I'm a broadly trained biologist with a strong background in ecology, genetics, and statistics. I also possess exceptional computational skills backed by the ability to communcate with both general and technical audiences. Most of my work focuses on analyses of wildlife species that are relevant to USGS and other DOI bureaus.
B.S. Auburn University (Zoology)
M.S. Virginia Tech (Biology)
Ph.D. Northern Arizona University (Biology)
- 18 years of post-PhD research experience in the life sciences (8 years in academia, 10 with U.S. Geological Survey).
- A well-documented record of productivity and achievement.
- 52 peer-reviewed scientific publications (additional under review or in press).
- Able to understand the complexities and subtle attributes of diverse systems.
- Research including taxa such as birds, mammals (including humans), amphibians, insects, crustaceans, fungi, fish, plants, and mollusks.
- Research environments including mountains, forests, deserts, wetlands, rivers and streams, and coastal systems.
- Research themes involving wildlife management, endangered species, agricultural systems, pest control, forensics, and human and wildlife disease.
- Topics of local, regional, national, and international importance.
- Exceptional computational and analytical skills backed by the ability to communicate with both general and technical audiences.
Since joining in 2008, I have been responsible for publishing peer-reviewed scientific papers that fulfill the mission of the USGS and inform policy and management decisions made by other Department of Interior bureaus. My record of productivity with USGS is consistent with the overall focus of my career to date, where I have published 52 peer-reviewed manuscripts (plus additional under review or in press).
Science and Products
This data release includes the data from simulations used to illustrate the behavior of inbreeding rate estimators and Python source code ("analytical expressions", "computer simulations", and "empricial data set") that can be used to analyze these data.
Isolation by distance versus landscape resistance: Understanding dominant patterns of genetic structure in Northern Spotted Owls (Strix occidentalis caurina)
Landscape genetics investigations examine how the availability and configuration of habitat influence genetic structure of plants and animals. We used landscape genetics to evaluate the role that forest connectivity plays in determining genetic structure of the federally-threatened Northern Spotted Owl (Strix occidentalis caurina) using genotypes...Miller, Mark P.; Davis, Raymond J.; Forsman, Eric D.; Mullins, Thomas D.; Haig, Susan M.
Variation in inbreeding rates across the range of Northern Spotted Owls (Strix occidentalis caurina): Insights from over 30 years of monitoring data
Inbreeding has been difficult to quantify in wild populations because of incomplete parentage information. We applied and extended a recently developed framework for addressing this problem to infer inbreeding rates in Northern Spotted Owls (Strix occidentalis caurina) across the Pacific Northwest, USA. Using pedigrees from 14,187 Northern Spotted...Miller, Mark P.; Haig, Susan M.; Forsman, Eric D.; Anthony, Robert G.; Diller, Lowell; Dugger, Katie M.; Franklin, Alan B.; Fleming, Tracy L.; Gremel, Scott; Lesmeister, Damon B.; Higley, Mark; Herter, Dale R.; Sovern, Stan G
A simplified field protocol for genetic sampling of birds using buccal swabs
DNA sampling is an essential prerequisite for conducting population genetic studies. For many years, blood sampling has been the preferred method for obtaining DNA in birds because of their nucleated red blood cells. Nonetheless, use of buccal swabs has been gaining favor because they are less invasive yet still yield adequate amounts of DNA for...Vilstrup, Julia T.; Mullins, Thomas D.; Miller, Mark P.; McDearman, Will; Walters, Jeffrey R.; Haig, Susan M.
Genetic differentiation and inferred dynamics of a hybrid zone between Northern Spotted Owls (Strix occidentalis caurina) and California Spotted Owls (S. o. occidentalis) in northern California
Genetic differentiation among Spotted Owl (Strix occidentalis) subspecies has been established in prior studies. These investigations also provided evidence for introgression and hybridization among taxa but were limited by a lack of samples from geographic regions where subspecies came into close contact. We analyzed new sets of samples from...Miller, Mark P.; Mullins, Thomas D.; Forsman, Eric D.; Haig, Susan M.
Estimating inbreeding rates in natural populations: Addressing the problem of incomplete pedigrees
Understanding and estimating inbreeding is essential for managing threatened and endangered wildlife populations. However, determination of inbreeding rates in natural populations is confounded by incomplete parentage information. We present an approach for quantifying inbreeding rates for populations with incomplete parentage information. The...Miller, Mark P.; Haig, Susan M.; Ballou, Jonathan D.; Steel, E. Ashley
Simulated data supporting inbreeding rate estimates from incomplete pedigrees
This data release includes:(1) The data from simulations used to illustrate the behavior of inbreeding rate estimators. Estimating inbreeding rates is particularly difficult for natural populations because parentage information for many individuals may be incomplete. Our analyses illustrate the behavior of a newly-described inbreeding rate...Miller, Mark P.
Ancient DNA reveals substantial genetic diversity in the California Condor (Gymnogyps californianus) prior to a population bottleneck
Critically endangered species that have undergone severe population bottlenecks often have little remaining genetic variation, making it difficult to reconstruct population histories to apply in reintroduction and recovery strategies. By using ancient DNA techniques, it is possible to combine genetic evidence from the historical population with...D'Elia, Jesse; Haig, Susan M.; Mullins, Thomas D.; Miller, Mark P.
Genetic diversity and population structure in the threatened Oregon silverspot butterfly (Speyeria zerene hippolyta) in western Oregon and northwestern California— Implications for future translocations and the establishment of new populations
Executive SummaryWe present results of population genetic analyses performed on Oregon silverspot butterflies (OSB; Speyeria zerene hippolyta) in western Oregon and northwestern California. We used DNA sequences from a 561-base pair region of the mitochondrial cytochrome oxidase subunit I (COI) gene for a dataset comprised of 112 S. z. hippolyta...Miller, Mark P.; Mullins, Thomas D.; Haig, Susan M.
U.S. Geological Survey science strategy for highly pathogenic avian influenza in wildlife and the environment (2016–2020)
IntroductionThrough the Science Strategy for Highly Pathogenic Avian Influenza (HPAI) in Wildlife and the Environment, the USGS will assess avian influenza (AI) dynamics in an ecological context to inform decisions made by resource managers and policymakers from the local to national level. Through collection of unbiased scientific information on...Harris, M. Camille; Pearce, John M.; Prosser, Diann J.; White, C. LeAnn; Miles, A. Keith; Sleeman, Jonathan M.; Brand, Christopher J.; Cronin, James P.; De La Cruz, Susan; Densmore, Christine L.; Doyle, Thomas W.; Dusek, Robert J.; Fleskes, Joseph P.; Flint, Paul L.; Guala, Gerald F.; Hall, Jeffrey S.; Hubbard, Laura E.; Hunt, Randall J.; Ip, Hon S.; Katz, Rachel A.; Laurent, Kevin W.; Miller, Mark P.; Munn, Mark D.; Ramey, Andrew M.; Richards, Kevin D.; Russell, Robin E.; Stokdyk, Joel P.; Takekawa, John Y.; Walsh, Daniel P.
Breeding sites and winter site fidelity of Piping Plovers wintering in The Bahamas, a previously unknown major wintering area
Most of the known wintering areas of Piping Plovers (Charadrius melodus) are along the Atlantic and Gulf coasts of the United States and into Mexico, and in the Caribbean. However, 1066 threatened/endangered Piping Plovers were recently found wintering in The Bahamas, an area not previously known to be important for the species. Although...Gratto-Trevor, Cheri; Haig, Susan M.; Miller, Mark P.; Mullins, Thomas D.; Maddock, Sidney; Roche, Erin A.; Moore, Predensa
The conservation genetics juggling act: Integrating genetics and ecology, science and policy
The field of conservation genetics, when properly implemented, is a constant juggling act integrating molecular genetics, ecology, and demography with applied aspects concerning managing declining species or implementing conservation laws and policies. This young field has grown substantially since the 1980’s following development of the...Haig, Susan M.; Miller, Mark P.; Bellinger, Renee; Draheim, Hope M.; Mercer, Dacey; Mullins, Thomas D.
Genetic structure, diversity, and interisland dispersal in the endangered Mariana Common Moorhen (Gallinula chloropus guami)
The Mariana Common Moorhen (Gallinula chloropus guami) is a highly endangered taxon, with fewer than 300 individuals estimated to occur in the wild. The subspecies is believed to have undergone population declines attributable to loss of wetland habitats on its native islands in the Mariana Islands. We analyzed mitochondrial DNA (mtDNA)...Miller, Mark P.; Mullins, Thomas D.; Haig, Susan M.; Takano, Leilani L.; Garcia, Karla
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.
Federal researchers used landscape genetics to evaluate the role that forest connectivity plays in determining genetic connectivity for the federally-threatened northern spotted owl.
Population genetic studies are driven by DNA sampling, and blood sampling has historically been the preferred method for obtaining DNA.