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At least 541 records · Page 30Linked to original sources
USGS1996

Concordance of seabird population parameters: Analytical methods and interpretation

In an ecological context, concordance may be defined as the tendency for paired values of some parameter, such as the annual productivity of bird species, to show similar directions and magnitudes of deviation from the mean. Where concordance among populations is high, there is an implied similarity of the ecological factors affecting performance. Conversely, if populations behave discordantly, dissimilarity of underlying ecological factors is likely. In evaluating birds as indicators of the marine environment, the biologist typically is confronted with a three-dimensional array of observations (species, areas, and years) in which there are more missing values than filled cells. This frustrates attempts to analyze concordance using existing methods (e.g., Kendall's coefficient, or correlation combined with cluster analysis), which are either impossible to apply to incomplete data sets or potentially misleading when applied to incomplete data sets. I suggest an alternative method for analyzing concordance that makes maximal use of available data. For a given data set partitioned into the smallest units containing information about concordance, one computes an index of concordance using a regression approach and tests for significance using randomization methods. This procedure would seem to have wide application to ecological studies generally and to seabird monitoring in particular.

Conference Paper↗
USGS1999

Implications of climate change for Alaska's seabirds

Seabirds are prominent and highly visible components of marine ecosystems that will be affected by global climate change. The Bering Sea region is particularly important to seabirds; populations there are larger and more diverse than in any similar region in North America—over 90% of seabirds breeding in the continental United States are found in this region. Seabirds, so named because they spend at least 80% of their lives at sea, are dependent upon marine resources for food. As prey availability changes in response to climatically driven factors such as surface sea temperature and extent of sea ice, so will populations of seabirds be affected. Seabirds are valued as indicators of healthy marine ecosystems and provide a “vicarious use value” or existence value—people appreciate and value seabirds simply because they are there and enjoy them through venues such as pictures, nature programs, and written accounts without ever directly observing seabirds in their native environment. A direct measure of this value is demonstrated by Federal legislation that established specific national wildlife refuges to protect seabirds and international treaty obligations that provide additional protection for seabirds. Seabirds are also an important subsistence resource for many who live within the Bering Sea region. Furthermore, the rich knowledge base about seabirds makes them a valuable resource as indicator species for measurement of change in the marine environment. Understanding this latter relationship is particularly important for seabirds as they can be dramatically affected by development-related activities (e.g., oil spills, fishing); understanding the population effects due to climatic change is critical to interpreting the actual effects of specific human activities or events.

Alaska↗
USGS2006

Geomorphic effects of large debris flows and flash floods, northern Venezuela, 1999

A rare, high-magnitude storm in northern Venezuela in December 1999 triggered debris flows and flash floods, and caused one of the worst natural disasters in the recorded history of the Americas. Some 15,000 people were killed. The debris flows and floods inundated coastal communities on alluvial fans at the mouths of a coastal mountain drainage network and destroyed property estimated at more than $2 billion. Landslides were abundant and widespread on steep slopes within areas underlain by schist and gneiss from near the coast to slightly over the crest of the mountain range. Some hillsides were entirely denuded by single or coalescing failures, which formed massive debris flows in river channels flowing out onto densely populated alluvial fans at the coast. The massive amount of sediment derived from 24 watersheds along 50 km of the coast during the storm and deposited on alluvial fans and beaches has been estimated at 15 to 20 million m3. Sediment yield for the 1999 storm from the approximately 200 km2 drainage area of watersheds upstream of the alluvial fans was as much as 100,000 m3/km2. Rapid economic development in this dynamic geomorphic environment close to the capital city of Caracas, in combination with a severe rain storm, resulted in the death of approximately 5% of the population (300,000 total prior to the storm) in the northern Venezuelan state of Vargas. ?? 2006 Gebru??der Borntraeger.

Zeitschrift fur Geomorphologie, Supplementband↗
USGS2024

Assessing the sustainability of Pacific walrus harvest in a changing environment

Harvest sustainability is a primary goal of wildlife management and conservation, and in a changing world, it is increasingly important to consider environmental drivers of population dynamics alongside harvest in cohesive management plans. This is particularly pertinent for harvested species that acutely experience effects of climate change. The Pacific walrus ( Odobenus rosmarus divergens ), a crucial subsistence resource for Indigenous communities, is simultaneously subject to rapid habitat loss associated with diminishing sea ice and an increasing anthropogenic footprint in the Arctic. We developed a theta-logistic population modeling-management framework to evaluate various harvest scenarios combined with 4 potential climate and disturbance scenarios (ranging from optimistic to pessimistic, based largely on sea ice projections from general circulation models) to simulate Pacific walrus population dynamics to the end of the twenty-first century, focusing on the independent-aged female subset of the population. We considered 2 types of harvest strategies: 1) state-dependent harvest scenarios wherein we calculated harvest as a percentage of the population and updated annual harvests at set intervals as the population was reassessed, and 2) annually consistent harvest scenarios wherein annual harvest levels remain consistent into the future. All climate and disturbance scenarios indicated declines of varying severity in Pacific walrus abundance to the end of the twenty-first century, even in the absence of harvest. However, we found that a state-dependent annual harvest of 1.23% of the independent-aged female subset of the population (e.g., 1,280 independent-aged females harvested in 2020, similar to contemporary harvest levels) met our criterion for sustainability under all climate and disturbance scenarios, considering a medium risk tolerance level of 25%. This indicates that the present rate of Pacific walrus harvest is sustainable and will continue to be—provided the population is assessed at regular intervals and harvest is adapted to match changes in population dynamics. Our simulations indicate that a sustainable annually-consistent harvest is also possible but only at low levels if the population declines as expected. Applying a constant annual harvest of 1,280 independent-aged females failed to meet our criterion for sustainability under 3 of the 4 climate and disturbance scenarios we evaluated and had a higher probability of quasi-extinction than an equivalent state-dependent harvest scenario (1.23%). We highlight the importance of state-dependent management strategies and suggest our modeling framework is useful for managing harvest sustainability in a changing climate.

Journal of Wildlife Management↗
USGS2024

Assessing the sustainability of Pacific walrus harvest in a changing environment

Harvest sustainability is a primary goal of wildlife management and conservation, and in a changing world it is increasingly important to consider environmental drivers of population dynamics alongside harvest in cohesive management plans. This is particularly pertinent for harvested species that are acutely experiencing effects of climate change. The Pacific walrus ( Odobenus rosmarus divergens ), a critical traditional subsistence resource for indigenous communities, is simultaneously subject to rapid habitat loss associated with diminishing sea ice and an increasing anthropogenic footprint in the Arctic. We developed a theta-logistic population modeling-management framework to evaluate various harvest scenarios combined with four potential climate/disturbance scenarios (ranging from optimistic–pessimistic) which simulates Pacific walrus population dynamics to the end of the 21 st century. We considered two types of harvest strategies: (1) adaptive harvest scenarios wherein harvest is calculated as a percentage of the population and annual harvests are updated at set intervals as the population is reassessed, and (2) non-adaptive harvest scenarios wherein annual harvest remains constant. All climate/disturbance scenarios indicated declines of varying severity in Pacific walrus abundance to the end of the 21 st century, even in the absence of harvest. However, we found that an adaptive annual harvest of 1.23% of the independent-aged female subset of the population (e.g., 1,280 independent-aged females harvested in 2020, representing contemporary harvest levels) met our criterion for sustainability (>70% probability of maintaining population abundance above maximum net productivity level) under all climate/disturbance scenarios, accepting a medium risk tolerance level of 25%. This suggests that the present rate of Pacific walrus harvest is sustainable and will continue to be—provided the harvest adapts to match changes in population dynamics. Our simulations suggest that a sustainable non-adaptive harvest is also possible, but only at low levels if the population declines as expected. Applying a constant annual harvest of 1,280 independent-aged females (equivalent to contemporary harvest levels of 1.23) exceeded our criterion for sustainability and resulted in a >5% chance of quasi-extinction by the end of the 21 st century under three of the four climate/disturbance scenarios we evaluated. Our results highlight the importance of adaptive co-management strategies, and we suggest such modeling frameworks are useful for managing for harvest sustainability in a changing climate.

BioRxiv↗
USGS2018

Vibrio population dynamics in Mid-Atlantic surface waters during Saharan dust events

Vibrio is a cosmopolitan genus of marine bacteria, highly investigated in coastal and estuarine environments. Vibrio have also been isolated from pelagic waters, yet very little is known about the ecology of these oligotrophic species. In this study we examined the relative change in bacterial abundance and more specifically the dynamics of Vibrio in the tropical North Atlantic in response to the arrival of pulses of Saharan dust aerosols, a major source of biologically important nutrients for downwind marine surface waters. Aerosol and surface water samples were collected over 1 month coinciding with at least two distinct dust events. Total bacterial counts increased by 1.6-fold correlating with the arrival of Saharan dust ( r = 0.76; p = 0.001). Virus-like particles (VLP) also followed this trend and were correlated with bacterial counts ( r = 0.67; p = 0.01). Vibrio specific qPCR targeting the 16S rRNA gene ranged from below detection limits to a high of 9,145 gene copies ml −1 with the arrival of dust. This increase equated to 6.5 × 10 2 −1.5 × 10 3 individual genome equivalents ml −1 based on the known range of 16S rRNA copies among this genus. Vibrio exhibited bloom-bust cycles potentially attributed to selective viral lysis or bloom depletion of organic carbon. This work is one of the few studies to examine the open ocean ecology of Vibrio , a conditionally rare taxon, whose bloom-bust lifestyle likely is a contributing factor in the flow of nutrients and energy in pelagic ecosystems.

Frontiers in Marine Science↗
USGS2021

Bat activity patterns relative to temporal and weather effects in a temperate coastal environment

The northeastern and mid-Atlantic coasts of the United States are important summer maternity habitat and seasonal migratory corridors for many species of bats. Additionally, the effects of weather on bat activity are relatively unknown beyond coarse nightly scales. Using acoustic detectors, we assessed nightly and hourly activity patterns for eight species of bats over 21 consecutive months at Fire Island National Seashore, New York. The site is an important bat conservation area because it hosts one of the few confirmed northern long-eared bat ( Myotis septentrionalis ) maternity colonies in the region despite their widespread extirpation due to white-nose syndrome (WNS). There have been no reported captures of little brown bats ( M. lucifugus ), Indiana bats ( M. sodalis ), or tri-colored bats ( Perimyotis subflavus ) at the site post-WNS. Overall, we found mean hourly temperature, time since sunset, day of year, and year to be the most important predictors of bat activity levels for all examined species. Most non-hibernating, migratory species in our study demonstrated a positive relationship to mean temperature at the hourly timescale, whereas cave-hibernating bats tended to show a negative relationship to mean temperature during the time of year when they are expected to be active. Although most bat activity occurred in the late spring through early autumn, peaking in summer, some activity occurred periodically in the winter months, mostly attributable to the big brown bat ( Eptesicus fuscus ) and silver-haired bat ( Lasionycteris noctivigans ) phonic group. Unexpectedly, relationships of bat activity to wind and precipitation were largely equivocal. Initial presence (as early as March 30) and departure (between November 1–4) for northern long-eared bats at our study area occurred earlier in the spring and later in the fall than occurs for inland populations, suggesting that the species overwinters on Long Island rather than at inland karst caves or mines. A peak in spring activity characteristic of migratory behavior in the central Appalachians and Atlantic Coast was not observed at Fire Island, although Eastern red bats ( Lasiurus borealis ) and hoary bats (L. cinereus ) – both migratory species – did show a notable rise in activity in the late summer and early fall, suggesting these populations may migrate to and from Fire Island. Understanding the temporal and weather relationships to bat activity in this coastal environment may have important implications for tailoring more effective conservation and management strategies by identifying optimal timing for surveys, tracking bats during peak migratory windows, and providing insights that minimizes impacts to extant bats from activities such as wind-energy development or land management, i.e., forestry.

New York↗
USGS2010

Milankovitch-scale correlations between deeply buried microbial populations and biogenic ooze lithology

The recent discoveries of large, active populations of microbes in the subseafloor of the world's oceans supports the impact of the deep biosphere biota on global biogeochemical cycles and raises important questions concerning the functioning of these extreme environments for life. These investigations demonstrated that subseafloor microbes are unevenly distributed and that cell abundances and metabolic activities are often independent from sediment depths, with increased prokaryotic activity at geochemical and/or sedimentary interfaces. In this study we demonstrate that microbial populations vary at the scale of individual beds in the biogenic oozes of a drill site in the eastern equatorial Pacific (Ocean Drilling Program Leg 201, Site 1226). We relate bedding-scale changes in biogenic ooze sediment composition to organic carbon (OC) and microbial cell concentrations using high-resolution color reflectance data as proxy for lithology. Our analyses demonstrate that microbial concentrations are an order of magnitude higher in the more organic-rich diatom oozes than in the nannofossil oozes. The variations mimic small-scale variations in diatom abundance and OC, indicating that the modern distribution of microbial biomass is ultimately controlled by Milankovitch-frequency variations in past oceanographic conditions. ?? 2010 Geological Society of America.

Geology↗
USGS2019

Decision-making in agent-based modeling: A current review and future prospectus

All basic processes of ecological populations involve decisions; when and where to move, when and what to eat, and whether to fight or flee. Yet decisions and the underlying principles of decision-making have been difficult to integrate into the classical population-level models of ecology. Certainly, there is a long history of modeling individuals' searching behavior, diet selection, or conflict dynamics within social interactions. When all the individuals are given certain simple rules to govern their decision-making processes, the resultant population–level models have yielded important generalizations and theory. But it is also recognized that such models do not represent the way real individuals decide on actions. Factors that influence a decision include the organism's environment with its dynamic rewards and risks, the complex internal state of the organism, and its imperfect knowledge of the environment. In the case of animals, it may also involve complex social factors, and experience and learning, which vary among individuals. The way that all factors are weighed and processed to lead to decisions is a major area of behavioral theory. While classic population-level modeling is limited in its ability to integrate decision-making in its actual complexity, the development of individual- or agent-based models (IBM/ABMs) (we use ABM throughout to designate both “agent-based modeling” and an “agent-based model”) has opened the possibility of describing the way that decisions are made, and their effects, in minute detail. Over the years, these models have increased in size and complexity. Current ABMs can simulate thousands of individuals in realistic environments, and with highly detailed internal physiology, perception and ability to process the perceptions and make decisions based on those and their internal states. The implementation of decision-making in ABMs ranges from fairly simple to highly complex; the process of an individual deciding on an action can occur through the use of logical and simple (if-then) rules to more sophisticated neural networks and genetic algorithms. The purpose of this paper is to give an overview of the ways in which decisions are integrated into a variety of ABMs and to give a prospectus on the future of modeling of decisions in ABMs.

Frontiers in Ecology and Evolution↗
USGS2015

Accuracy or precision: Implications of sample design and methodology on abundance estimation

Sampling by spatially replicated counts (point-count) is an increasingly popular method of estimating population size of organisms. Challenges exist when sampling by point-count method, and it is often impractical to sample entire area of interest and impossible to detect every individual present. Ecologists encounter logistical limitations that force them to sample either few large-sample units or many small sample-units, introducing biases to sample counts. We generated a computer environment and simulated sampling scenarios to test the role of number of samples, sample unit area, number of organisms, and distribution of organisms in the estimation of population sizes using N -mixture models. Many sample units of small area provided estimates that were consistently closer to true abundance than sample scenarios with few sample units of large area. However, sample scenarios with few sample units of large area provided more precise abundance estimates than abundance estimates derived from sample scenarios with many sample units of small area. It is important to consider accuracy and precision of abundance estimates during the sample design process with study goals and objectives fully recognized, although and with consequence, consideration of accuracy and precision of abundance estimates is often an afterthought that occurs during the data analysis process.

Ecological Modelling↗
USGS2004

Spatial-temporal population dynamics across species range: From centre to margin

Understanding the boundaries of species' ranges and the variations in population dynamics from the centre to margin of a species' range is critical. This study simulated spatial-temporal patterns of birth and death rates and migration across a species' range in different seasons. Our results demonstrated the importance of dispersal and migration in altering birth and death rates, balancing source and sink habitats, and governing expansion or contraction of species' ranges in changing environments. We also showed that the multiple equilibria of metapopulations across a species' range could be easily broken following climatic changes or physical disturbances either local or regional. Although we refer to our models as describing the population dynamics across whole species' range, they should also apply to small-scale habitats (metapopulations) in which species abundance follows a humped pattern or to any ecosystem or landscape where strong central-marginal (C-M) environmental gradients exist. Conservation of both central and marginal populations would therefore be equally important considerations in making management decisions.

Oikos↗
USGS2003

Challenges to reestablishment of free-ranging populations of black-footed ferrets

The black-footed ferret ( Mustela nigripes ) of North America is critically endangered due in part to its extreme specialization on formerly stable and abundant prairie dogs ( Cynomys ). Its close relative, the Siberian polecat ( M. eversmannii ) seems to have been subjected to a varying environment that was not conducive to specialization. One source of environmental variation in Asian steppes was plague (caused by Yersina pestis ), which was absent from North America. Introduction of plague to North America presents serious challenges to ferret recovery. Partial solutions to other biological and political problems have been found, resulting in improved production in captivity, increased survival post-release, and thriving populations in plague-free South Dakota.

Comptes Rendus - Biologies↗
USGS2016

California State Waters map series — Offshore of Aptos, California

Introduction In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within California’s State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar bathymetric data (the undersea equivalent of satellite remote-sensing data in terrestrial mapping), acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow subsurface geology. The Offshore of Aptos map area is located on the Pacific Coast, on the north side of Monterey Bay, about 105 km southeast of San Francisco. The largest incorporated city in the map area, Capitola, and numerous unincorporated towns including Aptos, lie on uplifted marine terraces between the shoreline, and the northwest-trending Santa Cruz Mountains, part of California’s Coast Ranges. The map area includes the northernmost part of Santa Cruz Harbor, and Moss Landing Harbor is located about 10 km south of the map area. The offshore part of the map area is entirely within California’s State Waters and is also part of the Monterey Bay National Marine Sanctuary. In the southern part of the map area, the Soquel Canyon State Marine Conservation Area extends eastward from the limit of California’s State Waters across Soquel Canyon. The Offshore of Aptos map area is on the western margin of North American Plate—the only continental margin in the world delineated largely by transform faults. The San Andreas Fault Zone cuts through the Santa Cruz Mountains just 3.5 km northeast of the map area. The San Gregorio Fault Zone, another major plate-boundary structure, cuts through Monterey Canyon about 13 km southwest of the map area. Ongoing deformation associated with and between these major fault zones has uplifted the Santa Cruz Mountains and formed well-developed sets of marine terraces that characterize almost the entire coastal zone of the map area. The offshore part of the map area consists of relatively flat and shallow continental shelf which is underlain by variable amounts (0 to 30 m) of upper Quaternary shelf, estuarine, and fluvial sediments deposited as sea level fluctuated in the late Pleistocene. Along the southern edge of the map area, the shelf is incised by the head of Soquel Canyon, a northeast-trending tributary to the west-trending Monterey Canyon. During the last sea-level lowstand (the Last Glacial Maximum [LGM], about 21,000 years ago) Soquel Creek flowed through a paleochannel across the emergent shelf into the head of Soquel Canyon. This canyon was disconnected from its onshore watershed during the post-LGM sea-level rise of about 125 m; the abandoned paleochannel was subsequently filled with marine sediment. Coastal sediment in the Offshore of Aptos map area is supplied by coastal watersheds and bluff erosion. Sediment transport in this part of the Santa Cruz littoral cell is primarily from the northwest to the southeast and terminates in the submarine Monterey Canyon. Longshore drift is impeded by jetties at Santa Cruz Harbor, resulting in high beach erosion rates east of the harbor. Sediment dredged from the harbor mouth (estimated 300,000 yds 3 /yr) is currently being used to nourish beaches directly to the east. Farther downcoast, the rapidly eroding beach at Capitola was stabilized by construction of an about 75-m-long groin. This part of central California is exposed to large North Pacific swells from the northwest throughout the year. North Pacific swell heights range from 2 to 10 meters, with larger swells occurring from October to May. During El Niño-Southern Oscillation (ENSO) events, winter storms track farther south than they do in normal (non-ENSO) years, thereby impacting the map area more frequently and with waves of larger heights. Bedrock exposed in coastal cliffs is relatively erosion-resistant, and significant erosional events primarily are restricted to storm-wave activity that also erodes the overlying unconsolidated marine-terrace sediments. The Offshore of Aptos map area lies within the cold-temperate biogeographic zone that is called either the “Oregonian” province or the “northern California ecoregion.” This biogeographic province is maintained by the long-term stability of the southward-flowing California Current, the eastern limb of the North Pacific subtropical gyre that flows from southern British Columbia to Baja California. At its midpoint off central California, the California Current transports subarctic surface (0–500 m deep) waters southward, about 150 to 1,300 km from shore. Seasonal northwesterly winds that are, in part, responsible for the California Current, generate coastal upwelling. The south end of the Oregonian province is at Point Conception (about 310 km southeast of the map area), although its associated phylogeographic group of marine fauna may extend beyond to the area offshore of Los Angeles in southern California. The ocean off of central California has experienced a warming over the last 50 years that is driving an ecosystem shift away from the productive subarctic regime towards a depopulated subtropical environment. Seafloor habitats in the Offshore of Aptos map area lie within the “Shelf” Megahabitat class and include patchy rocky habitats, gravel-rich scour depressions, minor bedrock habitat, and predominantly sandy inner shelf. Sandy shelf habitats grade offshore to mud-dominated habitats on the midshelf in deeper water. Biological productivity resulting from coastal upwelling supports populations of Sooty Shearwater, Western Gull, Common Murre, Cassin’s Auklet, and many other less populous bird species. In addition, an observable recovery of Humpback and Blue Whales has occurred in the area; both species are dependent on coastal upwelling to provide nutrients. California sea lions and Pacific harbor seals are abundant in the map area. Common bottlenose dolphins are often observed very close to shore and in the surf zone. The large extent of exposed inner shelf bedrock supports large forests of “bull kelp,” which is well adapted for high-wave-energy environments. The kelp beds are the northernmost known habitat for the population of southern sea otters. Common fish species found in the kelp beds and rocky reefs include blue rockfish, black rockfish, olive rockfish, kelp rockfish, gopher rockfish, black-and-yellow rockfish, painted greenling, kelp greenling, and lingcod.

California↗
USGS2019

Using environmental DNA (eDNA) to assess the presence of cavefish and cave crayfish populations in caves of the Ozark Highlands

Many cavefishes and cave crayfishes are considered of conservation concern; however, sampling these species is inherently difficult given their occupied environments. The goal of our project was to verify the presence of select karst organisms while developing the foundation for sampling approaches that might be useful to conservation and management agencies. Our project objectives were to develop assays to amplify deoxyribonucleic acid (DNA) from several species of Ozark cavefishes and cave crayfishes and complete an initial surveillance of locations across the Ozark Highlands using environmental DNA (eDNA). Using DNA either provided by agency cooperators or that we extracted from tissue samples, we PCR amplified and then sequenced the Cytochrome Oxidase 1 (CO1) gene for cave crayfishes and the NADH Dehydrogenase Subunit 2 (ND2) gene for cavefishes. We developed species-specific primers and probes for five cave crayfishes and two cavefishes. From February 2017 to May 2017, we sampled 1–5 sampling units from 42 caves, wells, and springs (i.e., sites) using eDNA and traditional visual surveys. We measured physicochemical parameters at each sampling unit to estimate detection probability associated with both techniques. We also calculated two occupancy covariates for each site using geospatial data. We successfully amplified Troglichthys rosae DNA from the environment and detected DNA representing this species at 24 of 40 sites. At 16 of the sites where we detected T. rosae DNA, we did not visually observe the species. Although our assay for Typlichthys eigenmanni successfully amplified the target DNA from the environment, it also resulted in false absences where the species was visually confirmed. Using eDNA to detect cave crayfishes was much more difficult. The assay for Cambarus subterraneus did not work for eDNA samples and we were unable to pick up DNA from the environment, even at locations where it was visually confirmed. Alternatively, the eDNA surveys worked well for C. tartarus and we were able to amplify DNA at every site where it was visually observed. Our assay for C. aculabrum was based on a single sample obtained from GenBank, and did not amplify eDNA from field samples. Lastly, our eDNA results from samples in the known range of Orconectes stygocaneyi suggested the species may be found at an additional cave. Detection using eDNA based on our O. stygocaneyi assay was likely low because it was designed from a pseudogene; however, positive eDNA samples were sequenced to confirm species-specific DNA. Detection probability of both cavefishes and cave crayfishes varied by survey technique and was influenced by water volume, water clarity, water velocity, and substrate. Detection of cavefishes and cave crayfishes via visual surveys decreased when water volume increased, whereas detection using eDNA increased with greater water volume. Detection between taxa using either sample method was highest in habitats classified by fine substrates, except for eDNA detection of crayfishes which was greatest in coarse substrates. Detection of cavefishes increased with water clarity, but detection of cave crayfishes increased with turbidity. Detection probability of both cavefishes and crayfishes using eDNA increased slightly with water velocity, but decreased with visual surveys as water velocity increased. Occupancy by both taxa was positively related to particular geologic series. Crayfish occupancy was negatively related to fine-scale anthropogenic disturbance (i.e., 500-m buffer around the site), whereas crayfish showed no relationship with disturbance. Our results suggest possible range extensions, provide insights to factors driving detection using both sample techniques, and suggest areas where recharge zones may be shared among caves. Future efforts focused on a comprehensive evaluation of genetic diversity among cave crayfishes to improve assay design could improve detection and the applicability of eDNA as a supplemental and non-invasive sampling approach.

Cooperator Science Series↗
USGS2020

Mitochondrial genome diversity and population mitogenomics of Polar cod (Boreogadus saida) and Arctic dwelling gadoids

High-latitude fish typically exhibit a narrow thermal tolerance window, which may pose challenges when coping with temperatures that shift outside of a species’ range of tolerance. Due to its role in aerobic metabolism and energy balance, the mitochondrial genome is likely critical for the acclimation and adaptation to differing temperature regimes in marine ectotherms. As oceans continue to warm, there is growing need to understand the ability of organisms to respond to changing environmental conditions given evidence that some species, in particular cold-water species, may already be experiencing difficulties. To assess how Arctic gadids in Alaska have responded to differential thermal preferences in the past and how regions are interconnected, we sequenced complete mitochondrial genomes for four Arctic gadids to determine the distribution of mitochondrial diversity and population-level structure as well as to detect signatures of selection acting on the mitochondrial genome. We found little population-level structure within all four species with the clear exception of Gulf of Alaska saffron cod ( Eleginus gracilis ). Northern localities exhibited higher levels of genetic diversity and primarily northern lineages were observed within polar cod ( Boreogadus saida ) and saffron cod, likely reflecting asymmetrical dispersal and potentially admixture of distinct lineages via ocean currents. The main evolutionary force shaping the evolution of the mitogenome appears to be purifying selection, but we also identified potential positive selection of candidate amino acid replacements primarily in complex I (ND genes) in polar cod. The high levels of mitochondrial diversity observed in our study and large population size may provide this species with the ability to respond evolutionarily (i.e. long-term) to a changing environment.

Alaska↗
USGS2004

Phenotypic variation and vulnerability to predation in juvenile bluegill sunfish (Lepomis macrochirus)

Bluegill sunfish (Lepomis macrochirus) are known to diversify into two forms specialized for foraging on either limnetic or littoral prey. Because juvenile bluegills seek vegetative cover in the presence of largemouth bass (Micropterus salmoides) predators, natural selection should favor the littoral body design at size ranges most vulnerable to predation. Yet within bluegill populations, both limnetic and littoral forms occur where vegetation and predators are present. While adaptive for foraging in different environments, does habitat-linked phenotypic variation also influence predator evasiveness for juvenile bluegills? We evaluate this question by quantifying susceptibility to predation for two groups of morphologically distinct bluegills; a limnetic form characteristic of bluegills inhabiting open water areas (limnetic bluegill) and a littoral form characteristic of bluegills inhabiting dense vegetation (littoral bluegill). In a series of predation trials, we found that bluegill behaviors differed in open water habitat but not in simulated vegetation. In open water habitat, limnetic bluegills formed more dense shoaling aggregations, maintained a larger distance from the predator, and required longer amounts of time to capture than littoral bluegill. When provided with simulated vegetation, largemouth bass spent longer amounts of time pursuing littoral bluegill and captured significantly fewer littoral bluegills than limnetic fish. Hence, morphological and behavioral variation in bluegills was linked to differential susceptibility to predation in open water and vegetated environments. Combined with previous studies, these findings show that morphological and behavioral adaptations enhance both foraging performance and predator evasiveness in different lake habitats.

Oecologia↗
USGS2018

Integrating animal movement with habitat suitability for estimating dynamic migratory connectivity

Context High-resolution animal movement data are becoming increasingly available, yet having a multitude of empirical trajectories alone does not allow us to easily predict animal movement. To answer ecological and evolutionary questions at a population level, quantitative estimates of a species’ potential to link patches or populations are of importance. Objectives We introduce an approach that combines movement-informed simulated trajectories with an environment-informed estimate of the trajectories’ plausibility to derive connectivity. Using the example of bar-headed geese we estimated migratory connectivity at a landscape level throughout the annual cycle in their native range. Methods We used tracking data of bar-headed geese to develop a multi-state movement model and to estimate temporally explicit habitat suitability within the species’ range. We simulated migratory movements between range fragments, and calculated a measure we called route viability. The results are compared to expectations derived from published literature. Results Simulated migrations matched empirical trajectories in key characteristics such as stopover duration. The viability of the simulated trajectories was similar to that of the empirical trajectories. We found that, overall, the migratory connectivity was higher within the breeding than in wintering areas, corroborating previous findings for this species. Conclusions We show how empirical tracking data and environmental information can be fused for meaningful predictions of animal movements throughout the year and even outside the spatial range of the available data. Beyond predicting migratory connectivity, our framework will prove useful for modelling ecological processes facilitated by animal movement, such as seed dispersal or disease ecology.

Landscape Ecology↗
USGS2011

Fire and vegetation shifts in the Americas at the vanguard of Paleoindian migration

Across North and South America, the final millennia of the Pleistocene saw dramatic changes in climate, vegetation, fauna, fire regime, and other local and regional paleo-environmental characteristics. Rapid climate shifts following the Last Glacial Maximum (LGM) exerted a first-order influence, but abrupt postglacial shifts in vegetation composition, vegetation structure, and fire regime also coincided with human arrival and transformative faunal extinctions in the Americas. We propose a model of post-glacial vegetation change in response to climatic drivers, punctuated by local fire regime shifts in response to megaherbivore-driven fuel changes and anthropogenic ignitions. The abrupt appearance of humans, disappearance of megaherbivores, and resulting changes in New World fire systems were transformative events that should not be dismissed in favor of climate-only interpretations of post-glacial paleo-environmental shifts in the Americas. Fire is a mechanism by which small human populations can have broad impacts, and growing evidence suggests that early anthropogenic influences on regional, even global, paleo-environments should be tested alongside other potential causal mechanisms.

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