Estimation of multiple male mating frequency using paternity skew: An example from a grey‐sided vole (Myodes rufocanus) population

Multiple male mating (MMM) causes sperm competition, which may play an important role in the evolution of reproductive traits. The frequency of multiple paternity (MP), where multiple males sire offspring within a single litter, has been used as an index of MMM frequency. However, MP frequency is necessarily lower than MMM frequency. The magnitude of the difference between MMM and MP frequency depends on litter size (LS) and fertilization probability skew (FPS), and this difference may be meaningfully large in animals with small LSs. In this study, we propose a method to estimate MMM frequency using an individual‐based model with three variables (MP frequency, LS and FPS). We incorporated observed paternity skew data to infer a possible range of FPS that cannot be measured in free‐living populations and tested the validity of our method using a data set from a grey‐sided vole (Myodes rufocanus) population and from hypothetical populations. MP was found in 50 out of 215 litters (23.3%) in the grey‐sided vole population, while MMM frequency was estimated in 67 of 215 litters (31.2%), with a certainty range of 59–88 (27.4%–40.9%). The point estimation of MMM frequency was realized, and the certainty range was limited within the practical range. The use of observed paternity skew was very effective at narrowing the certainty range of the estimate. Our method could contribute to a deeper understanding of the ecology of MMM in free‐living populations.     

Assessing probability of paternity and the product rule in DNA systems

The genetic resolution of paternity disputes begins with an intricate detection of inherited traits and finishes with a statistical inference (the probability of paternity,W). Notwithstanding some initial fanfare, statistical inference is a necessary component of DNA-based paternity tests because band patterns may be rare but not yet unique, and even rare events in a vacuum are meaningless. The genetic match must be combined with other evidence for relevancy, thus a Bayesian approach is preferred when computingW. This paper reviews the standard model used to computeW and discusses the model's various properties and assumptions. The standard model is extended to include DNA systems in which alleles are operationally continuous due to measurement error. This extension avoids problems associated with matched/non-matched binned decisions. After outlining the model assumptions for a single DNA system, particular attention is given to the product rule-the procedure of multiplying intermediate probabilities across genetic loci to form a combinedW. An empirical alternative to the product rule is also assessed and correlated with standard procedures.Editor's commentsThe authors present a carefully reasoned account of Bayesian inference in the paternity context. Their presentation of an alternative to the product rule for Paternity Index values offers a means of avoiding objections to the rule.     

Establishment of paternity testing system using microsatellite markers in Chinese Holstein

To estimate the efficiency of microsatellite markers in paternity testing among Chinese Holstein, 30 microsatellite loci were used to differentiate 330 Chinese Holstein genotypes, according to the calculation of the allele frequency, number of alleles, effective number of alleles, genetic heterozygosity, polymorphic information content (PIC), and the exclusion probability in this cattle population. The results demonstrated that the exclusion probability ranged from 0.620 in locus BM1818 to 0.265 in locus INRA005 with the average of 0.472 and 11 microsatellite markers exceeding 0.5. The combined exclusion probability of nine microsatellite markers was over 0.99. The result showed that paternity testing of Chinese Holstein was basically resolved using the nine microsatellite markers selected.     

Variation in social organization influences the opportunity for sexual selection in a social lizard

Social monogamy has traditionally been suggested to be maintained because of weak sexual selection on male partner acquisition. However, the ubiquitous incidence of extra-pair paternity suggests that sexual selection can be strong in monogamous systems, although studies partitioning variance in male reproductive success have come to mixed conclusions. Here, we use detailed field data to examine variance in male reproductive success and its implications for the maintenance of sociality in a population of the socially monogamous lizard Egernia whitii. We show that both within-pair and, to a lesser extent, extra-pair partner acquisition contribute to the variance in male reproductive success, resulting in considerable opportunity for sexual selection. Despite this, levels of multiple mating are lower in Egernia compared to other reptiles, suggesting that male partner acquisition is constrained. We suggest that this constraint may be a result of strong territoriality combined with sexual conflict over multiple mating generated by costs of extra-pair paternity to females as a result of facultative male care. This has the potential to limit sexual selection by reducing variance in male reproductive success and therefore contribute to the maintenance of complex social organization.     

Extra‐Pair Paternity Declines with Female Age and Wing Length in the Pied Flycatcher

Despite many studies of how male characteristics affect paternity in predominantly monogamous birds, relatively little attention has been given to the traits of females that may influence extra‐pair paternity (EPP). However, the occurrence of EPP may be the result of behavioural interactions in which both male and female traits are important for determining the outcome. If EPP is driven mainly by female choice of extra‐pair sires, older, more experienced or larger females would be better able to evade mate guarding tactics and more capable of selecting extra‐pair mates and resisting unwanted suitors. This would be especially noticeable in females paired with unattractive mates. On the other hand, if EPP is driven mainly by male pursuit, we should expect that young, inexperienced or small females would be more exposed to coercive male approaches independently of social mate traits. In a study of an Iberian population of the pied flycatcher Ficedula hypoleuca, we found that EPP affected 38% of the broods and 17% of the nestlings. These values are relatively high, allowing a relatively large number of affected within‐pair mates to be included. We found that EPP is related to both female and male traits although not to any interaction between male and female traits. EPP was higher at nests tended by both younger and short‐winged females and by browner males. Older females may be more experienced and dominant while long‐winged females may be faster fliers, these traits enabling them to avoid extra‐pair copulations, while brown males are less aggressive towards male intruders. In our study population, EPP appears to be caused by male pursuit, which in some cases may overwhelm female attempts to avoid extra‐pair copulations and their social partner's ability to prevent them.     

Estimations of the efficacy and reliability of paternity assignments from DNA microsatellite analysis of multiple-sire matings

It is important for bovine DNA testing laboratories to provide the cattle industry with accurate estimates of the efficacy and reliability of DNA tests offered so that end users of this technology can adequately assess the cost-benefits of testing. To address these issues for bovine paternity testing, paternity exclusion probability estimates were obtained from breed panel data and were predictive of the efficacy of the DNA tests used in 39 multiple-sire mating groups, involving 5960 calves and 505 bulls. Paternity testing of these mating groups has demonstrated that the majority involve a variable proportion of unknown sires and this impacts on the reliability of sire allocation. Mathematical models based on binomial or beta-binomial probability distributions were used to estimate the reliability of single-sire allocations from multiple-sire matings involving unknown sires. Reliability of 98-99% is achieved when the exclusion probability is 0.99 or greater, after allowing for up to 20% unknown sires. When the exclusion probability drops below 0.90 and there are 20% unknown sires, the reliability is poor, bringing into question the benefits of testing. This highlights the need for DNA testing laboratories to offer paternity tests with an exclusion power of at least 99%.     

Estimation of nonpaternity in the Mexican population of Nuevo Leon: A validation study with blood group markers

A method for estimating the general rate of nonpaternity in a population was validated using phenotype data on seven blood groups (A₁A₂BO, MNSs, Rh, Duffy, Lutheran, Kidd, and P) on 396 mother, child, and legal father trios from Nuevo León, Mexico. In all, 32 legal fathers were excluded as the possible father based on genetic exclusions at one or more loci (combined average exclusion probability of 0.694 for specific mother-child phenotype pairs). The maximum likelihood estimate of the general nonpaternity rate in the population was 0.118 ± 0.020. The nonpaternity rates in Nuevo León were also seen to be inversely related with the socioeconomic status of the families, i.e., the highest in the low and the lowest in the high socioeconomic class. We further argue that with the moderately low (69.4%) power of exclusion for these seven blood group systems, the traditional critical values of paternity index (PI ≥ 19) were not good indicators of true paternity, since a considerable fraction (307/364) of nonexcluded legal fathers had a paternity index below 19 based on the seven markers. Implications of these results in the context of genetic-epidemiological studies as well as for detection of true fathers for child-support adjudications are discussed, implying the need to employ a battery of genetic markers (possibly DNA-based tests) that yield a higher power of exclusion. We conclude that even though DNA markers are more informative, the probabilistic approach developed here would still be needed to estimate the true rate of nonpaternity in a population or to evaluate the precision of detecting true fathers. Am J Phys Anthropol 109:281–293, 1999. © 1999 Wiley-Liss, Inc.     

Multiple Paternity in Norway Lobster (<Emphasis Type="Italic">Nephrops norvegicus</Emphasis> L.) Assessed with Microsatellite Markers

We investigated genetic diversity and the mating system of the Norway lobster (Nephrops norvegicus) in a wild population off the Portuguese coast. Approximately 100 individuals were screened for 2 microsatellite loci. For 11 ovigerous lobsters both the female and a sample of her offspring (24 eggs) were genotyped. High genetic diversity was observed for the 2 markers in the population. Paternity within broods was analyzed by comparing multilocus genotypes of each egg with the corresponding mother, and the male parent contribution was then deduced. Multiple paternity was observed in 6 of the 11 broods studied. In those cases, 2 to 3 male parents were likely to have contributed to the fertilization of the eggs. When multiple paternity was involved, the comparative reproductive success of the male parents was quite even. This is the first report of multiple paternity in the Norway lobster. Comparisons with other taxa are presented, and consequences of multiple paternity are discussed.     

Development of microsatellite markers for parentage analysis in the great tinamou (Tinamus major)

Eighteen microsatellite loci were isolated from great tinamous (Tinamus major), which are large terrestrial birds found in the Neotropics. These are the first primers developed for the Order Tinamiformes. Paternity analyses are possible because the levels of heterozygosity are sufficiently high (0.29-0.90).     

Isolation of highly polymorphic autosomal microsatellite loci and a sex‐linked locus from sugarbirds

We describe the isolation of six tetranucleotide microsatellites from the Cape sugarbird (Promerops cafer) using an enrichment protocol. All loci were highly variable with number of alleles ranging from nine to 26 and values of observed heterozygosity ranging from 0.534 to 0.931. All loci were in Hardy–Weinberg equilibrium with the exception of Pro66 and Pro86. Further analysis of Pro86 indicated it was Z‐linked. All loci amplified and were variable in the congeneric Gurneys sugarbird (Promerops gurneyi). These loci will be used in mating system and phylogeographic studies of Cape sugarbirds in South Africa.     

Spatial distribution of nests constrains the strength of sexual selection in a warbler

In socially monogamous species, extra‐pair paternity may increase the strength of intersexual selection by allowing males with preferred phenotypes to monopolize matings. Several studies have found relationships between male signals and extra‐pair mating, but many others fail to explain variation in extra‐pair mating success. A greater appreciation for the role that ecological contingencies play in structuring behavioural processes may help to reconcile contradictory results. We studied extra‐pair mating in a spatial context in the common yellowthroat (Geothlypis trichas), a territorial wood warbler. Over the course of 6 years, we observed 158 breeding attempts by 99 males, resulting in a total of 369 nests and 520 sampled nestlings. The spatial distribution of territories varied greatly, with males having between 0 and 10 close neighbours and between three and 39 neighbouring nestlings close enough to represent extra‐pair siring opportunities. Both within‐pair and extra‐pair reproductive success increased with breeding density, but the opportunity for sexual selection and strength of selection varied with density. Total variance in reproductive success was highest at low density and was mostly explained by variation in within‐pair success. In contrast, at high density, both within‐pair and extra‐pair successes contributed substantially to variance in reproductive success. The relationships between plumage and extra‐pair mating also varied by density; plumage was under strong sexual selection via extra‐pair mating success at high density, but no selection was detected at low density. Thus, ecological factors that structure social interactions can drive patterns of sexual selection by facilitating or constraining the expression of mating preferences.     

Pedigree reconstruction in wild cichlid fish populations

It is common practice to use microsatellites to detect parents and their offspring in wild and captive populations, in order to reconstruct a pedigree. However, correct inference is often constrained by a number of factors, including the absence of demographic data and ignorance regarding the completeness of parental sampling. Here we present a new Bayesian estimator that simultaneously estimates the pedigree and the size of the unsampled population. The method is robust to genotyping error, and can estimate pedigrees in the absence of demographic data. Using a large-scale microsatellite assay in four wild cichlid fish populations of Lake Tanganyika (1000 individuals in total), we assess the performance of the Bayesian estimator against the most popular assignment program, Cervus. We found small but significant pedigrees in each of the tested populations using the Bayesian procedure, but Cervus had very high type I error rates when the size of the unsampled population was assumed to be lower than what it was. The need of pedigree relationships to infer adaptive processes in natural populations places strong constraints on sampling design and identification of multigenerational pedigrees in natural populations.     

The ecological-evolutionary interplay: density-dependent sexual selection in a migratory songbird

Little is understood about how environmental heterogeneity influences the spatial dynamics of sexual selection. Within human-dominated systems, habitat modification creates environmental heterogeneity that could influence the adaptive value of individual phenotypes. Here, we used the gray catbird to examine if the ecological conditions experienced in the suburban matrix (SM) and embedded suburban parks (SP) influence reproductive strategies and the strength of sexual selection. Our results show that these habitats varied in a key ecological factor, breeding density. Moreover, this ecological factor was closely tied to reproductive strategies such that local breeding density predicted the probability that a nest would contain extra-pair offspring. Partitioning reproductive variance showed that while within-pair success was more important in both habitats, extra-pair success increased the opportunity for sexual selection by 39% at higher breeding densities. Body size was a strong predictor of relative reproductive success and was under directional selection in both habitats. Importantly, our results show that the strength of sexual selection did not differ among habitats at the landscape scale but rather that fine-scale variation in an ecological factor, breeding density, influenced sexual selection on male phenotypes. Here, we document density-dependent sexual selection in a migratory bird and hypothesize that coarse-scale environmental heterogeneity, in this case generated by anthropogenic habitat modification, changed the fine-scale ecological conditions that drove the spatial dynamics of sexual selection.     

Isolation and characterization of 17 microsatellite loci for the house finch (Carpodacus mexicanus)

The house finch (Carpodacus mexicanus) has emerged recently as a model species in studies of sexual selection, reproductive physiology, population genetics, and epizootic disease ecology. Here we describe 17 highly polymorphic microsatellite loci for this species. In a sample of 36 individuals, we observed an average of 16 alleles per locus and heterozygosity ranged from 0.61 to 0.97. One locus showed significant deviation from Hardy-Weinberg proportions, but no significant gametic disequilibrium was observed among any of the loci. Amplification by polymerase chain reaction was optimized under similar parameters across loci, thereby facilitating multiplexing and rapid multilocus genotyping.     

Demographic correlates of paternity confidence and pregnancy outcomes among Albuquerque men

We examine the demographic correlates of paternity confidence, or men's assessment of the likelihood that they are the genetic father of a particular child. Evolutionary theory predicts that men will provide less parental investment for putative genetic offspring who are unlikely to be their actual offspring, but confidence of paternity has not been as extensively examined as its importance would merit. Using self-reported data on paternity confidence in 3,360 pregnancies reported by men living in Albuquerque, New Mexico, we find that low paternity confidence is more common among unmarried couples and for unplanned pregnancies. We also find that men are more likely not to state paternity confidence (i.e., they refuse to answer the question) if a pregnancy is unplanned. We additionally examine the pregnancy outcomes associated with confidence of paternity. We find that low paternity confidence pregnancies are significantly more likely to be aborted, and pregnancies for which paternity confidence is unstated are more likely to be aborted or to miscarry. Both abortion and miscarriage are associated with unmarried couples, with unplanned pregnancies, and with couples who have fewer children together.     

Performance of different SNP panels for parentage testing in two East Asian cattle breeds

The International Society for Animal Genetics (ISAG) proposed a panel of single nucleotide polymorphisms (SNPs) for parentage testing in cattle (a core panel of 100 SNPs and an additional list of 100 SNPs). However, markers specific to East Asian taurine cattle breeds were not included, and no information is available as to whether the ISAG panel performs adequately for these breeds. We tested ISAG's core (100 SNP) and full (200 SNP) panels on two East Asian taurine breeds: the Korean Hanwoo and the Japanese Wagyu, the latter from the Australian herd. Even though the power of exclusion was high at 0.99 for both ISAG panels, the core panel performed poorly with 3.01% false‐positive assignments in the Hanwoo population and 3.57% in the Wagyu. The full ISAG panel identified all sire–offspring relations correctly in both populations with 0.02% of relations wrongly excluded in the Hanwoo population. Based on these results, we created and tested two population‐specific marker panels: one for the Wagyu population, which showed no false‐positive assignments with either 100 or 200 SNPs, and a second panel for the Hanwoo, which still had some false‐positive assignments with 100 SNPs but no false positives using 200 SNPs. In conclusion, for parentage assignment in East Asian cattle breeds, only the full ISAG panel is adequate for parentage testing. If fewer markers should be used, it is advisable to use population‐specific markers rather than the ISAG panel.     

Mate guarding and frequent copulation in birds: A meta‐analysis of their relationship to paternity and male phenotype

In many birds, males are presumed to protect their paternity by closely guarding their mate or copulating frequently with her. Both these costly behaviors are assumed to reduce the risk and/or intensity of sperm competition. However, despite many studies on avian extra‐pair paternity, it remains unclear how strongly these behaviors are related to fitness and other key life‐history traits. Here, we conduct meta‐analyses to address two questions. First, are mate guarding and/or frequent copulation positively correlated with a male's share of paternity at his nest? We find a significant positive correlation between both presumed paternity protection behaviors and paternity share. The relationship is, however, weak (r = 0.08–0.23). This is perhaps unsurprising if the risk of partner infidelity, hence the need to protect paternity, varies among males. For example, more attractive males might have less need to protect their paternity. Second, do males with higher indices of so‐called male “quality” (phenotypic measures, usually subjectively defined by researchers as predictors of male attractiveness) exhibit lower levels of paternity protection behavior? We find a negative correlation between male quality and paternity protection. This finding might partly explain the weak relationship between paternity protection and paternity, although we discuss other, nonmutually exclusive possibilities.     

Do marker‐based paternity assignments favour heterozygous and unrelated males?

Genetic marker‐based parentage analyses are widely applied to studies of natural populations in the fields of evolutionary biology, conservation biology and ecology. When the same markers used in a parentage analysis are used together with the inferred parentage in a downstream analysis, such as the analysis of mate choice in terms of heterozygosity or relatedness, a bias may be incurred because a subset of the genotypes are favoured in parentage assignments or non‐exclusions. A previous simulation study shows that exclusion‐based paternity analyses are biased in favour of heterozygous males, and males less related to the mothers than expected under random mating. In this study, I investigated the biases of genetic paternity analyses achieved by both exclusion‐ and likelihood‐based methods, using both analytical and simulation approaches. It is concluded that while both exclusion‐ and likelihood‐based methods can lead to biased paternity assignments or non‐exclusions in favour of a subset of genotypes, the bias is not consistently towards heterozygous males or males apparently less related to mothers. Both the direction and extent of the bias depend heavily on the allele frequency distribution and the number of markers, the methods used for paternity assignments, and the estimators of relatedness. There exist important differences in the patterns of the biases between exclusion‐ and likelihood‐based paternity analysis methods. It is concluded that the markers, except when they are highly informative to yield accurate paternity assignments or exclusions, should be split into two subsets which are used separately in the paternity and downstream analyses.