Answers.Body: <p>Good answer.</p>
  <p>The common ancestor is not known due to the paucity of the fossil record at this point in evolutionary time. A reconstruction can be made using coalescent theory which is what @MaximillanPress describes. The level of uncertainty at that depth of calculation requires significant expertise. I would re-evaluate the comparison with related organisms that are heavily studied.</p>
  <p>Lobsters are decapods (Decapoda) and closely related to insects, moreover they are monophyletic with the Order Insecta. A lot is known about a lot of insects, many being model organisms, such as Drosophila melanogaster. Both decapods and insects exist within the arthropods (Arthropoda), along with spiders and the like. Their ancestors were marine arthropods, trilobites are arthropods. The major diversity of the arthropods was generated in the Cambrian Explosion and a lot of work has gone into identifying these fossils.</p>
  <p>Traversing between decapods and insects is as far as I'd go, which is likely the late stages of the Cambrian explosion. There are likely to be putative ancestral fossils - not that you can get any molecular sequence from them however. The closest living ancestor on the insect side is Colembola (beach hoppers).</p>
  <p>There are serious difficulties in major molecular calculations between decapods and mammals.</p>
  
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Answers.Text: I am interested in some of these notes, not being a well-trained systematist myself. Can you say more about the difficulties in molecular clock calculations? Maybe suggest citations for that, or for the beach hopper "living ancestor"?
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Answers.Text: For the palaeontology of the Cambrian Explosion the author is Simon Conway Morris, e.g. https://www.pnas.org/content/97/9/4426. The arthropod nuclear phylogeny and approximate dates https://www.sciencedirect.com/science/article/pii/S0960982219304865. This includes a guess at the molecular dating (which I'm not convinced by at all). The tree makes the point (which I'd forgotten) that waterfleas (Daphnia) are the more likely a 'living fossils'. Its the lines between the dark blue lines of the Malacostraca (including lobsters) and brown lines of the hexapods (insects).
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Answers.Body: <p>Because I've now posted several comments, I'll just roll them all up.</p>
  <p>For background on the approaches used to identify most recent common ancestors and a high-level look at how animal taxonomy has been inferred, I suggest <a href="https://onlinelibrary.wiley.com/doi/epdf/10.1111/j.1558-5646.1999.tb03768.x" rel="noreferrer">Lynch 1999</a>.</p>
  <p>I think that there are 2 interpretations of this question. If you are interested in <strong>just looking up a single MRCA of well-defined clades</strong>, such as lobster and human, here are some approaches:</p>
  <h2>Easy way:</h2>
  <ol>
  <li>Look at a tree diagram, e.g. this:</li>
  </ol>
  <p><a href="https://i.sstatic.net/iqoml.png" rel="noreferrer"><img src="https://i.sstatic.net/iqoml.png" alt="Animal phylogeny diagram" /></a></p>
  <ol start="2">
  <li><p>Find the tips that correspond to your species of interest (arthropods for lobster, chordata for humans).</p>
  </li>
  <li><p>Find where they join together in the diagram (the branch labeled &quot;true coelom&quot;).</p>
  </li>
  </ol>
  <p>You have your answer, the MRCA is the group of organisms with a true coelom,  coelomates.</p>
  <h2>A more involved way using a database</h2>
  <ol>
  <li>Go to <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&amp;id=33208&amp;lvl=3&amp;lin=f&amp;keep=1&amp;srchmode=1&amp;unlock" rel="noreferrer">this website</a>.</li>
  <li>Find the group of species 1 (arthropods, protostomes, etc. for lobster, chordata, deuterostomes etc. for human)</li>
  <li>navigate around until you see the group containing the two groups (in this case listed as &quot;bilateria&quot;). In this case you are looking for the bilaterian common ancestor.</li>
  </ol>
  <h2>another database</h2>
  <ol>
  <li>Go to <a href="http://lifemap-ncbi.univ-lyon1.fr/" rel="noreferrer">this website</a>.</li>
  <li>Point and click your way to a view where you see your 2 clades of interest (arthropods, chordates in this case). See figure.
  <a href="https://i.sstatic.net/0y23C.jpg" rel="noreferrer"><img src="https://i.sstatic.net/0y23C.jpg" alt="A view of a phylogenetic website" /></a></li>
  <li>Find where they join (in this case, it is less certain about the existence of a coelomate common ancestor, so it just says &quot;<strong>bilaterians</strong>&quot;).</li>
  </ol>
  <h2>In R</h2>
  <p>We might also want a programmatic procedure in case we need to automate it. The following gives a series of commands in R that do this.</p>
  <p>Get a newick/nexus tree from somewhere e.g. <a href="https://itol.embl.de/tree/129215302173073111930481660" rel="noreferrer">here</a> of animals (go &quot;control panel --&gt; export, format = &quot;newick tree&quot; --&gt; download).</p>
  <p>For this tree, we can approximate an answer as following:</p>
  <pre><code>library(ape)
  it = read.tree(&quot;~/Downloads/zUtVMYn3wJQBoP7E8fygTw_newick.txt&quot;)  # autogenerated filename from the website.
  getMRCA(it, c(&quot;Homo_sapiens&quot;, &quot;Drosophila_melanogaster&quot;))  # drosophila is one of only 2 arthropods in this tree, but arthropods all have an arthropod common ancestor
  # prints &quot;200&quot;, the node index of the MRCA.
  </code></pre>
  <p>You can use that node index to do things like look up a name in the <code>node.label</code> attribute of the tree (<code>it</code>) structure, or to do other operations on the tree.</p>
  
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Answers.Text: This is really helpful. I’ll have a good look at this tomorrow and give you a little more detail on what I’m trying to do.
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Body: <p>I want to specifically find the common ancestor between a lobster and a humans. I suspect it was an aquatic worm of some description. But I want to know about the nervous system of this common ancestor.</p>
  
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Comments.CreationDate: 2022-01-01T21:50:01.533Z
Comments.Text: can you give us some sense of what you've tried? what is the phylogeny you're using, if any? what's the level of resolution you want? For example, if you look e.g. at this little tree (https://www.researchgate.net/profile/Aiasha-Siddika-Arshi/publication/314095464/figure/fig1/AS:466667777073153@1488273676923/Phylogenetic-tree-of-the-Animal-kingdom-2.png), you can find an informatively labeled node, suggesting that the answer might be "the coelomate common ancestor". Another way would be to find an animal phylogeny, read it into R with `read.tree`, and then use `mrca()`. IDK which way you want.
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-01-01T21:55:38.313Z
Comments.Text: Sorry I’m a total novice at this I’ll digest your response and get back to you later.
Comments.UserDisplayName: syn_bio_delta
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Comments.CreationDate: 2022-01-01T23:04:51.983Z
Comments.Text: I guess, it would help to know exactly what you're trying to do. If you're looking for a single piece of factual information, there is a knowable right answer here that you can just look up (which I believe is "the coelomate common ancestor"). However, the fashion that you phrase this and the forum that you post it suggest that you want a more general workflow.
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-01-01T23:21:58.093Z
Comments.Text: for example, see this web app which computes common ancestors: http://www.timetree.org/. To state it a different way, your specific lobster/human question is finding the common ancestor of deuterostomes and protostomes in figure 1 here: https://onlinelibrary.wiley.com/doi/epdf/10.1111/j.1558-5646.1999.tb03768.x. I recommend that last paper if you want a general sense of how this stuff works.
Comments.UserDisplayName: Maximilian Press
Tags: <phylogenetics><genome><phylogeny>
Title: What is the most appropriate way to find the most recent common ancestor between two distantly related species
ThreadText: # What is the most appropriate way to find the most recent common ancestor between two distantly related species
  
  (Asked by: username_0 on 2021-12-29)
  
  I want to specifically find the common ancestor between a lobster and a humans. I suspect it was an aquatic worm of some description. But I want to know about the nervous system of this common ancestor.
  
  **Tags:** phylogenetics, genome, phylogeny
  
  > **Comments:**
  > **username_1**: can you give us some sense of what you've tried? what is the phylogeny you're using, if any? what's the level of resolution you want? For example, if you look e.g. at this little tree (https://www.researchgate.net/profile/Aiasha-Siddika-Arshi/publication/314095464/figure/fig1/AS:466667777073153@1488273676923/Phylogenetic-tree-of-the-Animal-kingdom-2.png), you can find an informatively labeled node, suggesting that the answer might be "the coelomate common ancestor". Another way would be to find an animal phylogeny, read it into R with `read.tree`, and then use `mrca()`. IDK which way you want.  
  > **username_0**: Sorry I’m a total novice at this I’ll digest your response and get back to you later.  
  > **username_1**: I guess, it would help to know exactly what you're trying to do. If you're looking for a single piece of factual information, there is a knowable right answer here that you can just look up (which I believe is "the coelomate common ancestor"). However, the fashion that you phrase this and the forum that you post it suggest that you want a more general workflow.  
  > **username_1**: for example, see this web app which computes common ancestors: http://www.timetree.org/. To state it a different way, your specific lobster/human question is finding the common ancestor of deuterostomes and protostomes in figure 1 here: https://onlinelibrary.wiley.com/doi/epdf/10.1111/j.1558-5646.1999.tb03768.x. I recommend that last paper if you want a general sense of how this stuff works.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2022-01-01. Score: 4 | Accepted answer
  
  Because I've now posted several comments, I'll just roll them all up.
  
  For background on the approaches used to identify most recent common ancestors and a high-level look at how animal taxonomy has been inferred, I suggest [Lynch 1999](https://onlinelibrary.wiley.com/doi/epdf/10.1111/j.1558-5646.1999.tb03768.x).
  
  I think that there are 2 interpretations of this question. If you are interested in **just looking up a single MRCA of well-defined clades**, such as lobster and human, here are some approaches:
  
  ## Easy way:
  
  1. Look at a tree diagram, e.g. this:
  
  [![Animal phylogeny diagram](https://i.sstatic.net/iqoml.png)](https://i.sstatic.net/iqoml.png)
  
  2. Find the tips that correspond to your species of interest (arthropods for lobster, chordata for humans).
  3. Find where they join together in the diagram (the branch labeled "true coelom").
  
  You have your answer, the MRCA is the group of organisms with a true coelom, coelomates.
  
  ## A more involved way using a database
  
  1. Go to [this website](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=33208&lvl=3&lin=f&keep=1&srchmode=1&unlock).
  2. Find the group of species 1 (arthropods, protostomes, etc. for lobster, chordata, deuterostomes etc. for human)
  3. navigate around until you see the group containing the two groups (in this case listed as "bilateria"). In this case you are looking for the bilaterian common ancestor.
  
  ## another database
  
  1. Go to [this website](http://lifemap-ncbi.univ-lyon1.fr/).
  2. Point and click your way to a view where you see your 2 clades of interest (arthropods, chordates in this case). See figure.
     [![A view of a phylogenetic website](https://i.sstatic.net/0y23C.jpg)](https://i.sstatic.net/0y23C.jpg)
  3. Find where they join (in this case, it is less certain about the existence of a coelomate common ancestor, so it just says "**bilaterians**").
  
  ## In R
  
  We might also want a programmatic procedure in case we need to automate it. The following gives a series of commands in R that do this.
  
  Get a newick/nexus tree from somewhere e.g. [here](https://itol.embl.de/tree/129215302173073111930481660) of animals (go "control panel --> export, format = "newick tree" --> download).
  
  For this tree, we can approximate an answer as following:
  
  ```
  library(ape)
  it = read.tree("~/Downloads/zUtVMYn3wJQBoP7E8fygTw_newick.txt")  # autogenerated filename from the website.
  getMRCA(it, c("Homo_sapiens", "Drosophila_melanogaster"))  # drosophila is one of only 2 arthropods in this tree, but arthropods all have an arthropod common ancestor
  # prints "200", the node index of the MRCA.
  
  ```
  
  You can use that node index to do things like look up a name in the `node.label` attribute of the tree (`it`) structure, or to do other operations on the tree.
  
  > **Comments:**
  > **username_0**: This is really helpful. I’ll have a good look at this tomorrow and give you a little more detail on what I’m trying to do.  
  
  ---
  
  ### Answer by username_2 on 2022-01-05. Score: 3
  
  Good answer.
  
  The common ancestor is not known due to the paucity of the fossil record at this point in evolutionary time. A reconstruction can be made using coalescent theory which is what @MaximillanPress describes. The level of uncertainty at that depth of calculation requires significant expertise. I would re-evaluate the comparison with related organisms that are heavily studied.
  
  Lobsters are decapods (Decapoda) and closely related to insects, moreover they are monophyletic with the Order Insecta. A lot is known about a lot of insects, many being model organisms, such as Drosophila melanogaster. Both decapods and insects exist within the arthropods (Arthropoda), along with spiders and the like. Their ancestors were marine arthropods, trilobites are arthropods. The major diversity of the arthropods was generated in the Cambrian Explosion and a lot of work has gone into identifying these fossils.
  
  Traversing between decapods and insects is as far as I'd go, which is likely the late stages of the Cambrian explosion. There are likely to be putative ancestral fossils - not that you can get any molecular sequence from them however. The closest living ancestor on the insect side is Colembola (beach hoppers).
  
  There are serious difficulties in major molecular calculations between decapods and mammals.
  
  > **Comments:**
  > **username_1**: I am interested in some of these notes, not being a well-trained systematist myself. Can you say more about the difficulties in molecular clock calculations? Maybe suggest citations for that, or for the beach hopper "living ancestor"?  
  > **username_2**: For the palaeontology of the Cambrian Explosion the author is Simon Conway Morris, e.g. https://www.pnas.org/content/97/9/4426. The arthropod nuclear phylogeny and approximate dates https://www.sciencedirect.com/science/article/pii/S0960982219304865. This includes a guess at the molecular dating (which I'm not convinced by at all). The tree makes the point (which I'd forgotten) that waterfleas (Daphnia) are the more likely a 'living fossils'. Its the lines between the dark blue lines of the Malacostraca (including lobsters) and brown lines of the hexapods (insects).  
  
  ---
  
  