gesp: A computer program for modelling genetic effective population size, inbreeding and divergence in substructured populations.
The genetically effective population size (Ne) is of key importance for quantifying rates of inbreeding and genetic drift and is often used in conservation management to set targets for genetic viability. The concept was developed for single, isolated populations and the mathematical means for analysing the expected Nein complex, subdivided populations have previously not been available. We recently developed such analytical theory and central parts of that work have now been incorporated into a freely available software tool presented here. gesp (Genetic Effective population size, inbreeding and divergence in Substructured Populations) is R-based and designed to model short- and long-term patterns of genetic differentiation and effective population size of subdivided populations. The algorithms performed by gesp allow exact computation of global and local inbreeding and eigenvalue effective population size, predictions of genetic divergence among populations (GST) as well as departures from random mating (FIS, FIT) while varying (i) subpopulation census and effective size, separately or including trend of the global population size, (ii) rate and direction of migration between all pairs of subpopulations, (iii) degree of relatedness and divergence among subpopulations, (iv) ploidy (haploid or diploid) and (v) degree of selfing. Here, we describe gesp and exemplify its use in conservation genetics modelling.
Department of Mathematics, Division of Mathematical Statistics, Stockholm University, Stockholm, Sweden.
Fredrik
F
Olsson
Department of Zoology, Division of Population Genetics, Stockholm University, Stockholm, Sweden.
Linda
L
Laikre
Department of Mathematics, Division of Mathematical Statistics, Stockholm University, Stockholm, Sweden.
Ola
O
Hössjer
Department of Zoology, Division of Population Genetics, Stockholm University, Stockholm, Sweden.
Nils
N
Ryman
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D014644:Genetic Variation; D007178:Inbreeding; D011156:Population Density; D012984:Software
eigenvalue effective size; inbreeding coefficient; inbreeding effective size; kinship coefficient; metapopulation effective size; migration; software; subpopulation differentiation