinction risk. Accurately quantifying genetic diversity is therefore crucial to assessing the viability of small populations. Diversity indices are typically calculated from the multilocus genotypes of all individuals sampled within discretely defined habitat patches or larger regional extents. Importantly, discrete population approaches do not capture the clinal nature of populations genetically isolated by distance or landscape resistance. Here, we introduce spatial Genetic Diversity (sGD), a new spatially explicit tool to estimate genetic diversity based on grouping individuals into potentially overlapping genetic neighbourhoods that match the population structure, whether discrete or clinal. We compared the estimates and patterns of genetic diversity using patch or regional sampling and sGD on both simulated and empirical populations. When the population did not meet the assumptions of an island model, we found that patch and regional sampling generally overestimated local heterozygosity, inbreeding and allelic diversity. Moreover, sGD revealed fine-scale spatial heterogeneity in genetic diversity that was not evident with patch or regional sampling. These advantages should provide a more robust means to evaluate the potential for genetic factors to influence the viability of clinal populations and guide appropriate conservation plans.

Temporal dynamics of genetic variability in a mountain goat (Oreamnos americanus) population

The association between population dynamics and genetic variability is of fundamental importance for both evolutionary and conservation biology. We combined long-term population monitoring and molecular genetic data from 123 offspring and their parents at 28 microsatellite loci to investigate changes in genetic diversity over 14 cohorts in a small and relatively isolated population of mountain goats (Oreamnos americanus) during a period of demographic increase. Offspring heterozygosity decreased while parental genetic similarity and inbreeding coefficients (F(IS) ) increased over the study period (1995-2008). Immigrants introduced three novel alleles into the population and matings between residents and immigrants produced more heterozygous offspring than local crosses, suggesting that immigration can increase population genetic variability. The population experienced genetic drift over the study period, reflected by a reduced allelic richness over time and an 'isolation-by-time' pattern of genetic structure. The temporal decline of individual genetic diversity despite increasing population size probably resulted from a combination of genetic drift due to small effective population size, inbreeding and insufficient counterbalancing by immigration. This study highlights the importance of long-term genetic monitoring to understand how demographic processes influence temporal changes of genetic diversity in long-lived organisms.

Does reduced heterozygosity influence dispersal? A test using spatially structured populations in an alpine ungulate

Despite having a profound effect on population dynamics, the reasons that animals disperse are poorly understood. Evolutionary explanations have focused on inbreeding and competition, where the potential cost of philopatry is negated through dispersal. Such scenarios lead to the prediction that less successful individuals preferentially disperse, termed 'fitness-associated dispersal'. Since heterozygosity is associated with fitness, we assessed whether dispersed animals had less observed heterozygosity (H(O)) than residents. We tested this prediction using both genetic and population-monitoring data of mountain goats (Oreamnos americanus). Individuals classified as dispersers through cross-assignment had the lowest mean H(O), followed by residents, and then admixed individuals. Dispersed individuals had 6.3 per cent less H(O) than their subpopulation of origin. In the long-term study of the mountain goat herd at Caw Ridge, Alberta, immigrants had the lowest H(O); however, the opposite pattern was seen in emigrants, which may be related to density dependence. This study is the first to provide empirical evidence that heterozygosity is associated with dispersal.

Inbreeding tolerance and fitness costs in wild bottlenose dolphins

In wild populations, inbreeding tolerance is expected to evolve where the cost of avoidance exceeds that of tolerance. We show that in a wild population of bottlenose dolphins found in East Shark Bay, Western Australia, levels of inbreeding are higher than expected by chance alone, and demonstrate that inbreeding is deleterious to female fitness in two independent ways. We found that inbred females, and females with inbred calves, have reduced fitness (lower calving success). We further show that one of the costs of inbreeding is extended weaning age, and that females' earlier calves are more likely to be inbred. While the exact causes of inbreeding remain obscure, our results indicate that one factor is female age, and thus experience. Any inbreeding avoidance mechanisms such as female evasion of kin, or male dispersal, do not seem to be completely effective in this population, which supports the view that inbreeding avoidance does not always evolve wherever inbreeding incurs a cost.

Father-offspring phenotypic correlations suggest intralocus sexual conflict for a fitness-linked trait in a wild sexually dimorphic mammal

In sexually dimorphic and polygynous mammals, sexual selection often favours large males with well-developed weaponry, as these secondary sexual characters confer advantages in intrasexual competition and are often preferred by females. Little is known, however, about the effects of sexually selected paternal traits on offspring phenotype in wild mammals, especially when considering that shared phenotypic traits and selection can also differ greatly between genders. Here, we conducted molecular parentage analyses in a long-term study population of mountain goats (Oreamnos americanus), an ungulate exhibiting high sexual dimorphism in mass, to first assess the determinants of yearly reproductive success (YRS) in males. We then examined the effects of paternal characteristics on offspring mass at 1 year of age. Paternity was highly skewed, with 9 per cent of 57 males siring 51 per cent of 96 offspring assigned over 12 years. Male YRS increased with age until apparent reproductive senescence at 9 years, but mass was a stronger determinant of siring success than age, horn length or social rank. Mass of sons increased with paternal mass, but the mass of daughters was negatively related to that of their father, a finding consistent with recent theory on intralocus sexual conflict. Because early differences in mass persisted to early adulthood, sex-specific effects of paternal mass can have important fitness consequences, as adult mass is positively linked with reproduction in both sexes. Divergent father-offspring phenotypic correlations may partly explain the maintenance of sexual dimorphism in mountain goats and the large variance observed for this homologous trait within each gender in polygynous mammals.