Effects of Overlapping Generations on Linkage Disequilibrium Estimates of Effective Population Size

Waples, R. S., Rodrigues Antao, Tiago and Luikart, G. (2014) 'Effects of Overlapping Generations on Linkage Disequilibrium Estimates of Effective Population Size'. Genetics, Vol 197, Issue 2, pp. 769-780.

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Abstract

Use of single-sample genetic methods to estimate effective population size has skyrocketed in recent years. Although the underlying models assume discrete generations, they are widely applied to age-structured species. We simulated genetic data for 21 iteroparous animal and plant species to evaluate two untested hypotheses regarding performance of the single-sample method based on linkage disequilibrium (LD): (1) estimates based on single-cohort samples reflect the effective number of breeders in one reproductive cycle (Nb), and (2) mixed-age samples reflect the effective size per generation (Ne). We calculated true Ne and Nb, using the model species’ vital rates, and verified these with individual-based simulations. We show that single-cohort samples should be equally influenced by Nb and Ne and confirm this with simulated results: Formula was a linear (r2 = 0.98) function of the harmonic mean of Ne and Nb. We provide a quantitative bias correction for raw Formula based on the ratio Nb/Ne, which can be estimated from two or three simple life history traits. Bias-adjusted estimates were within 5% of true Nb for all 21 study species and proved robust when challenged with new data. Mixed-age adult samples produced downwardly biased estimates in all species, which we attribute to a two-locus Wahlund effect (mixture LD) caused by combining parents from different cohorts in a single sample. Results from this study will facilitate interpretation of rapidly accumulating genetic estimates in terms of both Ne (which influences long-term evolutionary processes) and Nb (which is more important for understanding eco-evolutionary dynamics and mating systems).

Item Type:	Article
Additional Information:	The published article is available at www.genetics.org
Subjects:	QU Biochemistry > Genetics > QU 460 Genomics. Proteomics QU Biochemistry > Genetics > QU 475 Genetic processes QU Biochemistry > Genetics > QU 500 Genetic phenomena
Faculty: Department:	Biological Sciences > Vector Biology Department
Digital Object Identifer (DOI):	https://doi.org/10.1534/genetics.114.164822
Depositing User:	Lynn Roberts-Maloney
Date Deposited:	13 May 2015 08:54
Last Modified:	06 Feb 2018 13:09
URI:	https://archive.lstmed.ac.uk/id/eprint/5140

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