Biology subjects

van der Heyde, M.

Publications and source records attributed to van der Heyde, M..

4 recordsLinked to original sources

bioRxiv2025

eDNA on the go: a direct comparison of fixed and vehicle mounted airborne eDNA sampling methods for terrestrial vertebrate species detection at large spatial scales

Air is receiving increasing recognition as a biologically rich source of taxonomically diverse environmental DNA (eDNA). Multiple proof-of-concept studies have explored air as a medium for the detection of single terrestrial species, and even entire terrestrial communities, including mammals, non-anemophilous plants and insects. Airborne eDNA has been sampled using various stationary devices but if we can access it using mobile collection methods, we can rapidly assess biodiversity at large spatial scales. We therefore compared passive eDNA filters deployed for short (30 mins) and long periods (24 hrs) with filters attached to cars that sampled transects through natural and human-modified environments. Our metabarcoding procedure detected 49 vertebrate taxa (33 birds, 15 mammals and 1 amphibian) from all three eDNA air sampling approaches combined, with 29 of these taxa detected in samples collected using the mobile method. The total number of taxa, or proportions of unique taxa detected, did not differ by sampling method, land use or day. Community composition was not significantly impacted by sampling method or sampling day but differed significantly between land uses. We propose that our car-mounted air eDNA sampler could be a game changer for large scale, rapid biomonitoring efforts.

ecology↗

bioRxiv2024

Targeting terrestrial vertebrates with eDNA: Trends, perspectives, and considerations for sampling

Terrestrial vertebrates are experiencing worldwide population declines and species extinctions. To effectively conserve remaining populations and species, rapid, cost effective and scalable methods are needed to complement longstanding monitoring methods. Increasingly, environmental DNA (eDNA) based approaches are being used for terrestrial vertebrate biomonitoring within a range of environments. However, as we move eDNA biomonitoring onto land, we are presented with a new set of challenges. This necessitates the development of "best-practice" eDNA sample collection guidelines for terrestrial systems with the purpose of detecting terrestrial vertebrates. To address these needs we conducted a systematic literature review of 143 peer-reviewed papers applying eDNA to terrestrial vertebrate monitoring (excluding Lissamphibia) that were published between 2012 and 2023. We summarize the use of eDNA for terrestrial vertebrate biomonitoring, focusing on study design and field techniques. Over the decade we observe a steady growth in the annual number of publications, with 3 in 2012 and 33 in 2023. The majority of the reviewed studies targeted terrestrial mammals within temperate forest regions. While an equal number of studies focused on a metabarcoding approach to assess community taxon composition and/or species-specific eDNA detection methods, novel uses are increasingly published. These include studies of animal behaviour and population genetics. We record three types of sampling strategies, eight different substrate types and seven different preservation methods, suggesting there is no "one size fits all" eDNA based sampling methodology when detecting terrestrial vertebrates. With a multitude of study aims, across different environments, and target organisms with different ecologies, the standardization of eDNA sampling approaches in terrestrial systems is extremely challenging. We summarize in a table known factors influencing eDNA detection within terrestrial environments. Furthermore, we identify five key considerations to be addressed when sampling for eDNA studies targeting terrestrial vertebrate species, with the aim of guiding decision making.

ecology↗

bioRxiv2024

Towards a global barcode reference library for subterranean fauna

Implementation of environmental DNA (eDNA) metabarcoding for biodiversity discovery and assessment offers a unique opportunity to gain new insights into subterranean communities around the world. However, for effective and meaningful identification of species from anonymous eDNA barcodes, a library of known reference sequences with associated correct taxonomic metadata -also called a barcode reference library (BRL) - is required. Here we propose an open, publicly accessible information resource for eDNA biomonitoring of subterranean fauna following findable, accessible, interoperable and reusable (FAIR) principles that can be expanded globally. While similar proposals have been made by other authors for individual taxon groups, here we have analysed a curated BRL of subterranean fauna compiled from existing GenBank and BOLD DNA sequence databases for a minimum of four genes (COI, 18S, 12S, and 16S rRNA). We demonstrate the value of such an initiative to eDNA metabarcoding where custom libraries are used to characterise entire ecosystems under examination. To examine the effectiveness of a custom BRL, we generated metabarcoding data for an exemplar system at Bungaroo Creek in the Pilbara (Australia), a globally significant location of stygofaunal diversity. We compared results of BLAST queries of eDNA Operational Taxonomic Units (OTUs) to our BRL and the GenBank nucleotide database, and observed that for all barcoding regions, the custom BRL identified subterranean ZOTUs that could not be identified using GenBank and worked better in tandem. We use the BRL presented here to propose a four-stage plan for developing data infrastructure for subterranean fauna, especially with respect to eDNA metabarcoding data. To our knowledge, this represents the first published instance of a subterranean BRL being tested against real eDNA metabarcoding data. These findings provide a step forward towards robust DNA-based bioassessments for subterranean biodiversity and further emphasise the need for the eDNA community to work together in facilitating a global BRL.

evolutionary biology↗

bioRxiv2024

What are the best practices for curating eDNA custom barcode reference libraries? A case study using Australian subterranean fauna.

Identification of species for environmental assessment and monitoring is essential for understanding anthropogenic impacts on biodiversity, but for subterranean fauna this task is frequently difficult and time consuming. The implementation of environmental DNA (eDNA) metabarcoding for biodiversity discovery and assessment offers considerable promise for improving the rate, accuracy and efficiency of species detection in ecosystems both above and below the ground. Importantly, for a better understanding of the biodiversity and ecology of organisms detected using eDNA, a custom library of known reference sequences with associated correct taxonomic metadata--i.e., a barcode reference library (BRL)--is required. Yet, minimal guidance is currently available on how an effective (i.e. shareable, multi-sequence, that permits metadata and has a unified nomenclature) and accurate (i.e. verified) custom BRL can be achieved. Here, we present a detailed roadmap for curation of a BRL for subterranean fauna. To do this, we (1) curated a custom sequence database of subterranean fauna at an environmentally sensitive location, Bungaroo Creek in the Pilbara region of Western Australia, for four gene loci useful for eDNA metabarcoding (COI, 18S rRNA, 12S rRNA and 16S rRNA); (2) addressed major gaps in taxonomy and disparate nomenclature of subterranean fauna by estimating 17-29 putative new species with standard delimitation methods, including 34 Barcode Index Numbers (BINs) in BOLD, and (3) summarised a best practice workflow for curation of a custom BRL that has broad applicability and can be applied to any taxa. Scientific Significance StatementIn threatened ecosystems, environmental DNA (eDNA) metabarcoding for biodiversity discovery and assessment offers considerable promise for improvement in the rate, efficiency and accuracy of species detection. For a better understanding of the biodiversity and ecology of organisms detected using eDNA, a custom library of known reference sequences with associated correct taxonomic metadata is required. Minimal guidance is currently available on how an effective (i.e. shareable, multi-sequence, permits metadata and provides a unified nomenclature) custom barcode reference library (BRL) can be achieved for subterranean fauna. Here, we present a road map for sound and reliable curation of a BRL using subterranean fauna from Australia as a case study.

evolutionary biology↗