Bayesian sperm competition estimates

We introduce a Bayesian method for estimating parameters for a model of multiple mating and sperm displacement from genotype counts of brood-structured data. The model is initially targeted for Drosophila melanogaster, but is easily adapted to other organisms. The method is appropriate for use with field studies where the number of mates and the genotypes of the mates cannot be controlled, but where unlinked markers have been collected for a set of females and a sample of their offspring. Advantages over previous approaches include full use of multilocus information and the ability to cope appropriately with missing data and ambiguities about which alleles are maternally vs. paternally inherited. The advantages of including X-linked markers are also demonstrated.     

Field experiments on the distributions of eggs of different phosphoglucomutase (PGM) genotypes in the yellow dung fly Scathophaga stercoraria (L.)

Female yellow dung flies can, in the laboratory, influence the probability that stored sperm from different males are used to fertilize eggs. This matches offspring phosphoglucomutase genotypes to the environmental conditions in which the larvae will grow, increasing larval growth success. We conducted field experiments in which dung topology or shading conditions were controlled. The proportions of the five common phosphoglucomutase alleles in eggs laid in north-facing slopes or in shaded conditions was related to their electrophoretic mobility. We suggest that females lay eggs of different genotypes, by appropriately choosing their fathers, in different places.     

Microsatellite evidence for monogamy and sex-biased recombination in the Western Australian seahorse Hippocampus angustus

Four polymorphic microsatellite loci were used to assess biological parentage of 453 offspring from 15 pregnant males from a natural population of the Western Australian seahorse Hippocampus angustus . Microsatellite genotypes in the progeny arrays were consistent with a monogamous mating system in which both females and males had a single mate during a male brooding period. Multilocus genotypes implicated four females in the adult population sample as contributors of eggs to the broods of collected males, but there was no evidence for multiple mating by females. Based on genotypic data from the progeny arrays, two loci were linked tightly and the recombination rate appeared to be ≈ 10-fold higher in females than in males. The utility of linked loci for parentage analyses is discussed.     

Detection rates for genotyping errors in SNPs using the trio design

One well-known approach for the analysis of transmission-disequilibrium is the investigation of single nucleotide polymorphisms (SNPs) in trios consisting of an affected child and its parents. Results may be biased by erroneously given genotypes. Various reasons, among them sample swap or wrong pedigree structure, represent a possible source for biased results. As these can be partly ruled out by good study conditions together with checks for correct pedigree structure by a series of independent markers, the remaining main cause for errors is genotyping errors. Some of the errors can be detected by Mendelian checks whilst others are compatible with the pedigree structure. The extent of genotyping errors can be estimated by investigating the rate of detected genotyping errors by Mendelian checks. In many studies only one SNP of a specific genomic region is investigated by TDT which leaves Mendelian checks as the only tool to control genotyping errors. From the rate of detected errors the true error rate can be estimated. Gordon et al. [Hum Hered 1999;49:65-70] considered the case of genotyping errors that occur randomly and independently with some fixed probability for the wrong ascertainment of an allele. In practice, instead of single alleles, SNP genotypes are determined. Therefore, we study the proportion of detected errors (detection rate) based on genotypes. In contrast to Gordon et al., who reported detection rates between 25 and 30%, we obtain higher detection rates ranging from 39 up to 61% considering likely error structures in the data. We conclude that detection rates are probably substantially higher than those reported by Gordon et al.     

The leatherback turtle,Dermochelys coriacea,exhibits both polyandry and polygyny

The leatherback turtle (Dermochelys coriacea) is an endangered species, and world-wide populations are declining. To understand better the mating structure of this pelagic and fragile species, we investigated paternity in nearly 1000 hatchlings from Playa Grande in Parque Marino Nacional Las Baulas, Costa Rica. We collected DNA samples from 36 adult female leatherbacks and assessed allele frequency distributions for three microsatellite loci. For 20 of these 36 females, we examined DNA from hatchlings representing multiple clutches, and in some cases assessed up to four successive clutches from the same female. We inferred paternal alleles by comparing maternal and hatchling genotypes. We could not reject the null hypothesis of single paternity in 12 of 20 families (31 of 50 clutches), but we did reject the null hypothesis in two families (eight of 50 clutches). In the remaining six families, the null hypothesis could not be accepted or rejected with certainty because the number of hatchlings exhibiting extra nonmaternal alleles was small, and could thus be a result of mutation or sample error. Successive clutches laid by the same female had the same paternal allelic contribution, indicating sperm storage or possibly monogamy. None of 20 females shared the same three-locus genotype whereas there were two instances of shared genotypes among 17 inferred paternal three-locus genotypes. We conclude that both polyandry and polygyny are part of the mating structure of this leatherback sea turtle population.     

Kin recognition and adjustment of reproductive effort in zebra finches

The differential allocation theory predicts that females should invest more in offspring produced with attractive partners, and a number of studies support this prediction in birds. Females have been shown to increase reproductive investment when mated to males showing elaborated sexual traits. However, mate attractiveness might also depend on the interaction between male and female genotypes. Accordingly, females should invest more in offspring sired by individuals that are genetically dissimilar or carry superior alleles. Here, we show in zebra finches (Taeniopygia guttata) that pairs of unfamiliar genetic brothers and sisters are less likely to reproduce in comparison with randomly mated pairs. Among the brother–sister pairs, those that attempted to breed laid smaller clutches and of lower total clutch mass. Our results provide the first experimental evidence that females adjust their reproductive effort in response to the genetic similarity of their partners. Importantly, these results imply a female ability to assess relatedness of a social mate without prior association.     

Production of live offspring with predicted genotypes using PCR-RFLP analysis of polar bodies from mouse oocytes

Accurate identification of genotypes in gametes and early embryos could facilitate the efficient production of offspring with desirable traits. This study demonstrates the feasibility of producing offspring with predictable genotypes from micromanipulated mouse oocytes. The Polymerase Chain Reaction (PCR) was used to amplify genes in the IA subregion of the major histocompatibility complex of the mouse. The validity of the approach was demonstrated in experiment 1 with IA haplo-types of unfertilized mouse ova amplified via PCR and distinguished by restriction fragment length polymorphism (RFLP) analysis. In experiment 2, fertilized oocytes were micromanipulated to remove the first and second polar bodies, which were then genotyped by validated PCR-RFLP procedures. Primary oocytes of heterozygous females contain two copies of each of the different alleles. Following meiosis I and II, the genotype of the ovum was predicted by subtracting the alleles observed in micromanipulated polar body samples. Sixty-two fertilized ova were micromanipulated and transferred to recipient females resulting in 27 live offspring (44%). The correct maternal contribution to the embryonic genotype was predicted in 19 of 27 (71%) offspring as confirmed by PCR-RFLP analysis of DNA from pup tails. Predicted genotypes of two pups were not confirmed (7%), whereas no prediction could be made in six cases (22%). © 1995 Wiley-Liss, Inc.     

Evolution of cannibalism and female's response to oviposition-deterring pheromone in aphidophagous predators

1.  Egg cannibalism by larvae is common in Coccinellidae and is known to be advantageous for the cannibals. Furthermore, larvae of aphidophagous ladybirds usually produce an oviposition-deterring pheromone (ODP), which inhibits oviposition by adult females. It has been proposed that the response to ODP has evolved because of the high costs of cannibalism. However, this has never been formally proved.
2.  In this paper, we study the theoretical evolution of this system. We first look at the conditions under which cannibalism and the response to ODP can evolve. Subsequently, we examine the occurrence of polymorphism both in the production of larval tracks and in the sensitivity of females to specific pheromones.
3.  The models predict that the amount of cannibalism should not depend on prey density and that evolution should lead to a continuous increase in cannibalism, and consequently larvae should always cannibalize eggs when possible. In response to the cost of cannibalism, ODP recognition can evolve, so that females avoid laying eggs in patches of prey already occupied by conspecific larvae. The result is an arms race between larvae and adult females, which favours a diversification of ODP pheromones. Our models show that: (i) females should be able to recognize mixtures of hydrocarbons rather than a single molecule; and (ii) females should be more sensitive to the tracks of their own offspring than those of non-related larvae.     

Estimation of genotyping error rate from repeat genotyping,unintentional recaptures and known parent–offspring comparisons in 16 microsatellite loci for brown rockfish (Sebastes auriculatus)

Genotyping errors are present in almost all genetic data and can affect biological conclusions of a study, particularly for studies based on individual identification and parentage. Many statistical approaches can incorporate genotyping errors, but usually need accurate estimates of error rates. Here, we used a new microsatellite data set developed for brown rockfish (Sebastes auriculatus) to estimate genotyping error using three approaches: (i) repeat genotyping 5% of samples, (ii) comparing unintentionally recaptured individuals and (iii) Mendelian inheritance error checking for known parent–offspring pairs. In each data set, we quantified genotyping error rate per allele due to allele drop‐out and false alleles. Genotyping error rate per locus revealed an average overall genotyping error rate by direct count of 0.3%, 1.5% and 1.7% (0.002, 0.007 and 0.008 per allele error rate) from replicate genotypes, known parent–offspring pairs and unintentionally recaptured individuals, respectively. By direct‐count error estimates, the recapture and known parent–offspring data sets revealed an error rate four times greater than estimated using repeat genotypes. There was no evidence of correlation between error rates and locus variability for all three data sets, and errors appeared to occur randomly over loci in the repeat genotypes, but not in recaptures and parent–offspring comparisons. Furthermore, there was no correlation in locus‐specific error rates between any two of the three data sets. Our data suggest that repeat genotyping may underestimate true error rates and may not estimate locus‐specific error rates accurately. We therefore suggest using methods for error estimation that correspond to the overall aim of the study (e.g. known parent–offspring comparisons in parentage studies).     

Reconstruction of Parentage in a Band of Captive Hamadryas Baboons

The male leaders of free-ranging harem groups of hamadryas baboons are believed to mate exclusively with the female members of their harems, which typically contain no more than 2–3 females. Using no-parent parentage exclusion analysis (PEA) we identified the paternity of 25 offspring born in a captive band of hamadryas baboons (Papio hamadryas hamadryas) containing five adult males, each with a stable harem of about five females. Nine of 13 microsatellite (SSR) loci known to be highly polymorphic in rhesus macaques (Macaca mulatta) were successful in identifying the sires of all but two offspring without knowledge of the dams' genotypes, and we were able to determine the sires of all offspring when the dams' genotypes were considered. Mating success of the males ranged between 2 and 7 offspring and bore no clear relationship to the males' ages, ranks or the number of females in their harems. The males sired 7 of the 25 offspring with females outside their own harems, with higher-ranking males exhibiting greater success monopolizing access to females in their harem than lower-ranking males did. More surprisingly, the females assigned as the dams of 14 of the 25 offspring could be unequivocally excluded from parentage. The identity of the true dam could be determined for each of these 14 offspring using single-parent PEA and was uncorrelated with the ranks of these offsprings' sires and whether the offspring were born to dams outside the sires' harem groups. The combined effect of this extraharem mating and kidnapping was that only 12 of the 25 offspring were raised within their sires' harem groups. A second group of hamadryas baboons of identical structure exhibited the same high incidences of infant kidnapping and mating outside the harem group. It is unclear whether these behaviors provide an adaptive advantage or represent aberrant behavior resulting from captivity or other circumstances.     

Molecular genetic data provide support for a model of transmission dynamics in an Australian reptile tick, Bothriocroton hydrosauri

Bothriocroton hydrosauri is a three-host ixodid tick that infests large reptiles in southeastern Australia, where its most common host is a large scincid lizard Tiliqua rugosa . Based on previous ecological and behavioural studies of this system, we propose a 'ripple' model of tick population dynamics, where only a few female ticks succeed in producing surviving offspring. These females then are the centres of ripples of their progeny spreading into the broader landscape. The model predicts higher relatedness among larvae than among nymphs or adults on a host, and significant spatial autocorrelation in larvae extending further than for the later life stages. The model also predicts that adult ticks are likely to encounter related partners and that this will generate inbreeding within the population. We tested those predictions using nine polymorphic microsatellite loci on a sample of 848 ticks (464 larvae, 140 nymphs and 244 adults) collected from 98 lizard hosts from near Bundey Bore Station in South Australia. Our data support the predictions and indicate that the dynamics of transmission among hosts play an important role in parasite population structure.     

Inbreeding effective population size and parentage analysis without parents

An important use of genetic parentage analysis is the ability to directly calculate the number of offspring produced by each parent (k(i)) and hence effective population size, N(e). But what if parental genotypes are not available? In theory, given enough markers, it should be possible to reconstruct parental genotypes based entirely on a sample of progeny, and if so the vector of parental k(i) values. However, this would provide information only about parents that actually contributed offspring to the sample. How would ignoring the 'null' parents (those that produced no offspring) affect an estimate of N(e)? The surprising answer is that null parents have no effect at all. We show that: (i) The standard formula for inbreeding N(e) can be rewritten so that it is a function only of sample size and ∑(k(2)(i)); it is not necessary to know the total number of parents (N). This same relationship does not hold for variance N(e). (ii) This novel formula provides an unbiased estimate of N(e) even if only a subset of progeny is available, provided the parental contributions are accurately determined, in which case precision is also high compared to other single-sample estimators of N(e). (iii) It is not necessary to actually reconstruct parental genotypes; from a matrix of pairwise relationships (as can be estimated by some current software programs), it is possible to construct the vector of k(i) values and estimate N(e). The new method based on parentage analysis without parents (PwoP) can potentially be useful as a single-sample estimator of contemporary N(e), provided that either (i) relationships can be accurately determined, or (ii) ∑(k(2)(i)) can be estimated directly.     

Statistics of natural populations. III. Sequential sampling plans for the estimation of gene frequencies

In previous work several models have been developed for genetic surveys of natural populations. Parents of unknown genotype are collected from a natural population, polymorphic at a single genetic locus. From each of these N cryptic parents a number of offspring are identified for their genotype. Our problem is to select an efficient offspring sampling plan for estimating the frequency of an allele in the cryptic adult population based on the N family profiles of juvenile genotypes. A criterion called the information per unit cost of observation is introduced to evaluate sequential sampling plans, in which the number of offspring per family examined is random. Some simple, practical schemes for stopping the sampling of offspring from a collected parent are introduced; one example is stopping when: (i) the offspring are definitive about the parental genotype(s) for the first time; (ii) a fixed number of one genotype only is seen; or (iii) a fixed maximum feasible number of offspring have been genotyped. This sampling scheme is recommended. For each sampling scheme, the best linear unbiased estimator and the sequential maximum likelihood estimator of the allele frequency are characterized. From the moments of these estimators, it is then possible to tabulate efficient sequential sampling plans, which are better (in the sense of information per unit cost), just as simple, and less costly than corresponding fixed sampling plans in use.     

Non-Invasive Sampling of Schistosomes from Humans Requires Correcting for Family Structure

For ethical and logistical reasons, population-genetic studies of parasites often rely on the non-invasive sampling of offspring shed from their definitive hosts. However, if the sampled offspring are naturally derived from a small number of parents, then the strong family structure can result in biased population-level estimates of genetic parameters, particularly if reproductive output is skewed. Here, we document and correct for the strong family structure present within schistosome offspring (miracidia) that were collected non-invasively from humans in western Kenya. By genotyping 2,424 miracidia from 12 patients at 12 microsatellite loci and using a sibship clustering program, we found that the samples contained large numbers of siblings. Furthermore, reproductive success of the breeding schistosomes was skewed, creating differential representation of each family in the offspring pool. After removing the family structure with an iterative jacknifing procedure, we demonstrated that the presence of relatives led to inflated estimates of genetic differentiation and linkage disequilibrium, and downwardly-biased estimates of inbreeding coefficients (F_IS). For example, correcting for family structure yielded estimates of F_ST among patients that were 27 times lower than estimates from the uncorrected samples. These biased estimates would cause one to draw false conclusions regarding these parameters in the adult population. We also found from our analyses that estimates of the number of full sibling families and other genetic parameters of samples of miracidia were highly intercorrelated but are not correlated with estimates of worm burden obtained via egg counting (Kato-Katz). Whether genetic methods or the traditional Kato-Katz estimator provide a better estimate of actual number of adult worms remains to be seen. This study illustrates that family structure must be explicitly accounted for when using offspring samples to estimate the genetic parameters of adult parasite populations.     

Using molecular markers for pedigree reconstruction of the greater amberjack (Seriola dumerili) in the absence of parental information

Ensuring appropriate levels of genetic diversity in captive populations is essential to avoid inbreeding and loss of rare alleles by genetic drift. Pedigree reconstruction and parentage analysis in the absence of parental genotypes can be a challenging task that relies in the assignment of sibship relationships among the offspring. Here, we used eight highly variable microsatellite markers and three different assignment methods to reconstruct the most likely genotypes of a parental group of wild Seriola dumerili fish based on the genotypes of six cohorts of their offspring, to assess their relative contributions to the offspring. We found that a combination of the four most variable microsatellites was enough to identify the number of parents and their contribution to the offspring, suggesting that the variability of the markers can be more critical than the number of markers. Estimated effective population sizes were lower than the number of breeders and variable among years. The results suggest unequal parental contribution that should be accounted for breeding programs in the future.     

Brood development into sexual females depends on the presence of a queen but not on temperature in an ant dispersing by colony fission,Aphaenogaster senilis

Abstract. 1. In eusocial insects, colony fission is a mode of dispersal by which a young queen leaves her nest with some workers to found a new colony. In these species, adult females (workers and the queen) should allocate most resources to increasing their colony size, which constrains the possibility of fission. In contrast, developing diploid larvae should have a preference for becoming a queen and having their own offspring, rather than becoming workers and rearing the offspring of other females. 2. In the ant Aphaenogaster senilis, queens are produced in very small numbers, suggesting that adult females control larval development. We used a 6‐year series of data on more than 300 nests to determine the annual cycle of worker and queen production. Although both overlapped, the latter mostly occurred in the second half of the summer, after a major peak of worker emergence. Young queens were also often produced in nests whose reproductive queen had died, thus allowing her replacement. Overall, we estimate that only 0.07% of diploid larvae actually develop into gynes. 3. Laboratory experiments indicated that brood is bipotent until the second larval instar. Diploid larval development into queen was favoured by the removal of the mother queen, but was not affected by rearing temperature. 4. Our data suggest that most diploid broods are forced by the adults to develop into workers rather than into gynes. However, when the queen is not present due to death or after a fission event, a few larvae are allowed to develop into gynes. One way for workers to limit the development of larvae might be by controlling the amount of food they receive.     

Assigning alleles to different loci in amplifications of duplicated loci

Duplicated loci, for example those associated with major histocompatibility complex (MHC) genes, often have similar DNA sequences that can be coamplified with a pair of primers. This results in genotyping difficulties and inaccurate analyses. Here, we present a method to assign alleles to different loci in amplifications of duplicated loci. This method simultaneously considers several factors that may each affect correct allele assignment. These are the sharing of identical alleles among loci, null alleles, copy number variation, negative amplification, heterozygote excess or heterozygote deficiency, and linkage disequilibrium. The possible multilocus genotypes are extracted from the alleles for each individual and weighted to estimate the allele frequencies. The likelihood of an allele configuration is calculated and is optimized with a heuristic algorithm. Monte‐Carlo simulations and three empirical MHC data sets are used as examples to evaluate the efficacy of our method under different conditions. Our new software, mhc‐typer V1.1, is freely available at https://github.com/huangkang1987/mhc-typer .     

Analysis of Coyote Mitochondrial DNA Genotype Frequencies: Estimation of the Effective Number of Alleles

A restriction-site survey of 327 coyotes (Canis latrans) from most parts of their North American range reveals 32 mitochondrial DNA (mtDNA) genotypes. The genotypes are not strongly partitioned in space, suggesting that there is high gene flow among coyote subpopulations. Consequently, each new geographic location added to the study has a decreasing probability of containing a mtDNA genotype that had not been previously discovered. This being the case, by using Monte Carlo sampling experiments, we can estimate the total number of genotypes that would be found if all possible localities were surveyed. This estimate of total genotypic variability agrees qualitatively with estimates based on theoretical considerations of the expected number of alleles in a stable population. We also predict effective population sizes from genotype data. The accuracy of these estimates is thought to be dependent on the fact that coyotes are not highly genetically structured, a situation which may apply to highly mobile species.     

Differential effects of offspring and maternal inbreeding on egg laying and offspring performance in the burying beetle Nicrophorus vespilloides

We investigate the effect of offspring and maternal inbreeding on maternal and offspring traits associated with early offspring fitness in the burying beetle Nicrophorus vespilloides. We conducted two experiments. In the first experiment, we manipulated maternal inbreeding only (keeping offspring outbred) by generating mothers that were outbred, moderately inbred or highly inbred. Meanwhile, in the second experiment, we manipulated offspring inbreeding only (keeping females outbred) by generating offspring that were outbred, moderately inbred or highly inbred. In both experiments, we monitored subsequent effects on breeding success (number of larvae), maternal traits (clutch size, delay until laying, laying skew, laying spread and egg size) and offspring traits (hatching success, larval survival, duration of larval development and average larval mass). Maternal inbreeding reduced breeding success, and this effect was mediated through lower hatching success and greater larval mortality. Furthermore, inbred mothers produced clutches where egg laying was less skewed towards the early part of laying than outbred females. This reduction in the skew in egg laying is beneficial for larval survival, suggesting that inbred females adjusted their laying patterns facultatively, thereby partially compensating for the detrimental effects of maternal inbreeding on offspring. Finally, we found evidence of a nonlinear effect of offspring inbreeding coefficient on number of larvae dispersing. Offspring inbreeding affected larval survival and larval development time but also unexpectedly affected maternal traits (clutch size and delay until laying), suggesting that females adjust clutch size and the delay until laying in response to being related to their mate.     

Probable Community Transfer of Parous Adult Female Chimpanzees in the Budongo Forest, Uganda

Female chimpanzees with dependent offspring generally avoid border areas of their community's home range because they risk aggression and infanticide from extracommunity males. Typically, only nulliparous females risk crossing the boundary areas to transfer between communities; while immigration of parous females occurs, it is extremely rare and dangerous for the females and their offspring. In the Budongo Forest, Uganda, where researchers have continuously studied the Sonso community since 1990, our field data provide strong indications that ≥5 adult females with offspring have immigrated into the community. If the interpretation is correct, then it has fundamental implications for our understanding of female chimpanzee social strategies and dispersal patterns. Further, the identification of such a large number of new individuals within a short time frame is remarkable and suggests a major event, such as the breakup of a neighboring community or major habitat disturbance. We explore the evidence that points to the events as immigrations and discuss the implications for understanding the chimpanzee social system.