Allen Lab

Our Research

Invasive Largemouth Bass research in South Africa

Hargrove_bass_SA This research is being conducted by John Hargrove (PhD student, Univ. of Florida) and Mike Allen in conjunction with Dr. Olaf Weyl and his lab members at the South African Institute for Aquatic Biology, based out of the Eastern Cape of South Africa ( Largemouth bass, Micropterus salmoides, were brought to South Africa at the beginning of the 20th century to promote novel angling opportunities. Since that time, largemouth bass have been transferred extensively throughout the country and presently occur in all major river catchments in southern South Africa. Largemouth bass are considered an alien invasive species in South Africa due to their potential negative impacts on native animal communities. Historical records indicate that many modern bass populations in South Africa are the descendants of only 45 fingerlings used for hatchery production. This research will investigate if the significant genetic bottleneck experienced by largemouth bass in South Africa has negatively impacted population levels of success. Specifically, we will compare profiles of genetic diversity and life history characteristics (age-and-growth and size-at-sexual maturity) from a series of South African impoundments with the same data collected from populations within their native range. The products of these research efforts will enhance our understanding of the role of genotypic and environmental influences on population success of invasive fish species.


NOAA RTR Program at UF

We are excited to collaborate with a wide range of faculty and NOAA Personnel on the Recruiting, Training, and Research Program! This presents great opportunities for graduate students interested in quantitative fisheries methods and stock assessment. For more information about the RTR program and associated workshops, please see:

Climate change impacts on Florida freshwater fisheries

We have worked with the Bipartisan Policy Institute to evaluate the expected impacts of global climate change on warmwater fisheries in the USA. We evaluated climate predictions and expected impacts to fish habitat (e.g., water availability, aquatic plants), fish life history (e.g., spawning temperatures and range changes), and potential management agency responses to mitigate climate change impacts to freshwater fisheries. Our work was part of a broader effort to understand climate change impacts on fishing and hunting in the USA. A summary of those efforts can be found at We cooperated with BASS on the study regarding freshwater fisheries. A summary of that effort with special emphasis on impacts to Florida is found below. Mark Rogers, Galen Kaufman, and Chris Horton (BASS) cooperated on this effort. Download the presentation at: GCC impacts to Florida

Predicting Effects of Restoration Efforts for Florida Lakes

We developed Ecopath models that could be used to predict how habitat manipulations (herbicide use, drawdowns and muck removals) would influence lake fish communities. This project is led by Dr. Mark Rogers with Allen as a Co-Principal Investigator, and funding was provided by the Florida Fish and Wildlife Conservation Commission. Final Report

Murray cod fishery sustainability

We are working with cooperators from the Department of Primary Industries, Fisheries Victoria, Australia to develop sustainable harvest policies and stocking strategies for Murray cod and other native fishes of Australia. The Murray cod is of considerable cultural, environmental, economic and recreational importance in southeastern Australia. The species conservation status is classed as threatened in several jurisdictions, and the sustainability of the recreational fishery is of concern.  As such, the we are collaborating with the Victoria fisheries scientists to develop research and monitoring programs for this species.  Our approaches include simulation studies, analysis of historical data, and tagging studies. Our DPI cooperators include Paul Brown, Taylor Hunt, and John Douglas.


Evaluating factors influencing electrofishing catchability

MS Student - Matt Hansleben

Electrofishing is a widely used sampling method for monitoring programs. Our goal is to evaluate how electrofishing catchablilty (i.e., the fraction of the fish stock caught with a given amount of effort) varies between lakes with different aquatic macrophytes communities and other environmental variables.

This research will help FWC managers more accurately interpret their electrofishing catch per unit effort data from long-term
monitoring. Matt Hangsleben is a MS student working on this project, which is funded by the Florida Fish and Wildlife Conservation Commission.


Spawning microhabitats for American shad at the St. Johns River, Florida: Potential for use in establishing MFLs

American shad stocks along the Atlantic coast have displayed a slower than anticipated trend toward recovery despite large reductions in commercial harvest throughout their range. This may indicate that the quality and availability of riverine spawning habitat also plays a central role in American shad stock recovery. Presently, the St. Johns River is relatively un-regulated by dams and water control structures, but as the human populations continue to grow in Florida, the water within the St. Johns River basin is becoming increasingly valuable as a drinking water source. Diversion of some portion of flow in this system to Orlando is imminent.

We are using acoustic telemetry technology to track temporal and spatial components of annual American shad spawning migrations in the St. Johns River. As we identify key spawning locations, and characteristics of these locations, this information can be evaluated by state water management agencies. Ultimately, we wish to inform water use regulations such that human needs can be met in a responsible manner that continue to foster American shad stock recovery as well as the ecological integrity of the basin as a whole.

This study is funded by the St. Johns River Water Management District and the Florida Fish and Wildlife Conservation Commission.


Life history, population dynamics, and fishery management of the Golden Tilefish, Lopholatilus chamaeleonticeps, from the southeast Atlantic and Gulf of Mexico

Linda Lombardi-Carlson
Co-Chaired by Mike Allen and Bill Pine

My dissertation will focus on the description of life history characteristics and population modeling of golden tilefish from the Gulf of Mexico. The golden tilefish, Lopholatilus chamaeleonticeps, is a deep-water demersal fish found in the Atlantic from Nova Scotia through the Gulf of Mexico. This fish has a unique burrowing behavior and habitat preference, preferring malleable but stable sediments to form burrows, a mixture of clay and silt. My first objective will be to validate the timing of band deposition in sagittal otoliths using innovative radiochemical dating.  By verifying the timing of band deposition through the use of the natural decay of lead (210Pb) and radium (226Ra), a confirmation of the longevity of golden tilefish will be provided.  My second objective will be to describe the age, growth and reproduction; currently unknown for golden tilefish from the Gulf of Mexico.  Spatial comparisons of life history and population dynamics will also be conducted between the Gulf of Mexico and South Atlantic golden tilefish stocks.  I will also investigate the reproductive strategy of this species in hopes to provide evidence to support of the presence of hermaphroditism.  This research is essential for in the development stock-assessment models to make informed fishery management regulations. 

Currently, the status of the golden tilefish in the Gulf of Mexico is unknown and in South Atlantic golden tilefish has been undergoing overfishing since the 1980s. My final objective will be to create a population model of golden tilefish to determine if current harvest levels are sustainable.  Finally, the implications of management regulations on golden tilefish populations will be investigated.


Dissecting Mortality Components for Recreational Fisheries with High Rates of Released Fish

Ph.D. Student Janice Kerns

The purpose of this study is to assess the components of fishing mortality for fish populations with high rates of angler release and to evaluate the potential impact of all sources of fishing mortality on largemouth bass populations. To understand the general overall assumptions of size specific mortality our first objective is to evaluate directed fishing mortality due to harvest for largemouth bass in a large number of Florida lakes. Our second objective is to measure the components of total mortality including a) natural mortality, b) total fishing mortality including harvest, catch-and-release (discard deaths) and tournaments (discard deaths) components in two large lake systems. The second object will then estimate the specific portions of mortality and serve as an example for designing new methodologies for recreational fisheries where directed harvest is only one component of the fishing-related mortality. This study is funded by the Florida Fish and Wildlife Conservation Commission, and they are cooperating on all phases of the project.


A Largemouth Bass Model for the Kissimmee Chain of Lakes (KCOL)

This project seeks to use historical fisheries data from the KCOL to evaluate how changes in water level regimes and aquatic plant abundance and species composition would influence largemouth bass fisheries. The model includes a wide range of FWC and UF sampling efforts at the KCOL, and should provide resource managers with a tool that can be used to address policy options at this important Florida ecosystem. Patrick O'Rouke is an MS student working on this project, which is funded by the South Florida Water Management District.


Assessing Effects of Gizzard Shad Removal on Nutrient Cycling and Gizzard Shad Population Dynamics

Reversing the effects of eutrophication can be challenging and requires the reduction of external nutrient sources and internal nutrient loading. Omnivorous gizzard shad Dorosoma cepedianum can facilitate nutrient loading from the sediments as a consequence of their foraging activity at the sediment-water interface and subsequent excretion of nutrients in the water column.  This feeding activity may contribute considerably to the release of nutrients from the sediments in eutrophic Florida lakes.

Biomanipulation via removal of gizzard shad has been proposed as a management strategy for improving water clarity by reducing internal nutrient loading from the sediments.  Preliminary studies at Lake Denham, Florida, suggested that strong biomass reductions of gizzard shad using haul seines may reduce phytoplankton biomass.  Recently, biomanipulations have been attempted on several lakes of the Harris Chain of Lakes, Florida using gill nets, but the results of these efforts have yet to be experimentally evaluated.  Understanding how fish life history metrics respond to density reductions is critical to understanding the potential impact of biomanipulation on lake food webs.  We used a whole-lake gizzard shad reduction experiment (i.e., a biomanipulation) to 1) assess impacts of a commercial gizzard shad removal on their population dynamics (i.e., recruitment, growth, mortality), 2) measure diet contents of gizzard shad to indicate mode of feeding, 3) explore the potential for gizzard shad removal to influence lake water quality, and 4) evaluate the potential for bycatch impacts on black crappie Pomoxis nigromaculatus fisheries.  Matt Catalano is the Ph.D. candidate in charge of this project, which is funded by the SJRWMD, FWC, and SFWMD.

Final Report 2008

Final Report 2009


Size Selectivity of an Otter Trawl for Black Crappie at Five Florida Lakes

Otter trawls are a commonly employed assessment gear for black crappie in Florida. However, the selective properties of the gear have yet been defined. Our goal is to estimate the size selective properties of the bottom trawl and evaluate its utility for use as an assessment gear for crappie in Florida lakes. Data included in analysis occurs from five lakes with at least 5 and up to 25 years of fishery independent data. Cooperators include the Florida Fish and Wildlife Conservation Commission. 


Fish Community Composition in Tussock Forming Aquatic Macrophytes at Two South Florida Lakes

Understanding the mechanisms of how and why fish utilize aquatic macrophyte habitats under varying environmental conditions is important for management.  Tussocks negatively influence dissolved oxygen concentrations and influence the suitability of habitat for fish.  The Florida Fish and Wildlife Conservation Commission has provided funding for us to research tussocks and the impact they have on dissolved oxygen concentration and fish community at Lakes Kissimmee and Istokpoga.  The objectives of this project are to: 1) evaluate the temporal patterns in hypoxia with emergent aquatic macrophyte species and biomass levels, and 2) assess how fish community metrics (i.e., density, biomass, richness, and diversity) varies with emergent aquatic macrophyte species and biomass levels. 
Images: Tussock Habitat photo1, photo2, and Kissimmee Site Map