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Saving sharks with trees

Using evolutionary history and biogeography to refine conservation priorities for sharks, rays, and chimaeras

Go to the profile of Chris Mull
Jan 18, 2018
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The paper in Nature Ecology & Evolution is here: http://go.nature.com/2Dj5v5d

Sharks and rays have been around for almost 500 million years, and at times that’s how long it felt it took to complete this study. This colossal endeavor required the collaborative effort of experts in taxonomy, phylogenetics, natural history, biogeography, and conservation as well as computational centres from around the globe.

While we’ve all heard of white sharks and manta rays, how many of us have heard of the Colclough’s shark or the sharkray? Nearly one quarter of sharks and rays are threatened with extinction, primarily due to overfishing. However, despite the fact that 242 species are imperiled, most conservation attention goes towards a small handful of recognizable charismatic species. This bias in conservation effort means we aren’t currently conserving the majority of shark and ray biodiversity, and their unheralded ecological, morphological, and functional novelty. One way of shining the light on these unknown species has been to assess their evolutionary uniqueness in order to maximally conserve the tree of life.

A representative fully resolved tree containing all 1,192 species of sharks, rays, and chimaeras. Coloured branches represent ED (Myr).

To accomplish this we first had to develop phylogenetic trees that captured the full diversity of this group…sounds simple, right? To this end we set out to rank all 1,192 species based on their evolutionary distinctness (ED), a measure of the amount of evolutionary history that each species embodies. Our phylogeny construction and calculation of ED scores took place in three main stages. First, we constructed a "stage 1" molecular tree using publicly available DNA sequence data from GenBank. Since GenBank data can suffer from issues of misidentification we spent nearly one year running quality checks to ensure we were only using the best available sequence data. This included hand checking of countless interim trees, examining every branch and pruning out the rogue species. This left us with a carefully constructed shark and ray topiary of 610 species ready to add in all the taxa that do not have sequence data. While we might not have molecular data for these species, we do know their taxonomic affinity.

How do we create complete trees without molecular data? We simply infilled “data-free” species alongside their relatives. We coded a series of constraints based on our molecular phylogeny and the taxonomy, to ensure species were placed correctly. For example, hound sharks from the family Triakidae were coerced to form a monophyletic group.  After countless more visual checks to ensure that our species addition script was cooperating we were ready to submit over 1,000 jobs to our computing cluster.  Following weeks of running jobs there was juggling and organizing the vast amount of output that had to be summarized as a large "pseudoposterior" set of complete phylogenies. With that in hand, we generated and summarized ED scores for all 1192 species. Note to self, never start a project that only pays off at the very end!

How to calculate ED using Fair Proportion.

So what is the take home message? First, the extinction of a single chondrichthyan species would prune a median of 26 million years of unique evolutionary history from the shark and ray tree of life. With so much evolutionary history invested in each chondrichthyan species, a shark in hand is worth five birds (median bird ED approximately 8 Myr). Second, our list of high ED chondrichthyans encompasses a wide range of functional diversity, with a variety of morphologies, life history strategies, ecological roles, and habitats. For example we find the electric-generating coffin ray, the filter-feeding basking shark, and the deepwater frill shark in our Top 20.

Biological diversity in the Top 20 imperiled species.Images: D. Wackenfelt, G. Skomal, JNP Nuñez, DR Roberson.


Third, two taxonomic orders jumped out that deserve conservation consideration. Lamniformes are large-bodied, wide ranging, coastal and oceanic sharks including white, mako, basking, and thresher sharks. Rhinopristiformes are large, coastal-demersal rays including guitarfishes, wedgefishes, and sawfishes. Both of these groups account for large amounts of evolutionary history and a high proportion of their species are threatened with extinction mainly due to overfishing. Finally and importantly, by overlaying our ED scores with species’ range maps we were able to identify key regions that are important for conserving shark and ray evolutionary history. While not previously considered a chondrichthyan hotspot, the southwest Atlantic Ocean is a global hotspot for a large number of endemic, high ED imperiled species.

The most exciting thing about our study is that the outcome can benefit at least two future endeavors. Our primary goal was to produce ED scores to help prioritize species for conservation action. In conjunction with this publication the Zoological Society of London will soon launch an EDGE sharks conservation initiative under the EDGE of Existence Programme (www.edgeofexistence.org) to help build local expertise and capacity for the conservation of threatened high ED sharks and rays. However, in addition, our trees (both the stage 1 and stage 2 versions) present novel tools for comparative biologists to examine patterns of trait evolution and diversification in this remarkable (and remarkably old) radiation. We hope our study represents a jumping off point for both on-the-ground conservation, and new fundamental research into this diverse and unheralded group.

Go to the profile of Chris Mull

Chris Mull

Postdoctoral Scientist, Simon Fraser University

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