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Victor Bach

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Victor Bach last won the day on June 29 2020

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  1. An update on the classification of catsharks. A new paper by Soares, Marcelo and de Carvalho has just been published examining the phylogeny of the 16 species in the genus Scyliorhinus. The paper looked at 84 morphological characters on specimens of the 16 Scyliorhinus species, 4 of the 18 Cephaloscyllium species, the 2 species of Poroderma, specimens of almost all the other scyliorhinid genera and 1 specimen of proscyliid (to use as the root of the cladogram). A strict consensus cladogram supported that the genera Scyliorhinus, Cephaloscyllium and Poroderma compose a monophyletic clade: Scyliorhininae. This brings a few changes to the 3 previously made classifications I had entered in the Phylogeny Explorer's tree. This new paper seems to instead support a similar yet slightly different classification of the three major scyliorhinid clades: Scyliorhinidae I: Apristurus, Asymbolus, Bythaelurus, Cephalurus, Figaro, Halaelurus, Haploblepharus, Holohalaelurus, Parmaturus, Schroederichthys Scyliorhinidae II: Atelomycterus, Aulohalaerus Scyliorhininae: Cephaloscyllium, Poroderma, Scyliorhinus Nothing is written on stone however, and this classification will likely further change in the future with new research. Additionally, this paper doesn't address the classification of Pseudotriakidae, Gogolia filewoodi and Pentachus profundicolus, which the Chondrichthyan Tree of Life (https://sharksrays.org/) built by Dr Gavin Naylor has nestled in between these three major Scyliorhinid clades, while also making Scyliorhinidae a paraphyletic clade. Considering this is by far the most diverse group of extant selachimorphs (sharks), keeping track of these phylogenetics papers is important to ensure the accuracy of our tree. Soares,_Marcelo_&_de_Carvalho_(2020)_Phylogenetic_Relationship_of_Catshark_Species_of_the_Genus_Scyliorhinus.pdf
  2. Eugnathostomata was originally the clade branching into the three major clades of "true" jawed vertebrates: Osteichthyes (aka bony fish), Chondrichthyes (aka cartilaginous fish) and Acanthodii (aka "spiny sharks"). The latter of the three had always been a complex group to classify, since it shared features with both Osteichthyans and Chondrichthyans. Acanthodians had cartilaginous skeletons, an epidermis covered with small platelets (reminiscent of ganoid scales in extant Holosteans) and also fins with bony bases and large structural dentine spines (which gave them the nickname "spiny sharks"). At the beginning of this decade, closer inspection of certain fossils like Acanthodes' cranium where hinting at the possibility for Acanthodii to be ancestral to both Osteichthyes and Chondrichthyes. However, in 2013 the discovery of Entelognathus (a placoderm with bony fish jaw features) led to the revision of this clade, eventually leading to the conclusion that it was paraphyletic. Acanthodians are now believed to be stem Chondrichthyans and the clade from which sharks, rays and chimaeras evolved from. Chondrichthyans have been hypothesized to appear as early as the Ordovician, due to findings of isolated scales made of dentine and bone with a similar structure to that of cartilaginous fish, but these could also be remains of jawless fish like Thelodonts. The earliest "confirmed" Chondrichthyan fossil so far has been Kannathalepis from the early Silurian, but its remains consist mainly of scales found in the Canadian Arctic, which make classification of the specimen difficult. Doliodus was also originally labelled as a "conventionally defined Chondrichthyan" from the early Devonian due its shared features with sharks like expanded paired coracoids, successional replacement teeth and large basals and elongated radials on the pectoral fins. However, more recent papers have also pointed out similarities in its dermal skeleton with Acanthodians, which has left its exact classification unclear. Both Kannathalepis and Doliodus could potentially be classified as "spiny sharks", but Acanthodians were not sharks (not exactly). They were an ancient group of fish with physical adaptations that would lead to the evolution of Chondrichthyans; ancient relics of the evolutionary steps that produced some of the oceans' most successful predators. The line that separates Acanthodians from Chondrichthyans is getting more and more difficult to see as new discoveries keep providing new insights. This differentiation may as well not exist as more "Acanthodian fish" are being found to be nested among "conventionally defined Chondrichthyans" and vice-versa. Acanthodii should perhaps simply be seen as the clade that regroups all cartilaginous fish taxa and their "Acanthodian" ancestors and relatives, or it may be replaced completely by a new less confusing clade. Either way, extinct Acanthodians seem to guard the secrets of how Chondrichthyes progressively lost their bony skeletons to become the known extant cartilaginous fish. The phylogeny of these ancient fish is more than likely to be subject to constant changes and revisions as we learn more about the evolution of predominantly cartilaginous skeletons in fish, therefore I encourage anyone to share any news, papers, videos or other information that may help better build their clades in the PEP. I attached a couple images on the newly understood evolution and phylogeny of Acanthodians as well as a paper on Doliodus for those further interested in this topic. Maisey_et_al._(2017)_Doliodus,_Bridging_the_"Acanthodian"-Chondrichthyan_Divide.pdf
  3. 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?
  4. That sounds good to me! I'm in!
  5. 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
  6. I wouldn't be opposed to turn this into a blog, I am just not sure on how to proceed or what that would imply. My knowledge is limited (I am just a humble student that likes fish and, more specifically, sharks) and although I love to share this kind of information, I don't know if I would be able to share things of this relevance on a regular basis. But I am more than happy to post/share what I can find to be relevant to the PEP!
  7. Placodermi is a clade of ancient Gnathostomes that are famous for their hardened bony-plated skulls and for dominating the ocean ecosystems of the Devonian era. Placoderms have been considered one of the most basal Gnathostomes, being a sister clade to Eugnathostomata from which bony fish (Osteichthyes), cartilaginous fish (Chondrichthyes) and Acanthodians emerged from. It was thus initially though that Placoderms and bony fish evolved bony skulls separately while cartilaginous fish never evolved them at all. This was all believed to be true until the discovery of Entelognathus in 2013, a Placoderm from the Silurian era with a jaw structure very different from that of other Placoderms. While most Placoderms had a beak-like jaw (composed of gnathal plates), Entelognathus instead had jaw features consistent with that of bony fish like a maxilla, premaxilla and dentary. The implications were huge, as it redefined our understanding of ancient fish evolution. It is now (to my knowledge) believed that both cartilaginous and bony fish evolved from a Placoderm ancestor with bony jaws. Cartilaginous fish lost these traits in favor instead of a cartilaginous mandibular arch (known as the platoquadrate and Meckel's cartilage) while bony fish retained them and perfected them over time. This means that all extant Eugnathostomes (including sharks, rays, lizards, birds, mammals, etc.) are technically (from a cladistic point of view) Placoderms, with Eugnathostomata being a sister clade to Placoderm subtaxa like Arthrodira (which includes the awesome Dunkleosteus) and Antiarchi. This is extremely relevant for the construction of the PEP as it means that Placoderms actually never went extinct, but instead diversified to become one of the most successful clades of Earth's life history. And yes, that also means you and I are actually very evolved Placoderms. Placoderms have also been found to be some of the earliest species to show evidence of live birth, with Incisoscutum being found with unborn fetuses inside it and a female Materpiscis being found with a dead youngling still attached to its mother through a fossilized umbilical cord. They also seem to be the earliest clade of fish to have been reproducing through internal sexual fertilization, having claspers like extant cartilaginous fish. This also implies that internal fertilization may have been the norm with Gnathostomes and that cartilaginous fish retained the trait instead of evolving it independently, while bony fish lost the trait until Tetrapods eventually evolved it again when they left aquatic ecosystems. This is an example of how our understanding of evolution keeps changing, sometimes radically, as new discoveries come around. Feel free to add any new findings and share thoughts about the evolution of our Placoderm ancestors. I attached a few papers and images about Entelognathus, Placoderm evolution and claspers for those interested in learning directly from the sources. Long (2016) The First Jaws.pdf Zhu et al. (2013) A Silurian Placoderm with Osteichthyan-like Jaws.pdf Friedman & Brazeau (2013) A Jawdropping Fossil Fish.pdf
  8. 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.
  9. Hi everybody, I am a grad student at the University of Miami's Rosenstiel School of Marine & Atmospheric Sciences. I am currently part of the Shark Research & Conservation program (SRC) based off Virginia Key (https://sharkresearch.rsmas.miami.edu). I have always been fascinated with classification and encyclopedias and could not resist the opportunity to contribute to this project. So far I have entered and reviewed almost every taxa in Chondrichthyes (sharks, rays & chimeras) and I am hoping to continue entering data for these clades that passionate me personally. I have a background in marine biology and marine conservation. My goal is to specialize in sharks, hoping to (one day) get into a PhD to study Lamniformes (my personal favorites). I am also an underwater photographer and videographer particularly interested in audiovisual media to convey science. I have a small YouTube channel where I give hints on how to find marine life for non-specialist interested in having underwater wildlife encounters (https://www.youtube.com/channel/UCm5sLQXwzvNnDXE9cUzvCDg?view_as=subscriber). It isn't much, but I hope to be able to add more content as time goes by. Happy to be part of the team!
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