Parentage analysis with incomplete sampling of candidate parents and offspring

Many breeding systems include 'multiple mating' in which males or females mate with multiple partners. We identify two forms of multiple mating: 'single-sex', where the next-generation individuals (NGIs) are the product of multiple mating by one sex; and 'two-sex', where the NGIs are the product of multiple mating by both sexes. For both mating systems we develop models that estimate the proportion of NGIs that is fathered (paternity) or mothered (maternity) by the putative parents. The models only require genetic data from the parent or parents in question and the sample of NGIs, as well as an estimate of population allele frequencies. The models provide unbiased estimates, can accommodate loci with many alleles and are robust to violations of their assumptions. They allow researchers to address intractable problems such as the parentage of seeds found on the ground, juvenile fish in a stream, and nestlings in a communal breeding bird. We demonstrate the models using genetic data from a nest of the bluegill sunfish Lepomis macrochirus, where the NGIs may be from multiple females that have spawned with multiple males from different life histories (cuckolder and parental).     

Genetic evidence for cuckoldry in bluegill Lepomis macrochirus

In colonies of bluegill Lepomis macrochirus , some males provide parental care for broods in nests, whereas other males steal fertilizations and do not provide parental care. Using experimental pond populations of bluegill of known genotype (determined through protein electrophoresis), we demonstrate that cuckolder males successfully fertilize eggs in parental male nests. Using electrophoretic techniques to assess the fertilization success of nesting parental male bluegill in Lake Opinicon, Ontario, we demonstrate that paternity of these males ranges from 41% to 100% among four colonies studied. This difference among colonies is related to the density of cuckolder males.     

Increased performance of offspring sired by parasitic males in bluegill sunfish

Males of many species are characterized by alternative matingtactics. In bluegill sunfish (Lepomis macrochirus), some malesdelay maturation and become "parentals" while other males matureprecociously and become "cuckolders." Parentals use an overt,territorial mating tactic, defending a nest and courting females.Cuckolders instead use a sneaking tactic to parasitize parentals.It has previously been shown that parentals that are heavilycuckolded provide less care to their young, yet females do notappear to discriminate against cuckolders, and they may actuallyrelease more eggs when a cuckolder is present than when spawningonly with a parental. Here I examined growth rate of fry ofknown paternity through the yolk-sac stage of development usingcomplementary laboratory and field studies to assess a potentialindirect benefit for females that mate with cuckolders. Comparisonof maternal half-siblings sired in vitro shows that cuckolderoffspring grow faster and to a larger size than parental offspringwhile feeding endogenously on their yolk sac. Because both foodresource and maternal genes are equivalent across treatments,these data indicate a genetic difference in growth between thetwo male life histories. In the field, fry from nests that haveproportionately more cuckolder offspring are larger when theyemerge from the nest. This increased size can lead to threefoldhigher survivorship for cuckolder offspring than parental offspringfrom Hydra canadensis predation, a major predator of bluegillfry. These results are discussed in the context of mate choicefor direct and indirect benefits and in the context of the evolutionof alternative mating tactics.     

Statistical confidence in parentage analysis with incomplete sampling: how many loci and offspring are needed?

We have recently presented models to estimate parentage in breeding systems with multiple mating and incomplete sampling of the candidate parents. Here we provide formulas to calculate the statistical confidence and the optimal trade-off between the number of loci and offspring. These calculations allow an understanding of the statistical significance of the parentage estimates as well as the appropriate sampling regime required to obtain a desired level of confidence. We show that the trade-off generally depends on the parentage of the putative parents. When parentage is low, sampling effort should concentrate on increasing the number of loci. Otherwise, there are similar benefits from increasing the number of loci or offspring. We demonstrate these methods using genetic data from a nest of the bluegill sunfish (Lepomis macrochirus).     

A bayesian framework for parentage analysis: the value of genetic and other biological data

We develop fractional allocation models and confidence statistics for parentage analysis in mating systems. The models can be used, for example, to estimate the paternities of candidate males when the genetic mother is known or to calculate the parentage of candidate parent pairs when neither is known. The models do not require two implicit assumptions made by previous models, assumptions that are potentially erroneous. First, we provide formulas to calculate the expected parentage, as opposed to using a maximum likelihood algorithm to calculate the most likely parentage. The expected parentage is superior as it does not assume a symmetrical probability distribution of parentage and therefore, unlike the most likely parentage, will be unbiased. Second, we provide a mathematical framework for incorporating additional biological data to estimate the prior probability distribution of parentage. This additional biological data might include behavioral observations during mating or morphological measurements known to correlate with parentage. The value of multiple sources of information is increased accuracy of the estimates. We show that when the prior probability of parentage is known, and the expected parentage is calculated, fractional allocation provides unbiased estimates of the variance in reproductive success, thereby correcting a problem that has previously plagued parentage analyses. We also develop formulas to calculate the confidence interval in the parentage estimates, thus enabling the assessment of precision. These confidence statistics have not previously been available for fractional models. We demonstrate our models with several biological examples based on data from two fish species that we study, coho salmon (Oncorhychus kisutch) and bluegill sunfish (Lepomis macrochirus). In coho, multiple males compete to fertilize a single female's eggs. We show how behavioral observations taken during spawning can be combined with genetic data to provide an accurate calculation of each male's paternity. In bluegill, multiple males and multiple females may mate in a single nest. For a nest, we calculate the fertilization success and the 95% confidence interval of each candidate parent pair.     

Genetic life history effects on juvenile survival in bluegill

Foraging behaviour under the risk of predation has important consequences on an individual's survivorship and fitness. In bluegill (Lepomis macrochirus), we have recently shown that offspring sired by males of alternative life histories differ in their foraging behaviour. Specifically, offspring sired by 'cuckolder' males take fewer risks during foraging than do offspring sired by 'parental' males. This behavioural difference can have important consequences on the fitness of the two life histories and thus the underlying evolutionary mechanism. Here, we examine the consequences of this behavioural variation on growth rate, condition and survivorship during early development of juveniles. We used split in vitro fertilization to generate maternal half-sibs that differed in sire life history. The resulting 18 455 larvae from 50 families were released into a microcosm with safe and risky foraging areas for approximately 2 months. A total of 262 juveniles (1.4%) survived of which parentage was unambiguously determined using microsatellite genetic markers for 254 (97%). Although we found significant dam effects, there was no difference in apparent growth rate or condition of juveniles sired by males of the two life histories. Of the 25 paired half-sib families, 15 had higher survivorship when sired by a cuckolder male, seven had higher survivorship when sired by a parental male and three had no surviving offspring from either sire. Thus, although growth was similar between the two offspring types, survivorship was not. Combining the differential survivorship estimate with paternity data from natural nests and the frequency of males adopting each life history, we calculated that the cuckolder life history has 1.87 times higher fitness than the parental life history. As such, the life histories likely are not governed by a genetic polymorphism.     

Genetic perspectives on the natural history of fish mating systems

Molecular analyses of bird and mammal populations have shown that social mating systems must be distinguished from genetic mating systems. This distinction is important in fishes also, where the potential for extrapair spawning and intraspecific brood parasitism is especially great. We review studies on fishes that have used molecular markers to document biological parentage and genetic mating systems in nature, particularly in species with extended parental care of offspring. On average, nest-guarding adults parented about 70-95% of their custodial offspring, and approximately one-third of the nests were cuckolded to some extent. Furthermore, nearly 10% of the assayed nests contained offspring tended by foster fathers either because of nest takeovers or egg thievery. On average, fish that provide parental care on nests spawned with more mates than did fish with internal fertilization and pregnancy. Overall, genetic markers have both confirmed and quantified the incidence of several reproductive and other social behaviors of fishes, and have thereby enhanced our knowledge of piscine natural history.     

In Vitro Fertilization Reveals Offspring Recognition via Self-Referencing in a Fish with Paternal Care and Cuckoldry

Male bluegill sunfish (Lepomis macrochirus) exhibit alternative life histories: some males (parentals) delay maturation for up to 7 yr, then build nests, court females, and care for the eggs and fry, whereas other males (cuckolders) mature precociously, attempt to steal fertilizations from parentals, and provide no parental care. Parental males could avoid misdirecting their nepotism (i.e. caring for unrelated young) by abandoning entire broods if they were sired mainly by cuckolders or by discriminating between offspring and non‐kin fry within broods for which they care. We tested for kin discrimination by obtaining sperm from parental and cuckolder males and eggs from several females, and using them to conceive fry in vitro. In ‘blind’ laboratory tests, parental males (but not cuckolder males) distinguished between sources of dripping water that had been conditioned by their own offspring vs. unrelated fry. Parental males that were in the best physical condition were especially choosy. Because the only referents available to our experimental subjects were chemical cues emanating from their own body, our results imply that parental males can use self‐referent phenotype matching for kin recognition. This mechanism enables males to make the adaptive, nepotistic adjustments in paternal care that have been documented in previous studies.     

Dynamic adjustment of parental care in response to perceived paternity

Theories of parental care evolution predict that genetic relatedness will be an important variable in the amount of care a parent provides. However, current inferences of relatedness-based parental investment from studies in humans and birds remain challenged. No study has yet demonstrated parental care adjustment in a manner uncomplicated by life-history correlates or experimental design. We now present a unique test that controls for individual life histories and demonstrates paternity-related dynamic adjustments in parental care. Brood-rearing male bluegill sunfish (Lepomis macrochirus) that are cuckolded to a varying degree will either increase or decrease their parental investment in response to changing information on paternity during brood development. Specifically, as parental males detect paternity lost to cuckolders and, hence, a reduction in the value of their brood, they adaptively lower their level of parental care. Conversely, if they detect that their paternity is higher than previously assessed, they adaptively raise their level of parental care. This dynamic adjustment during brood rearing indicates the importance of genetic relatedness in parental investment decisions and provides needed empirical support for theoretical predictions.     

Isolation and characterization of polymorphic microsatellite loci for parentage analysis in a rhacophorid tree frog (Chirixalus eiffingeri) with unusual parental care

Chirixalus eiffingeri is an arboreal breeding rhacophorid frog with unique parental care behaviours. We developed 11 polymorphic microsatellites as genetic makers for parentage analysis to resolve the ecology of parental care. The numbers of alleles per locus ranged from two to 17. The observed and expected heterozygosities averaged 0.433 and 0.656, respectively. Total exclusionary probability of these loci is 0.984 when no parental genotypes are known, and is 0.999 when one of the parental genotypes is known. The results indicate that the 11 markers should provide sufficient resolution for inferring genetic parentage in C. eiffingeri.     

Polyandry in the wild: temporal changes in female mating frequency and sperm competition intensity in natural populations of the tettigoniid Requena verticalis

Empirical tests of sexual selection theory generally utilize model systems under laboratory settings, and extend conclusions to evolutionary processes occurring in nature. The biological significance of laboratory findings will depend largely on the mating rates of females and patterns of paternity in natural populations, information on which is generally lacking. Here we use microsatellite markers to provide rare estimates of female mating rates and patterns of parentage in a species of tettigoniid, Requena verticalis, which has been used extensively to test theory on the evolution of male parental investment and its influence on the direction of sexual selection. We found that although the number of males having a genetic representation in the female's sperm stores was higher for females collected late in the breeding season than those collected early in the season, overall the female mating rate was lower than that expected from laboratory observations. Analysis of parentage of offspring produced by females at the end of the breeding season revealed that all males represented in the sperm stores fathered offspring, although paternity was biased away from that expected from random sperm utilization. The data show that the complete first male sperm precedence documented in laboratory studies of this species does not persist in natural populations. Our data provide a solid underpinning for conclusions drawn from laboratory studies of this species.     

Bluegill Coloration as a Sexual Ornament: Evidence From Ontogeny,Sexual Dichromatism,and Condition Dependence

In aquatic environments, visual communication is expected in animals that inhabit clear, shallow waters. Here, we investigate variation in the colorful traits of bluegills, Lepomis macrochirus, to elucidate their possible function. Bluegills use alternative mating tactics whereby males develop into one of two irreversible phenotypes termed parental and cuckolder. Parentals build and defend nests and care for offspring whereas cuckolders obtain matings by sneaking copulations. We hypothesized that bluegill coloration might function as a sexual ornament in parental males and that ornamental coloration might serve as an honest indicator of male quality. We predicted that coloration should be more pronounced in parental males than in females and immature males and should be more pronounced during the breeding season. We also predicted that males in better condition should be more intensely colored than fish in poor condition. To test our predictions, we sampled 510 bluegills during the breeding and post‐breeding seasons at nine lakes in southern Ontario, Canada, in 2007. We used reflectance spectrometry to quantify the coloration of five body regions, aged and sexed each fish, and calculated Fulton’s condition factor from morphological measurements. A separate experiment showed that color did not fade several minutes post capture, suggesting that coloration could be measured reliably and consistently. We found that color was influenced by maturity, sex, and season, in the predicted direction, for three body regions (breast, cheek, and opercular flap). We also found that color varied with the condition of males such that males in better condition were darker for the sexually dichromatic ventral and facial regions. Our findings therefore suggest that some colorful traits in bluegills may serve as condition‐dependent sexual signals during the breeding season. Our research contributes to a growing appreciation of the importance of visual signaling in aquatic environments.     

Serial monogamy in the European long-snouted seahorse Hippocampus guttulatus

Seahorses (Hippocampus spp.) are non-sex-role-reversed members of the Syngnathidae family that provide extensive brood care. Previous studies of seahorses have revealed monogamy within a single brood, but their longer term mating system had not been comprehensively evaluated. The parental contribution to 29 wild-born broods of Hippocampus guttulatus, sampled from six Portuguese populations with differing seahorse densities and sex ratios, was assessed using microsatellite DNA markers. To assess the longer term genetic mating system of this species parentage was determined in eleven broods sampled from a captive population over two breeding seasons. Genetic data suggest that this socially polygamous seahorse is serially monogamous across breeding seasons, i.e. monogamous within a season but may switch mates between seasons, and that differing population densities and sex ratios do not affect the mating system.     

Mating systems and sexual selection in male-pregnant pipefishes and seahorses: insights from microsatellite-based studies of maternity

In pipefishes and seahorses (family Syngnathidae), the males provide all postzygotic care of offspring by brooding embryos on their ventral surfaces. In some species, this phenomenon of male "pregnancy" results in a reversal of the usual direction of sexual selection, such that females compete more than males for access to mates, and secondary sexual characteristics evolve in females. Thus the syngnathids can provide critical tests of theories related to the evolution of sex differences and sexual selection. Microsatellite-based studies of the genetic mating systems of several species of pipefishes and seahorses have provided insights into important aspects of the natural history and evolution of these fishes. First, males of species with completely enclosed pouches have complete confidence of paternity, as might be predicted from parental investment theory for species in which males invest so heavily in offspring. Second, a wide range of genetic mating systems have been documented in nature, including genetic monogamy in a seahorse, polygynandry in two species of pipefish, and polyandry in a third pipefish species. The genetic mating systems appear to be causally related to the intensity of sexual selection, with secondary sex characters evolving most often in females of the more polyandrous species. Third, genetic studies of captive-breeding pipefish suggest that the sexual selection gradient (or Bateman gradient) may be a substantially better method for characterizing the mating system than previously available techniques. Finally, these genetic studies of syngnathid mating systems have led to some general insights into the occurrence of clustered mutations at microsatellite loci, the utility of linked loci in studies of parentage, and the use of parentage data for direct estimation of adult population size.     

Steroid hormones in bluegill, a species with male alternative reproductive tactics including female mimicry

The proximate mechanisms underlying the evolution and maintenance of within-sex variation in mating behaviour are still poorly understood. Species characterized by alternative reproductive tactics provide ideal opportunities to investigate such mechanisms. Bluegill (Lepomis macrochirus) are noteworthy in this regard because they exhibit two distinct cuckolder (parasitic) morphs (called sneaker and satellite) in addition to the parental males that court females. Here we confirm previous findings that spawning cuckolder and parental males have significantly different levels of testosterone and 11-ketotestosterone. We also report, for the first time, that oestradiol and cortisol levels are higher in cuckolders than in parental males. The two cuckolder morphs did not differ in average levels of any of the four hormones. However, among satellite males which mimic females in appearance and behaviour, there was a strong negative relationship between oestradiol levels and body length, a surrogate for age. This finding suggests that for satellite males, oestradiol dependency of mating behaviour decreases with increasing mating experience. Although such decreased hormone dependence of mating behaviour has been reported in other taxa, our data represent the first suggestion of the relationship in fishes.     

Gene dispersal and outbreeding in a philopatric mammal

Extensive mark-recapture data from banner-tailed kangaroo rats, Dipodomys spectabilis, have shown that both males and females are highly philopatric and suggest the possibility of close inbreeding. However, indirect analyses based on genetic structure appear to contradict direct observations, suggesting longer dispersal distances. Using microsatellite genotypes from most members of a banner-tailed kangaroo rat population during five successive breeding seasons, we ask how relatedness is influenced by dispersal and how it in turn influences mating patterns. The data confirm that, because of philopatry, neighbours are often close relatives. However, patterns of parentage also show that the average distance between mates is large relative to natal dispersal distances and larger than the average distance between nearest opposite-sexed neighbours. Females' mates were often not their nearest male neighbour and many were less related than the nearest male neighbour. We detected multiple paternity in some females' litters; both sexes produce offspring with multiple mates within and between breeding seasons. At the population level, heterozygosities were high and estimates of F were low, indicating that levels of inbreeding were low. Using individual inbreeding coefficients of all juveniles to estimate their parents' relatedness, we found that parental relatedness was significantly lower than relatedness between nearest opposite-sexed adult neighbours. Thus in philopatric populations, long breeding forays can cause genes to move further than individuals disperse, and polyandry may serve to reduce relatedness between mates.     

Promiscuity drives self-referent kin recognition

Kin selection theory has been one of the most significant advances in our understanding of social behavior . However, the discovery of widespread promiscuity has challenged the evolutionary importance of kin selection because it reduces the benefit associated with helping nestmates . This challenge would be resolved if promiscuous species evolved a self-referent kin-recognition mechanism that enables individuals to differentiate kin and nonkin . Here, we take advantage of an asymmetry in the level of promiscuity among males of alternative life histories in the bluegill sunfish (Lepomis macrochirus). We show that, as a consequence of this asymmetry, offspring of "parental" males have a high level of relatedness to nestmates, whereas offspring of "cuckolder" males have a low level of relatedness to nestmates. We find that offspring of parentals do not use a direct recognition mechanism to discriminate among nestmates, whereas offspring of cuckolders use kin recognition by self-referent phenotype matching to differentiate between kin and nonkin. Furthermore, we estimate that the cost of utilizing such self-referent kin recognition is equivalent to a relatedness (R) of at least 0.06. These results provide compelling evidence for adaptive use of kin recognition by self-referent phenotype matching and confirm the importance of kinship in social behavior.     

Weak polygyny in California sea lions and the potential for alternative mating tactics

Female aggregation and male territoriality are considered to be hallmarks of polygynous mating systems. The development of genetic parentage assignment has called into question the accuracy of behavioral traits in predicting true mating systems. In this study we use 14 microsatellite markers to explore the mating system of one of the most behaviorally polygynous species, the California sea lion (Zalophus californianus). We sampled a total of 158 female-pup pairs and 99 territorial males across two breeding rookeries (San Jorge and Los Islotes) in the Gulf of California, Mexico. Fathers could be identified for 30% of pups sampled at San Jorge across three breeding seasons and 15% of sampled pups at Los Islotes across two breeding seasons. Analysis of paternal relatedness between the pups for which no fathers were identified (sampled over four breeding seasons at San Jorge and two at Los Islotes) revealed that few pups were likely to share a father. Thirty-one percent of the sampled males on San Jorge and 15% of the sampled males on Los Islotes were assigned at least one paternity. With one exception, no male was identified as the father of more than two pups. Furthermore, at Los Islotes rookery there were significantly fewer pups assigned paternity than expected given the pool of sampled males (p<0.0001). Overall, we found considerably lower variation in male reproductive success than expected in a species that exhibits behavior associated with strongly polygynous mating. Low variation in male reproductive success may result from heightened mobility among receptive females in the Gulf of California, which reduces the ability of males to monopolize groups of females. Our results raise important questions regarding the adaptive role of territoriality and the potential for alternative mating tactics in this species.     

Mate choice, genetic incompatibility, and outbreeding in the ornate dragon lizard, Ctenophorus ornatus

There has been recent interest in the role genetic incompatibility may play in mate or sperm choice. One source of incompatibility may be too similar or disparate genomes. An isolated population of the ornate dragon lizard, Ctenophorus ornatus, was followed over a breeding season and parentage assigned to the offspring using microsatellites. It was found that the adults in the population had an eight per cent chance of mating with a relative. I examined whether C. ornatus mate (or fertilize their eggs) with respect to genetic similarity. There was no difference in a female's relatedness to the male in whose territory she resided and her average relatedness to all other males. Neither was there a difference in the relatedness of the male that sired a female's offspring and the female's average relatedness to all other males. There was no evidence of a cost to mating with a more genetically similar mate, because offspring survival was not influenced by degree of inbreeding or outbreeding. However, females that were more outbred had fewer offspring survive. In this small population there are two possible explanations for the decreased fitness associated with outbreeding. First, the species may have an evolutionary history of inbreeding and thus may be susceptible to outbreeding depression. Second. as fitter individuals produce more offspring, these offspring have an increased probability of breeding with relatives, leading to an indirect relationship between fitness and outbreeding.     

Paternal Genetic Effects on Foraging Decision-Making Under the Risk of Predation

Foraging behavior under the risk of predation has interested biologists for decades. Here, we examine paternal genetic effects on foraging decisions of bluegill (Lepomis macrochirus) larvae sired by males adopting alternative life histories. We use split in vitro fertilization to generate maternal half‐siblings sired by either a ‘parental’ male or a ‘cuckolder’ male. Immediately, upon the switch to exogenous feeding, we fed the larvae ad libitum for 2 d. We then starved the larvae for between 12 and 17 h, following which we subjected them to a dichotomous choice foraging trial, where one side of a test tank posed a risky foraging habitat and the other posed a safe foraging habitat. Equal amounts of food were simultaneously introduced to both sides of the tank and the proportion of individuals on either side was recorded. There were significantly fewer cuckolder offspring foraging on the risky side of the tank when compared with their parental half‐siblings indicating that cuckolder offspring took fewer risks than parental offspring. These results demonstrate a paternal genetic effect (sire life history) on foraging behavior. We ruled out energetic state as a possible explanation for this difference because the half‐siblings did not differ in body length or mass. Instead, previous research suggests that cuckolder offspring have higher conversion efficiency (efficiency of converting food into soma) than parental offspring and therefore the differences in foraging behavior observed here may, in part, be attributed to genetic differences in conversion efficiency.