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USGS1994

Species diversity, selectivity, and habitat associations of small mammals from coastal California

Species diversity and habitat associations were documented for small mammals along 16 transects in a semiarid part of coastal California. Peromyscus were the most abundant, comprising 45.3% of all captures, followed by Dipodomys (21.2%), Neotoma (15.1%), and Perognathus (15.0%). Five additional genera made up the remaining captures (3.4%). Peromyscus truei and Perognathus californicus were both common and widespread, accounting for 42.1% of all captures. Both species were found on all but one transect. Neotoma lepida, the third most common species, was captured on rock transects 96% of the time. Dipodomys elephantinus was the fifth most common species, and was found exclusively in chamise chaparral. Species diversity (H') averaged 1.22 and ranged from 0.33 on a chamise chaparral transect to 1.74 on another chamise chaparral transect which crossed the edge of a burn. Nearly all transects demonstrated this same trend for diversity to vary widely both within and between habitats, indicating that local conditions were more of an influence on diversity than broad habitat types. Selectivity, averaged across the ten most common species, was only 0.06, indicating that habitat selectivity was quite low. The most geographically widespread species, Peromyscus maniculatus, was the least selective (0.03), whereas the two species with the smallest geographic ranges, D. venustus and D. elephantinus, showed the greatest habitat selectivity (0.11 and 0.20, respectively). These values are much lower than those reported from short-term studies and suggest that, like species diversity, brief studies may not accurately reflect community-level interactions.

Southwestern Naturalist↗

USGS1999

Radiotracking large wilderness mammals: Integration of GPS and Argos technology

We tested 30 prototype global positioning system (GPS) radiocollars on brown bears ( Ursus arctos ) over a 3-year period on the Kenai Peninsula, Alaska. Collars were of 2 design types: GPS with an Argos (Argos Data collection and Location System) satellite uplink ( n= 19) and GPS unites where the data were stored on board ( n =10) for retrieval at a later date. All units also contained a conventional VHF (very high frequency) transmitter and weighed 1.7 kg. GPS-Argos united obtained 10-82% of expected GPS fixes, and fix rate declined significantly ( P <0.05) with time after deployment. Argos uplink success (proportion of successful transmissions of stored data) was linearly related to GPS fix rate ( r =0.91, P <0.001). Store-on-board units obtained significantly more successful fixes when compared with the GPS-Argos units ( t =-4.009, P <0.001). Fix success rate for deployed store-on-board collars ranged from 13-96%; because of the increased number of attempted fixes per day, these collars obtained fixes on 97% of days deployed. Accuracy of the GPS units was less than predicted by the NAVSTAR GPS technology using the course acquisition code. Reduced accuracy was likely a result of the proportion of 2-dimensional versus 3-dimensional fixes obtained, although we could not determine this statistic from recorded data. Increased overstory closure was the only variable measured that partially explained the reduced likelihood of a successful fix. Stem density, stem diameter, and overstory height measured within 3 m of the collar did not affect fix success. GPS fix success rates for collars attached to bears varied more and were lower than fix rates for stationary collars placed in various vegetation types, suggesting that the bear, terrain, and movement all influence both fix and uplink success rate. Application of this new technology to grizzly and brown bear research and comparisons to studies with moose ( Alces alces ) are discussed.

Alaska↗

USGS1999

Radio-tracking large wilderness mammals: integration of GPS and Argos technologies

We tested 30 prototype global positioning system (GPS) radiocollars on brown bears ( Ursus arctos ) over a 3-year period on the Kenai Peninsula, Alaska. Collars were of 2 design types: GPS units with an Argos (Argos Data collection and Location System) satellite uplink ( n = 19) and GPS units where the data were stored on board ( n = 10) for retrieval at a later date. All units also contained a conventional VHF (very high frequency) transmitter and weighed 1.7 kg. GPS-Argos units obtained 10-82% of expected GPS fixes, and fix rate declined significantly ( P < 0.05) with time after deployment. Argos uplink success (proportion of successful transmissions of stored data) was linearly related to GPS fix rate ( r = 0.91, P < 0.001). Storeon-board units obtained significantly more successful fixes when compared with the GPS-Argos units ( t = -4.009, P < 0.001). Fix success rate for deployed store-on-board collars ranged from 13-96%; because of the increased number of attempted fixes per day, these collars obtained fixes on 97% of days deployed. Accuracy of the GPS units was less than predicted by the NAVSTAR GPS technology using the course acquisition code. Reduced accuracy was likely a result of the proportion of 2-dimensional versus 3-dimensional fixes obtained, although we could not determine this statistic from recorded data. Increased overstory closure was the only variable measured that partially explained the reduced likelihood of a successful fix. Stem density, stem diameter, and overstory height measured within 3 m of the collar did not affect fix success. GPS fix success rates for collars attached to bears varied more and were lower than fix rates for stationary collars placed in various vegetation types, suggesting that the bear, terrain, and movement all influence both fix and uplink success rate. Application of this new technology to grizzly and brown bear research and comparisons to studies with moose ( Alces alces ) are discussed.

Alaska↗

USGS2017

A genetic signature of the evolution of loss of flight in the Galapagos cormorant

INTRODUCTION Changes in the size and proportion of limbs and other structures have played a key role in the evolution of species. One common class of limb modification is recurrent wing reduction and loss of flight in birds. Indeed, Darwin used the occurrence of flightless birds as an argument in favor of his theory of natural selection. Loss of flight has evolved repeatedly and is found among 26 families of birds in 17 different orders. Despite the frequency of these modifications, we have a limited understanding of their underpinnings at the genetic and molecular levels. RATIONALE To better understand the evolution of changes in limb size, we studied a classic case of recent loss of flight in the Galapagos cormorant ( Phalacrocorax harrisi ). Cormorants are large water birds that live in coastal areas or near lakes, and P. harrisi is the only flightless cormorant among approximately 40 extant species. The entire population is distributed along the coastlines of Isabela and Fernandina islands in the Galapagos archipelago. P. harrisi has a pair of short wings, which are smaller than those of any other cormorant. The extreme reduction of the wings and pectoral skeleton observed in P. harrisi is an attractive model for studying the evolution of loss of flight because it occurred very recently; phylogenetic evidence suggests that P. harrisi diverged from its flighted relatives within the past 2 million years. We developed a comparative and predictive genomics approach that uses the genome sequences of P. harrisi and its flighted relatives to find candidate genetic variants that likely contributed to the evolution of loss of flight. RESULTS We sequenced and de novo assembled the whole genomes of P. harrisi and three closely related flighted cormorant species. We identified thousands of coding variants exclusive to P. harrisi and classified them according to their probability of altering protein function based on conservation. Variants most likely to alter protein function were significantly enriched in genes mutated in human skeletal ciliopathies, including Ofd1 , Evc , Wdr34 , and Ift122 . We carried out experiments in Caenorhabditis elegans to confirm that a missense variant present in the Galapagos cormorant IFT122 protein is sufficient to affect ciliary function. The primary cilium is essential for Hedgehog (Hh) signaling in vertebrates, and individuals affected by ciliopathies have small limbs and ribcages, mirroring the phenotype of P. harrisi . We also identified a 4–amino acid deletion in the regulatory domain of Cux1 , a highly conserved transcription factor that has been experimentally shown to regulate limb growth in chicken. The four missing amino acids are perfectly conserved in all birds and mammals sequenced to date. We tested the consequences of this deletion in a chondrogenic cell line and showed that it impairs the ability of CUX1 to transcriptionally up-regulate cilia-related genes (some of which contain function-altering variants in P. harrisi ) and to promote chondrogenic differentiation. Finally, we show that positive selection may have played a role in the fixation of the variants associated with loss of flight in P. harrisi . CONCLUSION Our results indicate that the combined effect of variants in genes necessary for the correct transcriptional regulation and function of the primary cilium likely contributed to the evolution of highly reduced wings and other skeletal adaptations associated with loss of flight in P. harrisi . Our approach may be generally useful for identification of variants underlying evolutionary novelty from genomes of closely related species.

Science↗

USGS2003

Protecting embryos from stress: Corticosterone effects and the corticosterone response to capture and confinement during pregnancy in a live-bearing lizard (Hoplodactylus maculatus)

Hormones in the embryonic environment, including those of the hypothalamo-pituitary-adrenal (HPA) axis, have profound effects on development in eutherian mammals. However, little is known about their effects in reptiles that have independently evolved viviparity. We investigated whether exogenous corticosterone affected embryonic development in the viviparous gecko Hoplodactylus maculatus, and whether pregnant geckos have a corticosterone response to capture and confinement that is suppressed relative to that in non-pregnant (vitellogenic) females and males. Corticosterone implants (5 mg, slow-release) administered to females in mid-pregnancy caused a large elevation of corticosterone in maternal plasma (P<0.001), probable reductions in embryonic growth and development (P=0.069-0.073), developmental abnormalities and eventual abortions. Cool temperature produced similar reductions in embryonic growth and development (P???0.036 cf. warm controls), but pregnancies were eventually successful. Despite the potentially harmful effects of elevated plasma corticosterone, pregnant females did not suppress their corticosterone response to capture and confinement relative to vitellogenic females, and both groups of females had higher responses than males. Future research should address whether lower maternal doses of corticosterone produce non-lethal effects on development that could contribute to phenotypic plasticity. Corticosterone implants also led to increased basking in pregnant females (P<0.001), and basal corticosterone in wild geckos (independent of reproductive condition) was positively correlated with body temperature (P<0.001). Interactions between temperature and corticosterone may have broad significance to other terrestrial ectotherms, and body temperature should be considered as a variable influencing plasma corticosterone concentrations in all future studies on reptiles. ?? 2003 Elsevier Inc. All rights reserved.

General and Comparative Endocrinology↗

USGS2007

Vascular Plant and Vertebrate Inventory of Coronado National Memorial

We conducted inventories for amphibians and reptiles, birds, and mammals; and summarized past inventories for vascular plants at Coronado National Memorial (NM) in Arizona. We used our data as well as data from previous research to compile species lists for the memorial, assess inventory completeness, and make suggestions on future monitoring efforts. There have been 940 species of plants and vertebrates recorded at Coronado NM (Table 1), of which 46 (5%) are non-native. The species richness of the memorial is one of the highest in the Sonoran Desert Network of park units, third only to park units that are two and one-half (Chiricahua National Monument), 19 (Saguaro National Park) and 70 (Organ Pipe Cactus National Monument) times larger in area. The high species diversities are due to the large elevational gradient, overlap of bigeographical regions, wide range of geology and soils, and diverse vegetation communities present at the memorial. Changes in species composition have occurred at the memorial over the last 20 years in all major taxonomic groups. These changes are likely due to increases in grassy plant species (both native and non-native) at the lower elevations of the memorial. We suspect that grassy plant cover has increased because of changes in grazing intensity, introduction of some non-native species, and a recent fire. All recent vertebrate inventories have yielded grassland obligate species not previously recorded at the memorial. Based on the review of past studies, we believe the inventory for most taxa, except bats, is nearly complete, though some rare or elusive species will likely be added with additional survey effort.

Open-File Report↗

USGS2018

Incorporating road crossing data into vehicle collision risk models for moose (Alces americanus) in Massachusetts, USA

Wildlife–vehicle collisions are a human safety issue and may negatively impact wildlife populations. Most wildlife–vehicle collision studies predict high-risk road segments using only collision data. However, these data lack biologically relevant information such as wildlife population densities and successful road-crossing locations. We overcome this shortcoming with a new method that combines successful road crossings with vehicle collision data, to identify road segments that have both high biological relevance and high risk. We used moose ( Alces americanus ) road-crossing locations from 20 moose collared with Global Positioning Systems as well as moose–vehicle collision (MVC) data in the state of Massachusetts, USA, to create multi-scale resource selection functions. We predicted the probability of moose road crossings and MVCs across the road network and combined these surfaces to identify road segments that met the dual criteria of having high biological relevance and high risk for MVCs. These road segments occurred mostly on larger roadways in natural areas and were surrounded by forests, wetlands, and a heterogenous mix of land cover types. We found MVCs resulted in the mortality of 3% of the moose population in Massachusetts annually. Although there have been only three human fatalities related to MVCs in Massachusetts since 2003, the human fatality rate was one of the highest reported in the literature. The rate of MVCs relative to the size of the moose population and the risk to human safety suggest a need for road mitigation measures, such as fencing, animal detection systems, and large mammal-crossing structures on roadways in Massachusetts.

Massachusetts↗

USGS2014

Effects of wildfire on sea otter (Enhydra lutris) gene transcript profiles

Wildfires have been shown to impact terrestrial species over a range of temporal scales. Little is known, however, about the more subtle toxicological effects of wildfires, particularly in downstream marine or downwind locations from the wildfire perimeter. These down-current effects may be just as substantial as those effects within the perimeter. We used gene transcription technology, a sensitive indicator of immunological perturbation, to study the effects of the 2008 Basin Complex Fire on the California coast on a sentinel marine species, the sea otter ( Enhydra lutris ). We captured sea otters in 2008 (3 mo after the Basin Complex Fire was controlled) and 2009 (15 mo after the Basin Complex Fire was controlled) in the adjacent nearshore environment near Big Sur, California. Gene responses were distinctly different between Big Sur temporal groups, signifying detoxification of PAHs, possible associated response to potential malignant transformation, and suppression of immune function as the primary responses of sea otters to fire in 2008 compared to those captured in 2009. In general, gene transcription patterns in the 2008 sea otters were indicative of molecular reactions to organic exposure, malignant transformation, and decreased ability to respond to pathogens that seemed to consistent with short-term hydrocarbon exposure.

California↗

USGS2008

Dolphin swimming: A review

Research into dolphin swimming has historically been guided by false assumptions of ‘effortless’, ‘high-speed’ swimming. These assumptions have instigated the development of drag-reduction hypotheses but tests of these hypotheses have generally had little success. The autecological approach has dominated recent efforts and has been more successful. In this review we summarize results of decades of research efforts to study these creatures. (1) Drag is minimized primarily by the streamlined shape of the body and appendages, with no known contributions from compliant dampening, dermal ridges, secretions, boundary layer heating, or skin folds. All indications are that the boundary layer is turbulent. (2) Muscles for the upstroke and downstroke of swimming dolphins provide approximately equal power. (3) Output force is enhanced by insertions occurring on the long processes of the vertebrae and on the subdermal connective tissue sheath. (4) Measured swimming speeds are lower than previously believed, with maximum reported routine speeds being approximately 3 m/s. (5) Porpoising behaviour appears to be the most energetically conservative manner in which to breathe when swimming at high speed. (6) Riding surf and wind waves involves the balance between the wave slope and the weight of the animal whereas riding the bow wave involves the interaction of the pressure wave in front of a ship and the drag of the dolphin.

Mammal Review↗

USGS1950

Raccoons of North and Middle America

The raccoons, genus Procyon, colloquially known as “coons,” belong to the carnivorous family Procyonidae, which also includes the American genera Nasua, Nasuella, Bassaricyon, and Potos, and the Old World genera Ailurus and Ailuropoda of the subfamily Ailurinae. The members of the Procyon lotor group (subgenus Procyon), with a transcontinental range from southern Canada to Panama, except in parts of the Rocky Mountain region, and including those inhabiting several distant islands, are among the most familiar and characteristic of North American mammals. This group is not known to occur south of Panama. It is overlapped in the Isthmian region by the so-called crab-eating raccoons of the subgenus Euprocyon, which range from that northern limit as far south as Paraguay in South America. The raccoons have been greatly reduced in numbers or have disappeared in many formerly wooded sections, owing to clearing and intensive human occupation. Despite adverse conditions, however, they have maintained themselves in many places with remarkable tenacity. Trapping for other fur bearers may have reduced the northern fringe to some extent, but the general range of the group has been little diminished. At the present time raccoons reach their northern limit in regular occurrence on Vancouver Island, B. C. The continental forms of the subgenus Procyon constitute a compact assemblage of closely allied geographic races all assignable to Procyon lotor. Complete intergradation is evident in numerous cases and the relative value and combination of characters presented indicate such close relationships that it can safely be assumed where lack of material leaves gaps in the known ranges. In the present revision of the raccoons are treated the North American continental species as far as the eastern border of Panama and the species on outlying islands along both the Atlantic and the Pacific coasts. Thirty species and subspccics are recognized. Twenty-nine of these are assigned to the subgenus Procyon and one to the subgenus Euproc yon. The revision is based mainly on a study of raccoon material in the collection of Biological Surveys, Fish and Wildlife Service, and in other collections in the United States National Museum. These and 358 specimens borrowed from other museums make a total of 1,337 examined. The assemblage included the types or topotypes of most of the known species and subspecies. For the loan of specimens the writer is especially indebted to Dr. Thomas Barbour, Museum of Comparative Zoology, Cambridge, Mass. ; the late Dr. Joseph Grinnell, Museum of Vertebrate Zoology, Berkeley, Calif.; Dr. W. H. Osgood, Chicago Natural History Museum, Chicago, Ill.; Dr. H. E. Anthony, American Museum of Natural History, New York City; Dr. R. M. Anderson, National Museum of Canada, Ottawa, Canada; the late Oldfield Thomas of the British Museum (Natural History) ; Francis Kermode, Provincial Museum, Vancouver, British Columbia; Dr. L. R. Dice, Museum of Zoology, University of Michigan, Ann Arbor, Mich.; and the late D. R. Dickey, Pasadena, Calif. Grateful acknowledgment is also due to Percy Shufeldt, La Cueva, N. Vex., for the generous donation of specimens collected by him in Campeche, Mexico. Notes on his examination of specimens in the British Museum have been kindly furnished by Dr. Remington Kellogg, United States National Museum, Washington, D. C. Stanley P. Young, Fish and Wildlife Service, Washington, D. C., generously supplied the photograph for the frontispiece. Dr. E. W. Nelson became keenly interested in the raccoons, as shown by his work on those inhabiting the Florida Keys (1930a).' During the same time and in the following year new subspecies were described jointly by Nelson and the writer in preparation for a revision of the group; but other projects claimed attention and our collaboration could not be carried beyond this preliminary stage

North American Fauna↗

USGS1981

Birds of the St. Croix River valley: Minnesota and Wisconsin

The St. Croix River Valley encompasses nearly 11,550 km2 in east-central Minnesota and northwestern Wisconsin. A wide range of habitats are available for birds including upland oak, lowland deciduous, maple-basswood, lowland and upland coniferous forests, natural basin wetlands, and grasslands. Situated in the north-central region of the United States, the valley is a biological 'crossroads' for many species. Because of the mixed affinities of plant communities, the valley includes the northern and southern range limits for a number of species. Also, because the valley lies near the forest-prairie transition zone, many typical western breeding species (e.g. pintail, western meadowlark, yellow-headed blackbird) breed in proximity to typical eastern species such as tufted titmouse, eastern meadowlark, and cardinal. From 1966 to 1980, I conducted extensive surveys of avian distribution and abundance in the St. Croix River Valley. I have supplemented the results of these surveys with published and unpublished observations contributed by many ornithologists. These additional data include compilations from Christmas Bird Counts sponsored by the National Audubon Society and from the Breeding Bird Survey coordinated by the U.S. Fish and Wildlife Service. Three hundred fourteen species have been recorded in the study area; data are presented on the migration period, nesting season distribution, winter distribution, relative abundance, and habitat use of each species. Recognizing the uniqueness of the area, and its importance not only to wildlife but also to man, the U.S. Congress designated the St. Croix a National Scenic Riverway. This action provided a considerable degree of protection to lands along and directly adjacent to the river. Unfortunately, no similar legal measure exists to protect lands away from the river. With the exception of the northern quarter of the St. Croix River Valley, agricultural interests have made significant inroads into the habitat base. The continuing expansion of the nearby Minneapolis-St. Paul metropolitan region has degraded or destroyed many woodlots, upland fields, and wetlands. In numerous instances, degradation of natural habitats has influenced the abundance and distribution of bird species. Because of these changes, both the Federal government and State Departments of Natural Resources have listed several species in various categories based on their current status. In the St. Croix River Valley, seven species are endangered, eight are threatened, and 29 are watch or priority status in either or both states. Data presented in this report are of value to land managers, land use specialists, and ornithologists, in assessing current and projected habitat alterations on the avifauna of this valley. The St. Croix River bisects a large region of western Wisconsin and east central Minnesota that exhibits a wide range of habitat types. This region supports not only birds, but many mammals, fishes, reptiles and amphibians, and several thousand species of vascular and nonvascular plants. The river itself is relatively clean through most of its course, and its natural flow is interrupted by only two small dams. Because the river lies within a 1-day drive of nearly 10 million people (Waters 1977), use of the area for recreational purposes is extremely heavy. Recreational pursuits include sunbathing, boating, and wild river kayaking in the summer, and ice fishing and cross-country skiing in the winter. The large number of unique and highly fragile habitats that exist there may never be compatible with the uses and abuses of the land that go with expanding human populations. Through the efforts of a number of citizens concerned with the quality of their environment and the foresightedness of several local, State, and Federal legislators, a portion of the upper St. Croix River Valley (hereafter termed 'the Valley') was established as a National Wild and Scenic River. Through establishment of t

North American Fauna↗

USGS2026

Quantifying southern sea otter (Enhydra lutris nereis) reactions to a quadcopter drone in central California

Drones are useful for wildlife research and management, but they can cause disturbance and harassment to wildlife. Sea otters ( Enhydra lutris ) are candidates for drone-based observation and monitoring but are vulnerable to disturbance. No studies have evaluated drone effects on sea otter behavior, but based on prior disturbance studies, we hypothesized: (1) sea otters would exhibit behaviors indicating higher reactivity in the presence of drones than when drones were absent and (2) drone disturbance to sea otters would be greater when drones were closer. At two sites in Monterey Bay, CA, we conducted 37 observational sessions, recording behavior codes for focal sea otters during a baseline (no drone) period and three consecutive drone flights. Data were analyzed using ANOVA and ordinal logistic regression models. At both locations, focal sea otters had higher behavior codes during drone trials compared to baseline, and behavior codes increased with descending drone altitude. Pup presence, group size, flight trial number, and gull presence were significant covariables. We calculated multipliers to predict drone-mediated behavioral responses at a range of drone altitudes. Our findings can inform best practices for a variety of uses of drones around sea otters, including population monitoring, oil spill response, and drone photography/videography.

California↗

USGS2019

Drift and beaching patterns of sea otter carcasses and car tire dummies

Enumerating and examining marine animal carcasses is important for quantifying mortality rates and determining causes of mortality. Drifter experiments are one tool for estimating at‐sea mortality and determining factors affecting carcass drift, but they require validation to confirm drifters accurately replicate the drift characteristics of the species of interest. The goal of this study was to determine whether dummies constructed from car tires were appropriate substitutes for sea otter ( Enhydra lutris ) carcasses. We released 33 sets of targets (carcasses and dummies) in a one‐to‐one ratio on 15 randomly chosen dates between January 1995 and December 1996. They were telemetrically tracked until they beached or were no longer detected. Beaching rates were similar between carcasses (69.7%) and dummies (66.7%). Our results indicated that there was no statistical difference in the drifting pattern, as measured by distance traveled and location, between carcasses and dummies, and that cumulative wind speed, days since release, and release month were predictors of drift patterns. We concluded that dummies constructed from car tires do imitate sea otter carcasses and could be used to estimate at‐sea mortality of sea otters, or, if released during or after an oil spill, could be used to direct search efforts for carcasses.

California↗

USGS2010

Evaluating abundance estimate precision and the assumptions of a count-based index for small mammals

Conservation and management of small mammals requires reliable knowledge of population size. We investigated precision of markrecapture and removal abundance estimates generated from live-trapping and snap-trapping data collected at sites on Guam (n 7), Rota (n 4), Saipan (n 5), and Tinian (n 3), in the Mariana Islands. We also evaluated a common index, captures per unit effort (CPUE), as a predictor of abundance. In addition, we evaluated cost and time associated with implementing live-trapping and snap-trapping and compared species-specific capture rates of selected live- and snap-traps. For all species, markrecapture estimates were consistently more precise than removal estimates based on coefficients of variation and 95 confidence intervals. The predictive utility of CPUE was poor but improved with increasing sampling duration. Nonetheless, modeling of sampling data revealed that underlying assumptions critical to application of an index of abundance, such as constant capture probability across space, time, and individuals, were not met. Although snap-trapping was cheaper and faster than live-trapping, the time difference was negligible when site preparation time was considered. Rattus diardii spp. captures were greatest in Haguruma live-traps (Standard Trading Co., Honolulu, HI) and Victor snap-traps (Woodstream Corporation, Lititz, PA), whereas Suncus murinus and Mus musculus captures were greatest in Sherman live-traps (H. B. Sherman Traps, Inc., Tallahassee, FL) and Museum Special snap-traps (Woodstream Corporation). Although snap-trapping and CPUE may have utility after validation against more rigorous methods, validation should occur across the full range of study conditions. Resources required for this level of validation would likely be better allocated towards implementing rigorous and robust methods.

Journal of Wildlife Management↗

USGS1999

Terrestrial predator alarm vocalizations are a valid monitor of stress in captive brown capuchins (Cebus apella)

The vocal behavior of captive animals is increasingly exploited as an index of well-being. Here we show that the terrestrial predator alarm (TPA) vocalization, a robust and acoustically distinctive anti-predation vocal response present in many mammal and bird species, offers useful information on the relative well-being and stress levels of captive animals. In a 16-week experiment evaluating the effects of varying levels of physical environmental enrichment (control < toys < foraging box < foraging box and toys) in the cages of eight singly housed adult male brown capuchins, we quantified the 1) emission rate of TPAs, 2) proportions of normal and abnormal behavior sample intervals, and 3) fecal and plasma cortisol levels. Variation in TPA emission across the experimental conditions was significant. We found significant reductions in the mean TPA production rate by the group in the enriched (toys, foraging box, and foraging box and toys) compared to the control condition; pre- and post-experimental conditions, however, did not differ from the control condition. Mean TPA production by the group was also significantly positively correlated to mean group levels of fecal cortisol and proportion of abnormal behavior sample intervals, and significantly negatively correlated to the average proportion of normal behavior sample intervals in the group. Based on group means, plasma cortisol levels were positively, but not significantly, related to increasing TPA rate. At the level of the responses of an individual subject, however, the covariation between the vocal and non-vocal behavioral measures and the cortisol assays seldom attained significance. Nevertheless, the direction of the relationships among these parameters within individual subjects typically mirrored those correlations based on group means. At both the group mean and individual levels, our results are consistent with the interpretation that in conditions of low environmental enrichment the study subjects were more stressed, and therefore more reactive to the presence of a threatening terrestrial stimulus (human observer), than when in more enriched conditions. We suggest that protocols to evaluate the effectiveness of enrichment for captive species other than brown capuchins could also profitably exploit TPAs as a first-line monitor or as corroboratory evidence of current well-being.

Zoo Biology↗

USGS2021

Genetic variation in sea otters (Enhydra lutris) from the North Pacific with relevance to the threatened Southwest Alaska Distinct Population Segment

For the sea otter ( Enhydra lutris ), genetic population structure is an area of research that has not received significant attention, especially in Southwest Alaska where that distinct population segment has been listed as threatened since 2005 pursuant to the U.S. Endangered Species Act. In this study, 501 samples from 14 locations from Prince William Sound, Alaska to the Commander Islands in Russia were analyzed for variation at 13 microsatellite loci. Our results indicate a high degree of genetic divergence among the 14 locations ( F ST = 0.120) with gene flow conforming to the isolation by distance (IBD) model ( r 2 = 0.491, p < .05). The 14 sampling locations formed six geographic associations in clustering and ordination analyses that likely correspond to remnant population lineages: (1) Southcentral Alaska, (2) Kodiak and North Alaska Peninsula, (3) South Alaska Peninsula and Bristol Bay, (4) Eastern Aleutian, (5) Western Aleutian, and (6) the Commander Islands. Except for South Alaska Peninsula and Bristol Bay, these clusters closely agree with previously defined stock and management unit boundaries. Our results reveal significant genetic population structure and are generally congruent with current management strategies for the threatened Southwest Alaska distinct population segment.

Alaska↗

USGS2008

Techniques for Monitoring Razorback Sucker in the Lower Colorado River, Hoover to Parker Dams, 2006-2007, Final Report

Trammel netting is generally the accepted method of monitoring razorback sucker in reservoirs, but this method is ineffective for monitoring this fish in rivers. Trammel nets set in the current become fouled with debris, and nets set in backwaters capture high numbers of nontarget species. Nontargeted fish composed 97 percent of fish captured in previous studies (1999-2005). In 2005, discovery of a large spawning aggregation of razorback sucker in midchannel near Needles, Calif., prompted the development of more effective methods to monitor this and possibly other riverine fish populations. This study examined the effectiveness of four methods of monitoring razorback sucker in a riverine environment. Hoop netting, electrofishing, boat surveys, and aerial photography were evaluated in terms of data accuracy, costs, stress on targeted fish, and effect on nontargeted fish as compared with trammel netting. Trammel netting in the riverine portion of the Colorado River downstream of Davis Dam, Arizona-Nevada yielded an average of 43 razorback suckers a year (1999 to 2005). Capture rates averaged 0.5 razorback suckers per staff day effort, at a cost exceeding $1,100 per fish. Population estimates calculated for 2003-2005 were 3,570 (95 percent confidence limits [CL] = 1,306i??i??i??-8,925), 1,768 (CL = 878-3,867) and 1,652 (CL = 706-5,164); wide confidence ranges reflect the small sample size. By-catch associated with trammel netting included common carp, game fish and, occasionally, shorebirds, waterfowl, and muskrats. Hoop nets were prone to downstream drift owing to design and anchoring problems aggravated by hydropower ramping. Tests were dropped after the 2006 field season and replaced with electrofishing. Electrofishing at night during low flow and when spawning razorback suckers moved to the shoreline proved extremely effective. In 2006 and 2007, 263 and 299 (respectively) razorback suckers were taken. Capture rates averaged 8.3 razorback suckers per staff day at a cost of $62 per fish. The adult population was estimated at 1,196 (925-1,546) fish. Compared with trammel netting, confidence limits narrowed substantially, from +or- 500 percent to +or- 30 percent, reflecting more precise estimates. By-catch was limited to two common carp. No recreational game fish, waterfowl, or mammals were captured or handled during use of electrofishing. Aerial photography (2006 and 2007) suggested an annual average of 580 fish detected on imagery. Identification of species was not possible; carp commonly have been mistaken for razorback sucker. Field verification determined that the proportion of razorback suckers to other fish was 3:1. On that basis, we estimated 435 razorback suckers were photographed, which equals 8.4 razorback suckers per staff day at a cost of $78 per fish. The data did not lend itself to population estimates. Fish were more easily identified from boats, where their lateral rather than their dorsal aspect is visible. On average, 888 razorback suckers were positively identified each year. Observation rates averaged 29.6 razorback suckers per staff day at a cost less than $18 per fish observed. Sucker densities averaged 20.5 and 9.6 fish/hectare which equated to an average spawning population at Needles, Calif., of 2,520 in 2006 and 1152 in 2007. The lower 2007 estimate reflected a refinement in sampling approach which removed a sampling bias. Electrofishing and boat surveys were more cost effective than other methods tested, and they provided more accurate information without the by-catch associated with trammel netting. However, they provided different types of data. Handling fish may be necessary for research purposes but unnecessary for general trend analysis. Electrofishing was extremely effective but can harm fish if not used with caution. Unnecessary electrofishing increases the likelihood of spinal damage and possible damage to eggs and potential young, and it may alter spawning behavior or duration. B

Open-File Report↗

USGS2024

Integrating presence-only and detection/non-detection data to estimate distributions and expected abundance of difficult-to-monitor species on a landscape-scale

Estimating species distribution and abundance is foundational to effective management and conservation. Using an integrated species distribution model that combines presence-only data from various sources with detection/non-detection data from structured surveys, we estimated the distribution and expected abundance of three difficult-to-monitor mammals of management concern across New York State, namely, coyotes ( Canis latrans ), bobcats ( Lynx rufus ) and black bears ( Ursus americanus ). Three distinct landscape-scale camera trap surveys provided detection/non-detection data over 9 years between 2013 and 2021, and we augmented those data with incidental records of our focal species from public repositories. We used an inhomogeneous Poisson point process to construct an integrated model that fit both data types simultaneously. We demonstrate a simple application of spatial point density of all species records in the accessed public databases to inform the thinning process to account for unknown spatial sampling in the presence-only data, often referred to as the ‘magic covariate’. Using this approach, we examine habitat associations and provide spatially explicit estimates in expected abundance across the entirety of New York State for all three focal species. As expected, coyotes were the most widely distributed and abundant species, with a strong positive association with agricultural land uses. Bobcats exhibited low expected abundance throughout the state and showed positive associations with deciduous forest and forest edge, and a negative association with road density. Finally, we observed considerable spatial variation in abundance of black bears with expected abundance increasing in association with various forest cover and composition covariates and decreasing with crop cover. We present insights into habitat associations and spatial variation in abundance, and provide management implications for each of the species of interest. Synthesis and applications . Our integrated modelling method allows for managers to use citizen sightings combined with detection/non-detection surveys to estimate robust indices of abundance for both high- and low-density, and wide-spread versus patchily distributed species. Through comparison with previous studies, we highlight how broad-scale programmes, such as the statewide efforts to estimate species distributions undertaken here, can benefit substantively from integrated models that leverage additional data (here, incidental records) from a larger region of space, and thus capture more landscape heterogeneity than is plausible within formalized surveys alone.

New York↗