Prediction and Estimation of Effective Population Size

Overview

Journal Heredity (Edinb)

Specialty Genetics

Date 2016 Jun 30

PMID 27353047

Citations 106

Authors

J Wang

E Santiago

A Caballero

Affiliations

Soon will be listed here.

Abstract

Effective population size (Ne) is a key parameter in population genetics. It has important applications in evolutionary biology, conservation genetics and plant and animal breeding, because it measures the rates of genetic drift and inbreeding and affects the efficacy of systematic evolutionary forces, such as mutation, selection and migration. We review the developments in predictive equations and estimation methodologies of effective size. In the prediction part, we focus on the equations for populations with different modes of reproduction, for populations under selection for unlinked or linked loci and for the specific applications to conservation genetics. In the estimation part, we focus on methods developed for estimating the current or recent effective size from molecular marker or sequence data. We discuss some underdeveloped areas in predicting and estimating Ne for future research.

Citing Articles

Rapid Evolution in Action: Environmental Filtering Supports Coral Adaptation to a Hot, Acidic, and Deoxygenated Extreme Habitat.

Leiva C, Torda G, Zhou C, Pan Y, Harris J, Xiang X Glob Chang Biol. 2025; 31(3):e70103.

PMID: 40028829 PMC: 11874183. DOI: 10.1111/gcb.70103.

Application of Genomic Selection in Beef Cattle Disease Prevention.

Kasimanickam R, Ferreira J, Kastelic J, Kasimanickam V Animals (Basel). 2025; 15(2).

PMID: 39858277 PMC: 11759163. DOI: 10.3390/ani15020277.

Spatio-Temporal Changes in Effective Population Size in an Expanding Metapopulation of Eurasian Otters.

Thomas N, Chadwick E, Bruford M, Hailer F Evol Appl. 2025; 18(1):e70067.

PMID: 39830484 PMC: 11742082. DOI: 10.1111/eva.70067.

Parallel genetic adaptation amid a background of changing effective population sizes in divergent yellow perch () populations.

Yin X, Schraidt C, Sparks M, Euclide P, Hoyt T, Ruetz Iii C Proc Biol Sci. 2025; 292(2038):20242339.

PMID: 39809312 PMC: 11732403. DOI: 10.1098/rspb.2024.2339.

Levels and Spatial Patterns of Effective Population Sizes in the Southern Damselfly (): On the Need to Carefully Interpret Single-Point and Temporal Estimations to Set Conservation Guidelines.

Leveque A, Duputie A, Vignon V, Duez F, Gode C, Mazoyer C Evol Appl. 2024; 17(12):e70062.

PMID: 39720624 PMC: 11667679. DOI: 10.1111/eva.70062.

References

Fernandez J, Toro M, Caballero A . Fixed contributions designs vs. minimization of global coancestry to control inbreeding in small populations. Genetics. 2003; 165(2):885-94. PMC: 1462774. DOI: 10.1093/genetics/165.2.885. View

Kamath P, Haroldson M, Luikart G, Paetkau D, Whitman C, van Manen F . Multiple estimates of effective population size for monitoring a long-lived vertebrate: an application to Yellowstone grizzly bears. Mol Ecol. 2015; 24(22):5507-21. DOI: 10.1111/mec.13398. View

Weir B, Hill W . Effect of mating structure on variation in linkage disequilibrium. Genetics. 1980; 95(2):477-88. PMC: 1214241. DOI: 10.1093/genetics/95.2.477. View

Caballero A . Developments in the prediction of effective population size. Heredity (Edinb). 1994; 73 ( Pt 6):657-79. DOI: 10.1038/hdy.1994.174. View

Schwartz M, Luikart G, Waples R . Genetic monitoring as a promising tool for conservation and management. Trends Ecol Evol. 2006; 22(1):25-33. DOI: 10.1016/j.tree.2006.08.009. View

Waples R, Waples R . Inbreeding effective population size and parentage analysis without parents. Mol Ecol Resour. 2011; 11 Suppl 1:162-71. DOI: 10.1111/j.1755-0998.2010.02942.x. View

Hill W . Effective size of populations with overlapping generations. Theor Popul Biol. 1972; 3(3):278-89. DOI: 10.1016/0040-5809(72)90004-4. View

Wang J, Santure A . Parentage and sibship inference from multilocus genotype data under polygamy. Genetics. 2009; 181(4):1579-94. PMC: 2666522. DOI: 10.1534/genetics.108.100214. View

Wray N, Thompson R . Prediction of rates of inbreeding in selected populations. Genet Res. 1990; 55(1):41-54. DOI: 10.1017/s0016672300025180. View

10.

Sanchez L, Bijma P, Woolliams J . Minimizing inbreeding by managing genetic contributions across generations. Genetics. 2003; 164(4):1589-95. PMC: 1462651. DOI: 10.1093/genetics/164.4.1589. View

11.

Wang Y, Pollak E . The effective number of a population that varies cyclically in size. II. Overlapping generations. Math Biosci. 2002; 179(2):161-81. DOI: 10.1016/s0025-5564(02)00106-2. View

12.

Pudovkin A, Zaykin D, Hedgecock D . On the potential for estimating the effective number of breeders from heterozygote-excess in progeny. Genetics. 1996; 144(1):383-7. PMC: 1207510. DOI: 10.1093/genetics/144.1.383. View

13.

Sved J . Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor Popul Biol. 1971; 2(2):125-41. DOI: 10.1016/0040-5809(71)90011-6. View

14.

Nei M, Murata M . Effective population size when fertility is inherited. Genet Res. 1966; 8(2):257-60. DOI: 10.1017/s0016672300010119. View

15.

Charlesworth B . Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation. Nat Rev Genet. 2009; 10(3):195-205. DOI: 10.1038/nrg2526. View

16.

Nomura T, Takahashi J . Effective population size in eusocial Hymenoptera with worker-produced males. Heredity (Edinb). 2012; 109(5):261-8. PMC: 3476667. DOI: 10.1038/hdy.2012.11. View

17.

Laporte V, Cuguen J, Couvet D . Effective population sizes for cytoplasmic and nuclear genes in a gynodioecious species. The role of the sex determination system. Genetics. 2000; 154(1):447-58. PMC: 1460890. DOI: 10.1093/genetics/154.1.447. View

18.

Laval G, SanCristobal M, Chevalet C . Maximum-likelihood and markov chain monte carlo approaches to estimate inbreeding and effective size from allele frequency changes. Genetics. 2003; 164(3):1189-204. PMC: 1462632. DOI: 10.1093/genetics/164.3.1189. View

19.

Pollak E . A new method for estimating the effective population size from allele frequency changes. Genetics. 1983; 104(3):531-48. PMC: 1202093. DOI: 10.1093/genetics/104.3.531. View

20.

Ghai G . Structure of populations under mixed random and sib mating. Theor Appl Genet. 2014; 39(4):179-82. DOI: 10.1007/BF00272526. View