Congruence between molecular and morphological phylogenies?

You know what this forum needs? More threads on evolution. To that end, I wanted to talk about a subject I've briefly mentioned before in more depth.One argument I've seen many times on this forum goes something like the below (posted by Taq, many years ago). The 'read more here' in this case was this section on phylogenetics on talk origins, which proudly points out the similarity between a cyt-b phylogeny and an extraordinarily selective 'consensus' tree based on morphology.Now, I think this is a poor argument to use. There are good points to be made about the congruence between different phylogenies, but they should be made very carefully. There is too much tendency to make these statements cavalierly absolute, as Taq did above (following the lead of talkorigins) and if any creationist or waverer reads such and looks into it carefully they are apt to feel deceived.The thing is, molecular phylogenetics is complicated; and any claim that its findings agree completely with traditional morphological understandings of relationships will ring false to anyone who does a bit of follow up reading.Let's take the example of humans. The traditional understanding of our relationships to other animals understood our closest relatives to be the pongids - that is, the great apes: gorillas, orangutans and chimpanzees. The first investigations of this with molecular techniques uncovered that pongids were not a natural group. The African apes, gorillas and chimps, were closer to humans than to orangs. Later, more sophisticated research clarified that chimps are closer to humans than gorillas. DNA did not confirm the traditional tree of great apes; it reshuffled it.But this is just one small example. Let's zoom out a bit to our order, Primates. Primates were traditionally classified in the group Archonta, which also included tree shrews, colugos and bats. All well and good. Except then came along molecular phylogenetics; and we realised that bats do not belong here at all. Bats belong elsewhere on the mammal tree, in a group dubbed Laurasiatheria (a grouping no one had ever suggested based on morphology). The remaining members of Archonta were renamed 'Euarchonta', 'eu' meaning 'true'. Except this might not be true either - since some studies suggest tree shrews are in fact closer to rodents.And what of the group where bats ended up? Who are they now classed with? They belong now with Insectivora and Ungulata. Well, except neither of those groups exist anymore. Some members of both (ie. tenrecs, golden moles, elephants, aardvarks) had to be moved off to a new group christened Afrotheria - yet another relationship which had never been proposed based on morphology. Of the rump groups left, the rest of Ungulata is probably not monophyletic. And whales and dolphins; traditionally considered the sister of even toed ungulates, appear instead to be nested deep within them. This sort of thing is common, incidentally. Groups traditionally classed separately due to a divergent feature or lifestyle, turn out to be nested within their more conventional relatives; rather than sister to them (ie. feylinine skinks, typhlonectid caecillians, pygopodids).This is only a very, very small selection of a couple of quick examples, since this is meant to be an OP. I could go on for many pages; but my point is simply that the talk origins argument is deceptive. And intentionally so. The phylogeny they show (below) is very, very, carefully selected to avoid any of the organisms that would give the lie to their claim of perfect congruence between molecules and morphology. And yet still they fail.Firstly, there's the fact that they have fungi closely related to animals. Which is true. But this is not the traditional morphological arrangement. Fungi used to be considered closer to plants. The relationship between animals and fungi is one established by DNA which upended our traditional understanding. It's fundamentally dishonest to present this as an example of molecular studies supporting the traditional understanding.What's more, even amongst the animal groups selected with such care; they have managed to produce a phylogeny rejected by modern molecular phylogenetics. The flaw was their decision to include iguanas; which morphological phylogenies placed as sister to other squamates. Molecular phylogenies have done away with this concept, however. Iguanas are deeply nested within Squamata; and are closer to snakes than are 'true lizards' of the family Lacertidae. The understanding of science is advanced by teaching people it's complexities. Burying them to make your argument look better has the opposite of effect of making creationist propaganda about evilutionists look true.Edited by caffeine, : typo

Thread copied here from the Congruence between molecular and morphological phylogenies? thread in the Proposed New Topics forum.Funny...I just now saw your thread and your complaint that you were being ignored. Sorry...it happens. Your thread seems like you could make it interesting for some. Let's give it a whirl here.Edited by AdminPhat, : No reason given.

This is an interesting topic that addresses an aspect of taxonomy that I have discussed with friends and colleagues on countless late nights drinking a few beers at dragonfly meetings and conferences.When I was young all we had was morphology along with some aspects of life histories as keys to phylogenetic relationships of dragonflies, but we realized that traditional Linnaean hierarchy was not a good description of evolutionary history for most species.Cladistics gave us a way to describe the evolutionary history of a species or groups of species based on speciation events.Molecular studies started being published and the technology advanced fairly rapidly. Early in the development of molecular methodology there were often results that disagreed with what we thought we knew from morphology. Sequencing multiple genes allowed better resolution and better confidence in the results.Recently (2016) some friends of mine published a revision of the genus Gomphus in North america. There are 5 authors, 2 of whom are molecular specialists and 3 of whom are morphological systematists, one who is also a nymph specialist. Phylogenetic relationships of North American Gomphidae and their close relatives A pdf is available at this site as well as the full text of the paper.Abstract:

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Intrafamilial relationships among clubtail dragonflies (Gomphidae) have been the subject of many morphological studies, but have not yet been systematically evaluated using molecular data. Here we present the first molecular phylogeny of Gomphidae. We include six of the eight subfamilies previously suggested to be valid, and evaluate generic relationships within them. We have included examples of all genera reported from the Nearctic except Phyllocycla. This sample includes all North American species of Ophiogomphus, which has allowed us to explore intrageneric relationships in that genus. Our particular focus is on the closest relatives of the genus Gomphus, especially those North American species groups that have been commonly treated as subgenera of Gomphus. The Gomphus complex is split into additional genera, supported by molecular and morphological evidence: Phanogomphus, Stenogomphurus, Gomphurus and Hylogomphus are here considered to be valid genera. The genus Gomphus, in our restricted sense, does not occur in the western hemisphere; in addition, G. flavipes is transferred to Stylurus.

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Multiple genetic sites were compared for each species.

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We used nuclear and mitochondrial protein coding [histone 3 (H3), and cytochrome c oxidase subunit I (COI)] and ribosomal (12S, 16S, and 28S) primers for amplification.

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Collaborations between gene jockies and morphologists makes these studies much more robust.Sometimes when you see a paper with a string of authors, the assumption is made that some of them may have been subordinate to others. That is not the case here. All five of these authors are considered to be at the top of their field.

It's actually remarkable how close the old boys got just by looking at the outside of beasts and drawing them.

Well they didn’t really get anywhere by looking at the outside, of course. Where they were right, the important clues were much more often based on internal anatomy, histology, embryology and life history. Vertebrate systematics in the days before protein and gene sequences relied heavily on skeletal structure; and in some senses it still does today since this is the only evidence we have to incorporate most extinct species.Traditional classifications based on just looking at the outside of beasts tend to be either blindingly obvious (you don’t need special training to figure out that lions and tigers are both cats); or wrong (such as putting pangolins with xenarthrans because they vaguely resemble armadillos).

Yeah, but hyenas are more closely related to cats than to dogs. Who would have thought that, except for those guys who actually studied hyenas closely? They were actually right.

Don't chuck it away that quickly; for example the keys that entomologists still use to distinguish between seemingly identiical species of hairy flying things were all built on detailed drawings but sure, just counting legs and wings narrows things down farly quickly.Of course the more we are able to see, the more complicated things become but it's still quite important to point out that the discovery of DNA and molecular genetics fully supports the original theory which was built primarily on observation and lists of parts.It's obvious that it should be that way but it didn't actually have to be. In the human world we build houses out of radically different materials and use different methods than cars; given the task, we probably would not make a an ant using the same building blocks as a whale a tree or a mushroom. The discovery of DNA could easily have disproved the ToE, but it didn't.

And this is what I meant in the first post about there being very good points to be made. My point was that they should be made carefully. If some impressionable young creationists hears the cavalier declaration that the phylogeny of some protein or gene perfectly matches the traditional morphological phylogeny; then I worry what they think should they read a bit further and discover that the phylogenies of different genes contradict one another and morphological phylogenies (or the fact that there isn't really one morphological phylogeny).On the subject of counting the legs of creepy-crawlies; I missed one more problem with the talk origins picture - one of the more surprising revelations of the molecular era of phylogenetics. Insects are placed wrongly above, since it turns out that they actually branch quite deep within crustaceans. Insects are, in a sense, weirdly modified flying land shrimp.