High Genetic Diversity Despite the Potential for Stepping-Stone Colonizations in an Invasive Species of Gecko on Moorea, French Polynesia

Invasive species often have reduced genetic diversity, but the opposite can be true if there have been multiple introductions and genetic admixture. Reduced diversity is most likely soon after establishment, in remote locations, when there is lower propagule pressure and with stepping-stone colonizations. The common house gecko (Hemidactylus frenatus) was introduced to Moorea, French Polynesia in the remote eastern Pacific within the last two decades and accordingly is expected to exhibit low diversity. In contrast, we show that H. frenatus on Moorea has exceptionally high genetic diversity, similar to that near the native range in Asia and much higher than reported for other Pacific island reptiles. The high diversity in this recently founded population likely reflects extensive genetic admixture in source population(s) and a life history that promotes retention of diversity. These observations point to the importance of understanding range-wide dynamics of genetic admixture in highly invasive species

Passerine_RawReads

Contains raw read Illumina output for Passerine samples

FinalAssemblies

Contains final assemblies for each sample. These are the outputs of pooling the ABySS assemblies for each sample and performing a local clustering and long-read assembly

Data from: Sequence Capture using PCR-generated Probes (SCPP): a cost-effective method of targeted high-throughput sequencing for non-model organisms

Recent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of non-model organisms. To multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in-solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture using PCR-generated probes (SCPP) protocol requires no specialized equipment, is highly flexible, and significantly reduces experimental costs for projects where a modest scale of genetic data is optimal (25-100 genomic loci). Our alterations enable application of this method across a wider phylogenetic range of taxa and result in higher capture efficiencies and coverage at each locus. Efficient and consistent capture over multiple SCPP experiments and at various phylogenetic distances is demonstrated, extending the utility of this method to both phylogeographic and phylogenomic studies

AbyssAssemblies

Contains the ABySS assembly output for each library. Each file has the following naming convention: LIBRARY_KMER_KMERCOV-contigs.f

Passerines_CleanReads

Contains the cleaned reads for the Passerine samples

Draco_CleanReads

Contains the cleaned reads for the Draco samples

Enyalius_CleanReads

Contains cleaned reads for the Enyalius samples

Passerines_Alignments

Contains alignments for the Passerine samples

References

Contains the references recovered for each locus for each sample