University textbook, Vertebrate Paleontology, by Michael J Benton: a focused review p2 – placentals

In the phylogenetic battle between traits and genes
author and paleontology professor Michael J Benton (2014) chose genes and lost fossils in his cladogram of placental mammals (Fig. 1). Benton writes, “The phylogeny of placental mammals has been substantially overturned by the application of molecular phylogenetic techniques.”

The resulting cladogram is a confusing mix
where university students are told that bats (Chiroptera) and horses (Perissodactyla) are close relatives (Fig. 1), among many other faults (see below). This should scare you if you plan on buying this book or paying tuition to attend Benton’s lectures.

Figure 1. From Benton 2014, a gene-based cladogram of placental mammals turned 90º. Colors added here. Green areas are supported by the LRT. Red areas are not supported.

This should also scare you away
from using suprageneric taxa in a cladogram. When you don’t use generic or species-grade taxa too much is left unsaid, leaving too large of a gap between taxa (e.g. no taxa nest between bats and whales in Benton’s cladogram, Fig. 1).

And don’t omit fossil taxa
for the same reason.

This is why
the large reptile tree (LRT) tests 1907 generic taxa (including fossils) based on traits. In the LRT bats are not related to horses, as every grade-schooler knows, but every university paleo student has to swallow and regurgitate on tests to get a good grade.

deep time analyses based on genes too often deliver false positives. Get used to it. It’s a fact of life. Gene results are based on trust with no correlates (at present) determining skull/orbit ratios, presence of a quadratojugal, etc. Benton trusts that someday a last common ancestor of horses and bats exclusive of whales and cows will be found. Good luck with that.

By contrast,
trait results in the LRT have no trust issues. Traits document evidence you can see and measure with calipers from snout to tail tip. Trait results deliver a gradual accumulation of evolving traits at every node of the LRT, and that includes fossil taxa.

Lets look at some other issues in Benton’s cladogram
from top to bottom:

= aardvarks. In the LRT aardvarks (Orycteropus) are naked armadillos in the clade Xenarthra.

= elephant shrews, but elephant shrews are diphyletic in the LRT. Macroscelides nests between Tupaia, the tree shrew and Chrysochloris, the golden mole. The unrelated Rhynchocyon nests with tenrecs, derived from fossil anagalids and leptictids.

= golden moles (Chrysochloris), tenrecs (Tenrec), hedgehog tenrecs (Echinops), otter shrews (Potamogale) and shrew tenrecs (Microgale). In the LRT many of these taxa nest at the bases of several trait-based clades, all with a tree shrew-like ancestor not recognized by Benton’s cladogram (Fig. 1).

Proboscidea, Hyracoidea and Sirenia
= elephants, hyraxes and manatees. In the LRT these taxa are also related, but they have a deep fossil history and are not closely related to the taxa listed above in Benton’s gene-based cladogram (Fig. 1).

= sloths, armadillos and anteaters. In the LRT these highly derived taxa are also related to each other, but they have a deep fossil history and do not give rise to elephants and golden moles. Based on skeletal traits aardvarks are xenarthrans.

Lipotyphyla = Eulipotyphla
(formerly ‘Lipotyphla’ – Afrosoricida = ‘Erinaceomorpha’ + ‘Soricomorpha’) = hedgehogs, moonrats, shrews, solenodons, and moles. In the LRT all are members of Glires (alongside shrews, rodents, rabbits, plesiadapiformes and multituberculates) in the LRT. One exception: Talpa, the mole, nests with mongooses in the Carnivora. Uropsilius, the shrew-like mole, still nests with other shrews (see below).

= pigs, camels, deer. In the LRT these taxa are also related. Hippos are not related.

= whales. In the LRT odontocetes arise from fossil pakicetids and echo-locating tenrecs. Mysticetes arise from fossil mesonychids, extant hippos and fossil desmostylians.

= bats. In the LRT bats and pangolins share a small, fossil tree shrew last common ancestor after the split from colugos. Horses and rhinos? No.

= horses and rhinos. In the LRT these taxa are related to each other, but are not related to bats.

= mongooses, bears, seals, sea lions, cats and dogs. In the LRT these taxa are related to each other (and add the mole, Talpa, see above), but are not related to horses and rhinos. This is the first clade to split from the others in the placental subset of the LRT, not one of the last (Fig. 1).

= pangolins. In the LRT pangolins are closer to bats and colugos than to carnivorans.

Rodentia, Lagomorpha
= rats, porcupines, squirrels, etc. In the LRT these taxa are also related to each other (plus the aye-aye, Daubentonia, hedgehogs, moonrats, Solenodon) in the clade Glires.

= tree shrews. In the LRT tree shrews are basal arboreal placentals arising from derived didelphid marsupials.

= colugos (flying lemurs). In the LRT dermopterans arise from tree shrews. So sometimes genes and traits match.

= lemurs, monkeys, apes. In the LRT these taxa are related to one another, but arise from tree shrews, not the other way around as shown in Benton (Fig. 1).

Who is to blame for this mess?
Author MJ Benton?
He borrowed gene studies from O’Leary et al. 2013 and they were published in Nature. So, if so, he was scammed. (See yesterday’s post for more of Benton’s backstory).

Professors around the world who ordered Benton 1990, 1997, 2005 and 2014?
Teaching is how professors make their living and Benton’s book is what they taught and were taught for the last thirty years. So, if so, they were scammed.

Students who bought Benton 2005 and 2014 without vocal objection?
Naive freshmen just want to learn all there is to learn about paleontology. They trust that their book and tuition monies are being spent properly. They don’t have the background to say, ‘that seems untenable.’ So, if so, they were scammed.

Outsiders armed with a wide-gamut trait analysis who point out the mess?
Funny. That’s who gets the name-calling and criticism for doing the work and trying to help.

A wide-gamut, trait-based cladogram based on traits and including fossils,
is a powerful tool. You should have one if you’re interested in vertebrate paleontology, if you teach vertebrate paleontology and especially if you write textbooks on vertebrate paleontology.

Benton MJ 2014. Vertebrate Paleontology 4th ed. Wiley-Blackwell 480pp.

wiki/Lipotyphla (wiki/Eulipotyphla)

12 thoughts on “University textbook, Vertebrate Paleontology, by Michael J Benton: a focused review p2 – placentals

  1. Maybe you should actually try and sit in on a lecture or lab class (they’re not brainwashing stations) or visit a professor (they’re not supervillains) before pretending to know about how university education works. These posts only demonstrate your complete ignorance of how biology classes are structured and taught, how educational institutions operate financially, as well as your intense and hostile anti-intellectualism and conspiracism. The world you are portraying resembles internet conspiracy theory videos and caricatures from movies and comic books, utterly detached from real life.

    As a side note, there are thousands of amateurs in the vertebrate zoology/paleontology community, none of these outsiders find your self-professed ‘outsider’ views compelling and for good reason; they are not, your methodology is bad. You have never actually ever paid any attention to anything they have been telling you (people would notice if you did), but there have been thousands of times when you were confronted about why your methods are bad and how you could improve them, often by those very amateurs and outsiders, you ignore everything they say and stubbornly or lazily (it’s often hard to figure out exactly which) refuse to improve your methods, insisting they are at fault and that there is a conspiracy afoot to rake in money for those villainous brainwashing professors.

    • You’re changing the subject from a textbook to a lecture class. Focus on the textbook. The only problem I have is with the textbook, nothing else.

      You say my methodology is bad. Running a wide-gamut, trait-based phylogenetic analysis is good methodology. This is something Professor Benton has not done for his textbooks. So, with that in mind, please direct your anger at Dr. Benton. Kindly encourage him to add taxa.

      When you say “thousands” I suspect hyperbole. You’re running on emotion. Come back down. Put your lab coat on and approach whatever irks you with the cool detachment of a scientist. Get real, then get back to me. There’s no place for hyperbole, invective and anonymity in science, that is, if you want to be taken seriously.

      • “This is something Professor Benton has not done for his textbooks.”

        Of course not. Nor should be expected to have done so. This is a textbook. It’s intended to summarize the literature for students new to the field. The kind of “wide-gamut” analysis you refer to – which should include more characters than taxa – belongs in the peer-reviewed literature, as all such analyses do.

        Benton did what I would have done, had I written this book – rather than try to work out relationships among sharks, temnospondyls, or early synapsids (for example) for myself, I’d have looked to what the actual experts who’ve seen the specimens for themselves have said about the subject. If someone’s devoted years or even decades to the study of a group, my confidence grows – though students and non-professionals with no substantial track record also make central contributions. If they made mistakes, or if new discoveries overturn what they concluded, I would expect subsequent analyses to add this information. This would prompt a revised edition.

        I’d be looking for consensus. What are the experts saying?

        There’s a lot of information out there. How would I assess the fitness of this information for consideration in any such textbook? First, I’d apply what I know about phylogenetics. Were taxon and character sampling adequate? Were appropriate methods applied? When was the analysis done? (This is important for contextualizing the first two questions. An analysis of, for example, cetacean phylogeny using molecular data including only 8 whale species would be marginal now, but in the 1990’s, that might have exhausted the data available to the researchers; capabilities to obtain data from large numbers of species, and to analyze them, have advanced quite a lot since then.)

        I would also insist that the analysis be published in the peer-reviewed literature.

        Textbooks should not be treated as though they’re the primary literature. They should be treated as an introduction to it.

      • Point well taken about textbooks vs primary literature, Chris, but the bottom line is this: Benton’s cladograms about evolution don’t show evolution. Bats with horses = magical thinking. Scleromochlus with pterosaurs = magical thinking and citation omission. Let’s leave students with the idea that we’ve thought this out. That we were critical of untenable results. That we put science and evidence ahead of money, peer group pressure, reputation, deadlines, etc. That we didn’t take the easy way out by citing the work of others as our excuse for adding untenable relationships to our textbooks. That we didn’t omit literature that overturned our pet hypotheses. When the primary literature is wrong, we should have the fortitude to point that out.

        I’m a little disappointed in the replies since no one, so far, has said, “Yeah, Benton was wrong and so were his sources. Bats don’t nest with horses. Thanks, Dave. I’ll send an email to Benton to make sure he changes that for the next edition.”

    • MG: May I suggest you contact paleontologist, Darren Naish? You’ll find in him a sympathetic ear. You seem to share views, cadence and tone. Both of you seem to be on the same page and need to move on to the next chapter.

      • Re: Benton’s (admittedly composite) cladograms allegedly “not showing” evolution:

        “…given the Hennigian convention that a parental species goes extinct when it undergoes speciation, it is de facto necessary that cladists acknowledge the existence of ancestral species. The trouble is, these are only diagnosable by symplesiomorphies, and so are difficult or impossible to identify unambiguously. Cladists’ rejection of ancestral species thus represents a razor of silence––we do not deny that they existed, but we cannot empirically discover them, so we omit them from our hypotheses of relationship. This also is the reason why fossils and extant taxa are treated as equivalent terminals in cladistic analyses…”

        “Another flashpoint for criticism is the notion that pattern cladists view cladograms as “atemporal synapomorphy schemes”, with the accompanying insinuation that this represents a denial of ancestry and descent, and an adoption of Platonism (e.g. Scott- Ram, 1990). Once again, the cladistic position is a razor of silence. Nobody denies that time is a real dimension, or believes that the objects of systematic study reside on a supernatural plane populated by atemporal Platonic forms (except, perhaps, those who believe phylogenetic relationships can be described with statistical models). Even Richard Owen considered his vertebrate archetype to represent a conceptual ground plan, rather than an idealized perfect form (Rupke, 1994). The cladists’ empiricist perspective leads them to treat fossils as remnants of organisms, with features that can be compared as homologues with those of other organisms, rather than as potential ancestors, by virtue of the fact that they are old. Thus, fossils appear as terminals on cladograms like any other taxon, and the vertical axis represents a simple empirical scale of relative degree of relationship or branching order that is implied by the evidence from the specimens themselves, rather than a chronogram’s theory-laden absolute time axis.

        When we consider the supposed differences of philosophy between pattern and process cladistics, we find that all of these also represent razors of silence on the part of pattern cladistics, rather than razors of denial. No cladist I am aware of has ever denied that evolution occurred. There may be some differences of opinion about particular mechanisms, but the general propositions of change through time and descent with modification are consistent with observable microevolutionary phenomena and with more inclusive patterns that systematists have discovered (Darwin, 1859). Even at his most dismissive, Colin Patterson (1982a:55) said only that “belief in, or knowledge of, evolution is clearly unnecessary for the analysis of homology”, and Nelson and Platnick (1981:159), “that, synapomorphy has the same empirical basis as homology, that both concepts are interdependent, that both may be considered without reference to evolutionism, and that an evolutionary element of interpretation may be added to them without necessarily changing their empirical basis.” These are plainly not denials that evolution is a good explanation of phylogenetic pat- terns, but merely statements that one does not need evolutionary theory to draw systematic inferences (cf. Brower, 2000).”

        – Brower, A. V. Z. (2019). Background knowledge: the assumptions of pattern cladistics. Cladistics, 35(6), 717-731

      • re: “The trouble is, these are only diagnosable by symplesiomorphies, and so are difficult or impossible to identify unambiguously.”
        I am guessing that you are talking about the software logic. In a cladogram, even one filled with convergent traits, the particular pattern of convergent traits is well-handled by PAUP.

        re: “The cladists’ empiricist perspective leads them to treat fossils as remnants of organisms, with features that can be compared as homologues with those of other organisms, rather than as potential ancestors”

        So, where do (and other extant taxa) come from? And which clades are no longer with us? These are questions that a cladogram answers through the blur of glasses that do not see every organism that ever lived, but see enough to make out patterns.

        re: “statements that one does not need evolutionary theory to draw systematic inferences.”

        Sorry Dr. Brower feels that way. Here a cladogram is a telescope time machine enabling one to see as many stages (as one is allowed and able to enter) describing in a detailed way descent through natural selection, subject to change with new data.

      • Just in case you’re implying that the comment above is from me and that I was using a pseudonym — nope. MG sounds to me like someone who knows what they’re talking about it and sees through your conspiratorial worldview and anti-intellectualism.

        Slow clap on your continual efforts to erode expertise and install yourself as new Science King of the World. Oh, and funny how yet again you forget to remind people that your hypotheses are _your hypotheses_ as posted on your blog, and are thus substantially inferior to the results Benton is talking about in his textbook.

        As usual, am screengrabbing and sharing this in case you delete it.

      • Darren, I hope you don’t continue to support hypotheses based on taxon exclusion. Come back to science. Create your own analysis. Add taxa. It’s not that hard. You’ve been complaining about since 2012. When are we going to see something from you to back up your claims?

        Some of my hypotheses do await confirmation. Others have been confirmed. A good hypothesis predicts results, so when others include the same taxa my hypothesis predicts others will find the same results. And they have. No matter the method. Unfortunately, many PhDs in your circle seem reticent to include pertinent taxa. The paper trail for that statement keeps getting longer and longer. Why is that? Why don’t PhDs and grad students test published contenders? Why do they borrow cladograms and illustrations from others, even some from 1870.

        re: new Science King of the World. The LRT is a powerful tool. Sarcasm is not. I worry that readers who see your comments will see you as spectator yelling at the players, rather than getting on the field, showing your stuff and being a player. It is not too late to turn that perception around.

      • PS re: “substantially inferior to the results Benton is talking about in his textbook”
        For starters, please support the pterosaur – Scleromochlus relationship — without omitting Cosesaurus.

        On a more general topic, please be aware of this thing called “projecting”. From Google: “Psychological projection is a defense mechanism people subconsciously employ in order to cope with difficult feelings or emotions. Psychological projection involves projecting undesirable feelings or emotions onto someone else, rather than admitting to or dealing with the unwanted feelings.” This is where vindictive name-calling comes from.

        On the same subject, your comment: “new Science King of the World” comes dangerously close to narcisism: “involving a sense of entitlement, a lack of empathy, and a need for admiration.” Reminds one of “Why the World has to ignore” from 2012. Evidently you live on a big stage, Darren. Try to bring it down to just a mouse skull or fish fin.

  2. As has been pointed out on innumerable previous occasions, the scope of the work required is vast (“the work” = the building of a well supported, taxonomically inclusive vertebrate phylogeny). I’m busy with lots of projects (quite funny for you to claim that I’m not a ‘player’, that I’m not active in the field), but one thing I’m not doing, nor planning to do, is build my own grand multi-taxon analysis. It’s just too much work. And don’t pretend that you’ve done it, because – as is pointed out to you in virtually every single comment left at this site – you’ve done a job that no specialist is happy with, for reasons you continue to ignore and explain away.

    As for the comments about projecting and my ‘Science King of the World’ thing — I’m deeply confused. You, dear David, are the one perpetually claiming everyone else to be wrong; _you_ are the one presenting your models as if they represent some ‘new truth’; _you_ are the one proclaiming the rest of us to be in some kind of blinkered conspiratorial cabal; you are the one making out that you’re on to something big. Difficult to see how drawing attention to this involves projecting on my part. Difficult because to do so would be wrong.

    • re: “It’s just too much work.” Darren: You can use your cladogram with the authority it will give you for the rest of your life. The other side of that coin is, when you do report what your cladogram results are, some young guy like you (without a cladogram) ten years from now will act like you’re acting. We call that convergence.

      re: “no specialist is happy with” Feelings are not science. Evidence is science. Bring on the evidence. I will add to the 150,000 changes I’ve already made over the past 11 years. Not happy about those errors, but I learn as I go and everything is new. The definition of research is studying things that have never been studied before.

      re: “everyone else to be wrong” I report results. Taxon exclusion is something that comes up alot. Ohhhh, Nowwww I see your point: specialists are not happy because I point that out. A simple oversight or two sometimes ruins an otherwise comprehensive paper. Sometimes that oversight is on purpose. And that is not so innocent.

      re: “new truth” The one thing you just said, “too much work,” is the one thing that will have you changing sides in this argument. So, all I can say is: it’s not too late. If you add a cladogram to your future, your entire outlook will change. Don’t be cross with someone who has done the work. People can see through that. It’s almost an Aesop Fable: the fox can’t get to the grapes, so he grumbles they must be sour.

      Looking forward to your progress and attitude change once that cladogram starts growing!

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