The role of taxonomic expertise in interpretation of metabarcoding studies

Abstract The performance of DNA metabarcoding approaches for characterizing biodiversity can be influenced by multiple factors. Here, we used morphological assessment of taxa in zooplankton samples to develop a large barcode database and to assess the congruence of taxonomic identification with metabarcoding under different conditions. We analysed taxonomic assignment of metabarcoded samples using two genetic markers (COI, 18S V1–2), two types of clustering into molecular operational taxonomic units (OTUs, ZOTUs), and three methods for taxonomic assignment (RDP Classifier, BLASTn to GenBank, BLASTn to a local barcode database). The local database includes 1042 COI and 1108 18S (SSU) barcode sequences, and we added new high-quality sequences to GenBank for both markers, including 109 contributions at the species level. The number of phyla detected and the number of taxa identified to phylum varied between a genetic marker and among the three methods used for taxonomic assignments. Blasting the metabarcodes to the local database generated multiple unique contributions to identify OTUs and ZOTUs. We argue that a multi-marker approach combined with taxonomic expertise to develop a curated, vouchered, local barcode database increases taxon detection with metabarcoding, and its potential as a tool for zooplankton biodiversity surveys

Rapidly Changing Range Limits in a Warming World: Critical Data Limitations and Knowledge Gaps for Advancing Understanding of Mangrove Range Dynamics in the Southeastern USA

Climate change is altering species’ range limits and transforming ecosystems. For example, warming temperatures are leading to the range expansion of tropical, cold-sensitive species at the expense of their cold-tolerant counterparts. In some temperate and subtropical coastal wetlands, warming winters are enabling mangrove forest encroachment into salt marsh, which is a major regime shift that has significant ecological and societal ramifications. Here, we synthesized existing data and expert knowledge to assess the distribution of mangroves near rapidly changing range limits in the southeastern USA. We used expert elicitation to identify data limitations and highlight knowledge gaps for advancing understanding of past, current, and future range dynamics. Mangroves near poleward range limits are often shorter, wider, and more shrublike compared to their tropical counterparts that grow as tall forests in freeze-free, resource-rich environments. The northern range limits of mangroves in the southeastern USA are particularly dynamic and climate sensitive due to abundance of suitable coastal wetland habitat and the exposure of mangroves to winter temperature extremes that are much colder than comparable range limits on other continents. Thus, there is need for methodological refinements and improved spatiotemporal data regarding changes in mangrove structure and abundance near northern range limits in the southeastern USA. Advancing understanding of rapidly changing range limits is critical for foundation plant species such as mangroves, as it provides a basis for anticipating and preparing for the cascading effects of climate-induced species redistribution on ecosystems and the human communities that depend on their ecosystem services

Adult life strategy affects distribution patterns in abyssal isopods – implications for conservation in Pacific nodule areas

With increasing pressure to extract minerals from the deep-sea bed, understanding the ecological and evolutionary processes that limit the spatial distribution of species is critical to assessing ecosystem resilience to mining impacts. The aim of our study is to gain a better knowledge about the abyssal isopod crustacean fauna of the central Pacific manganese nodule province (Clarion–Clipperton Fracture Zone, CCZ). In total, we examined 22 epibenthic sledge (EBS) samples taken at five abyssal areas located in the central northern Pacific including four contracting areas and one Area of Particular Environmental Interest (APEI3). Additional samples come from the DISturbance and reCOLonization experiment (DISCOL) area situated in the Peru Basin, southeastern Pacific. Using an integrative approach that combined morphological and genetic methods with species delimitation analyses (SDs) we assessed patterns of species range size, diversity, and community composition for four different isopod families (Munnopsidae Lilljeborg, 1864; Desmosomatidae Sars, 1897; Haploniscidae Hansen, 1916; and Macrostylidae Hansen, 1916) displaying different dispersal capacities as adults. Isopods are brooders, so their distribution and connectivity cannot be explained by larval dispersal but rather by adult locomotion. In particular, our objectives were to (1) identify potential differences in the distributional ranges of isopod families relative to their locomotory potential and to (2) evaluate the representativeness of the APEI for the preservation of regional biodiversity in the CCZ following mining disturbances. From 619 specimens, our SD analysis could distinguish 170 species, most of which were new to science (94.1 %). We found that increased locomotory ability correlated with higher species diversity with 9 species of Macrostylidae, 23 of Haploniscidae, 52 of Desmosomatidae, and 86 of Munnopsidae. This is supported by family-level rarefaction analyses. As expected, we found the largest species ranges in the families with swimming abilities, with a maximum recorded species range of 5245 and 4480 km in Munnopsidae and Desmosomatidae, respectively. The less motile Haploniscidae and Macrostylidae had maximal species ranges of 1391 and 1440 km, respectively. Overall, rarefaction analyses indicated that species richness did not vary much between areas, but the real number of species was still not sufficiently sampled. This is also indicated by the large proportion of singletons (40.5 %) found in this study. The investigated contractor areas in the CCZ were more similar in species composition and had a higher proportion of shared species between each other than the closely located APEI3 and the distantly located DISCOL area. In fact, the DISCOL area, located in the Peru Basin, had more species in common with the core CCZ areas than APEI3. In this regard, APEI3 does not appear to be representative as serving as a reservoir for the fauna of the investigated contractor areas, at least for isopods, as it has a different species composition. Certainly, more data from other APEIs, as well as preservation reference zones within contractor areas, are urgently needed in order to assess their potential as resources of recolonization of impacted seabed

Anchialine biodiversity in the Turks and Caicos Islands: New discoveries and current faunal composition

Lying at the southernmost point of the Lucayan Archipelago, the Turks and Caicos Islands are amongst the better studied localities for anchialine cave biodiversity. For nearly five decades, novel invertebrate fauna, comprised primarily of crustaceans, have been collected from these tidally influenced pools – but new findings are always on the horizon. Herein we present new records of crustaceans and annelids from anchialine blue holes and horizontal caves of the Turks and Caicos. These findings include two potentially new species of meiofaunal annelids and a new species of remipede collected from a shallow water cave pool. Our 2019 expedition additionally expands known faunal distributions for several taxa across the Caicos islands, and raises the biodiversity of the region to 35 species, 13 of them considered endemic. This is the first comprehensive faunal list for the anchialine systems in the Caicos Bank