Aquatic Vertebrate Integrative Conservation Laboratory (AVIC)

Environmental DNA (eDNA) refers to genetic material shed by organisms into their surroundings. As an organism moves through the water, it can leave behind DNA traces—such as fecal matter, skin or tissue cells, scales, mucus, or associated microbes—that can be collected, filtered and analyzed. These analyses can be directed aiming at detection of species of interest (species specific approaches), or to describe full biological communities (metabarcoding).  This is a non-invasive technique that allows the study of marine animals and biodiversity monitoring without physically seeing or capturing the organisms allowing monitoring distribution patterns.   eDNA is a powerful tool for assessing presence of species in a geographic area and can be combined with other methodological approaches.  A major benefit of eDNA metabarcoding for biodiversity surveys, is that it provides an efficient and non-invasive species detection with relatively small effort, at low cost for small to large scale surveys.

 

Some of the projects currently developed in this research line:

 

• Understanding shark and ray species distribution using eDNA metabarcoding and BRUvs in three locations of the Yucatán Peninsula, Mexico (In collaboration with Dr. Ramón Bonfil, Ecosur, Mexico).
• “Everglades Classroom”: understanding vertebrate community composition through eDNA analyses and hands-on citizen science opportunities for middle and high school students in Southeastern Florida (in collaboration with the Marine Environmental and Education Center at NSU, and “Eye of a Scientist” non-profit organization)
• Aquatic vertebrate diversity in coastal lagoons around Puerto Rico (in collaboration with Dr. Antonio Mignucci, Universidad Interamericana de Puerto Rico)
• eDNA detection of largetooth sawfish (Pristis pristis) in the Pacific Coast of Colombia (in collaboration with Dr. Diego Cardeñosa, FIU)
• Development of species-specific primers for eDNA qPCR detection of hard to see and study cetaceans (tucuxi dolphin, pigmy and dwarf sperm whales, Rice´s whale, in collaboration with Dr. Jeremy Kiszka, FIU)

 

It is important to emphasize that in this research line, there is an important component of education and citizen science opportunities, including training and participation of members from the local communities in sampling trips, as well as the development of an eDNA transversal school curriculum, teaching concepts related to genetics, biodiversity, ecology and conservation.

 

We recently finished generating the text for an illustrated book about eDNA directed to small children (7-12 years) and we hope to be able to publish it before the end of 2026. 

Fisheries management requires not only high-quality scientific information about target species abundance and other population trends, but also about their role in the ecosystems and their reproductive behavior.  Some of the most valuable fish species and populations are currently vulnerable to overexploitation or already seriously threatened with extinction.  Many of the methods used to obtain the type of information needed for management uses invasive or lethal techniques, generating more impact to already affected species.  Also, in many areas of the world, particularly in developing countries, there is a lack of fisheries information and little research about the status of fish species of commercially importance fish.  Genetic and genomic techniques allow development of minimally invasive techniques to obtain relevant information to improve management.  Also, fish population cannot be considered as independent entities, since they are immersed in a biological community and any threat to the whole community will impact the fish populations of interest.  For that reason, in this research line, we are developing projects aimed at understanding the diet, reproductive habits, population structure and genetic diversity of a variety of fish species.  In many of these projects we collaborate with artisanal, small and sport fishermen to obtain samples and biological information for focus species.

 

Among the species and projects, we are currently developing in this research line are:

 

• Investigating the diet of bonnethead sharks (Sphyrna tiburo) around Florida via fecal DNA and stable isotope analyses.
• Population genetic and genomic structure of small hammerheads (genus Sphyrna) in Panamá and the Caribbean (lead by Dr. Cindy González, postdoc in our lab)
• Phylogenomics of the shark family Sphyrnidae (lead by Dr. Cindy González, postdoc in our lab)
• Understanding philopatry, parentage and relatedness between bull sharks (Carcharhinus leucas) in nursery areas of the Everglades and adult females around Florida (in collaboration with Dr. Michael Heithaus (FIU), Dr. Catherine Macdonald (UM) and Dr. Toby Daly-Engel (FIT))
• Investigating philopatric behavior of tiger sharks (Galeocerdo cuvier) in Shark Bay, Western Australia (in collaboration with Dr. Michael Heithaus (FIU), Dr. Derek Burkholder (NSU) and Dr. Mahmood Shivji (NSU))
• Species and maternal lineage identification in sport fisheries in Southeast Florida: what are we catching? a citizen science initiative.
• First full genome and initial population genomic structure of the Atlantic Goliath grouper (Epinephelus itajara) in the Caribbean.

Understanding the genetic and genomic population structure and diversity of a species allows definition of significantly unique groups requiring specific conservation actions. With the development of next-generation sequencing techniques, we now have access to thousands of genes that can provide information not only on neutral genetic diversity, but also on adaptive genetic diversity.  This is important to increase our understanding of how particular species or populations will be able to cope with changing environmental conditions, including climate change.

 

Many long-lived species confront the issue of overexploitation.  In a few regions of the world, dolphins and whales are directly targeted and their meat is consumed by local communities.  One of the areas in which this direct hunt occurs is in the Caribbean islands of Saint Vincent and the Grenadines.  But how is this hunting of individuals from local population affect population connectivity in the Wider Caribbean?  Could hunting be driving local populations to fast reductions in abundance?  This information is key for decision makers and conservation conventions, such as the International Whaling Commission.

 

Introduced species can become invasive when they affect native species in a direct or indirect way, by competing with them directly or by introducing alien parasites and diseases into their habitats.  Florida is one of the areas in the world with higher rates of introductions. Genetic approaches can help understand the history of the introduction/invasion, the geographic region of origin of the introduced species and the levels of genetic diversity found in the introduced populations.  Such valuable information may provide clues on how to limit and manage introductions.

     

Among the species and projects, we are currently developing in this research line are:

 

• Genetic/genomic population structure of Delphinids in the Caribbean, affected by direct hunt (in collaboration with Dr. Jeremy Kiszka, (FIU) and Dr. Antonio Mignucci from Universidad Interamericana de Puerto Rico).
• Genomic diversity population structure and relatedness of freshwater otters (Lontra canadensis) in the Indian River Lagoon.
• Genomic diversity at immune genes (MHC) in leopard seals (Hydrurga leptonyx) from Antarctic Peninsula (in collaboration with the cruise company Hurtigruten)
• Understanding the history of introduction of the grey headed swamphen in Florida using genomic tools (in collaboration with Dr. David Kerstetter (NSU)).

The One Health initiatives are based on the observation that the health of humans, animals, plants and the wider environment is closely linked and interdependent. This interdependency means that no single discipline or sector can tackle threats to health that occur at the interface between humans, animals, plants and ecosystems in isolation. In the past, Dr. Caballero has conducted projects in the field of microbiology, investigating the gut microbiome of spectacled bears in Colombia, the skin microbiomes of sharks and rays and the manatee milk microbiomes.  Microbiome characterization can not only generate important information related with the health of endangered species, but it can have practical approaches to processes that lead to improvements in husbandry, survival and reintroduction of endangered species.  Dr. Caballero has also developed projects in molecular taxonomic identification of parasites in aquatic vertebrates, including marine birds and manatees, as well as identifying fungus that affect survival of sea turtle hatchlings.  Unfortunately, this fungus also affects the skin of humans and there is a likely connection between presence of this fungus on beaches with high human use.

 

We want to contribute to establish the OneHealth initiative that NSU is starting and leading in South Florida. Currently, we are starting to develop the following projects:

 

• Gut microbiomes of sick and healthy sea otters (Enhydra lutris) in Alaska
• eDNA to identify trematode larval stages of manatee parasites Chiorchis In Florida.
• Development of gut probiotics for orphaned baby manatees.
• Biomarkers of stress in dolphins and other vertebrates interacting in human swim with programs.

 

Thank you for your interest in our research group.