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1. Northeast Pacific eelgrass fish communities characterized by environmental DNA represent local diversity and show habitat specificity

   https://doi.org/10.1002/edn3.431  

   Beatty, Deanna S.; Deen, Emma; Gross, Collin; Stachowicz, John J. (July 2023, Environmental DNA)

   Abstract 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 (Gasterosteus aculeatus), Pacific staghorn sculpin (Leptocottus armatus), surfperches (Embiotocidae), gobies (Gobiidae), and a hound shark (Triakidae). We also compared fish biodiversity within the estuary with that from nearby Limantour Beach, a coastal site. Limantour beach differed in community composition from Drakes Estero and was characterized by high relative abundances of anchovy (Engraulissp.) and herring (Clupeasp.). Thus, we can distinguish estuarine and non‐estuarine sites (<10 km away) with eDNA surveys. Further, eDNA surveys accounted for greater fish diversity than seine surveys conducted at one site within the estuary. Environmental DNA surveys will likely be a useful tool to monitor fish biodiversity across eelgrass estuaries in the Northeast Pacific, especially as reference databases become better populated with regional species. 

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2. Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)

   https://doi.org/10.1038/s41477-023-01464-3  

   Yu, Lei; Khachaturyan, Marina; Matschiner, Michael; Healey, Adam; Bauer, Diane; Cameron, Brenda; Cusson, Mathieu; Emmett Duffy, J.; Joel Fodrie, F.; Gill, Diana; et al (August 2023, Nature Plants)

   Abstract Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marinaL.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Two west-to-east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival ofZ. marinain the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present there for ~243 ky (thousand years). Mediterranean populations were founded ~44 kya, while extant distributions along western and eastern Atlantic shores were founded at the end of the Last Glacial Maximum (~19 kya), with at least one major refuge being the North Carolina region. The recent colonization and five- to sevenfold lower genomic diversity of the Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans. 

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3. Effects of seagrass restoration on coastal fish abundance and diversity

   https://doi.org/10.1111/cobi.14147  

   Hardison, Sean B.; McGlathery, Karen J.; Castorani, Max C. (January 2023, Conservation Biology)

   Restoration is accelerating to reverse global declines of key habitats and recover lost ecosystem functions, particularly in coastal ecosystems. However, there is high uncertainty about the long-term capacity of restored ecosystems to provide habitat and increase biodiversity and the degree to which these ecosystem services are mediated by spatial and temporal environmental variability. We addressed these gaps by sampling fishes biannually for 5–7 years (2012–2018) at 16 sites inside and outside a rapidly expanding restored seagrass meadow in coastal Virginia (USA). Despite substantial among-year variation in abun-dance and species composition, seine catches in restored seagrass beds were consistently larger (6.4 times more fish, p<0.001) and more speciose (2.6 times greater species richness, p<0.001; 3.1 times greater Hill–Shannon diversity, p=0.03) than seine catches in adjacent unvegetated areas. Catches were particularly larger during summer than autumn(p<0.01). Structural equation modeling revealed that depth and water residence time interacted to control seagrass presence, leading to higher fish abundance and richness in shallow, well-flushed areas that supported seagrass. Together, our results indicate that seagrass restoration yields large and consistent benefits for many coastal fishes, but that restoration and its benefits are sensitive to the dynamic seascapes in which restoration is conducted. Consideration of how seascape-scale environmental variability affects the success of habitat restoration and subsequent ecosystem function will improve restoration outcomes and the provisioning of ecosystem services. 

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4. Molecular identity crisis: environmental DNA metabarcoding meets traditional taxonomy—assessing biodiversity and freshwater mussel populations (Unionidae) in Alabama

   https://doi.org/10.7717/peerj.15127  

   Hauck, Laura L.; Atkinson, Carla L.; Homyack, Jessica A.; Penaluna, Brooke E.; Mangum, Clay; Coble, Ashley A.; Nettles, Jami; Thornton-Frost, Jamie E.; Fix, Miranda J. (January 2023, PeerJ)

   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. 

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5. Spatial distribution, diversity, and taphonomy of clypeasteroid and spatangoid echinoids of the central Florida Keys

   https://doi.org/10.7717/peerj.14245  

   Grun, Tobias B.; Kowalewski, Michał (January 2022, PeerJ)

   Background Irregular echinoids are ecosystem engineers with diverse functional services. Documenting present-day distribution of those widespread organisms is important for understanding their ecological significance and enhancing our ability to interpret their rich fossil record. Methods This study summarizes SCUBA surveys of clypeasteroid and spatangoid echinoids conducted in 2020 and 2021 along the central part of the Florida Keys. The survey included observations on both live and dead specimens, their distribution, habitat preferences, abundance, and live-dead comparison. Results Echinoids were found at 17 out of 27 examined sites (63%) and occurred across a wide range of habitats including coastal seagrass meadows, subtidal sand and seagrass settings of the Hawk Channel, backreef sands, and fine muddy sands of deeper forereef habitats. The encountered species, both dead and alive, included Clypeaster rosaceus (four sites), Clypeaster subdepressus (five sites), Encope michelini (three sites), Leodia sexiesperforata (eight sites), Meoma ventricosa (nine sites), and Plagiobrissus grandis (four sites). All sites were dominated by one species, but some sites included up to five echinoid species. Live-dead fidelity was high, including a good agreement in species composition of living and dead assemblages, congruence in species rank abundance, and overlapping spatial distribution patterns. This high fidelity may either reflect long-term persistence of local echinoid populations or fragility of echinoid tests that could prevent post-mortem transport and the formation of time-averaged death assemblages. Regardless of causative factors, the live-dead comparisons suggest that irregular echinoid assemblages, from settings that are comparable to the study area, may provide a fossil record with a high spatial and compositional fidelity. The survey of live fauna is consistent with past regional surveys in terms of identity of observed species, their rank abundance, and their spatial distribution patterns. The results suggest that despite increasingly frequent hurricanes, active seasonal fisheries, massive tourism, and urban development, irregular echinoids continue to thrive across a wide range of habitats where they provide diverse ecosystem services by oxygenating sediments, recycling organic matter, supporting commensal organisms, and providing food to predators. Results reported here document the present-day status of local echinoid populations and should serve as a useful reference point for assessing future regional changes in echinoid distribution and abundance. 

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