Polygamy and an absence of fine-scale structure in Dendroctonus ponderosae (Hopk.) (Coleoptera: Curcilionidae) confirmed using molecular markers

An understanding of mating systems and fine-scale spatial genetic structure is required to effectively manage forest pest species such as Dendroctonus ponderosae (mountain pine beetle). Here we used genome-wide single-nucleotide polymorphisms to assess the fine-scale genetic structure and mating system of D. ponderosae collected from a single stand in Alberta, Canada. Fine-scale spatial genetic structure was absent within the stand and the majority of genetic variation was best explained at the individual level. Relatedness estimates support previous reports of pre-emergence mating. Parentage assignment tests indicate that a polygamous mating system better explains the relationships among individuals within a gallery than the previously reported female monogamous/male polygynous system. Furthermore, there is some evidence to suggest that females may exploit the galleries of other females, at least under epidemic conditions. Our results suggest that current management models are likely to be effective across large geographic areas based on the absence of fine-scale genetic structure.     

Punishment of polygyny

We investigated the evolution of monogamy (one male, one female) and polygyny (one male, more than one female). In particular, we studied whether it is possible for a mutant polygynous mating strategy to invade a resident population of monogamous breeders and, alternatively, whether a mutant monogamy can invade resident polygyny. Our population obeys discrete-time Ricker dynamics. The role of males and females in the breeding system is incorporated via the harmonic birth function. The results of the invasability analysis are straightforward. Polygyny is an evolutionarily stable strategy mating system; this holds throughout the examined range of numbers of offspring produced per female. So that the two strategies can coexist, polygyny has to be punished. The coexistence of monogamy and polygyny is achieved by reducing the offspring number for polygyny relative to monogamy. This yields long-term persistence of the strategies for all offspring numbers studied. An alternative punishment is to increase the sensitivity of polygynous breeders to population density. The coexistence is possible only with a limited range of offspring produced. The third way to achieve coexistence of the two mating strategies is to assume that individuals live in a spatially structured population, where dispersal links population subunits to a network. Reducing the dispersal rate of polygynous breeders relative to that of monogamous individuals makes the coexistence feasible. However, for monogamy to persist, the number of offspring produced has to be relatively high.     

The mating system of the Sichuan snub‐nosed monkey (Rhinopithecus roxellana)

This article reports the first genetic study of the mating system of the Sichuan snub‐nosed monkey (Rhinopithecus roxellana), an endemic and endangered species in China. The investigation was carried out in a population (WRT) in the Qinling Mountains using data from both field observation and paternity analysis through microsatellite DNA profiling. During a mating season, a male on an average copulated with 5.7 females. Approximately 18% of the females were observed to copulate with more than one male over the study period. The majority of copulations (94.5%) were initiated by females. Twenty‐eight of 430 observed matings were extra‐unit copulations. Eight polymorphic microsatellite loci were used for paternity analysis. The number of alleles at each locus ranged from 3 to 7 (mean=4.3). Observed heterozygosity ranged between 0.32 and 0.79. None of the loci showed significant deviation from Hardy–Weinberg equilibrium. Results from paternity exclusion showed that 12 of 21 (57.1%) immature individuals were sired by extra‐unit males. Although the basic social unit of snub‐nosed monkeys is consistent with a polygynous mating system, both field observation and genetic data suggests that their mating system is polygamous. Infanticide and inbreeding avoidance are the most likely explanations for the promiscuity of female snub‐nosed monkeys. Am. J. Primatol. 72:25–32, 2010. © 2009 Wiley‐Liss, Inc.     

ldne: a program for estimating effective population size from data on linkage disequilibrium

ldne is a program with a Visual Basic interface that implements a recently developed bias correction for estimates of effective population size (N(e) ) based on linkage disequilibrium data. The program reads genotypic data in standard formats and can accommodate an arbitrary number of samples, individuals, loci, and alleles, as well as two mating systems: random and lifetime monogamy. ldne calculates separate estimates using different criteria for excluding rare alleles, which facilitates evaluation of data for highly polymorphic markers such as microsatellites. The program also introduces a jackknife method for obtaining confidence intervals that appears to perform better than parametric methods currently in use.     

Sibship within samples of brown trout (<Emphasis Type="Italic">Salmo trutta</Emphasis>) and implications for supportive breeding

We analysed family relationships among brown trout from two small tributary populations that have been suggested as a source of individuals for supportive breeding, using variation at eight microsatellite loci. As a control, we analysed a sample of supposedly unrelated individuals representing a large anadromous population, and we simulated unrelated individuals based on the allelic distributions in all three samples. Two different approaches were used: (1) pairwise estimates of relatedness between individuals and (2) a method for partitioning individuals into half-sib and full-sib families. The anadromous population did not show evidence of a significant number of closely related individuals. In both tributary populations, however, the distributions of pairwise relatedness estimates suggested the presence of several related individuals, and sibship reconstruction suggested fewer families consisting of more individuals than were observed for the simulated individuals. The expected increase of inbreeding coefficient in the two samples due to family structure was 0.026 and 0.030 respectively. Moreover, tests for recent bottlenecks yielded significant outcomes in both populations suggesting a history of low effective population sizes. Depending on the effective population size of captive spawners and past effective population sizes in the populations it could be beneficial to conduct sib-avoidance matings, though this cannot eliminate inbreeding but only delay it. Alternatively, individuals from different populations could be crossed. Sibship reconstruction provided the clearest evidence for family structure, but pairwise relatedness is the best measure for designing mating schemes, as it allows for mating as unrelated individuals as possible rather than just avoiding mating between sibs.     

Reproductive specialization in multiple-queen colonies of the ant Formica exsecta

In polygynous (multiple queens per nest) colonies of socialinsects, queens can increase their reproductive share by layingmore eggs or by increasing the proportion of eggs that developinto reproductive individuals instead of workers. We used polymorphicmicrosatellite loci to determine the genetically effective contributionof queens to the production of gynes (new queens), males, and2 different cohorts of workers in a polygynous population ofthe ant Formica exsecta. For this purpose, we developed a newmethod that can be used for diploid and haplodiploid organismsto quantify the degree of reproductive specialization amongbreeders in societies where there are too many breeders to ascertainparentage. Using this method, we found a high degree of reproductivespecialization among nest-mate queens in both female- and male-producingcolonies (sex ratio is bimodally distributed in the study population).For example, a high effective proportion of queens (25% and79%, respectively) were specialized in the production of malesin female- and male-producing colonies. Our analyses furtherrevealed that in female-producing colonies, significantly fewerqueens contributed to gyne production than to worker production.Finally, we found significant changes in the identity of queenscontributing to different cohorts of workers. Altogether, thesedata demonstrate that colonies of F. exsecta, and probably thoseof many other highly polygynous social insect species, are composedof reproductive individuals differing in their investment togynes, males, and workers. These findings demonstrate a newaspect of the highly dynamic social organization of complexanimal societies.     

Sampling properties of the heterozygote-excess estimator of the effective number of breeders

The effective number of breeders (N _b) for a cohort of progeny can be estimated from an excess of heterozygotes that arises in progeny produced by finite numbers of parents. In principle, N _b is a simple function of the standardized deviation (D) of the proportion of heterozygous progeny from its expectation under random mating. We explored the sampling properties of this D-estimator of N _b through computer simulation. The accuracy of the D-estimator is remarkably robust to variation in numbers of alleles and loci and the presence of rare alleles, though precision can be low if, relative to a given N _b, the sample of progeny or the cumulative number of independent alleles (n _ci) sampled is too small. For N _b up to 30 parents, acceptable accuracy is achieved with sample sizes of 200 or more progeny and 80 or more independent alleles; for N _b of 50–100, a sample of 500–1,000 progeny and 450–900 independent alleles are required for similar accuracy and precision. Though the estimator is most applicable for the situation of random union of gametes (as may occur in some marine invertebrates or fish, for example), it works for other mating systems (monogamous or polygamous pairings, polygyny), when the effective number of breeders is small (N _b ≤ 20). Simulations reveal small overestimation biases with smaller sample sizes, rare alleles, or highly polymorphic loci (≥10 alleles). Despite this bias, multiallelic loci are preferable to many loci with few alleles, which have larger sampling errors.     

Mating frequency and mating system of the polygynous ant, Leptothorax acervorum

Multiple mating by queens (polyandry) and the occurrence of multiple queens in the same colony (polygyny) alter patterns of relatedness within societies of eusocial insects. This is predicted to influence kin-selected conflicts over reproduction. We investigated the mating system of a facultatively polygynous UK population of the ant Leptothorax acervorum using up to six microsatellite loci. We estimated mating frequency by genotyping 79 dealate (colony) queens and the contents of their sperm receptacles and by detailed genetic analysis of 11 monogynous (single-queen) and nine polygynous colonies. Results indicated that 95% of queens were singly mated and 5% of queens were doubly mated. The corrected population mean mating frequency was 1.06. Parentage analysis of adults and brood in 17 colonies (10 monogynous, 7 polygynous) showed that female offspring attributable to each of 31 queens were full sisters, confirming that queens typically mate once. Inbreeding coefficients, queen-mate relatedness of zero and the low incidence of diploid males provided evidence that L. acervorum sexuals mate entirely or almost entirely at random. Males mated to queens in the same polygynous colony were not related to one another. Our data also confirmed that polygynous colonies contain queens that are related on average and that their workers had a mixed maternity. We conclude that the mating system of L. acervorum involves queens that mate near nests with unrelated males and then seek readoption by those nests, and queens that mate in mating aggregations away from nests, also with unrelated males.     

Genetic consequences of polygyny and social structure in an Indian fruit bat, Cynopterus sphinx. II. Variance in male mating success and effective population size

Variance in reproductive success is a primary determinant of genetically effective population size (Ne), and thus has important implications for the role of genetic drift in the evolutionary dynamics of animal taxa characterized by polygynous mating systems. Here we report the results of a study designed to test the hypothesis that polygynous mating results in significantly reduced Ne in an age-structured population. This hypothesis was tested in a natural population of a harem-forming fruit bat, Cynopterus sphinx (Chiroptera: Pteropodidae), in western India. The influence of the mating system on the ratio of variance Ne to adult census number (N) was assessed using a mathematical model designed for age-structured populations that incorporated demographic and genetic data. Male mating success was assessed by means of direct and indirect paternity analysis using 10-locus microsatellite genotypes of adults and progeny from two consecutive breeding periods (n = 431 individually marked bats). Combined results from both analyses were used to infer the effective number of male parents in each breeding period. The relative proportion of successfully reproducing males and the size distribution of paternal sibships comprising each offspring cohort revealed an extremely high within-season variance in male mating success (up to 9.2 times higher than Poisson expectation). The resultant estimate of Ne/N for the C. sphinx study population was 0.42. As a result of polygynous mating, the predicted rate of drift (1/2Ne per generation) was 17.6% higher than expected from a Poisson distribution of male mating success. However, the estimated Ne/N was well within the 0.25-0.75 range expected for age-structured populations under normal demographic conditions. The life-history schedule of C. sphinx is characterized by a disproportionately short sexual maturation period scaled to adult life span. Consequently, the influence of polygynous mating on Ne/N is mitigated by the extensive overlap of generations. In C. sphinx, turnover of breeding males between seasons ensures a broader sampling of the adult male gamete pool than expected from the variance in mating success within a single breeding period.     

植物种质资源动态保存的数学分析

在假定植物群体中每个基因座上等可能出现N种不同等位基因,每一种等位基因的频率相等的前提下,用概率方法对在各种交配形式和不同异交率的情况下,动态地保持一个种群所需的基因库样本大小进行了数学分析,为保存和使用植物种质资源提供了一个有效方法。文中还给出了配子染色体数（n）为5—30的不同物种,在各种交配情况下维持动态基因库所需最小植株数目表,为植物育种家在实际运用本研究结果时提供便利。     

Stochastic modelling of shifts in allele frequencies reveals a strongly polygynous mating system in the re‐introduced Asiatic wild ass

Small populations are prone to loss of genetic variation and hence to a reduction in their evolutionary potential. Therefore, studying the mating system of small populations and its potential effects on genetic drift and genetic diversity is of high importance for their viability assessments. The traditional method for studying genetic mating systems is paternity analysis. Yet, as small populations are often rare and elusive, the genetic data required for paternity analysis are frequently unavailable. The endangered Asiatic wild ass (Equus hemionus), like all equids, displays a behaviourally polygynous mating system; however, the level of polygyny has never been measured genetically in wild equids. Combining noninvasive genetic data with stochastic modelling of shifts in allele frequencies, we developed an alternative approach to paternity analysis for studying the genetic mating system of the re‐introduced Asiatic wild ass in the Negev Desert, Israel. We compared the shifts in allele frequencies (as a measure of genetic drift) that have occurred in the wild ass population since re‐introduction onset to simulated scenarios under different proportions of mating males. We revealed a strongly polygynous mating system in which less than 25% of all males participate in the mating process each generation. This strongly polygynous mating system and its potential effect on the re‐introduced population's genetic diversity could have significant consequences for the long‐term persistence of the population in the Negev. The stochastic modelling approach and the use of allele‐frequency shifts can be further applied to systems that are affected by genetic drift and for which genetic data are limited.     

Polygamous mating system and protogynous sex change in the gobiid fish <Emphasis Type="Italic">Fusigobius neophytus</Emphasis>

Whereas mating behaviors and social structure have been studied extensively in monogamous hermaphroditic gobiid species, such studies are relatively limited for polygamous gobiid species. To investigate the reproductive strategy of polygamous gobies, mating groups of the common fusegoby Fusigobius neophytus were observed on reefs of Kuchierabu-jima Island, southern Japan. Males established mating nests on flat-rock surfaces within their territorial home ranges on sandy rubble flats. Females maintained independent home ranges outside the male home ranges during nonreproductive periods, but they shifted their home ranges to overlap with male ranges and actively visited male mating nests during their reproductive periods (1–3 days at ca. 7-day intervals). Females often changed mates during their serial mating. The mating system used by the common fusegoby fits with the definition of male-territory-visiting polygamy. The sex ratio within the study population was female-biased. Nest-holding males were significantly larger than females and were polygynous (mating with up to eight females). These characteristics fit well with the prediction of protogyny by the size-advantage model. Some of the females were observed to undergo functional sex changes to nest-holding males. In addition, small floating males demonstrated sneaking behavior. None of the floating males were derived from females that had changed sex, suggesting a diandric life-history pathway for F. neophytus.     

Heterozygote excess in small populations and the heterozygote-excess effective population size

It has been proposed that effective size could be estimated in small dioecious population by considering the heterozygote excess observed at neutral markers. When the number of breeders is small, allelic frequencies in males and females will slightly differ due to binomial sampling error. However, this excess of heterozygotes is not generated by dioecy but by the absence of individuals produced through selfing. Consequently, the approach can also be applied to self-incompatible monoecious species. Some inaccuracies in earlier equations expressing effective size as function of the heterozygote excess are also corrected in this paper. The approach is then extended to subdivided populations, where time of sampling becomes crucial. When adults are sampled, the effective size of the entire population can be estimated, whereas when juveniles are sampled, the average effective number of breeders per subpopulations can be estimated. The main limitation of the heterozygote excess method is that it will only perform satisfactorily for populations with a small number of reproducing individuals. While this situation is unlikely to happen frequently at the scale of the entire population, structured populations with small subpopulations are likely to be common. The estimation of the average number of breeders per subpopulations is thus expected to be applicable to many natural populations. The approach is straightforward to compute and independent of equilibrium assumptions. Applications to simulated data suggest the estimation of the number of breeders to be robust to mutation and migration rates, and to specificities of the mating system.     

Z chromosome divergence,polymorphism and relative effective population size in a genus of lekking birds

Sex chromosomes contribute disproportionately to species boundaries as they diverge faster than autosomes and often have reduced diversity. Their hemizygous nature contributes to faster divergence and reduced diversity, as do some types of selection. In birds, other factors (mating system and bottlenecks) can further decrease the effective population size of Z-linked loci and accelerate divergence (Fast-Z). We assessed Z-linked divergence and effective population sizes for two polygynous sage-grouse species and compared them to estimates from birds with various mating systems. We found lower diversity and higher F_ST for Z-linked loci than for autosomes, as expected. The π_Z/π_A ratio was 0.38 in Centrocercus minimus, 0.48 in Centrocercus urophasianus and 0.59 in a diverged, parapatric population of C. urophasianus, a broad range given the mating system among these groups is presumably equivalent. The full data set had unequal males and females across groups, so we compared an equally balanced reduced set of C. minimus and individuals pooled from both C. urophasianus subgroups recovering similar estimates: 0.54 for C. urophasianus and 0.38 for C. minimus. We provide further evidence that N_eZ/N_eA in birds is often lower than expected under random mating or monogamy. The lower ratio in C. minimus could be a consequence of stronger selection or drift acting on Z loci during speciation, as this species differs strongly from C. urophasianus in sexually selected characters with minimal mitochondrial divergence. As C. minimus also exhibited lower genomic diversity, it is possible that a more severe demographic history may contribute to its lower ratio.     

Sibship reconstruction for inferring mating systems,dispersal and effective population size in headwater brook trout (<Emphasis Type="Italic">Salvelinus fontinalis</Emphasis>) populations

Brook trout Salvelinus fontinalis populations have declined in much of the native range in eastern North America and populations are typically relegated to small headwater streams in Connecticut, USA. We used sibship reconstruction to infer mating systems, dispersal and effective population size of resident (non-anadromous) brook trout in two headwater stream channel networks in Connecticut. Brook trout were captured via backpack electrofishing using spatially continuous sampling in the two headwaters (channel network lengths of 4.4 and 7.7 km). Eight microsatellite loci were genotyped in a total of 740 individuals (80–140 mm) subsampled in a stratified random design from all 50 m-reaches in which trout were captured. Sibship reconstruction indicated that males and females were both mostly polygamous although single pair matings were also inferred. Breeder sex ratio was inferred to be nearly 1:1. Few large-sized fullsib families (>3 individuals) were inferred and the majority of individuals were inferred to have no fullsibs among those fish genotyped (family size = 1). The median stream channel distance between pairs of individuals belonging to the same large-sized fullsib families (>3 individuals) was 100 m (range: 0–1,850 m) and 250 m (range: 0–2,350 m) in the two study sites, indicating limited dispersal at least for the size class of individuals analyzed. Using a sibship assignment method, the effective population size for the two streams was estimated at 91 (95%CI: 67–123) and 210 (95%CI: 172–259), corresponding to the ratio of effective-to-census population size of 0.06 and 0.12, respectively. Both-sex polygamy, low variation in reproductive success, and a balanced sex ratio may help maintain genetic diversity of brook trout populations with small breeder sizes persisting in headwater channel networks.     

OPPORTUNITY FOR SEXUAL SELECTION AND EFFECTIVE POPULATION SIZE IN THE LEK-BREEDING EUROPEAN TREEFROG (HYLA ARBOREA).

Sexual selection in lek-breeding species might drastically lower male effective population size, with potentially important consequences for evolutionary and conservation biology. Using field-monitoring and parental-assignment methods, we analyzed sex-specific variances in breeding success in a population of European treefrogs, to (1) help understanding the dynamics of genetic variance at sex-specific loci, and (2) better quantify the risk posed by genetic drift in this species locally endangered by habitat fragmentation. The variance in male mating success turned out to be markedly lower than values obtained from other amphibian species with polygamous mating systems. The ratio of effective breeding size to census breeding size was only slightly lower in males (0.44) than in females (0.57), in line with the patterns of genetic diversity previously reported from H. arborea sex chromosomes. Combining our results with data on age at maturity and adult survival, we show that the negative effect of the mating system is furthermore compensated by the effect of delayed maturity, so that the estimated instantaneous effective size broadly corresponded to census breeding size. We conclude that the lek-breeding system of treefrogs impacts only weakly the patterns of genetic diversity on sex-linked genes and the ability of natural populations to resist genetic drift.     

Population bottleneck and effective size in Bonamia ostreae-resistant populations of Ostrea edulis as inferred by microsatellite markers

Genetic variability at five microsatellite loci was analysed in three hatchery-propagated populations of the flat oyster, Ostrea edulis. These populations were part of a selection programme for resistance to the protozoan parasite Bonamia ostreae and were produced by mass spawns, without control of the genealogy. Evidence for population bottlenecks and inbreeding was sought. A reduction in the number of alleles, mainly due to the loss of rare alleles, was observed in all selected populations, relative to the natural population from which they were derived. Heterozygote excesses were observed in two populations, and were attributed to substructuring of the population into a small number of families. Pedigree reconstruction showed that these two populations were produced by at most two spawning events involving a limited number of parents. Most individuals within these populations are half or full-sib, as shown by relatedness coefficients. The occurrence of population bottlenecks was supported by estimates of effective number of breeders derived by three methods: temporal variance in allelic frequencies, heterozygote excess, and a new method based on reduction in the number of alleles. The estimates from the different methods were consistent. The evidence for bottleneck and small effective number of breeders are expected to lead to increasing inbreeding, and have important consequences for the future management of the three O. edulis selected populations.     

Estimation of genetically effective breeding numbers using a rejection algorithm approach

Polygynous mating results in nonrandom sampling of the adult male gamete pool in each generation, thereby increasing the rate of genetic drift. In principle, genetic paternity analysis can be used to infer the effective number of breeding males (Nebm). However, this requires genetic data from an exhaustive sample of candidate males. Here we describe a new approach to estimate Nebm using a rejection algorithm in association with three statistics: Euclidean distance between the frequency distributions of maternally and paternally inherited alleles, average number of paternally inherited alleles and average gene diversity of paternally inherited alleles. We quantify the relationship between these statistics and Nebm using an individual-based simulation model in which the male mating system varied continuously between random mating and extreme polygyny. We evaluate this method using genetic data from a natural population of highly polygynous fruit bats (Cynopterous sphinx). Using data in the form of mother-offspring genotypes, we demonstrate that estimates of Nebm are very similar to independent estimates based on a direct paternity analysis that included data on candidate males. Our method also permits an evaluation of uncertainty in estimates of Nebm and thus facilitates inferences about the mating system from genetic data. Finally, we investigate the sensitivity of our method to sample size, model assumptions, adult population size and the mating system. These analyses demonstrate that the rejection algorithm provides accurate estimates of Nebm across a broad range of demographic scenarios, except when the true Nebm is high.     

On the Potential for Estimating the Effective Number of Breeders from Heterozygote-Excess in Progeny

The important parameter of effective population size is rarely estimable directly from demographic data. Indirect estimates of effective population size may be made from genetic data such as temporal variation of allelic frequencies or linkage disequilibrium in cohorts. We suggest here that an indirect estimate of the effective number of breeders might be based on the excess of heterozygosity expected in a cohort of progeny produced by a limited number of males and females. In computer simulations, heterozygote excesses for 30 unlinked loci having various numbers of alleles and allele-frequency profiles were obtained for cohorts produced by samples of breeders drawn from an age-structured population and having known variance in reproductive success and effective number. The 95% confidence limits around the estimate contained the true effective population size in 70 of 72 trials and the Spearman rank correlation of estimated and actual values was 0.991. An estimate based on heterozygote excess might have certain advantages over the previous estimates, requiring only single-locus and single-cohort data, but the sampling error among individuals and the effect of departures from random union of gametes still need to be explored.     

No difference between the sexes in fine-scale spatial genetic structure of roe deer

Background

Data on spatial genetic patterns may provide information about the ecological and behavioural mechanisms underlying population structure. Indeed, social organization and dispersal patterns of species may be reflected by the pattern of genetic structure within a population.

Methodology/Principal Findings

We investigated the fine-scale spatial genetic structure of a roe deer (Capreolus capreolus) population in Trois-Fontaines (France) using 12 microsatellite loci. The roe deer is weakly polygynous and highly sedentary, and can form matrilineal clans. We show that relatedness among individuals was negatively correlated with geographic distance, indicating that spatially proximate individuals are also genetically close. More unusually for a large mammalian herbivore, the link between relatedness and distance did not differ between the sexes, which is consistent with the lack of sex-biased dispersal and the weakly polygynous mating system of roe deer.

Conclusions/Significance

Our results contrast with previous reports on highly polygynous species with male-biased dispersal, such as red deer, where local genetic structure was detected in females only. This divergence between species highlights the importance of socio-spatial organization in determining local genetic structure of vertebrate populations.