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At least 1,387 records · Page 77Linked to original sources

USGS2004

Waterfowl migration on Klamath Basin National Wildlife Refuges 1953-2001

The Klamath Basin National Wildlife Refuge (NWR) complex, located in northeastern California and southern Oregon, is situated on a major Pacific Flyway migration corridor connecting waterfowl breeding grounds in the north with major wintering grounds in California and Mexico. The complex comprises five waterfowl refuges including Lower Klamath NWR, Tule Lake NWR, Upper Klamath NWR, Klamath Marsh NWR, and Clear Lake NWR, and one bald eagle refuge, Bear Valley NWR. Lower Klamath and Tule Lake NWRs are the largest refuges in the complex; historically, they supported some of the greatest autumn and spring concentrations of migrating waterfowl in North America. Starting in 1953, standardized waterfowl surveys from small aircraft have been conducted in autumn through spring. This report summarizes waterfowl migration activity (i.e., abundance, species composition, distribution on refuges, and chronology) over four time periods—the long-term (1953-2001), early (1953-76), recent (1977-2001), and the most recent (1998-2001)—to describe changing patterns of migration on Klamath Basin refuges from autumn 1953 to spring 2001. Over the long term, waterfowl abundance (birds per day) on the refuge complex averaged about 1.0 million in autumn and about 360,000 in spring. A record peak count of 5.8 million waterfowl was recorded September 24-25, 1958. Average abundance of autumn staging waterfowl for the refuge complex, after reaching record levels in the 1950s and early 1960s, began a decline that lasted until the 1980s. A gradual recovery occurred during the 1990s, but autumn abundance has not recovered to pre-1970 levels. In contrast to autumn, average spring abundance was generally lower in the early decades but has gradually increased through the 1990s, particularly on Lower Klamath NWR. Dabbling ducks represented an average of 68% of all waterfowl in autumn and 55% in spring for the long term. Northern pintail ( Anas acuta ) was dominant, representing 62% of all dabblers in autumn and 51% in spring. A significant decline in pintail abundance starting in the late 1950s altered waterfowl composition on Klamath Basin refuges. As pintail declined, other species such as mallard ( Anas platyrhynchos ) and green-winged teal ( Anas crecca ) increased in abundance. Although Arctic nesting geese, including white-fronted ( Anser albifrons ), cackling Canada ( Branta canadensis minima ), white geese (lesser snow [ Chen caerulescens caerulescens ], and Ross’s [ Chen rossii ]) have become less prominent in recent decades, they reached an historically high abundance during autumn in the 1960s and 1970s, particularly on Tule Lake NWR. Tule Lake NWR supported the highest average autumn waterfowl populations until surpassed by Lower Klamath NWR around 1980. During the recent period (1977-2001), Lower Klamath NWR accounted for 60% of all waterfowl using the refuge complex in autumn and 61% in spring. Habitat diversity and wetland productivity contributed to its greater waterfowl abundance. Tule Lake NWR supported the most geese over the long term, 79% in autumn and 66% in spring; however, total waterfowl abundance on this refuge in autumn has been in decline, likely because of reduced diversity and productivity of sumps in the refuge. Upper Klamath, Klamath Marsh, and Clear Lake NWRs accounted for less than 8% of total waterfowl use in autumn and spring but provided diverse habitats for migrants. Waterfowl use-days on Klamath Basin refuges typically peaked in mid-autumn, decreased as migrants passed through the basin, and then reached a lesser peak during spring passage. Waterfowl abundance reached a pronounced peak in autumn during the early period (1953-76), but spring peak buildup was much less pronounced. For the recent period the autumn peak was more subdued. Waterfowl abundance, species composition, and distribution on Klamath Basin refuges have fluctuated over the decades and have been influenced by events such as productivity on breeding grounds and habitat conditions on wintering grounds that cause shifts in migration patterns. A major challenge for the future appears to be the availability of adequate water for wetland management on Klamath Basin refuges.

California, Oregon↗

USGS2021

Extrinsically reinforced hybrid speciation within Holarctic ermine (Mustela spp.) produces an insular endemic

Aim Refugial isolation during glaciation is an established driver of speciation; however, the opposing role of interglacial population expansion, secondary contact, and gene flow on the diversification process remains less understood. The consequences of glacial cycling on diversity are complex and especially so for archipelago species, which experience dramatic fluctuations in connectivity in response to both lower sea levels during glacial events and increased fragmentation during glacial recession. We test whether extended refugial isolation has led to the divergence of genetically and morphologically distinct species within Holarctic ermine ( Mustela erminea ), a small cosmopolitan carnivore species that harbours 34 extant subspecies, 14 of which are insular endemics. Location Holarctic. Methods We use genetic sequences (complete mitochondrial genomes, four nuclear genes) from >100 ermine (stoats) and geometric morphometric data for >200 individuals (27 of the 34 extant subspecies) from across their Holarctic range to provide an integrative perspective on diversification and endemism across this complex landscape. Multiple species delimitation methods ( iBPP , bPTP ) assessed congruence between morphometric and genetic data. Results Our results support the recognition of at least three species within the M. erminea complex, coincident with three of four genetic clades, tied to diversification in separate glacial refugia. We found substantial geographic variation within each species, with geometric morphometric results largely consistent with historical infraspecific taxonomy. Main conclusions Phylogeographic structure mirrors patterns of diversification in other Holarctic species, with a major Nearctic‐Palearctic split, but with greater intraspecific morphological diversity. Recognition of insular endemic species M. haidarum is consistent with a deep history of refugial persistence and highlights the urgency of mindful management of island populations along North America's North Pacific Coast. Significant environmental modification (e.g. industrial‐scale logging, mining) has been proposed for a number of these islands, which may elevate the risk of extinction of insular palaeoendemics.

Diversity and Distributions↗

USGS2022

Increased landscape disturbance and streamflow variability threaten fish biodiversity in the Red River catchment, USA

Aim Stream fish distributions are hypothesized to be strongly associated with landscape characteristics at multiple scales. Variation in flow regimes and intensity of landscape disturbance are associated with stream fish distributions; however, relationships are poorly understood in many high-diversity regions. Our objective was to identify occurrence relationships between fish distributions and streamflow and landscape characteristics in the south-central United States. Location Our study area was the central Red River catchment in Oklahoma, Texas and Arkansas, USA. Methods We used existing fish surveys to model the occurrence of a diverse, warmwater assemblage among hydraulic response units (HRUs). We used multispecies occupancy modelling to identify variation in occurrence probability among 111 stream fishes in relation to landscape disturbance and flow regime characteristics. Results We found occurrence relationships with landscape disturbance and 11 metrics comprising all flow-regime components. The relationships varied within both major species groups and some genera. Frequency and duration were the most common metrics underlying flow regime relationships. More common stream fishes tended to be positively associated with higher levels of landscape disturbance and flow regime metrics representing variability; conversely, narrow-ranged fishes tended to be negatively associated. Occurrence relationships with flow metrics representing high-flow events were predominately negative. As expected, many species were strongly associated with ecoregion with landscape disturbance and flow relationships held constant. Main conclusions Our study informs land use and water management decisions and stream fish conservation at multiple spatial scales. Collectively, the findings suggest potential homogenization of the Red River fish assemblage with increased landscape disturbance and streamflow variability. A reduction in landscape disturbance and maintenance of natural flow patterns at coarser scales may benefit endemic and narrow-ranged fishes. Our findings also help guide finer-scale land use and water management decisions by identifying stream network areas with a high occurrence probability of less tolerant fishes.

Arkansas, Oklahoma, Texas↗

USGS2023

Limited hybridisation and introgression despite stocking among endemic Interior Highlands black basses (Centrarchidae: Micropterus)

Aim: Smallmouth Bass ( Micropterus dolomieu ; SMB) are globally popular among anglers and have been widely introduced (i.e. stocked) for population management and sportfishing. Importantly, stocking was prevalent before cryptic diversity within the SMB complex was known, which now includes three newly elevated species: Neosho Bass ( M. velox ; NB), Little River Bass ( M. sp. cf. dolomieu Little River; LRB) and Ouachita Bass ( M. sp. cf. dolomieu Ouachita River; OB). We sought to quantify population structure and hybridisation and introgression in these three recently described species. Location: Species-level diversity, particularly in the basin-restricted LRB and OB in the Ouachita Mountains within the Central Interior Highlands (CIH), North America, suggests the presence of distinct genetic variation that could be eroded by introgression. Methods: We estimated interspecific introgression and intraspecific population differentiation in the Smallmouth Bass species complex (SMB-C) using 472 specimens comprising SMB, NB, LRB and OB, including the naturally sympatric Spotted Bass ( M. punctulatus ; SPB). Genomic samples were genotyped on a SNP panel of 192 loci designed to detect allele-sharing on multiple hierarchical levels. Results: We found low range-wide hybridisation between species in the SMB-C and SPB (mostly SMB-C backcrosses), and interspecific heterozygosity varied, indicating differential introgression. Range-wide hybridisation between species in the CIH and SMB was similar overall (but mostly F 2 and CIH backcrosses) and was observed in streams with known SMB stocking in connected reservoirs. Interspecific heterozygosity in SMB hybrids was also generally lower, indicating later-generation backcrosses. We found strong population structure in the Ouachita Mountains (LRB and OB). Main conclusions: Despite isolated incidences of natural (SPB) and human-mediated (SMB) introgression, genomic identity appears intact in endemic LRB and OB, suggesting potential ecological or behavioural isolating mechanisms preventing cross-species reproduction. Our findings reveal that genetic variation remains in cryptic, basin-restricted species in the Ouachita Mountains ecoregion that may be managed for long-term conservation.

Arkansas, Missouri, Oklahoma↗

USGS2019

Comparing grasshopper (Orthoptera: Acrididae) communities on tallgrass prairie reconstructions and remnants in Missouri

Tallgrass prairies, which once occupied a large swath of central North America, face the combined challenges of habitat loss and fragmentation. In Missouri, where less than 1% the historical prairie remains, prairies are being reconstructed from agricultural or wooded land. Invertebrates are often assumed to colonise reconstructions if native vegetation returns; however, the limited mobility of many invertebrates, the isolation of many tallgrass remnants, and the difficulty in establishing prairie plants raise serious questions as to whether invertebrate communities on reconstructed prairies are and will be equivalent to those found on remnant prairies. Grasshoppers (Acrididae) display a range of dispersal capabilities and may be valuable for assessing the success of prairie restoration for invertebrates. Our first objective was to compare grasshopper communities on reconstructed and remnant prairies and, if differences existed, identify species or functional groups associated with each habitat type. The second objective was to evaluate the effect of time because prairie reconstruction on grasshopper communities to determine if communities on reconstructions are converging with communities on remnants. Our results suggest that prairie reconstructions in Missouri do not support the same communities of grasshoppers as prairie remnants. Grasshopper diversity was generally greater on remnants. Many species had not colonised nearby reconstructions. Communities on prairie reconstructions were characterised by a few long-winged, generalist species that are typically successful in agroecosystems. Further investigation into the habitat disparities driving low grasshopper diversity on reconstructions could help restore the grasshopper community of reconstructions.

Insect Conservation and Diversity↗

USGS2020

A comparative phylogeographic approach to facilitate recovery of an imperiled freshwater mussel (Bivalvia: Unionida: Potamilus inflatus)

North American freshwaters are among the world’s most threatened ecosystems, and freshwater mussels are among the most imperiled inhabiting these systems. A critical aspect of conservation biology is delineating patterns of genetic diversity, which can be difficult when a taxon has been extirpated from a significant portion of its historical range. In such cases, evaluating conservation and recovery options may benefit by using surrogate species as proxies when assessing overall patterns of genetic diversity. Here, we integrate the premise of surrogate species into a comparative phylogeographic framework to hypothesize genetic relationships between extant and extirpated populations of Potamilus inflatus by characterizing genetic structure in co-distributed congeners with similar life histories and dispersal capabilities. Our mitochondrial and nuclear sequence data exhibited variable patterns of genetic divergence between Potamilus spp. native to the Mobile and Pascagoula + Pearl + Pontchartrain (PPP) provinces. However, hierarchical Approximate Bayesian Computation indicated that the diversification between Mobile and PPP clades was synchronous and represents a genetic signature of a common history of vicariance. Recent fluctuations in sea-level appear to have caused Potamilus spp. in the PPP to form a single genetic cluster, providing justification for using individuals from the Amite River as a source of brood stock to re-establish extirpated populations of P. inflatus. Future studies utilizing eDNA and genome-wide molecular data are essential to better understand the distribution of P. inflatus and establish robust recovery plans. Given the imperilment status of freshwater mussels globally, our study represents a useful methodology for predicting relationships among extant and extirpated populations of imperiled species.

Florida, Alabama, Mississippi, Louisiana↗

USGS2021

Implications of historical and contemporary processes on genetic differentiation of a declining boreal songbird: The rusty blackbird

The arrangement of habitat features via historical or contemporary events can strongly influence genomic and demographic connectivity, and in turn affect levels of genetic diversity and resilience of populations to environmental perturbation. The rusty blackbird ( Euphagus carolinus ) is a forested wetland habitat specialist whose population size has declined sharply (78%) over recent decades. The species breeds across the expansive North American boreal forest region, which contains a mosaic of habitat conditions resulting from active natural disturbance regimes and glacial history. We used landscape genomics to evaluate how past and present landscape features have shaped patterns of genetic diversity and connectivity across the species’ breeding range. Based on reduced-representation genomic and mitochondrial DNA, genetic structure followed four broad patterns influenced by both historical and contemporary forces: (1) an east–west partition consistent with vicariance during the last glacial maximum; (2) a potential secondary contact zone between eastern and western lineages at James Bay, Ontario; (3) insular differentiation of birds on Newfoundland; and (4) restricted regional gene flow among locales within western and eastern North America. The presence of genomic structure and therefore restricted dispersal among populations may limit the species’ capacity to respond to rapid environmental change.

Diversity↗

USGS2009

Mine spoil prairies expand critical habitat for endangered and threatened amphibian and reptile species

Coal extraction has been occurring in the Midwestern United States for over a century. Despite the pre-mining history of the landscape as woodlands, spent surface coalfields are often reclaimed to grasslands. We assessed amphibian and reptile species on a large tract of coal spoil prairie and found 13 species of amphibians (nine frog and four salamander species) and 19 species of reptiles (one lizard, five turtle, and 13 snake species). Two state-endangered and three state species of special concern were documented. The amphibian diversity at our study site was comparable to the diversity found at a large restored prairie situated 175 km north, within the historic prairie peninsula.

Diversity↗

USGS1999

Temporal and spatial variability in thalweg profiles of a gravel-bed river

This study used successive longitudinal thalweg profiles in gravel-bed rivers to monitor changes in bed topography following floods and associated large sediment inputs. Variations in channel bed elevations, distributions of residual water depths, percentage of channel length occupied by riffles, and a spatial autocorrelation coefficient (Moran's I ) were used to quantify changes in morphological diversity and spatial structure in Redwood Creek basin, northwestern California. Bed topography in Redwood Creek and its major tributaries consists primarily of a series of pools and riffles. The size, frequency and spatial distribution of the pools and riffles have changed significantly during the past 20 years. Following large floods and high sediment input in Redwood Creek and its tributaries in 1975, variation in channel bed elevations was low and the percentage of the channel length occupied by riffles was high. Over the next 20 years, variation in bed elevations increased while the length of channel occupied by riffles decreased. An index [(standard deviation of residual water depth/bankfull depth) × 100] was developed to compare variations in bed elevation over a range of stream sizes, with a higher index being indicative of greater morphological diversity. Spatial autocorrelation in the bed elevation data was apparent at both fine and coarse scales in many of the thalweg profiles and the observed spatial pattern of bed elevations was found to be related to the dominant channel material and the time since disturbance. River reaches in which forced pools dominated, and in which large woody debris and bed particles could not be easily mobilized, exhibited a random distribution of bed elevations. In contrast, in reaches where alternate bars dominated, and both wood and gravel were readily transported, regularly spaced bed topography developed at a spacing that increased with time since disturbance. This pattern of regularly spaced bed features was reversed following a 12-year flood when bed elevations became more randomly arranged.

Earth Surface Processes and Landforms↗

USGS2000

Role of lake regulation on glacier fed rivers in enhancing salmon productivity: The Cook Inlet watershed south central Alaska, USA

Rivers fed by glaciers constitute a major part of the freshwater runoff into the Cook Inlet basin of south-central Alaska. This basin is very important to the economy of the State of Alaska because it is home to more than half of the population and it supports multi-million dollar commercial, subsistence and sport fisheries. Hence an understanding of how glacial runoff influences biological productivity is important for managing rivers that drain into Cook Inlet. This paper examines the ways in which the regulation of glacier-fed rivers by proglacial lakes affects salmon productivity, with particular reference to the Kenai River. Salmon escapement per unit channel length on the Kenai River is between two and ten times that found for rain-and-snowmelt dominated rivers and glacier-fed rivers lacking lake regulation. Lakes are shown to influence biological processes in glacier-fed rivers by attenuating peak flows, sustaining high flows throughout the summer, supplementing winter low flows, settling suspended sediment, and increasing river temperatures. Downstream from large lakes, glacier-fed rivers are less disturbed, channels are relatively stable and have well-developed salmonid habitats. The positive influences are indicated by the high diversity and abundances of benthic macroinvertebrates, which are important food resources for juvenile salmonids. High summer flows allow access for up-river salmon runs and lakes also provide both overwintering and rearing habitat. Copyright ?? 2000 John Wiley & Sons, Ltd.Rivers fed by glaciers constitute a major part of the freshwater runoff into the Cook Inlet basin of south-central Alaska. This basin is very important to the economy of the State of Alaska because it is home to more than half of the population and it supports multi-million dollar commercial, subsistence and sport fisheries. Hence an understanding of how glacial runoff influences biological productivity is important for managing rivers that drain into Cook Inlet. This paper examines the ways in which the regulation of glacier-fed rivers by proglacial lakes affects salmon productivity, with particular reference to the Kenai River. Salmon escapement per unit channel length on the Kenai River is between two and ten times that found for rain-and-snowmelt dominated rivers and glacier-fed rivers lacking lake regulation. Lakes are shown to influence biological processes in glacier-fed rivers by attenuating peak flows, sustaining high flows throughout the summer, supplementing winter low flows, settling suspended sediment, and increasing river temperatures. Downstream from large lakes, glacier-fed rivers are less disturbed, channels are relatively stable and have well-developed salmonid habitats. The positive influences are indicated by the high diversity and abundances of benthic macroinvertebrates, which are important food resources for juvenile salmonids. High summer flows allow access for up-river salmon runs and lakes also provide both overwintering and rearing habitat.

Hydrological Processes↗

USGS2014

Dynamics of the Yellowstone hydrothermal system

The Yellowstone Plateau Volcanic Field is characterized by extensive seismicity, episodes of uplift and subsidence, and a hydrothermal system that comprises more than 10,000 thermal features, including geysers, fumaroles, mud pots, thermal springs, and hydrothermal explosion craters. The diverse chemical and isotopic compositions of waters and gases derive from mantle, crustal, and meteoric sources and extensive water-gas-rock interaction at variable pressures and temperatures. The thermal features are host to all domains of life that utilize diverse inorganic sources of energy for metabolism. The unique and exceptional features of the hydrothermal system have attracted numerous researchers to Yellowstone beginning with the Washburn and Hayden expeditions in the 1870s. Since a seminal review published a quarter of a century ago, research in many fields has greatly advanced our understanding of the many coupled processes operating in and on the hydrothermal system. Specific advances include more refined geophysical images of the magmatic system, better constraints on the time scale of magmatic processes, characterization of fluid sources and water-rock interactions, quantitative estimates of heat and magmatic volatile fluxes, discovering and quantifying the role of thermophile microorganisms in the geochemical cycle, defining the chronology of hydrothermal explosions and their relation to glacial cycles, defining possible links between hydrothermal activity, deformation, and seismicity; quantifying geyser dynamics; and the discovery of extensive hydrothermal activity in Yellowstone Lake. Discussion of these many advances forms the basis of this review.

Idaho, Montana, Wyoming↗

USGS2016

The differing biogeochemical and microbial signatures of glaciers and rock glaciers

Glaciers and rock glaciers supply water and bioavailable nutrients to headwater mountain lakes and streams across all regions of the American West. Here we present a comparative study of the metal, nutrient, and microbial characteristics of glacial and rock glacial influence on headwater ecosystems in three mountain ranges of the contiguous U.S.: The Cascade Mountains, Rocky Mountains, and Sierra Nevada. Several meltwater characteristics (water temperature, conductivity, pH, heavy metals, nutrients, complexity of dissolved organic matter (DOM), and bacterial richness and diversity) differed significantly between glacier and rock glacier meltwaters, while other characteristics (Ca 2+ , Fe 3+ , SiO 2 concentrations, reactive nitrogen, and microbial processing of DOM) showed distinct trends between mountain ranges regardless of meltwater source. Some characteristics were affected both by glacier type and mountain range (e.g. temperature, ammonium (NH 4 + ) and nitrate (NO 3 - ) concentrations, bacterial diversity). Due to the ubiquity of rock glaciers and the accelerating loss of the low latitude glaciers our results point to the important and changing influence that these frozen features place on headwater ecosystems.

California, Colorado, Oregon, Washington, Wyoming↗

USGS2015

Predicting the resilience and recovery of aquatic systems: a framework for model evolution within environmental observatories

Maintaining the health of aquatic systems is an essential component of sustainable catchmentmanagement, however, degradation of water quality and aquatic habitat continues to challenge scientistsand policy-makers. To support management and restoration efforts aquatic system models are requiredthat are able to capture the often complex trajectories that these systems display in response to multiplestressors. This paper explores the abilities and limitations of current model approaches in meeting this chal-lenge, and outlines a strategy based on integration of ﬂexible model libraries and data from observationnetworks, within a learning framework, as a means to improve the accuracy and scope of model predictions.The framework is comprised of a data assimilation component that utilizes diverse data streams from sensornetworks, and a second component whereby model structural evolution can occur once the model isassessed against theoretically relevant metrics of system function. Given the scale and transdisciplinarynature of the prediction challenge, network science initiatives are identiﬁed as a means to develop and inte-grate diverse model libraries and workﬂows, and to obtain consensus on diagnostic approaches to modelassessment that can guide model adaptation. We outline how such a framework can help us explore thetheory of how aquatic systems respond to change by bridging bottom-up and top-down lines of enquiry,and, in doing so, also advance the role of prediction in aquatic ecosystem management.

Water Resources Research↗

USGS2014

Lianas as invasive species in North America

Liana diversity is typically low in the temperate zones; however, the influx of non-native invasive liana species in North America has increased local diversity at the expense of native habitats and species. Some of the most illustrative studies of invasive lianas in temperate North America compared the biological traits of invasive lianas with native congeners or ecological analogs. The majority of these studies focused on two species, Celastrus orbiculatus (oriental bittersweet) and Lonicera japonica (Japanese honeysuckle). Temperate zone lianas generally have higher photosynthetic rates than other early successional species and their host trees. Invasive lianas are having an increasing impact on the dynamics and trajectories of North American plant communities. They often exhibit superior growth and survival compared to their native counterparts, and in some cases, invasive lianas may directly contribute to the decline of their native correlates.

Book chapter↗

USGS2025

Performance comparisons for artificially propagated and wild Pacific lamprey juveniles and larvae

Artificially propagated Pacific lamprey ( Entosphenus tridentatus ) are produced for restoration and for use in dam passage studies to reduce the demand for wild fish. Such uses require that animals are representative of their wild counterparts. Previous work indicated that this is true for Pacific lamprey larvae and juveniles reared in the hatchery with respect to the length of sustained swimming. However, more subtle differences in behaviour and performance that lamprey need to survive have not been assessed. In this study, artificially propagated and wild fish were compared in laboratory tests under no-flow conditions to examine light avoidance, burrowing speed, burst swim speed, volitional routine swim speed and time to come to rest. Most larvae burrowed in less than a minute, and we found highly significant differences ( p < 0.001) between artificially propagated and wild larvae burrowing times, a critical escape behaviour. This could have implications for studies of larval entrainment at irrigation diversion canals or in turbine boils at dams. Interestingly, all of the wild juveniles tested came to rest quickly after introduction to the chamber (1.5 min), while artificially propagated lamprey swam robotically near the surface and 48% did not come to rest in the first 10 min (median time to rest = 9.5 min). In contrast, wild juveniles quickly (median = 1.47 min) sought areas near the tank bottom and attached strongly with their oral disc. Such behavioural differences could have important survival consequences for artificially propagated lamprey as they approach turbine intakes, bypass screens and irrigation diversion headgates. This study highlights the need to conduct behavioural assays that examine subtleties of fish behaviour that can be missed with traditional swim tunnel comparisons.

Aquaculture, Fish and Fisheries↗

USGS2025

Turning trash into treasure: Leveraging discarded filters for national-scale aquatic eDNA biomonitoring

Monitoring biodiversity changes over large spatiotemporal scales is critical for effective ecosystem conservation and management. This study investigates the potential of environmental DNA (eDNA) metabarcoding to enhance national-scale biomonitoring of freshwater diversity by leveraging discarded filters associated with routine water quality sampling from the U.S. Geological Survey's (USGS) National Water Quality Network (NWQN). We tested 375 samples from 103 NWQN sites for eDNA of native and non-native fish and found that 52% of the filters yielded fish eDNA for a total of 70 fish species detections. Of the filters that had fish eDNA present, an average of 3.7 species were detected. Benchmarking these results to USGS's Aquatic Gap Analysis Project (AGAP)—which includes both field-verified observations along with predictive models derived from fish capture and landscape predictor datasets—we found that eDNA from these filters detected only a fraction of the observed and expected fish diversity for these sites. Our results indicate that these discarded filters may not be sufficient for eDNA sampling of fish communities and posit that alternative filter types more appropriate for eDNA sampling may yield more valuable biomonitoring data. Nevertheless, we tested the efficacy of two novel approaches to facilitate large-scale biomonitoring. Though these filters did not yield adequate fish eDNA, the AGAP database provides a useful method for ground truthing fish species presence. The potential of integrating eDNA sampling into existing monitoring frameworks, which, when paired with more optimal eDNA methods, could be a cost-effective strategy to enhance biodiversity monitoring at large scales.

Aquaculture, Fish and Fisheries↗

USGS2012

Phylogeographic implications for release of critically endangered manatee calves rescued in Northeast Brazil

1. The Antillean manatee (Trichechus manatus manatus), a subspecies of the West Indian manatee, is a large-bodied marine mammal found in fresh, brackish, and marine habitats throughout the Caribbean Islands and Central and South America. Antillean manatees in Brazil are classified as critically endangered, with a census size of approximately 500 individuals. The population in the Northeast region of Brazil is suspected to have approximately 300 manatees and is threatened by habitat alteration and incidental entanglement in fishing gear. 2. A high incidence of dependent calf strandings have been identified near areas of altered critical manatee habitat. The majority of the calves are neonates, discovered alive, with no potential mothers nearby. These calves typically require human intervention to survive. Since 1989 the calves have been rescued (N=67), rehabilitated, and released (N=25) to supplement the small wild manatee population. The rescued calves, and those born in captivity, are typically, not released to their rescue location, mainly for logistical reasons. Therefore, phylogeographic analyses can help to identify related populations and appropriate release sites. 3. Here, mitochondrial DNA analyses identified low haplotype (h=0.08) and nucleotide (π=0.0026) genetic diversity in three closely related haplotypes. All three haplotypes (M01, M03, and a previously unidentified haplotype, M04) were found in the northern portion of the region, while only a single haplotype (M01) was represented in the south. This suggests the presence of two genetic groups with a central mixing zone. Release of rehabilitated calves to unrelated populations may result in genetic swamping of locally adapted alleles or genotypes, limiting the evolutionary potential of the population. 4. The small population size coupled with low genetic diversity indicates that the Northeast Brazil manatee population is susceptible to inbreeding depression and possible local extinction. Further conservation measures incorporating genetic information could be beneficial to the critically endangered Brazilian manatee population.

Aquatic Conservation: Marine and Freshwater Ecosys↗

USGS2018

Size-structured habitat selection by arapaima in floodplain lakes of the lower Amazon

Human modification of floodplain ecosystems is widespread and a major threat to fish populations, particularly in the tropics where fish diversity and rates of floodplain degradation are high. Identifying measures to minimize the susceptibility of floodplain fishes to habitat modification requires understanding dry-season lake habitat selection for species of conservation concern. This study examined the effects of environmental factors on dry-season floodplain lake habitat selection by arapaima ( Arapaima spp.) and determined the extent to which they differed across three size classes. In floodplain lakes of the lower Amazon River, variables were measured at locations representing habitat availability and compared with measurements taken where arapaima were observed during surface breathing. Regression models were used to account for between-lake variation in the presence of arapaima owing to nearby fishing communities. The probability of arapaima presence at each sample location was modelled based on the variables measured. The results indicated that arapaima expressed distinct habitat selection patterns, which differed significantly across size classes. The general pattern observed was that all arapaima were more likely to be found in deeper, more turbid, and higher conductivity locations, whereas smaller arapaima were more likely to remain near dense beds of floating macrophytes. The probability of arapaima presence differed among fishing community territories, reflecting differences in management schemes. Deeper, macrophyte-rich sections of floodplain lakes appear to provide key habitats for arapaima and deserve consideration for becoming priority targets for conservation of the rich diversity of fish species in these systems.

Pará↗