Fine-scale genetic structuring in a natural population of European wild rabbits (Oryctolagus cuniculus)

A Genetic Evaluation System for New Zealand White Rabbit Germplasm Resources Based on SSR Markers

Simple Summary

The New Zealand white rabbit (Oryctolagus cuniculus) is one of the most important breeds of commercial and experimental rabbits in the world, and also one of the most raised rabbit breeds in China. Our goal was to develop a suite of microsatellite markers to aid future conservation genetics research for the Oryctolagus cuniculus breeds. Based on the genetic diversity of 130 New Zealand white rabbits, we obtained a set combination of 22 markers. Then, we performed a genetic analysis of 200 New Zealand white rabbits corresponding to two generations with this combination. It can be used to evaluate the breed conservation of rabbit germplasm resources.

Abstract

At present, there is an abundance of quality domestic rabbit breeds in China. However, due to the lack of technical standards for the genetic evaluation of rabbit germplasm resources, there have been a number of problems, such as poor breed conservation. By studying the genetic diversity of 130 New Zealand white rabbits (regardless of generation), we obtained the best simple sequence repeat (SSR) marker combination. We found that, when using microsatellite markers for the effective genetic evaluation of domestic rabbits, the number of records should be greater than 60 and the marker number more than 22. Through the comparative analysis of 30 combinations of 22 markers, the optimal combination of 22 markers was determined, and the 22 SSR polymorphic loci were distributed on different chromosomes. We performed a genetic analysis of 200 New Zealand white rabbits corresponding to two generations, using the best SSR polymorphic loci combination. There were no significant differences in the genetic diversity parameters between the two generations of rabbits (p > 0.05), indicating that the characteristics of this excellent rabbit germplasm have been effectively preserved. At the same time, we verified that the established method can be used to evaluate the breed conservation of rabbit germplasm resources.

Cryptic population structure reveals low dispersal in Iberian wolves

Highly mobile mammalian carnivores are expected to have the capability to maintain high levels of gene flow across large geographic scales. Nonetheless, surprising levels of genetic structure have been found in many such populations. We combined genetic and spatial behavioural information from wolves (Canis lupus) in the Iberian Peninsula (Western Europe) during the last two decades to present a particular case of low dispersal levels in a large carnivore population persisting in human-dominated landscapes. We found an exceptionally reticulated pattern of cryptic population structure emerging at two hierarchical levels, in which four or eleven meaningful genetic clusters can be recognized, respectively. These clusters were characterized by moderate-high levels of differentiation (average pairwise F_ST = 0.09–0.19), low levels of admixture and varying degrees of genetic diversity. The number of dispersers identified among the 11 clusters was very low (<4% out of 218 wolves). Spatial information of tracked wolves further confirmed the geographical genetic patterns (only 2 out of 85 collared wolves overlapped with more than one genetic cluster). The high levels of genetic structure in this population may be determined by the recent demographic history of this population, among other factors. The identification of meaningful genetic clusters has implications for the delineation of conservation units and, consequently, on the conservation and management actions for Iberian wolves.

Pedigrees or markers: Which are better in estimating relatedness and inbreeding coefficient?

Individual inbreeding coefficient (F) and pairwise relatedness (r) are fundamental parameters in population genetics and have important applications in diverse fields such as human medicine, forensics, plant and animal breeding, conservation and evolutionary biology. Traditionally, both parameters are calculated from pedigrees, but are now increasingly estimated from genetic marker data. Conceptually, a pedigree gives the expected F and r values, FP and rP, with the expectations being taken (hypothetically) over an infinite number of individuals with the same pedigree. In contrast, markers give the realised (actual) F and r values at the particular marker loci of the particular individuals, FM and rM. Both pedigree (FP, rP) and marker (FM, rM) estimates can be used as inferences of genomic inbreeding coefficients FG and genomic relatedness rG, which are the underlying quantities relevant to most applications (such as estimating inbreeding depression and heritability) of F and r. In the pre-genomic era, it was widely accepted that pedigrees are much better than markers in delineating FG and rG, and markers should better be used to validate, amend and construct pedigrees rather than to replace them. Is this still true in the genomic era when genome-wide dense SNPs are available? In this simulation study, I showed that genomic markers can yield much better estimates of FG and rG than pedigrees when they are numerous (say, 10(4) SNPs) under realistic situations (e.g. genome and population sizes). Pedigree estimates are especially poor for species with a small genome, where FG and rG are determined to a large extent by Mendelian segregations and may thus deviate substantially from their expectations (FP and rP). Simulations also confirmed that FM, when estimated from many SNPs, can be much more powerful than FP for detecting inbreeding depression in viability. However, I argue that pedigrees cannot be replaced completely by genomic SNPs, because the former allows for the calculation of more complicated IBD coefficients (involving more than 2 individuals, more than one locus, and more than 2 genes at a locus) for which the latter may have reduced capacity or limited power, and because the former has social and other significance for remote relationships which have little genetic significance and cannot be inferred reliably from markers.

Spatial genetic structure across a hybrid zone between European rabbit subspecies

The Iberian Peninsula is the only region in the world where the two existing subspecies of the European rabbit (Oryctolagus cuniculus) naturally occur and hybridize. In this study we explore the relative roles of historical and contemporary processes in shaping the spatial genetic structure of the rabbit across its native distribution range, and how they differently affect each subspecies and the hybrid zone. For that purpose we obtained multilocus genotypes and mitochondrial DNA data from 771 rabbits across most of the distribution range of the European rabbit in Spain. Based on the nuclear markers we observed a hierarchical genetic structure firstly comprised by two genetic groups, largely congruent with the mitochondrial lineages and subspecies distributions (O. c. algirus and O. c. cuniculus), which were subsequently subdivided into seven genetic groups. Geographic distance alone emerged as an important factor explaining genetic differentiation across the whole range, without the need to invoke for the effect for geographical barriers. Additionally, the significantly positive spatial correlation up to a distance of only 100 km supported the idea that differentiation at a local level is of greater importance when considering the species overall genetic structure. When looking at the subspecies, northern populations of O. c. cuniculus showed more spatial genetic structure and differentiation than O. c. algirus. This could be due to local geographic barriers, limited resources, soil type and/or social behavior limiting dispersal. The hybrid zone showed similar genetic structure to the southern populations but a larger introgression from the northern lineage genome. These differences have been attributed to selection against the hybrids rather than to behavioral differences between subspecies. Ultimately, the genetic structure of the rabbit in its native distribution range is the result of an ensemble of factors, from geographical and ecological, to behavioral and molecular, that hierarchically interact through time and space.

Causes and consequences of fine-scale population structure in a critically endangered freshwater seal

Background

Small, genetically uniform populations may face an elevated risk of extinction due to reduced environmental adaptability and individual fitness. Fragmentation can intensify these genetic adversities and, therefore, dispersal and gene flow among subpopulations within an isolated population is often essential for maintaining its viability. Using microsatellite and mtDNA data, we examined genetic diversity, spatial differentiation, interregional gene flow, and effective population sizes in the critically endangered Saimaa ringed seal (Phoca hispida saimensis), which is endemic to the large but highly fragmented Lake Saimaa in southeastern Finland.

Results

Microsatellite diversity within the subspecies (H_E = 0.36) ranks among the lowest thus far recorded within the order Pinnipedia, with signs of ongoing loss of individual heterozygosity, reflecting very low effective subpopulation sizes. Bayesian assignment analyses of the microsatellite data revealed clear genetic differentiation among the main breeding areas, but interregional structuring was substantially weaker in biparentally inherited microsatellites (F_ST = 0.107) than in maternally inherited mtDNA (F_ST = 0.444), indicating a sevenfold difference in the gene flow mediated by males versus females.

Conclusions

Genetic structuring in the population appears to arise from the joint effects of multiple factors, including small effective subpopulation sizes, a fragmented lacustrine habitat, and behavioural dispersal limitation. The fine-scale differentiation found in the landlocked Saimaa ringed seal is especially surprising when contrasted with marine ringed seals, which often exhibit near-panmixia among subpopulations separated by hundreds or even thousands of kilometres. Our results demonstrate that population structures of endangered animals cannot be predicted based on data on even closely related species or subspecies.

Use of proximity loggers and network analysis to quantify social interactions in free-ranging wild rabbit populations

Context Social structure of group-living animals has important implications for processes such as gene flow, information transfer, resource utilisation, and disease spread. However, due to the difficulties associated with measuring relationships among wild animals and deriving meaningful estimates of social structure from these interactions, quantifying sociality of evasive species can be challenging. Aims Our aim was to quantify the pattern of social interactions among free-ranging European wild rabbits (Oryctolagus cuniculus) in a temperate region of Australia. Methods We used proximity logging devices to collect data on the dyadic interactions among two populations of rabbits. We then applied recently developed social structure and network analytical techniques to infer estimates of sociality and contact networks from recorded interactions. Key results We found large heterogeneities in the strength of association indices and network centrality measures within but not between populations. Network analytical techniques revealed clustering of rabbits into distinct social groups. Conclusions Most associations within social groups were strong and highly stable over time whereas interactions between groups were rare and transient, indicating low levels of inter-group mixing. Despite the apparent differences in habitat quality between sites, the network characteristics were extremely similar between the two populations. Implications Our results highlight the importance of heterogeneities in individual behaviour in determining the dynamics of directly transmitted diseases at the population level.

Fine-scale population genetic structure in a fission-fusion society

Nonrandom patterns of mating and dispersal create fine-scale genetic structure in natural populations - especially of social mammals - with important evolutionary and conservation genetic consequences. Such structure is well-characterized for typical mammalian societies; that is, societies where social group composition is stable, dispersal is male-biased, and males form permanent breeding associations in just one or a few social groups over the course of their lives. However, genetic structure is not well understood for social mammals that differ from this pattern, including elephants. In elephant societies, social groups fission and fuse, and males never form permanent breeding associations with female groups. Here, we combine 33 years of behavioural observations with genetic information for 545 African elephants (Loxodonta africana), to investigate how mating and dispersal behaviours structure genetic variation between social groups and across age classes. We found that, like most social mammals, female matrilocality in elephants creates co-ancestry within core social groups and significant genetic differentiation between groups (Phi(ST) = 0.058). However, unlike typical social mammals, male elephants do not bias reproduction towards a limited subset of social groups, and instead breed randomly across the population. As a result, reproductively dominant males mediate gene flow between core groups, which creates cohorts of similar-aged paternal relatives across the population. Because poaching tends to eliminate the oldest elephants from populations, illegal hunting and poaching are likely to erode fine-scale genetic structure. We discuss our results and their evolutionary and conservation genetic implications in the context of other social mammals.

Advances in our understanding of mammalian sex-biased dispersal

Sex-biased dispersal is an almost ubiquitous feature of mammalian life history, but the evolutionary causes behind these patterns still require much clarification. A quarter of a century since the publication of seminal papers describing general patterns of sex-biased dispersal in both mammals and birds, we review the advances in our theoretical understanding of the evolutionary causes of sex-biased dispersal, and those in statistical genetics that enable us to test hypotheses and measure dispersal in natural populations. We use mammalian examples to illustrate patterns and proximate causes of sex-biased dispersal, because by far the most data are available and because they exhibit an enormous diversity in terms of dispersal strategy, mating and social systems. Recent studies using molecular markers have helped to confirm that sex-biased dispersal is widespread among mammals and varies widely in direction and intensity, but there is a great need to bridge the gap between genetic information, observational data and theory. A review of mammalian data indicates that the relationship between direction of sex-bias and mating system is not a simple one. The role of social systems emerges as a key factor in determining intensity and direction of dispersal bias, but there is still need for a theoretical framework that can account for the complex interactions between inbreeding avoidance, kin competition and cooperation to explain the impressive diversity of patterns.

Establishing causes of eradication failure based on genetics: case study of ship rat eradication in Ste. Anne archipelago

Determining the causes of a failed eradication of a pest species is important because it enables an argued adjustment of the methodologies used and the improvement of the protocols for future attempts. We examined how molecular monitoring can help distinguish between the two main reasons for an eradication failure (i.e., survival of some individuals vs. recolonization after eradication). We investigated genetic variation in seven microsatellite loci in ship rat (Rattus rattus) populations from four islets off the Martinique coast (French Caribbean). In 1999 an eradication attempt was conducted on the four islets. Three years later rats were observed again on two of them. We compared the genetic signatures of the populations before and after the eradication attempt. On one of the islands, the new rat population was likely a subset of the pre-eradication population. A weak genetic differentiation was found between them, with almost no new alleles observed in the new population and moderate F(ST) values (0.15). Moreover, assignment procedures clustered the two populations together. In contrast, on the other islet, many new alleles were observed after the eradication attempt, resulting in an increase in genetic diversity (from 2.57 to 3.57 mean number of alleles per locus) and strong F(ST) values (0.39). Moreover, genetic clustering clearly separated the two samples (i.e., before and after the eradication attempt) in two different populations. Thus, to achieve long-term eradication on these islets, it seems necessary to redevelop the eradication procedure to avoid individuals surviving and to prevent reinvasion, probably from the mainland, by installing permanent trapping and poisoning devices and conducting regular monitoring. We strongly encourage wildlife managers conducting eradication campaigns to integrate molecular biological tools in their protocols, which can be done easily for most common invasive species.

Fine-scale genetic structure and dispersal in Canada lynx (Lynx canadensis) within Alberta, Canada

Although mammals are typically characterized by male-biased dispersal, field studies of lynx conflict as to whether dispersal is male-biased or lacks sex-bias. To resolve this issue we dissect fine-scale genetic structure and analyze dispersal in regard to gender using 19 microsatellite loci, teemed with extensive sampling (n = 272 adults) of Canada lynx ( Lynx canadensis Kerr, 1792) throughout Alberta. The level of genetic variation was high (mean He= 71.6%), as reported in previous genetic studies of lynx. No significant barriers to gene flow were detected within Alberta’s lynx population. Despite several reports of long-distance movements in lynx, we observed a slight significant negative correlation between pairwise relatedness values and geographic distance (rM= –0.025, P = 0.048), indicating a decrease in relatedness between individuals as their sampling distance increases. When the same analysis was performed separately on sexes, the slopes of the individual regressions did not differ significantly between males and females (P = 0.708). Our molecular results suggest a lack of sex-biased dispersal in Canada lynx, similar to reports on other lynx species.

Intrinsic Parent‐Offspring Correlation in Inbreeding Level in a Song Sparrow (Melospiza melodia) Population Open to Immigration

The extent to which offspring resemble their parents in genotype and phenotype underpins patterns of genetic and phenotypic variation, selection, and evolution in natural populations. Genetic and phenotypic resemblance can clearly result from additive genetic variance and can be shaped by nongenetic parental and common environmental influences. In contrast, there is no straightforward expectation that inbreeding coefficient (f), a nonadditive component of genetic "quality," should be correlated across parents and offspring in sexually reproducing species or consequently cause resemblance across generations. Here, we report a significant parent f-offspring f correlation within a free-living pedigreed population of song sparrows (Melospiza melodia) on Mandarte Island, Canada. Across 15 years, relatively inbred parents had relatively inbred offspring on average. We show that rather than requiring nonrandom pairing with respect to f and kinship, parent f-offspring f correlations arise as an intrinsic consequence of random pairing within Mandarte's open population, where immigrants interbreed with Mandarte-hatched natives. However, on Mandarte, parent f-offspring f correlations may have been exacerbated because relatively inbred individuals paired with more closely related mates than expected by chance. Such intrinsic parent f-offspring f correlations have major implications for the understanding of resemblance, selection, and evolution in natural populations.

Reduced Heterozygosity Depresses Sperm Quality in Wild Rabbits, Oryctolagus cuniculus

When close relatives are forced to reproduce, the resulting offspring inherit above average homozygosity and reduced fitness. Biologists now recognize inbreeding depression in the wild, a phenomenon that will probably increase as natural populations become depleted and fragmented. Inbreeding depression is most commonly expressed as compromised fertility and embryogenesis, but actual mechanisms remain poorly understood, especially for wild populations. Here, we examine how reduced heterozygosity influences spermatozoal and gonadal traits in wild rabbits (Oryctolagus cuniculus) sampled across the United Kingdom. By using a suite of 29 microsatellite markers (analyzed to confirm representation of individual heterozygosity across our sample), we found a significant negative relationship between heterozygosity and the production of normal sperm; the relationship was significant both between (n = 12) and within (n = 91 [total males], 42 [island], 49 [mainland]) populations. Reduced heterozygosity was also associated with decreased testis size across males (n = 112), but no relationship was seen at the population level, suggesting environmental confounds. Our results show, for a wild mammal, that inbreeding is associated with decreased sperm quality, confirming suggestions of links between inbreeding and elevated sperm abnormalities in rare felids . These findings could explain why inbreeding depression so frequently arises via compromised fertility and embryogenesis .

Microsatellite analyses reveal fine-scale genetic structure in grey mouse lemurs (Microcebus murinus)

Information on genetic structure can be used to complement direct inferences on social systems and behaviour. We studied the genetic structure of the solitary grey mouse lemur (Microcebus murinus), a small, nocturnal primate endemic to western Madagascar, with the aim of getting further insight on its breeding structure. Tissue samples from 167 grey mouse lemurs in an area covering 12.3 km2 in Kirindy Forest were obtained from trapping. The capture data indicated a noncontinuous distribution of individuals in the study area. Using 10 microsatellite markers, significant genetic differentiation in the study area was demonstrated and dispersal was found to be significantly male biased. Furthermore, we observed an overall excess of homozygotes in the total population (F(IT) = 0.131), which we interpret as caused by fine-scale structure with breeding occurring in small units. Evidence for a clumped distribution of identical homozygotes was found, supporting the notion that dispersal distance for breeding was shorter than that for foraging, i.e. the breeding neighbourhood size is smaller than the foraging neighbourhood size. In conclusion, we found a more complex population structure than what has been previously reported in studies performed on smaller spatial scales. The noncontinuous distribution of individuals and the effects of social variables on the genetic structure have implications for the interpretation of social organization and the planning of conservation activities that may apply to other solitary and endangered mammals as well.

The estimation of genetic relationships using molecular markers and their efficiency in estimating heritability in natural populations

Molecular marker data collected from natural populations allows information on genetic relationships to be established without referencing an exact pedigree. Numerous methods have been developed to exploit the marker data. These fall into two main categories: method of moment estimators and likelihood estimators. Method of moment estimators are essentially unbiased, but utilise weighting schemes that are only optimal if the analysed pair is unrelated. Thus, they differ in their efficiency at estimating parameters for different relationship categories. Likelihood estimators show smaller mean squared errors but are much more biased. Both types of estimator have been used in variance component analysis to estimate heritability. All marker-based heritability estimators require that adequate levels of the true relationship be present in the population of interest and that adequate amounts of informative marker data are available. I review the different approaches to relationship estimation, with particular attention to optimizing the use of this relationship information in subsequent variance component estimation.

Sex-biased dispersal of greater long-tailed hamster (Tscherskia triton) revealed by microsatellites

For 2 consecutive years we studied the effect of dispersal on the genetic diversity of greater long-tailed hamsters (Tscherskia triton (de Winton, 1899)) in farmland habitat, Hebei Province, People's Republic of China. Level of genetic diversity was estimated by analyzing six highly polymorphic microsatellite loci in terms of mean d2, allele number, allelic diversity, effective number of alleles, allelic richness, average observed heterozygosity, and expected heterozygosity. The genetic diversity in populations from both two sites and 2 years indicated that the males contained higher levels of genetic diversity than the females, which supported our prediction that male-biased dispersal increased population genetic diversity. We also found significant departures from Hardy–Weinberg equilibrium and a reduction in genetic diversity in samples from a partially isolated site, which was probably due to genetic drift, inbreeding, or a combination of these factors.

Construction of a cytogenetically anchored microsatellite map in rabbit

Rabbit (Oryctolagus cuniculus) represents a valuable source of biomedical models and corresponds to a small but active economic sector in Europe for meat and fur. The rabbit genome has not been thoroughly studied until recently, and high-resolution maps necessary for identification of genes and quantitative trait loci (QTL) are not yet available. Our aim was to isolate over 300 new and regularly distributed (TG)n or (TC)n rabbit microsatellites. To achieve this purpose, 164 microsatellite sequences were isolated from gene-containing bacterial artificial chromosome (BAC) clones previously localized by fluorescence in situ hybridization (FISH) on all the rabbit chromosomes. In addition, 141 microsatellite sequences were subcloned from a plasmid genomic library, and for 41 of these sequences, BAC clones were identified and FISH-mapped. TC repeats were present in 62% of the microsatellites derived from gene-containing BAC clones and in 22% of those from the plasmid genomic library, with an average of 42.9% irrespective of the microsatellite origin. These results suggest a higher proportion of (TC)n repeats and a nonhomogeneous distribution of (TG)n and (TC)n repeats in the rabbit genome compared to those in man. Among the 305 isolated microsatellites, 177 were assigned to 139 different cytogenetic positions on all the chromosomes except rabbit Chromosome 21. Sequence similarity searches provided hit locations on the Human Build 35a and hypothetical assignments on rabbit chromosomes for ten additional microsatellites. Taken together, these results report a reservoir of 305 new rabbit microsatellites of which 60% have a cytogenetic position. This is the first step toward the construction of an integrated cytogenetic and genetic map based on microsatellites homogeneously anchored to the rabbit genome.

To what extent does living in a group mean living with kin?

Chimpanzees live in large groups featuring remarkable levels of gregariousness and cooperation among the males. Because males stay in their natal communities their entire lives and are hence expected to be living with male relatives, cooperation is therefore assumed to occur within one large 'family' group. However, we found that the average relatedness among males within several chimpanzee groups as determined by microsatellite analysis is in fact rather low, and only rarely significantly higher than average relatedness of females in the groups or of males compared across groups. To explain these findings, mathematical predictions for average relatedness according to group size, reproductive skew and sex bias in dispersal were derived. The results show that high average relatedness among the philopatric sex is only expected in very small groups, which is confirmed by a comparison with published data. Our study therefore suggests that interactions among larger number of individuals may not be primarily driven by kin relationships.

Fine‐scale genetic pattern and evidence for sex‐biased dispersal in the túngara frog,Physalaemus pustulosus

Túngara frogs (Physalaemus pustulosus) are a model system for sexual selection and communication. Population dynamics and gene flow are of major interest in this species because they influence speciation processes and microevolution, and could consequently provide a deeper understanding of the evolutionary processes involved in mate recognition. Although earlier studies have documented genetic variation across the species' range, attempts to investigate dispersal on a local level have been limited to mark-recapture studies. These behavioural studies indicated high mobility at a scale of several hundred metres. In this study we used seven highly polymorphic microsatellite loci to investigate fine-scaled genetic variation in the túngara frog. We analysed the influence of geographical distance on observed genetic patterns, examined the influence of a river on gene flow, and tested for sex-biased dispersal. Data for 668 individuals from 17 populations ranging in distance from 0.26 to 11.8 km revealed significant levels of genetic differentiation among populations. Genetic differentiation was significantly correlated with geographic distance. A river acted as an efficient barrier to gene flow. Several tests of sex-biased dispersal were conducted. Most of them showed no difference between the sexes, but variance of Assignment Indices exhibited a statistically significant male bias in dispersal.

Assessing population structure and gene flow in Montana wolverines (Gulo gulo) using assignment‐based approaches

In North America, wolverines once occupied a continuous range from Alaska southward to New Mexico. In the lower 48 states, small remnant populations remain only in the northwestern United States. Among these remnant populations, the Montana population has the highest probability of long-term persistence given its size and proximity to healthy populations in Canada. In this study, we evaluate population genetic structure and gene flow among Montana wolverines using 10 polymorphic microsatellite loci. Bayesian and frequency-based assignment tests revealed significant population substructure and provide support for at least three subpopulations in Montana. FST values between subpopulations ranged from 0.08 to 0.10 and provide evidence for male-biased dispersal. The high degree of population substructure and low levels of gene flow contrast results from wolverine population genetic studies in less fragmented landscapes of Alaska and Canada. This study provides additional support for the hypothesis that large carnivore populations of Montana are becoming increasingly fragmented due to human development and disturbance.

Population genetic structure of male black grouse (Tetrao tetrix L.) in fragmented vs. continuous landscapes

We investigated the association of habitat fragmentation with genetic structure of male black grouse Tetrao tetrix. Using 14 microsatellites, we compared the genetic differentiation of males among nine localities in continuous lowland habitats in Finland to the genetic differentiation among 14 localities in fragmented habitats in the Alps (France, Switzerland and Italy). In both areas, we found significant genetic differentiation. However, the average differentiation, measured as theta, was more than three times higher in the Alps than in Finland. The greater differentiation found in the Alps is probably due to the presence of mountain ridges rising above natural habitats of the species, which form barriers to gene flow, and to a higher influence of genetic drift resulting from lower effective sizes in highly fragmented habitats. The detection of isolation by distance in the Alps suggests that gene flow among populations does occur. The genetic variability measured as gene diversity HE and allelic richness A was lower in the Alps than in Finland. This could result from the higher fragmentation and/or from the fact that populations in the Alps are isolated from the main species range and have a lower effective size than in Finland. This study suggests that habitat fragmentation can affect genetic structure of avian species with relatively high dispersal propensities.

Population genetic structure of rock ptarmigan Lagopus mutus in Northern and Western Europe

Alpine species may be losing habitat because of global warming. Setting management priorities for such species is thus urgent and cannot be achieved without data on population structure. We studied the structure of rock ptarmigan (Lagopus mutus) populations in the Pyrenees, Alps and Norway, using six microsatellites. We found that rock ptarmigan in the Pyrenees were genetically impoverished compared with those in the Alps and Norway, and displayed a greater divergence (Pyrenees vs. Alps or Norway: theta(ST) = 0.16, Alps vs. Norway, theta(ST) = 0.04). In the Alps, despite a weak genetic differentiation between localities up to 200 km apart (theta(ST) = 0.011), a significant isolation-by-distance (IBD) effect was detected. When computed for each sex separately this IBD effect was significant for males but not for females, suggesting that males are highly philopatric.

Fine-scale genetic structure in a free-living ungulate population

The fine-scale genetic structure of wild animal populations has rarely been analysed, yet is potentially important as a confounding factor in quantitative genetic and allelic association studies, as well as having implications for population dynamics, inbreeding and kin selection. In this study, we examined the extent to which the three spatial subunits, or hefts, of the Village Bay population of Soay sheep (Ovis aries) on St Kilda, Scotland, are genetically structured using data from 20 microsatellite and protein loci. Allele frequencies differed significantly among three hefts in all the study years we considered (1987-2000 inclusive). Small but significantly positive F(ST) and negative F(IS) values were observed in most years, indicating that the hefts are genetically differentiated, and that within each heft there is more observed heterozygosity than would be expected if each were an isolated breeding population. Males showed less fidelity to their natal heft, and as a consequence higher levels of relatedness within hefts were observed among females than among males. There was a significant negative relationship between geographical proximity and relatedness in pairwise comparisons involving females, and on average pairs of females located within 50 m of each other were related at the equivalent level of second cousins. Structure is therefore largely driven by incomplete postnatal dispersal by females. Mating appears to be random with respect to the spatial-genetic substructure of the hefts, and therefore genetic structure does not contribute to the overall rate of inbreeding in the population. However, genetic substructure can lead to allelic associations and generate environmental effects within lineages that have the potential to confound heritability analyses and allelic association studies.

Tests for sex-biased dispersal using bi-parentally inherited genetic markers

Understanding why dispersal is sex-biased in many taxa is still a major concern in evolutionary ecology. Dispersal tends to be male-biased in mammals and female-biased in birds, but counter-examples exist and little is known about sex bias in other taxa. Obtaining accurate measures of dispersal in the field remains a problem. Here we describe and compare several methods for detecting sex-biased dispersal using bi-parentally inherited, codominant genetic markers. If gene flow is restricted among populations, then the genotype of an individual tells something about its origin. Provided that dispersal occurs at the juvenile stage and that sampling is carried out on adults, genotypes sampled from the dispersing sex should on average be less likely (compared to genotypes from the philopatric sex) in the population in which they were sampled. The dispersing sex should be less genetically structured and should present a larger heterozygote deficit. In this study we use computer simulations and a permutation test on four statistics to investigate the conditions under which sex-biased dispersal can be detected. Two tests emerge as fairly powerful. We present results concerning the optimal sampling strategy (varying number of samples, individuals, loci per individual and level of polymorphism) under different amounts of dispersal for each sex. These tests for biases in dispersal are also appropriate for any attribute (e.g. size, colour, status) suspected to influence the probability of dispersal. A windows program carrying out these tests can be freely downloaded from http://www.unil.ch/izea/softwares/fstat.html

Inferring sex-biased dispersal from population genetic tools: a review

Sex-biased dispersal, where individuals of one sex stay or return to their natal site (or group) to breed while individuals of the other sex are prone to disperse, is a wide-spread pattern in vertebrate organisms. In general, mammals exhibit male-biased dispersal whereas birds exhibit female-bias. Dispersal estimates are often difficult to obtain from direct field observations. Here we describe different methods for inferring sex-specific dispersal using population genetic tools and discuss the problems they can raise. We distinguish two types of methods: those based on bi-parental markers (eg comparison of male/female relatedness, F(st) and assignment probabilities) and those relying on the comparison between markers with different modes of inheritance (eg mtDNA markers and microsatellites). Finally, we discuss statistical problems that are encountered with these different methods (eg pseudoreplication, problems due to the comparison of distinct markers). While the genetic methods to detect sex-biased dispersal are now relatively well developed, their interpretation can prove problematic due to the confounding effects of factors such as the mating system of the species. Moreover, the relative power of these methods is not well known and requires further investigation.

Sex-specific genetic differentiation and coalescence times: estimating sex-biased dispersal rates

I derive the equilibrium values of sex-specific FST parameters, in an island model for a dioecious species with sex-biased dispersal and binomial distribution of family size before dispersal (as assumed in a Wright-Fisher population). I show that FST may take different values among males and among females whenever dispersal is a trait conditioned on gender. This has not always been recognized, because some models assumed that genes are sampled before dispersal. In particular, the ratios of sex-specific FST parameters evaluated after dispersal over FST evaluated before dispersal are simple functions of sex-specific dispersal rates. Therefore, a simple moment-based estimator of sex-specific dispersal rate is proposed. This method is based on the comparison of FST estimated before and after dispersal and assumes equilibrium between migration and drift. I evaluate this method through stochastic simulations for a range of sex-specific dispersal rates and sampling effort (sample size, number of loci scored).

Distribution of individual inbreeding coefficients, relatedness and influence of stocking on native anadromous brown trout (Salmo trutta) population structure

We examined polymorphism at seven microsatellite loci in 4023 brown trout (Salmo trutta) collected from 32 tributaries to the Limfjord, Denmark (approximately 200 km) and from two hatcheries used for stocking. Populations differ in their estimated sizes and stocking histories. Mean individual inbreeding coefficients do not differ among locations within rivers. Relatedness varies between sites within rivers indicating varied local dynamics at a very small geographical scale. Relatedness is sometimes lower than expected among an equal number of simulated individuals with randomized genotypes, suggesting structure within locations. Five per cent of the genetic variance is distributed among rivers (F(ST) = 0.049), but in the western, less heavily stocked, area of the Limfjord a higher proportion of the genetic variance is distributed among rivers than among locations within rivers. The reverse is true of the eastern, more heavily stocked, area of the Limfjord. Here, a higher proportion of the genetic variance is distributed among locations within rivers than among rivers. Assignment tests reveal that the majority of trout (mean 77% of all fish) are more probably of local origin than hatchery origin but this proportion varies regionally, with rivers in the western area of the Limfjord showing a relatively high (mean 88%) and those in the eastern area showing a relatively low (mean 72%) proportion of locally assigned trout. These results can be interpreted as reflecting stocking impact. Also, the proportion of locally assigned trout correlates with the populations' stocking histories, with rivers presently subjected to stocking (hatchery trout) showing low (mean approximately 0.73), and rivers where stocking was discontinued showing high (mean approximately 0.84) proportions of local fish, probably reflecting lower survival of hatchery than of wild trout. There is evidence for isolation by distance at a large geographical scale when individual river populations are pooled into nine geographical regions but not at a small geographical scale when populations are considered individually. We reject the null hypothesis that stocking has had no impact on population structure but the relatively high proportion of locally assigned trout in populations where stocking with domestic fish no longer takes place suggests limited long-term success of stocking.

Molecular ecology of social behaviour: analyses of breeding systems and genetic structure

Molecular genetic studies of group kin composition and local genetic structure in social organisms are becoming increasingly common. A conceptual and mathematical framework that links attributes of the breeding system to group composition and genetic structure is presented here, and recent empirical studies are reviewed in the context of this framework. Breeding system properties, including the number of breeders in a social group, their genetic relatedness, and skew in their parentage, determine group composition and the distribution of genetic variation within and between social units. This group genetic structure in turn influences the opportunities for conflict and cooperation to evolve within groups and for selection to occur among groups or clusters of groups. Thus, molecular studies of social groups provide the starting point for analyses of the selective forces involved in social evolution, as well as for analyses of other fundamental evolutionary problems related to sex allocation, reproductive skew, life history evolution, and the nature of selection in hierarchically structured populations. The framework presented here provides a standard system for interpreting and integrating genetic and natural history data from social organisms for application to a broad range of evolutionary questions.

Marker-inferred relatedness as a tool for detecting heritability in nature

This paper presents a perspective of how inferred relatedness, based on genetic marker data such as microsatellites or amplified fragment length polymorphisms (AFLPs), can be used to demonstrate quantitative genetic variation in natural populations. Variation at two levels is considered: among pairs of individuals within populations, and among pairs of subpopulations within a population. In the former, inferred pairwise relatedness, combined with trait measures, allow estimates of heritability 'in the wild'. In the latter, estimates of QST are obtained, in the absence of known heritabilities, via estimates of pairwise FST. Estimators of relatedness based on the 'Kronecker operator' are given. Both methods require actual variation of relationship, a rarely studied aspect of population structure, and not necessarily present. Some conditions for appropriate population structures in the wild are identified, in part through a review of recent studies.

Absence of a genetic bottleneck in a wild rabbit (Oryctolagus cuniculus) population exposed to a severe viral epizootic

Infectious diseases and their demographic consequences are thought to influence the genetic diversity of populations. In Europe, during the last 50 years, the European rabbit (Oryctolagus cuniculus) has suffered two important viral epizootics: myxomatosis and rabbit viral haemorraghic disease (RVHD). Although mortality rates were very high, the impact of these diseases on genetic diversity has never been assessed directly. The subject of this paper is a wild rabbit population in France, which has been studied since the beginning of the 1980s. The first outbreak of RVHD occurred in 1995 and provoked a demographic crash. The population, sampled for the first time in 1982 and 1994, was sampled again at the end of 1996 to examine the impact of the epizootic on genetic diversity. In spite of the observed high mortality rate ( approximately 90%), analysis of 14 polymorphic loci (allozymes and microsatellites) showed no loss in genetic diversity after the epizootic. Determination of temporal changes in allele frequencies indicated that the population evolved under genetic drift. The temporal method of Waples demonstrated a significant decrease in the effective population size (Ne) correlated with the demographic crash due to the epizootic. However, the population had only been studied for two generations after the epizootic and the remnant population size probably stayed high enough ( approximately 50 individuals) to keep its genetic diversity at the precrash level. These results suggest that, contrary to what is usually thought and in spite of the subsequent high mortality rates, past epizootics (especially myxomatosis) may have had little effect on the genetic diversity of wild rabbit populations in Europe.

Microsatellite analysis of kinkajou social organization

Kinkajou social groups generally consist of one adult female, two males, one subadult and one juvenile. Based on analysis of variation in 11 microsatellite loci, we assess the degree of kinship within and between four social groups totaling 25 kinkajous. We use exclusion and likelihood analyses to assign parents for seven of the eight offspring sampled, five with >/= 95% certainty, and two with >/= 80% certainty. Five of six identified sires of group offspring came from the same social group as the mother and pup. Adult males and females within a group were unrelated and subadults and juveniles were offspring of the group adults, suggesting a family structure. All five identified paternities within a social group were by the dominant male of the group. However, this copulation asymmetry does not necessarily reflect cooperation due to kinship ties between the two adult males within a group as one of two adult male pairs sampled was unrelated. Neighbouring male kinkajous were more closely related to each other than neighbouring female kinkajous, suggesting that females disperse more often or farther than males.

Population structure and genetic variation of european wild rabbits (Oryctolagus cuniculus) in east anglia

The European wild rabbit (Oryctolagus cuniculus) is an introduced species in Britain, and populations have been profoundly influenced by both man and disease. In stable environmental conditions, distinct social behaviour is observed, and this social structure leads to significant genetic structuring at the intrapopulation level. In this study, European wild rabbits were sampled from 17 sites across the East Anglian region of Britain and genotyped with nine microsatellite loci. Genotypical proportions deviated significantly from Hardy-Weinberg equilibrium, reflecting a degree of population subdivision and non-random mating. Several estimates of measures of population genetic structure revealed that populations are genetically distinct and have small effective population sizes. These distinctive properties are seen to be the combined effects of the social structure and random drift acting on bottlenecked populations after myxomatosis. It is concluded that the genetic structure seen in rabbit populations today is unlikely to reflect historical structuring present before myxomatosis, but that it results from recent events.