How Well Do Molecular and Pedigree Relatedness Correspond, in Populations with Diverse Mating Systems, and Various Types and Quantities of Molecular and Demographic Data?

Authored by Anna M Kopps, William B Sherwin, Jungkoo Kang, Per J Palsboll

Date Published: 2015

DOI: 10.1534/g3.115.019323

Sponsors: Swiss National Science Foundation (SNSF)

Platforms: MATLAB

Model Documentation: Other Narrative

Model Code URLs: http://datadryad.org/resource/doi:10.5061/dryad.sr61r

Abstract

Kinship analyses are important pillars of ecological and conservation genetic studies with potentially far-reaching implications. There is a need for power analyses that address a range of possible relationships. Nevertheless, such analyses are rarely applied, and studies that use genetic-data-based-kinship inference often ignore the influence of intrinsic population characteristics. We investigated 11 questions regarding the correct classification rate of dyads to relatedness categories (relatedness category assignments; RCA) using an individual-based model with realistic life history parameters. We investigated the effects of the number of genetic markers; marker type (microsatellite, single nucleotide polymorphism SNP, or both); minor allele frequency; typing error; mating system; and the number of overlapping generations under different demographic conditions. We found that (i) an increasing number of genetic markers increased the correct classification rate of the RCA so that up to >80\% first cousins can be correctly assigned; (ii) the minimum number of genetic markers required for assignments with 80 and 95\% correct classifications differed between relatedness categories, mating systems, and the number of overlapping generations; (iii) the correct classification rate was improved by adding additional relatedness categories and age and mitochondrial DNA data; and (iv) a combination of microsatellite and single-nucleotide polymorphism data increased the correct classification rate if <800 SNP loci were available. This study shows how intrinsic population characteristics, such as mating system and the number of overlapping generations, life history traits, and genetic marker characteristics, can influence the correct classification rate of an RCA study. Therefore, species-specific power analyses are essential for empirical studies.
Tags
Simulation Generation Multilocus genotype data Reconstruction Natural-populations Single-nucleotide polymorphisms Parentage analysis Sibship inference Wild populations Genetic-markers