Research Interests

  • Population-level genetic variation in threatened species and species of management concern
  • Historical genetic variation (using museum DNA)
  • Relationships between genetic variation and fitness in individuals
  • Genetic aspects of behavioral ecology (inbreeding avoidance, extra-pair paternity)

Current Research

Seaside Sparrow & Marsh Rice Rat Response to the BP Oil Spill

Andrea Bonisoli Alquati, Post-doctoral Fellow (January 2015 – present)

Funding: Gulf of Mexico Research Initiative RFP IV
Collaborators: Phil Stouffer (co-PI; LSU AgCenter), GoMRI CWC Consortium, Stefan Woltmann (Austin Peay University), Christine Bergeon Burns (Indiana University)

AndreaBAThe Deepwater Horizon oil spill released a large amount of crude oil into the Gulf of Mexico, an event that could have an important and negative impact on coastal ecosystems. Andrea will focus on marsh bird and rat populations, using the Seaside Sparrow (Ammodramus maritimus) and the marsh rice rat (Oryzomys palustris) as model species to examine some potential effects of the oil spill. The Seaside Sparrow and the marsh rice rat are excellent marsh representatives because they spend all or most of their time in salt marsh, they are top-level consumers, and they are relatively abundant in the study area. Andrea will examine whether gene expression differs on oiled versus unoiled areas by targeting specific genes and using microarrays. Collaborative research includes an assessment of reproductive success, survival and stress hormones in sparrows and diet changes in rats and sparrows. The study area is nested within the ongoing sampling framework of our collaborators (Coastal Waters Consortium), and will include replication of unoiled and heavily oiled sites.

Mhc Variation and Mycoplasmal Upper Respiratory Tract Disease in Gopher Tortoises

Jean Elbers, PhD student (September 2011 – present)

Funding: Gilbert Fellowship
Collaborators: Rachel Wallace-Clostio (Louisiana State University)

The gopher tortoise, (Gopherus polyphemus), is a longleaf pine associated species that has experienced population declines and shows low levels of genetic diversity at microsatellite loci. Gopher tortoises are also susceptible to upper respiratory tract disease (URTD), which may decrease population viability and increase extinction risk. Jean is investigating the relationship between functional genetic variation and disease resistance in the gopher tortoise (Gopherus polyphemus). He will quantify genetic variation in several hundred immune genes and the major histocompatibility complex (Mhc), a genomic region in vertebrates that is closely related to disease resistance and immune response. He will relate observed Mhc variation to disease susceptibility to inform future management plans for gopher tortoises.

Response of marsh rice rats to the Deepwater Horizon oil spill

Anna Perez-Umphrey, PhD student (January 2016 – present)

Funding: Gulf of Mexico Research Institute RFP IV
Collaborators: Phil Stouffer (co-PI; LSU AgCenter), GoMRI CWC Consortium, Stefan Woltmann (Austin Peay University).

Marsh rice rats, (Oryzomys palustris), are top-level consumers and very common in coastal marshes, consequently they are excellent candidates to explore the effects of the Deepwater Horizon oil spill on terrestrial vertebrates. Anna will examine the relationship between genetic variation, susceptibility to hanta virus, and exposure to oil. She will also compare gene expression and estimates of population size between oiled and unoiled sites.

Genetic Structure of Bachman's Sparrows

Amie Settlecowski, M.Sc. student (August 2015 - present)

Funding: LSU and LSU Agcenter
Collaborators: Jeremy Brown (Louisiana State University), Jim Cox and James Tucker (Tall Timbers Research Station), Robb Brumfield (Louisiana State University),

SettlecowskiBachman’s Sparrow (Peucaea aestivalis) is a species-at-risk that has declined from fire suppression, timber harvesting, and fragmentation of the open longleaf pine savannahs that it occupies. Information on genetic population structure in Bachman’s sparrows is important for effective management at both broad and fine scales. Morphological data and distribution maps suggest genetic structure; however, microsatellite data suggest that the species is panmictic. Historic samples and markers associated with functional loci may reveal important genetic structure associated with local adaptation and morphological subspecific designations. Amie will explore these issues for her MS degree.

Genetic Variation and Effective Population Size in Smalltooth Sawfish

Kelcee Smith, M.Sc. student (August 2014 - present)

Funding: LSU Agcenter
Collaborators: Bill Kelso (LSU AgCenter), John Carlson (NOAA), Kevin Feldheim (Field Museum), Nicole Phillips (University of Southern Mississippi)

SmithSmalltooth sawfish (Pristis pectinata) are critically endangered yet information on population size is lacking despite its importance to population viability analyses and management strategies. Kelcee will examine genetic variation in historic and contemporary samples to estimate effective population size and to examine how genetic variation and structure may have changed over time. Smalltooth sawfish are unusual among fish in that historic samples are available from dried rostra, which have been kept as trophies: most fish are preserved in formalin, a chemical that crosslinks DNA and often makes it unusable for genetic analyses. Kelcee's work will contribute important information for conservation and may serve as a benchmark for other elasmobranchs for which historic DNA samples are unavailable.

Response of Seaside Sparrows to the Deepwater Horizon oil spill

Allison Snider, M.Sc. student (January 2016 - present)

Funding: Gulf of Mexico Research Institute RFP IV
Collaborators: Phil Stouffer (co-PI; LSU AgCenter), GoMRI CWC Consortium, Stefan Woltmann (Austin Peay University)

Seaside sparrows (Ammodramus maritimus) are the most common passserine found in coastal marshes and exposed to oil from the Deepwater Horizon oil spill. Feasting on a variety of insects and other invertebrates, the sparrows may have been affected by the oil spill through a loss or change in prey. Allison will examine sparrow diet on oiled and unoiled sites by sequencing insect remains in fecal, gut, and ligature samples in adult and young sparrows.

Genetic Structure of New Zealand Fernbirds

Sabrina Taylor

Funding: LSU Agcenter
Collaborators: Bruce Robertson (University of Otago), Colin O'Donnell (NZ Department of Conservation)

Fernbirds (Bowdleria punctata) are a species endemic to New Zealand frequently found in wetland areas. There are currently five described subspecies, several island populations, and considerable habitat loss and fragmentation. As such, there is considerable potential for genetic structure as a consequence of long-term reproductive isolation as well as more recent habitat fragmentation. I am collecting blood samples from the five subspecies as well as populations in the Te Anau Basin to examine whether subspecific designations have a genetic basis and whether fine-scale population differentiation exists as a consequence of habitat loss and isolation.

Former lab members


Dr. Christine Bergeon Burns
Former Postdoc, Seaside Sparrows and Marsh Rice Rats
Director, CISAB Lab
Indiana University
Jordan Hall 348
1001 E Third St, Bloomington IN 47405
812- 856-1139
cbergeon at



Dr. Kristin Brzeski
Former PhD student, Red Wolf immunogenetics
Postdoctoral Fellow, Princeton University








Blain Cerame
Former MS student, Bachman's Sparrow population structure
SWCA Environmental Consultants






Robert Ford
Former MS student, Mottled Duck population structure & hybridization with Mallards
Michigan Department of Natural Resources








Dr. Stefan Woltmann
Former Postdoc, Seaside Sparrows and Marsh Rice Rats
Assistant Professor
Dept. of Biology
Austin Peay State University
Clarksville, TN 37044
woltmanns at