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USGS2019

The power, potential, and pitfalls of open access biodiversity data in range size assessments: Lessons from the fishes

Geographic rarity is a driver of a species’ intrinsic risk of extinction. It encompasses multiple key components including range size, which is one of the most commonly measured estimates of geographic rarity. Range size estimates are often used to prioritize conservation efforts when there are multiple candidate species, because data for other components of rarity such as population size are sparse, or do not exist for species of interest. Range size estimates can provide rankings of species vulnerability to changing environments or threats, identifying rare species for future study or conservation initiatives. However, range sizes can be estimated by several different metrics, and the degree of overlap in the identification of the rarest or most common species across methodologies is not well understood. This knowledge gap compromises our ability to prioritize correctly rare species, and presents a particularly difficult challenge for stream-dwelling organisms with distributions constrained to river networks. We evaluated the relationship of multiple range size estimates of a subset of freshwater fishes native to the United States to determine the degree of overlap in rarity rankings using different data sources and grain sizes. We used publicly available, open access data from the Global Biodiversity Information Facility (GBIF) to calculate extent of occurrence (minimum convex polygons) and area of occupancy (total area occupied, measured across various grain sizes). We compared range sizes estimated using GBIF data with the best available estimates of current distributions described by publicly available digital maps (NatureServe) to evaluate the efficacy of GBIF data in assessments of range size. We found strong correlations between range size estimates across analytical approaches and data sources with no detectable bias of taxonomy. We found that variation among rarity rankings was highest for species with intermediate range sizes indicating that the approaches considered here generally converge when used to identify the rarest or the most common species. Importantly, our results show that the rarest, and perhaps the most vulnerable, species are consistently identified across common methodological approaches. More broadly, our results support the use of open access biodiversity data that include opportunistically collated and collected point occurrence records as a complement to coarse-grain (e.g., whole range map) approaches, as we observed no systematic bias or deviation across data sources in our analyses. This indicates databases such as the GBIF may help fill important fundamental and applied knowledge gaps for many poorly understood species, particularly in a broad-scale, multispecies framework.

Ecological Indicators↗

USGS2013

Estimates of future inundation of salt marshes in response to sea-level rise in and around Acadia National Park, Maine

Salt marshes are ecosystems that provide many important ecological functions in the Gulf of Maine. The U.S. Geological Survey investigated salt marshes in and around Acadia National Park from Penobscot Bay to the Schoodic Peninsula to map the potential for landward migration of marshes using a static inundation model of a sea-level rise scenario of 60 centimeters (cm; 2 feet). The resulting inundation contours can be used by resource managers to proactively adapt to sea-level rise by identifying and targeting low-lying coastal areas adjacent to salt marshes for conservation or further investigation, and to identify risks to infrastructure in the coastal zone. For this study, the mapping of static inundation was based on digital elevation models derived from light detection and ranging (LiDAR) topographic data collected in October 2010. Land-surveyed control points were used to evaluate the accuracy of the LiDAR data in the study area, yielding a root mean square error of 11.3 cm. An independent accuracy assessment of the LiDAR data specific to salt-marsh land surfaces indicated a root mean square error of 13.3 cm and 95-percent confidence interval of ± 26.0 cm. LiDAR-derived digital elevation models and digital color aerial photography, taken during low tide conditions in 2008, with a pixel resolution of 0.5 meters, were used to identify the highest elevation of the land surface at each salt marsh in the study area. Inundation contours for 60-cm of sea-level rise were delineated above the highest marsh elevation for each marsh. Confidence interval contours (95-percent,± 26.0 cm) were delineated above and below the 60-cm inundation contours, and artificial structures, such as roads and bridges, that may present barriers to salt-marsh migration were mapped. This study delineated 114 salt marshes totaling 340 hectares (ha), ranging in size from 0.11 ha (marshes less than 0.2 ha were mapped only if they were on Acadia National Park property) to 52 ha, with a median size of 1.0 ha. Inundation contours were mapped at 110 salt marshes. Approximately 350 ha of low-lying upland areas adjacent to these marshes will be inundated with 60 cm of sea-level rise. Many of these areas are currently freshwater wetlands. There are potential barriers to marsh migration at 27 of the 114 marshes. Although only 23 percent of the salt marshes in the study are on ANP property, about half of the upland areas that will be inundated are within ANP; most of the predicted inundated uplands (approximately 170 ha) include freshwater wetlands in the Northeast Creek and Bass Harbor Marsh areas. Most of the salt marshes analyzed do not have a significant amount of upland area available for migration. Seventy-five percent of the salt marshes have 20 meters or less of adjacent upland that would be inundated along most of their edges. All inundation contours, salt marsh locations, potential barriers, and survey data are stored in geospatial files for use in a geographic information system and are a part of this report.

Maine↗

USGS2022

Modeling impacts of drought-induced salinity intrusion on carbon dynamics in tidal freshwater forested wetlands

Tidal freshwater forested wetlands (TFFW) provide critical ecosystem services including essential habitat for a variety of wildlife species and significant carbon sinks for atmospheric carbon dioxide. However, large uncertainties remain concerning the impacts of climate change on the magnitude and variability of carbon fluxes and storage across a range of TFFW. In this study, we developed a process-driven Tidal Freshwater Wetlands DeNitrification-DeComposition model (TFW-DNDC) that has integrated new features, such as soil salinity effects on plant productivity and soil organic matter decomposition to explore carbon dynamics in TFFW in response to drought-induced saltwater intrusion. Eight sites along the floodplains of the Waccamaw River (USA) and the Savannah River (USA) were selected to represent TFFW transition from healthy to moderately and highly salt-impacted forests, and eventually to oligohaline marshes. TFW-DNDC was calibrated and validated using field observed annual litterfall, stem growth, root growth, soil heterotrophic respiration and soil organic carbon storage. Analyses indicate that plant productivity and soil carbon sequestration in TFFW could change substantially in response to increased soil porewater salinity and reduced soil water table due to drought, but in interactive ways dependent on the river simulated. Such responses are variable due to non-linear relationships between carbon cycling processes and environmental drivers. Plant productivity, plant respiration, soil organic carbon sequestration rate and storage in the highly salt-impacted forest sites decreased significantly under drought conditions compared to normal conditions. Considering the high likelihood of healthy and moderately salt-impacted forests becoming highly salt-impacted forests under future climate change and sea-level rise, it is very likely that TFFW will lose their capacity as carbon sinks without up-slope migration.

Georgia, South Carolina↗

USGS2017

Modeling the long-term effects of introduced herbivores on the spread of an invasive tree

Context Melaleuca quinquenervia (Cav.) Blake (hereafter melaleuca) is an invasive tree from Australia that has spread over the freshwater ecosystems of southern Florida, displacing native vegetation, thus threatening native biodiversity. Suppression of melaleuca appears to be progressing through the introduction of insect species, the weevil, Oxiops vitiosa , and the psyllid, Boreioglycaspis melaleucae . Objective To improve understanding of the possible effects of herbivory on the landscape dynamics of melaleuca in native southern Florida plant communities. Methods We projected likely future changes in plant communities using the individual based modeling platform, JABOWA-II, by simulating successional processes occurring in two types of southern Florida habitat, cypress swamp and bay swamp, occupied by native species and melaleuca, with the impact of insect herbivores. Results Computer simulations show melaleuca invasion leads to decreases in density and basal area of native species, but herbivory would effectively control melaleuca to low levels, resulting in a recovery of native species. When herbivory was modeled on pure melaleuca stands, it was more effective in stands with initially larger-sized melaleuca. Although the simulated herbivory did not eliminate melaleuca, it decreased its presence dramatically in all cases, supporting the long-term effectiveness of herbivory in controlling melaleuca invasion. Conclusions The results provide three conclusions relevant to management: (1) The introduction of insect herbivory that has been applied to melaleuca appears sufficient to suppress melaleuca over the long term, (2) dominant native species may recover in about 50 years, and (3) regrowth of native species will further suppress melaleuca through competition.

Landscape Ecology↗

USGS2006

Long-term surface fuel accumulation in burned and unburned mixed-conifer forests of the central and southern Sierra Nevada, CA (USA)

Summary of Conclusions and Recommendations: The levels of mercury contamination found in freshwater fish in Sweden and Finland are similar to those found in such fish in the United States. On the other hand, fish consumption in this country is regarded as generally somewhat less than in the region of Scandinavia. Medical examinations of heavy eaters of contaminated fish have not revealed conclusive evidence of mercury-related disease in either Sweden or Finland. Nevertheless, the body burdens of mercury of some of those having the heaviest intake of fish in both of those countries were as high as the lower levels reported in persons with methylmercury poisoning in Japan. The major conclusion derived from these and other findings was that it seems unlikely that we will find overt mercury poisoning from the consumption of fish or other food products, as normally marketed, in this country. This is not to say that there may not be a few individuals, who because of high consumption of contaminated fish may have signs of mercury poisoning or suffer possible subclinical effects, including delayed neurologic or intellectual damage. Also, possibly infants or children may have impaired development. As yet, no systematic studies have been undertaken, even in the known areas of human exposure in Sweden and Japan, to identify such subclinical effects. Although we appear to be on safe ground, it is urgent (1) to determine whether subtle health effects are present and (2) to use all possible means to reduce exposure to mercury immediately.

Fire Ecology↗

USGS2025

Stressor-driven changes in freshwater biological indicators inform spatial management strategies using expert knowledge, observational data, and hierarchical models

Stream ecosystems face continuous pressures from multiple anthropogenic stressors that reshape biological communities and impact ecosystem health and services. Managers can encounter challenges in stewarding ecosystems threatened by multiple stressors, in part because most multiple stressor studies are experimental and, while valuable, offer limited management relevance in targeting these stressors on the landscape. Recent advances in causal inference coupled with large biomonitoring data sets could further understanding of observational stressor-response relationships, aiding management. In this study, we use bioassessment data in the Chesapeake Bay watershed in the mid-Atlantic region of the United States to identify how water quality and physical habitat stressors influence key benthic macroinvertebrate response metrics, considering hierarchical relationships using Bayesian networks. Results suggest water temperature and specific conductivity were prevalent stressors in a mountainous region (northern Appalachians), whereas in an agriculturally dominated region (southern Appalachians) physical habitat alterations were the predominant stressor. In mixed-land use regions (Piedmont & Coastal Plains), specific conductivity was a key stressor, but habitat heterogeneity was important for macroinvertebrate metrics. To illustrate how these stressor-response relationships can be used to guide management decisions, we applied the resist-accept-direct (RAD) framework to develop a portfolio of management options based on predicted changes in macroinvertebrate metrics in response to physical habitat and water quality stressors. For example, accepting changes in areas with co-occurring stressors may be the most feasible option, whereas directing changes through stream restoration or water quality improvements may be effective in areas with single stressor groups. By leveraging observational bioassessment data and causal inference to identify key stressor-response relationships, this research supports decision making by building a simple, strategic management portfolio.

Delaware, Maryland, New York, Pennsylvania, Virgin↗

USGS2022

Disentangling direct and indirect effects of extreme events on coastal wetland communities

One of the primary ways in which climate change will impact coastal freshwater wetlands is through changes in the frequency, intensity, timing and distribution of extreme weather events. Disentangling the direct and indirect mechanisms of population- and community-level responses to extreme events is vital to predicting how species composition of coastal wetlands will change under future conditions. We extended static structural equation modelling approaches to incorporate system dynamics in a multi-year multispecies occupancy model to quantify the effects of extreme weather events on a coastal freshwater wetland system. We used data from an 8-year study (2009–2016) on St. Marks National Wildlife Refuge in Florida, USA, to quantify species-specific and community-level changes in amphibian and fish occupancy associated with two flooding events in 2012 and 2013. We examine how physical changes to the landscape, including potential changes in salinity and increased wetland connectivity, may have contributed to or exacerbated the effects of these extreme weather events on the biota of isolated coastal wetlands. We provide evidence that the primary effects of flooding on the amphibian community were through indirect mechanisms via changes in the composition of the sympatric fish community that may have had lethal (i.e. through direct predation) or non-lethal (i.e. through direct or indirect competitive interactions) effects. In addition, we have shown that amphibian species differed in their sensitivity to direct flooding effects and indirect changes in the fish community and wetland-specific conductance, which led to variable responses across the community. These effects led to the overall decline in amphibian species richness from 2009 to 2016, suggesting that wetland-breeding amphibian communities on St. Marks National Wildlife Refuge may not be resilient to predicted changes in coastal disturbance regimes because of climate change. Understanding both direct and indirect effects, as well as species interactions, is important for predicting the effects of a changing climate on individual species, communities and ecosystems.

Journal of Animal Ecology↗

USGS1955

The pygmy whitefish, Coregonus coulteri, in Lake Superior

Bottom trawling by the U. S. Fish and Wildlife Service motor vessel Cisco in Lake Superior in 1952–1953 revealed a large population of a tiny whitefish, Coregonus (Prosopium) coulteri, which has been reported previously only from northwestern North America. The hiatus in range, from Lake Superior to the Columbia River basin, is the greatest known for a North American freshwater fish. Although minor structural differences characterize the disjunct populations of the pygmy whitefish, these are not deemed worthy of nomenclatorial recognition. Comparisons with related species indicate that the pygmy whitefish is distinctive in the small size, large scales, few vertebrae, few pyloric caeca, and in other characters. The pygmy whitefish is widely distributed in Lake Superior, especially in semi-protected bays, such as Keweenaw Bay which yielded about 68 percent of the 1,623 specimens caught. The bathymetric range was 10 to 49 fathoms, with maximum abundance at the 25- to 39-fathom interval. Average length of fish increased progressively with water depth, chiefly because the number of yearlings declined from 100 percent at 10–14 fathoms to none at 45–49 fathoms. The average total length of pygmy whitefish caught by trawling was 3.4 inches (range 1.2 to 5.7). Extraordinarily slow growth was revealed by the examination of scales. Two fish from Keweenaw Bay, both nearing the end of their eighth growing season, were only 5.4 inches long. Compared to Keweenaw Bay, growth rate was about the same near Laughing Fish Point, faster in the Apostle Islands (and in Bull and McDonald Lakes, Montana), and slower in Siskiwit Bay, Isle Royale. Females grew more rapidly than males after the second year and had a longer life span. All male pygmy whitefish were mature at the age of 2 years and a total length of 3.6 or more inches. Most females were mature at 3 years and 4.2 inches; all older females were mature. Mean egg production was 362 (range, 93 to 597) per fish and 26 per gram of total weight for fish from 3.4 to 5.9 inches long. Spawning in 1953 occurred sometime in November or December. Crustacea (principally ostracods and amphipods–copepods in the young) occurred in 106 of 112 pygmy whitefish stomachs and made up 77 percent of the total food volume. When available, fish eggs appear to be important in the diet. Other cold-water fishes–cottids, ninespine sticklebacks, smelt, and four species of coregonines–were the most frequent associates of the pygmy whitefish. Lake trout and trout-perch were also taken with it at the same stations or in the same trawl hauls. Its closest relative in Lake Superior, the round whitefish, was not an ecological associate.

Transactions of the American Fisheries Society↗

USGS2015

Unifying research on the fragmentation of terrestrial and aquatic habitats: patches, connectivity and the matrix in riverscapes

While there is an increasing emphasis in terrestrial ecology on determining the influence of the area that surrounds habitat patches (the landscape ‘matrix’) relative to the characteristics of the patches themselves, research on these aspects in running waters is still rather underrepresented. Here we outline conceptual foundations of matrix ecology for stream and river ecosystems (‘riverscapes’). We discuss how a hierarchical, patch-based perspective is necessary for the delineation of habitat patches and the surrounding matrix, through which we may identify two classes of habitat edges in riverscapes (i.e. edges between the terrestrial–aquatic interface and edges within streams). Under this conceptual framework, we discuss the role of the matrix in influencing between-patch movement, and resource quality and quantity within and among habitat patches in riverscapes. We also review types of empirical and modelling approaches which may advance our understanding of fragmentation effects in these systems. We identify five key challenges for understanding fragmentation and matrix effects more completely: (i) defining populations and their status (i.e. quantifying the demographic contribution of habitat patches to metapopulation dynamics), (ii) scaling from metapopulations to metacommunities (particularly searching for generalities in species responses to landscape heterogeneity), (iii) scaling from metacommunities to metaecosystems (i.e. exploring the interactive role of the terrestrial–aquatic and within-stream matrix effects on the flow of material and energy at the network scale), (iv) understanding temporal dynamics in matrix permeability and (v) revealing the utility of different patch and matrix representations for modelling connectivity relationships. Fragmentation of habitats is a critical issue in the conservation and management of stream networks across spatial scales. Although the effects of individual barriers (e.g. dams) are well documented, we argue that a more comprehensive patch–matrix landscape model will improve our understanding of fragmentation effects and improve management in riverscapes.

Freshwater Biology↗

USGS2007

A gap analysis and comprehensive conservation strategy for riverine ecosystems of Missouri

North America harbors an astounding proportion of the world's freshwater species, but it is facing a freshwater biodiversity crisis. A first step to slowing the loss of biodiversity involves identifying gaps in existing efforts to conserve biodiversity and prioritizing opportunities to fill these gaps. In this monograph we detail two separate, but complementary, conservation planning efforts - a Gap Analysis (GAP) and a State Wildlife Action Plan (WAP) - for Missouri that address this first step. The goal of the Missouri Aquatic GAP Project was to identify riverine ecosystems, habitats, and species not adequately represented (i.e., gaps) within existing conservation lands. The goal of the freshwater component of the Missouri Wildlife Action Plan was to identify and map a set of conservation-opportunity areas (COAs) that holistically represent all riverine ecosystems, habitats, and species in Missouri. Since conservation planning is a geographical exercise, both efforts utilized geographic information systems (GIS). Four principal GIS data sets were used in each planning effort: (1) a hierarchical riverine ecosystem classification, (2) predicted species distributions, (3) public ownership/stewardship, and (4) a human-threat index. Results of the gap analyses are not encouraging. Forty five, mostly rare, threatened, or endangered, species are not represented in lands set aside for conserving biodiversity. Results also illustrate the fragmented nature of conservation lands, which are mainly situated in the uplands and fail to provide connectivity among riverine habitats. Furthermore, many conservation lands are severely threatened by an array of human disturbances. In contrast, results of the WAP provide hope that relatively intact riverine ecosystems still exist. A total of 158 COAs, representing &sim;6% of the total kilometers of stream in Missouri, were selected for the WAP. This illustrates that a wide spectrum of biodiversity can be represented within a small portion of the total resource base, but the area of conservation concern is often much larger. Identifying priority riverscapes for conservation is an important first step toward effective biodiversity conservation. Yet, achieving the ultimate goal of conserving biodiversity will require vigilance on the part of all responsible parties, with particular attention to addressing and coordinating the many remaining logistical tasks.

Missouri↗

USGS2012

Estimating risks to aquatic life using quantile regression

One of the primary goals of biological assessment is to assess whether contaminants or other stressors limit the ecological potential of running waters. It is important to interpret responses to contaminants relative to other environmental factors, but necessity or convenience limit quantification of all factors that influence ecological potential. In these situations, the concept of limiting factors is useful for data interpretation. We used quantile regression to measure risks to aquatic life exposed to metals by including all regression quantiles (τ = 0.05–0.95, by increments of 0.05), not just the upper limit of density (e.g., 90 th quantile). We measured population densities (individuals/0.1 m 2 ) of 2 mayflies (Rhithrogena spp., Drunella spp.) and a caddisfly (Arctopsyche grandis), aqueous metal mixtures (Cd, Cu, Zn), and other limiting factors (basin area, site elevation, discharge, temperature) at 125 streams in Colorado. We used a model selection procedure to test which factor was most limiting to density. Arctopsyche grandis was limited by other factors, whereas metals limited most quantiles of density for the 2 mayflies. Metals reduced mayfly densities most at sites where other factors were not limiting. Where other factors were limiting, low mayfly densities were observed despite metal concentrations. Metals affected mayfly densities most at quantiles above the mean and not just at the upper limit of density. Risk models developed from quantile regression showed that mayfly densities observed at background metal concentrations are improbable when metal mixtures are at US Environmental Protection Agency criterion continuous concentrations. We conclude that metals limit potential density, not realized average density. The most obvious effects on mayfly populations were at upper quantiles and not mean density. Therefore, we suggest that policy developed from mean-based measures of effects may not be as useful as policy based on the concept of limiting factors.

Colorado↗

USGS2009

A method to assess longitudinal riverine connectivity in tropical streams dominated by migratory biota

1. One way in which dams affect ecosystem function is by altering the distribution and abundance of aquatic species. 2. Previous studies indicate that migratory shrimps have significant effects on ecosystem processes in Puerto Rican streams, but are vulnerable to impediments to upstream or downstream passage, such as dams and associated water intakes where stream water is withdrawn for human water supplies. Ecological effects of dams and water withdrawals from streams depend on spatial context and temporal variability of flow in relation to the amount of water withdrawn. 3. This paper presents a conceptual model for estimating the probability that an individual shrimp is able to migrate from a stream's headwaters to the estuary as a larva, and then return to the headwaters as a juvenile, given a set of dams and water withdrawals in the stream network. The model is applied to flow and withdrawal data for a set of dams and water withdrawals in the Caribbean National Forest (CNF) in Puerto Rico. 4. The index of longitudinal riverine connectivity (ILRC), is used to classify 17 water intakes in streams draining the CNF as having low, moderate, or high connectivity in terms of shrimp migration in both directions. An in-depth comparison of two streams showed that the stream characterized by higher water withdrawal had low connectivity, even during wet periods. Severity of effects is illustrated by a drought year, where the most downstream intake caused 100% larval shrimp mortality 78% of the year. 5. The ranking system provided by the index can be used as a tool for conservation ecologists and water resource managers to evaluate the relative vulnerability of migratory biota in streams, across different scales (reach-network), to seasonally low flows and extended drought. This information can be used to help evaluate the environmental tradeoffs of future water withdrawals. ?? 2008 John Wiley & Sons, Ltd.

Aquatic Conservation: Marine and Freshwater Ecosys↗

USGS2013

Effects of future urban and biofuel crop expansions on the riverine export of phosphorus to the Laurentian Great Lakes

Increased phosphorus (P) loadings threaten the health of the world’s largest freshwater resource, the Laurentian Great Lakes (GL). To understand the linkages between land use and P delivery, we coupled two spatially explicit models, the landscape-scale SPARROW P fate and transport watershed model and the Land Transformation Model (LTM) land use change model, to predict future P export from nonpoint and point sources caused by changes in land use. According to LTM predictions over the period 2010–2040, the GL region of the U.S. may experience a doubling of urbanized areas and agricultural areas may increase by 10%, due to biofuel feedstock cultivation. These land use changes are predicted to increase P loadings from the U.S. side of the GL basin by 3.5–9.5%, depending on the Lake watershed and development scenario. The exception is Lake Ontario, where loading is predicted to decrease by 1.8% for one scenario, due to population losses in the drainage area. Overall, urban expansion is estimated to increase P loadings by 3.4%. Agricultural expansion associated with predicted biofuel feedstock cultivation is predicted to increase P loadings by an additional 2.4%. Watersheds that export P most efﬁciently and thus are the most vulnerable to increases in P sources tend to be found along southern Lake Ontario, southeastern Lake Erie, western Lake Michigan, and southwestern Lake Superior where watershed areas are concentrated along the coastline with shorter ﬂow paths. In contrast, watersheds with high soil permeabilities, fractions of land underlain by tile drains, and long distances to the GL are less vulnerable.

Laurentian Great Lakes↗

USGS2010

Fire, flow and dynamic equilibrium in stream macroinvertebrate communities

The complex effects of disturbances on ecological communities can be further complicated by subsequent perturbations within an ecosystem. We investigated how wildfire interacts with annual variations in peak streamflow to affect the stability of stream macroinvertebrate communities in a central Idaho wilderness, USA. We conducted a 4-year retrospective analysis of unburned (n = 7) and burned (n = 6) catchments, using changes in reflectance values (??NBR) from satellite imagery to quantify the percentage of each catchment's riparian and upland vegetation that burned at high and low severity. For this wildland fire complex, increasing riparian burn severity and extent were associated with greater year-to-year variation, rather than a perennial increase, in sediment loads, organic debris, large woody debris (LWD) and undercut bank structure. Temporal changes in these variables were correlated with yearly peak flow in burned catchments but not in unburned reference catchments, indicating that an interaction between fire and flow can result in decreased habitat stability in burned catchments. Streams in more severely burned catchments exhibited increasingly dynamic macroinvertebrate communities and did not show increased similarity to reference streams over time. Annual variability in macroinvertebrates was attributed, predominantly, to the changing influence of sediment, LWD, riparian cover and organic debris, as quantities of these habitat components fluctuated annually depending on burn severity and annual peak streamflows. These analyses suggest that interactions among fire, flow and stream habitat may increase inter-annual habitat variability and macroinvertebrate community dynamics for a duration approaching the length of the historic fire return interval of the study area. ?? 2009 Blackwell Publishing Ltd.

Freshwater Biology↗

USGS2022

Genetic structure and historic demography of endangered unarmoured threespine stickleback at southern latitudes signals a potential new management approach

Habitat loss, flood control infrastructure, and drought have left most of southern California and northern Baja California's native freshwater fish near extinction, including the endangered unarmoured threespine stickleback ( Gasterosteus aculeatus williamsoni ). This subspecies, an unusual morph lacking the typical lateral bony plates of the G. aculeatus complex, occurs at arid southern latitudes in the eastern Pacific Ocean and survives in only three inland locations. Managers have lacked molecular data to answer basic questions about the ancestry and genetic distinctiveness of unarmoured populations. These data could be used to prioritize conservation efforts. We sampled G. aculeatus from 36 localities and used microsatellites and whole genome data to place unarmoured populations within the broader evolutionary context of G. aculeatus across southern California/northern Baja California. We identified three genetic groups with none consisting solely of unarmoured populations. Unlike G. aculeatus at northern latitudes, where Pleistocene glaciation has produced similar historical demographic profiles across populations, we found markedly different demographics depending on sampling location, with inland unarmoured populations showing steeper population declines and lower heterozygosity compared to low armoured populations in coastal lagoons. One exception involved the only high elevation population in the region, where the demography and alleles of unarmoured fish were similar to low armoured populations near the coast, exposing one of several cases of artificial translocation. Our results suggest that the current “management-by-phenotype” approach, based on lateral plates, is incidentally protecting the most imperilled populations; however, redirecting efforts toward evolutionary units, regardless of phenotype, may more effectively preserve adaptive potential.

Baja California, California↗

USGS2013

A critique of the use of indicator-species scores for identifying thresholds in species responses

Identification of ecological thresholds is important both for theoretical and applied ecology. Recently, Baker and King (2010, King and Baker 2010) proposed a method, threshold indicator analysis (TITAN), to calculate species and community thresholds based on indicator species scores adapted from Dufrêne and Legendre (1997). We tested the ability of TITAN to detect thresholds using models with (broken-stick, disjointed broken-stick, dose-response, step-function, Gaussian) and without (linear) definitive thresholds. TITAN accurately and consistently detected thresholds in step-function models, but not in models characterized by abrupt changes in response slopes or response direction. Threshold detection in TITAN was very sensitive to the distribution of 0 values, which caused TITAN to identify thresholds associated with relatively small differences in the distribution of 0 values while ignoring thresholds associated with large changes in abundance. Threshold identification and tests of statistical significance were based on the same data permutations resulting in inflated estimates of statistical significance. Application of bootstrapping to the split-point problem that underlies TITAN led to underestimates of the confidence intervals of thresholds. Bias in the derivation of the z-scores used to identify TITAN thresholds and skewedness in the distribution of data along the gradient produced TITAN thresholds that were much more similar than the actual thresholds. This tendency may account for the synchronicity of thresholds reported in TITAN analyses. The thresholds identified by TITAN represented disparate characteristics of species responses that, when coupled with the inability of TITAN to identify thresholds accurately and consistently, does not support the aggregation of individual species thresholds into a community threshold.

Freshwater Science↗

USGS2018

Reestablishing a host–affiliate relationship: Migratory fish reintroduction increases native mussel recruitment

Co‐extirpation among host–affiliate species is thought to be a leading cause of biodiversity loss worldwide. Freshwater mussels (Unionida) are at risk globally and face many threats to survival, including limited access to viable host fish required to complete their life history. We examine the relationship between the common eastern elliptio mussel ( Elliptio complanata ) and its migratory host fish the American eel ( Anguilla rostrata ), whose distribution in the Chesapeake Bay watershed is limited, in part, by dams. We examined population demographics of E. complanata across locations in the Chesapeake Bay watershed, primarily in the Susquehanna River in the absence of American eels, and conducted experimental restocking of eels to assess potential impacts on mussel recruitment. Compared to surveys completed ~20 yr prior, E. complanata could be experiencing declines at several historically abundant sites. These sites also had extremely limited evidence of recruitment. Restoration of host fish improved recruitment, but results were not equivalent between stocking sites, indicating that host reintroduction alone may not be fully effective in reestablishing mussel populations. One site where eels were introduced (Pine Creek, Tioga County, Pennsylvania, USA) experienced an increase from 0 juveniles found during quantitative surveys prior to eel stocking to 151 (21% of individuals collected during quantitative surveys) E. complanata juveniles found four years after stocking. A second site (Buffalo Creek, Union County, Pennsylvania) experienced a more moderate increase from 2 to 7 juveniles found during 2010 and 2014 quantitative surveys, respectively. Continued examination of other potential interacting factors affecting recruitment, including water quality or habitat conditions, is necessary to target favorable sites for successful restoration.

Maryland, Pennsylvania↗

USGS2005

Modelling habitat associations with fingernail clam (Family: Sphaeriidae) counts at multiple spatial scales using hierarchical count models

1. Macroinvertebrate count data often exhibit nested or hierarchical structure. Examples include multiple measurements along each of a set of streams, and multiple synoptic measurements from each of a set of ponds. With data exhibiting hierarchical structure, outcomes at both sampling (e.g. within stream) and aggregated (e.g. stream) scales are often of interest. Unfortunately, methods for modelling hierarchical count data have received little attention in the ecological literature. 2. We demonstrate the use of hierarchical count models using fingernail clam (Family: Sphaeriidae) count data and habitat predictors derived from sampling and aggregated spatial scales. The sampling scale corresponded to that of a standard Ponar grab (0.052 m 2 ) and the aggregated scale to impounded and backwater regions within 38–197 km reaches of the Upper Mississippi River. Impounded and backwater regions were resampled annually for 10 years. Consequently, measurements on clams were nested within years. Counts were treated as negative binomial random variates, and means from each resampling event as random departures from the impounded and backwater region grand means. 3. Clam models were improved by the addition of covariates that varied at both the sampling and regional scales. Substrate composition varied at the sampling scale and was associated with model improvements, and reductions (for a given mean) in variance at the sampling scale. Inorganic suspended solids (ISS) levels, measured in the summer preceding sampling, also yielded model improvements and were associated with reductions in variances at the regional rather than sampling scales. ISS levels were negatively associated with mean clam counts. 4. Hierarchical models allow hierarchically structured data to be modelled without ignoring information specific to levels of the hierarchy. In addition, information at each hierarchical level may be modelled as functions of covariates that themselves vary by and within levels. As a result, hierarchical models provide researchers and resource managers with a method for modelling hierarchical data that explicitly recognises both the sampling design and the information contained in the corresponding data.

Illinois, Iowa, Minnesota, Wisconsin↗