Ancestor’s Tale list of concestors, revised

full_concestor

Some surprises in store for Concestor 23

When I helped write the Ancestor’s Tale, one of the big tasks was to make a human-centred tree of life: to list of all the point at which, backwards in time, the human lineage joined with lineages of other extant lifeforms. In February last year I was forwarded an email from someone using these “rendezvous points” as the basis for a song and story for children. She had seen the O’Leary  paper and wondered how much revision was needed to our original list.

For those who wish to skip to the chase, I’ve come up with a new list at the end of this post. I’m pleasantly surprised at how well most of the rendezvous points have held up, although there is still a lot of argument over their exact timing aFor example, O’Leary & the morphologists still seem to be arguing for the basal placental mammal spits to be post Cretaceous, whereas there is near-universal agreement among the molecular people that divergences go back to at least 90-100Mya.. Here, I summarise the major changes that have happened in the decade following the publication of The Ancestor’s Tale. I’ve tried to make sure that all the reference papers are available freely online, so that readers can check out the sources for themselves.

Tarsiers (Rendezvous 7).
This rendezvous point is now considered securely placed, in the position we originally had it .
Colugos/Tree Shrews (Rendezvous 9 & 10).
Gratifyingly, we actually used the colugo’s tale to point out how unsure we were of this particular bit of our evolutionary tree. The molecular data (including from “rare genomic changes”) marginally favour an extra RV point here, with colugos closer to primates . But some molecules, a chromosomal rearrangement , and the O’Leary  morphological analysis support grouping colugos & tree shrews together in a group called Sundatheria. Note that  also examine the sources of conflict in the placement of tree shrews. By explicitly modelling how genetic variation can go back beyond speciation events (trans-specific polymorphism), they agree that tree shrews are most closely related to Primates. It’s a shame that they didn’t include colugos in their analysis, however.
The uncertainty here needs flagging up, so in the book I’ll probably place both rendezvous in the same chapter, just to make the point. You can follow the paper trail from the references at the start of section 3 in . By the way, that paper also gives an interesting angle on the primate ancestor’s lifestyle.
Afrotheria / Xenarthra (Rendezvous 13).
I’m pleased that I noted in the book that this too was an unsure rendezvous. It’s still contentious  , and  provide reasonable evidence that the split was very close in time. They looked at medium-sized genomic changes caused by transposable elements, the sort of things that should give a clear phylogenetic answerbalthough I suspect that because transposition targets certain sites in the genome, there’s more parallel or convergent evolution than often acknowledged. The fact that they still get conflicting results suggests that different gene trees really do tell different stories, something that’s also been discussed by and . In the book, we tackle exactly this point in the Gibbon’s Tale. More molecular studies seem to be grouping Afrotheres and Xenarthrans together (the “Atlantogenata” hypothesis), e.g.  . I’m happy to place both at the same Rendezvous and almost treat it as a (hard) polytomy, while also noting that the previous order we had (afrotheres as the outgroup) is still being supported e.g. in a recent paper by  (and I find their dissection of the bias in genetic composition (fig 3) carefully done and pretty convincing).
Coelacanths/Lungfishes (Rendezvous 18 & 19)
There has been a recent suggestion that these should group together . However, most classifications still group lungfishes with tetrapods (Dipnotetrapodomorpha), and I find evidence from large-scale genomic changes  more convincing than small sequence changes, even if the Shan paper takes a technically more sophisticated Bayesian approach. A more recent analysis of larger numbers of genes, which additional considers the possibility of incomplete lineage sorting, also supports our original placement 
Lampreys/Hagfish (Rendezvous 22).
We took a punt on the lampreys and hagfishes being sister groups – what’s known as “cyclostome monophyly”. It turns out that we were probably right.  The last major opponent has graciously conceded defeat, as a result of higher-level DNA function & structure linking lampreys & hagfishes . This also has implications for the timing of Rendezvous 22.
Lancelets & Tunicates (Rendezvous 23 & 24) 

Not only fast-evolving, but a closer relative than we expected. © Biopix: N Sloth / CC-BY

This is the first massively unexpected change I’ve come across. Who would have have guessed that the squidgy sea squirts would be more closely related to us than the fish-like lancelets. But as a result of a couple of papers   this now seems to be the accepted order of events. The assumption is that tunicates later evolved a radically different, mostly static lifestyle. In fact, you might find it rather an anathema that tunicates in general show an accelerated rate of evolution compared to us vertebrates . Just goes to show…

Ctenophores (previously Rendezvous 29)

Beautiful iridescence. © Edith Widder / CC-BY-NC

Hot on the heels of one unexpected change is yet another. There was always a bit of a question mark over the relationships between bilaterally symmetrical animals, jellyfish, and ctenophores (comb jellies, of which a very pretty example on the right). But I wager that no-one would have placed the ctenophores as the most basal branch of the animals, splitting off even earlier than sponges. And yet that’s what analysis of the genome of Pacific sea gooseberry has shown, in a paper published last month . If it were just simple sequence similarity, I would be inclined to think of this as a statistical anomaly. But the paper looks at a whole host of important developmental genetic pathways, and concludes that the nervous system, and possibly even muscle development, evolved independently in ctenophores. I urge you to read the (freely available) paper online. It’s highly surprising, and I’m still not 100% convinced (Update: I’m less convinced now, see my comment to this post). But I’m convinced enough to alter the order and place ctenophores at Rendezvous 31.  Another paper gives a summary of some more conventional phylogenetic analyses and while it shows conflicting results, at least non-ribosomal genes support the idea of ctenophores at Rendezvous 31. Note that this last paper also finds that there could be multiple joining points for sponges (sponge paraphly), but I’m inclined to believe their conclusion that as more sponges are sequenced, sponge paraphyly is likely to lose support.

Filasterea
It’s not terribly surprising that there are many undiscovered, or at least unexamined, single-celled organisms floating around the place. There have always been various rag-bag eukaryotic groups whose evolutionary position was unclear, and this is fertile hunting ground for new discoveries. A paper by  claims to have placed two species Capsaspora and Ministeria in a new group named Filasterea, which is sister to (animals+choanoflagellates). It seems to me quite likely that groupings such as this exists.

Are these the stages to the evolution of animals?

What’s nice about the paper is that Filasterea is not just presented as another obscure group put in a new place. Instead the authors put this in the context of hypotheses about the sequence of evolutionary events which eventually led to the appearance of the animals (diagram to the right). Although I haven’t come across many papers substantiating their claims, I can’t find any refutations either. Since it seems to me quite plausible that obscure single-celled organisms would turn out to be closely related to animals, I’m happy to add this another rendezvous point, albeit one that could be subject to revision in the future.

Unclassified eukaryotes

The major eukaryote groups

In the same way that Filasterea have been given a provisional home, a few other eukaryotic groups are now thought to belong somewhere within the opisthokonts (animals, fungi, and a few single-celled relatives). There’s a recent summary in , and a nicer plot from   which I’ve reproduced here. I’m happy to reserve a rendezvous point for a selection from among the obscure eukaryotes Collodictyon, Rigidifilida, Apusomonads, and Ancyromonads (as labelled in the diagram). As to which of them actually belong here, I’m not sure anyone really knows yet.

Plants (previously Rendezvous 36, now incorporated into “all other eukaryotes”)
In the two papers above it seems to be acknowledged that plants belong in the other main group of eukaryotes: the SAR/Archaeplastida/Excavate grouping. Give the uncertainty 10 years ago, we deliberately fudged the order in the Ancestor’s Tale to give green plants their own rendezvous (this was discussed in the “Uncertain” rendezvous, 37. Now that the root of the tree seems a little more certain (although I suspect still not very solid), I think we should come clean. Hence I’m happy to bung the plants in with the rest of the eukaryotes in a new “uncertain” rendezvous, with potentially a few separate pranching points, depending on the root of the tree. 

In summary – one major change (lancelets and ctenophores), three expected alterations, and a satisfying number of correct guesses. In time, I hope that the evolutionary studies I’ve cited above, and any unexpected new trees, will filter down into the Open Tree of Life. That will give us a continuously updated list, reflecting the latest research. At the moment you can try browsing back from humans, but there are still a few unresolved branching points which are particularly visible when you get off the human/mammalian lineage.

The big list

For a more visible summary of the changes in the past 10 years, here is my revised list. Courtesy of EoL, the photos are all public domain, with larger versions easily available to use in presentations etc. Changes to the previous order are in red, and debatable branches have a question mark, typed in blue where on balance I think our original order still stands. I’m also interesting to see when the joining band contains more species than have accumulated so far: in those cases I’ve gone wild and put an exclamation mark. Protostomes of course, deserve even more exuberance, so they get two.

  1. Chimps
  2. Gorillas
  3. Orang-utans
  4. Gibbons!
  5. Old World Monkeys!
  6. New World MonkeyscI do wish that we could change the word “monkey” so that it also included apes. It’s one of the only cases where by chaining technical usage we could simultaneously make the term taxonomically valid (i.e. “monkeys are all descendants of concestor 6) and fit in with colloquial usage (most people think of a chimp as a “sort of monkey”)
  7. Tarsiers
  8. Lemurs and their kin
  9. Colugos
  10. & Tree Shrews?
  11. Rodents and rabbits!
  12. Laurasiatheres (most other mammals)
  13. Xenarthrans & Afrotheres (armadillos, tenrecs etc.)?
  14. Marsupials
  15. Monotremes
  16. Reptiles including birds!
  17. Amphibians
  18. Lungfishes
  19. Coelacanths?
  20. Ray finned fish!
  21. Sharks & rays
  22. Hagfishes and Lampreys
  23. Tunicates (was #24)
  24. Lancelets
  25. Ambulacraria (starfish etc.)
  26. Protostomes!!
  27. Acoelomorpha (maybe +Xenoturbella)?
  28. Jellyfish and sea anemones
  29. Ctenophores (see comments below)?
  30. Placozoa
  31. Sponges?dpossibly paraphyletic
  32. Choanoflagellates
  33. Filasterea (NEW GROUP)?
  34. Ichthyosporea (old name: DRIPs, was #33)
  35. Fungi (was #34)
  36. New uncertain eukaryoteseThere could be a number of branches in here. Possible taxa that have been suggested are Collodictyon, Rigidifilida, Apusomonads, and Ancyromonads??
  37. Amoebas (was #35)
  38. All other eukaryotes, including plants (were #36) ??
  39. Archaea. Possibly many RV points here (see comments)
  40. EubacteriafAs discussed in the original book, there could be many more branch points if archaea and eukaryotes derive from within the bacteria. It is unclear if a branching tree is a sensible description at this point anyway.

It’s also worth noting that the problem of finding the root of the Eukaryote tree is still a contentious issue, as we discussed in the book, and as re-highlighted in a recent paper . This could potentially add more rendezvous points between 38 and 39. And people are starting to suggest that we eukaryotes are nested within the Archaea, which would produce more points between 39 and 40.

References

Notes   [ + ]

a. For example, O’Leary & the morphologists still seem to be arguing for the basal placental mammal spits to be post Cretaceous, whereas there is near-universal agreement among the molecular people that divergences go back to at least 90-100Mya.
b. although I suspect that because transposition targets certain sites in the genome, there’s more parallel or convergent evolution than often acknowledged
c. I do wish that we could change the word “monkey” so that it also included apes. It’s one of the only cases where by chaining technical usage we could simultaneously make the term taxonomically valid (i.e. “monkeys are all descendants of concestor 6) and fit in with colloquial usage (most people think of a chimp as a “sort of monkey”)
d. possibly paraphyletic
e. There could be a number of branches in here. Possible taxa that have been suggested are Collodictyon, Rigidifilida, Apusomonads, and Ancyromonads
f. As discussed in the original book, there could be many more branch points if archaea and eukaryotes derive from within the bacteria. It is unclear if a branching tree is a sensible description at this point anyway.

12 thoughts on “Ancestor’s Tale list of concestors, revised

  1. Further update: there’s a recent strand of research (http://www.nature.com/nature/journal/v504/n7479/abs/nature12779.html) that argues that the original eukaryotic cell evolved as a result of a symbiosis between a Rickettisial-type eubacterium (we know that already), and a particular type of Archaeal bacterium, one that was nested within the rest of the Archaea. In other words that we are more closely related to some sorts of Archaea than others. I tend to believe this, which would add at least one (Euryarchaeota) – and maybe more then one – new rendezvous at the penultimate end of our pilgrimage. With recent probing of bacterial “dark matter” (http://www.nature.com/nature/journal/v499/n7459/full/nature12352.html), I suspect there may be a good range of Archaeal cousins out there to discover in the next 10 years.

  2. Yet another update: I’ve decided to place Afrotheres and Xenarthrans in the same Rendezvous point, and label culugos as 9 and tree shrews as 10, which changes a few numbers (and I’ve altered the post to reflect that).

  3. Helping my son design an up to date concestor chart for his science class. Have any of the assumptions changed since the last update?

    • Hi – thanks for your question. Within animals, there are still questions about the ctenophores the acoelomorphs (there’s the 4 new Xenoturbella species just discovered, and it’s still unclear where they go) and the sponges.

      There are a *load* of new bacterial discoveries, so that between my RV 39 and 40 we may now have a huge number of extra lineages – search under “candidate phyla radiation”, or CPR. But near to humans, e.g. within deuterostomes, I think the points are pretty secure. Have a look at the new Ancestor’s Tale edition if you like.

        • Are you more confident at this point grouping the xenoturbellids with the ambulacrarians or with the acoelomorphs? The oneZoom chart still shows them grouped with the former, but I was under the impression more recent studies went with the latter. Thanks.

  4. Thank you for bringing this info to life in such an engaging way!

    But I’m having a few problems with this page. I’m not getting what I guess are footnotes to work. I see spinning gears, without any footnote text, and clicking on them doesn’t take me to a footnote or anything. E.g. I read the text “Note that [spinning gear] also examine the sources of conflict in the placement of tree shrews”, which leaves out whoever it is that is examining the conflict. They are distinct from the tiny lettered “notes”, which I see when I scroll down to the “Notes” at the bottom, where there are 6 of them, a-f, and clicking on them goes back and forth in a way that is common on the web. Perhaps some javascript issue with class zp-InText-Citation?

    Also it seems your link to “browsing back from humans” (http://files.opentreeoflife.org/other/synth_viz_dyn.html?ottolID=770315) isn’t working. Perhaps it is now http://www.onezoom.org/life.html?init=zoom#Homininae

    The link to “unresolved branching points” (http://dev.opentreeoflife.org/opentree/otol.draft.22@386974/Holozoa) also isn’t working, and says “click for viz info” which leads to the help text at http://files.opentreeoflife.org/other/info.html

    This is all while browsing from Google Chrome on Linux, or Firefox.

    But I’m still having a blast exploring this!

    • Hi – apologies in getting back to you. I’ve been busy coding the OneZoom software, and rather neglected my blog recently. The footnotes should be corrected now. The Open Tree of Life have changed their URL format, so I’ve adjusted those links by hand. Thanks for spotting the problem. And also thanks for sponsoring the creeping barberry (http://www.onezoom.org/search_for_sponsor?query=McBurnett+&limit=6&display=5&type=all). Do see if any of your friends or colleagues would be interested in sponsoring, so that we can do more to develop the site.

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