Comparing the performance of analytical techniques for genetic parentage of half-sib progeny arrays

Abstract

The prevalence of female multiple mating in natural populations is important for many questions in mating system evolution. Several statistical techniques use genetic data to estimate the number of fathers that contribute gametes to broods, but they have not been widely compared to assess the magnitude of differences in their performance. With a combination of new data and reanalysis of previously published data, we compared five analytical approaches: (1) allele-counting, (2) parental reconstruction in GERUD, (3) a Bayesian probability model to estimate the frequency of multiple mating (FMM), (4) computer simulations based on population allele frequencies in HAPLOTYPES and (5) Bayesian parental reconstruction in PARENTAGE. The results show that choice of analysis technique can significantly affect estimates of sire number. Estimates from GERUD conformed exactly to results obtained from strict exclusion of potential sires in an experimental context. However, estimates yielded by HAPLOTYPES and PARENTAGE sometimes exceeded the numbers from GERUD by as much as 120 and 55%, respectively. We recommend GERUD over these other approaches for most purposes because of its accuracy and consistency in this analysis. Our novel genetic data set allowed us to investigate the extent and frequency of multiple paternity in a marbled salamander (Ambystoma opacum) population in South Carolina, USA. A. opacum contrasted with other salamander species by having relatively low levels of multiple paternity (only 31-54% compared with 71-96%). Although A. opacum had the lowest level of multiple paternity under all analytical approaches used here, the magnitude of differences among species varied.

Molecular Evidence for High Frequency of Multiple Paternity in a Freshwater Shrimp Species Caridina ensifera

“…Similar results were reported in several other studies on paternity [64], [65]. Although some studies suggested that GERUD outperformed over COLONY [66], [67], and vice versa [65], [68]. We would like to suggest using both software for parentage analysis, as previous studies demonstrated that the relative performances of software for parentage analysis depend on brood size, the true number of sires, the polymorphisms of DNA markers and the distribution of parental contributions between sires [65].…”

“…This analysis was conducted with the help of the GERUD software [38], as the software GERUD has been extensively used for parentage analysis in natural populations [28], [39], [40], [41], [42]. The occurrence of multiple paternity of a brood was unambiguously established by the occurrence of more than two paternal alleles across at least two loci, to allow for the possibility of mutation at one locus.…”

Molecular genetic evidence for polyandry in Ascaris suum

“…Estimates from GERUD conformed exactly to the results obtained from strict exclusion of potential sires in an experimental context. and it was recommended over other approaches for most purposes because of its accuracy and consistency analysis (Croshaw et al 2009). By using this technique, our analysis discovered that two out of three families of mothers had mated with multiple males.…”

“…The frequency of polyandry in natural populations is important in the evolution of mating system (Croshaw et al 2009). Multiple mating by females is known to be widespread across the animal kingdom (Simmons et al 2007).…”

Size does not matter for male Marbled Salamanders (Ambystomaopacum)

“…Males indiscriminately court all salamanders encountered by displaying a standard ritual that culminates in deposition of a spermatophore. Polyandrous mating by females and multiple paternity is common; roughly one-half of egg clutches are sired by more than one male (Croshaw et al 2009). …”