Evidence for an extreme founding effect in a highly successful invasive species: data and R code

The adaptive potential of invasive species is  thought to decrease during founding events due to reduced genetic diversity, limiting the new population’s ability to colonize novel habitats. Barbary ground squirrels (Atlantoxerus getulus) were purportedly introduced as a single breeding pair to the island of Fuerteventura but have expanded to over a million individuals spread across the island in just over 50 years. We estimated the number of founders and measured the level of genetic diversity in this population using the mitochondrial displacement loop and microsatellite markers. Island samples (n = 19) showed no variation in the d-loop, suggesting a single founding female, while Moroccan samples (n = 6) each had unique mitochondrial haplotypes. The microsatellite data of the island population (n = 256 individuals) revealed a small effective population size, low levels of heterozygosity, and high levels of inbreeding, supporting a founding population size of two to three individuals. Our results suggest that A. getulus has undergone an intense genetic bottleneck during their colonization of the island. They are one of the few species where introduction effort does not explain invasion success, although further investigation may explain how they have avoided the worst expected effects following an extreme genetic bottleneck.

Methods
(b) Genetic analysis – mitochondrial DNA

We extracted DNA from 85 samples using the E.Z.N.A.® Tissue DNA Kit (Omega Bio-tek, Norcross, GA), from which 45 were successfully amplified and sequenced (34 island, 11 mainland). We included 25 (19 island, six mainland) complete displacement loop sequences in our mtDNA analysis. We used four primers to target the d-loop (S. I. Table 3). We aligned d-loop sequences using the automatic ClustalW parameters in MEGA7 [53]. Samples with missing or ambiguous nucleotide data were removed from the analysis, and d-loop sequences were trimmed to a uniform length using the most closely related reference sequence available (Spermophilus dauricus, GenBank NC_027283.1).

(c) Genetic analysis – nuclear DNA

We isolated the genomic DNA of 256 individuals using Chelex beads (Bio-Rad) [54].Two microsatellite primers were previously designed for Cape ground squirrels (Xerus inauris; Xin09 and Xin10) [55] and we newly developed nine primers, which we labelled with fluorescent dyes and pooled according to annealing temperatures [51]. We examined nuclear DNA using GeneMarker (SoftGenetics, State College, PA, USA), which scored the loci semi-automatically. At least two observers scored the alleles in an objective scoring procedure [56]. We conducted tests for null alleles using Micro-Checker [36].