Genetic diversity and reproductive success in mandrills (Mandrillus sphinx)

Whole genome assessment of a declining game bird reveals cryptic genetic structure and insights for population management

Population genomics applied to game species conservation can help delineate management units, ensure appropriate harvest levels and identify populations needing genetic rescue to safeguard their adaptive potential. The ruffed grouse (Bonasa umbellus) is rapidly declining in much of the eastern USA due to a combination of forest maturation and habitat fragmentation. More recently, mortality from West Nile Virus may have affected connectivity of local populations; however, genetic approaches have never explicitly investigated this issue. In this study, we sequenced 54 individual low-coverage (~5X) grouse genomes to characterize population structure, assess migration rates across the landscape to detect potential barriers to gene flow and identify genomic regions with high differentiation. We identified two genomic clusters with no clear geographic correlation, with large blocks of genomic differentiation associated with chromosomes 4 and 20, likely due to chromosomal inversions. After excluding these putative inversions from the data set, we found weak but nonsignificant signals of population subdivision. Estimated gene flow revealed reduced rates of migration in areas with extensive habitat fragmentation and increased genetic connectivity in areas with less habitat fragmentation. Our findings provide a benchmark for wildlife managers to compare and scale the genetic diversity and structure of ruffed grouse populations in Pennsylvania and across the eastern USA, and we also reveal structural variation in the grouse genome that requires further study to understand its possible effects on individual fitness and population distribution.

The quest for good genes: Epigamic traits, fitness, MHC and multilocus heterozygosity in the guppy

The 'good genes' hypothesis for the evolution of male secondary sexual traits poses that female preferences for such traits are driven by indirect genetic benefits. However, support for the hypothesis remains ambiguous, and, in particular, the genetic basis for the benefits has rarely been investigated. Here, we use seminatural populations of Trinidadian guppies to investigate whether sexually selected traits (orange, black and iridescent colouration, gonopodium length and body size) predict fitness measured as the number of grandoffspring, a metric that integrates across fitness components and sexes. Furthermore, we tested whether two potential sources of genetic benefits-major histocompatibility complex (MHC) genotypes and multilocus heterozygosity (MLH)-are significant predictors of fitness and of the size of sexually selected traits. We found a significant, nonlinear effect of the area of black pigmentation and male body size on the number of grandoffspring, suggesting stabilizing selection on black area, and nonlinear selection favouring small body size. MLH was heritable (h2  = 0.14) and significantly predicted the number of grandoffspring, indicating the potential for genetic benefits based on heterozygosity. We also found support for local heterozygosity effects, which may reflect a noneven distribution of genetic load across the genome. MHC genotype was not significantly associated with any tested fitness component, or with the load of Gyrodactylus parasites. Neither MHC nor MLH was significant predictor of sexually selected traits. Overall, our results highlight the role of heterozygosity in determining fitness, but do not provide support for male sexually selected traits being indicators of genetic quality.

Coinfection patterns of two marine apicomplexans are not associated with genetic diversity of their polychaete host

Coinfections of two or more parasites within one host are more of a rule than an exception in nature. Interactions between coinfecting parasites can greatly affect their abundance and prevalence. Characteristics of the host, such as genetic diversity, can also affect the infection dynamics of coinfecting parasites. Here, we investigate for the first time the association of coinfection patterns of two marine apicomplexans, Rhytidocystis sp. and Selenidium pygospionis, with the genetic diversity of their host, the polychaete Pygospio elegans, from natural populations. Host genetic diversity was determined with seven microsatellite loci and summarized as allelic richness, inbreeding coefficient, and individual heterozygosity. We detected nonsignificant correlations between infection loads and both individual host heterozygosity and population genetic diversity. Prevalence and infection load of Rhytidocystis sp. were higher than those of S. pygospionis, and both varied spatially. Coinfections were common, and almost all hosts infected by S. pygospionis were also infected by Rhytidocystis sp. Rhytidocystis sp. infection load was significantly higher in dual infections. Our results suggest that factors other than host genetic diversity might be more important in marine apicomplexan infection patterns and experimental approaches would be needed to further determine how interactions between the apicomplexans and their host influence infection.

The long-standing significance of genetic diversity in conservation

Since allozymes were first used to assess genetic diversity in the 1960s and 1970s, biologists have attempted to characterize gene pools and conserve the diversity observed in domestic crops, livestock, zoos and (more recently) natural populations. Recently, some authors have claimed that the importance of genetic diversity in conservation biology has been greatly overstated. Here, we argue that a voluminous literature indicates otherwise. We address four main points made by detractors of genetic diversity's role in conservation by using published literature to firmly establish that genetic diversity is intimately tied to evolutionary fitness, and that the associated demographic consequences are of paramount importance to many conservation efforts. We think that responsible management in the Anthropocene should, whenever possible, include the conservation of ecosystems, communities, populations and individuals, and their underlying genetic diversity.

Female need for paternal care shapes variation in extra-pair paternity in a cooperative breeder

Socially monogamous females regularly mate with males outside the pair bond. The prevailing explanation for this behavior is that females gain genetic benefits resulting from increased fitness of extra-pair offspring. Furthermore, because of the risk of reduced paternal care in response to cuckoldry, females are expected to seek extra-pair copulations when they can rear offspring with little help from their social partner (“constrained female” hypothesis). We tested these hypotheses and analyzed variation in paternal care in the Afrotropical, facultative cooperative breeding placid greenbul (Phyllastrephus placidus). Overall, approximately 50% of the offspring resulted from extra-pair (and extra-group) mating. Identified extra-pair males were in most cases neighboring dominant males, yet never within-group subordinates. As predicted by the constrained female hypothesis, the occurrence of extra-pair paternity (EPP) increased with the number of cooperative helpers (and not with total group size). However, dominant males did not adjust their food provisioning rates in response to EPP. Although extra-pair males were more strongly related to the dominant female and less heterozygous than the latter’s social mate, this did not result in more inbred extra-pair offspring, likely because identified extra-pair males were not representative of the extra-pair male population. While earlier studies on EPP mainly focused on male genetic quality, results from this study provide evidence that female’s social context may affect extra-pair strategies too.

Genetic decline, restoration and rescue of an isolated ungulate population

Isolation of small populations is expected to reduce fitness through inbreeding and loss of genetic variation, impeding population growth and compromising population persistence. Species with long generation time are the least likely to be rescued by evolution alone. Management interventions that maintain or restore genetic variation to assure population viability are consequently of significant importance. We investigated, over 27 years, the genetic and demographic consequences of a demographic bottleneck followed by artificial supplementation in an isolated population of bighorn sheep (Ovis canadensis). Based on a long-term pedigree and individual monitoring, we documented the genetic decline, restoration and rescue of the population. Microsatellite analyses revealed that the demographic bottleneck reduced expected heterozygosity and allelic diversity by 6.2% and 11.3%, respectively, over two generations. Following supplementation, first-generation admixed lambs were 6.4% heavier at weaning and had 28.3% higher survival to 1 year compared to lambs of endemic ancestry. Expected heterozygosity and allelic diversity increased by 4.6% and 14.3% after two generations through new alleles contributed by translocated individuals. We found no evidence for outbreeding depression and did not see immediate evidence of swamping of local genes. Rapid intervention following the demographic bottleneck allowed the genetic restoration and rescue of this bighorn sheep population, likely preventing further losses at both the genetic and demographic levels. Our results provide further empirical evidence that translocation can be used to reduce inbreeding depression in nature and has the potential to mitigate the effect of human-driven environmental changes on wild populations.

Variance in Reproductive Success is Driven by Environmental Factors, not Mating System, in Bonytails

Studying the reproductive ecology of aggregate broadcast spawning fishes is difficult because it generally is not feasible to sample all potential parents and unambiguously assign their offspring. We used molecular-based parentage analysis to gain insights into the reproductive ecology of the endangered Bonytail, and to evaluate whether protected off-channel habitats could be used as an alternative to hatchery production. By genotyping adults and offspring stocked (n = 4130) into two experimental backwaters across three years, we determined that most adults (82-97%) contributed to progeny production across years and backwaters, with one exception. Both sexes mated multiply and the number of mates and family size were positively correlated. There was also a positive correlation between adult size and metrics of reproductive success. There were strong interactions between sample years and backwaters suggesting that environmental factors are the primary driver of variance in reproductive success. Knowledge of mating systems and sources of variance in reproductive success is important for management of endangered fish because high variance in reproductive success leads to substantial losses of genetic variation when few individuals reproduce successfully. Although variance in reproductive success was observed, most adults contributed to genetically diverse progeny in experimental backwaters. These results support the use of predator-free, but otherwise natural, backwaters as an effective conservation tool for reintroducing Bonytail to its native habitat.

Low incidence of inbreeding in a long-lived primate population isolated for 75 years

ABSTRACT

When close relatives mate, offspring are expected to suffer fitness consequences due to inbreeding depression. Inbreeding has previously been quantified in two ways: using a sufficiently large panel of markers or deep and complete pedigrees over several generations. However, the application of both approaches is still limited by the challenge of compiling such data for species with long generation times, such as primates. Here, we assess inbreeding in rhesus macaques living on Cayo Santiago (Puerto Rico), a population genetically isolated since 1938, but descendant of a large set of presumably unrelated founders. Using comprehensive genetic data, we calculated inbreeding coefficients (F) for 2669 individuals with complete three generation pedigrees and 609 individuals with complete four generation pedigrees. We found that 0.79 and 7.39% of individuals had an F > 0 when using data from three and four generation pedigrees, respectively. No evidence of an increase in inbreeding over the study period (up to 23 years) was found. Furthermore, the observed mean relatedness of breeding pairs differed significantly from the distribution of parental relatedness expected as simulated based on previous reproductive data, suggesting that kin generally avoid breeding with each other. Finally, inbreeding was not a predictor of early mortality measured as survival until weaning and sexual maturation, respectively. Our results remain consistent with three estimators of inbreeding (standardized heterozygosity, internal relatedness, and homozygosity by loci) using up to 42 highly polymorphic microsatellites for the same set of individuals. Together, our results demonstrate that close inbreeding may not be prevalent even in populations isolated over long periods when mechanisms of inbreeding avoidance can operate.

SIGNIFICANCE STATEMENT

When close relatives mate, offspring may suffer from such inbreeding, e.g., via lower survival and/or fertility. Using (i) a large panel of genetic markers and (ii) complete three or four generation pedigrees, respectively, we show that incidences of inbreeding in a long-lived primate population are rare, even after genetic isolation for 75 years. Moreover, our simulations suggest that kin in our population generally avoid breeding with each other. Finally, the few inbred individuals detected in our large sample did not suffer from lower survival. Given that many animal species face dramatic habitat loss combined with critical population declines, our study provides important implications for conservation biology in general and for population management in particular.

Male and Female Subpopulations of Salix viminalis Present High Genetic Diversity and High Long-Term Migration Rates between Them

Dioecy distributed in 157 flowering plant families and 959 flowering plant genera. Morphological and physiological differences between male and female plants have been studied extensively, but studies of sex-specific genetic diversity are relatively scarce in dioecious plants. In this study, 20 SSR loci were employed to examine the genetic variance of male subpopulations and female subpopulations in Salix viminalis. The results showed that all of the markers were polymorphic (Na = 14.15, He = 0.7566) and workable to reveal the genetic diversity of S. viminalis. No statistically significant difference was detected between male and female subpopulations, but the average genetic diversity of male subpopulations (Na = 7.12, He = 0.7071) and female subpopulations (Na = 7.31, He = 0.7226) were high. Under unfavorable environments (West Liao basin), the genetic diversity between male and female subpopulations was still not significantly different, but the genetic diversity of sexual subpopulations were lower. The differentiation of the ten subpopulations in S. viminalis was moderate (FST = 0.0858), which was conformed by AMOVA that most of genetic variance (94%) existed within subpopulations. Pairwise FST indicated no differentiation between sexual subpopulations, which was accompanied by high long-term migrate between them (M = 0.73~1.26). However, little recent migration was found between sexual subpopulations. Therefore, artificial crossing or/and transplantation by cutting propagation should be carried out so as to increase the migration during the process of ex situ conservation.

Social shaping of voices does not impair phenotype matching of kinship in mandrills

Kin selection theory provides a strong theoretical framework to explain the evolution of altruism and cooperative behaviour among genetically related individuals. However, the proximate mechanisms underlying kin discrimination, a necessary process to express kin-related behaviour, remain poorly known. In particular, no study has yet unambiguously disentangled mechanisms based on learned familiarity from true phenotype matching in kin discrimination based on vocal signals. Here we show that in addition to genetic background, social accommodation also shapes individual voices in an Old World monkey (Mandrillus sphinx), even though primate vocalizations were thought to be innate and little flexible. Nonetheless, social shaping of voice parameters does not impair kin discrimination through phenotype-matching of unknown relatives, revealing unexpected discriminatory versatility despite signal complexity. Accurate signal production and perception, therefore, provide a basis for kin identification and kin-biased behaviour in an Old World primate.

Heterozygosity-fitness correlations in a declining seabird population

Loss of genetic diversity is thought to lead to increased risk of extinction in endangered populations due to decreasing fitness of homozygous individuals. Here, we evaluated the presence of inbreeding depression in a long-lived seabird, the European shag (Phalacrocorax aristotelis), after a severe decline in population size by nearly 70%. During three reproductive seasons, 85 breeders were captured and genotyped at seven microsatellite loci. Nest sites were monitored during the breeding season to estimate reproductive success as the number of chicks surviving to full-size-grown per nest. Captured birds were tagged with a ring with an individual code, and resighting data were collected during 7-year period. We found a strong effect of multilocus heterozygosity on female reproductive performance, and a significant, although weaker, effect on breeder survival. However, our matrix population model suggests that this relatively small effect of genetic diversity on breeder survival may have a profound effect on fitness. This highlights the importance of integrating life history consequences in HFC studies. Importantly, heterozygosity was correlated across loci, suggesting that genomewide effects, rather than single loci, are responsible for the observed HFCs. Overall, the HFCs are a worrying symptom of genetic erosion in this declining population. Many long-lived species are prone to extinction, and future studies should evaluate the magnitude of fitness impact of genetic deterioration on key population parameters, such as survival of breeders.

Males and females contribute unequally to offspring genetic diversity in the polygynandrous mating system of wild boar

The maintenance of genetic diversity across generations depends on both the number of reproducing males and females. Variance in reproductive success, multiple paternity and litter size can all affect the relative contributions of male and female parents to genetic variation of progeny. The mating system of the wild boar (Sus scrofa) has been described as polygynous, although evidence of multiple paternity in litters has been found. Using 14 microsatellite markers, we evaluated the contribution of males and females to genetic variation in the next generation in independent wild boar populations from the Iberian Peninsula and Hungary. Genetic contributions of males and females were obtained by distinguishing the paternal and maternal genetic component inherited by the progeny. We found that the paternally inherited genetic component of progeny was more diverse than the maternally inherited component. Simulations showed that this finding might be due to a sampling bias. However, after controlling for the bias by fitting both the genetic diversity in the adult population and the number of reproductive individuals in the models, paternally inherited genotypes remained more diverse than those inherited maternally. Our results suggest new insights into how promiscuous mating systems can help maintain genetic variation.

High genetic diversity in a small population: the case of Chilean blue whales

It is generally assumed that species with low population sizes have lower genetic diversities than larger populations and vice versa. However, this would not be the case for long-lived species with long generation times, and which populations have declined due to anthropogenic effects, such as the blue whale (Balaenoptera musculus). This species was intensively decimated globally to near extinction during the 20th century. Along the Chilean coast, it is estimated that at least 4288 blue whales were hunted from an apparently pre-exploitation population size (k) of a maximum of 6200 individuals (Southeastern Pacific). Thus, here, we describe the mtDNA (control region) and nDNA (microsatellites) diversities of the Chilean blue whale aggregation site in order to verify the expectation of low genetic diversity in small populations. We then compare our findings with other blue whale aggregations in the Southern Hemisphere. Interestingly, although the estimated population size is small compared with the pre-whaling era, there is still considerable genetic diversity, even after the population crash, both in mitochondrial (N = 46) and nuclear (N = 52) markers (Hd = 0.890 and Ho = 0.692, respectively). Our results suggest that this diversity could be a consequence of the long generation times and the relatively short period of time elapsed since the end of whaling, which has been observed in other heavily-exploited whale populations. The genetic variability of blue whales on their southern Chile feeding grounds was similar to that found in other Southern Hemisphere blue whale feeding grounds. Our phylogenetic analysis of mtDNA haplotypes does not show extensive differentiation of populations among Southern Hemisphere blue whale feeding grounds. The present study suggests that although levels of genetic diversity are frequently used as estimators of population health, these parameters depend on the biology of the species and should be taken into account in a monitoring framework study to obtain a more complete picture of the conservation status of a population.

Preliminary study of the genetic diversity of eastern Assamese macaques (Macaca assamensis assamensis) in Thailand based on mitochondrial DNA and microsatellite markers

Human overpopulation, deforestation, invasion of agricultural areas, and livestock are the primary causes for population fragmentation of wildlife. The distribution range of species of the genus Macaca is constantly decreasing and becoming increasingly fragmented due to forest deterioration. Assamese macaques (M. assamensis) are classified as near threatened in the International Union for Conservation of Nature (IUCN) Red List of Threatened Animals (2008) and have been declared a protected wildlife animal according to Wildlife Preservation and Protection Act, B.E.2535 (1992) of Thailand. As studies of the population history and genetic diversity of Assamese macaques in Thailand are currently lacking, we aimed at a first investigation of their genetic diversity based on mitochondrial DNA [hypervariable regions 1 and 2 (HV1, HV2) and cytochrome B (CYTB) regions], as well as 15 microsatellite markers of five sampling sites distributed across Thailand. Our results indicate that Assamese macaques in Thailand are diverse, with eight maternal haplotypes and a low inbreeding coefficient in the Phu Khieo Wildlife Sanctuary (PKWS) population. Moreover, our phylogenetic and median-joining network analysis based on mitochondrial (mt)DNA suggests a population distribution in accordance with the evolutionary scenario proposed for M. sinica. Today, the population of Assamese macaques is fragmented, and conservation strategies are needed to ensure the maintenance of genetic diversity of this primate species.

Testing for post-copulatory selection for major histocompatibility complex genotype in a semi-free-ranging primate population

A large body of evidence suggests that major histocompatibility complex (MHC) genotype influences mate choice. However, few studies have investigated MHC-mediated post-copulatory mate choice under natural, or even semi-natural, conditions. We set out to explore this question in a large semi-free-ranging population of mandrills (Mandrillus sphinx) using MHC-DRB genotypes for 127 parent-offspring triads. First, we showed that offspring MHC heterozygosity correlates positively with parental MHC dissimilarity suggesting that mating among MHC dissimilar mates is efficient in increasing offspring MHC diversity. Second, we compared the haplotypes of the parental dyad with those of the offspring to test whether post-copulatory sexual selection favored offspring with two different MHC haplotypes, more diverse gamete combinations, or greater within-haplotype diversity. Limited statistical power meant that we could only detect medium or large effect sizes. Nevertheless, we found no evidence for selection for heterozygous offspring when parents share a haplotype (large effect size), genetic dissimilarity between parental haplotypes (we could detect an odds ratio of ≥1.86), or within-haplotype diversity (medium-large effect). These findings suggest that comparing parental and offspring haplotypes may be a useful approach to test for post-copulatory selection when matings cannot be observed, as is the case in many study systems. However, it will be extremely difficult to determine conclusively whether post-copulatory selection mechanisms for MHC genotype exist, particularly if the effect sizes are small, due to the difficulty in obtaining a sufficiently large sample.

Molecules and mating: positive selection and reproductive behaviour in primates

Sexual reproduction is generally thought to be more costly than asexual reproduction. However, it does have the advantage of accelerating rates of adaptation through processes such as recombination and positive selection. Comparative studies of the human and nonhuman primate genomes have demonstrated that positive selection has played an important role in the evolutionary history of humans and other primates. To date, many dozens of genes, thought to be affected by positive selection, have been identified. In this chapter, we will focus on genes that are associated with mating behaviours and reproductive processes, concentrating on genes that are most likely to enhance reproductive success and that also show evidence of positive selection. The genes encode phenotypic features that potentially influence mate choice decisions or impact the evolution and function of genes involved in the perception and regulation of, and the response to, phenotypic signals. We will also consider genes that influence precopulatory behavioural traits in humans and nonhuman primates, such as social bonding and aggression. The evolution of post-copulatory strategies such as sperm competition and selective abortion may also evolve in the presence of intense competition and these adaptations will also be considered. Although behaviour may not be solely determined by genes, the evidence suggests that the genes discussed in this chapter have some influence on human and nonhuman primate behaviour and that positive selection on these genes results in some degree of population differentiation and diversity.

Mixed-Ethnicity Face Shape and Attractiveness in Humans

Many studies show agreement within and between populations and cultures for general judgments of facial attractiveness. Studies that have examined the attractiveness of specific traits have also highlighted cross-cultural differences for factors such as symmetry, averageness, and masculinity. One trait that should be preferred across cultures is heterozygosity. Indeed, several studies suggest that mixed ethnicity, in terms of appearing to possess a mixture of traits from different human population groups, may be found attractive, which could reflect preferences for heterozygosity. We examined preferences for manipulated face shape associated with different populations in both Europeans (Britain) and Africans (Guinea-Bissau). We found that mixed-ethnicity face shapes were more attractive than enhanced single-ethnicity face shape across both populations. These results are consistent with evolutionary theories suggesting individuals should prefer heterozygosity in partners because facial cues to mixed-ethnicity are likely to indicate diverse genes compared to cues that indicate a face belongs to a single particular culture or population.

The evolution of the multicoloured face of mandrills: insights from the perceptual space of colour vision

Multicomponent signals consist of several traits that are perceived as a whole. Although many animals rely on multicomponent signals to communicate, the selective pressures shaping these signals are still poorly understood. Previous work has mainly investigated the evolution of multicomponent signals by studying each trait individually, which may not accurately reflect the selective pressures exerted by the holistic perception of signal receivers. Here, we study the design of the multicoloured face of an Old World primate, the mandrill (Mandrillus sphinx), in relation to two aspects of signalling that are expected to be selected by receivers: conspicuousness and information. Using reflectance data on the blue and red colours of the faces of 34 males and a new method of hue vectorisation in a perceptual space of colour vision, we show that the blue hue maximises contrasts to both the red hue and the foliage background colouration, thereby increasing the conspicuousness of the whole display. We further show that although blue saturation, red saturation and the contrast between blue and red colours are all correlated with dominance, dominance is most accurately indicated by the blue-red contrast. Taken together our results suggest that the evolution of blue and red facial colours in male mandrills are not independent and are likely driven by the holistic perception of conspecifics. In this view, we propose that the multicoloured face of mandrills acts as a multicomponent signal. Last, we show that information accuracy increases with the conspicuousness of the whole display, indicating that both aspects of signalling can evolve in concert.

The hidden benefits of sex: evidence for MHC-associated mate choice in primate societies

Major histocompatibility complex (MHC)-associated mate choice is thought to give offspring a fitness advantage through disease resistance. Primates offer a unique opportunity to understand MHC-associated mate choice within our own zoological order, while their social diversity provides an exceptional setting to examine the genetic determinants and consequences of mate choice in animal societies. Although mate choice is constrained by social context, increasing evidence shows that MHC-dependent mate choice occurs across the order in a variety of socio-sexual systems and favours mates with dissimilar, diverse or specific genotypes non-exclusively. Recent research has also identified phenotypic indicators of MHC quality. Moreover, novel findings rehabilitate the importance of olfactory cues in signalling MHC genes and influencing primate mating decisions. These findings underline the importance to females of selecting a sexual partner of high genetic quality, as well as the generality of the role of MHC genes in sexual selection.

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.

Inbreeding depresses sperm competitiveness, but not fertilization or mating success in male Tribolium castaneum

As populations decline to levels where reproduction among close genetic relatives becomes more probable, subsequent increases in homozygous recessive deleterious expression and/or loss of heterozygote advantage can lead to inbreeding depression. Here, we measure how inbreeding across replicate lines of the flour beetle Tribolium castaneum impacts on male reproductive fitness in the absence or presence of male-male competition. Effects on male evolution from mating pattern were removed by enforcing monogamous mating throughout. After inbreeding across eight generations, we found that male fertility in the absence of competition was unaffected. However, we found significant inbreeding depression of sperm competitiveness: non-inbred males won 57 per cent of fertilizations in competition, while inbred equivalents only sired 42 per cent. We also found that the P(2) 'offence' role in sperm competition was significantly more depressed under inbreeding than sperm 'defence' (P(1)). Mating behaviour did not explain these differences, and there was no difference in the viability of offspring sired by inbred or non-inbred males. Sperm length variation was significantly greater in the ejaculates of inbred males. Our results show that male ability to achieve normal fertilization success was not depressed under strong inbreeding, but that inbreeding depression in these traits occurred when conditions of sperm competition were generated.

Finger length ratios (2D:4D) in anthropoids implicate reduced prenatal androgens in social bonding

The second-to-fourth digit ratio (2D:4D) has been proposed as a biomarker reflecting prenatal androgen effects (PAE), such that individuals with lower ratios have experienced higher PAE than those with higher ratios. 2D:4D has been correlated with a number of sex-linked traits in humans such as aggression, promiscuity, and competitiveness. In addition, polygynous societies reportedly have lower 2D:4D (higher PAE) than more monogamous populations. This evidence suggests that PAE may be implicated in the development of sexually selected behaviors in humans. To place 2D:4D research into a broader context, we test the relationship between digit ratios and behavior across nonhuman anthropoids; polygynous species, with higher levels of intrasexual competition, should have more pronounced markers of PAE (lower 2D:4D) than pair-bonded species. Our results accord with those found in humans: 2D:4D is lower in polygynous species and higher (lower PAE) in pair-bonded species. Old World monkeys have low, and relatively invariant 2D:4D (high PAE), which is coupled with high levels of intrasexual competition. This contrasts with higher and more variable ratios in both great apes and New World monkeys. In addition, both male and female ratios decrease with increasing levels of intrasexual competition. Human ratios are intermediate between pair-bonded and more promiscuous hominoids. We propose that PAE may be involved in promoting species characteristic social behavior in anthropoids.

Opposites attract: MHC-associated mate choice in a polygynous primate

We investigated reproduction in a semi-free-ranging population of a polygynous primate, the mandrill, in relation to genetic relatedness and male genetic characteristics, using neutral microsatellite and major histocompatibility complex (MHC) genotyping. We compared genetic dissimilarity to the mother and genetic characteristics of the sire with all other potential sires present at the conception of each offspring (193 offspring for microsatellite genetics, 180 for MHC). The probability that a given male sired increased as pedigree relatedness with the mother decreased, and overall genetic dissimilarity and MHC dissimilarity with the mother increased. Reproductive success also increased with male microsatellite heterozygosity and MHC diversity. These effects were apparent despite the strong influence of dominance rank on male reproductive success. The closed nature of our study population is comparable to human populations for which MHC-associated mate choice has been reported, suggesting that such mate choice may be especially important in relatively isolated populations with little migration to introduce genetic variation.

Females prefer the scent of outbred males: good-genes-as-heterozygosity?

Background

There is increasing interest to determine the relative importance of non-additive genetic benefits as opposed to additive ones for the evolution of mating preferences and maintenance of genetic variation in sexual ornaments. The 'good-genes-as-heterozygosity' hypothesis predicts that females should prefer to mate with more heterozygous males to gain more heterozygous (and less inbred) offspring. Heterozygosity increases males' sexual ornamentation, mating success and reproduction success, yet few experiments have tested whether females are preferentially attracted to heterozygous males, and none have tested whether females' own heterozygosity influences their preferences. Outbred females might have the luxury of being more choosey, but on the other hand, inbred females might have more to gain by mating with heterozygous males. We manipulated heterozygosity in wild-derived house mice (Mus musculus musculus) through inbreeding and tested whether the females are more attracted to the scent of outbred versus inbred males, and whether females' own inbreeding status affects their preferences. We also tested whether infecting both inbred and outbred males with Salmonella would magnify females' preferences for outbred males.

Results

Females showed a significant preference for outbred males, and this preference was more pronounced among inbred females. We found no evidence that Salmonella infection increased the relative attractiveness of outbred versus inbred males; however, we found no evidence that inbreeding affected males' disease resistance in this study.

Conclusion

Our findings support the idea that females are more attracted to outbred males, and they suggest that such preferences may be stronger among inbred than outbred females, which is consistent with the 'good-genes-as-heterozygosity' hypothesis. It is unclear whether this odour preference reflects females' actual mating preferences, though it suggests that future studies should consider females' as well as males' heterozygosity. Our study has implications for efforts to understand how mate choice can provide genetic benefits without eroding genetic diversity (lek paradox), and also conservation efforts to determine the fitness consequences of inbreeding and the maintenance of genetic diversity in small, inbred populations.

Genetic variation in strains of zebrafish (Danio rerio) and the implications for ecotoxicology studies

There is substantial evidence that genetic variation, at both the level of the individual and population, has a significant effect on behaviour, fitness and response to toxicants. Using DNA microsatellites, we examined the genetic variation in samples of several commonly used laboratory strains of zebrafish, Danio rerio, a model species in toxicological studies. We compared the genetic variation to that found in a sample of wild fish from Bangladesh. Our findings show that the wild fish were significantly more variable than the laboratory strains for several measures of genetic variability, including allelic richness and expected heterozygosity. This lack of variation should be given due consideration for any study which attempts to extrapolate the results of ecotoxicological laboratory tests to wild populations.

Positive correlation between genetic diversity and fitness in a large, well-connected metapopulation

BACKGROUND

Theory predicts that lower dispersal, and associated gene flow, leads to decreased genetic diversity in small isolated populations, which generates adverse consequences for fitness, and subsequently for demography. Here we report for the first time this effect in a well-connected natural butterfly metapopulation with high population densities at the edge of its distribution range.

RESULTS

We demonstrate that: (1) lower genetic diversity was coupled to a sharp decrease in adult lifetime expectancy, a key component of individual fitness; (2) genetic diversity was positively correlated to the number of dispersing individuals (indicative of landscape functional connectivity) and adult population size; (3) parameters inferred from capture-recapture procedures (population size and dispersal events between patches) correlated much better with genetic diversity than estimates usually used as surrogates for population size (patch area and descriptors of habitat quality) and dispersal (structural connectivity index).

CONCLUSION

Our results suggest that dispersal is a very important factor maintaining genetic diversity. Even at a very local spatial scale in a metapopulation consisting of large high-density populations interconnected by considerable dispersal rates, genetic diversity can be decreased and directly affect the fitness of individuals. From a biodiversity conservation perspective, this study clearly shows the benefits of both in-depth demographic and genetic analyses. Accordingly, to ensure the long-term survival of populations, conservation actions should not be blindly based on patch area and structural isolation. This result may be especially pertinent for species at their range margins, particularly in this era of rapid environmental change.

Runs of homozygosity in European populations

Estimating individual genome-wide autozygosity is important both in the identification of recessive disease variants via homozygosity mapping and in the investigation of the effects of genome-wide homozygosity on traits of biomedical importance. Approaches have tended to involve either single-point estimates or rather complex multipoint methods of inferring individual autozygosity, all on the basis of limited marker data. Now, with the availability of high-density genome scans, a multipoint, observational method of estimating individual autozygosity is possible. Using data from a 300,000 SNP panel in 2618 individuals from two isolated and two more-cosmopolitan populations of European origin, we explore the potential of estimating individual autozygosity from data on runs of homozygosity (ROHs). Termed F(roh), this is defined as the proportion of the autosomal genome in runs of homozygosity above a specified length. Mean F(roh) distinguishes clearly between subpopulations classified in terms of grandparental endogamy and population size. With the use of good pedigree data for one of the populations (Orkney), F(roh) was found to correlate strongly with the inbreeding coefficient estimated from pedigrees (r = 0.86). Using pedigrees to identify individuals with no shared maternal and paternal ancestors in five, and probably at least ten, generations, we show that ROHs measuring up to 4 Mb are common in demonstrably outbred individuals. Given the stochastic variation in ROH number, length, and location and the fact that ROHs are important whether ancient or recent in origin, approaches such as this will provide a more useful description of genomic autozygosity than has hitherto been possible.

Age at maturity in wild baboons: genetic, environmental and demographic influences

The timing of early life-history events, such as sexual maturation and first reproduction, can greatly influence variation in individual fitness. In this study, we analysed possible sources of variation underlying different measures of age at social and physical maturation in wild baboons in the Amboseli basin, Kenya. The Amboseli baboons are a natural population primarily comprised of yellow baboons (Papio cynocephalus) that occasionally hybridize with anubis baboons (Papio anubis) from outside the basin. We found that males and females differed in the extent to which various factors influenced their maturation. Surprisingly, we found that male maturation was most strongly related to the proportion of anubis ancestry revealed by their microsatellite genotypes: hybrid males matured earlier than yellow males. In contrast, although hybrid females reached menarche slightly earlier than yellow females, maternal rank and the presence of maternal relatives had the largest effects on female maturation, followed by more modest effects of group size and rainfall. Our results indicate that a complex combination of demographic, genetic, environmental, and maternal effects contribute to variation in the timing of these life-history milestones.

Quantifying the increase in average human heterozygosity due to urbanisation

The human population is undergoing a major transition from a historical metapopulation structure of relatively isolated small communities to an outbred structure. This process is predicted to increase average individual genome-wide heterozygosity (h) and could have effects on health. We attempted to quantify this increase in mean h. We initially sampled 1001 examinees from a metapopulation of nine isolated villages on five Dalmatian islands (Croatia). Village populations had high levels of genetic differentiation, endogamy and consanguinity. We then selected 166 individuals with highly specific personal genetic histories to form six subsamples, which could be ranked a priori by their predicted level of outbreeding. The measure h was then estimated in the 166 examinees by genotyping 1184 STR/indel markers and using two different computation methods. Compared to the value of mean h in the least outbred sample, values of h in the remaining samples increased successively with predicted outbreeding by 0.023, 0.038, 0.058, 0.067 and 0.079 (P<0.0001), where these values are measured on the same scale as the inbreeding coefficient (but opposite sign). We have shown that urbanisation was associated with an average increase in h of up to 0.08-0.10 in this Croatian metapopulation, regardless of the method used. Similar levels of differentiation have been described in many populations. Therefore, changes in the level of heterozygosity across the genome of this magnitude may be common during isolate break-up in humans and could have significant health effects through the established genetic mechanism of hybrid vigour/heterosis.

Genetic heterozygosity and sociality in a primate species

The relationship between an individual's genotype and its phenotype is a central issue in biology, but one that is largely unexplored for the important phenotype of complex social behavior. Here we examine the relationship between heterozygosity and social behavior among unrelated adult female rhesus macaques living on the island of Cayo Santiago (Puerto Rico). We show that female macaques with lower mean neutral heterozygosity were discriminated against by their unrelated conspecifics: less heterozygous females received aggressive behavior at higher rates and received affiliation at lower rates than more heterozygous females. We demonstrate that these results are likely due to local genomic effects associated with particular microsatellite loci. Our study suggests that genetic characteristics can impact the way an individual experiences its social environment and that female macaques that are homozygous at two microsatellite loci appear to be less attractive social partners based on grooming and aggression received by unrelated conspecifics.

Inbreeding depression in non-human primates: a historical review of methods used and empirical data

Offspring born to related parents may show reduced fitness due to inbreeding depression. Although evidence of inbreeding depression has accumulated for a variety of taxa during the past two decades, such analyses remain rare for primate species, probably because of their long generation time. However, inbreeding can have important fitness costs and is likely to shape life-history traits in all living species. As a consequence, selection should have favored inbreeding avoidance via sex-biased dispersal, extra-group paternity, or kin discrimination. In this paper, we review empirical studies on the effects of inbreeding on fitness traits or fitness correlates in primate species. In addition, we report the methods that have been used to detect inbreeding in primate populations, and their development with the improvement of laboratory techniques. We focus particularly on the advantages and disadvantages using microsatellite loci to detect inbreeding. Although the genetic data that are typically available (partial pedigrees, use of microsatellite heterozygosity as an estimate of genomewide inbreeding) tend to impose constraints on analyses, we encourage primatologists to explore the potential effects of inbreeding if they have access to even partial pedigrees or genetic information. Such studies are important because of both the value of basic research in inbreeding depression in the wild and the conservation issues associated with inbreeding, particularly in threatened species, which include more than half of the currently living primate species.

Are indirect genetic benefits associated with polyandry? Testing predictions in a natural population of lemon sharks

Multiple mating has clear fitness benefits for males, but uncertain benefits and costs for females. We tested for indirect genetic benefits of polyandry in a natural population, by using data from a long-term genetic and demographic study of lemon sharks (Negaprion brevirostris) at Bimini, Bahamas. To do so, we followed the fates of individuals from six cohorts (450 age-0 and 254 age-1 fish) in relation to their individual level of genetic variation, and whether they were from polyandrous or monoandrous litters. We find that offspring from polyandrous litters did not have a greater genetic diversity or greater survival than did the offspring of monoandrous litters. We also find no evidence of positive associations between individual offspring genetic diversity metrics and our surrogate measure of fitness (i.e. survival). In fact, age-1 individuals with fewer heterozygous microsatellite loci and more genetically similar parents were more likely to survive to age-2. Thus, polyandry in female lemon sharks does not appear to be adaptive from the perspective of indirect genetic benefits to offspring. It may instead be the result of convenience polyandry, whereby females mate multiply to avoid harassment by males. Our inability to find indirect genetic benefits of polyandry despite detailed pedigree and survival information suggests the need for similar assessments in other natural populations.

Female extrapair mate choice in a cooperative breeder: trading sex for help and increasing offspring heterozygosity

Sexual conflict between males and females over mating is common. Females that copulate with extrapair mates outside the pair-bond may gain (i) direct benefits such as resources or increased paternal care, (ii) indirect genetic benefits for their offspring, or (iii) insurance against infertility in their own social mate. Few studies have been able to demonstrate the different contexts in which females receive varying types of benefits from extrapair mates. Here, I examined sexual conflict, female extrapair mate choice, and patterns of extrapair paternity in the cooperatively breeding superb starling Lamprotornis superbus using microsatellite markers. Although extrapair paternity was lower than many other avian cooperative breeders (14% of offspring and 25% of nests), females exhibited two distinct mating patterns: half of the extrapair fertilizations were with males from inside the group, whereas half were with males from outside the group. Females with few potential helpers copulated with extrapair mates from within their group and thereby gained direct benefits in the form of additional helpers at the nest, whereas females paired to mates that were relatively less heterozygous than themselves copulated with extrapair mates from outside the group and thereby gained indirect genetic benefits in the form of increased offspring heterozygosity. Females did not appear to gain fertility insurance from copulating with extrapair mates. This is the first study to show that individuals from the same population mate with extrapair males and gain both direct and indirect benefits, but that they do so in different contexts.

Egg production and individual genetic diversity in lesser kestrels

Fecundity is an important component of individual fitness and has major consequences on population dynamics. Despite this, the influence of individual genetic variability on egg production traits is poorly known. Here, we use two microsatellite-based measures, homozygosity by loci and internal relatedness, to analyse the influence of female genotypic variation at 11 highly variable microsatellite loci on both clutch size and egg volume in a wild population of lesser kestrels (Falco naumanni). Genetic diversity was associated with clutch size, with more heterozygous females laying larger clutches, and this effect was statistically independent of other nongenetic variables such as female age and laying date, which were also associated with fecundity in this species. However, egg volume was not affected by female heterozygosity, confirming previous studies from pedigree-based breeding experiments which suggest that this trait is scarcely subjected to inbreeding depression. Finally, we explored whether the association between heterozygosity and clutch size was due to a genome-wide effect (general effect) or to single locus heterozygosity (local effect). Two loci showed a stronger influence but the correlation was not fully explained by these two loci alone, suggesting that a main general effect underlies the association observed. Overall, our results underscore the importance of individual genetic variation for egg production in wild bird populations, a fact that could have important implications for conservation research and provides insights into the study of clutch size evolution and genetic variability maintenance in natural populations.

Effects of genome-wide heterozygosity on a range of biomedically relevant human quantitative traits

The dramatic changes in human population structure over the last 200 years have resulted in significant levels of outbreeding, which, in turn, is predicted to lead to increased levels of individual genetic diversity (genome-wide heterozygosity, h). To investigate possible effects of these large demographic changes on global health, we studied the effect of h, measured as relative heterozygosity, h(R), on 15 disease-related traits in four groups of individuals with widely differing ancestral histories (ranging from outbred to inbred) from the Dalmatian islands in Croatia. Higher levels of h(R), estimated using 1184 STR/indel markers, were found in the outbred group (P < 0.0001) and were associated with lower blood pressure (BP) and total/LDL cholesterol (P = 0.01 and 0.01, respectively) after controlling for other factors, with BP showing a strong sex effect (males P > 0.5 and females P = 0.002). These findings, if replicated, suggest that h(R) be considered as a genetic risk factor in genetic epidemiological studies on common disease traits. They are consistent with the well-known effects of heterosis (hybrid vigour) described when outcrossing animals and plants. Outbreeding resulting from urbanization and migration from traditional population subgroups may be leading to increasing h(R) and may have beneficial effects on a range of traits associated with human health and disease. Other traits, such as age at menarche, IQ and lifespan, which have been changing during the decades of urbanization, may also have been influenced by demographic factors.

Elevation and connectivity define genetic refugia for mountain sheep as climate warms

Global warming is predicted to affect the evolutionary potential of natural populations. We assessed genetic diversity of 25 populations of desert bighorn sheep (Ovis canadensis nelsoni) in southeastern California, where temperatures have increased and precipitation has decreased during the 20th century. Populations in low-elevation habitats had lower genetic diversity, presumably reflecting more fluctuations in population sizes and founder effects. Higher-elevation habitats acted as reservoirs of genetic diversity. However, genetic diversity was also affected by population connectivity, which has been disrupted by human development. Restoring population connectivity may be necessary to buffer the effects of climate change on this desert-adapted ungulate.