Effects of Overlapping Generations on Linkage Disequilibrium Estimates of Effective Population Size. Issue 2 (1st June 2014)

• Record Type: Journal Article
• Authors: Waples, Robin S; Antao, Tiago; Luikart, Gordon
• Is Part Of: Genetics. Volume 197:Issue 2(2014)
• Page Start: 769
• Page End: 780
• Publication Date: 2014-06-01
• Subjects: age structure -- life history -- iteroparity -- ldne -- computer simulations -- AgeNe -- effective number of breeders; Genetics -- Periodicals; 576.5
• DOI: 10.1534/genetics.114.164822
• Languages: English
• ISSNs: 0016-6731

Abstract

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 ( N b ), and (2) mixed-age samples reflect the effective size per generation ( N e ). We calculated true N e and N b, using the model species' vital rates, and verified these with individual-based simulations. We show that single-cohort samples should be equally influenced by N b and N e and confirm this with simulated results: N ^ b was a linear ( r 2 = 0.98) function of the harmonic mean of N e and N b . We provide a quantitative bias correction for raw N ^ b based on the ratio N b / N e, which can be estimated from two or three simple life history traits. Bias-adjusted estimates were within 5% of true N b 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 N e (which influences long-term evolutionary processes) and N b (which is more important for understanding eco-evolutionary dynamics and mating systems).