Michael Bunce

Ancient DNA provides insights into 4,000 years of resource economy across Greenland

Publisher: Springer Science and Business Media LLC

Date: 06-10-2022

DOI: 10.1038/S41562-022-01454-Z

Abstract: The success and failure of past cultures across the Arctic was tightly coupled to the ability of past peoples to exploit the full range of resources available to them. There is substantial evidence for the hunting of birds, caribou and seals in prehistoric Greenland. However, the extent to which these communities relied on fish and cetaceans is understudied because of taphonomic processes that affect how these taxa are presented in the archaeological record. To address this, we analyse DNA from bulk bone s les from 12 archaeological middens across Greenland covering the Palaeo-Inuit, Norse and Neo-Inuit culture. We identify an assemblage of 42 species, including nine fish species and five whale species, of which the bowhead whale (Balaena mysticetus) was the most commonly detected. Furthermore, we identify a new haplotype in caribou (Rangifer tarandus), suggesting the presence of a distinct lineage of (now extinct) dwarfed caribou in Greenland 3,000 years ago.

Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient

Publisher: PeerJ

Date: 06-02-2019

DOI: 10.7717/PEERJ.6379

Abstract: Effective bio ersity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine bio ersity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna. We here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment s les to provide snapshots of eukaryotic subtropical bio ersity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA. Using 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m ( p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most erse class (contributing 81% of species) within the phylum Porifera the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on s ling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases. Overall, our pilot study demonstrates the importance of exploring depth effects in eDNA and suggest that RUMS may be applied to provide a baseline of information on eukaryotic marine taxa at coastal sites of economic and conservation importance.

eDNA metabarcoding survey reveals fine‐scale coral reef community variation across a remote, tropical island ecosystem

Publisher: Wiley

Date: 03-2020

DOI: 10.1111/MEC.15382

Towards a macroscope: Leveraging technology to transform the breadth, scale and resolution of macroecological data

Publisher: Wiley

Date: 12-11-2019

DOI: 10.1111/GEB.13025

Complementary molecular and visual sampling of fish on oil and gas platforms provides superior biodiversity characterisation

Publisher: Elsevier BV

Date: 07-2022

DOI: 10.1016/J.MARENVRES.2022.105692

Abstract: Offshore oil and gas platforms have the potential to provide complex refugia for fish and benthic colonisers. We compare two methods of bio ersity assessment for fish and elasmobranchs at seven decommissioned oil and gas platforms as well as five sediment sites, located 5 km from platforms, in the Gulf of Thailand. Using surveys from stereo-video ROV transects, and data from Environmental DNA (eDNA) water-column s les, we detected fish and elasmobranch taxa from 39 families and 66 genera across both platform and sediment sites with eDNA, compared with 18 families and 29 genera by stereo-ROV with platforms yielding significantly greater species richness. This study demonstrates that the combination of stereo-video ROV and eDNA provide effective, non-extractive and complementary methods to enhance data capture. This approach sets new benchmarks for evaluating fish assemblages surrounding platforms and will enhance measurements of biota to inform decisions on the fate of oil/gas infrastructure.

Beyond Biodiversity: Can Environmental DNA (eDNA) Cut it as a Population Genetics Tool?

Publisher: MDPI AG

Date: 05-02-2019

DOI: 10.20944/PREPRINTS201902.0048.V1

Abstract: Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations and contribute to effective conservation management. However, collecting genetic s les can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way to s le genetic material non-invasively without requiring visual observation. While eDNA has been trialed extensively as a bio ersity and biosecurity monitoring tool with a strong taxonomic focus, it has yet to be fully explored as a means for obtaining population genetic information. Here, we review current research that employs eDNA approaches for the study of populations. We outline challenges facing eDNA-based population genetic methodologies, and suggest avenues of research for future developments. We advocate that with further optimizations, this emergent field holds great potential as part of the population genetics toolkit.

Evidence for fungi and gold redox interaction under Earth surface conditions

Publisher: Springer Science and Business Media LLC

Date: 23-05-2019

DOI: 10.1038/S41467-019-10006-5

Abstract: Microbial contribution to gold biogeochemical cycling has been proposed. However, studies have focused primarily on the influence of prokaryotes on gold reduction and precipitation through a detoxification-oriented mechanism. Here we show, fungi, a major driver of mineral bioweathering, can initiate gold oxidation under Earth surface conditions, which is of significance for dissolved gold species formation and distribution. Presence of the gold-oxidizing fungus TA_pink1, an isolate of Fusarium oxysporum , suggests fungi have the potential to substantially impact gold biogeochemical cycling. Our data further reveal that indigenous fungal ersity positively correlates with in situ gold concentrations. Hypocreales, the order of the gold-oxidizing fungus, show the highest centrality in the fungal microbiome of the auriferous environment. Therefore, we argue that the redox interaction between fungi and gold is critical and should be considered in gold biogeochemical cycling.

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

Publisher: CSIRO Publishing

Date: 2021

DOI: 10.1071/MF20288

The influence of diet and environment on the gut microbial community of field crickets

Publisher: Wiley

Date: 16-04-2018

DOI: 10.1002/ECE3.3977

Arctic shrub colonization lagged peak postglacial warmth: Molecular evidence in lake sediment from Arctic Canada

Publisher: Wiley

Date: 11-10-2019

DOI: 10.1111/GCB.14836

Abstract: Arctic shrubification is an observable consequence of climate change, already resulting in ecological shifts and global-scale climate feedbacks including changes in land surface albedo and enhanced evapotranspiration. However, the rate at which shrubs can colonize previously glaciated terrain in a warming world is largely unknown. Reconstructions of past vegetation dynamics in conjunction with climate records can provide critical insights into shrubification rates and controls on plant migration, but paleoenvironmental reconstructions based on pollen may be biased by the influx of exotic pollen to tundra settings. Here, we reconstruct past plant communities using sedimentary ancient DNA (sedaDNA), which has a more local source area than pollen. We additionally reconstruct past temperature variability using bacterial cell membrane lipids (branched glycerol dialkyl glycerol tetraethers) and an aquatic productivity indicator (biogenic silica) to evaluate the relative timing of postglacial ecological and climate changes at a lake on southern Baffin Island, Arctic Canada. The sedaDNA record tightly constrains the colonization of dwarf birch (Betula, a thermophilous shrub) to 5.9 ± 0.1 ka, ~3 ka after local deglaciation as determined by cosmogenic

Dense sampling of bird diversity increases power of comparative genomics

Publisher: Springer Science and Business Media LLC

Date: 11-11-2020

DOI: 10.1038/S41586-020-2873-9

Comprehensive evidence for subspecies designations in Cook’s Petrel Pterodroma cookii with implications for conservation management

Publisher: Cambridge University Press (CUP)

Date: 05-10-2020

DOI: 10.1017/S0959270920000350

Abstract: Cook’s Petrel Pterodroma cookii is an endemic New Zealand seabird that has experienced a large range decline since the arrival of humans and now only breeds on two offshore islands (Te Hauturu-o-Toi/Little Barrier Island and Whenua Hou/Codfish Island) at the extreme ends of its former distribution. Morphological, behavioural, and mitochondrial cytochrome oxidase 1 (CO1) sequence data led a previous study to recognise the two extant populations as distinct conservation management units. Here, we further examine the genetic relationship between the extant populations using two nuclear introns ( β-fibint7 and PAX ). Using one mitochondrial locus (CO1), we also investigate the past distribution of a single nucleotide polymorphism (SNP) that differentiates the modern populations using bone and museum skins sourced from within its former range across New Zealand’s North and South Islands. We found significant population genetic structure between the two extant Cook’s Petrel populations for one of the two nuclear introns ( β-fibint7 ). The mitochondrial DNA CO1 analysis indicated that the SNP variant found in the Codfish Island population was formerly widely distributed across both the North and South Islands, whereas the Little Barrier Island variant was detected only in North Island s les. We argue that these combined data support the recognition of the extant populations as different subspecies. Previous names for these taxa exist, thus Cook’s Petrel from Little Barrier Island becomes Pterodroma cookii cookii and Cook’s Petrel from Codfish Island becomes P. c. orientalis . Furthermore, we suggest that both genetic and non-genetic data should be taken into consideration when planning future mainland translocations. Namely, any translocations on the South Island should be sourced from Codfish Island and future translocations on the North Island should continue to be sourced from Little Barrier Island only.

Rapid range shifts and megafaunal extinctions associated with late Pleistocene climate change

Publisher: Springer Science and Business Media LLC

Date: 02-06-2020

DOI: 10.1038/S41467-020-16502-3

Abstract: Large-scale changes in global climate at the end of the Pleistocene significantly impacted ecosystems across North America. However, the pace and scale of biotic turnover in response to both the Younger Dryas cold period and subsequent Holocene rapid warming have been challenging to assess because of the scarcity of well dated fossil and pollen records that covers this period. Here we present an ancient DNA record from Hall’s Cave, Texas, that documents 100 vertebrate and 45 plant taxa from bulk fossils and sediment. We show that local plant and animal ersity dropped markedly during Younger Dryas cooling, but while plant ersity recovered in the early Holocene, animal ersity did not. Instead, five extant and nine extinct large bodied animals disappeared from the region at the end of the Pleistocene. Our findings suggest that climate change affected the local ecosystem in Texas over the Pleistocene-Holocene boundary, but climate change on its own may not explain the disappearance of the megafauna at the end of the Pleistocene.

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

Publisher: Cold Spring Harbor Laboratory

Date: 10-2020

DOI: 10.1101/2020.09.29.319525

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 s les collected at multiple s ling 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 s led 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 s led 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 reflects common haplotypic variation

Publisher: Cold Spring Harbor Laboratory

Date: 03-2022

DOI: 10.1101/2022.02.26.481856

Abstract: Analysis of environmental DNA (eDNA) has gained widespread usage for taxonomically based bio ersity assessment. While interest in applying non-invasive eDNA monitoring for population genetic assessments has grown, its usage in this sphere remains limited. One barrier to uptake is that the effectiveness of eDNA detection below the species level remains to be determined for multiple species and environments. Here, we test the utility of this emergent technology in a population genetic framework using eDNA s les derived from water along New Zealand’s South Island (Otago Coast: n=9 Kaikōura: n=7) and DNA obtained from tissue s les (n=76) of in idual blackfoot pāua ( Haliotis iris) s led from New Zealand’s Otago coast. We recovered four mitochondrial haplotypes from eDNA versus six from the tissue s les collected. Three common haplotypes were recovered with both eDNA and tissue s les, while only one out of three rare haplotypes – represented in tissue s les by one in idual each – was recovered with our eDNA methods. We demonstrate that eDNA monitoring is an effective tool for recovering common genetic ersity from pāua, although rare ( 5%) haplotypes are seldom recovered. Our results show the potential of eDNA to identify population-level haplotypes for gastropods in the marine environment identification below the species level and for studying the population genetic ersity of gastropods. This work supports eDNA methods as effective, non-invasive tools for genetic monitoring. Non-invasive eDNA s ling could minimize target organism stress and human interaction enabling population genetic research for hard-to-s le, delicate, or sensitive species.

Mitochondrial Genomes from New Zealand’s Extinct Adzebills (Aves: Aptornithidae: Aptornis) Support a Sister-Taxon Relationship with the Afro-Madagascan Sarothruridae

Publisher: MDPI AG

Date: 15-02-2019

DOI: 10.3390/D11020024

Abstract: The recently extinct New Zealand adzebills (Aptornithidae, Aptornis spp.) were an enigmatic group of large flightless birds that have long eluded precise taxonomic assignment as they do not closely resemble any extant birds. Adzebills were nearly wingless, weighed approximately 16–19 kg, and possessed massive adze-like reinforced bills whose function remains unknown. Using hybridisation enrichment and high-throughput sequencing of DNA extracted from subfossil bone and eggshell, near-complete mitochondrial genomes were successfully assembled from the two Quaternary adzebill species: the North Island Adzebill (Aptornis otidiformis) and South Island Adzebill (A. defossor). Molecular phylogenetic analyses confirm that adzebills are members of the Ralloidea (rails and allies) and are sister-taxon to the Sarothruridae, which our results suggest comprises the Madagascan wood rails (Mentocrex, two likely sp.) in addition to the tiny ( gram) rail-like Afro-Madagascan flufftails (Sarothrura, 9 spp.). Node age estimates indicate that the split between adzebills and Sarothruridae occurred ~39.6 Ma, suggesting that the ancestors of the adzebills arrived in New Zealand by long-distance dispersal rather than continental vicariance. This newly identified biogeographic link between physically distant New Zealand and Afro-Madagascar, echoed by the relationship between the New Zealand kiwi (Apterygiformes) and Madagascan elephant-birds (Aepyornithiformes), suggests that the adzebill’s near relatives were formerly more widespread. In addition, our estimate for the ergence time between the two Quaternary adzebill species (0.2–2.3 Ma) coincides with the emergence of a land-bridge between the North and South islands of New Zealand (ca. 1.5–2 Ma). This relatively recent ergence suggests that North Island adzebills are the result of a relatively recent dispersal from the South Island, from which the earliest (Miocene) adzebill fossil has been described.

Gut content metabarcoding of specialized feeders is not a replacement for environmental DNA assays of seawater in reef environments

Publisher: PeerJ

Date: 27-09-2023

DOI: 10.7717/PEERJ.16075

Towards reproducible metabarcoding data: Lessons from an international cross-laboratory experiment.

Publisher: Wiley

Date: 31-08-2022

DOI: 10.1111/1755-0998.13485

Abstract: Advances in high-throughput sequencing (HTS) are revolutionizing monitoring in marine environments by enabling rapid, accurate and holistic detection of species within complex biological s les. Research institutions worldwide increasingly employ HTS methods for bio ersity assessments. However, variance in laboratory procedures, analytical workflows and bioinformatic pipelines impede the transferability and comparability of results across research groups. An international experiment was conducted to assess the consistency of metabarcoding results derived from identical s les and primer sets using varying laboratory procedures. Homogenized biofouling s les collected from four coastal locations (Australia, Canada, New Zealand and the USA) were distributed to 12 independent laboratories. Participants were asked to follow one of two HTS library preparation workflows. While DNA extraction, primers and bioinformatic analyses were purposefully standardized to allow comparison, many other technical variables were allowed to vary among laboratories ( lification protocols, type of instrument used, etc.). Despite substantial variation observed in raw results, the primary signal in the data was consistent, with the s les grouping strongly by geographical origin for all data sets. Simple post hoc data clean-up by removing low-quality s les gave the best improvement in s le classification for nuclear 18S rRNA gene data, with an overall 92.81% correct group attribution. For mitochondrial COI gene data, the best classification result (95.58%) was achieved after correction for contamination errors. The identified critical methodological factors that introduced the greatest variability (preservation buffer, s le defrosting, template concentration, DNA polymerase, PCR enhancer) should be of great assistance in standardizing future bio ersity studies using metabarcoding.

Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity

Publisher: Wiley

Date: 12-09-2019

DOI: 10.1111/COBI.13183

A large scale temporal and spatial environmental DNA biodiversity survey of marine vertebrates in Brazil following the Fundão tailings dam failure

Publisher: Elsevier BV

Date: 10-2023

DOI: 10.1016/J.MARENVRES.2023.106239

Debugging diversity – a pan‐continental exploration of the potential of terrestrial blood‐feeding leeches as a vertebrate monitoring tool

Publisher: Wiley

Date: 05-07-2018

DOI: 10.1111/1755-0998.12912

Abstract: The use of environmental DNA (eDNA) has become an applicable noninvasive tool with which to obtain information about bio ersity. A subdiscipline of eDNA is iDNA (invertebrate-derived DNA), where genetic material ingested by invertebrates is used to characterize the bio ersity of the species that served as hosts. While promising, these techniques are still in their infancy, as they have only been explored on limited numbers of s les from only a single or a few different locations. In this study, we investigate the suitability of iDNA extracted from more than 3,000 haematophagous terrestrial leeches as a tool for detecting a wide range of terrestrial vertebrates across five different geographical regions on three different continents. These regions cover almost the full geographical range of haematophagous terrestrial leeches, thus representing all parts of the world where this method might apply. We identify host taxa through metabarcoding coupled with high-throughput sequencing on Illumina and IonTorrent sequencing platforms to decrease economic costs and workload and thereby make the approach attractive for practitioners in conservation management. We identified hosts in four different taxonomic vertebrate classes: mammals, birds, reptiles and hibians, belonging to at least 42 different taxonomic families. We find that vertebrate blood ingested by haematophagous terrestrial leeches throughout their distribution is a viable source of DNA with which to examine a wide range of vertebrates. Thus, this study provides encouraging support for the potential of haematophagous terrestrial leeches as a tool for detecting and monitoring terrestrial vertebrate bio ersity.

Maximising fish detection with eDNA metabarcoding

Publisher: Wiley

Date: 20-02-2020

DOI: 10.1002/EDN3.74

Plumbing the depths with environmental DNA (eDNA): Metabarcoding reveals biodiversity zonation at 45–60 m on mesophotic coral reefs

Publisher: Wiley

Date: 20-09-2023

DOI: 10.1111/MEC.17140

Protein and carbohydrate intakes alter gut microbial community structure in crickets: a Geometric Framework approach

Publisher: Oxford University Press (OUP)

Date: 04-07-2019

DOI: 10.1093/FEMSEC/FIZ106

Abstract: Proteins and carbohydrates have profound impacts on the ecology of gut microbiota, but disentangling the single and interactive effects of different dietary constituents is challenging. Here, we used a multidimensional approach, the Geometric Framework, to study the interactions between nutrition and bacterial abundances with respect to protein and carbohydrate intakes in field cricket, Teleogryllus oceanicus. Our study revealed that species richness decreased as crickets consumed more macronutrients, and species evenness peaked at high intake of protein-rich diets. Sex and protein:carbohydrate (P:C) ratios in diets were the primary factors influencing the gut bacterial community, but most of the microbial operational taxonomic units (OTUs) that were significantly different between males and females were present in low abundance. In contrast, protein intake had a greater influence than carbohydrate consumption on the relative abundances of the core bacterial taxa, as an increase in dietary protein availability could remove the growth constraint imposed by limited nitrogen. Taken together, the use of the Geometric Framework provides a deeper insight into how nutritional intakes influence the relative abundances of gut microbes, and could be a useful tool to integrate the study of gut microbiome and fitness traits in a host.

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

Publisher: Wiley

Date: 05-02-2021

DOI: 10.1002/ECE3.7162

Author Correction: Early Pastoral Economies and Herding Transitions in Eastern Eurasia

Publisher: Springer Science and Business Media LLC

Date: 06-03-2020

DOI: 10.1038/S41598-020-60516-2

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Characterizing the distribution of the critically endangered estuarine pipefish (Syngnathus watermeyeri) across its range using environmental DNA

Publisher: Wiley

Date: 07-10-2023

DOI: 10.1002/EDN3.365

Abstract: The effective management of rare and threatened species, especially in areas where population sizes have diminished, relies on knowledge of their population size, threats, and distribution. Robust mapping of distribution presents a particular challenge in aquatic environments for cryptic species, especially those with low abundance. Environmental DNA (eDNA) approaches can offer improved detection rates of many rare and threatened species when compared with traditional s ling approaches. In this study, we developed and optimized a targeted eDNA assay for the critically endangered estuarine pipefish ( Syngnathus watermeyeri ). eDNA s ling and seine netting were undertaken at 39 sites across the historical range of S. watermeyeri in the Eastern Cape of South Africa in 2019. At each site, five water s les were collected for eDNA analysis ( n = 195) along with three seine netting hauls ( n = 117). Habitat and environmental data were collected at each location to explore what physical and biotic parameters might correlate with pipefish presence/absence. We successfully detected S. watermeyeri in two estuaries (Kariega and Bushmans) using both survey methods. Importantly, the positive detection rate of eDNA (66.7%) was four times that of seine netting (16.7%), highlighting the value of eDNA as a monitoring tool for rare and cryptic species. Null detections in the Kasouga, East Kleinemonde, and West Kleinemonde estuaries add to the growing body of evidence that the estuarine pipefish has been extirpated from these locations and is now only found in two estuarine systems. The occurrence of S. watermeyeri was found to be highly dependent on the cover of submerged macrophytes such as Zostera capensis (eelgrass). By providing a more complete picture of the conservation status of this critically endangered species, this work facilitates the development of a long‐term monitoring program and the identification of priority conservation areas.

It is time for ancient DNA to sweat the small stuff

Publisher: Wiley

Date: 28-04-2023

DOI: 10.1111/MEC.16970

Abstract: When one thinks of the field of ancient DNA it conjures images of extinct megafauna, from mammoths and woolly rhinos, through to the giant, flightless elephant bird (but hopefully not dinosaurs – despite the pervasive idea of ‘dino DNA’ from Jurassic park). These taxa have fascinating evolutionary histories, and their extinction stories need to be told. At the other end of the vertebrate scale, however, is the often neglected ‘small stuff’ – lizards, frogs, and other herpetofauna. But here's the rub – extracting DNA from the bones of this ‘small stuff’ is not only difficult, it often destroys the s le. In this issue, Scarsbrook et al. (2023) describe a new way to study the ancient (or historical) DNA of small vertebrates that is minimally destructive. The authors use the method to reconstruct the dynamic evolutionary history of New Zealand geckos and make new insights into how remnant populations should be managed. This work provides some key insights into New Zealand geckos but also opens up opportunities of biomolecular research on the smallest of vouchered vertebrate s les held within museum collections.

Evaluating restoration trajectories using DNA metabarcoding of ground-dwelling and airborne invertebrates and associated plant communities.

Publisher: Wiley

Date: 17-02-2022

DOI: 10.1111/MEC.16375

Abstract: Invertebrates are important for restoration processes as they are key drivers of many landscape-scale ecosystem functions including pollination, nutrient cycling and soil formation. However, invertebrates are often overlooked in restoration monitoring because they are highly erse, poorly described, and time-consuming to survey, and require increasingly scarce taxonomic expertise to enable identification. DNA metabarcoding is a relatively new tool for rapid survey that is able to address some of these concerns, and provide information about the taxa with which invertebrates are interacting via food webs and habitat. Here, we evaluate how invertebrate communities may be used to determine ecosystem trajectories during restoration. We collected ground-dwelling and airborne invertebrates across chronosequences of mine-site restoration in three ecologically disparate locations in Western Australia and identified invertebrate and plant communities using DNA metabarcoding. Ground-dwelling invertebrates showed the clearest restoration signals, with communities becoming more similar to reference communities over time. These patterns were weaker in airborne invertebrates, which have higher dispersal abilities and therefore less local fidelity to environmental conditions. Although we detected directional changes in community composition indicative of invertebrate recovery, patterns observed were inconsistent between study locations. The inclusion of plant assays allowed identification of plant species, as well as potential food sources and habitat. We demonstrate that DNA metabarcoding of invertebrate communities can be used to evaluate restoration trajectories. Testing and incorporating new monitoring techniques such as DNA metabarcoding is critical to improving restoration outcomes.

Time to Spread Your Wings: A Review of the Avian Ancient DNA Field

Publisher: MDPI AG

Date: 18-07-2017

DOI: 10.3390/GENES8070184

Strategies for sample labelling and library preparation in DNA metabarcoding studies

Publisher: Wiley

Date: 13-10-2021

DOI: 10.1111/1755-0998.13512

Abstract: Metabarcoding of DNA extracted from environmental or bulk specimen s les is increasingly used to profile biota in basic and applied bio ersity research because of its targeted nature that allows sequencing of genetic markers from many s les in parallel. To achieve this, PCR lification is carried out with primers designed to target a taxonomically informative marker within a taxonomic group, and s le‐specific nucleotide identifiers are added to the licons prior to sequencing. The latter enables assignment of the sequences back to the s les they originated from. Nucleotide identifiers can be added during the metabarcoding PCR and during “library preparation”, that is, when licons are prepared for sequencing. Different strategies to achieve this labelling exist. All have advantages, challenges and limitations, some of which can lead to misleading results, and in the worst case compromise the fidelity of the metabarcoding data. Given the range of questions addressed using metabarcoding, ensuring that data generation is robust and fit for the chosen purpose is critically important for practitioners seeking to employ metabarcoding for bio ersity assessments. Here, we present an overview of the three main workflows for s le‐specific labelling and library preparation in metabarcoding studies on Illumina sequencing platforms one‐step PCR, two‐step PCR, and tagged PCR. Further, we distill the key considerations for researchers seeking to select an appropriate metabarcoding strategy for their specific study. Ultimately, by gaining insights into the consequences of different metabarcoding workflows, we hope to further consolidate the power of metabarcoding as a tool to assess bio ersity across a range of applications.

MobiSeq: De novo SNP discovery in model and non‐model species through sequencing the flanking region of transposable elements

Publisher: Wiley

Date: 06-02-2019

DOI: 10.1111/1755-0998.12984

Abstract: In recent years, the availability of reduced representation library (RRL) methods has catalysed an expansion of genome-scale studies to characterize both model and non-model organisms. Most of these methods rely on the use of restriction enzymes to obtain DNA sequences at a genome-wide level. These approaches have been widely used to sequence thousands of markers across in iduals for many organisms at a reasonable cost, revolutionizing the field of population genomics. However, there are still some limitations associated with these methods, in particular the high molecular weight DNA required as starting material, the reduced number of common loci among investigated s les, and the short length of the sequenced site-associated DNA. Here, we present MobiSeq, a RRL protocol exploiting simple laboratory techniques, that generates genomic data based on PCR targeted enrichment of transposable elements and the sequencing of the associated flanking region. We validate its performance across 103 DNA extracts derived from three mammalian species: grey wolf (Canis lupus), red deer complex (Cervus sp.) and brown rat (Rattus norvegicus). MobiSeq enables the sequencing of hundreds of thousands loci across the genome and performs SNP discovery with relatively low rates of clonality. Given the ease and flexibility of MobiSeq protocol, the method has the potential to be implemented for marker discovery and population genomics across a wide range of organisms-enabling the exploration of erse evolutionary and conservation questions.

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

Publisher: Wiley

Date: 24-01-2021

DOI: 10.1111/DDI.13228

Abstract: 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. North‐western Australia (NWA). We applied metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes to 284 surface seawater eDNA s les collected from 71 mid‐shelf, inshore, coastal and nearshore estuarine sites over 700 km of the NWA coastline. 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 ). 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 bio ersity in this unique marine region.

eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA sequences exploiting Nextflow and Singularity

Publisher: Wiley

Date: 09-03-2021

DOI: 10.1111/1755-0998.13356

Abstract: Metabarcoding of environmental DNA (eDNA) when coupled with high throughput sequencing is revolutionising the way bio ersity can be monitored across a wide range of applications. However, the large number of tools deployed in downstream bioinformatic analyses often places a challenge in configuration and maintenance of a workflow, and consequently limits the research reproducibility. Furthermore, scalability needs to be considered to handle the growing amount of data due to increase in sequence output and the scale of project. Here, we describe eDNAFlow, a fully automated workflow that employs a number of state‐of‐the‐art applications to process eDNA data from raw sequences (single‐end or paired‐end) to generation of curated and noncurated zero‐radius operational taxonomic units (ZOTUs) and their abundance tables. This pipeline is based on Nextflow and Singularity which enable a scalable, portable and reproducible workflow using software containers on a local computer, clouds and high‐performance computing (HPC) clusters. Finally, we present an in‐house Python script to assign taxonomy to ZOTUs based on user specified thresholds for assigning lowest common ancestor (LCA). We demonstrate the utility and efficiency of the pipeline using an ex le of a published coral ersity biomonitoring study. Our results were congruent with the aforementioned study. The scalability of the pipeline is also demonstrated through analysis of a large data set containing 154 s les. To our knowledge, this is the first automated bioinformatic pipeline for eDNA analysis using two powerful tools: Nextflow and Singularity. This pipeline addresses two major challenges in the analysis of eDNA data scalability and reproducibility.

Using dietary metabarcoding analyses to characterise waterbirds–agriculture interactions

Publisher: Wiley

Date: 26-09-2022

DOI: 10.1111/1365-2664.14272

Abstract: Globally, the use of agricultural fields by waterbirds has increased, resulting in conflicts with farmers. Designing effective management strategies to resolve these conflicts requires understanding the species' resource use. Dietary analyses can shed light on the extent of consumption of agricultural crops and surrounding natural resources, as well as the potential relationship between diet and an in idual's body condition and ultimately its fitness. We examined the dietary composition of the tropical magpie goose Anseranas semipalmata , seasonally utilising a mixed natural‐agricultural landscape of northern Australia. We used DNA metabarcoding of intestinal contents from hunted geese to reconstruct in idual diets and evaluated body condition from morphometric measurements. We compared the relative contribution of agricultural and natural foods to dietary composition, and investigated how this contribution varied spatially, temporally and among in iduals that differed in body condition. We found that geese consumed both agricultural and naturally occurring plants assigned to at least 35 taxa. The most frequent and abundant taxa belonged to three families: Poaceae (grasses), Cyperaceae (sedges) and Anacardiaceae (mangoes). Dietary composition varied substantially among s ling sites and over time but not with body condition of geese. Synthesis and applications . We used a novel approach to investigate the diet of a waterbird perceived as problematic across an agricultural landscape in tropical Australia. We showed that in iduals forage opportunistically, and that agricultural crops, while eaten, may not represent an essential part of geese diet across the study region. The knowledge acquired provides new insights into the species' foraging ecology offering clear alternatives for mitigating goose–agriculture interactions. Providing disturbance‐free alternative foraging areas or minimising the attractiveness of targeted agricultural fields (e.g. shorter grass, alternative ground cover) may alleviate crop consumption while benefiting the species' long‐term conservation. While also highlighting the limitations of DNA metabarcoding, our dietary study emphasises the potential of this methodology to improve our understanding of crop damage by wildlife, allowing effective evaluation of management requirements.

New insights into 4,000 years of resource economy across Greenland using ancient DNA

Publisher: Cold Spring Harbor Laboratory

Date: 25-02-2022

DOI: 10.1101/2022.02.23.480846

Abstract: The success and failure of past cultures across the Arctic was tightly coupled to the ability of past people to exploit the full range of resources available to them, and to adapt to fluctuations in resource availability. There is substantial evidence for the hunting of birds, caribou and a wide range of marine mammals in pre-historic Greenland from bone remains preserved in ancient middens. However, the extent to which these communities relied on marine resources such as fish and large cetaceans is understudied because of the taphonomic processes and bias that affect how these taxa present themselves in the archaeological record. To address this, we analyse DNA from bulk bone s les from 12 archaeological sites across Greenland dating from Paleo-Inuit to Neo-Inuit periods. Using a combination of metabarcoding and shotgun metagenomics we identify an assemblage of 43 species consisting of birds, fish, and both marine and terrestrial mammals. We find genetic evidence of five different whale species, of which the bowhead whale ( Balaena mysticetus ) was the most commonly detected. Furthermore, we detect nine fish species, of which four have not previously been identified in any of the studied sites. Lastly, we identify a novel haplotype in caribou ( Rangifer tarandus ) at the 3,000-year-old site Itinnera, suggesting the presence of a distinct lineage of (now extinct) dwarfed caribou that colonised Greenland after the last ice age 9,000 years ago. Collectively, these findings provide a rare insight into whaling and fishing practices in Greenland and demonstrate that prehistoric Greenlandic communities had the social and technological capacity to target the largest whales available in the waters around them.

Species‐level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization

Publisher: Wiley

Date: 15-01-2019

DOI: 10.1002/ECE3.4843

Genomic and life-history discontinuity reveals a precinctive lineage for a deep-water grouper with gene flow from tropical to temperate waters on the west coast of Australia

Publisher: Elsevier BV

Date: 12-2018

DOI: 10.1016/J.EGG.2018.09.001

Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool?

Publisher: MDPI AG

Date: 03-2019

DOI: 10.3390/GENES10030192

Abstract: Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations and contribute to effective conservation management. However, collecting genetic s les can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way to s le genetic material non-invasively without requiring visual observation. While eDNA has been trialed extensively as a bio ersity and biosecurity monitoring tool with a strong taxonomic focus, it has yet to be fully explored as a means for obtaining population genetic information. Here, we review current research that employs eDNA approaches for the study of populations. We outline challenges facing eDNA-based population genetic methodologies, and suggest avenues of research for future developments. We advocate that with further optimizations, this emergent field holds great potential as part of the population genetics toolkit.

Comparing environmental DNA collection methods for sampling community composition on marine infrastructure

Publisher: Elsevier BV

Date: 04-2023

DOI: 10.1016/J.ECSS.2023.108283

Author Correction: Dense sampling of bird diversity increases power of comparative genomics

Publisher: Springer Science and Business Media LLC

Date: 08-04-2021

DOI: 10.1038/S41586-021-03473-8

Abstract: A Correction to this paper has been published: 0.1038/s41586-021-03473-8.

Early Pastoral Economies and Herding Transitions in Eastern Eurasia

Publisher: Springer Science and Business Media LLC

Date: 22-01-2020

DOI: 10.1038/S41598-020-57735-Y

Abstract: While classic models for the emergence of pastoral groups in Inner Asia describe mounted, horse-borne herders sweeping across the Eurasian Steppes during the Early or Middle Bronze Age (ca. 3000–1500 BCE), the actual economic basis of many early pastoral societies in the region is poorly characterized. In this paper, we use collagen mass fingerprinting and ancient DNA analysis of some of the first stratified and directly dated archaeofaunal assemblages from Mongolia’s early pastoral cultures to undertake species identifications of this rare and highly fragmented material. Our results provide evidence for livestock-based, herding subsistence in Mongolia during the late 3rd and early 2nd millennia BCE. We observe no evidence for dietary exploitation of horses prior to the late Bronze Age, ca. 1200 BCE – at which point horses come to dominate ritual assemblages, play a key role in pastoral diets, and greatly influence pastoral mobility. In combination with the broader archaeofaunal record of Inner Asia, our analysis supports models for widespread changes in herding ecology linked to the innovation of horseback riding in Central Asia in the final 2nd millennium BCE. Such a framework can explain key broad-scale patterns in the movement of people, ideas, and material culture in Eurasian prehistory.

Assessing the utility of eDNA as a tool to survey reef-fish communities in the Red Sea

Publisher: Springer Science and Business Media LLC

Date: 23-08-2017

DOI: 10.1007/S00338-017-1618-1

DNA metabarcoding assays reveal a diverse prey assemblage for Mobula rays in the Bohol Sea, Philippines

Publisher: Wiley

Date: 30-01-2019

DOI: 10.1002/ECE3.4858

Development and evaluation of fish eDNA metabarcoding assays facilitate the detection of cryptic seahorse taxa (family: Syngnathidae)

Publisher: Wiley

Date: 19-06-2020

DOI: 10.1002/EDN3.93

Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding

Publisher: Wiley

Date: 06-03-2020

DOI: 10.1111/1755-0998.13148

Marine environmental DNA biomonitoring reveals seasonal patterns in biodiversity and identifies ecosystem responses to anomalous climatic events

Publisher: Public Library of Science (PLoS)

Date: 08-02-2019

DOI: 10.1371/JOURNAL.PGEN.1007943

Environmental DNA metabarcoding studies are critically affected by substrate selection

Publisher: Wiley

Date: 21-12-2019

DOI: 10.1111/1755-0998.12971

Abstract: Effective biomonitoring is critical for driving management outcomes that ensure long-term sustainability of the marine environment. In recent years, environmental DNA (eDNA), coupled with metabarcoding methodologies, has emerged as a promising tool for generating biotic surveys of marine ecosystems, including those under anthropogenic pressure. However, more empirical data are needed on how to best implement eDNA field s ling approaches to maximize their utility for each specific application. The effect of the substrate chosen for eDNA s ling on the ersity of marine taxa detected by DNA metabarcoding has not yet been systematically analysed, despite aquatic systems being those most commonly targeted for eDNA studies. We investigated the effect of four commonly used eDNA substrates to explore taxonomic ersity: (a) surface water, (b) marine sediment, (c) settlement plates and (d) planktonic tows. With a focus on coastal ports, 332 eDNA s les from Australia (Indian and Southern oceans) and Kazakhstan (Caspian Sea) were collected and analysed by multi-assay DNA metabarcoding. Across study locations, between 30% and 52% of eukaryotic families detected were unique to a particular substrate and <6% of families were found in all four substrates. Taxonomic composition varied significantly depending on the substrate s led implying that the suitability (and bias) of an eDNA substrate will depend on the focal taxa. These findings demonstrate that single substrate eDNA metabarcoding likely underestimates the total eukaryotic ersity. Future eDNA experimental design should consider incorporating multiple substrates or select substrate(s) best suited to the specific detection of target taxa.

DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea)

Publisher: Wiley

Date: 12-06-2017

DOI: 10.1002/ECE3.3123

Unlocking the phylogenetic diversity, primary habitats, and abundances of free‐living Symbiodiniaceae on a coral reef

Publisher: Wiley

Date: 29-11-2020

DOI: 10.1111/MEC.15719

University Of Oxford

Location: United Kingdom of Great Britain and Northern Ireland

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McMaster University

Location: Canada

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New Zealand Ministry Of Health

Location: New Zealand

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Australian National University

Location: Australia

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New Zealand Environmental Protection Authority

Location: New Zealand

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Murdoch University

Location: Australia

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Curtin University

Location: Australia

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Lincoln University

Location: New Zealand

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ESR

Location: New Zealand

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Testing For Fishing-Induced Evolution Using DNA From Ancient And Modern Snapper

Start Date: 2017

End Date: 2020

Funder: Marsden Fund

Discovery Projects - Grant ID: DP0771971

Start Date: 2007

End Date: 12-2010

Amount: $192,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP160101508

Start Date: 11-2017

End Date: 10-2021

Amount: $221,973.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP130100050

Start Date: 11-2013

End Date: 12-2017

Amount: $294,263.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP160104473

Start Date: 2016

End Date: 09-2019

Amount: $340,425.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP120103725

Start Date: 2012

End Date: 12-2015

Amount: $152,000.00

Funder: Australian Research Council

ARC Future Fellowships - Grant ID: FT0991741

Start Date: 06-2010

End Date: 12-2014

Amount: $686,400.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP160100839

Start Date: 09-2016

End Date: 09-2019

Amount: $292,169.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP120104435

Start Date: 2012

End Date: 12-2014

Amount: $380,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE150100158

Start Date: 2015

End Date: 12-2015

Amount: $670,000.00

Funder: Australian Research Council