Biology subjects

Barber, P. H.

Publications and source records attributed to Barber, P. H..

4 recordsLinked to original sources

bioRxiv2021

Environmental DNA in a Global Biodiversity Hotspot: Lessons from Coral Reef Fish Diversity Across the Indonesian Archipelago

Indonesia is the heart of the Coral Triangle, the worlds most diverse marine ecosystem. Preserving the biological and economic value of this marine biodiversity requires efficient and economical ecosystem monitoring, yet our understanding of marine biodiversity in this region remains limited. This study uses environmental DNA (eDNA) to survey fish communities across a pronounced biodiversity gradient in Indonesia. A total of 12,939,690 sequence reads of MiFish 12S rRNA from 39 sites spanning 7 regions of Indonesia revealed 4,146 Amplified Sequence Variants (ASVs). Regional patterns of fish diversity based on eDNA broadly conformed to expectations based on traditional biodiversity survey methods, with the highest fish biodiversity in Raja Ampat and generally lower diversity in Western Indonesia. However, eDNA performed relatively poorly compared to visual survey methods in site-by-site comparisons, both in terms of total number of taxa recovered and ability to assign species names to ASVs. This result stands in a stark contrast to eDNA studies of temperate and tropical ecosystems with lower diversity. Analyses show that while sequencing depth was sufficient to capture all fish diversity within individual seawater samples, variation among samples from individual localities was high, and sampling effort was insufficient to capture all fish diversity at a given sampling site. Interestingly, mean ASVs recovered per one-liter seawater was surprisingly similar across sites, despite substantial differences in total diversity, suggesting a limit to total ASVs (~200) per one-liter eDNA sample. Combined, results highlight two major challenges of eDNA in highly diverse ecosystems such as the Coral Triangle. First, reference databases are incomplete and insufficient for effective ASV taxonomic assignment. Second, eDNA sampling design developed from lower diversity temperate marine ecosystems are inadequate to fully capture diversity of biodiversity hotspots like the Coral Triangle.

ecology↗

bioRxiv2020

Investigating temporal and spatial variation of eDNA in a nearshore rocky reef environment

Environmental DNA (eDNA) is increasingly used to measure biodiversity of marine ecosystems. However, key aspects of spatial and temporal dynamics of eDNA remain unknown. Particularly, it is unclear how long eDNA signals persist locally in dynamic marine environments, since degradation rates have predominantly been quantified through mesocosm studies. To determine in situ eDNA residence times, we introduced an eDNA signal from a non-native fish into a Southern California rocky reef ecosystem, and then measured changes in both introduced and background eDNA signals over 96 hours. Foreign eDNA signal could no longer be detected 7.5 hours after introduction, far exceeding disappearance rates quantified in laboratory studies. In addition, native vertebrate eDNA signals varied greatly over the 96 hours of observation, but time of day and tidal direction did not drive this variation in community structure. Species accumulation curves showed that standard sampling protocols using 3 replicate 1 L sea water samples were insufficient to capture full diversity of local marine vertebrates, capturing only 76% of all taxa. Despite this limitation, a single eDNA sample captured greater vertbrate diversity than 18 SCUBA based underwater visual transect surveys conducted at a nearby site. There was no significant difference in species richness between temporal replicates and spatial replicates, suggesting a space for time substitution may be effective for fully capturing the diversity of local marine vertebrate communities in nearshore rocky reef environments. This result is particularly important in designing eDNA metabarcoding sampling protocols to capture local marine species diversity.

ecology↗

bioRxiv2020

MiSebastes: An eDNA metabarcoding primer set for rockfishes (genus Sebastes)

Environmental DNA (eDNA) is a promising biomonitoring tool for marine ecosystems, but its effectiveness for North Pacific coastal fishes is limited by the inability of existing barcoding primers to differentiate among rockfishes in the genus Sebastes. Comprised of 110 commercially and ecologically important species, this recent radiation is exceptionally speciose, and exhibits high sequence similarity among species at standard barcoding loci. Here, we report new Sebastes-specific metabarcoding primers that target mitochondrial cytochrome B. Amongst the 110 Sebastes species, 85 unique barcodes (of which 62 are species-specific) were identified in our amplicon region based on available reference sequences. The majority of the remaining barcodes are shared by only two species. Importantly, MiSebastes yield unique barcodes for 28 of 44 commercially harvested species in California, a dramatic improvement compared to the widely employed MiFish 12S primers which only recover one of 44. Tests of these primers in an aquarium mesocosm containing 16 rockfish species confirms the utility of these new primers for eDNA metabarcoding, providing an important biomonitoring tool for these key coastal marine fishes.

ecology↗

bioRxiv2020

eDNA metabarcoding as a biomonitoring tool for marine protected areas

Monitoring of marine protected areas (MPAs) is critical for marine ecosystem management, yet current protocols rely on SCUBA-based visual surveys that are costly and time consuming, limiting their scope and effectiveness. Environmental DNA (eDNA) metabarcoding is a promising alternative for marine ecosystem monitoring, but more direct comparisons to visual surveys are needed to understand the strengths and limitations of each approach. This study compares fish communities inside and outside the Scorpion State Marine Reserve off Santa Cruz Island, CA using eDNA metabarcoding and underwater visual census surveys. Results from eDNA captured 76% (19/25) of fish species and 95% (19/20) of fish genera observed during pairwise underwater visual census. Species missed by eDNA were due to the inability of MiFish 12S barcodes to differentiate species of rockfishes (Sebastes, n=4) or low site occupancy rates of crevice-dwelling Lythrypnus gobies. However, eDNA detected an additional 30 fish species not recorded in paired visual surveys, but previously reported from prior visual surveys, highlighting the sensitivity of eDNA. Significant variation in eDNA signatures by location (50m) and site (~1000m) demonstrates the sensitivity of eDNA to address key questions such as community composition inside and outside MPAs. Interestingly, eDNA results recorded higher species richness outside the MPA while visual surveys observed the opposite pattern. This result is likely caused by swamping effects of high fish abundance in MPAs that reduce detection probabilities of pelagic and intertidal taxa. Results demonstrate the utility of eDNA metabarcoding for monitoring marine ecosystems, providing an important complementary tool to visual methods.

molecular biology↗