Ancient environmental DNA indicates limited human impact on marine biodiversity in pre-industrial Iceland.

Human activities are affecting marine biodiversity globally by accelerating extinction rates, altering ecosystem conditions and changing community structures. These changes can only be understood through establishing the ecosystem state prior to significant anthropogenic impact and by disentangling the anthropogenic effect from natural climatic changes. Here, we reconstruct marine biodiversity in Iceland across three millennia (1315 BCE-1785 CE), encompassing periods of climatic fluctuation and human settlement, to explore the comparative effect of natural and anthropogenic forces on marine biodiversity.

Shifting seas: understanding deep-time human impacts on marine ecosystems.

Humans have interacted with, and impacted, marine ecosystems for millennia. During this time, the oceans have experienced ecosystem degradation through harvesting, habitat change, pollution, the introduction of invasive species and climate change. Despite extensive documentation of substantial recent anthropogenic impacts, our understanding of ancient marine biodiversity remains limited for many ocean regions.

Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA.

The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human-impacted oceans. Sequencing sedimentary ancient DNA (sedaDNA) is an emerging method for generating high-resolution biodiversity time-series data, offering insights into past ecosystems. However, few studies directly compare the two predominant sedaDNA sequencing approaches: metabarcoding and shotgun-metagenomics, and it remains unclear if these methodological differences affect diversity metrics.

Diet components associated with specific bacterial taxa shape overall gut community compositions in omnivorous African viverrids.

Gut bacterial communities provide flexibility to hosts during dietary changes. Despite the increasing number of studies exploring the associations between broader dietary guilds of mammalian hosts and their gut bacteria, it is generally unclear how diversity and variability in consumed diets link to gut bacterial taxa in wild non-primate mammals, particularly in omnivores. Here, we contribute to filling this gap by exploring consumed diets and gut bacterial community compositions with metabarcoding of faecal samples for two African mammals, and spp.

Analysing the effects of distance, taxon and biomass on vertebrate detections using bulk-collected carrion fly iDNA.

Invertebrate-derived DNA (iDNA) metabarcoding from carrion flies is a powerful, non-invasive tool that has value for assessing vertebrate diversity. However, unknowns exist around the factors that influence vertebrate detections, such as spatial limits to iDNA signals or if detections are influenced by taxonomic class or estimated biomass of the vertebrates of interest. Using a bulk-collection method, we captured flies from within a zoo and along transects extending 4 km away from this location.

Vertebrate environmental DNA from leaf swabs.

Terrestrial vertebrates are threatened by anthropogenic activities around the world. The rapid biodiversity loss that ensues is most intense in the tropics and affects ecosystem functions, such as seed dispersal, or may facilitate pathogen transmission. Monitoring vertebrate distributions is essential for understanding changes in biodiversity and ecosystems and also for adaptive management strategies.

Airborne environmental DNA captures terrestrial vertebrate diversity in nature.

The current biodiversity and climate crises highlight the need for efficient tools to monitor terrestrial ecosystems. Here, we provide evidence for the use of airborne eDNA analyses as a novel method for detecting terrestrial vertebrate communities in nature. Metabarcoding of 143 airborne eDNA samples collected during 3 days in a mixed forest in Denmark yielded 64 bird, mammal, fish and amphibian taxa, of which the detected 57 'wild' taxa represent over a quarter of the around 210 terrestrial vertebrates that occur in the overall area.

Use of carrion fly iDNA metabarcoding to monitor invasive and native mammals.

Severely fragmented habitats increase the risk of extirpation of native mammal populations through isolation, increased edge effects, and predation. Therefore, monitoring the movement of mammal populations through anthropogenically altered landscapes can inform conservation. We used metabarcoding of invertebrate-derived DNA (iDNA) from carrion flies (Calliphoridae and Sarcophagidae) to track mammal populations in the wheat belt of southwestern Australia, where widespread clearing for agriculture has removed most of the native perennial vegetation and replaced it with an agricultural system.

Transforming terrestrial biodiversity surveys using airborne eDNA.

Studies show that land-living animals, plants, fungi, and bacteria leave DNA traces in the air. These results imply that sequencing of bioaerosols might be a powerful tool for simultaneous surveys of terrestrial biodiversity across lifeforms, but in parallel, it highlights the need to carefully control for possible contaminants.

Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods.

Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-scale syntheses may be compromised if metabarcoding workflows differ from each other.

Shunning the scoop: Sidestepping the race to publish.

What happens when a researcher finds out that research very similar to their own is already being conducted? What if they find out that the said research is also very close to being published? First, there is probably anxiety and panic. Maybe, there are frantic calls to collaborators. Perhaps Twitter rants about the phenomenon of scooping that plagues all researchers, especially those early-career researchers who often feel they are in a race to get their best work out to the world.

Airborne environmental DNA for terrestrial vertebrate community monitoring.

Biodiversity monitoring at the community scale is a critical element of assessing and studying species distributions, ecology, diversity, and movements, and it is key to understanding and tracking environmental and anthropogenic effects on natural ecosystems. Vertebrates in terrestrial ecosystems are experiencing extinctions and declines in both population numbers and sizes due to increasing threats from human activities and environmental change. Terrestrial vertebrate monitoring using existing methods is generally costly and laborious, and although environmental DNA (eDNA) is becoming the tool of choice to assess biodiversity, few sample types effectively capture terrestrial vertebrate diversity.

Strategies for sample labelling and library preparation in DNA metabarcoding studies.

Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this, PCR amplification is carried out with primers designed to target a taxonomically informative marker within a taxonomic group, and sample-specific nucleotide identifiers are added to the amplicons prior to sequencing. The latter enables assignment of the sequences back to the samples they originated from.

The potential of aquatic bloodfeeding and nonbloodfeeding leeches as a tool for iDNA characterisation.

Leeches play important roles in food webs due to their abundance, diversity and feeding habits. Studies using invertebrate-derived DNA (iDNA) extracted from leech gut contents to target vertebrate DNA have focused on the Indo-Pacific region and mainly leveraged the leech family Haemadipsidae, composed of bloodfeeding terrestrial leeches, while predatory, fluid/tissue-feeding and aquatic bloodfeeding species have been largely disregarded. While there is some general knowledge regarding the taxonomic groups that leeches prefer to feed on, detailed taxonomic resolution is missing and, therefore, their potential use for monitoring animals is unknown.

Metagenomics: A viable tool for reconstructing herbivore diet.

Metagenomics can generate data on the diet of herbivores, without the need for primer selection and PCR enrichment steps as is necessary in metabarcoding. Metagenomic approaches to diet analysis have remained relatively unexplored, requiring validation of bioinformatic steps. Currently, no metagenomic herbivore diet studies have utilized both chloroplast and nuclear markers as reference sequences for plant identification, which would increase the number of reads that could be taxonomically informative.

Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis.

High-throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge.

Tagsteady: A metabarcoding library preparation protocol to avoid false assignment of sequences to samples.

Metabarcoding of environmental DNA (eDNA) and DNA extracted from bulk specimen samples is a powerful tool in studies of biodiversity, diet and ecological interactions as its inherent labelling of amplicons allows sequencing of taxonomically informative genetic markers from many samples in parallel. However, the occurrence of so-called 'tag-jumps' can cause incorrect assignment of sequences to samples and artificially inflate diversity. Two steps during library preparation of pools of 5' nucleotide-tagged amplicons have been suggested to cause tag-jumps: (a) T4 DNA polymerase blunt-ending in the end-repair step and (b) postligation PCR amplification of amplicon libraries.

An appetite for pests: Synanthropic insectivorous bats exploit cotton pest irruptions and consume various deleterious arthropods.

Conservation biological control (CBC) seeks to minimize the deleterious effects of agricultural pests by enhancing the efficiency of natural enemies. Despite the documented potential of insectivorous bats to consume pests, many synanthropic bat species are still underappreciated as beneficial species. We investigated the diet of Kuhl's pipistrelle (Pipistrellus kuhlii), a common synanthropic insectivorous bat that forages in urban and agricultural areas, to determine whether it may function as a natural enemy in CBC.

Skmer: assembly-free and alignment-free sample identification using genome skims.

The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally. This approach discards the nuclear DNA, which constitutes the vast majority of the data.

Promises and pitfalls of using high-throughput sequencing for diet analysis.

The application of high-throughput sequencing-based approaches to DNA extracted from environmental samples such as gut contents and faeces has become a popular tool for studying dietary habits of animals. Due to the high resolution and prey detection capacity they provide, both metabarcoding and shotgun sequencing are increasingly used to address ecological questions grounded in dietary relationships. Despite their great promise in this context, recent research has unveiled how a wealth of biological (related to the study system) and technical (related to the methodology) factors can distort the signal of taxonomic composition and diversity.

Using metabarcoding to compare the suitability of two blood-feeding leech species for sampling mammalian diversity in North Borneo.

The application of high-throughput sequencing (HTS) for metabarcoding of mixed samples offers new opportunities in conservation biology. Recently, the successful detection of prey DNA from the guts of leeches has raised the possibility that these, and other blood-feeding invertebrates, might serve as useful samplers of mammals. Yet little is known about whether sympatric leech species differ in their feeding preferences, and whether this has a bearing on their relative suitability for monitoring local mammalian diversity.

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

The use of environmental DNA (eDNA) has become an applicable noninvasive tool with which to obtain information about biodiversity. A subdiscipline of eDNA is iDNA (invertebrate-derived DNA), where genetic material ingested by invertebrates is used to characterize the biodiversity 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 samples from only a single or a few different locations.

Using DNA metabarcoding for simultaneous inference of common vampire bat diet and population structure.

Metabarcoding diet analysis has become a valuable tool in animal ecology; however, co-amplified predator sequences are not generally used for anything other than to validate predator identity. Exemplified by the common vampire bat, we demonstrate the use of metabarcoding to infer predator population structure alongside diet assessments. Growing populations of common vampire bats impact human, livestock and wildlife health in Latin America through transmission of pathogens, such as lethal rabies viruses.

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat.

Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat (Desmodus rotundus), one of the only three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary adaptation. Specifically, we assembled its high-quality reference genome (scaffold N50 = 26.