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Hulse L, Tomsett C, Roser A, Clark L, Meer H, Pyne M, Fenelon JC, Renfree MB, Johnston S. An evaluation of DNA sample source and molecular markers to determine gender in the short-beaked echidna (Tachyglossus aculeatus). Zoo Biol 2024; 43:92-99. [PMID: 37905691 DOI: 10.1002/zoo.21809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 08/16/2023] [Accepted: 10/21/2023] [Indexed: 11/02/2023]
Abstract
The short-beaked echidna is sexually monomorphic such that gender identification without veterinary intervention is challenging. The aim of this study was to evaluate and compare the most optimal noninvasive genetic source by extracting echidna genomic DNA (gDNA) from fecal scats, plucked hair, and quills to perform genetic sex testing using a range of molecular markers. Sex determination of 14 captive short-beaked echidnas was determined by amplifying isolated DNA from noninvasive samples, targeting two Y chromosome (male-specific) genes (mediator complex subunit 26 Y-gametologue [CRSPY] and anti-Müllerian hormone Y-gametologue [AMHY]), in addition to four confirmed sex-specific RADseq markers. Results of noninvasive samples were compared with blood samples and clinical records. Receiver operating characteristic curves were used to assess accuracy of sex determination of markers for each sample type. The gender of the echidnas was successfully identified on 75% of occasions using fecal samples, 90.6% occasions using hair, and 84.6% occasions with quills. Overall, the male-specific RADseq markers accurately identified the sex of echidnas with all sample types for 90% of animals; compared with 81.5% using CRSPY, and 82.0% using AMHY to identify sex. Collection of hair, quills, and feces provides a useful alternative to invasively collected samples, however, the accuracy of results depends on sample type and genetic marker selected. We found gender determination in the short-beaked echidna was most accurate using four male-specific RADseq markers on gDNA isolated from blood and hair. The noninvasive genetic sexing techniques documented here will inform and facilitate husbandry and genetic management of captive echidna populations.
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Affiliation(s)
- Lyndal Hulse
- School of Agriculture and Food Science, The University of Queensland, Gatton, Australia
| | - Caitlin Tomsett
- School of Agriculture and Food Science, The University of Queensland, Gatton, Australia
| | - Alice Roser
- Currumbin Wildlife Sanctuary, Currumbin, Australia
| | - Lauren Clark
- Currumbin Wildlife Sanctuary, Currumbin, Australia
| | - Haley Meer
- Currumbin Wildlife Sanctuary, Currumbin, Australia
| | - Michael Pyne
- Currumbin Wildlife Sanctuary, Currumbin, Australia
| | - Jane C Fenelon
- School of BioSciences, The University of Melbourne, Victoria, Australia
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Victoria, Australia
| | - Stephen Johnston
- School of Agriculture and Food Science, The University of Queensland, Gatton, Australia
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Perry T, West E, Eisenhofer R, Stenhouse A, Wilson I, Laming B, Rismiller P, Shaw M, Grützner F. Characterising the Gut Microbiomes in Wild and Captive Short-Beaked Echidnas Reveals Diet-Associated Changes. Front Microbiol 2022; 13:687115. [PMID: 35847103 PMCID: PMC9279566 DOI: 10.3389/fmicb.2022.687115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/16/2022] [Indexed: 12/23/2022] Open
Abstract
The gut microbiome plays a vital role in health and wellbeing of animals, and an increasing number of studies are investigating microbiome changes in wild and managed populations to improve conservation and welfare. The short-beaked echidna (Tachyglossus aculeatus) is an iconic Australian species, the most widespread native mammal, and commonly held in zoos. Echidnas are cryptic animals, and much is still unknown about many aspects of their biology. Furthermore, some wild echidna populations are under threat, while echidnas held in captivity can have severe gastric health problems. Here, we used citizen science and zoos to collect echidna scats from across Australia to perform the largest gut microbiome study on any native Australian animal. Using 16S rRNA gene metabarcoding of scat samples, we characterised and compared the gut microbiomes of echidnas in wild (n = 159) and managed (n = 44) populations, which were fed four different diets. Wild echidna samples were highly variable, yet commonly dominated by soil and plant-fermenting bacteria, while echidnas in captivity were dominated by gut commensals and plant-fermenting bacteria, suggesting plant matter may play a significant role in echidna diet. This work demonstrates significant differences between zoo held and wild echidnas, as well as managed animals on different diets, revealing that diet is important in shaping the gut microbiomes in echidnas. This first analysis of echidna gut microbiome highlights extensive microbial diversity in wild echidnas and changes in microbiome composition in managed populations. This is a first step towards using microbiome analysis to better understand diet, gastrointestinal biology, and improve management in these iconic animals.
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Affiliation(s)
- Tahlia Perry
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, SA, Australia
| | - Ella West
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Raphael Eisenhofer
- Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, SA, Australia
| | - Alan Stenhouse
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Isabella Wilson
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | | | - Peggy Rismiller
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
- Pelican Lagoon Research and Wildlife Centre, Penneshaw, SA, Australia
| | - Michelle Shaw
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
- Taronga Wildlife Nutrition Centre, Taronga Conservation Society Australia, Mosman, NSW, Australia
| | - Frank Grützner
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, SA, Australia
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Keating SE, Fenelon JC, Pyne M, Pinto BJ, Guzmán-Méndez IA, Johnston SD, Renfree MB, Gamble T. Research Article Genetic sex test for the short-beaked echidna (Tachyglossus aculeatus). CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01258-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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