Abstract
The concept of kinship permeates many domains of fundamental and applied biology ranging from social evolution to conservation science to quantitative and human genetics. Until recently, pedigrees were the gold standard to infer kinship, but the advent of next‐generation sequencing and the availability of dense genetic markers in many species make it a good time to (re)evaluate the usefulness of genetic markers in this context. Using three published data sets where both pedigrees and markers are available, we evaluate two common and a new genetic estimator of kinship. We show discrepancies between pedigree values and marker estimates of kinship and explore via simulations the possible reasons for these. We find these discrepancies are attributable to two main sources: pedigree errors and heterogeneity in the origin of founders. We also show that our new marker‐based kinship estimator has very good statistical properties and behaviour and is particularly well suited for situations where the source population is of small size, as will often be the case in conservation biology, and where high levels of kinship are expected, as is typical in social evolution studies.
Highlights
Kinship, known as coancestry or half‐relatedness, is important to many fields of biology (Csilléry et al, 2006; Speed & Balding, 2015)
The most frequently used estimator varies from field to field: GCTA (Genome‐wide Complex Trait Analysis) (Yang et al, 2010) and Ritland (1996) estimators are commonly used by human geneticists, while Queller‐Goodnight's (Queller & Goodnight, 1989) is common in conservation biology and social evolution (Weir & Goudet, 2017)
Heterogeneity of genetic origin among founders is likely to be common in populationsestablished for conservation, and it seems that much is to be gained by using genetic markers rather than pedigrees in these situations
Summary
Known as coancestry or half‐relatedness, is important to many fields of biology (Csilléry et al, 2006; Speed & Balding, 2015). A common estimation approach (Milligan, 2003; Thompson, 1975) is to use allele frequencies in the current population as surrogates for reference population values, with the justification that “realistic samples will often involve enough individuals that errors in the allele‐frequency distribution will be quite small” (Milligan, 2003). Frentiu et al (2008) compared the use of pedigree‐ and marker‐ based kinship values to estimate quantitative genetic variances and covariances for a set of traits in a wild bird population They describe the advantage of marker‐based methods as avoiding the difficulties of reconstructing pedigrees of wild populations, but they claimed only mixed success with those methods. The aim of this study was threefold: (a) to examine the properties of kinship estimators for real pedigrees of varying size, structure and completeness; (b) to explore, using simulations, the causes underlying different estimator properties; and (c) to evaluate the usefulness of pedigree‐based estimates of kinship
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
