Effective conservation management relies on robust understanding of a wide breadth of topics, including species’ life history, vital rates, population structure & connectivity, habitat use, and threats. The fields of population genetics and ecology have long played integral roles in ascertaining these key parameters, and recent technological advances have swung the door wide open to new and exciting integrated approaches across these disciplines. Our research group conducts molecular ecology research across a diverse spectrum of applications to address critical knowledge gaps in animal conservation.
We particularly use a a variety of techniques that employ high-throughput sequencing technologies (HTS). These approaches allow us to interrogate thousands of loci across the entire genome (including nuclear SNPs and mitogenomes) to investigate critical neutral and adaptive processes, and/or reliably quantify fewer markers across thousands of samples (e.g., for individual genotyping or species barcoding). These tools build on previous markers to offer powerful approaches to address knowledge gaps in animal conservation through identifying significant population units to conserve, estimating critical demographic rates, and population assignment of unknown individuals.
marine turtle conservation genomics
In addition to being iconic marine species, sea turtles are fascinating for many ecological, evolutionary, and physiological reasons. Unfortunately, human activities have negative impacts on these animals, and many populations are greatly reduced below historical levels and/or still declining. However, science and conservation efforts are helping to identify and address these problems, ultimately working to restore and protect these species. In collaboration with NOAA Pacific Islands and Southwest Fisheries Science Centers, we are developing HTS methods for rapid sea turtle genotyping. In addition to refining our understanding of fine-scale population structure and connectivity, these tools can be used for a variety of genotyping applications, such as assessing climate change impacts, determining vital rates via genetic mark-recapture, and conducting genetic stock assignment.
To learn more about recent and upcoming marine turtle genetic conservation applications, check our review paper!
development of a sustainable Golden Dorado recreational fishery in South America
Catch-and-release (C&R) recreational fisheries are rapidly growing in popularity and economic value around the globe, and ultimately strive to provide sustainable livelihood alternatives to traditional extractive activities in many developing regions. However, frequently key biological information is missing for targeted C&R species, making it challenging to determine best practices and management to support these endeavors. Golden Dorado (Salminus brasiliensis) is a native, freshwater predatory fish in Neotropical South America and the focus of a rapidly expanding C&R fishery due to characteristics such as their vibrant appearance and intense fight. Additionally, many river ecosystems that Golden Dorado inhabit have been heavily fragmented by hydroelectric dams, but it is not known how these human impacts have altered their movements or population connectivity. As demand for Golden Dorado C&R recreational fishing increases, so do the potential benefits for local communities and regional economies, but many aspects key to the development of a sustainable recreational fishery are not well understood- including their basic biology, response to disturbance, and the social capacity to adopt and support best practices. In collaboration with Drs. Andy Danylchuk and Ezra Markowitz, we are (1) using genomic tools to understand historical and human-driven connectivity patterns to identify ‘conservation units’ (led by PhD student Nadia Fernandez), and (2) employing quantitative and qualitative social science methods to explore key factors that influence social norms and practices within the Golden Dorado recreational angling community. This research not only supports the development of sustainable practices and management strategies for Golden Dorado, but also serves as a case study for similar circumstances with other developing C&R recreational around the world.
evaluating close-kin mark-recapture for elasmobranch abundance estimation
Successful marine resource management relies on population assessments that evaluate the status of marine fisheries stocks and species of concern. One of the greatest challenges in marine conservation and management is accurately estimating abundance and assessing trends over time. Without a way to track the size of populations through time, it is very difficult to manage species in an informed and sustainable way. This is especially true in elasmobranchs, where the majority of species are classified as ‘data-poor’, largely because traditional methods for estimating abundance are intractable in this group. Close-kin mark-recapture (CKMR; Bravington et al., 2016) has recently been proposed as a tool for estimating population size that alleviates the sources of error that accompany fisheries-dependent methods (such as CPUE) as well as the logistical challenges associated with traditional mark-recapture. Using genetic tags, CKMR examines the proportion of observed vs. expected kin among sampled individuals, then analyzes these data in a mark-recapture framework to estimate the size of the population from which the samples were taken. However, like any new method, before the CKMR framework can be broadly applied, it first needs to be validated in different biological systems to ensure that it reliably produces robust parameter estimates that can be incorporated into population assessments and stock projections. CKMR models are heavily dependent on the biology of the species of interest and this method has not yet been validated in longer-lived slow-to-mature species like elasmobranchs. Led by PhD student John Swenson and in collaboration with Drs. Dovi Kacev (UC San Diego-SIO), Michael Kinney (NOAA SWFSC), Charlotte Boyd (NOAA AFSC) and Kevin Feldheim (Field Museum, Chicago), we are testing central assumptions of the CKMR framework using genetic data drawn from a population of Lemon Sharks that has been intensively sampled and studied for over 20 years. Using simulation and empirical approaches, we are testing the reliability of CKMR-based abundance estimates under various scenarios that reflect realistic challenges associated with sampling marine populations. These results will help establish best practices for designing and implementing future CKMR studies in elasmobranches and other challenging data-poor marine species.
habitat restoration impacts on anadromous river herring connectivity
Fragmentation of riverine habitat from dams and other barriers has negatively impacted many aquatic species, particularly anadromous fishes that reproduce in freshwater rivers but spend most of their lives at sea and must be able to move freely in both directions between life stages. Efforts to restore habitat connectivity through the installation of fish ladders, dam removals and other means hold great promise, but require effective monitoring of populations prior, during and after the changes to quantify positive impacts. In the St. Croix River system along the Maine-New Brunswick (Canada) border, dam construction over the past century or more has created multiple barriers to movement for populations of river herring (Alosa pseudoharengus), also known as alewife. Although anadromous river herring have been blocked from moving upstream to spawn, some river herring have succeeded in living out their entire life cycle above these dams, leading to several interesting questions about their ecological role and origin. Partnering with the Passamaquoddy Tribe, Dr. Adrian Jordaan and the Headwaters to Oceans Lab, and led by UMass Darwin fellow Dr. Sarah Emel, we are using genomic tools to understand the spatial genetic structure of this system both prior to and following recent efforts to restore connectivity using fish ladders. We aim to determine the relatedness between anadromous and land-locked populations of river herring, the effects of isolation and possible contemporary mixing on their genetic diversity, and the implications of these findings for the conservation of this culturally important native species.
Want to learn more about river herring? Check out this NFWF video to learn just how incredible they are!
Population connectivity of Western Atlantic cownose rays (Rhinoptera bonasus)
Cownose rays in the Western Atlantic Ocean are highly migratory, moving south as one large aggregation during the fall to overwintering grounds near Cape Canaveral, Florida and then migrating north during the spring to disperse into various estuaries where they give birth and then mate throughout the summer. Tracking data suggest that individual rays return to the same estuary each summer to breed; however, it is unknown whether this philopatric behavior has resulted in reduced population connectivity among estuaries and the formation of genetically distinct subpopulations. In collaboration with Drs. Charles Bangley and Matt Ogburn at the Smithsonian Environmental Research Center and led by PhD student John Swenson, we are using Restriction-site Associated DNA Sequencing (RAD-Seq) to assess whether the Western Atlantic cownose ray population is structured according to summer reproductive habitat. If so, then the long-term sustainability of cownose rays will likely depend on managing each subpopulation at the appropriate spatial scale to preserve genetic diversity of the stock. On the other hand, if Western Atlantic cownose rays represent a mixed population, then effective conservation may require coordination between regulatory agencies across their range. This project is made possible through an amazing network of agencies and researchers helping to collect cownose ray samples across their broad range, and is supported with funding from the North Carolina Aquarium Society.