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Geology topics

James A. Powell

Publications and source records attributed to James A. Powell.

16 recordsLinked to original sources
USGS2022

The first assessment of the genetic diversity and structure of the endangered West Indian manatee in Cuba

The coastal waters of Cuba are home to a small, endangered population of West Indian manatee, which would benefit from a comprehensive characterization of the population’s genetic variation. We conducted the first genetic assessment of Cuban manatees to determine the extent of the population's genetic structure and characterize the neutral genetic diversity among regions within the archipelago. We genotyped 49 manatees at 18 microsatellite loci, a subset of 27 samples on 1703 single nucleotide polymorphisms (SNPs), and sequenced 59 manatees at the mitochondrial control region. The Cuba manatee population had low nuclear (microsatellites H E = 0.44, and SNP H E = 0.29) and mitochondrial genetic diversity ( h = 0.068 and π = 0.00025), and displayed moderate departures from random mating (microsatellite F IS = 0.12, SNP F IS = 0.10). Our results suggest that the western portion of the archipelago undergoes periodic exchange of alleles based on the evidence of shared ancestry and low but significant differentiation. The southeast Guantanamo Bay region and the western portion of the archipelago were more differentiated than southwest and northwest manatees. The genetic distinctiveness observed in the southeast supports its recognition as a demographically independent unit for natural resource management regardless of whether it is due to historical isolation or isolation by distance. Estimates of the regional effective population sizes, with the microsatellite and SNP datasets, were small (all N e < 60). Subsequent analyses using additional samples could better examine how the observed structure is masking simple isolation by distance patterns or whether ecological or biogeographic forces shape genetic patterns.

Genetica↗
USGS2022

Connecting regional-scale tree distribution models with seed dispersal kernels

Regional scale forest distribution models are important tools for biogeography and understanding the structure of forest communities in space. These models take climate and geographic variables as input and are therefore helpful for long-term decision support and climate adaptation planning. Generally, local processes of tree germination and seedling survival are resolved probabilistically with explanatory variables such as elevation, latitude, exposure, soil type, moisture availability, climate and weather inputs and `trained’ using landscape and regional presence-absence data and machine learning techniques. How seeds are distributed in these models, that is, determining the dispersal kernel, is far more problematic. The challenge is that variables conditioning vertebrate seed dispersal (motility and probability of utilization or caching in response to cover type) are not represented in large scale distribution models, and in fact vary on scales (10-100 meters) that are much smaller than the smallest pixel size for the distribution model (1-10 kilometers). We present a homogenized seed digestion kernel (HSDK) which incorporates this scale separation. Homogenization naturally links highly variable small-scale processes (like seed foraging and caching by birds and rodents) with large scale effects (like dispersal of seeds over tens of kilometers). We develop a homogenization strategy to predict seed dispersal on landscape scales, analytically linking small-scale variables (landscape fraction cover by tree type, gut residence times and cover type utilization by frugivorous birds) with large scale behaviors. Closed form approximations are developed in two dimensions for two limiting cases of seed handling behavior, and the approach is illustrated using landscape data and piñon-pine dispersal in a 630,000 square kilometer region in the southwestern US.

Applied Mathematics and Computation↗
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↗
USGS2020

Animal movement models with mechanistic selection functions

A suite of statistical methods are used to study animal movement. Most of these methods treat animal trajectory data in one of three ways: as discrete pro- cesses, as continuous processes, or as point processes. We brie y review each of these approaches and then focus in on the latter. In the context of point processes, so-called resource selection analyses are among the most common way to statis- tically treat animal trajectory data. However, most resource selection analyses provide inference based on approximations of point process models. The forms of these models have been limited to a few types of specications that provide infer- ence about relative resource use and, less commonly, probability of use. For more general spatio-temporal point process models, the most common type of analysis often proceeds with a data augmentation approach that is used to create a binary data set that can be analyzed with conditional logistic regression. We show that the conditional logistic regression likelihood can be generalized to accommodate a variety of alternative specications related to resource selection. We then provide an example of a case where a spatio-temporal point process model coincides with that implied by a mechanistic model for movement expressed as a partial dier- ential equation derived from rst principles of movement. We demonstrate that inference from this form of point process model is intuitive (and could be useful for management and conservation) by analyzing a set of telemetry data from a mountain lion in Colorado, USA, to understand the eects of spatially explicit environmental conditions on movement behavior of this species.

Spatial Statistics↗
USGS2019

Nonlinear reaction–diffusion process models improve inference for population dynamics

Partial differential equations (PDEs) are a useful tool for modeling spatiotemporal dynamics of ecological processes. However, as an ecological process evolves, we need statistical models that can adapt to changing dynamics as new data are collected. We developed a model that combines an ecological diffusion equation and logistic growth to characterize colonization processes of a population that establishes long-term equilibrium over a heterogeneous environment. We also developed a homogenization strategy to statistically upscale the PDE for faster computation and adopted a hierarchical framework to accommodate multiple data sources collected at different spatial scales. We highlighted the advantages of using a logistic reaction component instead of a Malthusian component when population growth demonstrates asymptotic behavior. As a case study, we demonstrated that our model improves spatiotemporal abundance forecasts of sea otters in Glacier Bay, Alaska. Furthermore, we predicted spatially varying local equilibrium abundances as a result of environmentally driven diffusion and density-regulated growth. Integrating equilibrium abundances over the study area in our application enabled us to infer the overall carrying capacity of sea otters in Glacier Bay, Alaska.

Alaska↗
USGS2018

Effects of climate change on ecological disturbance in the Northern Rockies Region [Chapter 8]

This chapter describes the ecology of important disturbance regimes in the Forest Service, U.S. Department of Agriculture (USFS) Northern Region and the Greater Yellowstone Area, hereafter called the Northern Rockies region, and potential shifts in these regimes as a consequence of observed and projected climate change. The term disturbance regime describes the general temporal and spatial characteristics of a disturbance agent - insect, disease, fire, weather, even human activity - and the effects of that agent on the landscape (table 8.1). More specifically, a disturbance regime is the cumulative effect of multiple disturbance events over space and time (Keane 2013). Disturbances disrupt an ecosystem, community, or population structure and change elements of the biological environment, physical environment, or both (White and Pickett 1985). The resulting shifting mosaic of diverse ecological patterns and structures in turn affects future patterns of disturbance, in a reciprocal, linked relationship that shapes the fundamental character of landscapes and ecosystems. Disturbance creates and maintains biological diversity in the form of shifting, heterogeneous mosaics of diverse communities and habitats across a landscape (McKinney and Drake 1998), and biodiversity is generally highest when disturbance is neither too rare nor too frequent on the landscape (Grime 1973).

General Technical Report↗
USGS2017

Effects of climate change on ecological disturbance in the northern Rockies

Disturbances alter ecosystem, community, or population structure and change elements of the biological and/or physical environment. Climate changes can alter the timing, magnitude, frequency, and duration of disturbance events, as well as the interactions of disturbances on a landscape, and climate change may already be affecting disturbance events and regimes. Interactions among disturbance regimes, such as the cooccurrence in space and time of bark beetle outbreaks and wildfires, can result in highly visible, rapidly occurring, and persistent changes in landscape composition and structure. Understanding how altered disturbance patterns and multiple disturbance interactions might result in novel and emergent landscape behaviors is critical for addressing climate change impacts and for designing land management strategies that are appropriate for future climates This chapter describes the ecology of important disturbance regimes in the Northern Rockies region, and potential shifts in these regimes as a consequence of observed and projected climate change. We summarize five disturbance types present in the Northern Rockies that are sensitive to a changing climate--wildfires, bark beetles, white pine blister rust (Cronartium ribicola), other forest diseases, and nonnative plant invasions—and provide information that can help managers anticipate how, when, where, and why climate changes may alter the characteristics of disturbance regimes.

Rocky Mountains↗
USGS2017

Diet of the Antillean manatee (Trichechus manatus manatus) in Belize, Central America

Belize contains important habitat for Antillean manatees (Trichechus manatus manatus) and provides refuge for the highest known population density of this subspecies. As these animals face impending threats, knowledge of their dietary habits can be used to interpret resource utilization. The contents of 13 mouth, 6 digestive tract (stomach, duodenum and colon), and 124 fecal samples were microscopically examined using a modified point technique detection protocol to identify key plant species consumed by manatees at two important aggregation sites in Belize: Southern Lagoon and the Drowned Cayes. Overall, 15 different items were identified in samples from manatees in Belize. Five species of seagrasses (Halodule wrightii, Thalassia testudinum, Ruppia maritima, Syringodium filiforme, and Halophila sp.) made up the highest percentage of items. The red mangrove (Rhizophora mangle), was also identified as an important food item. Algae (Ulva sp., Chara sp., Lyngbya sp.) and invertebrates (sponges and diatoms) were also consumed. Variation in the percentage of seagrasses, other vascular plants, and algae consumption was analyzed as a 4-factor analysis of variance (ANOVA) with main effects and interactions for locality, sex, size classification, and season. While sex and season did not influence diet composition, differences for locality and size classification were observed. These results suggest that analysis of diet composition of Antillean manatees may help to determine critical habitat and use of associated food resources which, in turn can be used to aid conservation efforts in Belize.

Journal of the Marine Biological Association of th↗
USGS2017

When mechanism matters: Bayesian forecasting using models of ecological diffusion

Ecological diffusion is a theory that can be used to understand and forecast spatio-temporal processes such as dispersal, invasion, and the spread of disease. Hierarchical Bayesian modelling provides a framework to make statistical inference and probabilistic forecasts, using mechanistic ecological models. To illustrate, we show how hierarchical Bayesian models of ecological diffusion can be implemented for large data sets that are distributed densely across space and time. The hierarchical Bayesian approach is used to understand and forecast the growth and geographic spread in the prevalence of chronic wasting disease in white-tailed deer ( Odocoileus virginianus ). We compare statistical inference and forecasts from our hierarchical Bayesian model to phenomenological regression-based methods that are commonly used to analyse spatial occurrence data. The mechanistic statistical model based on ecological diffusion led to important ecological insights, obviated a commonly ignored type of collinearity, and was the most accurate method for forecasting.

Ecology Letters↗
USGS2016

Baseline reference range for trace metal concentrations in whole blood of wild and managed West Indian Manatees ( Trichechus manatus ) in Florida and Belize

The West Indian manatee ( Trichechus manatus ) is exposed to a number of anthropogenic influences, including metals, as they inhabit shallow waters with close proximity to shore. While maintaining homeostasis of many metals is crucial for health, there is currently no baseline reference range that can be used to make clinical and environmental decisions for this endangered species. In this study, whole blood samples from 151 manatees were collected during health assessments performed in Florida and Belize from 2008 through 2011. Whole blood samples (n = 37) from managed care facilities in Florida and Belize from 2009 through 2011 were also used in this study. The concentrations of 17 metals in whole blood were determined, and the data were used to derive a baseline reference range. Impacts of capture location, age, and sex on whole blood metal concentrations were examined. Location and age were related to copper concentrations as values were significantly higher in habitats near urban areas and in calves. Copper may also be a husbandry concern as concentrations were significantly higher in managed manatees (1.17 ± 0.04 ppm) than wild manatees (0.73 ± 0.02 ppm). Zinc (11.20 ± 0.30 ppm) was of special interest as normal concentrations were two to five times higher than other marine mammal species. Arsenic concentrations were higher in Belize (0.43 ± 0.07 ppm), with Placencia Lagoon having twice the concentration of Belize City and Southern Lagoon. Selenium concentrations were lower (0.18 ± 0.09 ppm) than in other marine mammal species. The lowest selenium concentrations were observed in rehabilitating and managed manatees which may warrant additional monitoring in managed care facilities. The established preliminary baseline reference range can be used by clinicians, biologists, and managers to monitor the health of West Indian manatees.

Aquatic Mammals↗
USGS2013

Computationally efficient statistical differential equation modeling using homogenization

Statistical models using partial differential equations (PDEs) to describe dynamically evolving natural systems are appearing in the scientific literature with some regularity in recent years. Often such studies seek to characterize the dynamics of temporal or spatio-temporal phenomena such as invasive species, consumer-resource interactions, community evolution, and resource selection. Specifically, in the spatial setting, data are often available at varying spatial and temporal scales. Additionally, the necessary numerical integration of a PDE may be computationally infeasible over the spatial support of interest. We present an approach to impose computationally advantageous changes of support in statistical implementations of PDE models and demonstrate its utility through simulation using a form of PDE known as “ecological diffusion.” We also apply a statistical ecological diffusion model to a data set involving the spread of mountain pine beetle (Dendroctonus ponderosae) in Idaho, USA.

Journal of Agricultural, Biological, and Environme↗
USGS2013

Blood mineral concentrations in manatees ( Trichechus manatus latirostris and Trichechus manatus manatus )

Limited information is available regarding the role of minerals and heavy metals in the morbidity and mortality of manatees. Whole-blood and serum mineral concentrations were evaluated in apparently healthy, free-ranging Florida ( Trichechus manatus latirostris , n = 31) and Belize ( Trichechus manatus manatus , n = 14) manatees. Toxicologic statuses of the animals and of their environment had not been previously determined. Mean mineral whole-blood (WB) and serum values in Florida (FL) and Belize (BZ) manatees were determined, and evaluated for differences with respect to geographic location, relative age, and sex. Mean WB and serum silver, boron, cobalt, magnesium, molybdenum, and WB cadmium concentrations were significantly higher in BZ versus FL manatees ( P ≤ 0.05). Mean WB aluminum, calcium, manganese, sodium, phosphorus, vanadium, and serum zinc concentrations were significantly lower in BZ versus FL manatees. Adult manatees had significant and higher mean WB aluminum, manganese, sodium, antimony, vanadium, and serum manganese and zinc concentrations compared to juvenile animals. Significant and lower mean WB and serum silver, boron, cobalt, and serum copper and strontium concentrations were present in adults compared to juveniles ( P ≤ 0.05). Females had significant and higher mean WB nickel and serum barium compared to males ( P ≤ 0.05). Mean WB arsenic and zinc, and mean serum iron, magnesium, and zinc concentrations fell within toxic ranges reported for domestic species. Results reveal manatee blood mineral concentrations differ with location, age, and sex. Influence from diet, sediment, water, and anthropogenic sources on manatee mineral concentration warrant further investigation.

Journal of Zoo and Wildlife Medicine↗
USGS2013

Diversidad haplotípica en el manatí Trichechus manatus en Cuba: resultados preliminares

The aim of this analysis was to obtain information regarding the mtDNA haplotype composition of the manatee (T. manatus) occupying the Cuban archipelago. A fragment of 410 bp of the non-coding region was analyzed for 12 individual manatees from Cuba and one from Florida, USA. Only two haplotypes were identified. Haplotype A1, found exclusively in Florida (including in the sample analyzed here) but also found in Mexico, the Dominican Republic and Puerto Rico, was the most frequent haplotype (11 of the 12 samples from Cuba) and widely distributed. The second haplotype A3, previously referred to as endemic from Belize, was identified from an individual stranded in Isabela de Sagua, north of Cuba. These preliminary results provide information about three major aspects of manatee biology: (1) the mtDNA genetic diversity of T. manatus in Cuba seems low as compared to other regions of the Caribbean; (2) the Cuban population likely belongs to the group comprising Florida and the portions of the Greater Antilles; and (3) the territories of Belize and Cuba have exchanged individuals at present or in a relatively recent past.

Revista de investigación↗
USGS2012

Monitoring oral temperature, heart rate, and respiration rate of West Indian manatees (Trichechus manatus) during capture and handling in the field

West Indian manatees (Trichechus manatus) are captured, handled, and transported to facilitate conservation, research, and rehabilitation efforts. Monitoring manatee oral temperature (OT), heart rate (HR), and respiration rate (RR) during out-of-water handling can assist efforts to maintain animal well-being and improve medical response to evidence of declining health. To determine effects of capture on manatee vital signs, we monitored OT, HR, and RR continuously for a 50-min period in 38 healthy, awake, juvenile and adult Florida manatees (T. m. latirostris) and 48 similar Antillean manatees (T. m. manatus). We examined creatine kinase (CK), potassium (K+), serum amyloid A (SAA), and lactate values for each animal to assess possible systemic inflammation and muscular trauma. OT range was 29.5 to 36.2° C, HR range was 32 to 88 beats/min, and RR range was 0 to 17 breaths/5 min. Antillean manatees had higher initial OT, HR, and RR than Florida manatees (p < 0.001). As monitoring time progressed, mean differences between the subspecies were no longer significant. High RR over monitoring time was associated with high lactate concentration. Antillean manatees had higher overall lactate values ([mean ± SD] 20.6 ± 7.8 mmol/L) than Florida manatees (13.7 ± 6.7 mmol/L; p < 0.001). We recommend monitoring manatee OT, HR, and RR during capture and handling in the field or in a captive care setting.

Aquatic Mammals↗
USGS2010

First report of a Florida manatee (Trichechus manatus latirostris) in Cuba

Manatees ( Trichechus manatus latirostris ) in Florida utilize intake and effluent canals of power plants as resting and thermoregulatory habitat. We report the use of a power plant canal in Cuba by a known Florida manatee, the first documented case of movement by a manatee between Florida and Cuba. In January, February, and April 2007, two manatees (mother and calf) were reported entering a power plant canal in north Havana, Cuba. The larger manatee had several distinctive scars which were photographed. Digital images were matched to a previously known Florida manatee (CR131) with a sighting history dating from December 1979 to July 2006. Exchanges of individuals between Florida and Cuba may have important genetic implications, particularly since there appears to be little genetic exchange between the Florida manatee subspecies with populations of the Antillean manatee subspecies ( T. m. manatus ) in Puerto Rico and the Dominican Republic.

Aquatic Mammals↗