A new individual‐based spatial approach for identifying genetic discontinuities in natural populations

Abstract

The population concept is central in evolutionary and conservation biology, but identifying the boundaries of natural populations is often challenging. Here, we present a new approach for assessing spatial genetic structure without the a priori assumptions on the locations of populations made by adopting an individual-centred approach. Our method is based on assignment tests applied in a moving window over an extensively sampled study area. For each individual, a spatially explicit probability surface is constructed, showing the estimated probability of finding its multilocus genotype across the landscape, and identifying putative migrants. Population boundaries are localized by estimating the mean slope of these probability surfaces over all individuals to identify areas with genetic discontinuities. The significance of the genetic discontinuities is assessed by permutation tests. This new approach has the potential to reveal cryptic population structure and to improve our ability to understand gene flow dynamics across landscapes. We illustrate our approach by simulations and by analysing two empirical datasets: microsatellite data of Ursus arctos in Scandinavia, and amplified fragment length polymorphism (AFLP) data of Rhododendron ferrugineum in the Alps.

Genetic diversity analysis of Rhododendron aureum Georgi (Ericaceae) located on Changbai Mountain using ISSR and RAPD markers

“…Many naturally distributed populations of Rhododendrons have been collected and their genetic variations studied in recent years (Escaravage et al 1998;Kameyama et al 2001;Wolf et al 2004;Manel et al 2007;Delmas et al 2011;De Keyser et al 2010), but there is little information available on the genetic variation of R. aureum. Presently, a few studies have focused on its life history (Kudo 1993;Hirao et al 2006) and chemical composition (Olennikov et al 2010).…”

Re-Evaluating Causal Modeling with Mantel Tests in Landscape Genetics

“…CDPOP is an individual-based, spatially explicit, landscape genetic model that simulates birth, death, mating and dispersal of individuals in complex landscapes as probabilistic functions of movement cost among them. The model represents landscape structure as resistance surfaces and simulates mate selection and dispersal as probabilistic functions of cumulative cost across these resistance surfaces (breeding is simulated with Mendelian inheritance and a k-allele mutation-mutation rate = 0.0005), a commonly used mutation model for microsatellite loci [35,36]. The user specifies the locations and genotypes of the initial population, and the model simulates spatially-explicit population genetic change through time as a function of individual-based movement (mate choice and dispersal), mating, mutation and mortality.…”

Research Article Genetic diversity of arboreal cotton populations of the Brazilian semiarid: a remnant primary gene pool for cotton cultivars.

“…The individual-centred approach proposed by Manel et al (2007), in which there is no need to pre assume the population size based on states boundaries, lead to further investigate the population concept. The geographical diversity distribution was studied using unbiased estimates of gene diversity (Nei, 1978) obtained within a moving window of 200-km radius (Rodriguez et al, 2015) over the sampling area.…”