Comparative Analyses of Effective Population Size Within and Among Species: Ranid Frogs as a Case Study

Abstract

A key parameter in the theory and application of population genetics is the effective population size (N e ): the number of breeding individuals in a conceptual, ideal population that would lose genetic diversity at the same rate as the real population being studied (Wright 1931;Charlesworth 2009). How a population responds to evolutionary forces depends on N e , rather than the actual number of individuals in the population (N, the census population size). Although direct estimates of N e can be calculated from demographic data, such data are often prohibitively difficult to obtain (Wang 2005). Given this limitation, and the importance of N e in population and conservation genetics, it is not surprising that considerable effort has been put into developing methods of using molecular genetic data to obtain indirect estimates of N e .With advances in these methods and with the increasing accessibility of multilocus genotype data, it has recently become practicable to estimate the effective sizes of many populations of the same species (Luikart et al. 2010;Waples and Do, 2010). Such an effort is highly worthwhile for a couple of reasons. First, by gathering estimates from multiple populations, investigators might identify a reasonably narrow range of typical N e values for a species, an "educated guess" for the value of this parameter in any given population. This information could be used to approximate N e in evolutionary modeling of the species. For example, an expected N e could be used as input for simulations of evolutionary processes or as a Bayesian prior in analyses used to infer other population genetic parameters, such as migration rates or selection coefficients. Expected N e values for a species would also be useful in conservation and management, in situations in which an estimate of N e for a population is desired but genetic and demographic data are unavailable. In such cases, it would be helpful to know if populations of the focal species typically have, for example, N e estimates less than 100. Furthermore, when estimates of both N e and N (census size) can be obtained for multiple populations, it may be possible to identify the typical range of N e /N for the species. If so, estimates of N for the species might then be used as proxies for N e , when the former are easier to obtain that the latter.Second, a comparative analysis of N e estimates from multiple populations across more than one species can help generate hypotheses about what particular biological factors influence N e within species. Consistent differences in N e among species might correspond to differences in habitat, dispersal capabilities, or breeding behaviors. Hypotheses generated in a comparative analysis could then be tested in subsequent studies. Similarly, the factors that influence N e within species can also be investigated by evaluating correlations between environmental variables and N e for multiple populations of a species.Despite the fact that such multipopulation, empirical investigations of N e can lead to valuable...

Variable rates of random genetic drift in protected populations of English yew: implications for gene pool conservation

“…On the other hand, low frequency alleles could cause overestimated N e(LD) (although we applied the heuristic correction, as suggested by Waples and Do 2010, see M&M). Interestingly, similar trends were also noted in the recent study of ranid frogs (Phillipsen et al 2011), suggesting that further attention is needed to determine susceptibility of a particular method to an information content of genetic markers.…”

Amphibian molecular ecology and how it has informed conservation

“…A key element of this method is that the true N e need not remain stable across sampling periods, although the harmonic mean N e will be returned in that case (Waples 2005). The effective population size for a population is usually lower than the census population size, with estimates of <100 (and often far less) for many amphibian populations (Phillipsen et al 2011).…”

“…First, effective population sizes are often quite low in amphibians-usually under 100 and frequently closer to 10-and this pattern is heavily influenced by the natural history of many amphibian populations (Schmeller & Meril€ a 2007;Phillipsen et al 2011;Richmond et al 2014). Because this is a 'natural' trait of some amphibian populations, it is important to understand, on a case-by-case basis, whether effective population size has remained constant through time or if it has recently crashed (Beebee & Rowe 2001;Phillipsen et al 2011). Amphibian populations have a varied history of bottlenecking, with strong evidence of recent population bottlenecks for some populations (Schoville et al 2011).…”

Conservation of the endangered Mediterranean tortoise Testudo hermanni hermanni: The contribution of population genetics and historical demography

“…Because reptiles and amphibians are often difficult to count in the wild, direct estimates of the number of breeding individuals are rare (Shaffer et al, 2015). The application of genetic methods can not only help to estimate the effective breeding size of a population, but for several species also offers a valuable alternative that allows the historical patterns of population expansion or decline to be inferred (Funk et al, 1999;Phillipsen et al, 2011;Casas-Marce et al, 2013;Kamath et al, 2015). From a conservation perspective, the identification of demographic bottlenecks is crucial because these lessen the chance of survival of populations that have undergone significant declines (Peery et al, 2012).…”