matesoft: a program for deducing parental genotypes and estimating mating system statistics in haplodiploid species

With the advent of sophisticated genetic markers, studies on mating systems and reproductive apportionment have become increasingly feasible. In particular, paternity analyses in haplodiploid species have gained in power as hemizygous paternal genotypes allow maternal and paternal genotypes to be directly inferred from offspring genotypes. The computer program matesoft offers both newly developed algorithms for inferring maternal and paternal genotypes, and integrated estimation and correction procedures for calculating mating frequency statistics. Standard data are offspring genotypes of male‐haplodiploid organisms, including social Hymenoptera.     

Isolation and characterization of highly polymorphic microsatellites in the chokka squid, Loligo reynaudii

The chokka squid, Loligo reynaudii, is the target of a commercially valuable fishery in South Africa, but little information is available on population structure and mating system. We developed 11 polymorphic microsatellite markers using both standard nonenrichment and enrichment protocols. Numbers of alleles per locus ranged from 11 to 30, and levels of expected heterozygosity ranged between 0.77 and 0.98. Three loci developed using an enriched library displayed significant departure from Hardy-Weinberg genotype proportions suggesting high frequencies of null alleles. The remaining loci should prove useful for population and parentage studies.     

Parentage assignment and extra-group paternity in a cooperative breeder: the Seychelles warbler (Acrocephalus sechellensis)

We describe the development and initial application of a semiautomated parentage testing system in the Seychelles warbler (Acrocephalus sechellensis). This system used fluorescently labelled primers for 14 polymorphic microsatellite loci in two multiplex loading groups to genotype efficiently over 96% of the warbler population on Cousin island. When used in conjunction with the program CERVUS, this system provided sufficient power to assign maternity and paternity within the Seychelles warbler, despite the complications associated with its cooperative breeding system and a relatively low level of genetic variation. Parentage analyses showed that subordinate 'helper' females as well as the dominant 'primary' females laid eggs in communal nests, indicating that the Seychelles warbler has an intermediate level of female reproductive skew, in between the alternative extremes of helper-at-the-nest and joint nesting systems. Forty-four per cent of helpers bred successfully, accounting for 15% of all offspring. Forty per cent of young resulted from extra-group paternity.     

Microsatellite inheritance and multiple paternity in the deep-sea octopus Graneledone boreopacifica (Mollusca: Cephalopoda)

Abstract. Octopodids are a globally distributed group of marine molluscs. Despite this, our knowledge of their reproductive biology rests heavily on inference, as all phases of copulation, beginning with sperm transfer, occur within the mantle cavity. Male octopuses insert a spermatophore into the female's oviduct, which is predicted to release a sperm-filled sac that either bursts to release sperm for storage or to itself be stored in a gland in the middle of the oviduct. To test whether female octopuses use sperm from multiple males to fertilize their eggs, as may be predicted from anatomy and anecdotal accounts, we apply microsatellite analysis to a partial clutch of Graneledone boreopacifica collected at 1600-m depth to test for multiple paternity. At least two genetically distinct sires contributed sperm to the hatchlings analyzed, demonstrating for the first time multiple paternity in octopodids.     

爬行动物多父性生殖策略研究进展

动物生殖策略是多种多样的.对一个种群交配体系的调查有助于了解生殖模式的进化情况,并为一些濒危物种的保护计划提供理论依据,同时也为经济养殖动物的人工繁育提供理论支持.多父性( multiple paternity)现象是一种重要的生殖策略,在爬行类动物中普遍存在,并且在主要类群中多父性的水平也比较高,特别是多数有鳞类动物存在多父性现象的窝数可占到总检测窝数的50％以上,这种现象强烈地支持雌性存在混交的进化过程.本文对多父性产生的组织结构、可能机制和多父性的检测手段等进行综述,并对未来的研究方向提出了建议.     

Molecular determination of paternity in a natural population of the multiply mating polygynous lizard Eulamprus heatwolei

We studied the mating system of the southern water skink, Eulamprus heatwolei, during spring and summer (encompassing the breeding season) in a population in southeastern Australia. We examined potential attributes that might influence the mating system and male reproductive success including home range size, physical proximity of adults and body size, and then genotyped all mothers, offspring and potential sires. Home range overlap of both sexes was extensive, with adult females sharing the greatest amount of space with each other and adult males the least amount of space with each other. However, not all adults hold home ranges. We classified approximately one quarter of adult males as home range holders and the rest as 'floaters'. Adult females occupy home ranges more than males, with approximately three-quarters classified as home range holders. Home range ownership is not correlated with body size for either sex, however, male body size is positively correlated with the number of adult female home ranges that his home range overlaps and adult male home ranges are larger than those of females. We used microsatellite genotyping to assign paternities to 55 offspring from 17 litters and then compared this data with our home range and behavioural observations. This species displays extreme levels of multiple paternity given the small mean clutch size of three. Multiple paternity was confirmed in 11 (64.7%) of 17 clutches but three other clutches (for a total of 82.4%) also may display multiple paternity. A total of 30 offspring from 12 litters were assigned to 10 of the 32 genotyped adult males from our study site. Of these 10 adult males, half were home range holders. Five complete clutches and a total of 25 out of the 55 offspring could not be positively assigned to any male surveyed as part of the study and were attributed to floater males or resident males adjacent to our study site that had not been genotyped. While sample sizes are small, neither male home range ownership nor body size is significantly correlated with the number of paternities a male obtained. Our study suggests a polygynous mating system for this species.     

gerud1.0: a computer program for the reconstruction of parental genotypes from progeny arrays using multilocus DNA data

We have no standard computer algorithm for the reconstruction of parental genotypes from the data generated by molecular studies of progeny arrays. Here I present a computer program that uses the multilocus genotypes of parents and offspring to reconstruct the genotypes of unknown parents contributing gametes to a progeny array for which one parent is known a priori. A second program performs simulations to assess the reliability of the algorithm under various scenarios. These programs will aid scientists engaged in parentage analyses, particularly in species with large clutches.     

Isolation and characterization of polymorphic microsatellite loci for the study of paternity and population structure in the little penguin Eudyptula minor

We isolated and characterized eight novel microsatellite loci in the little penguin Eudyptula minor, using nonradioactive polymerase chain reaction‐based techniques to screen GA and GAAA repeats from enriched genomic DNA libraries. All eight loci were polymorphic and seven were variable in our main study population (mean H_E = 0.613, mean N_A = 7.14). Cross‐amplification using a microsatellite primer developed in Spheniscus demersus (African penguin) yielded one additional polymorphic locus. This locus combined with six of the little penguin loci is suitable for paternity assignment in little penguins (exclusion probability for seven unlinked loci = 0.993).     

gerud 2.0: a computer program for the reconstruction of parental genotypes from half‐sib progeny arrays with known or unknown parents

Large groups of related progeny, as can be collected from discrete egg masses or fruits, present excellent opportunities for parentage analysis by allowing the reconstruction of parental genotypes. Current techniques of parental genotypic reconstruction require the knowledge of at least one parental genotype. Here, I present a new computer program that reconstructs parental genotypes when no parents are known, provided that the progeny array contains only full and half siblings. The prospects for successfully reconstructing parental genotypes for such progeny arrays with unknown parents are nearly as good as those for the case when one parent is known with certainty.     

Evolutionary transition from single to multiple mating in fungus-growing ants

Queens of leafcutter ants exhibit the highest known levels of multiple mating (up to 10 mates per queen) among ants. Multiple mating may have been selected to increase genetic diversity among nestmate workers, which is hypothesized to be critical in social systems with large, long-lived colonies under severe pressure of pathogens. Advanced fungus-growing (leafcutter) ants have large numbers (104-106 workers) and long-lived colonies, whereas basal genera in the attine tribe have small (< 200 workers) colonies with probably substantially shorter lifespans. Basal attines are therefore expected to have lower queen mating frequencies, similar to those found in most other ants. We tested this prediction by analysing queen mating frequency and colony kin structure in three basal attine species: Myrmicocrypta ednaella, Apterostigma collare and Cyphomyrmex longiscapus. Microsatellite marker analyses revealed that queens in all three species were single mated, and that worker-to-worker relatedness in these basal attine species is very close to 0.75, the value expected under exclusively single mating. Fungus growing per se has therefore not selected for multiple queen mating. Instead, the advanced and highly productive social structure of the higher attine ants, which is fully dependent on the rearing of an ancient clonal fungus, may have necessitated high genetic diversity among nestmate workers. This is not the case in the lower attines, which rear fungi that were more recently derived from free-living fungal populations.     

Inter-population variation in multiple paternity and reproductive skew in the guppy

We use microsatellite loci to detail the multiple paternity patterns in broods from 10 wild populations of the guppy ( Poecilia reticulata ) found in Northern Trinidad. The populations span two major drainages comprising the Caroni and the Oropouche, and include sites that are characterized by either high or low predation. Across the populations the frequency of multiple paternity is high with 95% (range: 70%–100%) of broods having multiple sires. Broods have an average of 3.5 sires (range: 1–9) and a mixed-model analysis suggests that broods from high predation sites have marginally more sires than do those from low predation sites, but this is true only in the Oropouche drainage. There is no difference in sire number between predation sites in the Caroni drainage. Brood size, but not female body length, is correlated with the number of sires and the correlation cannot be attributed solely to the stochastic process associated with sperm competition and a 'fair raffle'. Within broods there is significant skew in reproductive success among males, which may reflect variation in sperm competitiveness or female choice. There is, however, no difference in the skew among populations from different predation regimes or drainages. Finally, high predation populations were characterized by increased genetic variability at the microsatellite loci, suggesting a larger effective population size. We discuss explanations for the high degree of multiple paternity but the general lack of any major differences among broods from ecologically different populations.     

High prevalence of multiple paternity in the invasive crayfish species,Procambarus clarkii

Reproductive strategy is a central feature of the ecology of invasive species as it determines the potential for population increase and range expansion. The red swamp crayfish, Procambarus clarkii, has invaded many countries and caused serious problems in freshwater ecosystems. However, little is known about the effects of environmental conditions on crayfish paternity and offspring traits in the wild. We studied these reproductive characteristics of P. clarkii in wild populations from two different habitats (ponds and ditches) in three locations with different environmental conditions in China. Genotyping of 1,436 offspring and 30 mothers of 30 broods was conducted by using four microsatellites. An analysis of genotyping results revealed that gravid females were the exclusive mother of the progeny they tended. Twenty-nine of 30 mothers had mated with multiple (2-4) males, each of which contributed differently to the number of offspring in a brood. The average number of fathers per brood and the number of offspring per brood were similar (P > 0.05) among six sampling sites, indicating that in P. clarkii multiple paternity and offspring number per brood are independent of environmental conditions studied. Indirect benefits from increasing the genetic diversity of broods, male and sperm competition, and cryptic female choice are a possible explanation for the high level multiple paternity and different contribution of fathers to offspring in this species.     

Characterization of microsatellite markers in the squid,Loligo bleekeri (Cephalopoda: Loliginidae)

Loligo bleekeri has a long spawning season and the size of mature males changes during the season: dimorphic (large/small) early in the spawning season and monomorphic (small) later in the spawning season. To understand how copulatory behaviours relate to the dimorphism, we developed five polymorphic microsatellite loci in L. bleekeri. The level of polymorphism ranged from 10 to 22 alleles with expected heterozygosities ranging from 0.79 to 0.93, suggesting that the novel polymorphic loci should be useful for parentage analysis of L. bleekeri.     

Detection of multiple paternity in the Kemp's ridley sea turtle with limited sampling

An important question in sea turtle biology is the number of males that contribute to the fertilization of a clutch of eggs. Previous studies on other sea turtle species have indicated little to no multiple paternity. We conclude here that female Kemp's ridleys, Lepidochelys kempi , are polyandrous. DNA from 26 mother and offspring groups was analysed at three microsatellite loci to identify paternal alleles. Three paternal alleles were observed among 14 of the clutches; four paternal alleles were observed among the offspring of an additional female. A maximum likelihood analysis not only rejects the model of single paternity, but also rejects the model of equal paternal contribution to the clutch. By explicitly addressing the high mutation rate of microsatellite markers, our analysis rejected mutation as the sole cause of multiple paternal alleles.     

Evidence of multiple paternity in spiny dogfish (Squalus acanthias) broods based on microsatellite analysis

An understanding of alternative mating systems is a fundamental requirement for the effective management of vulnerable species. Microsatellite analysis of spiny dogfish Squalus acanthias broods from the north‐west Atlantic provides novel evidence of polyandry in this species.     

Relatedness in wild chimpanzees: influence of paternity, male philopatry, and demographic factors

In chimpanzees (Pan troglodytes), high-ranking males are expected to have high reproductive success and females typically emigrate upon reaching maturity. Although high average relatedness among males in the same social groups has been assumed, previous reports have indicated that relatedness among males is not necessarily significantly higher than that among females. The paternity of 11 offspring and the relatedness of 50 individuals in the M group of chimpanzees at Mahale Mountains National Park, Tanzania, were investigated using DNA analyses. We determined the fathers of 10 offspring. Two different alpha males sired a total of five offspring, whereas the other males had low reproductive success. The proportion of paternal half-sibling pairs among the 10 offspring was 15.6%. The average relatedness among mature males was significantly higher than that among mature females. The existence of an old male and the long tenure of one alpha male may have contributed to this significant difference. The average dyadic relatedness among mature natal individuals was significantly higher than that in natal-immigrant pairs in which the individuals came from different groups. The average relatedness among immigrant females was similar to that in pairs of natal and immigrant females, suggesting that the immigrants came from various groups. Thus, female transfer acts to maintain low average relatedness within the group. A comparison of our results to those from other study sites suggests that although the average relatedness among adult males does not reach the level of half-siblings, under some circumstances it can exceed the relatedness of females.