riverscape community genomics

comparative population genomics of stream fishes

Our ancestors were more likely to have kids with people nearby, e.g., from the same country/region. This resulted in people being more closely related (on average) to their compatriots, which means that today, we can actually infer the nationalities of our ancestors based on the DNA we carry. Many folks do not realize that other organisms, like fish, also have 'countries.' (Biologists call them populations.)

But we are typically unaware of these 'countries' because other animals do not make maps or express their regional differences in a way we readily perceive. (Imagine fish with accents.) If we remain ignorant of these borders, then, at best, our management strategies will be ineffective and, at worst, detrimental because fish from different places may have particular adaptations to their unique environments.

Therefore, to preserve the rich diversity across these 'countries' within a species, we must make maps to help guide conservation and management. We rely on information gathered from DNA samples collected across a species range to construct these maps. (Like 23andMe for fish!)

Check out the tabs below and my publications page for more details, and see this Molecular Ecology article.
But you might be thinking, "aren't many species out there, and wouldn't that take a lot of time and resources to make all those maps?"

Exactly! This project aims to understand what shapes fish countries by studying the maps of dozens of species along with multitudes of other data and approaches.

Suppose we can understand and model these general principles. In that case, we can make predictions about what maps for other species look like—even when we don't have any genetic data for them—and we can forecast how the countries might change in the future, for example, under various climate change scenarios.
Preliminary results indicate different species show variability in how their genetic variation is structured across the riverscape, likely due to differences in population histories and connectivity via gene flow. Exploratory models suggest this pattern is primarily explained by differences in species' ecological and life-history traits and not necessarily morphological features, such as body size.
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  • landscape genomics
    of white-tailed deer

    applying genomics to epidemiology

    White-tailed deer are one of North America's most recreationally valuable species and are prized for their lean and healthy meat. Despite the widespread extirpation of deer populations across the U.S. in the early twentieth century, subsequent management efforts helped deer rebound.

    But now, populations are increasingly threatened by a fatal neurodegenerative disease known as chronic wasting disease (CWD; a prion disease similar to 'mad cow'). If we do not respond quickly and in earnest to the spread of this disease, then it may once again drive deer extirpation and have cascading effects on ecosystems, economies, and potentially human health.

    To contain and mitigate the effects of CWD, we need to be able to forecast how it will spread. I work in collaboration with the Arkansas Game and Fish Commission (AGFC) and Arkansas Conservation and Molecular Ecology Lab (ACaMEL) to develop genomic-based tools for studying generational patterns of deer movement across the Arkansas landscape because this can help us predict the most likely routes for the future spread of CWD. These forecasts will help us put containment efforts in the right places.

    Check out my publications page for more details, and see this AGFC Wildlife Magazine article.

    stream fish ecology

    exploring the factors that affect fish assemblage change in time and space



    As a master’s student at the University of Oklahoma, working alongside Bill Matthews, I led a project funded by a state wildlife grant that aimed to assess the diversity of fish species of greatest conservation need (SGCN) in the most speciose part of Oklahoma. This project resulted in rich data sets of fish species occurrence and environmental characteristics at over 160 stream/river reaches. These data are being used to address questions about how groups of fish, or assemblages, fluctuate in their composition across the riverscape and over time.
    The primary objective was first to identify high diversity areas and those that harbor high numbers of SGCN. Additional objectives have evolved, including 1) identifying major environmental drivers of fish assemblage structure; 2) comparing diversity and spatial dynamics among drainages; 3) comparing contemporary diversity to that from 40 years earlier and investigating the effect of spatial scale on estimating assemblage change; 4) identifying non-randomly associated species, inferring their likely causes, and exploring their stability through time.
    Headwater streams are critical for the maintenance of regional biodiversity. Although headwaters may be relatively depauperate of species at an individual location (alpha diversity), these streams have large species turnover among sites (beta diversity) and contribute significantly to overall drainage richness (gamma diversity). Furthermore, comparisons of change through time indicate the importance of spatial scale in estimating shifts in diversity and assemblage composition. While individual sites can differ dramatically through time due to stochasticity and fish movement, larger scales such as entire catchments remain more stable. Therefore, spatial scale is paramount to understanding and responding to change in the diversity of any organism.

    Check out my publications page for more details.

    migration
    of trans-himalayan fishes

    conservation genomics

    In partnership with the Arkansas Conservation and Molecular Ecology Lab, the National Research Center for Riverine and Lake Fisheries, the Ministry of Agriculture and Forests, and the Royal Government of Bhutan, I have had the pleasure of visiting the "Land of the Thunder Dragon" and making expeditions to its streams and rivers in search of culturally important fish such as the Golden Mahseer.

    The aim is to use genetics to understand how fish migrate among steep rivers that drain the Himalayas. This information is critical in the face of the increasing development of hydroelectric dams in India and Bhutan. Importantly, our work also aims to build the fisheries research capacity in Bhutan.

    conservation genomics
    of a threatened fish

    connectivity and adaptation

    In partnership with the Arkansas Conservation and Molecular Ecology Lab, Illinois Natural History Survey, Kansas Department of Wildlife & Parks, and US Fish & Wildlife Service I am studying the range-wide population genomics of the federally threatened Neosho Madtom.

    This project delves into the conservation of the Neosho Madtom, a threatened catfish species in the Neosho River system. Employing a population genomic approach, our study aims to understand the genetic diversity, population boundaries, connectivity, and adaptation of the Neosho Madtom. Through extensive field sampling and genetic analysis, we've identified distinct genetic populations, assessed their viability, and explored environmental influences on their dispersal. Our objectives also include determining demographic trends and testing for local adaptation to inform effective conservation strategies for this unique species.

    unique highland lineages
    of smallmouth bass

    distinct lineages of the interior highlands

    In collaboration with the Arkansas Conservation and Molecular Ecology Lab and Arkansas Game and Fish Commission, I am researching the regional population genetics and phylogeography of Smallmouth Bass.

    The study aims to determine distinct lineages of the species across the interior highlands, where these lineages occur geographically, and where these lineages may be mixing. This information will help inform black bass management and help maintain evolutionarily significant units (ESUs) of diversity in the Ozarks.

    fish diversity
    in a contaminated drainage

    Tar Creek Superfund site

    Two world wars required raw materials for ammunition provided by lead mines near Picher, OK. Unfortunately, groundwater was contaminated due to these operations and eventually turned the surface water of Tar Creek into an orange disaster.

    However, thanks to Robert Nairin and his team using environmental engineering to remediate parts of the watershed, the fish are returning to the once toxic waters. I sampled Tar Creek and surrounding areas while at the University of Oklahoma to assess re-establishment of fish populations. In parts of the watershed once utterly devoid of fish, the communities have recovered and harbor diversity similar to neighboring regions.

    See the related story published in Sooner Magazine:
    Fish Are Coming Back to Tar Creek

    Yes, that is me in the orange soup. No, I did not like it any more than the fish.