Research

In examining the effects of environmental change, our research focuses on three types of questions:

We use a variety of approaches to answer these questions including standardized sampling across regional scales and along disturbance gradients, collecting trait data from natural history collections, and testing mechanisms in experiments. Overall, we are interested in how ecological understanding can contribute to the conservation of aquatic ecosystems and the sustainable management of fisheries.

Current Research


By some measures, freshwater biodiversity is declining at rates at least double its terrestrial and marine counterparts. Our research examines how multiple and interacting environmental stressors contribute to changes in freshwater fish populations and communities across spatial scales and over time. We use ecological frameworks to contribute to management and conservation decision making. Most of our work focuses on fish communities in the Laurentian Great Lakes Basin, but we also collaborate on research elsewhere, including the Guiana Shield of South America.

Research in the lab is organized into three primary topics. First, we use historical long-term and large-scale data sets to examine changes in fish populations and communities. This includes projects examining both changes related to environmental degradation and responses to restoration. Second, work in the lab has focused on understanding the mechanisms which control the vulnerability of fish to climate change. Third, we develop tools to use species traits to understand patterns of ecological change. Here are more details about the different aspects of our work:

Leveraging historical data to examine how changes in biological communities can inform predictions and improve resilience

CHANGES is an interdisciplinary project , initially funded by the Michigan Institute for Data Sciences, and in collaboration with Andrea Thomer (School of Information), Hernán López-Fernández and Randy Singer (Ecology and Evolutionary Biology and Museum of Zoology), Justin Schell (Library, Shapiro Design Lab) and Kevin Wehrly (Institute for Fisheries Research (IFR), a cooperative with the Michigan Department of Natural Resources (MDNR)). One aim of the project is investigating whether forecasts of the impacts of climate change on species distributions can be improved by using historical ecological data to examine patterns through time rather than solely using spatial correlations. To do this we are using more than a century of historical lake survey data.  

We have developed methods for digitizing, curating and analyzing heterogeneous survey data. We have developed transcription workflows to digitize historical data using Zooniverse, a community science crowdsourcing platform. The dataset we have assembled includes lake-scale data on fish community composition, population abundance, fish growth rates, plant and invertebrate resources, habitat structure, shoreline development and water quality, which can be paired with specimens from the UM Museum of Zoology. Katelyn King, postdoctoral research fellow, used these data to test the validity of space-time substitutions in predicting the impacts of climate change impacts on the distribution and abundance of Largemouth Bass. She developed and hindcasted SDMs to historical climate conditions. Examining mismatches between hindcasts and long-term data tests the validity of models and allows refining them by examining ecological patterns through time. 

Elise Grabda, MSc thesis student, has used historical data from this project to examine the factors controlling changes in Bluegill growth over time. We are also starting an NSF funded project to collect growth data for non-game fish species from museum specimens and examine the environmental factors and species traits which control changes in growth.

Informing and evaluating Great Lakes fish habitat restoration

We are involved in several other projects using long-term and historical data to examine changes in fish populations and communities. As part of the Great Lakes Coregonine Restoration Framework, Karen Alofs and Cory Brant (USGS Great Lakes Science Center) co-lead a science team which is developed a methodology for examining differences in historical and contemporary habitat use by coregonine fishes which includes important forage species, like cisco and bloater, and commercial fish species, like whitefish. Postdoctoral research fellow, Katelyn King, is developing models under using this methodology. This work will be used to inform restoration priorities across the Great Lakes Basin.

In collaboration with the Friends of the Rouge, Olivia Williams, MSc thesis student, is examining changes in fish communities throughout the Rouge watershed over several decades and following habitat restoration projects. The Rouge River watershed covers a large portion of Southeastern Michigan and runs through the City of Detroit. The watershed is a Great Lakes ‘Area of Concern’ and has been designated with a series of ‘Beneficial Use Impairments’ that recognize the degradation of ecosystems services that they provide to human communities. This work will help to assess the impacts of prior restoration on fish populations and prioritize future projects and monitoring efforts.

With funding through the Cooperative Institute for Great Lakes Research (CIGLR), we are working with the NOAA Restoration Center to understand how spatial benchmarks can be used in informing and evaluating Great Lakes shoreline restoration projects. Andy Miller, postdoctoral research fellow, has built species distribution models to understand the drivers of habitat use for fish species which are common restoration targets.

Investigating the mechanisms controlling the vulnerability of fish to climate change

Temperature controls many biological rates, processes, and patterns from biochemical reactions and metabolism to species distributions and ecosystem productivity-- because of this the impacts of climate change on biodiversity are expected to be profound. Recent calls have emphasized the need to move beyond correlation-based predictions (from SDMs) to understanding and incorporating mechanisms into predictions of the impacts of climate change. Evidence suggests that both sensitivity and adaptive capacity can vary significantly among populations across a species range, but we have a poor understanding of how this variation will contribute to individual fitness and population viability in the context of climate change. 

Our work on this topic, thus far focuses on Walleye (Sander vitreus), a cool-water adapted fish species which, in recent decades, has declined in northern temperate lakes with climate warming. Scott Jackson, PhD student and MI Sea Grant Fellow, is experimentally examining how measures of sensitivity (gene expression, metabolic rates, and temperature tolerance) change with differences in acclimation, rearing temperatures, and genetic backgrounds. 

Using species traits to understand patterns of ecological change and the impacts of invasions

Changes in biological diversity often indicate the impact of environmental stressors on ecosystem function and ecosystem services. Examining changes in functional diversity, measured through the diversity of species traits (e.g., habitat use, trophic interactions and life history), can reveal more information about the resilience of ecosystems and the mechanisms controlling ecological change than comparisons of species composition (e.g. species richness or the number of species). In recent collaborations, we have examined differences in functional diversity among lake fish communities across bioregions and along climate gradients (Lamothe et al. 2018) and within versus outside of protected areas (Lamothe et al. 2019). Cameron Leitz, MSc Thesis Student, has examined how traits predict the success of invasive species in lake and stream ecosystems in the Great Lakes Basin.

Fish morphological diversity (e.g., variation in body, head and fin shape) has been used as a proxy of functional diversity as it is correlated with swimming and feeding mechanics, and consequently both diet and habitat use. Studying fish morphology allows us to use natural history collections and field samples to examine functional changes both within and among species. We have several projects which are investigating changes in fish morphological diversity in relation to environmental change. As an NSF Postdoctoral Research Fellow, Kelsey Lucas, examined functional changes in morphology in relation to lake shoreline conditions. 

In collaboration with Hernán López-Fernández, from Ecology and Evolutionary Biology, and Aline Cotel, from Civil and Environmental Engineering we are also examining how changes in habitat conditions due to the impacts of goldmining are reflected in the morphological and functional diversity of stream fish communities in the Upper Mazaruni River, on the Guiana Shield in northern South America. We have previously found that highly endemic and poorly understood fish communities on the Guiana Shield are threatened by increasing gold mining (Alofs et al. 2014, Diversity & Distributions).

Previous Research

Resilience of lake fish communities in a changing climate

Temperature acts as a filter that prevents warmwater-adapted species, like Smallmouth Bass, from establishing self-sustaining populations in northern-latitude lakes by limiting the length of the growing season and the overwinter survival of young-of-the-year. Climate change is expected to extend the suitable thermal habitat conditions for cool and warmwater-adapted fish and create more stressful conditions for coldwater-adapted fish. We have used data from the Ontario Ministry of Natural Resources and Forestry  and the Royal Ontario Museum, to show that the northern range limit of cool and warmwater sportfishes has shifted northward by a mean of nearly half a degree latitude over ~ 30 years (Alofs et al. 2014, Diversity & Distributions). In agreement with life history and invasion theory, our work shows faster range expansions in species with greater dispersal ability and higher reproductive rates. In contrast to predatory sportfishes, cool- and warmwater prey fishes have not shifted northward as expected. Instead, the range limit of many of these species has contracted southward. These contractions may be the result of range expansions by predatory sportfishes. By developing a method for predicting the vulnerability of species to climate-induced species introductions, we found smaller bodied prey fishes are more likely to go extinct in lakes where predatory fishes have been introduced (Alofs and Jackson 2015, Proc. R. Soc B). This work suggests that the importance of biotic interactions on species distributions in changing climates is underestimated. 

Investigating biotic resistance to inform invasive species management

The concept of biotic resistance suggests that species introduced outside of their historical range limits may be less likely to establish in more diverse communities. Overlap with resident species in resource requirements (niche overlap) should prevent introduced species from establishing. Biotic resistance and mechanisms controlling community invasibility have most often been investigated in terrestrial systems. In  meta-analysis, we found that biotic resistance in freshwater systems seems to be controlled more by predation than by competition and that biotic resistance is significantly stronger in lentic than lotic habitats (Alofs & Jackson 2014, Ecology). We also tested the influence of biotic resistance on the establishment of predatory fishes which have expanded their northern range limits (Alofs & Jackson 2015, Global Change Biology). We found that, across a regional scale, establishment was primarily determined by abiotic factors (e.g. temperature and lake size). Controlling for abiotic factors, however, we found Bass are less likely to establish in lakes that already contain other top predators. 

Native diversity, habitat loss and habitat fragmentation  

Maximizing landscape connectivity to minimize the negative effects of habitat fragmentation on native biodiversity may also facilitate the spread of invasive species. However, few studies have empirically tested the effects of fragmentation on the spread of invasive species. Woody plant encroachment, a change occurring in savannas across the globe, leads to habitat loss and fragmentation for herbaceous plant communities. In central Texas, I demonstrated that with woody plant encroachment an invasive grass occurs less frequently in more fragmented landscapes (Alofs & Fowler 2010, Journal of Applied Ecology). I analysed a temporal series of aerial photographs taken as woody plant encroachment proceeded over ~ 60 years and found that present patterns of native diversity are more strongly related to past than present habitat distribution (evidence of extinction debt). Further, in this system, native species richness declines with habitat loss and fragmentation and the effects of the former are stronger and occur more quickly than those of the latter (Alofs et al. 2014, Plant Ecology). Theory suggests that less diverse communities may be more susceptible to invasions due to reduced competition and more resources or ‘niches’ being available to invading species (‘biotic resistance’). But the effects of realistic and observed species losses on community invasibility are rarely tested. I experimentally demonstrated that habitat loss and fragmentation indirectly promote invasion through their negative effects on local species richness (Alofs & Fowler 2013, Ecology). Overall, as woody plant encroachment proceeds, fragmentation reduces the likelihood of an invasive grass spreading between patches. However, in the event that seed spreads to a new location, reduced native species richness facilitates establishment of the invasive grass.