Delimiting cryptic species within the brown-banded bamboo shark, Chiloscyllium punctatum in the Indo-Australian region with mitochondrial DNA and genome-wide SNP approaches

Abstract

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.

Cryptic diversity within two widespread diadromous freshwater fishes (Teleostei: Galaxiidae)

“…Cryptic diversity has been previously suggested in widespread and vagile taxa—those that are less affected by barriers. This includes both non‐migratory and migratory bird species (Irwin et al., 2011; Lohman et al., 2010), planktonic marine copepods (Halbert et al., 2013), and marine and freshwater bony and cartilaginous fishes (D'Aloia et al., 2017; Fahmi et al., 2021; Neilson & Stepien, 2009). For example, migratory populations of the Wilson's warbler (a bird) exhibit strong genetic differentiation, perhaps reflecting differences in migratory patterns (Irwin et al., 2011).…”

First Evidence of Cryptic Species Diversity and Population Structuring of Selaroides leptolepis in the Tropical Western Pacific

“…For instance, additional collections from Eastern Java, Indonesia corresponded with the widely distributed Asian haplotype-H01. This sampling locality is known to exhibit continuous coral and rocky reef bottoms that extend to the Nusa Tenggara region (Fahmi et al, 2021). The Eastern Indian Ocean and the Timor Sea separate Eastern Java, Indonesia from North Australia, which is the southernmost range of the species in TWP.…”

“…Specimens from Eastern Java grouped with the widespread Asian haplogroup suggested that this lineage might be the originally described S. leptolepis, and the Australian lineage is another putative species. Species complexes were considered recently diverged; therefore, their morphological differentiation is believed to have develop later due to new environment adaptations (Fahmi et al, 2021). A comprehensive and adequate collection on the S. leptolepis full range would also help us understand its global structure and detect the presence of any possible intermediate populations.…”

Reply to Soldo, A.; Lipej, L. Comment on “Balàka et al. Updated Checklist of Chondrichthyan Species in Croatia (Central Mediterranean Sea). Biology 2023, 12, 952”

“…Cryptic shark species are known to have relatively low levels of genetic differentiation [ 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 ], which might be the reason why previous population genetic studies of C. canicula were cautious to suggest a species distinct to S. canicula , although all of them found strong genetic differentiation [ 27 , 37 , 38 ]. Future studies might require a whole-genome-wide sequencing approach to cover as much genetic depth as possible [ 34 ].…”