Work

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

Year: 2014

Type: article

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: see text] was a linear (r(2) = 0.98) function of the harmonic mean of Ne and Nb. We provide a quantitative bias correction for raw [Formula: see text] 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).

Source: Genetics

DOI: 10.1534/genetics.114.164822

Authors: Robin S Waples, Tiago Antao, Gordon Luikart

Institutions: NOAA National Marine Fisheries Service, National Oceanic and Atmospheric Administration, NOAA National Marine Fisheries Service Northwest Fisheries Science Center, Liverpool School of Tropical Medicine, University of Montana

Language: English

Topic: Genetic diversity and population structure

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Estimated APC paid: $1,189

Funders: National Science Foundation, National Evolutionary Synthesis Center, Wellcome Trust