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  3. Hi Don. The concept of ancestry is one of relationship and phylogeny, which (by/like the question implies), assumes evolution and so an answer can potentially be sought, though the further back in time we go, especially at some junctures, it can be tricky, for various reasons, but this question is precisely a key one which you will be able to find with this programme. When I say tricky, I in no way mean that the whole concept could be wrong or major, distinct alternatives are open to consideration. By way of example or comparison, it is like a child walking home from school and being seen by multiple CCTV cameras, which can track people’s whereabouts in terms of time and location. There may be some specific points along the way where there were no cameras or some obscuring took place, but the route and times are not in dispute, merely what may have occurred, if anything different, at these specific points. The gaps are natural, explainable and expected ones. Are you an enquiring creationist? If so, or my advice for those who are, is to analyse how anyone can see and trace this lineage (with no pre-conceptions) and examine how life is or is not interrelated., and consider that, if anyone thinks not, how such results are shown as they are, and what other explanation can possibly result from them and the statistical improbability of such occurring. To give an indication of an answer to your question, we share a Eukaryotic ancestor which in turn stemmed from an Archean one, but it would not be possible to tell you what species, but please note that this is not a failure, any more than asking you to name the individual from 1000 years ago, from whom you descended. I am not sure as to the reason or motive for the question, so I am not sure how helpful my answer is, though Steve
  4. Greetings everyone! I've started working as a volunteer in the Phylogeny Explorer Project, in Data Entry, in January and I've loved it since the beginning. I've joined due to being a science enthusiast and due to my passion of Biology. I've worked on the Lagomorpha clade for a few months and from that moment on I've started meeting and knowing a considerable amount of good and dedicated people that are passionate about what they are doing. It's an ambitious project and I'm honored for being a part of such a good and professional team that has helped me adapt and learn a lot about the project and its vision! As of now I'm the Data Entry Manager along with my fellow Gabe Stroup. There's a lot of work to be done, but with great effort and will the PEP will be very first website that presents a grand tree of life! Regarding my background, it's pretty simple. My name is João Ferreira, and I'm from Portugal. I've finished my Bachelor's Degree in Political Science in 2017, and I'm finishing my Post-Graduation in Strategy. I've always wanted to pursue Biology, but due to the low employability in my country on that field I had to pursue something else. I'm passionate about Biology, Genetics and Animal Behaviour and I try to read and stay in touch with that area of interest of mine. I'm also passionate about Philosophy and Religion (the study of it). I hope everybody who comes to the Project feels good about being part of such an amazing team and I look forward with working with everybody who has an interest in contributing to Science! Cheers!
  5. Last week
  6. 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
  7. Welcome Joe enjoy your stay. Where always looking for volunteers.
  8. I am a software engineer by trade but find joy in studying cosmology, some math (I enjoy numberphile) and biology. My dad would spend hours showing me plants and such as we would hike. I like visiting zoos and now finding amazement by the deversity of life. I am hoping to spend some time helping with the software
  9. Great. Will get that sorted. It was my Heinz 57. It is a British joke about the number of varieties of naked beans and I had plnned it to be used by Aron Ra on one of his videos. Thanksd for removing.
  10. Yes it was. I assumed it was some kind of vandalism. Anyway, I've submitted an application to become a data entry volunteer.
  11. Hi Ross. I see. You need to register as a volunteer and for data entry, so the data entry team know of your existence and can log you and any work done. You can do as much or little as you like and will get updates in the forum and you'll get a personal project email. I will speak to the social media manager anmd wed w8ill work on clarifying onbosarding, based on your experience/feedback, too. We are working on documenation and it will be shared/available when ready. Was the joke, 'Heinz 57' in the dog clade? I really appreciate your help, Ross. Please stick with us. You can continue to edit until/unless any other update comes up, which will be in the data entry forum. Hope that helps.
  12. I signed up for the project back in August 2018 (after talking to Aron Ra on the YouTube comments of one of his phylogeny videos), but I think at that time the Explorer was not editable for me. There also was no forums then, and since I wasn't on Facebook or anything, I didn't become a member of the community. I think you sent me an email back then saying that things were soon going to be starting up and you would send me more information in future. But that was the last communication (I understand you were probably busy trying to organise many other things). Anyway, I then did a small bit of editing the Explorer on my own over the last few months (and a bit more in the last week or so). Just minor things like marking living species as Extant, etc. I also deleted one obvious joke/vandalism entry. By Volunteering do you mean this applications page?: https://phylogenyexplorerproject.org/application/ I'm not entirely sure what I could do there. I also couldn't promise to commit a large amount of time to a role here. I was more intending to just casually edit the Explorer from time to time (add species and subspecies, correctly mark extinct/extant, maybe write some info and find picture, and what not). Is that basically what "data entry" is? I don't have any real programming/coding skills, I can edit stuff like Wikipedia and the basic stuff on the Explorer, but that's about it. BTW, is there some general editing guide or rule-set available for the project?
  13. Sure. Will let you know. Yes. No,
  14. Hi Ross. Yes, I'm Steve Registering on the Website gives you access tg0o additional forums. You'll need to register as a volunteer if you haven't already. As a data entry person for example. This will then give you access to the data entry team forum. You can then receive a personal project e-mail. If you have any questions about onboarding, please let me know. W We want to make things as easy and clear and well signposted as possible, and this appolies to everything, so if any of this wasn't or isn't clear, I'd really like to know (you can include screen shots if you like) and I will look into making this better. Did you get edit access recently? Pleaase make yourself known to the data entry team. Gabe and Joao are running it and they can advice on what can be done on the explorer.
  15. 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?
  16. That sounds good to me! I'm in!
  17. Ok, I've registered for the forums. I was signed up to the project by someone called Stephen Owen, was that you? (the system is a bit silly that it doesn't register you with the forum at the same time as registering you for the Explorer itself, but ok). Unfortunately I'm not on Facebook or any other social media. When you say data entry is being suspended, does that mean I should not try to edit the explorer at the moment? Where is the Data entry forum?
  18. 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.
  19. A blog is so diverse and open in termns of length, depth, topic etc. I'm looking for interesting stories, information, news, research and related. It doesn't need to be a regular thing. I'm thinking of doing a weekly one with different contributors who can revisit or do a new blog anytime. So, you can put something together or use all or parts of what you posted, withy or without pics. And I'll post the blog with your name.
  20. 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
  21. 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!
  22. A fascinating read, Victor. Read all of both posts. There are data fields for images (when the white screen fix is done). I'd say this is worthy of a blog. You are welcome/invited to make one or turn this into one. Let me or Borg know.
  23. 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.
  24. Earlier
  25. 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
  26. 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.
  27. Hi Ross. Have we communicated before? Thank you so much for helping out. Are you in the Facebook group? You highlight a well-known key problem area. A development update included the ability to make the extinct function work as a clade. As you may well know, if ANY clade node is denoted as extinct, then NOTHING subordinate to that clade node can be extant. The problem was, that the new function which enables this, was put in after many annotations had already been entered, some wrongly. The data entry team are suspending much of the data entry imminently in order to prepare some exciting new things. If you haven’t already, please (with Weare Borg’s help) get into the Data entry forum which is a communication hub for data entry where all relevant things will be raised. Data entry are also looking for help in preparing the ground with various roles available which may interest you. They will no doubt post in the forum shortly. Thanks,
  28. If you can goto https://phylogenyexplorerproject.org/register you can signup there or at the right side you can use Facebook or Twitter to register.
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