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Victor Bach

Catshark Classification

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Scyliorhinidae (commonly known as catsharks) are probably the largest extant family of sharks, with at least 160 species in 17 genera (according to knowledge from 2014) and with new species being described every year as commercial fisheries and scientific research move into deeper waters. These cartilaginous fish can be found worldwide from tropical to arctic waters, usually near the seabed. However, our understanding of these animals is greatly limited, as many are deep sea species living below 2000m (6000 feet) depths. For instance, about a third of the species in Apristurus are known from only one scientifically described specimen and in several cases the original and only specimen has been lost. These limitations in taxonomic information have obvious repercussions in identification and classification, as certain species can be very difficult to tell apart without knowledge of very specific taxonomic details. For instance, one of the few ways to tell Scyliorhinus canicula and Scyliorhinus stellaris apart taxonomically are the size of their nasal flaps (skin folds near their nostrils), yet one species is one of the most common in the Mediterranean Sea while the other is one of the rarest.

Genetic tests can obviously shed some light on the identification and classification of these animals, but that requires some form of DNA samples for analysis. Until relatively recently, most specimens where preserved in formaldehyde solutions or formalin, which damages DNA by causing single-strand breaks. Although most labs and collections (that I am aware of) seem to be transitioning specimens to either isopropyl or ethyl alcohol for the safety of both specimens and scientists/students, the damage on those old yet unique specimens has already been done, limiting the information we can get from DNA analyses. Yet, DNA analyses have been able to provide new insights on the classification of catsharks and even challenge our understanding of those animals' phylogeny. Dr Gavin Naylor runs the Chondrichthyan Tree of Life (https://sharksrays.org/), an online phylogenetic tree for all extant cartilaginous fish and the baseline from which I have been building the extant clades in the PEP. If you try to find Scyliorhinidae in Naylor's website (inside Carcharhiniformes) you will see that the clade is turning out to be polyphyletic, with genera being organized in three "Scyliorhinidae" clades:

Scyliorhinidae I: Apristurus, Asymbolus, Bythaelurus, Figaro, Halaelurus, Haploblepharus, Holohalaelurus, Parmaturus.

Scyliorhinidae II: Atelomycterus, Aulohalaerus, Schroederichthys

Scyliorhinidae III: Cephaloscyllium, Cephalurus, Poroderma, Scyliorhinus

These "temporary clades" are still flawed, but they are good starting point for a better understanding of the phylogeny and evolution of catsharks. It seems that the standard "catshark phenotype" has either been selected through convergent evolution multiple times in Carcharhiniformes or is closer to the basal phenotype of the clade from which other taxa evolved from and has been retained in certain benthic species (I still need to find more information on this). Either way, these little sharks are a bit of a phylogenetic headache when it come to placing them in a phylogenetic tree.

If anyone has additional information (papers, news, presentations, videos, etc...) on these sharks and their phylogeny please share them here, as any help is welcomed when it comes to solving the issues for the classification of these mysterious marine predators.

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Hi Victor. It might be good to have a summary of this in the appropriate clades for reference, though I'm sure Gavin Naylor will have been referenced by you.

Do you know if any species of Scyliorhinidae has had its gemome analysed as yet?

Do you know if Gavin Naylor's cartaligenous fish phylogeny has been put or is available in the Newark format?

Are you in contact with him (if he's still active/around)?

Would you like to learn some new science in phylogenetic analysis from an expert and consider being a consultant and focus on this fish clade?

I'd like you to join a select group of scientists in a forum regarding some aspecrts of the tree/data entry and which data fields to add.

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I am planning on adding this to the clades' descriptions when the "blank screen" issue is fixed. Almost all of my references include Gavin Naylor's website since it was my baseline, and I believe he is a trustworthy source for shark phylogenetics (he was recommended to me by the PI of my lab).

To my knowledge, there is only one paper that explores the genome of a Scyliorhinid species (Scyliorhinus torazame), I attached it to this post. I am not an expert in genomics at all, but to my understanding genomes are difficult and expensive to get, and to have true insight on the evolution and phylogeny of these animals we would need large libraries of genetic data (in other words, there is still a lot of work to do to get a clear picture).

Dr Naylor's papers on sharks and rays phylogeny definitely present data under what looks like a Newick format (I attached some of his contributions to the post), but I personally don't know for sure.

I don't know Dr Naylor personally and although I tried to reach him several times through emails, he has unfortunately not been answering me. It is not too surprising, researchers are very busy people and they can be very hard to reach. I do know that he is still active however.

I am always open to learn new science! However, it all depends on how much time that may take (my "expertise" is mainly focused on behavioral ecology). I would love to become a consultant, I just do not know if I have the skills to be one (at least yet). I may know someone that could be interested however: Dr Claudio Barria. He is a friend from Barcelona who studies Mediterranean sharks and rays and he confessed to me that he has a soft spot for paleontology. Once the "blank screen" issue gets fixed, I will tell him about the PEP and encourage him to take a closer look into it, he may be willing to become a consultant (and he is definitely qualified for that).

I would love to join that forum, just send me the invitation or tell me where I need to click. Just for the record, I do not really consider myself a scientist (at least yet) since I do not conduct active research or publish papers regularly, but I would love to help wherever and however I can!

Hara et al. (2018) Elasmobranch Evolution & the Origin of Vertebrates.pdf Martin & Naylor (1997) Independent Origins of Filter-Feeding Sharks.pdf Naylor et al. (2005) Phylogenetic Relationships Among Modern Elasmobranchs.pdf Lopez et al. (2006) Phylogeny of Triakidae.pdf

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Thanks, Victor. All that sounds fine.

Genomes for virtually everything is free/open source on some sites. Dr Rob Leigh is a project consultant with us and specialises, for the purpose of our project, on phylogenetic analysis and building the tree baeed entirely on peer reviewed sources or informatrion and the results will be our own. Rob is going to teach interested folk and produce guidance in how to do this and provide access to the software and is looking for people to help and learn, so that we have continuiuty. It seemeded like a gresat opportunity for you to see a new side to some science you masy not be familiar with which may bode well on your resume and potentiaslly be a new interest focus.

Regarding consultancy. I am looking for people who have a good knowledge or interest in an area of the tree. You do not need to be the most knowledgable or even have a specialism, but your dedication has shown me a lot and you know vhow to research or get access to informatrion that you donm't know, and as we grow and may get people who are better qualified, you can remain a consultant as we are not limited to one. You would provide different or shared vfunctions. Many queries are at a level you can more than adequetly address and you can grow and learn from those around you. Being a consultant/associated with or being an active member of the PEP team also looks good i9n many ways for you, and increasingly so as we grow. I wantb to reward dedication as well as qualified placements.

I will sort the forum out.

 

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Thank you, Steve. Yes, I would love to learn from Dr Leigh, I am sure this type of knowledge will only benefit me and my career. Is there anything I should know in advance with this software? For instance, is it compatible with Apple products or does it require very high RAM speeds?

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