Close-kin and cownose ray conservation

  • Rays & Skates
Years funded
  • 2020
  • Active
Project types
  • Conservation
  • Research

John is developing a set of targeted ‘capture panels’ that focus DNA sequencing efforts on specific regions of the cownose ray genome that can be used to identify related individuals. These panels will facilitate construction of a close-kin mark-recapture model to estimate abundance of cownose rays along the US East Coast.

Close-kin and cownose ray conservation

John Swenson

Project leader
About the project leader

I don’t know why or where it came from, but I have felt drawn to the ocean and captivated by elasmobranchs (sharks and rays) for as long as I can remember. Over the years, as I studied elasmobranch biology and sought opportunities to interact with the animals, my casual interest transformed into a passion; the more I’ve learnt, the more I’ve come to realise how exceptional sharks and rays are. Their uniqueness arises from their evolutionary history. Sharks and rays (and chimaeras) took their own evolutionary path relative to other vertebrates about 450 million years ago. This does not mean...

PROJECT LOCATION : Northwest Atlantic Ocean/East Coast of United States
Project details

Counting Cownose Rays with Close-Kin Mark-Recapture

Key objective

Concurrent with development of a species management plan in Maryland, this project will assess population connectivity of cownose rays in the Western Atlantic Ocean and use the data to develop targeted DNA capture panels that can be used for kinship identification. The methods and results from this project will aid future efforts to estimate population abundance using close-kin mark-recapture (CKMR).

Why is this important

This project is unique because it combines cutting-edge genomic techniques with new advances in statistical modeling to address a critical issue that has plagued effective elasmobranch conservation for decades: estimating population abundance. As CKMR becomes more popular among elasmobranch researchers, it is important to clarify the data requirements of the models while demonstrating how the findings translate into real-world applications. As a species with a well-understood life history, cownose rays are ideal candidates for applying CKMR in the field.

In addition, we are developing resources that will streamline future genomics and CKMR work in cownose rays and other closely-related species of conservation concern, such as eagle rays and mobula rays. In developing capture panels and testing their versatility, this project is expected to produce a valuable resource for the elasmobranch research community and also provide a road map for other researchers wishing to integrate these tools into their programs.


The threats facing elasmobranchs are numerous and complex, from targeted fishing for consumption, to non-target removal as bycatch and recreational fishing for sport, all of which contribute to the alarming decline of elasmobranch populations. As solutions are sought and ways to implement them explored, populations continue to be exploited at rates that are difficult to quantify because tracking abundance of these elusive animals has proven very difficult. This makes it challenging to manage elasmobranch populations in a sustainable way. However, recent breakthroughs in technology may offer a solution to this conundrum.

Close-kin mark-recapture (CKMR) is an emerging approach that is likely to revolutionize elasmobranch conservation. CKMR fuses the burgeoning fields of genomics and population modeling by analyzing genomic data in a mark-recapture framework to give estimates of population abundance and survival. Importantly, CKMR can be applied in settings where samples are obtained lethally or non-lethally, making it useful for species that are culled as bycatch and also endangered species that are caught and released alive. Further, CKMR allows researchers to estimate adult abundance using samples from juveniles alone, and therefore could be a great tool for researchers studying elasmobranchs that are most easily caught as juveniles in nursery habitats.

Though the method has been applied to a handful of elasmobranch populations already, the widespread adoption of this technique would be assisted by guidelines regarding how to apply it effectively. The overarching goal of this project is to examine the data requirements of CKMR models for elasmobranchs with varied, often complex life histories using simulation, and then apply the method to a species of growing conservation concern: cownose rays. In so doing, we will develop a set of best practice guidelines for constructing CKMR models to estimate abundance of elasmobranch populations. Once these guidelines are established, CKMR can potentially be used to estimate abundance of other threatened species for which robust tissue collections already exist, including smalltooth sawfish and spotted eagle rays. In the end, we hope this project will encourage elasmobranch researchers to incorporate this exciting technique into their programs.

Aims & objectives
  • Develop capture panels that facilitate cost-effective high-throughput genotyping of cownose rays by targeting regions of the genome that are informative for population-level analysis and identification of relatives (e.g. parent-offspring, half-sibling) for future application with CKMR
  • Test the capture panels in tissue samples representing a range of conditions (e.g. DNA quality), as well as life history traits (sex, life stage), and species (eagle ray, mobula ray) to determine panel versatility