DOI: 10.5061/dryad.wh70rxwn3
title: Delimiting cryptic species within the brown-banded bamboo shark, Chiloscyllium punctatum in the Indo-Australian region with mitochondrial DNA and genome-wide SNP approaches

description: Background Delimiting cryptic species in elasmobranchs is a major
 challenge in modern taxonomy due the lack of available phenotypic
 features. Employing stand-alone genetics in splitting a cryptic species
 may prove problematic for further studies and for implementing
 conservation management. In this study, we examined mitochondrial DNA and
 genome-wide nuclear single nucleotide polymorphisms (SNPs) in the
 brown-banded bambooshark, Chiloscyllium punctatum to evaluate potential
 cryptic species and the species-population boundary in the group. Results
 Both mtDNA and SNP analyses showed potential delimitation within C.
 punctatum from the Indo-Australian region and consisted of four
 operational taxonomic units (OTUs), i.e. those from Indo-Malay region, the
 west coast of Sumatra, Lesser Sunda region, and the Australian region.
 Each OTU can be interpreted differently depending on available supporting
 information, either based on biological, ecological or geographical data.
 We found that SNP data provided more robust results than mtDNA data in
 determining the boundary between population and cryptic species.
 Conclusion To split a cryptic species complex and erect new species based
 purely on the results of genetic analyses is not recommended. The
 designation of new species needs supportive diagnostic morphological
 characters that allow for species recognition, as an inability to
 recognise individuals in the field creates difficulties for future
 research, management for conservation and fisheries purposes.
  Moreover, we recommend that future studies use a comprehensive
 sampling regime that encompasses the full range of a species complex. This
 approach would increase the likelihood of identification of operational
 taxonomic units rather than resulting in an incorrect designation of new
 species.
description: Tissue samples from <i>Chiloscyllium punctatum</i>
 were obtained from 17 localities within the Indo-Australian region. 
 Samples from Thailand, Malaysia, and Indonesia (Sumatra, Java, Kalimantan,
 South Sulawesi, and Lombok) were sourced from local fish markets. Samples
 were from Moreton Bay, eastern Australia, samples from Papua New Guinea
 and Western Australia were provided by the national fish collection
 (CSIRO, Hobart). A total of 34 tissue samples collected
 from 12 locations during 2017 was analysed with the mtDNA gene marker NADH
 dehydrogenase subunit 2 (NADH2). Samples were amplified using MyTaq DNA
 polymerase (Bioline Reagents, London) and primers from Naylor et al.(18)
 with a modified forward primer: ILEM Chilo2 (5'- AAG GAT CAC TTT GAT
 AGA GT- 3'), and modified reverse primer: ASNM Chilo (5'- AAC
 ACT TAG CTG TTA ACT AA- 3'). A total of 148
 extracted DNA samples (50–150 ng.µl<sup>-1</sup>) were
 genotyped with the DArT-seq approach by Diversity Arrays Technologies
 (DArT Pty Ltd, Canberra, Australia). The SNP data were filtered using the
 R package 'dartR'. Loci with 100% repeatability (repAvg=1.0) and
 without missing values (call rate=1.0) were retained for subsequent
 analysis.  Monomorphic loci and secondary SNPs within loci were removed,
 the latter to reduce the possibility of linked fragments. SNP loci with
 ≤1% minor allele frequency were removed.
description: The dataset
 contains: The sequence of the
 mtDNA ND2 marker of <i>Chiloscyllium punctatum</i> from 34
 samples were aligned with 3 reference sequences from genebank (GN2590,
 GN4616, GN4446) and exported to nexus format using Geneious
 software.   SNP data
 of <i>C. punctatum</i> from DArT were filtered using R package
 ‘dartR’ and converted to nexus file using PGDspider
 software.  Filtered SNP data from DArT (in
 csv. file)