THE CHONDRICHTHYAN TREE OF LIFE

The goal of this project is to reconstruct the pattern and timing of lineage diversification that gave rise to modern elasmobranchs. The project has 6 major components:
• Revision of alpha taxonomy of extant sharks, skates, rays and chimaeras
• Estimation of phylogenetic relationships among all extant chondrichthyan species based on molecular data  (complete mitogenomes and 1000 nuclear genes used as input data)
• Estimates of times of divergence among major groups
• Updated range maps for all species
• Comparative Skeletal Anatomy of major groups
• Exploration of the forces responsible for driving diversification and species distributions

The project was funded by the US National Science Foundation from 2011-2017 and is still ongoing: Two major products have resulted to date. A book entitled “Rays of the World” edited by Last, White, Carvalho, Seret, Stehmann and Naylor and (2) An interactive website: https://sharksrays.org designed by Gavin Naylor and Jason Davies.

POPULATION GENETICS

• Historical demography of endangered sawfish species around the world from DNA sequence data
  This is a global population genetics project that will determine population structure based on both historical and contemporary samples of all 5 species of sawfish. We are using ancient DNA and contemporary next generation sequencing approaches to better understand how sawfish populations were distributed in the past relative to present day populations. We will also use the genetic data to assess the genetic health of different contemporary populations. These data will be used to inform conservation management policy to ensure the long-term survival of these animals.
• Colonization of the Indian and Pacific Oceans by Black Tip Reef Sharks.
  We are using population genetic approaches to understand the colonization patterns that gave rise to the current distribution of black tip reef sharks in the Pacific and Indian Oceans
• Understanding the history of shark and ray population expansion and contraction from meta-population data.
  DNA sequence data are frequently used to infer changes in effective population size. The technique is commonly applied to identify populations that have undergone recent bottlenecks and that consequently are deemed to be at risk of extinction. The technique has been applied to number of elasmobranch populations. However, the technique can be misleading suggesting that populations are at risk when they are not. This occurs when populations are structured. We have been exploring new ways to improve assessments of population health that do not suffer from these biases. This is a collaboration with Stefano Mona in France and Pierpaolo Maisano-Delser in the UK.
• Inferring long term patterns of White shark movements around the world.
  White shark populations exhibit striking geographic structure in mitochondrial gene sequences. Populations in Australia, California South Africa and New England are all highly distinct. However, it remains unclear what has driven these patterns. We are using gene capture applied to nuclear gene markers to infer demographic history of white sharks around the world and contrasting these data with movement data derived from tagging studies. This work is a collaboration between scientists in Mexico, (Mauricio Hoyos) South Africa (Geremy Cliff and Sabine Wintner) The Atlantic White Shark Conservancy in Massachusetts (Greg Skomal) and Australia (Pierre Feutry, Floriaan Devlo and Charleie Huvenners and Italy (Stefano Mona and Pierre Maisano-Delser).
• Thorny Skate Population structure and Historical Demography.
  We will use recently developed genomic technologies to determine the population structure, migration patterns, and changes in population size over time for the Thorny Skate Amblyraja radiata, a species of intense interest to commercial fisheries, conservation biologists, government agencies (NOAA, NMFS and NAFO) and resource managers. We will (1) distinguish between patterns of genetic variation that are due to contemporary pressures such as fishing and climate change from those that due to historical influences (2) test for historical associations between changes in demography and changes in climatic variables. (3) identify genomic regions under selection that may be associated with adaptation to climate change in the past (4) provide a region-by-region framework for the long-term sustainable management of Thorny Skates across its entire range. This project is funded by the Lenfest Ocean Foundation of the Pew Charitable Trust.

E-DNA

We are developing target gene capture tools using RNA baits to assess marine biodiversity based on environmental DNA (eDNA)samples. Environmental DNA is extracted from filtered seawater samples and genomic libraries are prepared. Libraries are then interrogated using elasmobranch specific RNA probes that bind to target sequences. The bound target DNA is sequenced using a Next-Generation Sequencing platform, bioinformatically sorted, and mapped to an independently curated reference database of ~800 verified elasmobranch whole mitogenome sequences in order to determine the species composition of the original eDNA sample. We are currently testing the efficacy of our protocols. This works is being done in collaboration with Demian Chapman at FIU and Stefano Mariani at Salford University in the UK.

FORENSIC IDENTIFICATION OF FINS AND SHARK PRODUCTS

We are working with Demian Chapman (FIU) to identify genetic polymorphisms that are unique to particular species that will allow us to develop cheap and effective diagnostic test that can be used to forensically identify when fins (or shark products) come from CITES protected elasmobranchs.

OVERT

This is an NSF funded project to generate high-resolution digital three-dimensional data for internal and external anatomy across vertebrate diversity using high resolution CT scan data.We are contributing to the elasmobranch component of the project and are currently exploring the use of different staining protocols to optimally visualize soft tissues. See link

HIGH QUALITY ELASMOBRANCH REFERENCE GENOMES

We are working with the Vertebrate Genome Project based at Rockefeller University to assemble high quality genomes for representatives of all Vertebrates. Most of the genomes that have been sequenced to date are not of high enough quality to be used in downstream applications (such as the development of probes for molecular biology or development). The VGP initiative has set out to establish reference genomes for all the major groups of vertebrates that meet the highest standards of contiguity and coverage.

The FPSR oversees the chondrichthyan component of the VGP project. We have 4 genome assembly projects that are at different stages of completion.

(1) Thorny Skate (Amblyraja radiata) with Jeff Kneebone and Olivier Fedrigo. All PacBio, HiC, 10x data in hand. assembly in progress
(2) White shark (Carcharhodon carcharias) with Chris Lowe and Olivier Fedrigo.100x Illumina data, HiC in hand. Initial assembly complete. Still requires PacBio gap filling.
(3) Epaulette shark (Hemiscyllium occelatum) in collaboration with Pete Currie, Shawn Burgess, Olivier Fedrigo, Adam Phillipy.
(4) Smalltooth Sawfish (Pristis pectinata). Frozen tissues in hand. Not yet started.

INTERNATIONAL SAWFISH ENCOUNTER DATABASE

We continue to document sawfish encounters around the world. These encounters collectively allow us to monitor the incidence and trends in sawfish distributions over time. These data are used to inform policy makers about habitat preferences and how best to manage the long-term health of the world’s sawfishes, all of which are listed as endangered. See interactive sawfish map

INTERNATIONAL SHARK ATTACK FILE

The FPSR has maintained the International Shark Attack Files for over 40 years. We continue to monitor shark bites around the world and have a team of international collaborators in Hawaii, California, New England, Australia, South Africa, Brazil and Reunion. See interactive map of shark attacks by species and by year

COMPARATIVE DEVELOPMENTAL BIOLOGY

Comparative analysis of branchial rays in sharks. This is a collaboration with Dr. Andrew Gillis as part of his ongoing exploration of gill arch patterning and the origin of fins (https://www.gillislab.org/people.html). We are collecting high resolution CT scan data from branchial ray elements in sharks.

ECOLOGY AND MOVEMENT BIOLOGY

• Influence of Spatial and Environmental Factors in Shark Attacks.
  In this project, spatial models have been applied to shark attack data from the International Shark Attack File (ISAF) to examine their distribution and density in relation to environmental and spatial factors.

• Turing patterns in freshwater stingrays of the genus Potamotrygon.
  Freshwater Stingrays (Potamotrygon) have striking colour patterns that are highly variable across species. Many observed patterns are consistent with those generated by Turing-Like Reaction-Diffusion (RD) processes. We will use simulation to estimate models and their associated parameter values for a variety of RD models. We will identify those that best account for the patterns observed across different species of Potamotrygon and then infer how parameters change for the best fitting models over the phylogenetic tree that describes their relationships. This project is part of a project aimed at better characterizing the genotype-phenotype map by incorporating models of self assembly into selection models.
• Karotype Evolution.
  We are planning to use cell culture to grow elasmobranch cells which will be arrested at metaphase, harvested and stained to determine karyotpes for all of the major lineages of elasmobranchs. Probes will be developed based on whole genome sequences to identify homologous regions. These will be used to reconstruct chromosome evolution among elasmobranchs. This project will be carried out in conjunction with Marty Cohn’s lab in the Genetics Institute at UF.
• Sex Determination.
  It has not yet been established how sex is determined in elasmobranchs, or indeed if sex is determined in the same way across all chondrichthyans. Initial work carried out in collaboration with Dr. Tony Gamble has shown that there are unique sex specific markers in male skates (based on the identification of ddRadSeq cut sites that are present in males and the absence of unique cut sites in females). We plan to extend these types of analyses to a broader diversity of chondrichthyans.
• Epigenetic regulation.
  IRecent work by Jackie Lighten suggests that the winter skate (Leucoraja ocellata) may respond to climate change through epigenetic regulation of gene expression. Epigenetic responses make sense for K selected animals that cannot rapidly respond to environmental challenges through classical mutation-selection mechanisms. We plan to examine the distribution and extent of epigenetic expression across elasmobranchs to see if there are patterns associated with longevity, mode of reproduction and life history traits(Lighten, Jackie & Incarnato, Danny & Ward, Ben & Van Oosterhout, Cock & Bradbury, Ian & Hanson, Mark & Bentzen, Paul. (2016). Adaptive phenotypic response to climate enabled by epigenetics in a K-strategy species, the fish Leucoraja ocellata (Rajidae). Royal Society Open Science. 3. 10.1098/rsos.160299.)
• Speciation in Epaulette sharks.
  Epaulette sharks (Genus Hemiscyllium) are distributed in Northern Australia and Papua New Guinea. They also constitute some of the most closely related elasmobranchs that are accessible to field work. As such Epaulette sharks are the group that can best provide insight into the mechanisms that underlie speciation and phenotypic differentiation in chondrichthyan fishes. We will use the high -resolution genome we are assembling with Pete Currie’s group to design markers that will allow us to assess gene flow, historical demography and the incidence of selection within and among different species of Epaulette sharks.
• Comparative anatomy across the Chondrichtyan Tree of Life.
  The comparative anatomy of elasmobranchs has not been extensively explored. Modern CT scanning techniques now allow us to use a variety of staining techniques to obtain high quality CT scans of both skeletal material and the soft tissue. We are looking for a student interested in staining, CT scanning and analyzing a variety of different elasmobranchs across the Chondrichthyan Tree of Life to assess phylogenetic trends and tendencies in anatomical features and to identify adaptations that are associated with environmental conditions.

ECOLOGY AND MOVEMENT BIOLOGY

• Habitat Use and Behavioral Studies.
  This study examines migration and movement of elasmobranchs found within the Indian River Lagoon and elasmobranch nursery areas within the Cedar Key region of the Gulf of Mexico.
• Elasmobranch Nursery Areas Within the Cedar Key Region of the Gulf of Mexico.
  This study will provide a unique and comprehensive view of a multi-species nursery area, along with competitive interactions that structure the community.