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Genetics. 2014 Jun;197(2):769-80. doi: 10.1534/genetics.114.164822. Epub 2014 Apr 8.

Effects of overlapping generations on linkage disequilibrium estimates of effective population size.

Author information

1
Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington 98112 robin.waples@noaa.gov.
2
Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, L3 5QA United Kingdom.
3
Flathead Lake Biological Station, Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Polson, Montana 59860.

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).

KEYWORDS:

AgeNe; age structure; computer simulations; effective number of breeders; iteroparity; ldne; life history

PMID:
24717176
PMCID:
PMC4063931
DOI:
10.1534/genetics.114.164822
[Indexed for MEDLINE]
Free PMC Article

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