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
Filter Total Items: 75
SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data
SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains 3 analysis modules along with a fourth control module that can automate analyses of large volumes of data. The modules are used to 1) identify the subset of paired-end sequences...
Authors
Mark P. Miller, Brian J. Knaus, Thomas D. Mullins, Susan M. Haig
Population genetics and evaluation of genetic evidence for subspecies in the Semipalmated Sandpiper (Calidris pusilla) Population genetics and evaluation of genetic evidence for subspecies in the Semipalmated Sandpiper (Calidris pusilla)
Semipalmated Sandpipers (Calidris pusilla) are among the most common North American shorebirds. Breeding in Arctic North America, this species displays regional differences in migratory pathways and possesses longitudinal bill length variation. Previous investigations suggested that genetic structure may occur within Semipalmated Sandpipers and that three subspecies corresponding to...
Authors
Mark P. Miller, Cheri Gratto-Trevor, Susan M. Haig, David S. Mizrahi, Melanie M. Mitchell, Thomas D. Mullins
SSR_pipeline--computer software for the identification of microsatellite sequences from paired-end Illumina high-throughput DNA sequence data 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. The program suite contains three analysis modules along with a fourth control module that can be used to automate analyses of large volumes of data. The modules are used to (1) identify the...
Authors
Mark P. Miller, Brian J. Knaus, Thomas D. Mullins, Susan M. Haig
Evaluation of a new model of aeolian transport in the presence of vegetation Evaluation of a new model of aeolian transport in the presence of vegetation
Aeolian transport is an important characteristic of many arid and semiarid regions worldwide that affects dust emission and ecosystem processes. The purpose of this paper is to evaluate a recent model of aeolian transport in the presence of vegetation. This approach differs from previous models by accounting for how vegetation affects the distribution of shear velocity on the surface...
Authors
Junran Li, Gregory S. Okin, Jeffrey E. Herrick, Jayne Belnap, Mark E. Miller, Kimberly Vest, Amy E. Draut
Assessing the risk of nitrogen deposition to natural resources in the Four Corners area Assessing the risk of nitrogen deposition to natural resources in the Four Corners area
Nitrogen (N) deposition in the western U.S. is on the rise and is already dramatically affecting terrestrial ecosystems. For example, N deposition has repeatedly been shown to lower air and water quality, increase greenhouse gas emissions, alter plant community composition, and significantly modify fire regimes. Accordingly, the effects of N deposition represent one of our largest...
Authors
Sasha C. Reed, Jayne Belnap, Lisa Floyd-Hanna, Tim Crews, Jack Herring, Dave Hanna, Mark E. Miller, Michael C. Duniway, Carla M. Roybal
Variation in migratory behavior influences regional genetic diversity and structure among American kestrel populations (Falco sparverius) in North America Variation in migratory behavior influences regional genetic diversity and structure among American kestrel populations (Falco sparverius) in North America
Birds employ numerous strategies to cope with seasonal fluctuations in high-quality habitat availability. Long distance migration is a common tactic; however, partial migration is especially common among broadly distributed species. Under partial migration systems, a portion of a species migrates, whereas the remainder inhabits breeding grounds year round. In this study, we identified...
Authors
Mark P. Miller, Thomas D. Mullins, John G. Parrish, Jeffrey R. Walters, Susan M. Haig
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.
Science and Products
Filter Total Items: 75
SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data
SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains 3 analysis modules along with a fourth control module that can automate analyses of large volumes of data. The modules are used to 1) identify the subset of paired-end sequences...
Authors
Mark P. Miller, Brian J. Knaus, Thomas D. Mullins, Susan M. Haig
Population genetics and evaluation of genetic evidence for subspecies in the Semipalmated Sandpiper (Calidris pusilla) Population genetics and evaluation of genetic evidence for subspecies in the Semipalmated Sandpiper (Calidris pusilla)
Semipalmated Sandpipers (Calidris pusilla) are among the most common North American shorebirds. Breeding in Arctic North America, this species displays regional differences in migratory pathways and possesses longitudinal bill length variation. Previous investigations suggested that genetic structure may occur within Semipalmated Sandpipers and that three subspecies corresponding to...
Authors
Mark P. Miller, Cheri Gratto-Trevor, Susan M. Haig, David S. Mizrahi, Melanie M. Mitchell, Thomas D. Mullins
SSR_pipeline--computer software for the identification of microsatellite sequences from paired-end Illumina high-throughput DNA sequence data 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. The program suite contains three analysis modules along with a fourth control module that can be used to automate analyses of large volumes of data. The modules are used to (1) identify the...
Authors
Mark P. Miller, Brian J. Knaus, Thomas D. Mullins, Susan M. Haig
Evaluation of a new model of aeolian transport in the presence of vegetation Evaluation of a new model of aeolian transport in the presence of vegetation
Aeolian transport is an important characteristic of many arid and semiarid regions worldwide that affects dust emission and ecosystem processes. The purpose of this paper is to evaluate a recent model of aeolian transport in the presence of vegetation. This approach differs from previous models by accounting for how vegetation affects the distribution of shear velocity on the surface...
Authors
Junran Li, Gregory S. Okin, Jeffrey E. Herrick, Jayne Belnap, Mark E. Miller, Kimberly Vest, Amy E. Draut
Assessing the risk of nitrogen deposition to natural resources in the Four Corners area Assessing the risk of nitrogen deposition to natural resources in the Four Corners area
Nitrogen (N) deposition in the western U.S. is on the rise and is already dramatically affecting terrestrial ecosystems. For example, N deposition has repeatedly been shown to lower air and water quality, increase greenhouse gas emissions, alter plant community composition, and significantly modify fire regimes. Accordingly, the effects of N deposition represent one of our largest...
Authors
Sasha C. Reed, Jayne Belnap, Lisa Floyd-Hanna, Tim Crews, Jack Herring, Dave Hanna, Mark E. Miller, Michael C. Duniway, Carla M. Roybal
Variation in migratory behavior influences regional genetic diversity and structure among American kestrel populations (Falco sparverius) in North America Variation in migratory behavior influences regional genetic diversity and structure among American kestrel populations (Falco sparverius) in North America
Birds employ numerous strategies to cope with seasonal fluctuations in high-quality habitat availability. Long distance migration is a common tactic; however, partial migration is especially common among broadly distributed species. Under partial migration systems, a portion of a species migrates, whereas the remainder inhabits breeding grounds year round. In this study, we identified...
Authors
Mark P. Miller, Thomas D. Mullins, John G. Parrish, Jeffrey R. Walters, Susan M. Haig
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.