Pedigree reconstruction in wild cichlid fish populations

Abstract

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.

Estimating offspring production using capture‐mark‐recapture and genetic methods in red squirrels

“…In this case, categorical allocation of mothers using CERVUS is indicated (Jones and Ardren 2003). However, erroneous assignment or nondetection of candidate parents (CPs) will be affected by: (1) the number of microsatellites loci used and their polymorphic information content (e.g., Lemos et al 2006); (2) absence of demographic data and/or ignorance regarding the completeness of parental sampling (e.g., Koch et al 2008); and (3) rate of scoring error in genotype assessment (e.g., Oddou-Muratorio et al 2003). To reduce these types of errors, we combined detailed demographic data with a maximum likelihood estimator that accounted for genotyping error (CERVUS vs 3.0, Kalinowski et al 2007) and with allelic mismatching between offspring and CPs.…”

“…The type of samples obtained from natural populations has great implications for the reconstruction of parentage in studies using a combination of polymorphic molecular markers (DNA microsatellites), parentage analysis methods based on maximum likelihood estimators, and exclusion of individuals as potential parents (Jones and Ardren 2003;Telfer et al 2003;Koch et al 2008). Although the joint combination of these methods greatly increases the correct parentage assignment, the risk of two types of errors remains: false parentage assignment and the nondetection of true parents, in our case mothers (e.g., Oddou-Muratorio et al 2003;Shurtliff et al 2005).…”

Reconstruction of pedigrees in clonal plant populations

“…With (partially) missing age data, to ensure irreducibility of the MCMC sampler, it is necessary to perform swap steps in which the direction of a random arc ( j, k) of the pedigree is reversed (Koch et al, 2008). Note that age data implies the direction of an pedigree arc, so a swap step would always return an invalid pedigree in the case that age data is available.…”

Can Parentage Analysis Facilitate Breeding Activities in Root and Tuber Crops?

“…It requires care for the assurance of sufficiently adequate power. Unlike the conservative technique, full probability models and sibship reconstruction methods of the categorical or fractional assignment build a model of error into likelihood estimates or posterior probabilities [137,138].…”