Geology topics

William L. Miller

Publications and source records attributed to William L. Miller.

7 recordsLinked to original sources

USGS2021

Comparison of sample types from white-tailed deer (Odocoileus virginianus) for DNA extraction and analyses

Collection of biological samples for DNA is necessary in a variety of disciplines including disease epidemiology, landscape genetics, and forensics. Quantity and quality of DNA varies depending on the method of collection or media available for collection (e.g., blood, tissue, fecal). Blood is the most common sample collected in vials or on Whatman Flinders Technology Associates (FTA) cards with short- and long-term storage providing adequate DNA for study objectives. The focus of this study was to determine if biological samples stored on Whatman FTA Elute cards were a reasonable alternative to traditional DNA sample collection, storage, and extraction. Tissue, nasal swabs, and ocular fluid were collected from white-tailed deer ( Odocoileus virginianus ). Tissue samples and nasal swabs acted as a control to compare extraction and DNA suitability for microsatellite analysis for nasal swabs and ocular fluid extracted from FTA Elute cards. We determined that FTA Elute cards improved the extraction time and storage of samples and that nasal swabs and ocular fluid containing pigmented fluid were reasonable alternatives to traditional tissue DNA extractions.

Pennsylvania↗

USGS2020

Assessment of spatial genetic structure to identify populations at risk for infection of an emerging epizootic disease

Understanding the geographic extent and connectivity of wildlife populations can provide important insights into the management of disease outbreaks but defining patterns of population structure is difficult for widely distributed species. Landscape genetic analyses are powerful methods for identifying cryptic structure and movement patterns that may be associated with spatial epizootic patterns in such cases. We characterized patterns of population substructure and connectivity using microsatellite genotypes from 2,222 white-tailed deer ( Odocoileus virginianus ) in the Mid-Atlantic region of the United States, a region where chronic wasting disease was first detected in 2009. The goal of this study was to evaluate the juxtaposition between population structure, landscape features that influence gene flow, and current disease management units. Clustering analyses identified four to five subpopulations in this region, the edges of which corresponded to ecophysiographic provinces. Subpopulations were further partitioned into 11 clusters with subtle ( F ST ≤ 0.041), but significant genetic differentiation. Genetic differentiation was lower and migration rates were higher among neighboring genetic clusters, indicating an underlying genetic cline. Genetic discontinuities were associated with topographic barriers, however. Resistance surface modeling indicated that gene flow was diffuse in homogenous landscapes, but the direction and extent of gene flow were influenced by forest cover, traffic volume, and elevational relief in subregions heterogeneous for these landscape features. Chronic wasting disease primarily occurred among genetic clusters within a single subpopulation and along corridors of high landscape connectivity. These results may suggest a possible correlation between population substructure, landscape connectivity, and the occurrence of diseases for widespread species. Considering these factors may be useful in delineating effective management units, although only the largest features produced appreciable differences in subpopulation structure. Disease mitigation strategies implemented at the scale of ecophysiographic provinces are likely to be more effective than those implemented at finer scales.

Maryland, Pennsylvania, Virginia↗

USGS2019

Can genetic assignment tests provide insight on the influence of captive egression on epizootiology of chronic wasting disease?

Identifying the sources of ongoing and novel disease outbreaks is critical for understanding the diffusion of epizootic diseases. Identifying infection sources is difficult when few physical differences separate individuals with different origins. Genetic assignment procedures show great promise for assessing transmission dynamics in such situations. Here, we use genetic assignment tests to determine the source of chronic wasting disease infections in free-ranging white-tailed deer ( Odocoileus virginianus ) populations. Natural dispersal is thought to facilitate the geographic diffusion of chronic wasting disease, but egression from captive cervid populations represents an alternative source of infection that is difficult to detect due to physical similarities with wild deer. Simulated reference populations were created based on allele frequencies from 1,912 empirical microsatellite genotypes collected in four sampling subregions and five captive facilities. These reference populations were used to assess the likelihood of ancestry and assignment of 1,861 free-ranging deer (1,834 noninfected and 27 infected) and 51 captive individuals to captive or wild populations. The ancestry ( Q ) and assignment scores ( A ) for free-ranging deer to wild populations were high (average Q wild = 0.913 and average A wild = 0.951, respectively), but varied among subregions ( Q wild = 0.800–0.947, A wild = 0.857–0.976). These findings suggest that captive egression and admixture are rare, but risk may not be spatially uniform. Ancestry and assignment scores for two free-ranging deer with chronic wasting disease sampled in an area where chronic wasting disease was previously unobserved in free-ranging herds indicated a higher likelihood of assignment and proportion of ancestry attributable to captive populations. While we cannot directly assign these individuals to infected facilities, these findings suggest that rare egression events may influence the epizootiology of chronic wasting disease in free-ranging populations. Continued disease surveillance and genetic analyses may further elucidate the relative disease risk attributable to captive and wild sources.

Maryland, Pennsylvania, Virginia, West Virginia↗

USGS2019

Evaluation of a microsatellite panel for use across North American populations of white-tailed deer (Odocoileus virginianus)

Background Microsatellite loci have been used extensively over the past two decades to study the genetic characteristics of non-model species. The relative ease of microsatellite development and ability to adapt markers from related species has led to the proliferation of available markers, particularly for those species that are intensively studied and managed. Because it is often infeasible to genotype individuals across all available loci, researchers generally rely on subsets of markers. Marker choice and genotyping errors can bias inferences made using disparate suites of microsatellite loci. This can limit comparative and collaborative efforts among research groups and has been a primary motivation for panel standardization efforts. Here, we develop a methodology for identifying a suite of markers from previous literature that can be generalizable across the range of commonly studied organisms. We specifically focus on producing a broadly applicable microsatellite panel for white-tailed deer ( Odocoileus virginianus ). Results We reviewed microsatellite panels from 58 previous or ongoing projects and identified a total of 106 candidate loci. We developed a multiplex protocol and evaluated the efficacy of 17 of the most commonly used loci using 720 DNA samples collected from the Mid-Atlantic region of the United States, an area where few previous studies were conducted. Amplification errors were detected in six of these loci. The properties of the remaining 11 loci suggest that they are applicable for many common research objectives. Specifically, this panel is highly polymorphic (eight to 20 alleles per locus, polymorphic information criterion = 0.492 to 0.917), exhibits low frequencies of genotyping errors (null alleles < 10%), and is relatively easy to interpret with the aid of allele binning software. Conclusions We were able to identify a panel of microsatellite markers that show potential for broad applicability over the geographic range of white-tailed deer, as evidenced by the distribution of previous studies that utilized them. Validation in an additional region confirmed this. These results suggest that marker standardization and evaluation procedures based on literature reviews offers an effective method for identifying consolidated panels for future studies. This simple procedure addresses previous concerns about the infeasibility of standardization efforts.

Maryland, Pennsylvania, Virginia↗

USGS2019

Spatial heterogeneity of prion gene polymorphisms in an area recently infected by chronic wasting disease

Genetic variability in the prion protein ( Prnp ) gene influences host susceptibility to many pathogenic prion diseases. Understanding the distribution of susceptible Prnp variants and determining factors influencing spatial genetic patterns are important components of many chronic wasting disease mitigation strategies. Here, we describe Prnp variability in white-tailed deer ( Odocoileus virginianus ) from the Mid-Atlantic region of the United States of America, an area with a recent history of infection and low disease incidence. This population is characterized by lower rates of polymorphism and significantly higher frequencies of the more susceptible 96GG genotype compared to previously surveyed populations. The prevalence of the most susceptible genotypes at disease-associated loci did vary among subregions, indicating that populations have innate differences in genotype-dictated susceptibility.

Maryland, Pennsylvania, Virginia, West Virginia↗

USGS2018

Limited hatchery introgression into wild brook trout (Salvelinus fontinalis) populations despite reoccurring stocking

Due to increased anthropogenic pressures on many fish populations, supplementing wild populations with captive‐raised individuals has become an increasingly common management practice. Stocking programs can be controversial due to uncertainty about the long‐term fitness effects of genetic introgression on wild populations. In particular, introgression between hatchery and wild individuals can cause declines in wild population fitness, resiliency, and adaptive potential, and contribute to local population extirpation. However, low survival and fitness of captive‐raised individuals can minimize the long‐term genetic consequences of stocking in wild populations, and to date the prevalence of introgression in actively stocked ecosystems has not been rigorously evaluated. We quantified the extent of introgression in 30 populations of wild brook trout ( Salvelinus fontinalis ) in a Pennsylvania watershed, and examined the correlation between introgression and 11 environmental covariates. Genetic assignment tests were used to determine the origin (wild vs. captive‐raised) for 1742 wild‐caught and 300 hatchery brook trout. To avoid assignment biases, individuals were assigned to two simulated populations that represented the average allele frequencies in wild and hatchery groups. Fish with intermediate probabilities of wild ancestry were classified as introgressed, with threshold values determined through simulation. Even with reoccurring stocking at most sites, over 93% of wild‐caught individuals probabilistically assigned to wild origin, and only 5.6% of wild‐caught fish assigned to introgressed. Models examining environmental drivers of introgression explained less than 3% of the among‐population variability, and all estimated effects were highly uncertain. This was not surprising given overall low introgression observed in this study. Our results suggest that introgression of hatchery‐derived genotypes can occur at low rates, even in actively stocked ecosystems and across a range of habitats. However, a cautious approach to stocking may still be warranted, as the potential effects of stocking on wild population fitness and the mechanisms limiting introgression are not known.

Evolutionary Applications↗

USGS2017

CWDPRNP: A tool for cervid prion sequence analysis in program R

Chronic wasting disease is a fatal, neurological disease caused by an infectious prion protein, which affects economically and ecologically important members of the family Cervidae. Single nucleotide polymorphisms within the prion protein gene have been linked to differential susceptibility to the disease in many species. Wildlife managers are seeking to determine the frequencies of disease-associated alleles and genotypes and delineate spatial genetic patterns. The CWDPRNP package, implemented in program R, provides a unified framework for analyzing prion protein gene variability and spatial structure.

Bioinformatics↗