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Efficient detection and management of non-indigenous species are critical for mitigating their ecological impacts. Environmental DNA (eDNA) techniques have transformed biodiversity monitoring by enabling sensitive and cost-effective surveys. This study compares the efficacy of passive eDNA samplers (PEDS) to conventional active filtration methods for detecting the cryptogenic macroalga Chondria tumulosa within the Papahānaumokuākea Marine National Monument, Hawaiʻi, USA. Three components of the species-specific eDNA assay were evaluated: clinical sensitivity, DNA yield, and overall performance. Site-level detection sensitivity of 15-minute PEDS deployments matched that of 2-L active filtration, with both methods detecting C. tumulosa in all cases where it was known to present. Site-occupancy models provided a robust framework for evaluating overall performance, offering critical insights into the tradeoffs of PEDS for detecting rare taxa. The success of PEDS is largely dependent on the increased number of qPCR replicates employed in this study compared to the previously developed eDNA assay for C. tumulosa . Passive method performance resulted in lower qPCR detection rates with higher probabilities of false-positives and false-negatives. Model estimates for C. tumulosa eDNA occupancy were similar between PEDS affixed to stationary buoys and PEDS attached to roving SCUBA divers. There was, however, a decrease in the eDNA capture rate among samples collected while on SCUBA. We also tested two passive membrane types—research-grade mixed cellulose ester filters and low-cost cotton rounds. The absorbent cotton rounds yielded greater target eDNA yields and were more reliable for inferring the presence of C. tumulosa . However, DNA yields from PEDS were consistently lower than actively filtered samples, indicating the importance of optimizing sampling and processing protocols to balance erroneous detections. Despite these limitations, passive sampling successfully detected C. tumulosa at low abundances (<1%), demonstrating its utility for uncovering cryptic taxa. PEDS are a cost-effective, versatile, and scalable alternative to active filtration, particularly in remote or resource-limited settings.

Climate change is causing shifts in the spatial distribution of species and a reshuffling of the composition of multiple community types. On coral reefs, deep water can act as both refuges and refugia for corals from the combined negative effects of heat and light stress. Phenotypically plastic generalists that can tolerate both low and high light environments could be disproportionately important on future reefs, persisting in refugia and colonizing vacant shallow reefs. We performed a common garden experiment to investigate the effect of light on three different wild-collected genotypes of the abundant, depth-generalist coral Pavona varians . We measured the growth response and reaction norms of six other morphological and functional traits in full sunlight, 75%, and 90% shade. We also modeled the combined effects of light and temperature on growth. P. varians had positive growth in all three treatments, but increased both skeletal mass and 2-D colony footprint most in 90% shade, with a higher density of corallites, and a less rugose skeleton that may enhance light capture. Areas of the colony corresponding to new growth had greater fluorescence of Symbiodiniaceae communities in the darkest treatment. Light did not alter the functional lipid ratio, nor did communities of Symbiodiniaceae vary with light treatments. The model revealed additively negative, but not synergistic, effects of light and temperature on growth. This additively negative relationship in the model is consistent with the hypothesis that reductions in bleaching at depth could be the product of reduced light stress at depth rather than reduced temperature stress. Light-associated plasticity likely allows P.varians to live in a wide variety of habitats and across a broad depth gradient. In reduced light conditions, this species may mitigate some of the negative effects of bleaching temperatures on growth. We predict that P. varians is likely one of a minority of species that may benefit from deep reef refugia.

Background Cytochrome P450s (CYPs) in animals fall into two categories: those that synthesize or metabolize endogenous molecules and those that interact with exogenous chemicals from the diet or the environment. The latter form a critical component of detoxification systems. Results Data mining and manual curation of the Daphnia pulex genome identified 75 functional CYP genes, and three CYP pseudogenes. These CYPs belong to 4 clans, 13 families, and 19 subfamilies. The CYP 2, 3, 4, and mitochondrial clans are the same four clans found in other sequenced protostome genomes. Comparison of the CYPs from D. pulex to the CYPs from insects, vertebrates and sea anemone ( Nematostella vectensis ) show that the CYP2 clan, and to a lesser degree, the CYP4 clan has expanded in Daphnia pulex , whereas the CYP3 clan has expanded in insects. However, the expansion of the Daphnia CYP2 clan is not as great as the expansion observed in deuterostomes and the nematode C. elegans . Mapping of CYP tandem repeat regions demonstrated the unusual expansion of the CYP370 family of the CYP2 clan. The CYP370s are similar to the CYP15s and CYP303s that occur as solo genes in insects, but the CYP370s constitute ~20% of all the CYP genes in Daphnia pulex . Lastly, our phylogenetic comparisons provide new insights into the potential origins of otherwise mysterious CYPs such as CYP46 and CYP19 (aromatase). Conclusion Overall, the cladoceran, D. pulex has a wide range of CYPs with the same clans as insects and nematodes, but with distinct changes in the size and composition of each clan.

Early detection of nuisance species is crucial for managing threatened ecosystems and preventing widespread establishment. Environmental DNA (eDNA) data can increase the sensitivity of biomonitoring programs, often at minimal cost and effort. However, eDNA analyses are prone to errors that can complicate their use in management frameworks. To address this, eDNA studies must consider imperfect detections and estimate error rates. Detecting nuisance species at low abundances with minimal uncertainty is vital for successful containment and eradication. We developed a novel eDNA assay to detect a nuisance marine macroalga across its colonization front using surface seawater samples from Papahānaumokuākea Marine National Monument (PMNM), one of the world’s largest marine reserves. Chondria tumulosa is a cryptogenic red alga with invasive traits, forming dense mats that overgrow coral reefs and smother native flora and fauna in PMNM. We verified the eDNA assay using site-occupancy detection modeling from quantitative polymerase chain reaction (qPCR) data, calibrated with visual estimates of benthic cover of C . tumulosa that ranged from < 1% to 95%. Results were subsequently validated with high-throughput sequencing of amplified eDNA and negative control samples. Overall, the probability of detecting C . tumulosa at occupied sites was at least 92% when multiple qPCR replicates were positive. False-positive rates were 3% or less and false-negative errors were 11% or less. The assay proved effective for routine monitoring at shallow sites (less than 10 m), even when C . tumulosa abundance was below 1%. Successful implementation of eDNA tools in conservation decision-making requires balancing uncertainties in both visual and molecular detection methods. Our results and modeling demonstrated the assay’s high sensitivity to C . tumulosa , and we outline steps to infer ecological presence-absence from molecular data. This reliable, cost-effective tool enhances the detection of low-abundance species, and supports timely management interventions.

Calibration of nucleotide sequence divergence rates provides an important method by which to test many hypotheses of evolution. In the absence of an adequate fossil record, geological events, rather than the first appearances of sister taxa in the geological record, are often used to calibrate molecular clocks. The formation of the Isthmus of Panama, which isolated the tropical western Atlantic and eastern Pacific oceans, is one such event that is frequently used to infer rates of nucleotide sequence divergence. Isthmian calibrations assume that morphologically similar “geminate” species living now on either side of the isthmus were isolated geographically by the latest stages of seaway closure 3.1–3.5 MYA. Here, I have applied calibration dates from the fossil record to cytochrome c oxidase-1 (CO1) and nuclear histone-3 (H3) divergences among six pairs of geminates in the Arcidae to test this hypothesis. Analysis of CO1 first and third positions yield geminate divergences that predate final seaway closure, and on the basis of CO1 first positions, times for all six geminates are significantly greater than 3.5 Myr. H3 sequences produce much more recent geminate divergences, some that are younger than 3.1 Myr. But H3-derived estimates for all arcid geminates are not significantly different from both 0 and 15 Myr. According to CO1, one of the two most divergent pairs, Arca mutabilis and A. imbricata, split more than 30 MYA. This date is compatible with the fossil record, which indicates that these species were morphologically distinct at least 16–21 MYA. Across all CO1 nucleotide sites, divergence rates for arcids are slower than the rates reported for other taxa on the basis of isthmian calibrations, with the exception of rates determined from the least divergent species pair in larger surveys of multiple transisthmian pairs. Rate differences between arcids and some taxa may be real, but these data suggest that divergence rates can be greatly overestimated when dates corresponding to final closure of the Central American Seaway are used to calibrate the molecular clocks of marine organisms.

Ecological patterns in biodiversity are primarily based on conspicuous organisms. Few methods are used to survey the taxonomically rich cryptobiome, which is made up of inhabitants from within microhabitats. One way that cryptic marine biodiversity can be non‐invasively surveyed is by analyzing environmental DNA (eDNA) present in seawater. Using coral reefs as a model system, here we compare estimates of cryptic diversity among community biomass and eDNA metabarcoding sampling methods with a broad eukaryotic marker (COI). First, contributions to eDNA were investigated across cryptobiomes through a comparison of community metabarcoded biomass from standardized autonomous reef monitoring structures (ARMS) to eDNA acquired from seawater in which individual ARMS were soaked. Second, we compared these results to those from eDNA samples taken from within reef crevices and the ambient water column. Metabarcoding of community biomass from ARMS and eDNA from the two types of water samples revealed significantly different communities of cryptic coral reef habitat with little overlap between methods. Taxa that were unique to metabarcoding of ARMS biomass were predominantly from chitinous and calcifying groups (polychaetes, palaemonid shrimp, mollusks, brittle stars, and red algae), which suggests that these taxa are underrepresented in eDNA surveys. Other than the corals themselves, sponges and red algae were significant drivers of reef crevice community differences, while ambient seawater samples detected mostly planktonic organisms and reef fishes. Our data indicate that both eDNA and ARMS provide incomplete accounting of cryptic diversity. Direct sampling of biomass is best suited for building taxonomies and improving databases, whereas eDNA methods offer rapid insights into the composition of cryptobiomes. Because each method likely captures different taxa, multiple targeted assays can be used to provide the greatest estimates of metazoan and macroalgal richness. Cryptic diversity of coral reef habitat was compared among metabarcoding methods using standardized autonomous reef monitoring structures (ARMS) and eDNA applying a broad eukaryotic marker (COI). Metabarcoding of biomass from ARMS and eDNA from water samples revealed fundamentally different communities of cryptic coral reef habitat with little overlap between methods. Our data and analysis indicate that eDNA from the water column should not be used as a standalone method to assess coral reef cryptic diversity.

Genetic diversity (θ), effective population size (N(e)), and contemporary levels of gene flow are important parameters to estimate for species of conservation concern, such as the globally endangered scalloped hammerhead shark, Sphyrna lewini. Therefore, we have reconstructed the demographic history of S. lewini across its Eastern Pacific (EP) range by applying classical and coalescent population genetic methods to a combination of 15 microsatellite loci and mtDNA control region sequences. In addition to significant population genetic structure and isolation-by-distance among seven coastal sites between central Mexico and Ecuador, the analyses revealed that all populations have experienced a bottleneck and that all current values of θ are at least an order of magnitude smaller than ancestral θ, indicating large decreases in N(e) (θ = 4N(e)μ), where μ is the mutation rate. Application of the isolation-with-migration (IM) model showed modest but significant genetic connectivity between most sampled sites (point estimates of Nm = 0.1-16.7), with divergence times (t) among all populations significantly greater than zero. Using a conservative (i.e., slow) fossil-based taxon-specific phylogenetic calibration for mtDNA mutation rates, posterior probability distributions (PPDs) for the onset of the decline in N(e) predate modern fishing in this region. The cause of decline over the last several thousand years is unknown but is highly atypical as a post-glacial demographic history. Regardless of the cause, our data and analyses suggest that S. lewini was far more abundant throughout the EP in the past than at present.

The European eel ( Anguilla anguilla ) has declined by over 90% since the early 1980s and has been listed as critically endangered. Yet, despite strict export bans from the European Union, the European eel is still sold illegally in many countries. Efforts to monitor the trade of European eels have been primarily concentrated in Asian markets where concerningly high rates of European eel have been reported. Comparably fewer studies have assessed the identities of eel samples from the United States (US), despite the obvious implications for eel conservation. To address this knowledge gap, we purchased 137 eel products (134 freshwater eels and three saltwater eels) from grocers, sushi bars, and restaurants in nine states across the US from 2019 to 2021. Seven samples (5.2%) labeled as freshwater eels (or “unagi”) were identified as European eels using a combination of mitochondrial (cytochrome b) and nuclear (18S rRNA) restriction digestion assays, a fast and inexpensive molecular tool for seafood identification that can identify hybrids between European eels ( A. anguilla ) and American eels ( A. rostrata ). No hybrids between European and American eels were found and all seven samples identified with restriction digestion as European eels were confirmed by sequencing of cytochrome b and 18S rRNA. Frequency of European eels in US markets did not significantly correlate with state or retail type. Although illegal eel exports are likely reaching US consumers, the frequency of European eel samples in this study of the US market is much lower than found in other non-European countries.

Seafood mislabeling distorts the true abundance of fish in the sea, defrauds consumers, and can also cause unwanted exposure to harmful pollutants. By combining genetic data with analyses of total mercury content, we have investigated how species substitutions and fishery-stock substitutions obscure mercury contamination in Patagonian toothfish (Dissostichus eleginoides), also known as \"Chilean sea bass\". Patagonian toothfish show wide variation in mercury concentrations such that consumers may be exposed to either acceptable or unacceptable levels of mercury depending on the geographic origins of the fish and the allowable limits of different countries. Most notably, stocks of Patagonian toothfish in Chile accumulate significantly more mercury than stocks closer to the South Pole, including the South Georgia/Shag Rocks stock, a fishery certified by the Marine Stewardship Council (MSC) as sustainably fished. Consistent with the documented geography of mercury contamination, our analysis showed that, on average, retail fish labeled as MSC-certified Patagonian toothfish had only half the mercury of uncertified fish. However, consideration of genetic data that were informative about seafood substitutions revealed a complex pattern of contamination hidden from consumers: species substitutions artificially inflated the expected difference in mercury levels between MSC-certified and uncertified fish whereas fishery stock substitutions artificially reduced the expected difference in mercury content between MSC-certified and uncertified fish that were actually D. eleginoides. Among MSC-certified fish that were actually D. eleginoides, several with exogenous mtDNA haplotypes (i.e., not known from the certified fishery) had mercury concentrations on par with uncertified fish from Chile. Overall, our analysis of mercury was consistent with inferences from the genetic data about the geographic origins of the fish, demonstrated the potential negative impact of seafood mislabeling on unwanted mercury exposure for consumers, and showed that fishery-stock substitutions may expose consumers to significantly greater mercury concentrations in retail-acquired fish than species substitutions.