Assignment of paternity groups without access to parental genotypes: multiple mating and developmental plasticity in squid

Abstract

We present a novel approach to investigating sibling relationships and reconstructing parental genotypes from a progeny array. The Bayesian method we have employed is flexible and may be applicable to a variety of situations in addition to the one presented here. While mutation rates and breeding population allele frequencies can be taken into account, the model requires relatively few loci and makes few assumptions. Paternity of 270 veined squid (Loligo forbesi) hatchlings from three egg strings collected from one location was assigned using five microsatellite loci. Paternal and maternal genotypes reconstructed for each of the three strings were identical, strongly indicating that a single female produced the strings that were fertilized by the same four males. The proportion of eggs fertilized was not equal between males in all three strings, with male 1 siring most offspring (up to 68% in string 1), through to male 4 siring the least (as low as 2.4% in string 1). Although temperature had a profound effect on incubation time, paternity did not affect this trait at 12 degrees C or 8 degrees C.

Joint analysis of spatial genetic structure and inbreeding in a managed population of Scots pine

“…Paternal genotypes were reconstructed using the Bayesian program Parentage 1.0 (Emery et al, 2001). We used two chains and the Metropolis-coupled MCMC option.…”

Parentage and sibship exclusions: higher statistical power with more family members

“…Some of the offspring sampled from a mother may be full siblings fathered by the same male, and their genotypes can be used jointly to infer the paternity more accurately. Although the full-and HS relationships among the offspring from a mother are usually unknown, they can be identified and utilized to infer their paternity by some recently developed statistical methods (Emery et al, 2001;Sieberts et al, 2002). In such cases, therefore, parentage exclusion probabilities calculated using previous equations assuming a single offspring underestimate the statistical power of parentage analyses and undervalue the amount of information of markers.…”

“…The probability that at least one copy of each parental allele is represented in a set n offspring is 1À2 1Àn , and the potential of the parental genotype being fully inferable increases rapidly with n. Therefore, genotyping multiple offspring increases parentage exclusion probability for any given marker system. Some statistical methods have been developed to use the genotypes of multiple offspring in inferring their common parentage (Emery et al, 2001;Jones, 2001;Sieberts et al, 2002). Calculating P E for multiple offspring helps in determining more accurately the power of a parentage analysis, in screening markers by their informativeness, and in deciding on the appropriate numbers of offspring and markers to be genotyped in designing a parentage assignment experiment.…”

Recent developments in genetic data analysis: what can they tell us about human demographic history?

“…An example of this use is the moment-based method of Vitalis and Couvet (2001), which allows for separate identification of effective population size and immigration rate into populations. Related developments, possibly of less use in human population genetics but of great utility elsewhere, are methods that use multilocus information to infer the number of sibships in a sample ) and the number of parents in a sample (Emery et al, 2001). …”