Prediction and estimation of effective population size

Abstract

Effective population size (N e ) 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 N e for future research.Heredity ( INTRODUCTIONThe concept of effective population size, introduced by Sewall Wright (1931, 1933), is central to plant and animal breeding (Falconer and Mackay, 1996), conservation genetics (Frankham et al., 2010;Allendorf et al., 2013) and molecular variation and evolution (Charlesworth and Charlesworth, 2010), as it quantifies the magnitude of genetic drift and inbreeding in real-world populations. A substantial number of extensions to the basic theory and predictions were made since the seminal work of Wright, with main early developments by James Crow and Motoo Kimura (Kimura and Crow, 1963a;Crow and Kimura, 1970) and later by a list of contributors. Several review papers (Crow and Denniston, 1988;Caballero, 1994;Wang and Caballero, 1999;Nomura, 2005a) and population genetic books (Fisher, 1965;Wright, 1969;Ewens, 1979;Nagylaki, 1992) have summarised the existing theory in predicting the effective size of a population at different spatial and timescales under various inheritance modes and demographies. Comparatively, methodological developments (reviewed by Schwartz et al., 1999;Beaumont, 2003a;Wang, 2005;Palstra and Ruzzante, 2008;Luikart et al., 2010;Gilbert and Whitlock, 2015) in estimating the effective size of natural populations from genetic data lag behind but are accelerating in the past decade, thanks to the rapid developments of molecular biology.The classical developments of effective population size theory are based on the rate of change in gene frequency variance (genetic drift) or the rate of inbreeding. The effective population size is defined in reference to the Wright-Fisher idealised population, that is, a hypothetical population with very simplifying characteristics where genetic drift is the only factor in operation, and the dynamics of allelic and genotypic frequencies across generations merely depend on the population census (N) size. The effective size of a real population is then defined as the size of an idealised population, which would give rise to the rate of inbreeding and the rate of change in variance of gene frequencies actually observed in the population under consideration,

Prelude to a panzootic: Gene flow and immunogenetic variation in northern little brown myotis vulnerable to bat white-nose syndrome

“…In contrast, NeEstimator V2 (Do et al 2014) does not assume that all samples are from a single cohort, and has been previously used to estimate N e in bats (Plecotus auritus; Razgour et al 2014). We, therefore, chose this method as the most appropriate for our data set, recognizing that methods for estimating N e each have their own strengths and weaknesses (Wang et al 2016;Waples 2016). …”

Spatial differences in genetic diversity and northward migration suggest genetic erosion along the boreal caribou southern range limit and continued range retraction

“…The mitochondrial DNA study by Klütsch et al (2012) found that while both Manitoba and Ontario animals expanded from (Wang, Santiago, & Caballero, 2016). The mitochondrial DNA study by Klütsch et al (2012) found that while both Manitoba and Ontario animals expanded from (Wang, Santiago, & Caballero, 2016).…”

Historical Processes and Contemporary Anthropogenic Activities Influence Genetic Population Dynamics of Nassau Grouper (Epinephelus striatus) within The Bahamas

“…Although estimates of genetic diversity were mostly high and fairly uniform, temporal analyses of changes in N e show that contemporary populations have dramatically reduced effective population sizes compared to historic levels. Because N e accuracy is affected by sample size, marker numbers, and marker polymorphism Waples et al, 2014;Wang et al, 2016), performing cohort analysis, increasing the numbers of polymorphic molecular markers, sample size, and spatial coverage throughout the archipelago would allow for enhanced assessments of the genetic population dynamics of Nassau grouper. The application of more sophisticated molecular techniques than microsatellites, for example, RAD-sequencing, which can identify thousands of single nucleotide polymorphisms (SNPs), could help to resolve potential fine-scale intraspecific genetic structure (e.g., Larson et al, 2013).…”