Patterns of relatedness and parentage in an asocial, polyandrous striped hyena population

We investigated patterns of relatedness and reproduction in a population of striped hyenas in which individuals are behaviourally solitary but form polyandrous spatial groups consisting of one adult female and multiple adult males. Group-mate males were often close relatives, but were unrelated or distantly related in some cases, indicating that male coalitions are not strictly a result of philopatry or dispersal with cohorts of relatives. Most male-female pairs within spatial groups were unrelated or only distantly related. Considering patterns of relatedness between groups, relatedness was significantly higher among adult males living in non-neighbouring ranges than among neighbouring males. Mean relatedness among male-female dyads was highest for group-mates, but relatedness among non-neighbouring males and females was also significantly higher than among dyads of opposite-sex neighbours. Female-female relatedness also increased significantly with increasing geographic separation. These unusual and unexpected patterns may reflect selection to settle in a nonadjacent manner to reduce inbreeding and/or competition among relatives for resources (both sexes), or mates (males). Finally, resident males fathered the majority of the resident female's cubs, but extra-group paternity was likely in 31% of the cases examined, and multiple paternity was likely in half of the sampled litters.     

Male reproductive suppression in the cooperatively breeding fish Neolamprologus pulcher

In most cooperative breeders, dominants suppress the reproductionof subordinates. However, two previous studies of Neolamprologuspulcher, a cooperatively breeding cichlid fish, have suggestedthat socially subordinate helper males sneak fertilizationsfrom dominant breeding males. If such sneaking does occur, boththeoretical work and empirical studies of other fish speciessuggest that sperm competition will select for increased reproductiveinvestment by sneaker males, relative to more dominant males.To address these issues, we quantified gonadal investment andsperm characteristics of 41 N. pulcher male breeders and 62male helpers from 55 groups in Lake Tanganyika. Gonadal investmentfollowed patterns consistent with reproductive suppression,with breeders having considerably larger testes masses thanhelpers. Breeders also had faster and longer swimming spermand a higher percentage of motile sperm compared to helpers.However, sperm characteristics of large helpers were similarto those of breeders, but these same helpers had lower testesmasses. Thus, large helpers had sperm that were physiologicallyequivalent to that of breeders, but their relatively small gonadsimply that they were reproductively suppressed.     

Group composition affects male reproductive partitioning in a cooperatively breeding cichlid

Individuals within groups of cooperatively breeding species may partition reproduction, with the dominant pair often taking the largest share. The dominant's ability to reproductively control subordinates may depend on differences in competitive ability, due to, e.g. body size differences, but may also depend on the number of same‐sex competitors inside the group. We tested experimentally whether subordinates reproduce more when these subordinates are large or when a second subordinate of the same sex need to be controlled by the dominants, using the cooperatively breeding cichlid Neolamprologus pulcher. Dominant pairs were assisted by a large and a small unrelated subordinate; sexes of these fish were varied in a full‐factorial design (giving four treatments). Dominant males lost significantly more parentage to the large subordinate male when a small subordinate male was also present, compared to when a small subordinate female was present. However, subordinate paternity was generally low and did not significantly curb total dominant male reproductive output, which was more affected by the sizes and numbers of reproductive females present inside his group. Dominant female maternity, clutch sizes and total output did not depend on the treatments. Subordinate–subordinate reproduction was virtually absent (one out of 874 offspring). Female subordinates were more likely to provide care for their own broods. In contrast, male subordinates did not adjust their level of care to their parentage. Variability in female subordinate alloparental brood care was particularly high, with females showing more care than males in general. We also detected effects of growth rate and food ration on parentage independent of the treatments, most notably: (i) a trade‐off between dominant male growth rate and paternity; (ii) a decrease in dominant male paternity with increasing food ration; (iii) a positive effect of growth rate on paternity in small males. We conclude that dominant males should be sensitive to the number and sizes of subordinate males present in their group, particularly when these subordinates are not helpful or grow fast, and food is plentiful. Dominant females should be less sensitive, because female subordinates do not appear to impose reproductive costs and can be helpful through alloparental brood care.     

Liver size reveals social status in the African cichlid Neolamprologus pulcher

Wild groups ( n = 167) of the cooperatively breeding Lake Tanganyika cichlid, Neolamprologus pulcher , were used to investigate how social status and sex influence liver investment. In contrast to expectations, males and females (controlling for body size) had similar liver investment and subordinates (both sexes) had relatively larger livers compared with dominants. Three hypotheses were considered for why social status results in liver size disparity: liver mass might reflect status-dependent differences in (1) energy expenditure, (2) energy storage and (3) energy acquisition. First, dominants performed more energetically costly behaviours ( e.g . social policing and care) compared with subordinates, supporting the notion that energy expenditure drives liver investment. Moreover, dominants in large groups (with many subordinates to monitor) and those holding multiple territories (with large areas to patrol), tended to have smaller livers. Second, subordinates did not appear to use the liver as a strategic energy storage organ. In laboratory and field experiments, subordinates ascending in rank had similar or larger livers during periods of rapid growth compared with non-ascending controls. Third, although subordinates fed more frequently than dominants, a negative relationship was found between feeding rates and liver size. Hence, these results contrast with previous liver studies and suggest that liver investment patterns were linked to status-driven differences in energy expenditure but not to energy intake or storage in N. pulcher .     

Insights into the mating habits of the tiger salamander (Ambystoma tigrinum tigrinum) as revealed by genetic parentage analyses

Among urodeles, ambystomatid salamanders are particularly amenable to genetic parentage analyses because they are explosive aggregate breeders that typically have large progeny arrays. Such analyses can lead to direct inferences about otherwise cryptic aspects of salamander natural history, including the rate of multiple mating, individual reproductive success, and the spatial distribution of clutches. In 2002, we collected eastern tiger salamander (Ambystoma tigrinum tigrinum) egg masses (> 1000 embryos) from a approximately 80 m linear transect in Indiana, USA. Embryos were genotyped at four variable microsatellite loci and the resulting progeny array data were used to reconstruct multilocus genotypes of the parental dams and sires for each egg mass. UPGMA analysis of genetic distances among embryos resolved four instances of egg mass admixture, where two or more females had oviposited at exactly the same site resulting in the mixing of independent cohorts. In total, 41 discrete egg masses were available for parentage analyses. Twenty-three egg masses (56%) consisted exclusively of full-siblings (i.e. were singly sired) and 18 (44%) were multiply sired (mean 2.6 males/clutch). Parentage could be genetically assigned to one of 17 distinct parent pairs involving at least 15 females and 14 different males. Reproductive skew was evident among males who sired multiply sired clutches. Additional evidence of the effects of sexual selection on male reproductive success was apparent via significant positive correlations between male mating and reproductive success. Females frequently partitioned their clutches into multiple discrete egg masses that were separated from one another by as many as 43 m. Collectively, these data provide the first direct evidence for polygynandry in a wild population of tiger salamanders.     

Methods of parentage analysis in natural populations

The recent proliferation of hypervariable molecular markers has ushered in a surge of techniques for the analysis of parentage in natural and experimental populations. Consequently, the potential for meaningful studies of paternity and maternity is at an all-time high. However, the details and implementation of the multifarious techniques often differ in subtle ways that can influence the results of parentage analyses. Now is a good time to reflect on the available techniques and to consider their strengths and weaknesses. Here, we review the leading techniques in parentage analysis, with a particular emphasis on those that have been implemented in readily useable software packages. Our survey leads to some important insights with respect to the utility of the different approaches. This review should serve as a useful guide to anyone who wishes to embark on the study of parentage.     

Dispersal patterns and status change in a co‐operatively breeding cichlid Neolamprologus pulcher: evidence from microsatellite analyses and behavioural observations

Genetic techniques and long‐term behavioural observations were combined to investigate dispersal patterns and changes in social position in Neolamprologus pulcher , a co‐operatively breeding cichlid from Lake Tanganyika. Comparisons of genetic variance ( F _ST) across sub‐populations demonstrated that fish were genetically more similar to individuals from proximate sub‐populations compared to individuals from distant sub‐populations. Microsatellite analyses revealed year‐long philopatry for some individuals and that other individuals dispersed to new territories and sub‐populations. Individuals appeared to disperse farther (across many territories in a sub‐population or to new sub‐populations) to achieve breeding status. Non‐breeding group members (or helpers) were observed to inherit breeding positions and male breeders were replaced faster than female breeders. These results demonstrate that important and difficult to obtain life‐history information can be obtained from genetic sampling.     

A genetic assessment of parentage in a natural population of dollar sunfish (Lepomis marginatus) based on microsatellite markers

We employ microsatellite markers to assess mating tactics in Lepomis marginatus. Genetic assignments for 1015 progeny in 23 nests indicate that about 95% of the offspring were sired by their respective nest-guardians, a finding consistent with the apparent absence of a brood parasitic morphotype in this species. Allopaternal care was documented in two nests, one resulting from a nest takeover, the other from cuckoldry by an adjoining nest-tender. Clustered de novo mutations also were identified. About 2.5 females (range 1-7) contributed to the offspring pool within a typical nest. Results are compared to those for other Lepomis species.     

Towards unbiased parentage assignment: combining genetic, behavioural and spatial data in a Bayesian framework

Inferring the parentage of a sample of individuals is often a prerequisite for many types of analysis in molecular ecology, evolutionary biology and quantitative genetics. In all but a few cases, the method of parentage assignment is divorced from the methods used to estimate the parameters of primary interest, such as mate choice or heritability. Here we present a Bayesian approach that simultaneously estimates the parentage of a sample of individuals and a wide range of population-level parameters in which we are interested. We show that joint estimation of parentage and population-level parameters increases the power of parentage assignment, reduces bias in parameter estimation, and accurately evaluates uncertainty in both. We illustrate the method by analysing a number of simulated test data sets, and through a re-analysis of parentage in the Seychelles warbler, Acrocephalus sechellensis. A combination of behavioural, spatial and genetic data are used in the analyses and, importantly, the method does not require strong prior information about the relationship between nongenetic data and parentage.     

Comparing parentage inference software: reanalysis of a red deer pedigree

Knowledge of the parentage of individuals is required to address a variety of questions concerning the evolutionary dynamics of wild populations. A major advance in parentage inference in natural populations has been the use of molecular markers and the development of statistical methods to analyse these data. Cervus, one of the most widely used parentage inference programs, uses molecular data to determine parent–offspring relationships. However, Cervus does not make use of all available information: additional phenotypic information may exist predicting parent–offspring relationships, and additional genetic information may be exploited by simultaneously considering multiple types of relationships rather than just pairwise or just parent–offspring relationships. Here we reanalyse data from a wild red deer population using two programs capable of using this additional information, MasterBayes and COLONY2, and quantify the impact of these alternative approaches by comparison with a ‘known pedigree’ estimated using a larger suite of microsatellite makers for a subset of the population. The use of phenotypic information and multiple relationships increased the number of correct assignments. We highlight the differences between programs, particularly the use of population‐ rather than individual‐level statistical confidence in Cervus. We conclude that the use of additional information allows MasterBayes and COLONY2 to assign more correct paternities, whereas their use of individual‐ rather than population‐level confidence generates fewer erroneous assignments. We suggest that maximal information may be gained by combining outputs from different programs. Higher accuracy and completeness of pedigree information will improve parameters estimated from pedigree information in studies of natural populations.     

A practical guide to methods of parentage analysis

The use of molecular techniques for parentage analysis has been a booming science for over a decade. The most important technological breakthrough was the introduction of microsatellite markers to molecular ecology, an advance that was accompanied by a proliferation and refinement of statistical techniques for the analysis of parentage data. Over the last several years, we have seen steady progress in a number of areas related to parentage analysis, and the prospects for successful studies continue to improve. Here, we provide an updated guide for scientists interested in embarking on parentage analysis in natural or artificial populations of organisms, with a particular focus on computer software packages that implement various methods of analysis. Our survey of the literature shows that there are a few established methods that perform extremely well in the analysis of most types of parentage studies. However, particular experimental designs or study systems can benefit from some of the less well-known computer packages available. Overall, we find that parentage analysis is feasible and satisfying in most systems, and we try to provide a simple roadmap to help other scientists navigate the confusing topography of statistical techniques.     

Power of 22 microsatellite markers in fluorescent multiplexes for parentage testing in goats (Capra hircus)

Two multiplex systems, each containing 11 microsatellite loci, were developed for semiautomated parentage testing in goats. Eight of the loci originate from goats, nine from cattle and five from sheep. Eighteen of the loci have been mapped to 16 different autosomes (in goats and cattle). Parentage exclusion probabilities were computed from allele frequencies in approximately 30 unrelated individuals from each of four economically important breeds: Mongolian Native Cashmere, Turkish Angora, Swiss Saanen, and Spanish Murciana-Grenadina. In cases where genotypes are known for one parent and an offspring, the 22 markers will exclude an (erroneously) alleged parent with a probability of > 0.999999 in the cashmere breed, > 0.99999 in Angora and Murciana-Grenadina, and > 0.9999 in Saanen. The multiplexes provide very high power for individual identification as the probability of finding two identical genotypes for the 22 loci is < 1 in 1.10(15) in each of the four breeds. The multiplexes will also be useful for studies of population structure, history, and diversity in goats and also in wild Capra species that represent important resources for genetic improvement of domestic breeds.     

Concessions of an alpha male? Cooperative defence and shared reproduction in multi-male primate groups

By living in social groups with potential competitors, animals forgo monopolizing access to resources. Consequently, debate continues over how selection might favour sociality among competitors. For example, several models exist to account for the evolution of shared reproduction in groups. The 'concession model' hypothesizes that dominant reproducers benefit from the presence of subordinates, and hence tolerate some reproduction by subordinates. This mutual benefit to both dominants and subordinates may provide a foundation for the formation of social groups in which multiple members reproduce-a necessary step in the evolution of cooperation. To date, however, the concession model has received virtually no support in vertebrates. Instead, the vast majority of vertebrate data support 'limited control models', which posit that dominant reproducers are simply unable to prevent subordinates from reproducing. Here we present the most comprehensive evidence to date in support of the concession model in a vertebrate. We examined natural variation in the number of adult males in gelada (Theropithecus gelada) reproductive units to assess the extent of reproductive skew in multi-male units. Dominant ('leader') males in units that also had subordinate ('follower') males had a 30 per cent longer tenure than leaders in units that did not have followers, mainly because followers actively defended the group against potential immigrants. Follower males also obtained a small amount of reproduction in the unit, which may have functioned as a concession in return for defending the unit. These results suggest that dominants and subordinates may engage in mutually beneficial reproductive transactions, thus favouring male-male tolerance and cooperation.     

Genetic parentage assessment in the crayfish Orconectes placidus,a high-fecundity invertebrate with extended maternal brood care

Microsatellite data have recently been introduced in the context of genetic maternity and paternity assignments in high-fecundity fish species with single-parent-tended broods. Here we extend such analyses to an aquatic invertebrate, the crayfish Orconectes placidus, in which gravid females carry large numbers of offspring. Genetic parentage analyses of more than 900 progeny from 15 wild crayfish broods revealed that gravid females were invariably the exclusive dams of the offspring they tended (i.e. there was no allomaternal care), and that most of the females had mated with multiple (usually two) males who contributed sometimes highly skewed numbers of offspring to a brood. Within any multiply sired brood, the unhatched eggs (or the hatched juveniles) from different fathers were randomly distributed across the mother's brood space. All of these genetic findings are discussed in the light of observations on the mating behaviours and reproductive biology of crayfish.     

Subordinate male meerkats prospect for extra-group paternity: alternative reproductive tactics in a cooperative mammal

In cooperatively breeding species, subordinates typically suffer strong constraints on within-group reproduction. While numerous studies have highlighted the additional fitness benefits that subordinates might accrue through helping, few have considered the possibility that subordinates may also seek extra-group matings to improve their chances of actually breeding. Here, we show that subordinate males in cooperative meerkat, Suricata suricatta, societies conduct frequent extraterritorial forays, during periods of peak female fertility, which give rise to matings with females in other groups. Genetic analyses reveal that extra-group paternity (EGP) accrued while prospecting contributes substantially to the reproductive success of subordinates: yielding the majority of their offspring (approx. 70%); significantly reducing their age at first reproduction and allowing them to breed without dispersing. We estimate that prospecting subordinates sire 20-25% of all young in the population. While recent studies on cooperative birds indicate that dominant males accrue the majority of EGP, our findings reveal that EGP can also arise from alternative reproductive tactics employed exclusively by subordinates. It is important, therefore, that future attempts to estimate the fitness of subordinate males in animal societies quantify the distribution of extra-group as well as within-group paternity, because a substantial proportion of the reproductive success of subordinates may otherwise go undetected.     

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.     

The evolution of cooperative breeding in the African cichlid fish,Neolamprologus pulcher

The conundrum of why subordinate individuals assist dominants at the expense of their own direct reproduction has received much theoretical and empirical attention over the last 50 years. During this time, birds and mammals have taken centre stage as model vertebrate systems for exploring why helpers help. However, fish have great potential for enhancing our understanding of the generality and adaptiveness of helping behaviour because of the ease with which they can be experimentally manipulated under controlled laboratory and field conditions. In particular, the freshwater African cichlid, Neolamprologus pulcher, has emerged as a promising model species for investigating the evolution of cooperative breeding, with 64 papers published on this species over the past 27 years. Here we clarify current knowledge pertaining to the costs and benefits of helping in N. pulcher by critically assessing the existing empirical evidence. We then provide a comprehensive examination of the evidence pertaining to four key hypotheses for why helpers might help: (1) kin selection; (2) pay‐to‐stay; (3) signals of prestige; and (4) group augmentation. For each hypothesis, we outline the underlying theory, address the appropriateness of N. pulcher as a model species and describe the key predictions and associated empirical tests. For N. pulcher, we demonstrate that the kin selection and group augmentation hypotheses have received partial support. One of the key predictions of the pay‐to‐stay hypothesis has failed to receive any support despite numerous laboratory and field studies; thus as it stands, the evidence for this hypothesis is weak. There have been no empirical investigations addressing the key predictions of the signals of prestige hypothesis. By outlining the key predictions of the various hypotheses, and highlighting how many of these remain to be tested explicitly, our review can be regarded as a roadmap in which potential paths for future empirical research into the evolution of cooperative breeding are proposed. Overall, we clarify what is currently known about cooperative breeding in N. pulcher, address discrepancies among studies, caution against incorrect inferences that have been drawn over the years and suggest promising avenues for future research in fishes and other taxonomic groups.     

A commitment model of reproductive inhibition in cooperatively breeding groups

Cooperatively breeding groups include individuals that giveup some current reproductive opportunities while remaining ina group. In some cases, these individuals are physiologicallyor morphologically unable to reproduce. Empirical and theoreticalevidence suggest that this inability often does not result fromstress or manipulation by dominants against the interests ofsubordinates. I argue that such reproductive inhibition canrepresent a commitment not to reproduce in exchange for a reductionin costs imposed by dominants. I present a model that allowssubordinates to choose whether to inhibit their own reproduction("self-inhibition") and accept no direct reproduction whilein the group or to remain flexible and attempt to take a shareof group productivity. If dominants assess the reproductivestatus of subordinates and punish those that reproduce, thismodel predicts self-inhibition when group members are closelyrelated, opportunities for independent breeding are poor, assessmentof reproductive status and eviction are costly, and the chanceof being detected when cheating is high. However, dominantsare less likely to assess the reproductive status of subordinatesthat are closely related, resulting in a narrow window of relatednessin which self-inhibition is favored. Counterintuitively, thiswindow is wider when flexible subordinates would be able totake a large share of group production. Although the model assumesthat dominants are able to reliably detect commitment, it isgenerally robust against mistakes in the form of dominants failingto assess uncommitted subordinates, or even low frequenciesof deception by flexible subordinates.     

Bayesian parentage analysis reliably controls the number of false assignments in natural populations

Parentage analysis in natural populations is a powerful tool for addressing a wide range of ecological and evolutionary questions. However, identifying parent–offspring pairs in samples collected from natural populations is often more challenging than simply resolving the Mendelian pattern of shared alleles. For example, large numbers of pairwise comparisons and limited numbers of genetic markers can contribute to incorrect assignments, whereby unrelated individuals are falsely identified as parent–offspring pairs. Determining which parentage methods are the least susceptible to making false assignments is an important challenge facing molecular ecologists. In a recent paper, Harrison et al. (2013a) address this challenge by comparing three commonly used parentage methods, including a Bayesian approach, in order to explore the effects of varied proportions of sampled parents on the accuracy of parentage assignments. Unfortunately, Harrison et al. made a simple error in using the Bayesian approach, which led them to incorrectly conclude that this method could not control the rate of false assignment. Here, I briefly outline the basic principles behind the Bayesian approach, identify the error made by Harrison et al., and provide detailed guidelines as to how the method should be correctly applied. Furthermore, using the exact data from Harrison et al., I show that the Bayesian approach actually provides greater control over the number of false assignments than either of the other tested methods. Lastly, I conclude with a brief introduction to solomon , a recently updated version of the Bayesian approach that can account for genotyping error, missing data and false matching.     

Assessment of microsatellite and SNP markers for parentage assignment in ex situ African Penguin (Spheniscus demersus) populations

Captive management of ex situ populations of endangered species is traditionally based on pedigree information derived from studbook data. However, molecular methods could provide a powerful set of complementary tools to verify studbook records and also contribute to improving the understanding of the genetic status of captive populations. Here, we compare the utility of single nucleotide polymorphisms (SNPs) and microsatellites (MS) and two analytical methods for assigning parentage in ten families of captive African penguins held in South African facilities. We found that SNPs performed better than microsatellites under both analytical frameworks, but a combination of all markers was most informative. A subset of combined SNP (n = 14) and MS loci (n = 10) provided robust assessments of parentage. Captive or supportive breeding programs will play an important role in future African penguin conservation efforts as a source of individuals for reintroduction. Cooperation among these captive facilities is essential to facilitate this process and improve management. This study provided us with a useful set of SNP and MS markers for parentage and relatedness testing among these captive populations. Further assessment of the utility of these markers over multiple (>3) generations and the incorporation of a larger variety of relationships among individuals (e.g., half‐siblings or cousins) is strongly suggested.