Mark Miller
Mark Miller is an RGE-EDGE Senior Scientist with the USGS Office of Science Quality and Integrity (OSQI).
Mark Miller is a broadly trained biologist with a strong background in ecology, genetics, and statistics. He also possesses exceptional computational skills backed by the ability to communicate with both general and technical audiences. Prior to joining OSQI, his research primarily focused on analyses of wildlife and endangered species that are relevant to USGS and other DOI bureaus. Mark has been located in Lakewood, Colorado since 2020.
Education and Certifications
B.S. Auburn University (Zoology)
M.S. Virginia Tech (Biology)
Ph.D. Northern Arizona University (Biology)
Science and Products
Developing a "fire-aware" stream gage network by integrating USGS enterprise databases
Wildfires affect streams and rivers when they burn vegetation and scorch the ground. This makes floods more likely to happen and reduces water quality. Public managers, first responders, fire scientists, and hydrologists need timely information before and after a fire to plan for floods and water treatment. This project will create a method to combine national fire databases with the...
Amplified Fragment Length Polymorphism (AFLP) data obtained for 34 long-tailed vole (Microtus longicaudus) individuals at 91 loci
Prior to removal of pest species from an area, resource managers must determine if re-immigration from another population is possible. Voles inhabiting Saddle Rock on the southern Oregon coast are suspected to be partially responsible for declines in the Leach's storm petrel colony on the island. The island is very close to the mainland, and it is potentially accessible during below...
Nuclear microsatellite genotypes of six populations of yellow rail (Coturnicops noveboracensis) sampled 2005-2008
These data reflect nuclear microsatellite genotypes for specimens of yellow rails (Coturnicops noveboracensis) sampled in 2005-2008. Data from six populations are included.
Variables pertaining to establishment success of non-native fishes introduced to the Hawaiian Islands and Guam for use in risk analysis modeling
Data represent dependent and independent variables used in logistic modeling for a study entitled "Evaluating Establishment Success of Non-native Fishes Introduced to Inland Aquatic Habitats of Tropical Pacific Islands." The phases of invasion of nonnative species are transport, introduction, establishment, and spread. To understand likelihood of establishment of species moved to new...
Genetic data from Red-cockaded woodpeckers (Dryobates borealis) used to assess changes in population genetic differentiation and diversity over the past century throughout the southeastern United States
These data include nuclear microsatellite data and mitochondrial DNA sequences (mtDNA) for specimens of Red-cockaded woodpeckers collected from three time points: 1881-1969 (mtDNA only), 1992-1994, and 2010-2014. Additional information regarding individual identifiers, population assignment, regional assignment, and eco-regional assignment are included as are longitude/latitude...
DNA yields and concentrations from buccal swab samples of red-cockaded woodpeckers
The data were generated as part of a study to determine if buccal (oral) swabs could be used to obtain genetic material from Red-Cockaded Woodpecker chicks. Different swab types were investigated to determine if any specific type gave the highest DNA yields.
Microsatellite markers, habitat quality, and sample location data for Northern Spotted Owls (Strix occidentalis caurina)
The data are included in 8 separate text files: 1) "Sample_coordinates.txt". The file contains sample identifiers along with geographic coordinates associated with each sample. Coordinates are specified as UTM Zone 10 values (WGS84). 2) "Sample_genotypes.txt". The file contains a sample identifier along with microsatellite genotypes associated with each sample. 3) "uniform_conductances...
Data and source code from "Estimating inbreeding rates in natural populations: addressing the problem of incomplete pedigrees"
We used Monte Carlo simulations to compare properties of the two estimators and determine their utility for empirical analyses. Simulations were performed using idealized populations that were tracked over 15 generations. Separate simulations were performed using generation sizes of 100 individuals (50 male and 50 females) or 20 individuals (10 males and 10 females). In each generation...
Evaluating rehabilitation efforts following the Milford Flat Fire: Successes, failures, and controlling factorsData
Uncontrolled wildfire in arid and semiarid ecosystems has become an increasing concern in recent decades. Active rehabilitation of fire-affected areas is often quickly initiated to minimize long-term ecosystem damage. However, the complex soil-geomorphic-vegetation patterns and low and variable moisture conditions in these regions makes restoration challenging. To further inform these...
Filter Total Items: 75
The U.S. Geological Survey Water Resources Research Act Program—Meeting local, State, and national needs for water resources science and training
IntroductionThe U.S. Geological Survey (USGS) has a broad research portfolio that addresses water resource issues that are critical to our Nation’s prosperity and quality of life. Socioeconomics, geopolitical stressors, population growth, climate variability, and other factors provide challenges for the management of water resources. Working collaboratively with partners, the USGS...
Authors
Mark P. Miller, Earl A. Greene, Tanja N. Williamson
Ecosystem resilience to invasion and drought: Insights after 24 years in a rare never-grazed grassland
Understanding the resilience of ecosystems globally is hampered by the complex and interacting drivers of change characteristic of the Anthropocene. This is true for drylands of the western US, where widespread alteration of disturbance regimes and spread of invasive non-native species occurred with westward expansion during the 1800s, including the introduction of domestic livestock and...
Authors
Michael Duniway, Rebecca A Finger-Higgens, Erika L. Geiger, David L. Hoover, Alix Pfennigwerth, Anna C. Knight, Matthew W. Van Scoyoc, Mark P. Miller, Jayne Belnap
Geologic, geomorphic, and edaphic underpinnings of dryland ecosystems: Colorado Plateau landscapes in a changing world
Drylands represent more than 41% of the global land surface and are at degradation risk due to land use and climate change. Developing strategies to mitigate degradation and restore drylands in the face of these threats requires an understanding of how drylands are shaped by not only soils and climate, but also geology and geomorphology. However, few studies have completed such a...
Authors
Michael Duniway, Christopher Benson, Travis Nauman, Anna C. Knight, John Bradford, Seth Munson, Dana L. Witwicki, Carolyn Livensperger, Matthew W. Van Scoyoc, Terry T Fisk, David P. Thoma, Mark P. Miller
Water priorities for the Nation—U.S. Geological Survey Integrated Water Prediction science program
The U.S. Geological Survey Integrated Water Prediction science program focuses on the development of advanced models for forecasting water use and other components of the water cycle along with water quality attributes such as temperature, water constituents, and ecological conditions. The program also is developing the cyberinfrastructure required to implement national and local-scale...
Authors
Mark P. Miller, Katherine Skalak, David P. Lesmes
Water priorities for the Nation—The USGS National Water Dashboard
The U.S. Geological Survey National Water Dashboard supplies critical information to decision makers, emergency managers, and the public during extreme hydrologic events (such as droughts and floods) and during normal hydrologic conditions. It informs decision making that can help protect lives and property before and during extreme hydrologic events. The National Water Dashboard draws...
Authors
Mark P. Miller, Thomas E. Burley, Brian E. McCallum
Visit the U.S. Geological Survey's National Water Dashboard
The U.S. Geological Survey National Water Dashboard supplies critical information to decision makers, emergency managers, and the public during extreme hydrologic events (such as droughts and floods) and during normal hydrologic conditions. It informs decision making that can help protect lives and property before and during extreme hydrologic events. The National Water Dashboard draws...
Authors
Mark P. Miller, Thomas E. Burley, Brian E. McCallum
Evaluating establishment success of non-native fishes introduced to inland aquatic habitats of tropical Pacific islands
An information-theoretic approach was used to evaluate non-native freshwater fish species introduced to insular habitats of Hawaii and Guam comparing successful establishments vs. failures. Since the late 1800s, as many as 81 non-native freshwater fish species have been recorded as introduced to Hawaii and Guam (combined) and 50 (62%) of these are documented as having one or more...
Authors
Stephen J. Walsh, Leo Nico, Mark P. Miller
Water priorities for the Nation—USGS Integrated Water Science basins
The United States faces growing challenges to its water supply, infrastructure, and aquatic ecosystems because of population growth, climate change, floods, and droughts. To help address these challenges, the U.S. Geological Survey Water Resources Mission Area is integrating recent advances in monitoring, research, and modeling to improve assessments of water availability throughout the...
Authors
Mark P. Miller, Sandra M. Eberts, Lori A. Sprague
U.S. Geological Survey wildland fire science strategic plan, 2021–26
The U.S. Geological Survey (USGS) Wildland Fire Science Strategic Plan defines critical, core fire science capabilities for understanding fire-related and fire-responsive earth system processes and patterns, and informing management decision making. Developed by USGS fire scientists and executive leadership, and informed by conversations with external stakeholders, the Strategic Plan is...
Authors
Paul F. Steblein, Rachel A. Loehman, Mark P. Miller, Joseph R. Holomuzki, Suzanna C. Soileau, Matthew Brooks, Mia Drane-Maury, Hannah M. Hamilton, Jason W. Kean, Jon E. Keeley, Robert R. Mason,, Alexa McKerrow, James Meldrum, Edmund B. Molder, Sheila F. Murphy, Birgit Peterson, Geoffrey S. Plumlee, Douglas J. Shinneman, Phillip van Mantgem, Alison York
By
Ecosystems Mission Area, Natural Hazards Mission Area, Science Synthesis, Analysis and Research Program, Science Analytics and Synthesis (SAS) Program, Alaska Science Center, Earth Resources Observation and Science (EROS) Center , Forest and Rangeland Ecosystem Science Center, Fort Collins Science Center, Geologic Hazards Science Center, Geology, Geophysics, and Geochemistry Science Center, Western Ecological Research Center (WERC), Wildland Fire Science
Conservation genetics of imperiled striped whipsnake in Washington
Conservation of wide-ranging species is aided by population genetic information that provides insights into adaptive potential, population size, interpopulation connectivity, and even extinction risk in portions of a species range. The Striped Whipsnake (Masticophis taeniatus) occurs across 11 western U.S. states and into Mexico but has experienced population declines in parts of its...
Authors
David Pilliod, Lisa A. Hallock, Mark P. Miller, Thomas D. Mullins, Susan M. Haig
Water priorities for the Nation—U.S. Geological Survey Integrated Water Availability Assessments
The United States faces growing challenges to its water supply, infrastructure, and aquatic ecosystems because of population growth, climate change, floods and droughts, and aging water delivery systems. To help address these challenges, the U.S. Geological Survey (USGS) Water Resources Mission Area has established new strategic priorities that capitalize on the operational and...
Authors
Mark P. Miller, Brian R. Clark, Sandra M. Eberts, Patrick Lambert, Patricia Toccalino
Genetic identification of African pangolins and their origin in illegal trade
To track the illegal pangolin trade from Africa to Asia, we analyzed 1800 DNA samples from 30 seizures of African pangolin scales in Hong Kong during the period 2012–2016. We concluded that all four African pangolin species were present in trade, and that the white-bellied pangolin (Phataginus tricuspis) appeared most frequently (88.5%) in our samples. All six previously described...
Authors
Huarong Zhang, Gary Ades, Mark P. Miller, Feng Yang, Kwok-wai Lai, Gunter A. Fischer
Non-USGS Publications**
Safner, T., Miller, M.P., McRae, B.H., Fortin, M., Manel, S., 2011, Comparison of Bayesian clustering andedge detection methods for inferring boundaries in landscape genetics: International Journal of Molecular Sciences, v. 12, p. 865-889.
Fernandes, E., Keyser, C.A., Chong, J.P., Rangel, D., Miller, M.P., Roberts, D.W., 2010, Characterization of Metarhiziumspecies and varieties based on molecular analysis, heat tolerance and cold activity: Journal of Applied Microbiology, v. 108, p. 115-128.
Fernandes, E., Moraes, A.L., Pacheco, R.S., Rangel, D., Miller, M.P., Bittencourt, V., Roberts, D.W., 2009, Genetic diversity among Brazilian isolates of Beauveria bassiana - comparisons with non-Brazilian isolates and other Beauveria species: Journal of Applied Microbiology, v. 107, p. 760-774.
Schultheis, A.S., Booth, J.Y., Vinson, M.R., Miller, M.P., 2008, Genetic evidence for cohort splitting in the merovoltine stonefly Pteronarcys californica (Newport) in Blacksmith Fork, Utah: Aquatic Insects, v. 30, no. 3, p. 187-195.
Miller, M.P., Vincent, R., 2008, Rapid natural selection for resistance to an introduced parasite of rainbow trout: Evolutionary Applications, v. 1, p. 336-341.
Barni, F., Berti, A., Pianese, A., Boccellino, A., Miller, M.P., Caperna, A., Lago, G., 2007, Allele frequencies of 15 autosomal STR loci in the Iraq population with comparisons to other populations from the middle-eastern region: Forensic Science International, v. 167, p. 87-92.
Wagner, E.J., Wilson, C., Arndt, R., Goddard, P., Miller, M.P., Hodgson, A., Vincent, R., Mock, K., 2006, Evaluation of disease resistance of the Fish Lake–DeSmet, Wounded Man, and Harrison Lake strains of rainbow trout exposed to Myxobolus cerebralis: Journal of Aquatic Animal Health, v. 18, p. 128-135.
Miller, M.P., Weigel, D.E., Mock, K., Roth, B., 2006, Evidence for an outcrossing reproductive strategy in the hermaphroditic heterobranch gastropod Valvata utahensis (Valvatidae), with notes on the genetic differentiation of V. utahensis and V. humeralis: Journal of Molluscan Studies, v. 72, p. 397-403.
Miller, M.P., Weigel, D.E., Mock, K., 2006, Patterns of genetic structure in the endangered aquatic gastropod Valvata utahensis (Mollusca - Valvatidae) at small and large spatial scales: Freshwater Biology, v. 51, p. 2362-2375.
Miller, M.P., 2005, Alleles In Space (AIS) - Computer software for the joint analysis of interindividual spatial and genetic information: Journal of Heredity, v. 96, no. 6, p. 722-724.
Mock, K., Miller, M.P., 2005, Patterns of molecular diversity in naturally occurring and refugial populations of the least chub: Transactions of the American Fisheries Society, v. 134, p. 267-278.
Shuster, S.M., Miller, M.P., Lang, B.K., Zorich, N., Huynh, L., Keim, P., 2005, The effects of controlled propagation on an endangered species - genetic differentiation and divergence in body size among native and captive populations of the Socorro Isopod (Crustacea- Flabellifera): Conservation Genetics, v. 6, p. 355-368.
Mock, K., Brim-Box, J.C., Miller, M.P., Downing, M.E., Hoeh, W.R., 2004, Genetic diversity and divergence among freshwater mussel (Anodonta) populations in the Bonneville Basin of Utah: Molecular Ecology, v. 13, p. 1085-1098.
Miller, M.P., Parker, J.D., Kumar, S., 2003, Quantifying the intragenic distribution of human disease mutations: Annals of Human Genetics, v. 67, p. 567-579.
Miller, M.P., Blinn, D.W., Keim, P., 2002, Correlations between observed dispersal capabilities and patterns of genetic differentiation in populations of four aquatic insect species from the Arizona White Mountains, USA: Freshwater Biology, v. 47, p. 1660-1673.
Miller, M.P., Kumar, S., 2001, Understanding human disease mutations through the use of interspecific genetic variation: Human Molecular Genetics, v. 10, no. 21, p. 2319-2328.
Miller, M.P., Stevens, L.E., Busch, J., Sorensen, J.A., Keim, P., 2000, Amplified fragment length polymorphism and mitochondrial sequence data detect genetic differentiation and relationships in endangered southwestern USA ambersnails (Oxyloma spp.): Canadian Journal of Zoology, v. 78, p. 1845-1854.
Busch, J., Miller, M.P., Paxton, E.H., Sogge, M.K., Keim, P., 2000, Genetic variation in the endangered southwestern willow flycatcher: Auk, v. 117, no. 3, p. 586-595.
Miller, M.P., 1999, MANTEL-STRUCT- A program for the detection of population structure via mantel tests: Journal of Heredity, v. 90, no. 1, p. 258-259.
Miller, M.P., Kimberling, D.N., Keim, P., 1999, Re-analysis of genetic structure among populations of Rana pipiens in Arizona and Utah: The Southwest Naturalist, v. 44, no. 4, p. 527-530.
Miller, M.P., Hendricks, A.C., 1996, Zinc resistance in Chironomus riparius - Evidence for physiological and genetic components: Journal of the North American Benthological Society, v. 15, no. 1, p. 106-116.
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
SSR_pipeline: Computer Software for the Identification of Microsatellite Sequences from Paired-End Illumina High-Throughput DNA Sequence Data
SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (SSRs; for example, microsatellites) from paired-end high-throughput Illumina DNA sequencing data.
Science and Products
Developing a "fire-aware" stream gage network by integrating USGS enterprise databases
Wildfires affect streams and rivers when they burn vegetation and scorch the ground. This makes floods more likely to happen and reduces water quality. Public managers, first responders, fire scientists, and hydrologists need timely information before and after a fire to plan for floods and water treatment. This project will create a method to combine national fire databases with the...
Amplified Fragment Length Polymorphism (AFLP) data obtained for 34 long-tailed vole (Microtus longicaudus) individuals at 91 loci
Prior to removal of pest species from an area, resource managers must determine if re-immigration from another population is possible. Voles inhabiting Saddle Rock on the southern Oregon coast are suspected to be partially responsible for declines in the Leach's storm petrel colony on the island. The island is very close to the mainland, and it is potentially accessible during below...
Nuclear microsatellite genotypes of six populations of yellow rail (Coturnicops noveboracensis) sampled 2005-2008
These data reflect nuclear microsatellite genotypes for specimens of yellow rails (Coturnicops noveboracensis) sampled in 2005-2008. Data from six populations are included.
Variables pertaining to establishment success of non-native fishes introduced to the Hawaiian Islands and Guam for use in risk analysis modeling
Data represent dependent and independent variables used in logistic modeling for a study entitled "Evaluating Establishment Success of Non-native Fishes Introduced to Inland Aquatic Habitats of Tropical Pacific Islands." The phases of invasion of nonnative species are transport, introduction, establishment, and spread. To understand likelihood of establishment of species moved to new...
Genetic data from Red-cockaded woodpeckers (Dryobates borealis) used to assess changes in population genetic differentiation and diversity over the past century throughout the southeastern United States
These data include nuclear microsatellite data and mitochondrial DNA sequences (mtDNA) for specimens of Red-cockaded woodpeckers collected from three time points: 1881-1969 (mtDNA only), 1992-1994, and 2010-2014. Additional information regarding individual identifiers, population assignment, regional assignment, and eco-regional assignment are included as are longitude/latitude...
DNA yields and concentrations from buccal swab samples of red-cockaded woodpeckers
The data were generated as part of a study to determine if buccal (oral) swabs could be used to obtain genetic material from Red-Cockaded Woodpecker chicks. Different swab types were investigated to determine if any specific type gave the highest DNA yields.
Microsatellite markers, habitat quality, and sample location data for Northern Spotted Owls (Strix occidentalis caurina)
The data are included in 8 separate text files: 1) "Sample_coordinates.txt". The file contains sample identifiers along with geographic coordinates associated with each sample. Coordinates are specified as UTM Zone 10 values (WGS84). 2) "Sample_genotypes.txt". The file contains a sample identifier along with microsatellite genotypes associated with each sample. 3) "uniform_conductances...
Data and source code from "Estimating inbreeding rates in natural populations: addressing the problem of incomplete pedigrees"
We used Monte Carlo simulations to compare properties of the two estimators and determine their utility for empirical analyses. Simulations were performed using idealized populations that were tracked over 15 generations. Separate simulations were performed using generation sizes of 100 individuals (50 male and 50 females) or 20 individuals (10 males and 10 females). In each generation...
Evaluating rehabilitation efforts following the Milford Flat Fire: Successes, failures, and controlling factorsData
Uncontrolled wildfire in arid and semiarid ecosystems has become an increasing concern in recent decades. Active rehabilitation of fire-affected areas is often quickly initiated to minimize long-term ecosystem damage. However, the complex soil-geomorphic-vegetation patterns and low and variable moisture conditions in these regions makes restoration challenging. To further inform these...
Filter Total Items: 75
The U.S. Geological Survey Water Resources Research Act Program—Meeting local, State, and national needs for water resources science and training
IntroductionThe U.S. Geological Survey (USGS) has a broad research portfolio that addresses water resource issues that are critical to our Nation’s prosperity and quality of life. Socioeconomics, geopolitical stressors, population growth, climate variability, and other factors provide challenges for the management of water resources. Working collaboratively with partners, the USGS...
Authors
Mark P. Miller, Earl A. Greene, Tanja N. Williamson
Ecosystem resilience to invasion and drought: Insights after 24 years in a rare never-grazed grassland
Understanding the resilience of ecosystems globally is hampered by the complex and interacting drivers of change characteristic of the Anthropocene. This is true for drylands of the western US, where widespread alteration of disturbance regimes and spread of invasive non-native species occurred with westward expansion during the 1800s, including the introduction of domestic livestock and...
Authors
Michael Duniway, Rebecca A Finger-Higgens, Erika L. Geiger, David L. Hoover, Alix Pfennigwerth, Anna C. Knight, Matthew W. Van Scoyoc, Mark P. Miller, Jayne Belnap
Geologic, geomorphic, and edaphic underpinnings of dryland ecosystems: Colorado Plateau landscapes in a changing world
Drylands represent more than 41% of the global land surface and are at degradation risk due to land use and climate change. Developing strategies to mitigate degradation and restore drylands in the face of these threats requires an understanding of how drylands are shaped by not only soils and climate, but also geology and geomorphology. However, few studies have completed such a...
Authors
Michael Duniway, Christopher Benson, Travis Nauman, Anna C. Knight, John Bradford, Seth Munson, Dana L. Witwicki, Carolyn Livensperger, Matthew W. Van Scoyoc, Terry T Fisk, David P. Thoma, Mark P. Miller
Water priorities for the Nation—U.S. Geological Survey Integrated Water Prediction science program
The U.S. Geological Survey Integrated Water Prediction science program focuses on the development of advanced models for forecasting water use and other components of the water cycle along with water quality attributes such as temperature, water constituents, and ecological conditions. The program also is developing the cyberinfrastructure required to implement national and local-scale...
Authors
Mark P. Miller, Katherine Skalak, David P. Lesmes
Water priorities for the Nation—The USGS National Water Dashboard
The U.S. Geological Survey National Water Dashboard supplies critical information to decision makers, emergency managers, and the public during extreme hydrologic events (such as droughts and floods) and during normal hydrologic conditions. It informs decision making that can help protect lives and property before and during extreme hydrologic events. The National Water Dashboard draws...
Authors
Mark P. Miller, Thomas E. Burley, Brian E. McCallum
Visit the U.S. Geological Survey's National Water Dashboard
The U.S. Geological Survey National Water Dashboard supplies critical information to decision makers, emergency managers, and the public during extreme hydrologic events (such as droughts and floods) and during normal hydrologic conditions. It informs decision making that can help protect lives and property before and during extreme hydrologic events. The National Water Dashboard draws...
Authors
Mark P. Miller, Thomas E. Burley, Brian E. McCallum
Evaluating establishment success of non-native fishes introduced to inland aquatic habitats of tropical Pacific islands
An information-theoretic approach was used to evaluate non-native freshwater fish species introduced to insular habitats of Hawaii and Guam comparing successful establishments vs. failures. Since the late 1800s, as many as 81 non-native freshwater fish species have been recorded as introduced to Hawaii and Guam (combined) and 50 (62%) of these are documented as having one or more...
Authors
Stephen J. Walsh, Leo Nico, Mark P. Miller
Water priorities for the Nation—USGS Integrated Water Science basins
The United States faces growing challenges to its water supply, infrastructure, and aquatic ecosystems because of population growth, climate change, floods, and droughts. To help address these challenges, the U.S. Geological Survey Water Resources Mission Area is integrating recent advances in monitoring, research, and modeling to improve assessments of water availability throughout the...
Authors
Mark P. Miller, Sandra M. Eberts, Lori A. Sprague
U.S. Geological Survey wildland fire science strategic plan, 2021–26
The U.S. Geological Survey (USGS) Wildland Fire Science Strategic Plan defines critical, core fire science capabilities for understanding fire-related and fire-responsive earth system processes and patterns, and informing management decision making. Developed by USGS fire scientists and executive leadership, and informed by conversations with external stakeholders, the Strategic Plan is...
Authors
Paul F. Steblein, Rachel A. Loehman, Mark P. Miller, Joseph R. Holomuzki, Suzanna C. Soileau, Matthew Brooks, Mia Drane-Maury, Hannah M. Hamilton, Jason W. Kean, Jon E. Keeley, Robert R. Mason,, Alexa McKerrow, James Meldrum, Edmund B. Molder, Sheila F. Murphy, Birgit Peterson, Geoffrey S. Plumlee, Douglas J. Shinneman, Phillip van Mantgem, Alison York
By
Ecosystems Mission Area, Natural Hazards Mission Area, Science Synthesis, Analysis and Research Program, Science Analytics and Synthesis (SAS) Program, Alaska Science Center, Earth Resources Observation and Science (EROS) Center , Forest and Rangeland Ecosystem Science Center, Fort Collins Science Center, Geologic Hazards Science Center, Geology, Geophysics, and Geochemistry Science Center, Western Ecological Research Center (WERC), Wildland Fire Science
Conservation genetics of imperiled striped whipsnake in Washington
Conservation of wide-ranging species is aided by population genetic information that provides insights into adaptive potential, population size, interpopulation connectivity, and even extinction risk in portions of a species range. The Striped Whipsnake (Masticophis taeniatus) occurs across 11 western U.S. states and into Mexico but has experienced population declines in parts of its...
Authors
David Pilliod, Lisa A. Hallock, Mark P. Miller, Thomas D. Mullins, Susan M. Haig
Water priorities for the Nation—U.S. Geological Survey Integrated Water Availability Assessments
The United States faces growing challenges to its water supply, infrastructure, and aquatic ecosystems because of population growth, climate change, floods and droughts, and aging water delivery systems. To help address these challenges, the U.S. Geological Survey (USGS) Water Resources Mission Area has established new strategic priorities that capitalize on the operational and...
Authors
Mark P. Miller, Brian R. Clark, Sandra M. Eberts, Patrick Lambert, Patricia Toccalino
Genetic identification of African pangolins and their origin in illegal trade
To track the illegal pangolin trade from Africa to Asia, we analyzed 1800 DNA samples from 30 seizures of African pangolin scales in Hong Kong during the period 2012–2016. We concluded that all four African pangolin species were present in trade, and that the white-bellied pangolin (Phataginus tricuspis) appeared most frequently (88.5%) in our samples. All six previously described...
Authors
Huarong Zhang, Gary Ades, Mark P. Miller, Feng Yang, Kwok-wai Lai, Gunter A. Fischer
Non-USGS Publications**
Safner, T., Miller, M.P., McRae, B.H., Fortin, M., Manel, S., 2011, Comparison of Bayesian clustering andedge detection methods for inferring boundaries in landscape genetics: International Journal of Molecular Sciences, v. 12, p. 865-889.
Fernandes, E., Keyser, C.A., Chong, J.P., Rangel, D., Miller, M.P., Roberts, D.W., 2010, Characterization of Metarhiziumspecies and varieties based on molecular analysis, heat tolerance and cold activity: Journal of Applied Microbiology, v. 108, p. 115-128.
Fernandes, E., Moraes, A.L., Pacheco, R.S., Rangel, D., Miller, M.P., Bittencourt, V., Roberts, D.W., 2009, Genetic diversity among Brazilian isolates of Beauveria bassiana - comparisons with non-Brazilian isolates and other Beauveria species: Journal of Applied Microbiology, v. 107, p. 760-774.
Schultheis, A.S., Booth, J.Y., Vinson, M.R., Miller, M.P., 2008, Genetic evidence for cohort splitting in the merovoltine stonefly Pteronarcys californica (Newport) in Blacksmith Fork, Utah: Aquatic Insects, v. 30, no. 3, p. 187-195.
Miller, M.P., Vincent, R., 2008, Rapid natural selection for resistance to an introduced parasite of rainbow trout: Evolutionary Applications, v. 1, p. 336-341.
Barni, F., Berti, A., Pianese, A., Boccellino, A., Miller, M.P., Caperna, A., Lago, G., 2007, Allele frequencies of 15 autosomal STR loci in the Iraq population with comparisons to other populations from the middle-eastern region: Forensic Science International, v. 167, p. 87-92.
Wagner, E.J., Wilson, C., Arndt, R., Goddard, P., Miller, M.P., Hodgson, A., Vincent, R., Mock, K., 2006, Evaluation of disease resistance of the Fish Lake–DeSmet, Wounded Man, and Harrison Lake strains of rainbow trout exposed to Myxobolus cerebralis: Journal of Aquatic Animal Health, v. 18, p. 128-135.
Miller, M.P., Weigel, D.E., Mock, K., Roth, B., 2006, Evidence for an outcrossing reproductive strategy in the hermaphroditic heterobranch gastropod Valvata utahensis (Valvatidae), with notes on the genetic differentiation of V. utahensis and V. humeralis: Journal of Molluscan Studies, v. 72, p. 397-403.
Miller, M.P., Weigel, D.E., Mock, K., 2006, Patterns of genetic structure in the endangered aquatic gastropod Valvata utahensis (Mollusca - Valvatidae) at small and large spatial scales: Freshwater Biology, v. 51, p. 2362-2375.
Miller, M.P., 2005, Alleles In Space (AIS) - Computer software for the joint analysis of interindividual spatial and genetic information: Journal of Heredity, v. 96, no. 6, p. 722-724.
Mock, K., Miller, M.P., 2005, Patterns of molecular diversity in naturally occurring and refugial populations of the least chub: Transactions of the American Fisheries Society, v. 134, p. 267-278.
Shuster, S.M., Miller, M.P., Lang, B.K., Zorich, N., Huynh, L., Keim, P., 2005, The effects of controlled propagation on an endangered species - genetic differentiation and divergence in body size among native and captive populations of the Socorro Isopod (Crustacea- Flabellifera): Conservation Genetics, v. 6, p. 355-368.
Mock, K., Brim-Box, J.C., Miller, M.P., Downing, M.E., Hoeh, W.R., 2004, Genetic diversity and divergence among freshwater mussel (Anodonta) populations in the Bonneville Basin of Utah: Molecular Ecology, v. 13, p. 1085-1098.
Miller, M.P., Parker, J.D., Kumar, S., 2003, Quantifying the intragenic distribution of human disease mutations: Annals of Human Genetics, v. 67, p. 567-579.
Miller, M.P., Blinn, D.W., Keim, P., 2002, Correlations between observed dispersal capabilities and patterns of genetic differentiation in populations of four aquatic insect species from the Arizona White Mountains, USA: Freshwater Biology, v. 47, p. 1660-1673.
Miller, M.P., Kumar, S., 2001, Understanding human disease mutations through the use of interspecific genetic variation: Human Molecular Genetics, v. 10, no. 21, p. 2319-2328.
Miller, M.P., Stevens, L.E., Busch, J., Sorensen, J.A., Keim, P., 2000, Amplified fragment length polymorphism and mitochondrial sequence data detect genetic differentiation and relationships in endangered southwestern USA ambersnails (Oxyloma spp.): Canadian Journal of Zoology, v. 78, p. 1845-1854.
Busch, J., Miller, M.P., Paxton, E.H., Sogge, M.K., Keim, P., 2000, Genetic variation in the endangered southwestern willow flycatcher: Auk, v. 117, no. 3, p. 586-595.
Miller, M.P., 1999, MANTEL-STRUCT- A program for the detection of population structure via mantel tests: Journal of Heredity, v. 90, no. 1, p. 258-259.
Miller, M.P., Kimberling, D.N., Keim, P., 1999, Re-analysis of genetic structure among populations of Rana pipiens in Arizona and Utah: The Southwest Naturalist, v. 44, no. 4, p. 527-530.
Miller, M.P., Hendricks, A.C., 1996, Zinc resistance in Chironomus riparius - Evidence for physiological and genetic components: Journal of the North American Benthological Society, v. 15, no. 1, p. 106-116.
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
SSR_pipeline: Computer Software for the Identification of Microsatellite Sequences from Paired-End Illumina High-Throughput DNA Sequence Data
SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (SSRs; for example, microsatellites) from paired-end high-throughput Illumina DNA sequencing data.