Inference from paternity and sibships accounting for uncertainty in genealogy Journal Article

Author(s): Ellis, Thomas; Field, David L; Barton, Nicholas H
Article Title: Inference from paternity and sibships accounting for uncertainty in genealogy
Affiliation IST Austria
Abstract: Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov-chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time consuming. Here we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically-derived error rates, the method performs as well as the widely-used package Colony, but is faster by two orders of magnitude. Using simulations we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open pollinated arrays of the snapdragon Antirrhinum majus, and find evidence for a high degree of multiple mating. Though we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in non-model systems.
Journal Title: Molecular Ecology Resources
ISSN: 1471-8286
Publisher: Wiley-Blackwell  
Date Published: 2018-01-01
Start Page: Epub ahead of print
Sponsor: This work was partially supported by ERC grant 250152 to NHB.
DOI: 10.1111/1755-0998.12782
Notes: We thank a large number of field volunteers involved in data collection of the A. majus population, and Matthew Couchman and Harald Ringbauer for their help in processing and cleaning these data. We are also grateful to four anonymous reviewers whose comments significantly improved the quality of the manuscript.
Open access: yes (OA journal)