Inference from paternity and sibships accounting for uncertainty in genealogy

T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999.

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Journal Article | Published | English
Department
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.
Publishing Year
Date Published
2018-09-01
Journal Title
Molecular Ecology Resources
Acknowledgement
This work was partially supported by ERC grant 250152 to NHB. 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.
Volume
18
Issue
5
Page
988-999
IST-REx-ID

Cite this

Ellis T, Field D, Barton NH. Inference from paternity and sibships accounting for uncertainty in genealogy. Molecular Ecology Resources. 2018;18(5):988-999. doi:10.1111/1755-0998.12782
Ellis, T., Field, D., & Barton, N. H. (2018). Inference from paternity and sibships accounting for uncertainty in genealogy. Molecular Ecology Resources, 18(5), 988–999. https://doi.org/10.1111/1755-0998.12782
Ellis, Thomas, David Field, and Nicholas H Barton. “Inference from Paternity and Sibships Accounting for Uncertainty in Genealogy.” Molecular Ecology Resources 18, no. 5 (2018): 988–99. https://doi.org/10.1111/1755-0998.12782.
T. Ellis, D. Field, and N. H. Barton, “Inference from paternity and sibships accounting for uncertainty in genealogy,” Molecular Ecology Resources, vol. 18, no. 5, pp. 988–999, 2018.
Ellis T, Field D, Barton NH. 2018. Inference from paternity and sibships accounting for uncertainty in genealogy. Molecular Ecology Resources. 18(5), 988–999.
Ellis, Thomas, et al. “Inference from Paternity and Sibships Accounting for Uncertainty in Genealogy.” Molecular Ecology Resources, vol. 18, no. 5, Wiley-Blackwell, 2018, pp. 988–99, doi:10.1111/1755-0998.12782.

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