Best Mammal Evolutionary Trees?

These mammaless days mean I finally have some time to improve the taxonomy of my global mammal checklist  (with generous help from Don Roberson and others). At the moment it lists the genera alphabetically within families, rather than by how closely they are related. I’m using the Handbook of the Mammals of the World to fix that.

At the same time I would like to use the “best” family tree (cladogram) out there to organise the whole list but there are several to turn to.  There is this one from 2011 or these two from the American Natural History Museum, and doubtless more.

I have two questions for those more expert than me (i.e. pretty much everyone)

Is there any (near) consensus yet on whether morphology or genetics is the way to go when ordering these?

And what is the leading (or your favourite) evolutionary tree?

Jon

15 Comments
  1. Morgan Churchill 5 months ago

    I have also been going through and reorganizing my lists due to COVID limiting my many of my hobbies. I haven’t gotten to mammals yet, focusing on bird and herps so far. I am also not going down to organizing things by genera and species, merely making sure orders, families, and subfamilies are arranged in proper order. When I do finish the mammals, I would be more than happy to share the classification.

    For higher level relationships (How orders are related to one another), I would almost certainly go with molecular trees. The early radiation of mammals after the extinction of the dinosaurs was so rapid and extreme that its hard to sort out how major clades are related to one another.

    I am not aware of the differences in morphology versus molecules for most groups of mammals, only those I have experience with. In general, among marine mammals the most recent comprehensive morphological analyses, especially those with fossils, generally agree with one another. The biggest conflict is generally with how many genera should be recognized, which is especially problematic with delphinids and phocids. I believe there is general genus level concordance for carnivores in general as well. Once you get down to species, all bets are off. If I were you, I would not worry about ordering of taxa beyond the generic level…we often don’t have a lot of data available for many species. I would just live species within a genus in alphabetical order.

    Overall, I would go with molecular data, but try to stick with more recent studies and preferably those which use both nuclear and morphological.

    • Profile photo of Jon Hall Author
      Jon Hall 5 months ago

      THanks Morgan – I was hoping you would comment! I certainly won’t even try going below genus level. Would be very useful to see what you have done when you finish your organizing. Thanks

  2. Profile photo of Vladimir Dinets
    Vladimir Dinets 5 months ago

    Historically, mammalian systematics were heavily based on skull morphology, particularly teeth. In a few cases it created strong bias that was (and still is) corrected by molecular studies. Also, many mammalian orders branched off at roughly the same time (likely just after the dino extinction), so building the high-level cladogram was difficult. Until molecular methods became available we didn’t know about Afrotheria etc. Anyway, you can’t just stick to morphology nowadays.
    I have constantly-updated checklist where everything is listed by relatedness rather than alphabetically, in case you are interested, but it is simplified (only species, genera, families and orders).

  3. Manuel Ruedi 5 months ago

    Dear Jon, Dear Morgan,

    As you certainly know, bat phylogenies are part of my main job, and placing them
    into the biggest view of mammal radiation inevitably comes with it… I concur with Morgan that the deeper nodes of the mammal radiation could certainly be better resolved with multiple genes rather than by getting new key fossils, although actually both approaches generally illuminate each others.
    The problem is having both a species-level phylogeny (i.e. crown groups resolved), and the deeper nodes resolved on the same tree. Technically, it is almost an impossible endeavor, even with entire genomes (not only because a tiny fraction of those species have been sequenced so far). A very good paper addressing this question is to be found here (https://www.researchgate.net/publication/304557527_Mammal_madness_Is_the_mammal_tree_of_life_not_yet_resolved). So the usual way is to build backbone trees with supermatrices, etc. But beyond few groups (primates, carnivorans), you will end-up with choosing to mix alternative and incomplete trees with conflicting relationships…
    My preferred global phylogeny for bats has been constructed this way and is really remarkably reasonably resolved (https://link.springer.com/article/10.1007/s10914-016-9363-8) but the trees used are already 5-6 years old, and many new phylogenies (and species/genera/even families) have been published since then.
    So a global phylogeny of all species of mammals would be really cool (like the one which exists for birds), but it does not exist yet (to my knownledge), and a lot of more or less manual input will be necessary. For sure, I’ll stay tuned on this discussion!
    Take care.
    Manuel Ruedi, Geneva

    • Jens Krause 5 months ago

      Hi Manuel,

      It is interesting that you should say that about birds when especially birds have come under renewed scrutiny and it is suspected that up to twice the number of species exists:
      George F. Barrowclough, Joel Cracraft, John Klicka, Robert M. Zink. How Many Kinds of Birds Are There and Why Does It Matter? PLOS ONE, 2016; 11 (11): e0166307 DOI: 10.1371/journal.pone.0166307

      best wishes

      Jens

  4. Paul Carter 5 months ago

    Hi Jon. Over the last 4-5 years I have slowly been ordering my data down to species group levels in parts (not advised if you have a real job in the real world); currently working on neatening it up, and revisiting parts neglected for a while. The AMNH figure (morphology vs genetics) that you referred to is from Springer et al 2004 (Trends in Ecology and Evolution, 19 (8): 430–438). Re Q2 – I like the style of the tree shown as Fig 1 in Graphodatsky et al (2011; Molecular Cytogenetics 2011 4: 22), also 10 years old, ignoring Chiroptera and Perissodactyla grouping etc. Paul

  5. Paul Carter 5 months ago

    Hi Jon. Fig 1 in Esselstn et al (2017) – Genome Biol. Evol. 9(9):2308–2321 doi:10.1093/gbe/evx168 is also useful.

  6. Paul Carter 5 months ago

    Hi Jon. I don’t think my last post went through; referring to “Esselstyn et al (2017 Aug). Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements. Genome Biol. Evol. 9(9):2308–2321”. Fig 1 is useful. In my data though I have Laurasiatheria before Euarchontoglires (as in the Foley 2016 paper referred to by Manuel above). Paul

  7. Michael Kessler 4 months ago

    Hi Jon, I won’t comment on the phylogeny, that is beyond my scope. In fact, I am very happy with the current arrangement; makes it easy to find things. But I have another suggestion, in case you are really bored: what I would find very helpful in the list would be short distributional notes (such as “Sahel zone from Senegal to South Sudan”) for each species. I enjoy going through the list to see what I haven’t seen yet and while I know where Okapi occurs, for many species I don’t know the ranges off the top of my head. Michael

    • Profile photo of Jon Hall Author
      Jon Hall 4 months ago

      I hope I won’t have that sort of time or boredom! Though if COVID is around for another 6 months then maybe. That said the guys at IGOTERRA are adding range info for a lot of mammals in their system and there will soon be a post about this.

  8. Profile photo of Vladimir Dinets
    Vladimir Dinets 4 months ago

    BTW, an interesting paper I missed: Schiaffini et al., 2013, Zool. J. Linn. Soc. 167:327-344. The authors show that there is only one species of skunk in southern S America; Conepatus rex and C. humboldti are synonyms of C. chinga.

  9. Profile photo of Paul Carter
    Paul Carter 4 months ago

    Thanks Vladimir. I checked red list and they concluded (on a 2016 assessment) that “A recent revision including morphological, molecular and pelage coloration analyses proposed that Conepatus chinga and C. humboldtii are conspecific, and as C. chinga has page priority, this should be the valid name for the species (Schiaffini et al. 2013). The same authors (p. 341) wrote that “samples from Chile, DNA samples from this country and from north-west Argentina, and other genes will help to test this hypothesis and the conclusions presented in this paper” and pending such corroboration, the Red List maintains the treatment as two species”. Paul

  10. Profile photo of Paul Carter
    Paul Carter 4 months ago

    Thanks Vladimir – I will have a look.

  11. Profile photo of twilighter
    twilighter 4 months ago

    Very interesting discussion!
    The last 5th edition of Mammalogy: Adaptation, Diversity, Ecology have quite up to date Classification of mammals above the species level, including Superorders and Magnaorders arrangement.

    An updated Manual of the Mammalia An Homage to Lawlor’s “Handbook to the Orders and Families of Living Mammals” also coming out soon. You can see the list in the description below:

    https://www.nhbs.com/3/academic-and-professional-books?q=&hPP=60&idx=titles_date_desc&p=0&fR%5Bhide%5D%5B0%5D=false&fR%5Bhide%5D%5B1%5D=false&fR%5Blive%5D%5B0%5D=true&fR%5Blive%5D%5B1%5D=true&fR%5Bshops.id%5D%5B0%5D=3&fR%5Bshops.id%5D%5B1%5D=3&hFR%5Bsubjects_books.lvl1%5D%5B0%5D=Mammals%20%3E%20Mammals%3A%20General&qtview=219304

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