Historical biogeography and genetic status of the enigmatic pig-nosed turtle (Carettochelys insculpta) within the Australo-Papuan region

This dataset was used to examine the phylogeographic genetic structure of an iconic species, the pignosed turtle Carettochelys insculpta, the last remaining member of a once globally widespread family, now restricted to a region with a dynamic and complex geological and geographical history – the Australo-Papuan region. It comprises aligned sequences of mtDNA data (Nd4 and Control Region) and SNP data used for population genetics and phylogenetic reconstruction., SNP analyses
Skin tissues and extracted DNA were provided to DArT for processing, sequencing and informative SNP marker identification using DArTseqTM (Kilian et al., 2012). DArT performed a genome complexity reduction technique using double digestion of genomic DNA with two restriction endonucleases PstI (5′- CTGCA|G- 3′) and SphI (5′- GCATG|C- 3′), fragment-size selection and next-generation sequencing on an Illumina HiSeq2500 (CA, USA). Sequences were processed using proprietary DArT analytical pipelines (for full details refer to Georges et al. (2018). Initial filtering was based primarily on average and variance of sequencing depth, average allele counts and call rate across samples. Approximately one third of samples were sequenced twice as technical replicates, with scoring consistency identifying high quality SNP markers with low error rates. We applied further quality control filtering using the R package dartR 2.7.2 (Gruber et al., 2018; Mijangos et al., 2022).  These fil..., , # Data from: Historical biogeography and genetic status of the enigmatic pig-nosed turtle (Carettochelys insculpta) within the Australo-Papuan region

[https://doi.org/10.5061/dryad.qrfj6q5pb](https://doi.org/10.5061/dryad.qrfj6q5pb)

This Dryad entry contains the data files and associated R script to prepare the data in a form conducive to analysis, including the analyses presented in the companion review article. They include SNP datasets for the pignosed turtle and aligned mtDNA sequences.

## Description of the data and file structure

**SNP analyses**

The turtle SNP data comprises a matrix of entities (individuals) versus attributes (loci) taking on the states 0 for homozygous reference allele, 2 for homozygous alternate allele and 1 for the heterozygous state. The data are stored in compressed form as an adegenet genlight object with associated locus metadata (e.g. callrate, reproducibility) and individual metadata (e.g. latitude, longitude, population). The SNP scores can be exa...