For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least 7 and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways. [Brachyura; convergent evolution; crustaceans; divergence times; fossil calibration; molecular phylogeny; terrestrialization; threshold model.].

Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications.

Ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. Using modern ecological models and community science, we integrate environmental DNA and Earth observations to produce a time snapshot of regional biodiversity patterns and provide multi-scalar community-level characterization. We collected 278 samples in spring 2017 from coastal, shrub, and lowland forest sites in California, a complex ecosystem and biodiversity hotspot. We recovered 16,118 taxonomic entries from eDNA analyses and compiled associated traditional observations and environmental data to assess how well they predicted alpha, beta, and zeta diversity. We found that local habitat classification was diagnostic of community composition and distinct communities and organisms in different kingdoms are predicted by different environmental variables. Nonetheless, gradient forest models of 915 families recovered by eDNA analysis and using BIOCLIM variables, Sentinel-2 satellite data, human impact, and topographical features as predictors, explained 35% of the variance in community turnover. Elevation, sand percentage, and photosynthetic activities (NDVI32) were the top predictors. In addition to this signal of environmental filtering, we found a positive relationship between environmentally predicted families and their numbers of biotic interactions, suggesting environmental change could have a disproportionate effect on community networks. Together, these analyses show that coupling eDNA with environmental predictors including remote sensing data has capacity to test proposed Essential Biodiversity Variables and create new landscape biodiversity baselines that span the tree of life.

Climate change is leading to habitat shifts that threaten species persistence throughout California's unique ecosystems. Baseline biodiversity data would provide opportunities for habitats to be managed under short-term and long-term environmental change. Aiming to provide biodiversity data, the UC Conservation Genomics Consortium launched the California Environmental DNA (CALeDNA) program to be a citizen and community science biomonitoring initiative that uses environmental DNA (eDNA, DNA shed from organisms such as from fur, feces, spores, pollen or leaves). Now with results from 1,000 samples shared online, California biodiversity patterns are discoverable. Soil, sediment and water collected by researchers, undergraduates and the public reveal a new catalog of thousands of organisms that only slightly overlap with traditional survey bioinventories. The CALeDNA website lets users explore the taxonomic diversity in different ways, and researchers have created tools to help people new to eDNA to analyze community ecology patterns. Although eDNA results are not always precise, the program team is making progress to fit it into California's biodiversity management toolbox, such as for monitoring ecosystem recovery after invasive species removal or wildfire.

Unique ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. We offer a way to use environmental DNA, community science and remote sensing together as methods to reduce the discrepancy between the magnitude of change and historical approaches to measure it. Taking advantages of modern ecological models, we integrate environmental DNA and Earth observations to evaluate regional biodiversity patterns for a snapshot of time, and provide critical community-level characterization. We collected 278 samples in Spring 2017 from coastal, shrub and lowland forest sites in California, a large-scale biodiversity hotspot. We applied gradient forest to model 915 family occurrences and community composition together with environmental variables and multi-scalar habitat classifications to produce a statewide biodiversity-based map. 16,118 taxonomic entries recovered were associated with environmental variables to test their predictive strength on alpha, beta, and zeta diversity. Local habitat classification was diagnostic of community composition, illuminating a characteristic of biodiversity hotspots. Using gradient forest models, environmental variables predicted 35% of the variance in eDNA patterns at the family level, with elevation, sand percentage, and greenness (NDVI32) as the top predictors. This predictive power was higher than we found in published literature at global scale. In addition to this indication of substantial environmental filtering, we also found a positive relationship between environmentally predicted families and their numbers of biotic interactions. In aggregate, these analyses showed that strong eDNA community-environment correlation is a general characteristic of temperate ecosystems, and may explain why communities easily destabilize under disturbances. Our study provides the first example of integrating citizen science based eDNA with biodiversity mapping across the tree of life, with promises to produce large scale, high resolution assessments that promote a more comprehensive and predictive understanding of the factors that influence biodiversity and enhance its maintenance.

Habitat degradation and land-use change severely threaten the survival of fairy shrimp and the vernal pools in which they live. Limiting effective fairy shrimp conservation management efforts is the ability to readily identify species without the capture and sacrifice of individuals for microscopy. Here we demonstrate that eDNA metabarcoding is an effective non-invasive tool for monitoring fairy shrimp. Results from ten Southern California vernal pools comparing eDNA and traditional dip-net methods showed that eDNA metabarcoding with16SrDNA provides exceptional species-level resolution. Importantly, while the two methods were concordant during early hydroperiods where adults were present, eDNA detected fairy shrimp for up to 2 months after dip-nets failed to detect any adults, expanding the time period for vernal pool monitoring. Together, these results provide resource managers a simple, cost-effective, and non-invasive method for biomonitoring endangered fairy shrimp species.

Environmental DNA (eDNA) metabarcoding is emerging as a biomonitoring tool available to the citizen science community that promises to augment or replace photographic observation. However, eDNA results and photographic observations have rarely been compared to document their individual or combined power. Here, we use eDNA multilocus metabarcoding, a method deployed by the CALeDNA Program, to inventory and evaluate biodiversity variation along the Pillar Point headland near Half Moon Bay, California. We describe variation in presence of 13,000 taxa spanning 82 phyla, analyze spatiotemporal patterns of beta diversity, and identify metacommunities. Inventory and measures of turnover across space and time from eDNA analysis are compared to the same measures from Global Biodiversity Information Facility (GBIF) data, which contain information largely contributed by iNaturalist photographic observations. We find eDNA depicts local signals with high seasonal turnover, especially in prokaryotes. We find a diverse community dense with pathogens and parasites in the embayment, and a State Marine Conservation Area (SMCA) with lower species richness than the rest of the beach peninsula, but with beta diversity signals showing resemblance to adjacent unprotected tidepools. The SMCA differs in observation density, with higher density of protozoans, and animals in Ascidiacea, Echinoidea, and Polycladida. Local contributions to beta diversity are elevated in a section of East-facing beach. GBIF observations are mostly from outside the SMCA, limiting some spatial comparisons. However, our findings suggest eDNA samples can link the SMCA sites to sites with better GBIF inventory, which may be useful for imputing species from one site given observations from another. Results additionally support >3800 largely novel biological interactions. This research, and accompanying interactive website support eDNA as a gap-filling tool to measure biodiversity that is available to community and citizen scientists.

The digitization of biocollections is a critical task with direct implications for the global community who use the data for research and education. Recent innovations to involve citizen scientists in digitization increase awareness of the value of biodiversity specimens; advance science, technology, engineering, and math literacy; and build sustainability for digitization. In support of these activities, we launched the first global citizen-science event focused on the digitization of biodiversity specimens: Worldwide Engagement for Digitizing Biocollections (WeDigBio). During the inaugural 2015 event, 21 sites hosted events where citizen scientists transcribed specimen labels via online platforms (DigiVol, Les Herbonautes, Notes from Nature, the Smithsonian Institution's Transcription Center, and Symbiota). Many citizen scientists also contributed off-site. In total, thousands of citizen scientists around the world completed over 50,000 transcription tasks. Here, we present the process of organizing an international citizen-science event, an analysis of the event's effectiveness, and future directions—content now foundational to the growing WeDigBio event.

231 Bioinventory (the enumeration and identification of species in an area) has long been a function of museum-based researchers, and in some ways there’s nothing new about sampling an area to determine what kinds of insects live there. At the Natural History Museum of Los Angeles County (LACM), however, we are trying to push the boundaries of inventory in unusual ways. Through our two programs discussed below, we hope not only to obtain interesting results, but also to set precedents that can be followed for other inventories.

Taxonomy is a fundamental science that provides the scaffolding for biology. But the true value of taxonomic data remains unrealized because basic biodiversity information remains fragmented and unevenly accessible. Taxonomy helps us recognize species and map their distributions by generating text descriptions, images, and records of when and where they have been observed. Current rates of species extinction, habitat loss, and climate change mean that taxonomy has never been more relevant. Biodiversity is one of the most information-rich fields of human knowledge, but advances in basic cybertaxonomic infrastructure have only recently provided the tools to organize biodiversity information in ways that respond to a wide range of user groups, including ecologists, land managers, and interested citizens, not to mention the benefits of readily accessible information to the global taxonomic community. The call to revitalize taxonomy by embracing the internet has been sounded for more than a decade. The time is ripe to significantly increase the volume of taxonomic information freely available online. But simply posting information online will not automatically reinvigorate taxonomy. There are myriad online sites dedicated to particular taxa or projects. These are useful to users interested in questions within the site’s domains. But the greater potential lies in mechanisms for aggregating primary source data in ways that allow users to filter and recombine data easily and flexibly for whatever purposes they imagine.

It is time for us to take full advantage of the investment that our societies have made in documenting the biodiversity of the world. It is time for us to fully, and legally, make systematic literature available worldwide. Using U.S. "Fair Use" guidelines, we can.

We present an updated classification for the entire Crustacea Decapoda, listing all known families and genera organized by higher taxonomic groups and including estimates of the number of species in every genus. All taxonomic names are also linked to the verified literature in which they were described, the first compilation of its kind for the Decapoda. To arrive at this compilation, we began with the classification scheme provided by Martin & Davis (2001) for extant families,, updated the higher classification and included the fossil taxa. The resultant framework was then populated with the currently valid genera and an estimate of species numbers within each genus. Our resulting classification, spanning both extant (living) and fossil taxa, is the first comprehensive estimate of taxonomic diversity within the entire Decapoda. The classification consists of 233 families of decapods containing 2,725 genera and an estimated 17,635 species (including both extant and fossil species). Of the families in our classification, 53 are exclusively fossil, 109 contain both fossil and extant species, and 71 are extant only. The current estimate for extant species is 14,756, whereas 2,979 species are known exclusively as fossils.

We provide evidence from field experiments that within-coral colony variation in light, limited electron transport rates through Photosystem II is positively correlated with water flow over the coral surface. We made in situ paired measurements of water flow and photosynthetic electron transport rates (rETR) over the upstream and downstream faces of several coral colonies at Conch Reef, Key Largo, Florida, USA. Using pulse amplitude modulated (PAM) fluorometry, we estimated rETR at increasing levels of photosynthetically active radiation (PAR). The rETR versus PAR relationship was fitted to a negative exponential curve parameterized by the initial slope (a) and the asymptotic maximum (rETR(max)). We showed that flow speeds measured at 3 mm above the upstream faces of multiple branching colonies of Porites porites and hemispherical colonies of Siderastrea siderea were more than double those over the downstream faces. In both P. porites and S, siderea, these higher upstream flow speeds were associated with a values that were 4 and 12% higher, respectively, than those over the downstream faces. In contrast, there were no differences inflow speed, or in a between the upstream and downstream faces of plate-like colonies of Montastrea annularis. Ancillary measurements of oxygen concentrations over intact coral colonies in the field demonstrated that oxygen concentrations within 2 mm of the coral surface were between 2 to 110% higher than ambient (measured > 1 m from the coral). Moreover, paired measurements over a single colony of S. siderea showed steeper velocity gradients over the upstream face relative to the downstream face, accompanied by lower oxygen concentrations, a thinner diffusion boundary layer, and higher a. Our results support the hypothesis that within-colony variation in photosynthesis by corals is related to water flow, and suggests that oxygen flux from the coral may be important.

Recent studies indicate that the incidence and persistence of damage from coral reef bleaching are often highest in areas of restricted water motion, and that resistance to and recovery from bleaching is increased by enhanced water motion. We examined the hypothesis that water motion increases the efflux of oxygen from coral tissue thereby reducing oxidative stress on the photosynthetic apparatus of endosymbiotic zooxanthellae. We experimentally exposed colonies of Montastrea annularis and Agaricia agaricites to manipulations of water flow, light intensity, and oxygen concentration in the field using a novel mini-flume. We measured photosynthetic efficiency using a pulse amplitude modulated fluorometer to test the short-term response of corals to our manipulations. Under normal oxygen concentrations, A. agaricites showed a significant 8% increase in photosynthetic efficiency from 0.238 (± 0.032) in still water to 0.256 (± 0.037) in 15 cm s−1 flow, while M. annularis exhibited no detectable change. Under high-ambient oxygen concentrations, the observed effect of flow on A. agaricites was reversed: photosynthetic efficiencies showed a significant 11% decrease from 0.236 (± 0.056) in still water to 0.211 (± 0.048) in 15 cm s−1 flow. These results support the hypothesis that water motion helps to remove oxygen from coral tissues during periods of maximal photosynthesis. Flow mitigation of oxidative stress may at least partially explain the increased incidence and severity of coral bleaching in low flow areas and observations of enhanced recovery in high-flow areas.

Biological specimens are identified by a printed label detailing their collection and curation information. Deterioration of specimen labels can render specimens scientifi- cally valueless. Given that this problem is a threat to wet-preserved collections, it is critically important to know which label preparation techniques will withstand decades of immersion in common preservatives. Traditional print methods that have lasted for centuries, such as writing in pencil or India ink on cotton rag paper, are time-consuming and not amenable to producing multiple copies of labels. Laser-printing technology greatly increases label pro- duction rates, but its durability on assorted label papers or stored in common preservatives has not been quantitatively tested. This 14-yr study examines the durability of laser print on five museum-quality papers. We evaluate the effects of post-printing heat and acrylic-coating treatments on print dura- bility in the presence of two preservative types, formalin and ethanol. All treatments re- mained legible at the end of the trial. The treatments that maintained the greatest print legibility were acrylic-coated (vs. uncoated) labels and labels immersed in ethanol (vs. formalin solution). Paper type and microwave treatment did not affect print durability.