Northwest Fisheries Science Center

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Document Type: Journal Article
Center: NWFSC
Document ID: 7480
Title: Effects of overlapping generations on linkage disequilibrium estimates of effective population size
Author: Robin S. Waples, Tiago Antao, G. Luikart
Publication Year: 2014
Journal: Genetics
Volume: 197
Issue: 2
Pages: 769-780
Keywords: Effective population size,overlapping generations,age structure,computer simulations,bias

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: Nb^  was a linear (r2 = 0.98) function of the harmonic mean of Ne and Nb.  We provide a quantitative bias correction for raw Nb^  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).

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Notes: Open access
Theme: Recovery and rebuilding of marine and coastal species
Foci: Characterize the population biology of species, and develop and improve methods for predicting the status of populations.
Develop methods to use physiological, biological and behavioral information to predict population-level processes.