Pairwise Relatedness Research Articles

Re‐mating across years and intralineage polygyny are associated with greater than expected levels of inbreeding in wild red deer

The interaction between philopatry and nonrandom mating has important consequences for the genetic structure of populations, influencing co-ancestry within social groups but also inbreeding. Here, using genetic paternity data, we describe mating patterns in a wild population of red deer (Cervus elaphus) which are associated with marked consequences for co-ancestry and inbreeding in the population. Around a fifth of females mate with a male with whom they have mated previously, and further, females frequently mate with a male with whom a female relative has also mated (intralineage polygyny). Both of these phenomena occur more than expected under random mating. Using simulations, we demonstrate that temporal and spatial factors, as well as skew in male breeding success, are important in promoting both re-mating behaviours and intralineage polygyny. However, the information modelled was not sufficient to explain the extent to which these behaviours occurred. We show that re-mating and intralineage polygyny are associated with increased pairwise relatedness in the population and a rise in average inbreeding coefficients. In particular, the latter resulted from a correlation between male relatedness and rutting location, with related males being more likely to rut in proximity to one another. These patterns, alongside their consequences for the genetic structure of the population, have rarely been documented in wild polygynous mammals, yet they have important implications for our understanding of genetic structure, inbreeding avoidance and dispersal in such systems.

Utilizing Graph Theory to Select the Largest Set of Unrelated Individuals for Genetic Analysis

Many statistical analyses of genetic data rely on the assumption of independence among samples. Consequently, relatedness is either modeled in the analysis or samples are removed to "clean" the data of any pairwise relatedness above a tolerated threshold. Current methods do not maximize the number of unrelated individuals retained for further analysis, and this is a needless loss of resources. We report a novel application of graph theory that identifies the maximum set of unrelated samples in any dataset given a user-defined threshold of relatedness as well as all networks of related samples. We have implemented this method into an open source program called Pedigree Reconstruction and Identification of a Maximum Unrelated Set, PRIMUS. We show that PRIMUS outperforms the three existing methods, allowing researchers to retain up to 50% more unrelated samples. A unique strength of PRIMUS is its ability to weight the maximum clique selection using additional criteria (e.g. affected status and data missingness). PRIMUS is a permanent solution to identifying the maximum number of unrelated samples for a genetic analysis.

Small-scale dispersal and population structure in stream-living brown trout (Salmo trutta) inferred by mark–recapture, pedigree reconstruction, and population genetics

Many animals move among habitats, and even small-scale dispersal of individuals between habitat patches may have strong implications for population dynamics and structure. Here, we use long-term mark–recapture data combined with extensive genotyping and parentage assignment to investigate the importance of small-scale location change of resident brown trout ( Salmo trutta ) in a small stream (1500 m). During the first summer, juvenile fish dispersed downstream (mean displacement 200 m), with smaller juveniles dispersing longer distances. Downstream movement was also predominant during the first winter, but older fish moved little. This limited dispersal resulted in a significant isolation-by-distance structure for ages 1 and 2, but not for older age groups or for the mature fish. Individual pairwise relatedness coefficients decreased with waterway distance for mature fish during the 2002 and 2003 spawning seasons, but only weakly. Overall, between-site genetic differentiation was stronger for the younger age classes, and the signal decayed with age, indicating that the genetic structure observed in the stream is mainly driven by spatial aggregation of close relatives.

The familiality of pelvic organ prolapse in the Utah Population Database

Pelvic organ prolapse (POP) in women is a common condition whose etiology is poorly understood. There is increasing evidence that POP is heritable. The aim of our study was to define and evaluate familial clustering of POP. Using a population-based Utah genealogy linked to more than a decade of hospital data, we calculated relative risks (RR) of POP in female relatives of women with POP using age- and birth year-specific rates of POP. We compared the average pairwise relatedness of all POP cases to the population using a measure of genetic distance. We identified 1,292 women with diagnostic and procedure codes for POP. The RR of POP was significantly elevated in first- and third-degree female relatives (RR 4.15, p < 0.001; RR 1.24, p = 0.05). The average pairwise relatedness for all individuals with POP was significantly higher than expected (p < 0.001). These results strongly support a significant heritable contribution to POP.

Kinship in a social bee mediates ovarian differentiation and has implications for reproductive skew theories

Understanding how social species differentially allocate reproduction within groups is a major problem in evolutionary biology. A key issue is whether relatedness among nestmates can be assessed by group members and then used to determine levels of skew. Several studies have shown a relationship between skew and relatedness, but this might indicate correlational rather than causal relationships. For example, if fecundity has a genetic component, then more closely related females might have similar reproductive outputs, and hence low skew, owing to genetic similarity in genes controlling reproduction, rather than relatedness per se. Here we show that in a facultatively social bee ovarian differentiation between queens and secondary reproductives, prior to egg-laying declines with increasing relatedness. This finding could not be explained by genetically determined similarities in fecundity, by variation in body size or age, or by selective execution of brood by workers. Our results indicate that females are able to assess pairwise relatedness, either directly or indirectly, and use this information to mediate ovarian development. This points a way forward for future developments in skew theory by throwing attention onto what has been largely treated as a ‘black box’: the ability of organisms to acquire and process the kinds of information needed for skew theories to operate. ► We examine ovary size in colonies of a social bee, prior to egg laying. ► We show that ovarian skew is correlated with pairwise relatedness. ► This correlation is not due to genetic similarity in fecundities. ► Our data concord with earlier studies, but show that skew precedes egg laying. ► The effect of relatedness on skew meets a critical assumption in many skew theories.

Relatedness does not predict vigilance in a population of the social rodent Octodon degus

The possibility that social foragers adjust and coordinate their scanning activity when in the presence of close relatives to attain inclusive fitness benefits remains controversial and scarcely examined. To this aim, we first tested the null hypothesis of no association between foraging individuals of the diurnal rodent, Octodon degus and their pairwise relatedness (six microsatellite loci), under natural conditions. Secondly, we examined the influence of relatedness on scan effort (percent overlapping) and temporal distribution of scanning using linear regression. Finally, we evaluated whether temporal distributions of scanning were significantly lower (coordination) or higher (synchrony) than random expectations using bootstrapping. We found that pairwise relatedness between focal degus and their foraging partner did not influence the scan effort or the temporal distribution of scanning. These original, field-based findings imply that vigilance behavior in socially foraging degus is unlikely to be kin-selected and adds to results from previous lab studies in that kinship remains a poor predictor of social behavior in these animals. Overall, our study adds to others revealing that kin selection may not have had an impact on aspects of social behavior such as vigilance during social foraging.

The female perspective of mating in A. femoralis, a territorial frog with paternal care--a spatial and genetic analysis.

The adaptive significance of sequential polyandry is a challenging question in evolutionary and behavioral biology. Costs and benefits of different mating patterns are shaped by the spatial distribution of individuals and by genetic parameters such as the pairwise relatedness between potential mating partners. Thus, females should become less choosy as costs of mating and searching for mates increase. We used parentage assignments to investigate spatial and genetic patterns of mating across a natural population of the Neotropical frog Allobates femoralis, a species characterized by male territoriality and care and female iteroparity. There was no correlation between genetic and spatial distances between adult individuals across the population. In 72% of cases, females mated with males available within a radius of 20 m. Mean pairwise relatedness coefficients of successful reproducers did not differ from random mating but had a lower variance than expected by chance, suggesting maximal reproductive output at intermediate genetic divergence. We also found evidence for selection in favor of more heterozygous individuals between the embryo and adult stage. The level of sequential polyandry significantly increased with the number of spatially available males. Females that had more candidate males also produced more adult progeny. We hypothesize that the benefits associated with female multiple mating outweigh the costs of in- and outbreeding depression, and consequently precluded the evolution of ‘choosy’ mate selection in this species.

Translocation of wild populations: conservation implications for the genetic diversity of the black‐lipped pearl oysterPinctada margaritifera

Translocation has been widely studied as a tool for conservation management to restore or enhance degraded populations. On the contrary, few studies have been conducted on translocation for commercial purposes. In this study, we evaluate the genetic consequences of translocation of wild individuals of Pinctada margaritifera on farmed and adjacent wild populations. We tested the hypotheses that translocations would induce high genetic heterogeneity in farmed populations and this heterogeneity would then leak into the adjacent wild populations. In fact, farmed samples exhibit high levels of heterogeneity and low pairwise relatedness compared to wild populations, highlighting the pooling of genetically divergent populations into farms. We also demonstrate that this heterogeneity is transmitted to adjacent wild populations as a result of interbreeding. Adjacent wild populations tend to have higher genetic diversity values and greater pairwise relatedness coefficient with farmed populations than wild populations. Overall, pearl culture in French Polynesia promotes the mixing of unrelated individuals in farmed locations and reduces genetic divergence among geographically distant populations as well as among farmed and wild populations of a same lagoon. We also studied for the first time a farmed population originating from spat collected in a lagoon where release of hatchery-produced larvae occurred 10 years ago and we were able to identify four distinct genetic groups. These groups contribute highly to reproduction and caused considerable genetic drift in the lagoon, suggesting that hatchery-produced larvae are neither sustainable method for pearl culture nor for conserving the diversity of P. margaritifera in French Polynesia.

Fine-scale genetic population structure of an understory rainforest bird in Costa Rica

We studied five populations of a rainforest understory insectivorous bird (Myrmeciza exsul, chestnut-backed antbird) in a fragmented landscape in northeastern Costa Rica in order to test hypotheses about the influence of forest fragmentation on population genetic structure using 16 microsatellite loci. Bayesian assignment approaches—perhaps the most conservative analyses we performed—consistently grouped the sites into two distinct groups, with all individuals from the smallest and most isolated population clustering separately from the other four sites. Additional analyses revealed (1) overall significant genetic structure; (2) a pattern of population differentiation consistent with a hypothesis of isolation by resistance (landscape connectivity), but not distance; and (3) relatively short dispersal distances indicated by elevated mean pairwise relatedness in several of the sites. Our results are somewhat surprising given the small geographic distances between sites (11–34 km) and the short time (~60 years) since wide-spread deforestation in this landscape. We suspect fine-scale genetic structure may occur in many resident tropical bird species, and in the case of the chestnut-backed antbird it appears that anthropogenic habitat fragmentation has important population genetic implications. It appears that chestnut-backed antbirds may persist in fragmented landscapes in the absence of significant migration among patches, but mechanisms that allow this species to persist when many other similar species do not are not well understood.

Building genetic networks using relatedness information: a novel approach for the estimation of dispersal and characterization of group structure in social animals

Natal dispersal is an important life history trait driving variation in individual fitness, and therefore, a proper understanding of the factors underlying dispersal behaviour is critical to many fields including population dynamics, behavioural ecology and conservation biology. However, individual dispersal patterns remain difficult to quantify despite many years of research using direct and indirect methods. Here, we quantify dispersal in a single intensively studied population of the cooperatively breeding chestnut-crowned babbler (Pomatostomus ruficeps) using genetic networks created from the combination of pairwise relatedness data and social networking methods and compare this to dispersal estimates from re-sighting data. This novel approach not only identifies movements between social groups within our study sites but also provides an estimation of immigration rates of individuals originating outside the study site. Both genetic and re-sighting data indicated that dispersal was strongly female biased, but the magnitude of dispersal estimates was much greater using genetic data. This suggests that many previous studies relying on mark-recapture data may have significantly underestimated dispersal. An analysis of spatial genetic structure within the sampled population also supports the idea that females are more dispersive, with females having no structure beyond the bounds of their own social group, while male genetic structure expands for 750 m from their social group. Although the genetic network approach we have used is an excellent tool for visualizing the social and genetic microstructure of social animals and identifying dispersers, our results also indicate the importance of applying them in parallel with behavioural and life history data.

Kin selection may contribute to lek evolution and trait introgression across an avian hybrid zone

Understanding the mechanism(s) that favour cooperation among individuals competing for the same resources provides direct insights into the evolution of grouping behaviour. In a hybrid zone between golden-/yellow-collared (Manacus vitellinus) and white-collared (Manacus candei) manakins, males form aggregations composed of white and yellow males solely to attract females ('mixed leks'). Previous work shows that yellow males in these mixed leks experience a clear mating advantage over white males, resulting in the preferential introgression of yellow plumage allele(s) into the white species. However, the yellow male mating advantage only occurs in mixed leks with high frequencies of yellow males, and only a few of these males probably mate. Hence, it remains unclear why unsuccessful males join leks. Here, we used microsatellite markers to estimate pairwise relatedness among males within and between leks to test whether indirect genetic benefits of helping kin ('kin selection') can promote grouping. We found that yellow males are significantly more related to each other within than between leks, while relatedness among white males did not differ within and between leks. This suggests that yellow males may indirectly enhance their own reproductive success by preferentially lekking with relatives because yellow plumage is under positive frequency-dependent selection (positive FDS). Our results are consistent with the hypothesis that kin selection may promote grouping and facilitate positive FDS for yellow males, mediating the movement of yellow plumage across this hybrid zone.

Genetic Consequences of Group Living in Mongolian Gerbils

Social behavior can shape the local population genetic structure of mammals. Group living can increase pairwise genetic relatedness of mammals at a local level but differentiate the genetic structure at a population level through offspring philopatry and nonrandom mating. Our study aimed to test the hypothesis that social groups of Mongolian gerbils (Meriones unguiculatus) would consist of genetically related individuals due to offspring philopatry and would have distinct genetic structures because of restricted gene flow among social groups and nonrandom mating. We genotyped 327 wild gerbils, live captured from 28 social groups in Inner Mongolia, China, using nine microsatellite loci. The within-group pairwise genetic relatedness coefficient averaged 0.28 ± 0.14 (standard deviation), whereas the average pairwise genetic relatedness coefficient of the whole gerbil population was 0.0 ± 0.2. Additionally, the value of the global F statistic (F(st)) was 0.21, suggesting a substantial genetic differentiation among social groups of Mongolian gerbils. The Bayesian clustering divided the 327 gerbils into 23 distinct genetic clusters. Therefore, our results show that high within-group genetic relatedness and among-group genetic differentiation are the genetic consequences of group living in social mammals because of restricted gene flow, female philopatry, and nonrandom mating within social groups.

Willow tit Parus montanus extrapair offspring are more heterozygous than their maternal half-siblings

Through extrapair matings, males can sire additional offspring with low cost and females may look for direct benefits in form of food or additional paternal care or gain genetic benefits that increase offspring fitness. We studied the patterns of female mate choice and frequency of extrapair paternity in the socially monogamous willow tit Parus montanus using microsatellites. We also examined the effect of heterozygosity on the growth rate and survival of the chicks. We found 25 mixed-paternity broods out of 117 broods of which both parents were sampled. Altogether, 6.7% of sampled chicks were classified as extrapair young. The pairwise relatedness of social pairs did not correlate with the percentage of extrapair young in the brood and there was no difference in heterozygosity between promiscuous and monogamous parents. However, the extrapair young were more heterozygous than the within-pair young in the mixed-paternity broods. The maternal half-siblings in mixed paternity broods were similar in body size. Thus, there was no indication for different growth rate between the siblings, but there were indications that heterozygosity affects survival.

Genetic diversity and population structure of Glossina pallidipes in Uganda and western Kenya

BackgroundGlossina pallidipes has been implicated in the spread of sleeping sickness from southeastern Uganda into Kenya. Recent studies indicated resurgence of G. pallidipes in Lambwe Valley and southeastern Uganda after what were deemed to be effective control efforts. It is unknown whether the G. pallidipes belt in southeastern Uganda extends into western Kenya. We investigated the genetic diversity and population structure of G. pallidipes in Uganda and western Kenya.ResultsAMOVA indicated that differences among sampling sites explained a significant proportion of the genetic variation. Principal component analysis and Bayesian assignment of microsatellite genotypes identified three distinct clusters: western Uganda, southeastern Uganda/Lambwe Valley, and Nguruman in central-southern Kenya. Analyses of mtDNA confirmed the results of microsatellite analysis, except in western Uganda, where Kabunkanga and Murchison Falls populations exhibited haplotypes that differed despite homogeneous microsatellite signatures. To better understand possible causes of the contrast between mitochondrial and nuclear markers we tested for sex-biased dispersal. Mean pairwise relatedness was significantly higher in females than in males within populations, while mean genetic distance was lower and relatedness higher in males than females in between-population comparisons. Two populations sampled on the Kenya/Uganda border, exhibited the lowest levels of genetic diversity. Microsatellite alleles and mtDNA haplotypes in these two populations were a subset of those found in neighboring Lambwe Valley, suggesting that Lambwe was the source population for flies in southeastern Uganda. The relatively high genetic diversity of G. pallidipes in Lambwe Valley suggest large relict populations remained even after repeated control efforts.ConclusionOur research demonstrated that G. pallidipes populations in Kenya and Uganda do not form a contiguous tsetse belt. While Lambwe Valley appears to be a source population for flies colonizing southeastern Uganda, this dispersal does not extend to western Uganda. The complicated phylogeography of G. pallidipes warrants further efforts to distinguish the role of historical and modern gene flow and possible sex-biased dispersal in structuring populations.

Mass-Intrusion-Induced Temporary Shift in the Genetic Structure of an Asian Black Bear Population

Abstract. Some Asian black bears inhabiting Japan are known to invade residential areas, a phenomenon known as mass intrusion. Although mass intrusion occurs in autumn, it can result in genetic mingling. We examined the influence of intrusion on the genetic structure of black bears. Tissue samples were collected from invasive bears in central Japan in the autumn of two mass-intrusion years, 2004 and 2006. We also set hair traps overlapping an area where tissue samples were collected in the summers of 2005, 2006, and 2008. The genotypes of eight microsatellite loci were determined by PCR. Pairwise relatedness (rxy ) was negatively correlated with distance among resident bears, whereas no such relationship was observed among invasive bears. Spatial autocorrelation analysis of the normal bears in 2006 revealed a significantly positive rc value within the 0–65-km-distance class, whereas that of invasive bears in 2006 revealed significantly positive rc values between the 0–15- and 0–65-km-distance classes. We ...

Evidence for a heritable predisposition to Chronic Fatigue Syndrome

BackgroundChronic Fatigue Syndrome (CFS) came to attention in the 1980s, but initial investigations did not find organic causes. Now decades later, the etiology of CFS has yet to be understood, and the role of genetic predisposition in CFS remains controversial. Recent reports of CFS association with the retrovirus xenotropic murine leukemic virus-related virus (XMRV) or other murine leukemia related retroviruses (MLV) might also suggest underlying genetic implications within the host immune system.MethodsWe present analyses of familial clustering of CFS in a computerized genealogical resource linking multiple generations of genealogy data with medical diagnosis data of a large Utah health care system. We compare pair-wise relatedness among cases to expected relatedness in the Utah population, and we estimate risk for CFS for first, second, and third degree relatives of CFS cases.ResultsWe observed significant excess relatedness of CFS cases compared to that expected in this population. Significant excess relatedness was observed for both close (p <0.001) and distant relationships (p = 0.010). We also observed significant excess CFS relative risk among first (2.70, 95% CI: 1.56-4.66), second (2.34, 95% CI: 1.31-4.19), and third degree relatives (1.93, 95% CI: 1.21-3.07).ConclusionsThese analyses provide strong support for a heritable contribution to predisposition to Chronic Fatigue Syndrome. A population of high-risk CFS pedigrees has been identified, the study of which may provide additional understanding.

Relatedness and Demography of African Forest Elephants: Inferences from Noninvasive Fecal DNA Analyses

African forest elephants (Loxodonta cyclotis) are genetically and morphologically distinct from their savannah counterparts, but their biology remains poorly understood. In this study, I use noninvasive fecal DNA analyses to examine the relatedness structure and historical demography of forest elephants at 2 sites in SW Gabon, central Africa. Pairwise relatedness values calculated between 162 elephant individuals genotyped at 8 microsatellite loci were significantly higher within spatially associated dung piles than between random pairings for one site. First- and second-order relatives were most commonly detected among dung piles from adult female pairs and adult females and juveniles. Pairwise relatedness estimates suggested that, like savannah elephants, forest groups are largely composed of adult females, their sisters, and juvenile offspring. Associations between males, and groups containing juveniles from multiple related females, were detected but at much lower frequency. Analysis of mitochondrial d-loop sequences from 70 elephant individuals identified 2 haplogroups in SW Gabon.

Dispersal Patterns of Orang-utans (Pongo spp.) in a Bornean Peat-swamp Forest

Knowledge regarding dispersal patterns in great apes may help in understanding the evolution of dispersal patterns and social grouping in early hominoids, as well as in our own species. However, the social structure and dispersal system of orang-utans (Pongo spp.) remains little understood despite past research. We addressed this question by conducting genetic analyses on a wild orang-utan (Pongo pygmaeus wurmbii) population from the Sabangau peat-swamp in Borneo. We estimated pairwise relatedness among 16 adult individuals using 19 polymorphic microsatellite markers. Mean relatedness among females was significantly higher than in males, irrespective of the relatedness estimator used, following the pattern predicted for male dispersal. Our results support field observations that average dispersal distance for females is less than for males, suggesting that female orang-utans are philopatric, whereas males disperse. This contrasts with previous findings from other sites where anthropogenic influences were present. Based on qualitative mitochondrial DNA analyses, it appears that unflanged adult males show some degree of site fidelity compared to flanged males. Thus, male orang-utans may disperse permanently from their natal range once they are fully flanged. Male-biased dispersal and female philopatry in orang-utans differ from those of extant African apes and are more similar to many Old World monkey species. Hence we hypothesize that this system may represent the ancestral state of early hominoids.

Genetic evidence for male‐biased dispersal in the Siberian jay (Perisoreus infaustus) based on autosomal and Z‐chromosomal markers

Sex-bias in natal dispersal patterns can have important genetic and evolutionary consequences; however, reliable information about sex-biased dispersal can be difficult to obtain with observational methods. We analysed the sex-specific patterns of genetic differentiation among three Siberian jay (Perisoreus infaustus) populations, using 11 autosomal and six Z-chromosomal microsatellite markers. Irrespective of marker-type and indices used (viz. F(ST), average pairwise relatedness and effective number of immigrants), all analyses provided strong evidence for male-biased dispersal. Population structuring at autosomal loci (F(ST) =0.046, P<0.05) exceeded that at Z-chromosomal loci (F(ST) =0.033, P<0.05), and levels of introgression were inferred to be significantly higher for Z-chromosomal when compared to autosomal loci. Of the three populations studied, levels of genetic variability were the lowest in the southernmost fringe population, despite the fact that it harboured a group of divergent Z-chromosomal haplotypes that were not found in the other two populations. In general, the results provide strong genetic evidence for male-biased dispersal in Siberian jays, where observational data have previously suggested male philopatry. The results also highlight the utility of Z-chromosomal markers for gaining insights into the genetic diversity and structuring of populations.

Social and genetic structure in colonies of the social wasp Microstigmus nigrophthalmus

Microstigmus (Hymenoptera: Crabronidae) is a genus of social apoid wasps which represents an origin of sociality independent from vespoids, but which has so far received little attention. Though group-nesting is widespread in Microstigmus, genetic relatedness has so far been studied in only one species, M. comes. We report on the social biology of M. nigrophthalmus, drawing from behavioural observations and molecular genetic analyses of relatedness and kinship. There was no evidence of distinctive behavioural suites that distinguished reproductive and non-reproductive individuals. Females could mate more than once, but mating frequency was low. Mean relatedness within nests was high, particularly between females (close to 0.5), but pairwise relatedness values were very variable, as nestmates displayed a wide range of relationships. Such high levels of relatedness should be a factor promoting social nesting and cooperative brood care in this species, as females gain only a slight genetic advantage through rearing their own offspring rather than those of nestmates. This study provides the finest analysis of genetic structure so far in an apoid wasp, and indicates that the form of sociality varies greatly between species of Microstigmus.