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VisTrails SAHM: visualization and workflow management for species habitat modeling

The Software for Assisted Habitat Modeling (SAHM) has been created to both expedite habitat modeling and help maintain a record of the various input data, pre- and post-processing steps and modeling options incorporated in the construction of a species distribution model through the established workflow management and visualization VisTrails software. This paper provides an overview of the VisTrails:SAHM software including a link to the open source code, a table detailing the current SAHM modules, and a simple example modeling an invasive weed species in Rocky Mountain National Park, USA.

Ecography: Pattern and Diversity in Ecology↗

Linking rapid magma reservoir assembly and eruption trigger mechanisms at evolved Yellowstone-type supervolcanoes

The geological record contains evidence of volcanic eruptions that were as much as two orders of magnitude larger than the most voluminous eruption experienced by modern civilizations, the A.D. 1815 Tambora (Indonesia) eruption. Perhaps nowhere on Earth are deposits of such supereruptions more prominent than in the Snake River Plain–Yellowstone Plateau (SRP-YP) volcanic province (northwest United States). While magmatic activity at Yellowstone is still ongoing, the Heise volcanic field in eastern Idaho represents the youngest complete caldera cycle in the SRP-YP, and thus is particularly instructive for current and future volcanic activity at Yellowstone. The Heise caldera cycle culminated 4.5 Ma ago in the eruption of the ∼1800 km 3 Kilgore Tuff. Accessory zircons in the Kilgore Tuff display significant intercrystalline and intracrystalline oxygen isotopic heterogeneity, and the vast majority are 18 O depleted. This suggests that zircons crystallized from isotopically distinct magma batches that were generated by remelting of subcaldera silicic rocks previously altered by low-δ 18 O meteoric-hydrothermal fluids. Prior to eruption these magma batches were assembled and homogenized into a single voluminous reservoir. U-Pb geochronology of isotopically diverse zircons using chemical abrasion–isotope dilution–thermal ionization mass spectrometry yielded indistinguishable crystallization ages with a weighted mean 206 Pb/ 238 U date of 4.4876 ± 0.0023 Ma (MSWD = 1.5; n = 24). These zircon crystallization ages are also indistinguishable from the sanidine 40 Ar/ 39 Ar dates, and thus zircons crystallized close to eruption. This requires that shallow crustal melting, assembly of isolated batches into a supervolcanic magma reservoir, homogenization, and eruption occurred extremely rapidly, within the resolution of our geochronology (10 3 –10 4 yr). The crystal-scale image of the reservoir configuration, with several isolated magma batches, is very similar to the reservoir configurations inferred from seismic data at active supervolcanoes. The connection of magma batches vertically distributed over several kilometers in the upper crust would cause a substantial increase of buoyancy overpressure, providing an eruption trigger mechanism that is the direct consequence of the reservoir assembly process.

Geology↗

Development and validation of a spatially-explicit agent-based model for space utilization by African savanna elephants (Loxodonta africana) based on determinants of movement

African elephants (Loxodonta africana) are well-studied and inhabit diverse landscapes that are being transformed by both humans and natural forces. Most tools currently in use are limited in their ability to predict how elephants will respond to novel changes in the environment. Individual-, or agent-based modeling (ABM), may extend current methods in addressing and predicting spatial responses to environmental conditions over time. We developed a spatially explicit agent-based model to simulate elephant space use and validated the model with movement data from elephants in Kruger National Park (KNP) and Chobe National Park (CNP). We simulated movement at an hourly scale, as this scale can reflect switches in elephant behavior due to changes in internal states and short-term responses to the local availability and distribution of critical resources, including forage, water, and shade. Known internal drivers of elephant movement, including perceived temperature and the time since an individual last visited a water source, were linked to the external environment through behavior-based movement rules. Simulations were run on model landscapes representing the wet season and the hot, dry season for both parks. The model outputs, including home range size, daily displacement distance, net displacement distance, and maximum distance traveled from a permanent water source, were evaluated through qualitative and quantitative comparisons to actual elephant movement data from both KNP and CNP. The ABM was successful in reproducing the differences in daily displacements between seasons in each park, and in distances traveled from a permanent water source between parks and seasons. Other movement characteristics, including differences in home range sizes and net daily displacements, were partially reproduced. Out of the all the statistical comparisons made between the empirical and simulated movement patterns, the majority were classified as discrepancies of medium or small effect size. We have shown that a resource-driven model with relatively simple decision rules generates trajectories with movement characteristics that are mostly comparable to those calculated from empirical data. Simulating hourly movement (as our model does) may be useful in predicting how finer-scale patterns of space use, such as those created by foraging movements, are influenced by finer spatio-temporal changes in the environment.

Chobe National Park, Kruger National Park↗

Modelling community dynamics based on species-level abundance models from detection/nondetection data

1. In large‐scale field surveys, a binary recording of each species’ detection or nondetection has been increasingly adopted for its simplicity and low cost. Because of the importance of abundance in many studies, it is desirable to obtain inferences about abundance at species‐, functional group‐, and community‐levels from such binary data. 2. We developed a novel hierarchical multi‐species abundance model based on species‐level detection/nondetection data. The model accounts for the existence of undetected species, and variability in abundance and detectability among species. Species‐level detection/nondetection is linked to species‐level abundance via a detection model that accommodates the expectation that probability of detection (at least one individuals is detected) increases with local abundance of the species. We applied this model to a 9‐year dataset composed of the detection/nondetection of forest birds, at a single post‐fire site (from 7 to 15 years after fire) in a montane area of central Japan. The model allocated undetected species into one of the predefined functional groups by assuming a prior distribution on individual group membership. 3. The results suggest that 15–20 species were missed in each year, and that species richness of communities and functional groups did not change with post‐fire forest succession. Overall abundance of birds and abundance of functional groups tended to increase over time, although only in the winter, while decreases in detectabilities were observed in several species. 4. Synthesis and applications . Understanding and prediction of large‐scale biodiversity dynamics partly hinge on how we can use data effectively. Our hierarchical model for detection/nondetection data estimates abundance in space/time at species‐, functional group‐, and community‐levels while accounting for undetected individuals and species. It also permits comparison of multiple communities by many types of abundance‐based diversity and similarity measures under imperfect detection.

Journal of Applied Ecology↗

Genomic identity of white oak species in an eastern North American syngameon

The eastern North American white oaks, a complex of approximately 16 potentially interbreeding species, have become a classic model for studying the genetic nature of species in a syngameon. Genetic work over the past two decades has demonstrated the reality of oak species, but gene flow between sympatric oaks raises the question of whether there are conserved regions of the genome that define oak species. Does gene flow homogenize the entire genome? Do the regions of the genome that distinguish a species in one part of its range differ from the regions that distinguish it in other parts of its range, where it grows in sympatry with different species? Or are there regions of the genome that are relatively conserved across species ranges? In this study, we revisit seven species of the eastern North American white oak syngameon using a set of 80 single-nucleotide polymorphisms (SNPs) selected in a previous study because they show differences among, and consistency within, the species. We test the hypothesis that there exist segments of the genome that do not become homogenized by repeated introgression, but retain distinct alleles characteristic of each species. We undertake a range-wide sampling to investigate whether SNPs that appeared to be fixed based on a relatively small sample in our previous work are fixed or nearly fixed across the range of the species. Each of the seven species remains genetically distinct across its range, given our diagnostic set of markers, with relatively few individuals exhibiting admixture of multiple species. SNPs map back to all 12 Quercus linkage groups (chromosomes) and are separated from each other by an average of 7.47 million bp (± 8.74 million bp, SD), but are significantly clustered relative to a random null distribution, suggesting that our SNP toolkit reflects genome-wide patterns of divergence while potentially being concentrated in regions of the genome that reflect a higher-than-average history of among-species divergence. This application of a DNA toolkit designed for the simple problem of identifying species in the field has two important implications. First, the eastern North American white oak syngameon is composed of entities that most taxonomists would consider “good species.” Second, and more fundamentally, species in the syngameon are genetically coherent because characteristic portions of the genome remain divergent despite a history of introgression. Understanding the conditions under which some loci diverge while others introgress is key to understanding the origins and maintenance of global tree diversity.

Estern United States↗

Effectiveness of rapid 'ōhi'a death management strategies at a focal disease outbreak on Hawai'i Island

The ongoing spread of rapid ‘ōhi‘a death (ROD) in the Hawaiian Islands threatens the long-term sustainability of ‘ōhi‘a lehua (Metrosideros polymorpha) forests throughout the state. First identified in the Puna district of Hawai‘i Island in 2014, the disease caused by the novel fungi Ceratocystis lukuohia and Ceratocystis huliohia has now spread island-wide and was recently detected on Kaua‘i, O‘ahu, and Maui. The leading hypothesis for the spread of ROD is through airborne ambrosia beetle frass particles that contain viable Ceratocystis propagules, thus management efforts focus on containing this frass. At the time of this study (2017–2018), the Waipunalei site was the northernmost outbreak of ROD on Hawai‘i Island. The focal nature of the outbreak and accessibility of the location provided the opportunity to monitor the effectiveness of two types of proposed management methods to reduce the airborne spread of potentially infective ambrosia beetle frass: tree felling and insecticide treatments. We placed 23 passive environmental samplers (PES), which monitored for airborne frass and wood particles containing C. lukuohia and C. huliohia in a grid that spanned the outbreak area over 22 weeks. Cross-vane panel traps with 1:1 methanol:ethanol lures were attached to nine of the PES to document wood-boring ambrosia and cerambycid beetle populations during the latter three months of the study. Monitoring with PES began three weeks before management and continued for one month after the last infected trees were felled. Glass microscope slides from the 23 PES were examined for airborne ambrosia beetle frass and wood particles by microscopy. DNA was extracted from the slides and tested by qPCR (quantitative polymerase chain reaction) for C. lukuohia and C. huliohia. We also investigated the correlation of beetle gallery counts with tree height and tested the efficacy of Bifen I/T insecticide (active ingredient: bifenthrin 7.9%) for preventing beetle attacks on the cut surface of ‘ōhi‘a bolts (tree stem sections). Beetle trapping data revealed that the area supports a diverse community of wood-boring beetles, some of which likely attack ‘ōhi‘a and may facilitate the spread of ROD. The number of beetle galleries on felled ‘ōhi‘a trees decreased linearly as tree height increased. We also observed significantly fewer beetle attacks on Bifen I/T treated ‘ōhi‘a bolts than non-treated bolts, but gallery formation nearly ceased in both treated and control bolts by week three. Ceratocystis lukuohia DNA was detected twenty-six times and C. huliohia was detected five times in the PES throughout this study. DNA detections were correlated to frass and wood counts, and the number of felled trees were correlated to wood particle counts but not frass counts. Both the timing and distribution of detections across the sampling grid indicate that tree felling may have reduced airborne detections of Ceratocystis DNA soon after tree felling was completed. A subsequent increase in detections after tree felling ceased may indicate that incomplete removal of infected trees and the appearance of new infections in previously asymptomatic trees could have allowed airborne detections of potentially infectious fungal propagules to once again increase.

Hawaii↗

Anthropogenic organic compounds in source water of select community water systems in the United States, 2002-10

Drinking water delivered by community water systems (CWSs) comes from one or both of two sources: surface water and groundwater. Source water is raw, untreated water used by CWSs and is usually treated before distribution to consumers. Beginning in 2002, the U.S. Geological Survey’s (USGS) National Water-Quality Assessment Program initiated Source Water-Quality Assessments (SWQAs) at select CWSs across the United States, primarily to characterize the occurrence of a large number of anthropogenic organic compounds that are predominantly unregulated by the U.S. Environmental Protection Agency. Source-water samples from CWSs were collected during 2002–10 from 20 surface-water sites (river intakes) and during 2002–09 from 448 groundwater sites (supply wells). River intakes were sampled approximately 16 times during a 1-year sampling period, and supply wells were sampled once. Samples were monitored for 265 anthropogenic organic compounds. An additional 3 herbicides and 16 herbicide degradates were monitored in samples collected from 8 river intakes and 118 supply wells in areas where these compounds likely have been used. Thirty-seven compounds have an established U.S. Environmental Protection Agency (EPA) Maximum Contaminant Level (MCL) for drinking water, 123 have USGS Health-Based Screening Levels (HBSLs), and 29 are included on the EPA Contaminant Candidate List 3. All compounds detected in source water were evaluated both with and without an assessment level and were grouped into 13 categories (hereafter termed as “use groups”) based on their primary use or source. The CWS sites were characterized in a national context using an extract of the EPA Safe Drinking Water Information System to develop spatially derived and system-specific ancillary data. Community water system information is contained in the EPA Public Supply Database, which includes 2,016 active river intakes and 112,099 active supply wells. Ancillary variables including population served, watershed size, land use, population density, and recharge were characterized for each of the watersheds for river intakes and contributing areas for supply wells. A total of 313 samples were collected from 20 river intakes. Between the years of 2002 through 2010, samples were collected approximately 16 times over the course of a year. Seventy-one compounds from 12 of the 13 use groups commonly occurred (detected in greater than or equal to 1 percent of samples using an assessment level of 0.05 microgram per liter or when a compound was detected in greater than or equal to 10 percent of samples without an assessment level) indicating a wide variety of sources and pathways to these rivers and highlighting the importance of source-water protection strategies. A total of 448 supply wells were sampled once during 2002–10 as part of 30 independent groundwater studies. About 15 CWS supply wells were sampled for each independent groundwater study. Twenty-eight compounds from 7 of the 13 use groups commonly occurred indicating a wide variety of sources and pathways exist for these compounds to reach these wells and highlighting the importance of wellhead protection strategies. About one-half the 265 compounds monitored (122) were detected in both surface water and groundwater samples. A more diverse suite of compounds were detected in surface water in comparison to groundwater. However, herbicides and herbicide degradates were the most frequent group of compounds detected in both surface water and groundwater. Sixty-five of the most commonly occurring compounds were detected in one or more samples from both surface water and groundwater. Human-health benchmarks (MCLs for regulated compounds and HBSLs for unregulated compounds) were available for more than one-half the compounds (160 of the 265) monitored in this study. Fifty-eight percent (41 of 71) of the commonly occurring compounds in surface water have a human-health benchmark to which concentrations can be compared; 19 have MCLs and 22 have HBSLs. Eighty-three percent (24 of 28) of the most commonly occurring compounds in groundwater have a human-health benchmark for which concentrations can be compared; 14 have MCLs and 10 have HBSLs. To put results from this study into context with the national distribution of river intakes and supply wells used by CWSs, sites were grouped into the respective national population of land-use quartiles. The increase in compound occurrence with increasing urban and agricultural land use in the watershed or contributing area was more evident for rivers than for supply wells. The increase in detection frequency of herbicides and herbicide degradates with increasing agricultural land use was more evident for rivers than for supply wells. The occurrence of solvents did not change substantially with increasing urban land use for rivers or supply wells. Basic co-occurrence analyses were completed with and without an assessment level. Considering all detections in surface water without an assessment level, approximately 86 percent of source-water samples contained 2 or more compounds, and 50 percent of samples contained at least 14 compounds. Considering all detections in groundwater without an assessment level, 50 percent of samples contained at least three compounds. For the most part, the compounds detected most frequently as individual compounds in the environment often composed the most frequent unique mixtures. Five of the 10 most frequently co-occurring unique mixtures in both surface water and groundwater were the same: atrazine and deethylatrazine; atrazine and chloroform; deethylatrazine and simazine; atrazine and simazine; and deethylatrazine, atrazine, and simazine. Because similar mixtures were identified in both surface water and groundwater without an assessment level, future studies could be directed toward better understanding the toxicological importance of these unique mixtures. Summed concentrations of herbicide degradates were compared to concentrations of the parent herbicides in surface-water and groundwater samples collected from 8 river intakes and 118 CWS wells, from which samples were analyzed for an additional 3 herbicides and 16 degradates. The toxicity to humans for many of these degradate products is largely unknown and thus points to the importance of monitoring these compounds (both the parent and degradate) in the environment. This study highlights the importance of anthropogenic organic compounds in source water of select CWSs in the United States by characterizing their occurrence in surface-water and groundwater samples. Compound concentrations and occurrence are summarized and evaluated in a human-health context, when possible. Additionally, compounds found to co-occur as mixtures for both surface water and groundwater highlight the significance of low-level compound co-occurrence.

Scientific Investigations Report↗

Vegetation affects water movement in the Florida Everglades

Introduction The Florida Everglades is a vast, diverse wetland ecosystem characterized by small ground-surface slopes, slowly moving surface waters, and dense aquatic vegetation. Both submersed and emergent vegetation are found in sawgrass and cattail marshes, wet prairies, and sloughs. The south Florida ecosystem has been greatly altered during the last 100 years. A complex water-management system that includes levees, canals, pumps, and water-control structures now regulates flooding and provides a steady supply of fresh water to urban areas and agriculture. Drainage projects have diverted much of the water that originally flowed slowly southward from Lake Okeechobee through the Everglades. Restoration and management of the Everglades ecosystem requires understanding and manipulating the amount and timing of water flows throughout the ecosystem. The spatial and temporal distribution of water and water-borne contaminants in the Everglades must be understood if degradation of the ecosystem is to be halted and reversed. To understand how water moves through the Everglades, it is necessary to quantify the forces affecting the flow. The resistance exerted on the flow by the vegetation through which the water moves is one of the dominant but least understood forces affecting Everglades surface-water flows. The aquatic vegetation of the Everglades affects both the depth of water and the rate at which it moves. The presence of living and dead plant material in the water column creates drag forces on the moving water. Water flows most slowly and the water-surface slope is largest in areas where vegetation is most dense.

Florida↗

Cascadia Margin cold seeps: Subduction zone fluids, gas hydrates, and chemosynthetic habitats

Priority Geographic Area: The outer continental shelf and upper continental slope from Canada/U.S. border offshore Washington State to the Mendocino Fracture Zone (Northern California), entirely within the U.S. Exclusive Economic Zone (EEZ), from the outermost shelf to at least 2000 m water depth (Figure 1). Description of Priority Area: Since 2015, over a thousand water column gas plumes originating at seafloor gas seeps have been discovered landward of the Cascadia deformation front (e.g., Embley et al., 2016; Johnson et al., 2015, 2019; Merle and Embley, 2016; NA-95 Cruise Report, 2018; Riedel et al., 2018), adding to those that had long been known on Hydrate Ridge (e.g., Heeschen et al., 2003; Tréhu et al., 2004). The recently-discovered seeps stretch from offshore Vancouver Island to the Mendocino Fracture Zone and from the outer shelf to ~2000 m water depth, occurring both landward and seaward of the nominal limit for gas hydrate stability zone on the upper continental slope (Figure 1). Hundreds of seeps likely remain undiscovered. Water column imaging is incomplete both within the target geographic area and farther seaward, between the 2000 m isobath and the deformation front, which is the subject of an imaging study described in a white paper by Watt et al. The recently-discovered Cascadia Margin cold seeps partially overlap an important active margin gas hydrate province (Spence et al., 2001; Tréhu et al., 2003, 2004), as well as an area where sediments on the North American plate are folded and faulted and affected by fluids generated in the subduction complex beneath the Cascadia forearc (e.g., Saffer and Tobin, 2011). Several Ocean Drilling Program expeditions have focused on hydrate systems offshore Vancouver and Oregon (e.g., Riedel et al., 2009; Tréhu et al., 2004) and on the connection between the shallow and deep hydrogeologic systems. Cabled observatories now continuously monitor physical, chemical, and venting processes on south Hydrate Ridge (OOI; e.g., Philip et al., 2016a) and offshore Vancouver Island (NEPTUNE; e.g. Römer et al., 2016). Outside of these well-studied gas hydrate areas, a subset of the recently-discovered Cascadia seeps, including some that we visited with R/V Falkor in 2019 (e.g., https://schmidtocean.org/cruise/methane-seeps-at-edge-of-hydrate-stability/), also likely emit methane associated with shallow subseafloor gas hydrate systems. Other seeps are delivering not only methane, but also deep-derived gases (Baumberger et al., 2018, 2020) to the seafloor. Many Cascadia Margin seeps have also been recognized at water depths too shallow (e.g., 175 m) to be connected to gas hydrate dynamics. These seeps are postulated to be emitting gas and fluids that originated deep in accretionary wedge before migrating up normal faults generated during forearc extension associated with large earthquakes (Johnson et al., 2019). Only a small fraction of the recently discovered U.S. Cascadia Margin water column gas plumes has so far been verified by ROVs (Hercules from E/V Nautilus in 2016 and 2018; SuBastian from R/V Falkor in 2018 and 2019) to correspond to seafloor seeps. Careful scientific mapping, investigation, and sampling at the seeps have also been limited (e.g., Baumberger et al., 2018, 2020; Merle and Embley, 2016; Seabrook et al., 2018; Greinert et al. 2019). This white paper focuses on expanding exploration of already-identified U.S. Cascadia Margin cold seeps through a multipronged and multidisciplinary discovery program that could be accomplished with a variety of NOAA assets. The goals of the proposed exploration activities are to develop high-resolution maps of seep fields from deep ocean vehicles; to verify (and sample) seafloor gas emissions at the locations of water column plumes for compositional and isotopic studies; to map, sample, and conduct analyses on chemosynthetic communities and deep-sea coral habitats near seep sites to document species distributions and habitats as a function of depth and latitude along the margin; to collect seep geologic samples that can constrain the timing of methane emissions through geochronology; and to record environmental data (e.g., CTD) near the seafloor and in the water column above the seeps. Seafloor mapping using shipboard systems (multibeam/backscatter) would be needed to characterize seafloor features near seep sites. Water column imaging (EK60/80 and/or multibeam WCD data) conducted before and after seafloor explorations would capture active methane plumes and constrain temporal variations in seep emissions (e.g., Kannberg et al., 2013; Philip et al., 2016a, 2016b), which are known to vary on time scales as rapid as tidal cycles on this margin (e.g., Römer et al., 2016). What are the characterization and data needs in this area? Check all that apply: __x_ Biology, Geology, Physical Oceanography, Chemistry ___ Marine Archaeology ___ Other Provide a list or brief description of the data needed within this area, from your perspective: 1. Water column backscatter to image active gas plumes 2. High-resolution multibeam bathymetry, seafloor backscatter, and shallow sub-bottom imaging 3. Visual characterization and ground truthing of potential seeps, including high-resolution mapping and photography from near-seafloor vehicles; collection of seep-associated species, corals, sediments, authigenic carbonates, gases, and seawater Describe relevance to national security, conservation, and/or the economy: The Cascadia margin seeps provide significant ecosystem services, including habitat for commercially important fishes and support for diversity along the continental margin. Methane seeps are also biological hotspots for krill, plankton, and crustaceans, which in turn sustain higher trophic levels (e.g., whales). Methane-derived authigenic carbonates serve as a hard substrate for deep-sea corals and sponges on millennial time scales. The studies proposed here will elucidate the relationship among seep environments, deep-sea corals, sponges, fisheries, and other organisms and provide new insight into subduction zone and hydrate-associated fluids in this important seismogenic zone. The studies address fishery management concerns and inform future conservation of sensitive species (e.g., deep-sea corals) and benthic habitats. From your perspective, what makes this area unique? The Cascadia Margin seeps are a critical component of the leaky margin that stretches from Baja California to the Aleutian Arc along the Pacific coastline of North America. Cold seeps have been intensely studied on the Gulf of Mexico and U.S. Atlantic passive margins with a focus on chemosynthetic communities, deep-sea corals, and leakage of microbially-generated and/or thermogenic hydrocarbons; however, the recently-discovered Cascadia Margin seeps, as well as active margin seep systems in general, remain more poorly characterized. Such seeps not only contribute to the ocean carbon cycle (e.g., Pohlman et al., 2011), thereby fueling the base of the food chain in these settings, but also emit subduction zone fluids that provide clues about processes within the seismogenic zone and the accretionary complex. The Cascadia seeps area allows both biological (e.g., benthic habitats, coral distributions) and physical processes (e.g., generation of subduction zone fluids) to be studied along both depth (perpendicular to the deformation front) and latitudinal gradients.

California, Oregon, Washington↗

Seasonal occurrence and distribution of submerged aquatic macrophytes in the tidal Potomac River

A systematic survey was conducted in the Tidal Potomac River in 1978 to determine the presence, abundance, and phenology of submersed aquatic macrophytes. The survey covered 81.5 km of main river and 59.3 km of tributary on the Maryland shore. Four regions were selected for the study: (1) Piscataway - Mattawoman Creek region (fresh-tidal river), (2) Nanjemoy Creek-Port Tobacco River region (transition zone), (3) Wicomico River region (estuary), and (4) St. Marys River region (estuary). The Wicomico River region was subdivided into fresh tidal river, transition zone and estuary for purposes of date analysis. Data were gathered by sampling each 15 m along transects running perpendicular to shore for a maximum distance of 300 m. Modified oyster tongs were used to sample both plants and benthic soils from an outboard boat. A total of 131 transects were established with a total of approximately 3500 grabs being taken per sampling period. Sampling was initiated in the spring and repeated in the summer and fall. Highest plant diversity and productivity were measured in the transition zone extending from Lower Cedar Point to beyond Maryland Point, a distance of approximately 30 km, and in the transition zone of the Wicomico River above Chaptico Bay. Fresh tidal areas were devoid of plants. The estuary had a sparse growth of horned pondweed (Zannichellia palustris) and widgeon grass (Ruppia maritima) in the spring: horned pondweed was not found in summer or fall. Redhead grass (Potomageton perfoliatus) was the most abundant pondweed; it matured in early summer and died back in mid-to-late summer. Wild celery (Vallisneria americana) and widgeon grass matured in early-to-late fall and were the most abundant plants during that period. Data analysis is being finalized and a publication is in preparation. This research will be continued over the next several seasons as part of the long term USGS effort on the Potomac

Book chapter↗

Physiological basis of climate change impacts on North American inland fishes

Global climate change is altering freshwater ecosystems and affecting fish populations and communities. Underpinning changes in fish distribution and assemblage-level responses to climate change are individual-level physiological constraints. In this review, we synthesize the mechanistic effects of climate change on neuroendocrine, cardiorespiratory, immune, osmoregulatory, and reproductive systems of freshwater and diadromous fishes. Observed climate change effects on physiological systems are varied and numerous, including exceedance of critical thermal tolerances, decreased cardiorespiratory performance, compromised immune function, and altered patterns of individual reproductive investment. However, effects vary widely among and within species because of species, population, and even sex-specific differences in sensitivity and resilience and because of habitat-specific variation in the magnitude of climate-related environmental change. Research on the interactive effects of climate change with other environmental stressors across a broader range of fish diversity is needed to further our understanding of climate change effects on fish physiology.

Fisheries↗

Give and take: Effects of genetic admixture on mutation load in endangered Florida panthers

Genetic admixture is a biological event inherent to genetic rescue programs aimed at the long-term conservation of endangered wildlife. Although the success of such programs can be measured by the increase in genetic diversity and fitness of subsequent admixed individuals, predictions supporting admixture costs to fitness due to the introduction of novel deleterious alleles are necessary. Here, we analyzed nonsynonymous variation from conserved genes to quantify and compare levels of mutation load (i.e. proportion of deleterious alleles and genotypes carrying these alleles) among endangered Florida panthers and non-endangered Texas pumas. Specifically, we used canonical (i.e. non-admixed) Florida panthers, Texas pumas, and F 1 (canonical Florida × Texas) panthers dating from a genetic rescue program and Everglades National Park panthers with Central American ancestry resulting from an earlier admixture event. We found neither genetic drift nor selection significantly reduced overall proportions of deleterious alleles in the severely bottlenecked canonical Florida panthers. Nevertheless, the deleterious alleles identified were distributed into a disproportionately high number of homozygous genotypes due to close inbreeding in this group. Conversely, admixed Florida panthers (either with Texas or Central American ancestry) presented reduced levels of homozygous genotypes carrying deleterious alleles but increased levels of heterozygous genotypes carrying these variants relative to canonical Florida panthers. Although admixture is likely to alleviate the load of standing deleterious variation present in homozygous genotypes, our results suggest that introduced novel deleterious alleles (temporarily present in heterozygous state) in genetically rescued populations could potentially be expressed in subsequent generations if their effective sizes remain small.

Journal of Heredity↗

Status of the California Red-legged Frog (Rana draytonii) in the State of Baja California, México

The California Red-legged Frog ( Rana draytonii ) is a threatened species in the United States that has undergone population declines, especially in southern California. Due to the lack of information on the status of Mexican populations, we surveyed for the presence of R. draytonii in Baja California and assessed possible threats to population persistence. Our study area extended from the U.S.-Mexican border to the southern end of the distribution of the species in the Sierra San Pedro Mártir. We found R. draytonii at six of 15 historical sites, none at five proxy sites (i.e., alternative sites chosen because the historical record lacked precise locality data), and four at 24 additional sites. The 10 occupied sites are within three watersheds in the Sierra San Pedro Mártir (two sites at Arroyo San Rafael, two sites at Arroyo San Telmo, and six sites at Arroyo Santo Domingo). We did not detect R. draytonii at 60% of historical sites, including the highest elevation site at La Encantada and multiple low-elevation coastal drainages, suggesting the species has declined in Baja California. The threats we noted most frequently were presence of exotic aquatic animal species, water diversion, and cattle grazing. Management of remaining populations and local education is needed to prevent further declines.

Baja California↗

Stormwater management network effectiveness and implications for urban watershed function: A critical review

Deleterious effects of urban stormwater are widely recognized. In several countries, regulations have been put into place to improve the conditions of receiving water bodies, but planning and engineering of stormwater control is typically carried out at smaller scales. Quantifying cumulative effectiveness of many stormwater control measures on a watershed scale is critical to understanding how small-scale practices translate to urban river health. We review 100 empirical and modelling studies of stormwater management effectiveness at the watershed scale in diverse physiographic settings. Effects of networks with stormwater control measures (SCMs) that promote infiltration and harvest have been more intensively studied than have detention-based SCM networks. Studies of peak flows and flow volumes are common, whereas baseflow, groundwater recharge, and evapotranspiration have received comparatively little attention. Export of nutrients and suspended sediments have been the primary water quality focus in the United States, whereas metals, particularly those associated with sediments, have received greater attention in Europe and Australia. Often, quantifying cumulative effects of stormwater management is complicated by needing to separate its signal from the signal of urbanization itself, innate watershed characteristics that lead to a range of hydrologic and water quality responses, and the varying functions of multiple types of SCMs. Biases in geographic distribution of study areas, and size and impervious surface cover of watersheds studied also limit our understanding of responses. We propose hysteretic trajectories for how watershed function responds to increasing imperviousness and stormwater management. Even where impervious area is treated with SCMs, watershed function may not be restored to its predevelopment condition because of the lack of treatment of all stormwater generated from impervious surfaces; non-additive effects of individual SCMs; and persistence of urban effects beyond impervious surfaces. In most cases, pollutant load decreases largely result from run-off reductions rather than lowered solute or particulate concentrations. Understanding interactions between natural and built landscapes, including stormwater management strategies, is critical for successfully managing detrimental impacts of stormwater at the watershed scale.

Europe↗

Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria-resistant introduced birds

Of the estimated 55 Hawaiian honeycreepers (subfamily Carduelinae) only 17 species remain, nine of which the International Union for Conservation of Nature considers endangered. Among the most pressing threats to honeycreeper survival is avian malaria, caused by the introduced blood parasite Plasmodium relictum , which is increasing in distribution in Hawaiʻi as a result of climate change. Preventing further honeycreeper decline will require innovative conservation strategies that confront malaria from multiple angles. Research on mammals has revealed strong connections between gut microbiome composition and malaria susceptibility, illuminating a potential novel approach to malaria control through the manipulation of gut microbiota. One honeycreeper species, Hawaiʻi ʻamakihi ( Chlorodrepanis virens ), persists in areas of high malaria prevalence, indicating they have acquired some level of immunity. To investigate if avian host-specific microbes may be associated with malaria survival, we characterized cloacal microbiomes and malaria infection for 174 ʻamakihi and 172 malaria-resistant warbling white-eyes ( Zosterops japonicus ) from Hawaiʻi Island using 16S rRNA gene metabarcoding and quantitative polymerase chain reaction. Neither microbial alpha nor beta diversity covaried with infection, but 149 microbes showed positive associations with malaria survivors. Among these were Escherichia and Lactobacillus spp . , which appear to mitigate malaria severity in mammalian hosts, revealing promising candidates for future probiotic research for augmenting malaria immunity in sensitive endangered species.

Hawaii↗

Estimating changes in riparian and channel features along the Trinity River downstream of Lewiston Dam, California, 1980 to 2011

Dam construction, flow diversion, and legacy landuse effects reduced the transport capacity, sediment supply, channel complexity and floodplain-connectivity along the Trinity River, CA below Lewiston Dam. This study documents the geomorphic evolution of the Trinity River Restoration Program’s intensively managed 65-km long restoration reach from 1980 to 2011. The nature and extent of riparian and channel changes were assessed using a series of geomorphic feature maps constructed from ortho-rectified photography acquired at low flow conditions in 1980, 1997, 2001, 2006, 2009, and 2011. Since 1980 there has been a general conversion of riparian to channel features and expansion of the active channel area. The primary mechanism for expansion of the active channel was bank erosion from 1980 to 1997 and channel widening was well distributed longitudinally throughout the study reach. Subsequent net bar accretion from 1997 to 2001, followed by slightly higher net bar scour from 2001 to 2006, occurred primarily in the central and lower reaches of the study area. In comparison, post-2006 bank and bar changes were spatially-limited to reaches with sufficient local transport capacity or sediment supply supported by gravel augmentation, mechanical channel rehabilitation, and tributary contributions to flow and sediment supply. A series of tributary floods in 1997, 1998 and 2006 were the primary factors leading to documented increases in channel complexity and floodplain connectivity. During the post-2006 period managed flow releases, in the absence of large magnitude tributary flooding, combined with gravel augmentation and mechanical restoration caused localized increases in sediment supply and transport capacity leading to smaller but measurable increases in channel complexity and floodplain connectivity primarily in the upper river below Lewiston Dam.

California↗

Digital model of the Bayou Bartholomew alluvial aquifer stream system, Arkansas

A digital model of the Bayou Bartholomew aquifer-stream system in Arkansas was calibrated for the purpose of predicting hydrologic responses to stresses of water development. The simulated-time span for model calibration was from 1953 to 1970, during which time the system was stressed largely by ground- and surface-water diversions for rice irrigation. The model was calibrated by comparing groundwater-level and streamflow data with model-derived groundwater levels and streamflow. In the calibrated model, the ratio of model-derived to observed streamflows for 17 subbasins averaged 1.1; the ratios among the subbasins ranged from 0.8 to 1.6. The average deviation of the differences between model-derived and observed groundwater levels at 47 nodes was 0.2; the average among the nodes ranged from -2.3 to 10.4. The average standard deviation of the differences between the model-derived and observed groundwater levels was 3.5; the average among the nodes ranged from 0.4 to 10.5. The model will provide projections of changes in the potentiometric surface resulting from (1) changes in the rate or distribution of groundwater pumpage or (2) changes in the stage of streams and reservoirs. The model will provide only approximate projections of the streamflow.

Arkansas↗

Evaluation of selected model constraints and variables on simulated sustainable yield from the Mississippi River Valley alluvial aquifer system in Arkansas

An existing conjunctive use optimization model of the Mississippi River Valley alluvial aquifer was used to evaluate the effect of selected constraints and model variables on ground-water sustainable yield. Modifications to the optimization model were made to evaluate the effects of varying (1) the upper limit of ground-water withdrawal rates, (2) the streamflow constraint associated with the White River, and (3) the specified stage of the White River. Upper limits of ground-water withdrawal rates were reduced to 75, 50, and 25 percent of the 1997 ground-water withdrawal rates. As the upper limit is reduced, the spatial distribution of sustainable pumping increases, although the total sustainable pumping from the entire model area decreases. In addition, the number of binding constraint points decreases. In a separate analysis, the streamflow constraint associated with the White River was optimized, resulting in an estimate of the maximum sustainable streamflow at DeValls Bluff, Arkansas, the site of potential surface-water withdrawals from the White River for the Grand Prairie Area Demonstration Project. The maximum sustainable streamflow, however, is less than the amount of streamflow allocated in the spring during the paddlefish spawning period. Finally, decreasing the specified stage of the White River was done to evaluate a hypothetical river stage that might result if the White River were to breach the Melinda Head Cut Structure, one of several manmade diversions that prevents the White River from permanently joining the Arkansas River. A reduction in the stage of the White River causes reductions in the sustainable yield of ground water.

Arkansas↗