Environmental DNA analysis confirms extant populations of the cryptic Irwin’s turtle within its historical range

Abstract

Background Approximately 50% of freshwater turtles worldwide are currently threatened by habitat loss, rural development and altered stream flows. Paradoxically, reptiles are understudied organisms, with many species lacking basic geographic distribution and abundance data. The iconic Irwin’s turtle, Elseya irwini, belongs to a unique group of Australian endemic freshwater turtles capable of cloacal respiration. Water resource development, increased presence of saltwater crocodiles and its cryptic behaviour, have made sampling for Irwin’s turtle in parts of its range problematic, resulting in no confirmed detections across much of its known range for > 25 years. Here, we used environmental DNA (eDNA) analysis for E. irwini detection along its historical and contemporary distribution in the Burdekin, Bowen and Broken River catchments and tributaries. Five replicate water samples were collected at 37 sites across those three river catchments. Environmental DNA was extracted using a glycogen-aided precipitation method and screened for the presence of E. irwini through an eDNA assay targeting a 127 base pair-long fragment of the NADH dehydrogenase 4 (ND4) mitochondrial gene. Results Elseya irwini eDNA was detected at sites within its historic distribution in the lower Burdekin River, where the species had not been formally recorded for > 25 years, indicating the species still inhabits the lower Burdekin area. We also found higher levels of E. iriwni eDNA within its contemporary distribution in the Bowen and Broken Rivers, matching the prevailing scientific view that these areas host larger populations of E. irwini. Conclusions This study constitutes the first scientific evidence of E. irwini presence in the lower Burdekin since the original type specimens were collected as part of its formal description, shortly after the construction of the Burdekin Falls Dam. From the higher percentage of positive detections in the upper reaches of the Broken River (Urannah Creek), we conclude that this area constitutes the core habitat area for the species. Our field protocol comprises a user-friendly, time-effective sampling method. Finally, due to safety risks associated with traditional turtle sampling methods in the Burdekin River (e.g., estuarine crocodiles) we propose eDNA sampling as the most pragmatic detection method available for E. irwini.

A needle in a haystack: A new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)

“…Because eDNA facilitates the retrieval of high amounts of molecular data at species level with minimal effort, it represents an ideal approach to these applications, as well as to increase the existing knowledge of the ecology or distribution of species. These practices are much more common in plants and animals, and bring along many applications, for instance to invasive species monitoring (Ficetola et al, 2008), food regime studies (Roffler et al, 2021) and even to the rediscovery of critically endangered species (Turunen et al, 2021; Villacorta‐Rath et al, 2022). The diversity of these applications suggests the immense potential that lies in the application of species level metabarcoding to protists.…”

A needle in a haystack: a new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)

“…Because eDNA facilitates the collection of high amounts of species molecular data with minimal effort, it represents an ideal approach to these applications, as well as to increase the existing knowledge of the ecology or distribution of species. These practices are much more common in plants and animals, and bring along many applications, for instance to invasive species monitoring (Ficetola et al, 2008), food regime studies (Roffler et al, 2021) and even to the rediscovery of critically endangered species (Turunen et al, 2021; Villacorta-Rath et al, 2022). The diversity of these applications suggests the immense potential that lies in the application of species level metabarcoding to new protist groups.…”

Opportunities for research and conservation of freshwater turtles in Australia

“…These knowledge gaps are true even for species for which there are substantial publication outputs (e.g., Emydura macquarii ). With the advent of new technologies, such as camera trapping (McKnight et al, 2023), tissue stable isotope analysis (Micheli‐Campbell et al, 2017), passive acoustic tracking (Micheli‐Campbell et al, 2017; Van Dyke et al, This issue), environmental DNA (Villacorta‐Rath et al, 2022), and underwater baited video cameras (Coleman, This issue), we are beginning to unravel the mysteries of turtle behaviour. In addition, the reduction in cost and increase in the capability of genetic techniques have enabled better resolution of phylogenetic relationships among and within turtle species, providing clarity around systematics and nomenclature (Georges et al, 1999, 2018; Thomson et al, 2021).…”