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USGS2014

A reference system for animal biometrics: application to the northern leopard frog

Reference systems and public databases are available for human biometrics, but to our knowledge nothing is available for animal biometrics. This is surprising because animals are not required to give their agreement to be in a database. This paper proposes a reference system and database for the northern leopard frog (Lithobates pipiens). Both are available for reproducible experiments. Results of both open set and closed set experiments are given.

Conference Paper↗

USGS2020

Applications of deep convolutional neural networks to predict length, circumference, and weight from mostly dewatered images of fish

Simple biometric data of fish aid fishery management tasks such as monitoring the structure of fish populations and regulating recreational harvest. While these data are foundational to fishery research and management, the collection of length and weight data through physical handling of the fish is challenging as it is time consuming for personnel and can be stressful for the fish. Recent advances in imaging technology and machine learning now offer alternatives for capturing biometric data. To investigate the potential of deep convolutional neural networks to predict biometric data, several regressors were trained and evaluated on data stemming from the FishL™ Recognition System and manual measurements of length, girth, and weight. The dataset consisted of 694 fish from 22 different species common to Laurentian Great Lakes. Even with such a diverse dataset and variety of presentations by the fish, the regressors proved to be robust and achieved competitive mean percent errors in the range of 5.5 to 7.6% for length and girth on an evaluation dataset. Potential applications of this work could increase the efficiency and accuracy of routine survey work by fishery professionals and provide a means for longer‐term automated collection of fish biometric data.

Illinois, Michigan, Ohio↗

USGS2010

Uncovering a latent multinomial: Analysis of mark–recapture data with misidentification

Natural tags based on DNA fingerprints or natural features of animals are now becoming very widely used in wildlife population biology. However, classic capture-recapture models do not allow for misidentification of animals which is a potentially very serious problem with natural tags. Statistical analysis of misidentification processes is extremely difficult using traditional likelihood methods but is easily handled using Bayesian methods. We present a general framework for Bayesian analysis of categorical data arising from a latent multinomial distribution. Although our work is motivated by a specific model for misidentification in closed population capture-recapture analyses, with crucial assumptions which may not always be appropriate, the methods we develop extend naturally to a variety of other models with similar structure. Suppose that observed frequencies f are a known linear transformation f=A'x of a latent multinomial variable x with cell probability vector pi= pi(theta). Given that full conditional distributions [theta | x] can be sampled, implementation of Gibbs sampling requires only that we can sample from the full conditional distribution [x | f, theta], which is made possible by knowledge of the null space of A'. We illustrate the approach using two data sets with individual misidentification, one simulated, the other summarizing recapture data for salamanders based on natural marks.

Biometrics↗

USGS2007

Hierarchical spatiotemporal matrix models for characterizing invasions

The growth and dispersal of biotic organisms is an important subject in ecology. Ecologists are able to accurately describe survival and fecundity in plant and animal populations and have developed quantitative approaches to study the dynamics of dispersal and population size. Of particular interest are the dynamics of invasive species. Such nonindigenous animals and plants can levy significant impacts on native biotic communities. Effective models for relative abundance have been developed; however, a better understanding of the dynamics of actual population size (as opposed to relative abundance) in an invasion would be beneficial to all branches of ecology. In this article, we adopt a hierarchical Bayesian framework for modeling the invasion of such species while addressing the discrete nature of the data and uncertainty associated with the probability of detection. The nonlinear dynamics between discrete time points are intuitively modeled through an embedded deterministic population model with density-dependent growth and dispersal components. Additionally, we illustrate the importance of accommodating spatially varying dispersal rates. The method is applied to the specific case of the Eurasian Collared-Dove, an invasive species at mid-invasion in the United States at the time of this writing. ?? 2006, The International Biometric Society.

Biometrics↗

USGS2008

Modeling unobserved sources of heterogeneity in animal abundance using a Dirichlet process prior

In surveys of natural populations of animals, a sampling protocol is often spatially replicated to collect a representative sample of the population. In these surveys, differences in abundance of animals among sample locations may induce spatial heterogeneity in the counts associated with a particular sampling protocol. For some species, the sources of heterogeneity in abundance may be unknown or unmeasurable, leading one to specify the variation in abundance among sample locations stochastically. However, choosing a parametric model for the distribution of unmeasured heterogeneity is potentially subject to error and can have profound effects on predictions of abundance at unsampled locations. In this article, we develop an alternative approach wherein a Dirichlet process prior is assumed for the distribution of latent abundances. This approach allows for uncertainty in model specification and for natural clustering in the distribution of abundances in a data-adaptive way. We apply this approach in an analysis of counts based on removal samples of an endangered fish species, the Okaloosa darter. Results of our data analysis and simulation studies suggest that our implementation of the Dirichlet process prior has several attractive features not shared by conventional, fully parametric alternatives. ?? 2008, The International Biometric Society.

Biometrics↗

USGS1982

Optimum nonparametric estimation of population density based on ordered distances

The asymptotic mean and error mean square are determined for the nonparametric estimator of plant density by distance sampling proposed by Patil, Burnham and Kovner (1979, Biometrics 35 , 597-604. On the basis of these formulae, a bias-reduced version of this estimator is given, and its specific form is determined which gives minimum mean square error under varying assumptions about the true probability density function of the sampled data. Extension is given to line-transect sampling.

Biometrics↗

USGS1986

Constant-parameter capture-recapture models

Jolly (1982, Biometrics 38, 301-321) presented modifications of the Jolly-Seber model for capture-recapture data, which assume constant survival and/or capture rates. Where appropriate, because of the reduced number of parameters, these models lead to more efficient estimators than the Jolly-Seber model. The tests to compare models given by Jolly do not make complete use of the data, and we present here the appropriate modifications, and also indicate how to carry out goodness-of-fit tests which utilize individual capture history information. We also describe analogous models for the case where young and adult animals are tagged. The availability of computer programs to perform the analysis is noted, and examples are given using output from these programs.

Biometrics↗

USGS2006

Site occupancy models with heterogeneous detection probabilities

Models for estimating the probability of occurrence of a species in the presence of imperfect detection are important in many ecological disciplines. In these ?site occupancy? models, the possibility of heterogeneity in detection probabilities among sites must be considered because variation in abundance (and other factors) among sampled sites induces variation in detection probability (p). In this article, I develop occurrence probability models that allow for heterogeneous detection probabilities by considering several common classes of mixture distributions for p. For any mixing distribution, the likelihood has the general form of a zero-inflated binomial mixture for which inference based upon integrated likelihood is straightforward. A recent paper by Link (2003, Biometrics 59, 1123?1130) demonstrates that in closed population models used for estimating population size, different classes of mixture distributions are indistinguishable from data, yet can produce very different inferences about population size. I demonstrate that this problem can also arise in models for estimating site occupancy in the presence of heterogeneous detection probabilities. The implications of this are discussed in the context of an application to avian survey data and the development of animal monitoring programs.

Biometrics↗

USGS2022

A critical review of bioaccumulation and biotransformation of organic chemicals in birds

A literature review of bioaccumulation and biotransformation of organic chemicals in birds was undertaken, aiming to support scoping and prioritization of future research. The objectives were to characterize available bioaccumulation/biotransformation data, identify knowledge gaps, determine how extant data can be used, and explore the strategy and steps forward. An intermediate approach balanced between expediency and rigor was taken given the vastness of the literature. Following a critical review of > 500 peer-reviewed studies, > 25,000 data entries and 2 million information bytes were compiled on > 700 organic compounds for ~ 320 wild species and 60 domestic breeds of birds. These data were organized into themed databases on bioaccumulation and biotransformation , field survey , microsomal enzyme activity , metabolic pathway , and bird taxonomy and diet . Significant data gaps were identified in all databases at multiple levels. Biotransformation characterization was largely fragmented over metabolite/pathway identification and characterization of enzyme activity or biotransformation kinetics. Limited biotransformation kinetic data constrained development of an avian biotransformation model. A substantial shortage of in vivo biotransformation kinetics has been observed as most reported rate constants were derived in vitro. No metric comprehensively captured all key contaminant classes or chemical groups to support broad-scope modeling of bioaccumulation or biotransformation. However, metrics such as biota-feed accumulation factor, maximum transfer factor, and total elimination rate constant were more readily usable for modeling or benchmarking than other reviewed parameters. Analysis demonstrated the lack of bioaccumulation/biotransformation characterization of shorebirds, seabirds, and raptors. In the study of bioaccumulation and biotransformation of organic chemicals in birds, this review revealed the need for greater chemical and avian species diversity, chemical measurements in environmental media, basic biometrics and exposure conditions, multiple tissues/matrices sampling, and further exploration on biotransformation. Limitations of classical bioaccumulation metrics and current research strategies used in bird studies were also discussed. Forward-looking research strategies were proposed: adopting a chemical roadmap for future investigations, integrating existing biomonitoring data, gap-filling with non-testing approaches, improving data reporting practices, expanding field sampling scopes, bridging existing models and theories, exploring biotransformation via avian genomics, and establishing an online data repository.

Reviews of Environmental Contamination and Toxicol↗

USGS2007

Evapotranspiration in a cottonwood (Populus fremontii) restoration plantation estimated by sap flow and remote sensing methods

Native tree plantations have been proposed for the restoration of wildlife habitat in human-altered riparian corridors of western U.S. rivers. Evapotranspiration (ET) by riparian vegetation is an important, but poorly quantified, term in river water budgets. Native tree restoration plots will potentially increase ET. We used sap flow sensors and satellite imagery to estimate ET in a 8 ha, cottonwood (Populus fremontii) restoration plot on the Lower Colorado River. Biometric methods were used to scale leaf area to whole trees and stands of trees. This technique was used to validate our estimates of ET obtained by scaling from branch level to stand (or plot) level measurements of ET. Cottonwood trees used 6-10 mm day-1 of water during the peak of the growing season as determined by sap flow sensors, and annual rates scaled by time-series MODIS satellite imagery were approximately 1.2 m year-1. Although irrigation was not quantified, the field had been flood irrigated at 2 week intervals during the 3 years prior to the study, receiving approximately 2 m year-1 of water. A frequency-domain electromagnetic induction survey of soil moisture content showed that the field was saturated (26-28% gravimetric water content) at the 90-150 cm soil depth under the field. Trees were apparently rooted into the saturated soil, and considerable saving of water could potentially be achieved by modifying the irrigation regime to take into account that cottonwoods are phreatophytes. The study showed that cottonwood ET can be monitored by remote sensing methods calibrated with ground measurements with an accuracy or uncertainty of 20-30% in western riparian corridors. ?? 2007 Elsevier B.V. All rights reserved.

Agricultural and Forest Meteorology↗

USGS2021

Analysis of body condition indices reveals different ecotypes of the Antillean manatee

Assessing the body condition of wild animals is necessary to monitor the health of the population and is critical to defining a framework for conservation actions. Body condition indices (BCIs) are a non-invasive and relatively simple means to assess the health of individual animals, useful for addressing a wide variety of ecological, behavioral, and management questions. The Antillean manatee ( Trichechus manatus manatus ) is an endangered subspecies of the West Indian manatee, facing a wide variety of threats from mostly human-related origins. Our objective was to define specific BCIs for the subspecies that, coupled with additional health, genetic and demographic information, can be valuable to guide management decisions. Biometric measurements of 380 wild Antillean manatees captured in seven different locations within their range of distribution were obtained. From this information, we developed three BCIs (BCI 1 = UG/SL, BCI 2 = W/SL 3 , BCI 3 = W/(SL*UG 2 )). Linear models and two-way ANCOVA tests showed significant differences of the BCIs among sexes and locations. Although our three BCIs are suitable for Antillean manatees, BCI 1 is more practical as it does not require information about weight, which can be a metric logistically difficult to collect under particular circumstances. BCI 1 was significantly different among environments, revealing that the phenotypic plasticity of the subspecies have originated at least two ecotypes—coastal marine and riverine—of Antillean manatees.

Puerto Rico↗

USGS2008

Fidelity and breeding probability related to population density and individual quality in black brent geese Branta bernicla nigricans

1. Patterns of temporary emigration (associated with non-breeding) are important components of variation in individual quality. Permanent emigration from the natal area has important implications for both individual fitness and local population dynamics. 2. We estimated both permanent and temporary emigration of black brent geese (Branta bernicla nigricans Lawrence) from the Tutakoke River colony, using observations of marked brent geese on breeding and wintering areas, and recoveries of ringed individuals by hunters. We used the likelihood developed by Lindberg, Kendall, Hines & Anderson 2001 (Combining band recovery data and Pollock's robust design to model temporary and permanent emigration. Biometrics, 57, 273-281) to assess hypotheses and estimate parameters. 3. Temporary emigration (the converse of breeding) varied among age classes up to age 5, and differed between individuals that bred in the previous years vs. those that did not. Consistent with the hypothesis of variation in individual quality, individuals with a higher probability of breeding in one year also had a higher probability of breeding the next year. 4. Natal fidelity of females ranged from 0.70 ?? 0.07-0.96 ?? 0.18 and averaged 0.83. In contrast to Lindberg et al. (1998), we did not detect a relationship between fidelity and local population density. Natal fidelity was negatively correlated with first-year survival, suggesting that competition among individuals of the same age for breeding territories influenced dispersal. Once females nested at the Tutakoke River, colony breeding fidelity was 1.0. 5. Our analyses show substantial variation in individual quality associated with fitness, which other analyses suggest is strongly influenced by early environment. Our analyses also suggest substantial interchange among breeding colonies of brent geese, as first shown by Lindberg et al. (1998).

Journal of Animal Ecology↗

USGS2006

Heteropolaria colisarum Foissner and Schubert, 1977 (Protozoa: Epistylididae) or North American freshwater fishes

The peritrichous ciliate ‘Epistylis sp.’ involved in the‘red-sore’ disease of various North American freshwater fishes is identified as Heteropolaria colisarum Foissner & Schubert, 1977. Its morphology is redescribed from observations of living and silver-stained organisms and biometrically analysed individuals. Extended zooids can be easily identified by their highly characteristic (elongated) body. Silver impregnations show a very high number of silverlines and a band-like, irregularly formed macronucleus. The genus Heteropolaria belongs to the family Epistylididae and is characterized by the eccentric location of the scopula of the swarmer and a peculiar myoneme in the peristomal disc that branches off the myoneme of the peristomal collar. Autochthonous occurrences of this species are known only from North America. In Europe only the related species H. lwoffi has been found. Histological sections give some evidence that the terminal platelet of the stalk is embedded in the dermal epithelium. This suggests that H. colisarum could be a parasite rather than an epizoon and that the often associated bacterium Aeromonas hydrophila is a secondary invader. However, further studies are necessary. Experiments showed a high infectivity of the ciliate and no host specificity. These characteristics are supported by the observations of other researchers. Preliminary laboratory tests showed that a single treatment with salt solution (NaCl) at a rate of 1.5% for 3h controlled H. colisarum.

Journal of Fish Diseases↗

USGS2023

Juvenile sea lamprey (Petromyzon marinus) have a wide window of elevated salinity tolerance that is eventually limited during springtime warming

The present study examined changes in biometric characteristics, osmoregulatory capacity, and seawater (SW) tolerance of juvenile sea lamprey ( Petromyzon marinus ) throughout the varying thermal changes from late autumn to late spring. Body length, mass, and condition factor were maintained until April, when significant declines in mass and condition factor were observed to correspond with increases in temperature. Nearly 100% survival in SW was maintained through April. In May, after river and estuarine temperatures had increased, significant mortality in SW (up to 50%) was observed. After SW acclimation, plasma chloride was maintained at an elevated set point, and gill Na + /K + -ATPase activity was elevated. Neither parameter appeared to be affected during springtime warming. Together, these results provide a first characterization of the sustained osmoregulatory performance of juvenile sea lamprey after metamorphosis and show that the window of increased hypo-osmoregulatory performance for SW entry lasts for at least 5 months but may ultimately be limited by increases in river water temperatures in late spring.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2006

A review of the population estimation approach of the North American landbird conservation plan

As part of their development of a continental plan for monitoring landbirds (Rich et al. 2004), Partners in Flight (PIF) applied a new method to make preliminary estimates of population size for all 448 species of landbirds present in the continental United States and Canada (Table 1). Estimation of the global population size of North American landbirds was intended to (1) identify the degree of vulnerability of each species, (2) provide estimates of the current population size for each species, and (3) provide a starting point for estimating population sizes in states, provinces, territories, and Bird Conservation Regions (Rich et al. 2004). A method proposed by Rosenberg and Blancher (2005) was used to derive population estimates from available survey data. To enhance the credibility of these estimates, PIF organized a review of the methodology used to estimate North American landbird population sizes. A planning committee selected members from the ornithological and biometrical communities (hereafter “the panel”), with the aim of selecting individuals from academia, state natural-resource agencies, and the U.S. and Canadian federal governments, including the Canadian Wildlife Service, the U.S. Geological Survey, and the U.S. Department of Agriculture Forest Service. The panel addressed three questions: (1) Were the methods of population estimation proposed by PIF reasonable? (2) What actions could be taken to improve the data or analyses on which the PIF population estimates were based? and (3) How should the PIF population estimates be interpreted?

The Auk↗

USGS2018

Influencia de factores ambientales y biométricos en la capacidad de nado del barbo ibérico (Luciobarbus bocagei Steindachner, 1864), un ciprínido potamódromo endémico de la Península Ibérica

El presente trabajo analiza la capacidad voluntaria de nado del barbo ibérico ( Luciobarbus bocagei Steindachner, 1864) en un canal abierto durante su época de migración, relacionándola con factores ambientales y biométricos. La temperatura del agua, la velocidad de flujo y la longitud del pez fueron los factores de mayor importancia que condicionaron la velocidad de nado de los barbos y su tiempo de fatiga. Dentro del rango de valores estudiado, el barbo ibérico pudo mantener velocidades de nado en sprint (> 15 BL/s) durante 3-10 s, y de 17-117 s en el modo de natación prolongada (7-15 BL/s). Los resultados aportados pueden ser empleados como una herramienta útil para la gestión de sus poblaciones, principalmente para el diseño de pasos para peces. This paper analyzes the volitional swimming capacity of the Iberian barbel ( Luciobarbus bocagei Steindachner, 1864) in an open flume during its migration period, in relation to environmental and biometric factors. Water temperature, flow velocity and fish length were the most important factors which affected the swimming speed of barbels and their fatigue time. Within the range of values studied, the Iberian barbel was able to maintain sprint swim speeds (> 15 BL/s) for 3-10 s, and 17-117 s in prolonged swim mode (7-15 BL/s). The results can be used as a tool for the management of barbel populations, mainly in the design of fishways.

Limnetica↗

USGS2003

Monitoring amphibians in Great Smoky Mountains National Park

Amphibian species have inexplicably declined or disappeared in many regions of the world, and in some instances, serious malformations have been observed. In the United States, amphibian declines frequently have occurred even in protected areas. Causes for the declines and malformations probably are varied and may not even be related. The seemingly sudden declines in widely separated areas, however, suggests a need to monitor amphibian populations as well as identify the causes when declines or malformations are discovered. In 2000, the President of the United States and Congress directed Department of the Interior (DOI) agencies to develop a plan to monitor the trends in amphibian populations on DOI lands and to conduct causes of declines. The DOI has stewardship responsibilities over vast land holdings in the United States, much of it occupied by, or potential habitat for, amphibians. The U.S. Geological Survey (USGS) was given lead responsibility for planning and organizing this program, named the Amphibian Research and Monitoring Initiative (ARMI). Authorization carried the mandate to set up a national amphibian monitoring program on Federal lands, to develop the sampling techniques and biometrical analyses necessary to determine status and trends, and to identify possible causes of amphibian declines and malformations. The biological importance of Great Smoky Mountains National Park has been recognized by its designation as an International Biosphere Reserve. As such, it is clearly the leading region of significance for amphibian research. Although no other region shares the wealth of amphibians as found in the Great Smokies (31 species of salamanders, and 13 of frogs), the entire southern and mid-section of the Appalachian Mountain chain is characterized by a high diversity of amphibians, and inventories and monitoring protocols developed in the Smokies likely will be applicable to other Appalachian National Park Service properties. From 1998 to 2001, USGS biologists carried out a pilot inventory and monitoring research project in Great Smoky Mountains National Park. A variety of inventory, sampling, and monitoring techniques were employed and tested. These included wide-scale visual encounter surveys of amphibians at terrestrial and aquatic sites, intensive monitoring of selected plots, randomly placed small-grid plot sampling, litterbag sampling in streams, monitoring nesting females of selected species, call surveys, and monitoring specialized habitats, such as caves. Coupled with information derived from amphibian surveys on Federal lands using various other techniques (automated frog call data loggers, PVC pipes, drift fences, terrestrial and aquatic traps), an amphibian monitoring program was designed to best meet the needs of biologists and natural resource managers after taking into consideration the logistics, terrain, and life histories of the species found within Great Smoky Mountains National Park. This report provides an overview of the Park’s amphibians, the factors affecting their distribution, a review of important areas of biodiversity, and a summary of amphibian life history in the Southern Appalachians. In addition, survey techniques are described as well as examples of how the techniques are set up, a critique of what the results tell the observer, and a discussion of the limitations of the techniques and the data. The report reviews considerations for site selection, outlines steps for biosecurity and for processing diseased or dying animals, and provides resource managers with a decision tree on how to monitor the Park’s amphibians based on different levels of available resources. It concludes with an extensive list of references for inventorying and monitoring amphibians. USGS and Great Smoky Mountains National Park biologists need to establish cooperative efforts and training to ensure that congressionally mandated amphibian surveys are performed in a statistically rigorous and biologically meaningful manner, and that amphibian populations on Federal lands are monitored to ensure their long-term survival. The research detailed in this report will aid these cooperative efforts.

North Carolina, Tennessee↗

USGS2003

Occurrence of the diamondback terrapin ( Malaclemys terrapin littoralis ) at South Deer Island in Galveston Bay, Texas, April 2001-May 2002

One-hundred thirty-five terrapins were captured (116 individuals, 19 recaptures) in occurrence and nesting and basking surveys at South Deer Island in Galveston Bay, Texas, during April 2001–May 2002. Along the southern shore of the island, terrapins were captured in crab traps placed in shallow water offshore; in the lagoon on the island, terrapins were captured by hand while walking along the shore. In the nesting and basking surveys, areas of the island with continuous patches of exposed shell typically were checked twice a day for nesting and basking terrapins, except during the last 2 months of the study, when more intensive monitoring was conducted. The occurrence surveys resulted in 119 terrapins captured in crab traps and nine captured by hand around the lagoon. The nesting and basking surveys yielded seven terrapins. Only one was nesting, although the nest is believed to be the first documented terrapin nest found in Texas. Three terrapins were captured swimming near shell beaches, and three more were captured basking on shell beaches. The most terrapins were captured during April–May 2001 and April–May 2002. Biometric data collected on terrapins captured showed size dimorphism on the basis of sex. The median female straight-line carapace length was 17.8 centimeters, 1.4 times larger than the median male carapace length, 13.1 centimeters. The median female mass was 1,021 grams, 2.9 times larger than the median male mass, 354 grams. Intra-specific variation occurred in the colorations and markings of terrapins captured. Anomalies - lesions, deformities, barnacles, and algae - were common among terrapins captured. Both lesions and deformities were more common among males than females. Dominant vegetation or substrate associated with terrapin habitat included saltwort, slender seapurslane, seabeach orache, shell, and woody debris.

Texas↗