Schaefer Lab

Evolutionary Ecology of Fishes
The University of Southern Mississippi


118 College Dr. #5018
Hattiesburg, MS 39406


USM Department of Biological Sciences

Evolutionary Ecology, Physiology and Ichthyology


Research in my lab focuses on the evolutionary ecology, physiology and conservation of freshwater fishes. Much of the research utilizes species in the Fundulus notatus species complex (F. notatus, F. olivaceus and F. euryzonus) to address basic questions in evolutionary ecology. The species in this complex are closely related and known to hybridize in numerous replicate hybrid zones throughout their broadly overlapping ranges. Within areas of coexistence, the species usually segregate along the river continuum with areas of hybridization and coexistence focused on confluences. Interestingly, in some areas of the distribution, typical up and downstream distributions may be reversed. Thus, hybrid zones in this system are replicated and replicate hybrid zones vary in the degree of genetic divergence and ecology of the parental species.

While hybrid zones have long been of interest to evolutionary biologists (“natural laboratories of evolution”), their ultimate role in the evolutionary process is not clear. Hybridization is increasingly recognized as common, and can be either detrimental through erosion of existing genetic structure, or beneficial through the formation of novel allele combinations (adaptive hybridization or hybrid speciation). The factors that differentiate these disparate outcomes is still debated and one of the more pressing questions in evolutionary biology.

Courses Taught


    Ichthyology (BSC 414/514L)

  • Taught fall semester of even years
  • Objectives
    • Recognize all major taxonomic groups of fishes
    • Ability to identify freshwater fishes of the Southeastern US
    • General knowledge of the science of ichthyology
    • Understanding of basic anatomy and physiology of fishes
    • Understanding of the evolution, systematics, and zoogeography of major groups of fishes
    • Appreciation of current issues concerning conservation and fisheries applications
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    Population and Community Ecology (BSC 441/541L)

  • Taught fall semester of odd years
  • Objectives
    • Understanding of the mechanisms regulating the abundance, distribution and demographics of populations
    • Understanding of the mechanisms regulating the dynamics, composition and organization of groups of species (communities)
    • Introduction to some of the tools necessary for the design of population/community ecology experiments. These tools include sampling procedures, data collection, data analysis and hypothesis testing.
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    Environmental Physiology (BSC 452/552)

  • Taught spring semester of odd years
  • Objectives
    • Udnderstand the nature and mechanisms for physiological adaptation in an environmental context
    • An introduction to physiology and the issues of size and scale
    • Understanding of specific adaptations to environmental extremes
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    Multivariate Applications in Ecology (BSC 747)

  • Taught spring semester of even years
  • Objectives
    • Know the proper use, data assumptions and method of reporting results
    • Know how to interpret analyses presented in the literature and apply that interpretation to the research question being asked
    • Be able to compile a dataset, format it appropriately, analyze it in R and extract the components necessary for reporting
  • Syllabus (Course material in Canvas)
  • Schedule and Course Materials (Course material in Canvas)

Recent Publications



  • Schmidt, B.V., and J. Schaefer. 2017. Ecological and landscape effects on genetic distance in an assemblage of headwater fishes. Ecology of Freshwater Fish     
  • Schmidt, B. V. and J.F. Schaefer. 2018. Comparative genetic isolation patterns for multiple headwater fishes in three geographic regions. Journal of Fish Biology      .
  • Clark, S. R., W.T. Slack, B. R. Kreiser, J. F. Schaefer, and M. A. Dugo. 2018. Stability, persistence and habitat associations of the Pearl Darter Percina aurora in the Pascagoula River System, southeastern USA. Endangered Species Research 36: 99-109      .
  • Schaefer, J., B. Kreiser, S. Flanagan. 2018. Population genomics of Fundulus grandis exposed to oil from Deepwater Horizon. Journal of Experimental Marine Biology and Ecology 509, 82–90.      .


  • Clark, S.R., B.R. Kreiser, J. F. Schaefer and L.K. Stewart. 2019. Scale dependence of sex‐specific movement in a small‐bodied stream fish. Freshwater Biology 64 (7):1342-1353.     
  • Duvernell, D.D., E. Westhafer and J. F. Schaefer. 2019. Late Pleistocene range expansion of North American topminnows accompanied by admixture and introgression. Journal of Biogeography      
  • Hubbell, J.P., J. Schaefer, M. Warren and K. Sterling. 2020. Modeling patterns of coexistence of three congeneric headwater fishes. Freshwater Biology      .
  • Cashner, R., J. Schaefer, A. Echelle, F. Galvez, and M. Ghedotti. 2020. Fundulidae: Topminnows. In: Freshwater Fishes of North America: Volume 2: Characidae to Poeciliidae. Ed. by M Warren and B Burr. Vol. 2. Baltimore, Maryland: Johns Hopkins University Press      
  • Hubbell, J.P., Melvin Warren, J. Schaefer, K. Sterling and P. J. Flood. 2020. Fragmentation alters ecological gradients and headwater fish assemblage composition relative to land use in a dendritic river systemCanadian Journal of Fisheries and Aquatic Sciences      .


  • Hubble, J. P., J. F. Schaefer and B. Kreiser. 2022. The Influence of Habitat Characteristics on the Occupancy and Dispersal of Two Headwater Fishes in a Dendritic Network. Ecosphere     
  • Stearman, L. W., and J. F. Schaefer. 2022. Long‐term minnow community trait shifts and metacommunity dynamics in a geomorphically unstable river. Ecology of Freshwater Fishes     
  • Hubbell, J. P., and J. F. Schaefer. 2022. Confluences and land cover as agents of change: habitat change modifies the movement and assemblage stability of headwater fishes. Urban Ecosyst     
  • Matamoros, W. A., S. Fenoglio, S. R. Clark, and J. F. Schaefer. 2021. Ontogenetic shift in the diet of Dajaus monticola (Mugiliformes: Mugilidae) with comments in the recruitment of young individuals in the Honduran Caribbean coast. Neotropical Biodiversity     7:546-553.
  • Kreiser, B. R., S. R. Clark, and J. F. Schaefer. 2021. Microsatellite Loci for the Threatened Pearl Darter and Cross Amplification in Channel and Coal Darters. Journal of Fish and Wildlife Management 12:257-262.     
  • Hubbell, J., L. Stearman, and J. Schaefer. 2021. Updated status of Bayou darter, a narrowly ranged endemic in a geomorphically active watershed. Endang. Species. Res. 44:137-148.    


  • Stearman, L.W. and J.F. Schaefer. 2023. Fluvial geomorphic evolution and stream fish community trajectories in the Bayou Pierre, Mississippi Freshwater Biology 70: 1051-1063.      
  • Duvernell, D. D., N. S. Remex, J. T. Miller and J. F. Schaefer. 2023. Ecology and Evolution. Variable rates of hybridization among contact zones between a pair of topminnow species, Fundulus notatus and F. olivaceus.     

Ichthyological Collection


The ichthyological collections at USM contain over 85,000 cataloged lots and support a variety of research and education needs. The collection is split among the Hattiesburg (primarily freshwater) and Gulf Coast Research Lab (GCRL; primarily estuarine and marine) campuses. The majority of the freshwater collection was collected and cataloged by Dr. Stephen T. Ross and his students from 1974 until 2004. By 1998, the collection contained a total of 20,325 lots and a large uncurated backlog from Black Creek and Horn Island, as well as larval collections from a variety of sources. At that time, Dr. Ross and Dr. Stuart G. Poss (former curator at GCRL) received Nation al Science Foundation (NSF) funding to process the backlog of material and improve the overall curation of the collections. The collection was improved by: 1) cataloging backlogged material into both USM collections, 2) installing new shelving and storage infrastructure, and 3) transfer lots from 45% isopropyl to 70% ethanol at Hattiesburg. By the end of the project in 2001, a total of 7,200 new lots had been cataloged and the entire collection is now stored in 70% ethanol.

The collection continued to grow under the direction of Dr. Ross until his retirement in the spring of 2004 at which time the collection held approximately 28,000 lots. Since then, the collection has roughly doubled in size (currently ~53,000). Additional NSF funds (2007 award to myself and Sara LeCroy at GCRL) supported the purchase of compact shelving, complete georeferencing of all sites, and relabeling of older lots. In 2013 the collection (and USM Herbarium) was relocated to the Lake Thoreau Environmental Center.




PhD Students

  • Paul Mickle (2010)
    • Mississippi State University
  • Wilfredo Matamoros (2010)
    • Universidad de Ciencias y Artes de Chiapas
  • Scott Clark (2016)
    • U.S. Fish and Wildlife Service
  • Bjorn Schmidt (2016)
    • Texas A&M Commerce, Department of Biology
  • Josh Hubbell (2020)
    • U.S. Geological Survey
  • Loren Stearman (2023)
    • Postdoctoral Researcher, University of Southern Mississippi
  • Langston Haden (current)
  • River Watson (current)

Postdoctoral Researchers

  • Nate Franssen
    • U. S. Fish and Wildlife Service
  • Wilfredo Matamoros
    • Universidad de Ciencias y Artes de Chiapas
  • Paul Mickle
    • Mississippi State University