The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“
This content will become publicly available on July 1, 2024
Fish biodiversity is an important indicator of ecosystem health and a priority for the National Park Service in Drakes Estero, a shallow estuary within Point Reyes National Seashore, Marin County, California. However, fish diversity has yet to be described following the removal of oyster aquaculture infrastructure within Drakes Estero from 2016 to 2017. We used environmental DNA (eDNA) to characterize fish biodiversity within Drakes Estero. We amplified fish eDNA with MiFish primers and classified sequences with a 12S rRNA reference database. We identified 110 unique operational taxonomic units (OTUs, at 97% similarity) within the estuary from 40 samples across 4 sites. From these 110 OTUs, we identified 9 species and 13 taxonomic groups at the genus, family, order, or class level within the estuary. Species‐level assignments are limited by a lack of representative sequences targeted by the MiFish primers for 42% of eelgrass fishes in our region that we identified from a literature review in the Northeast Pacific (NEP) from Elkhorn Slough to Humboldt Bay. Despite this limitation, we identified some common Drakes Estero fishes with our eDNA surveys, including the three‐spined stickleback (
- Award ID(s):
- 1829992
- NSF-PAR ID:
- 10482471
- Publisher / Repository:
- Wiley
- Date Published:
- Journal Name:
- Environmental DNA
- Volume:
- 5
- Issue:
- 4
- ISSN:
- 2637-4943
- Page Range / eLocation ID:
- 706 to 722
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
Abstract HTS ”) platforms now enable the rapid sequencing ofDNA from diverse kinds of environmental samples (termed “environmentalDNA ” or “eDNA ”). CouplingHTS with our ability to associate sequences fromeDNA with a taxonomic name is called “eDNA metabarcoding” and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use ofeDNA metabarcoding for surveying animal and plant richness, and the challenges in usingeDNA approaches to estimate relative abundance. We highlighteDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of differenteDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss theeDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications ofeDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and howeDNA metabarcoding can empower citizen science and biodiversity education. -
The use of environmental DNA (eDNA) to assess aquatic biodiversity is a growing field with great potential for monitoring and managing threatened species, like freshwater mussel (Unionidae) populations. Freshwater mussels are globally imperiled and serve essential roles in aquatic systems as a food source and as a natural water filter making their management essential for ecosystem health. Unfortunately, mussel populations are often understudied, and challenges exist to accurately and efficiently describe the full suite of species present. Multispecies eDNA approaches may also be more challenging where freshwater mussel populations are most diverse due to ongoing and significant taxonomic restructuring that has been further complicated by molecular phylogenies using mitochondrial genes. For this study, we developed a microfluidic metabarcoding array that targets a wide range of species, from invertebrates to fishes, with an emphasis on detecting unionid mussels known to be present in the Sipsey River, Alabama. We compared mussel species diversity across six sites with well-studied mussel assemblages using eDNA surveys and traditional quadrat surveys in 2016. We examined how factors such as mussel population density, biomass and location in the river substrate impacted our ability to detect certain species; and investigated unexpected eDNA detections through phylogenetic analysis. Our eDNA results for fish and mussel species were broadly consistent with the data from traditional electrofishing and quadrat-based field surveys, although both community eDNA and conventional sampling detected species unique to that method. Our phylogenetic analysis agreed with other studies that treat Pleurobema decisum and P. chattanoogaense as synonymous species; however, they are still listed as unique species in molecular databases which complicates their identity in a metabarcoding assay. We also found that Fusconaia flava and F. cerina are indistinguishable from one another using a portion of the NADH dehydrogenase Subunit 1 (ND1) marker, which may warrant further investigation into whether or not they are synonymous. Our results show that many factors impacted our ability to detect and correctly identify Unionidae mussel species. Here we describe the obstacles we faced, including the murky phylogeny of Unionidae mussels and turbid river conditions, and our development of a potentially impactful freshwater mussel monitoring eDNA assay.more » « less
-
Biodiversity of Philippine marine fishes: A DNA barcode reference library based on voucher specimensmore » « less
Abstract Accurate identification of fishes is essential for understanding their biology and to ensure food safety for consumers. DNA barcoding is an important tool because it can verify identifications of both whole and processed fishes that have had key morphological characters removed (e.g., filets, fish meal); however, DNA reference libraries are incomplete, and public repositories for sequence data contain incorrectly identified sequences. During a nine-year sampling program in the Philippines, a global biodiversity hotspot for marine fishes, we developed a verified reference library of cytochrome c oxidase subunit I (COI) sequences for 2,525 specimens representing 984 species. Specimens were primarily purchased from markets, with additional diversity collected using rotenone or fishing gear. Species identifications were verified based on taxonomic, phenotypic, and genotypic data, and sequences are associated with voucher specimens, live-color photographs, and genetic samples catalogued at Smithsonian Institution, National Museum of Natural History. The Biodiversity of Philippine Marine Fishes dataset is released herein to increase knowledge of species diversity and distributions and to facilitate accurate identification of market fishes.
-
more » « less
Abstract Biodiversity surveys may require the use of multiple types of sampling gear to maximize the efficiency of species detections, yet few studies have investigated how to optimally distribute effort among gear. In this study, we conducted eDNA metabarcoding and capture‐based sampling surveys (electrofishing, fyke netting, gillnetting, and seining) to sample fish species richness in a large northern temperate lake. We evaluated the success of the sampling methods individually and in combination to determine the allocation of effort and cost across sampling gear that provides the optimal approach for lake‐wide species inventories. We found that eDNA metabarcoding detected more species than any other sampling method, including 11 species that were not detected with any capture‐based approach. Optimal gear combination analyses revealed that detected species richness is maximized when most of the effort or budget is allocated to eDNA metabarcoding, with smaller allocations to seining and fyke netting. eDNA metabarcoding and capture sampling gear showed similar patterns of spatial heterogeneity in the fish community across habitat types, with pelagic samples forming a group that was distinct from nearshore samples. Our results indicate that eDNA metabarcoding is a rapid and cost‐efficient tool for biodiversity monitoring and that assessing the complementarity of multiple sampling types can inform the development of optimal approaches for measuring fish species richness.
-
more » « less
Abstract Aim Identification of the processes that generate and maintain species diversity within the same region can provide insight into biogeographic patterns at broader spatiotemporal scales. Hawkfishes in the genus
Paracirrhites are a unique taxon to explore with respect to niche differentiation, exhibiting diagnostic differences in coloration, and an apparent center of distribution outside of the Indo–Malay–Philippine (IMP) biodiversity hotspot for coral reef fishes. Our aim is to use next‐generation sequencing methods to leverage samples of a taxon at their center of maximum diversity to explore phylogenetic relationships and a possible mechanism of coexistence.Location Flint Island, Southern Line Islands, Republic of Kiribati.
Methods A comprehensive review of museum records, the primary literature, and unpublished field survey records was undertaken to determine ranges for four “arc‐eye” hawkfish species in the
Paracirrhites species complex and a potential hybrid. Fish from fourParacirrhites species were collected from Flint Island in the Southern Line Islands, Republic of Kiribati. Hindgut contents were sequenced, and subsequent metagenomic analyses were used to assess the phylogenetic relatedness of the host fish, the microbiome community structure, and prey remains for each species.Results Phylogenetic analyses conducted with recovered mitochondrial genomes revealed clustering of
P. bicolor withP. arcatus andP. xanthus withP. nisus , which were unexpected on the basis of previous morphological work in this species complex. Differences in taxonomic composition of gut microbial communities and presumed prey remains indicate likely separation of foraging niches.Main Conclusions Our findings point toward previously unidentified relationships in this cryptic species complex at its proposed center of distribution. The three species endemic to the Polynesian province (
P. nisus ,P. xanthus , andP. bicolor ) cluster separately from the more broadly distributedP. arcatus on the basis of relative abundance of metazoan sequences in the gut (presumed prey remains). Discordance between gut microbial communities and phylogeny of the host fish further reinforce the hypothesis of niche separation.
