Matthew J. Heydenrych

University of Western Australia

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Michael Bunce

Curtin University

Nicole E. White

Curtin University

Simon Jarman

University of Western Australia

Zoe T. Richards

Western Australian Museum

Katrina M. West

Australian National Fish Collection

Morten E. Allentoft

University of Copenhagen

Georgia Nester

Curtin University

Paul Nevill

Curtin University

Joshua P. Newton

Curtin University

Benjamin Mayne

Commonwealth Scientific and Industrial Research Organisation

Cooperative Institutions

Curtin University

University of Western Australia

Commonwealth Scientific and Industrial Research Organisation

Western Australian Marine Science Institution

Murdoch University

James Cook University

Australian Institute of Marine Science

University of Copenhagen

Bentley (Canada)

John Wiley & Sons (United States)

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Development of a 16S metabarcoding assay for the environmental DNA (eDNA) detection of aquatic reptiles across northern Australia

Marine and Freshwater Research (2021)

Katrina M. West Matthew J. Heydenrych Rose Lines Anton D. Tucker Sabrina Fossette

A severe lack of distribution data for aquatic reptiles in northern Australia leaves many taxa vulnerable to extirpation and extinction. Environmental DNA (eDNA) technologies offer sensitive and non-invasive genetic alternatives to trapping and visual surveys and are increasingly employed for the detection of aquatic and semi-aquatic reptiles. However, these eDNA approaches have largely applied species-specific primers that do not provide a cost-effective avenue for the simultaneous detection of multiple reptilian taxa. Here, we present a mitochondrial 16S rRNA metabarcoding assay for the broad detection of aquatic and semi-aquatic reptile species. This assay is tested on water samples collected at multiple sampling sites at two tropical locations, including 12 marine and estuarine sites in Roebuck Bay, Western Australia, and four estuarine sites in Cooktown, Queensland, Australia. In total, nine reptile taxa were detected from 10 of the 16 sampled sites, including marine and freshwater turtles, aquatic, semi-aquatic and terrestrial snakes, and terrestrial skinks. However, inconsistencies in the detection of previously observed aquatic reptiles at our sampled sites, such as saltwater crocodile and sea snakes, indicated that further research is required to assess the reliability, strengths and limitations of eDNA methods for aquatic reptile detection before it can be integrated as a broad-scale bioassessment tool.

Environmental DNA

DNA Barcoding

10.1071/mf20288

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Citations (17)

Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution

The Science of The Total Environment (2023)

Miwa Takahashi Mattia Saccò Joshua H. Kestel Georgia Nester Matthew A. Campbell

Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly 'distillation' of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.

Environmental DNA

10.1016/j.scitotenv.2023.162322

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Citations (132)

Monitoring the birds and the bees: Environmental DNA metabarcoding of flowers detects plant–animal interactions

Environmental DNA (2023)

Joshua P. Newton Philip W. Bateman Matthew J. Heydenrych Joshua H. Kestel Kingsley W. Dixon

Abstract Animal pollinators are vital for the reproduction of ~90% of flowering plants. However, many of these pollinating species are experiencing declines globally, making effective pollinator monitoring methods more important than ever before. Pollinators can leave DNA on the flowers they visit, and metabarcoding of these environmental DNA (eDNA) traces provides an opportunity to detect the presence of flower visitors. Our study, collecting flowers from seven plant species with diverse floral morphologies, for eDNA metabarcoding analysis, illustrated the value of this novel survey tool. eDNA metabarcoding using three assays, including one developed in this study to target common bush birds, recorded more animal species visiting flowers than visual surveys conducted concurrently, including birds, bees, and other species. We also recorded the presence of a flower visit from a western pygmy possum; to our knowledge this is the first eDNA metabarcoding study to simultaneously identify the interaction of insect, mammal, and bird species with flowers. The highest diversity of taxa was detected on large inflorescence flower types found on Banksia arborea and Grevillea georgeana. The study demonstrates that the ease of sample collection and the robustness of the metabarcoding methodology has profound implications for future management of biodiversity, allowing us to monitor both plants and their attendant cohort of potential pollinators. This opens avenues for rapid and efficient comparison of biodiversity and ecosystem health between different sites and may provide insights into surrogate pollinators in the event of pollinator declines.

Environmental DNA

10.1002/edn3.399

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Citations (35)

Ancient DNA preserved in small bone fragments from the P.W. Lund collection

Ecology and Evolution (2021)

Frederik Valeur Seersholm Kasper Lykke Hansen Matthew J. Heydenrych Anders J. Hansen Michael Bunce

Abstract The Lund collection is one of the oldest subfossil collections in the world. The vast assemblage of subfossils was collected in the 1830s and 1840s by Peter Wilhelm Lund in Lagoa Santa, Brazil, and was shipped to Copenhagen in 1848, where it was stored in various locations around the city with little attention for the future preservation of the collection. So far, successful genetic research on the material collected by Lund has been limited to two samples of human petrous bone. However, less is known about the preservation conditions of the vast amounts of small and fragmentary bones stored in the collection. To address this, we studied ancient DNA from bulk bone samples of approximately 100 bone fragments from the P.W. Lund collection from boxes with varying degrees of physical preservation conditions. Using bulk bone metabarcoding, we found a high species diversity in all samples. In total, we identified 17 species, representing 11 mammals, two birds, one fish, and three frogs. Of these, two species are new to the collection. Collectively, these results exhibit the potential of future genetic studies on the famous P.W. Lund collection and suggest that the effects of poor storage conditions are probably negligible compared with the long‐term in situ degradation that specimens undergo before excavation.

Subfossil

Ancient DNA

Assemblage (archaeology)

10.1002/ece3.7162

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Citations (11)

Metazoan diversity in Chilean hypersaline lakes unveiled by environmental DNA

Frontiers in Ecology and Evolution (2025)

Mattia Saccò Matthew A. Campbell Pablo Aguilar Gonzalo Salazar Tina E. Berry

Saline and hypersaline wetlands are biodiversity hotspots for metazoans such as aquatic invertebrates and wading birds. However, the survival of these habitats and their biota is increasingly threatened by a combination of pressures from climate change and extractive processes. With the goal of improving conservation efforts in hypersaline ecosystems, this study tests the use of eDNA methods for metazoan biomonitoring. We employed a multi-assay approach utilizing three genetic markers—12S rRNA, 18S rRNA, and COI —to analyze biodiversity in sediment and water. Samples were collected from three hypersaline lakes in Northern Chile: Salar de Atacama (Laguna Puilar), Salar de Pujsa, and Salar de Tara. eDNA outputs were also compared with results generated from aquatic macroinvertebrate assessments using kick-nets. Our eDNA analyses revealed a total of 21 and 22 taxa across the three hypersaline lakes in sediment and water, respectively. The highest diversity was found in Salar de Tara (15 taxa within sediment and 13 taxa from water). Our multi-assay design detected a range of resident hypersaline taxa with different conservation status, spanning from rotifers to endangered snails, to amphipods and flamingos. Macroinvertebrate data via kick-net surveys further validated Salar de Tara as the most biodiverse system. Compared to net-based assessments, eDNA analysis allowed more refined taxonomic assignments for copepods and ostracods, while certain taxa such as Ephydridae or Hirudinea were not detected through molecular tests. Overall, this study provides evidence that eDNA is an effective tool to elucidate fine scale taxa assemblages and can refine conservation efforts in hypersaline lakes.

Biota

Environmental DNA

10.3389/fevo.2025.1504666

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Large‐scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north‐western Australia

Diversity and Distributions (2021)

Katrina M. West Michael J. Travers Michael Stat Euan S. Harvey Zoe T. Richards

Abstract Aim Environmental DNA (eDNA) metabarcoding has demonstrated its applicability as a highly sensitive biomonitoring tool across small spatial and temporal scales in marine ecosystems. However, it has rarely been tested across large spatial scales or biogeographical barriers. Here, we scale up marine eDNA metabarcoding, test its ability to detect a major marine biogeographic break and evaluate its use as a regional biomonitoring tool in Australia. Location North‐western Australia (NWA). Methods We applied metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes to 284 surface seawater eDNA samples collected from 71 mid‐shelf, inshore, coastal and nearshore estuarine sites over 700 km of the NWA coastline. Results Metabarcoding detected a wide range of bony fish (404 taxa), elasmobranchs (44) and aquatic reptiles (5). We detected bioregional and depth differentiation within inshore bony fish communities. These findings support the presence of a marine biogeographic break, which is purported to occur in the vicinity of Cape Leveque, demarcating the border between the Kimberley and Canning bioregions. Inshore bony fish and elasmobranch communities, as well as coastal bony fish assemblages, were additionally found to differ between the South and North Kimberley regions suggesting previously unrecognized subregional differentiation amongst these taxa. The overall compositional data have been used to update distribution information for a number of endangered, elusive and data‐deficient taxa, including sawfish (family: Pristidae), northern river shark ( Glyphis garricki ) and wedgefish (genus: Rhynchobatus ). Main conclusions eDNA metabarcoding demonstrated a high level of sensitivity that was able to discern fine‐scale patterns across the large‐scale, remote and oceanographically complex region of North‐western Australia. Importantly, this study highlights the potential of integrating broad‐scale eDNA metabarcoding alongside other baseline surveys and long‐term monitoring approaches, which are crucial for the sustainable management and conservation of marine biodiversity in this unique marine region.

Environmental DNA

10.1111/ddi.13228

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Citations (114)

Environmental DNA for Biodiversity Monitoring of Coral Reefs

Coral reefs of the world (2022)

Zoe T. Richards Michael Stat Matthew J. Heydenrych Joseph D. DiBattista

Environmental DNA

10.1007/978-3-031-07055-6_13

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Citations (7)

Development of a 16S metabarcoding assay for the environmental DNA (eDNA) detection of aquatic reptiles across northern Australia

bioRxiv (Cold Spring Harbor Laboratory) (2020)

Katrina M. West Matthew J. Heydenrych Rose Lines Anton D. Tucker Sabrina Fossette

Abstract A severe lack of distribution data for aquatic reptiles in northern Australia leaves many taxa vulnerable to extirpation and extinction. Environmental DNA (eDNA) technologies offer sensitive and non-invasive genetic alternatives to trapping and visual surveys and are increasingly employed for the detection of aquatic and semi-aquatic reptiles. However, at present, these studies have largely applied species-specific primers which do not provide a cost-effective avenue for the simultaneous detection of multiple reptilian taxa. Here, we present a 16S rRNA metabarcoding assay for the broad detection of aquatic and semi-aquatic reptile species. This assay is tested on water samples collected at multiple sampling sites at two tropical locations: 12 marine/estuarine sites in Roebuck Bay, Western Australia, and 4 estuarine sites in Cooktown, Queensland, Australia. A total of nine reptile taxa were detected from 10 of the 16 sampled sites, including marine and freshwater turtles, aquatic and semi-aquatic/terrestrial snakes, and terrestrial skinks. However, inconsistencies in the detection of previously observed aquatic reptiles at our sampled sites, such as saltwater crocodile and sea snakes, indicates that further research is required to assess the reliability, strengths and limitations of eDNA methods for aquatic reptile detection before it can be integrated as a broad-scale bioassessment tool.

Environmental DNA

10.1101/2020.09.29.319525

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Citations (4)

A genomic predictor for age at sexual maturity for mammalian species

Evolutionary Applications (2024)

Matthew J. Heydenrych Alyssa Budd Benjamin Mayne Simon Jarman

Age at sexual maturity is a key life history trait that can be used to predict population growth rates and develop life history models. In many wild animal species, the age at sexual maturity is not accurately quantified. This results in a reduced ability to accurately model demography of wild populations. Recent studies have indicated the potential for CpG density within gene promoters to be predictive of other life history traits, specifically maximum lifespan. Here, we have developed a machine learning model using gene promoter CpG density to predict the mean age at sexual maturity in mammalian species. In total, 91 genomes were used to identify 101 unique gene promoters predictive of age at sexual maturity across males and females. We found these gene promoters to be most predictive of age at sexual maturity in females (

Sexual maturity

Trait

Life History Theory

10.1111/eva.13635

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Citations (4)

Universal prediction of vertebrate species age at maturity

Research Square (Research Square) (2024)

Alyssa Budd Suk Yee Yong Matthew J. Heydenrych Benjamin Mayne Oliver Berry

Abstract Animal age at maturity can be used as a universal and simple predictor of species extinction risk. At present, methods to estimate age at maturity are typically species-specific, limiting comparisons among species or are infeasible to do practical constraints. To overcome this, we developed a universal predictor of vertebrate species age at maturity. We show that the frequency of ‘CG’ sequences (CpG sites) in gene promoter regions is a rapid predictor of vertebrate age at maturity. Our models predict age at maturity with remarkable accuracy and generalisability, with median error rates of 30% (less than 1 year) and are robust to genome assemblies of varying quality. We generate age at maturity predictions for 1912 vertebrate species for which this information was previously absent from online databases and envisage these predictions will help to inform management decisions for the many species for which more detailed population information is currently unavailable.

Limiting

Extinction (optical mineralogy)

10.21203/rs.3.rs-4448358/v1

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