Schwartz, Molecules, and Morphology: There Can Be Only One

Connor MacLeod: How do you fight such a savage?
Ramirez: With heart, faith and steel. In the end there can be only one.

Rudolf Raff, in The Shape of Life, has an interesting discussion on attempts to iron out the relationships between lungfish, trout, and humans. On the surface it is quite simple. Lungfish are more closely related to humans than trout are. The lungfish has some adaptations to air breathing and one of the questions raised by the above relationship is whether these adaptations are homologous to those of tetrapods, or are they independent solutions to the same problem.

Enter the coelacanth. Morphological analyses of where the coelacanth fit into the above scheme yielded conflicting results as did various and sundry molecular analyses. One of the keys to solving the problem came in a mitochondrial DNA analysis that indicated a lungfish-tetrapod clade with coelacanths as the next branch and finally ray-finned fish. Assuming this is true, what can the fossil record and morphology tell us? This is where the story gets interesting. According to Raff, the lungfish, the coelacanth, and tetrapods are the few surviving members of a, once, more diverse rhipidistian clade. Early lungfish were deep sea forms that had gills, while modern forms are air breathers. Getting back to the question above, this means that the adaptations to air breathing are convergent with tetrapods. Raff concludes:

An especially striking demonstration of this conclusion is that the earliest know tetrapod, Acanthostega from the upper Devonian of Greenland has been shown by Coates and Clack to have had functional internal gills. It probably also possessed lungs, which were a primitive feature shared by bony fishes. Tetrapods have lost their gills in becoming more terrestrial. The first tetrapods thus convergently resembled modern lungfishes more than they resembled the earliest lungfishes. [page 162 - afarensis]

The molecular data wasn’t wrong, just incomplete due to missing taxa. In this case the taxa were missing due to extinction and this problem also, one thinks, affected the morphological analyses. I suspect that one could achieve the same affect by simply omitting some species from a morphological analysis. The point to take away from this is that in order to untangle the problem, both molecules and morphology were required. Not to mention more data. All to often, morphology and molecular analysis have been presented as being in some kind of zero sum conflict where there can be only one.

Which brings me to an article, published in the Journal of Biogeography, by Grehan and Schwartz called Evolution of the Second Orangutan: Phylogeny and Biogeography of Hominid Origins. [Note: It was open access at one time but doesn't seem to be anymore - at least the link I have doesn't seem to work]. Schwartz has been arguing for years that humans are more closely related to orangutans than to chimps and gorillas. Schwartz is engaged in just such a zero sum conflict as I mentioned above. For Schwartz the morphological evidence relating humans and orangutans is overwhelming and if the molecular evidence (as far as I know he doesn’t mention the chromosomal evidence) indicates otherwise, it is just plain wrong. At any rate, in this paper Grehan and Schwartz examine 56 traits from the species listed below:

Sahelanthropus, Ardipithecus, Kenyanthropus, Lufengpithecus, Pongo, Sivapithecus, Ankarapithecus, human, Homo, australopiths, Orrorin, Hispanopithecus, Ouranopithecus, Khoratpithecus, Gigantopithecus, Dryopithecus, Pan, Gorilla, Hylobates (Hylobatidae), monkeys. [Note: This information comes from the supplementary material]

A number of these, such as Lufengpithecus, Sivapithecus, Ankarapithecus, and Khoratpithecus are related to orangutans. Hispanopithecus may or may not be in the orangutan clade and has a number of traits linking them to orangutans, although some have placed them in the Dryopithecines. Ouranopithecus, also called Graecopithecus, has been considered to be either in the orangutan clade or the sister group of Plio-Pleistocene hominids (I’m skeptical of this), among other things. Taxa with more than one species, such as the austalopiths and Dryopithecus were analyzed as a single taxonomic unit. Basically, the analysis is orangutan heavy and, truth be told, not very informative. Grehan and Schwartz present the results of four analyses:

Figure 2 Phylogenetic relationships and bootstrap values for living and fossil large-bodied hominoids. (a) Single most parsimonious tree for extant large-bodied hominoids supporting the monophyly, respectively, of humans (Hominidae) and orangutans (Pongidae) and of the African apes (Panidae). (b) Consensus tree for large-bodied hominoids supporting the monophyly of living (humans) and fossil hominids (Homo, australopiths) as the sister-group to orangutans. (c) Consensus tree supporting the monophyly of hominids and various Miocene–Pliocene fossil apes and orangutans into a ‘dental-hominoid clade’, with the African apes as a sister clade along with the putative hominids Ardipithecus and Sahelanthropus. The heuristic search was made with a random seed = 100, replicates = 50,000, saved trees/ replication = 10, tree bisection–reconnection (TBR) option and replacement of existing trees. (d) Consensus tree for fossil and living largebodied hominoids with fossil taxa limited to those with 14 or more shared character states as the maximum number of taxa providing resolution of relationships within the dental-hominoid clade.

Figure 2 Phylogenetic relationships and bootstrap values for living and fossil large-bodied hominoids. (a) Single most parsimonious tree for extant large-bodied hominoids supporting the monophyly, respectively, of humans (Hominidae) and orangutans (Pongidae) and of the African apes (Panidae). (b) Consensus tree for large-bodied hominoids supporting the monophyly of living (humans) and fossil hominids (Homo, australopiths) as the sister-group to orangutans. (c) Consensus tree supporting the monophyly of hominids and various Miocene–Pliocene fossil apes and orangutans into a ‘dental-hominoid clade’, with the African apes as a sister clade along with the putative hominids Ardipithecus and Sahelanthropus. The heuristic search was made with a random seed = 100, replicates = 50,000, saved trees/ replication = 10, tree bisection–reconnection (TBR) option and replacement of existing trees. (d) Consensus tree for fossil and living largebodied hominoids with fossil taxa limited to those with 14 or more shared character states as the maximum number of taxa providing resolution of relationships within the dental-hominoid clade.

The first (a in the picture above) is relatively straight forward. Chimps and gorillas are the sister group to a clade composed of humans and orangutans. The trouble becomes apparent when Grehan and Schwartz start introducing fossil species into the analyses. In the second analysis (b in the picture above) chimps and gorilla are the sister group to a clade composed of orangutans and fossil and modern humns. The analysis could not resolve the relationships between australopiths, fossil homo, and modern humans. In the third (c in the picture above), chimps, gorillas, Ardipithecus, Dryopithecus, and Sahelanthropus form a clade that is the sister group to a clade containing, well, everything else (Grehan and Schwartz’s dental hominoid clade). Of this result Grehan and Schwartz have this to say:

While our morphological analysis of living taxa contradicts the interpretations of an array of recent studies based on molecular comparisons, the proposed monophyly of hominids (Homo and australopiths) and orangutans to the exclusion of the African apes is further corroborated by the analysis of fossil taxa – including several Miocene hominoids that have otherwise been largely marginalized in the biogeographical exploration of hominid origins and evolution – which collectively comprise a clade we descriptively refer to as ‘dental hominoids’. Monophyly of a dental hominoid clade encompassing all living and fossil representatives is only weakly supported because many taxa are known only from partial remains and there is currently only one character state (thick molar enamel) represented in all fossil members.

In the fourth analysis (d in the picture above) most of the non-australopith (Orrorin, Kenyanthropus, etc) non-orangutan fossils (Dryopithecus, etc), were excluded, although chimps and gorillas were allowed to stay, and the character set was reduced to 14 or more traits. The results are that humans (and related fossils) are the sister group to orangutans (and related fossils) – hardly surprising.

Grehan and Schwartz also have to deal with the molecular evidence and they have one section devoted to critiquing this evidence (although, again the evidence from chromosomal analysis is not discussed). I mentioned some of their critiques in a previous post and won’t go into too many details here. Several other points in their discussion are worth mentioning. One of the problems Grehan and Schwartz have to deal with is that phylogenetic analysis of a wide variety of different genes all indicate that chimps and humans are more closely related to each other than they are to other groups. In essence, there is a consilience between a wide variety of different data sets. Grehan and Schwartz argue that that these comparisons are not between homologous derived character states and are probably primitive retentions. Kind of mind boggling when you consider that they accept a dental hominoid clade based on one character with nor discussion of the homology of that character – or even of trait polarity of the character. They go on to say:

Our study cannot resolve such questions, but we do show that if morphology is critically examined using the cladistic principle of restricting analysis to character states that are absent or very rare in the outgroup (Hennig, 1966; Kitching et al., 1998), the preponderance of evidence not only supports a human orangutan sister relationship among living taxa, but it is also congruent with a cladistic analysis of living and fossil taxa, which can be analysed only through the study of morphology. In this regard, we are compelled to point out that it is precisely when one incorporates fossil evidence into the analysis that the limits of molecular data become apparent, precisely because molecular data cannot speak to, much less falsify or corroborate, any morphological analysis of the relationships between extinct and extant taxa.

And later:

Robust morphological support for phylogenetic relationships that run counter to interpretations of molecular data (as we suggest is the case for humans and orangutans) represents a viable falsifier of molecular similarity, particularly when the morphological evidence of relationship among living taxa (as between human and orangutan) is not contradicted by (indeed is consistent with) hypothesized phylogenetic relationships between fossil and living taxa.

There have been a number of conflicts between morphology and molecules in the past 20-30 years and there are a wide variety of reasons for such conflicts. Resolution of those conflicts, at least in the cases I am familiar with, came through taking the results of both at face value and using each to shed light on the other. The example I gave at the beginning of this post is a good example. Grehan and Schwartz, like the immortals in Highlander, think there can be only one and that one is morphology.

Update 1: A couple of extra points stand out. First, New Scientist has a story on the paper. This quote by Robin Crompton backs up one of my criticisms of the paper:

According to Robin Crompton, an anatomist at the University of Liverpool, UK, Grehan and Schwartz’s selection of species for phylogenetic analysis is “strange”, and misses out key extinct species such as Proconsul, considered to be the ancestor of all great apes. Even so, the paper appears to contain some good ideas, he says. “The biogeographic ideas are really quite interesting.”

The last sentence about the biogeography brings to mind Carl Sagan’s discussion of reactions to Velikovsky. Scientist thought the science sucked but were impressed by Velikovsky’s discussion of various myths. People familiar with the myths Velikovsky used thought his discussion of them sucked but were impressed with the science.

The second point comes from a quote by Malte Ebacj on MSNBC:

“They criticize molecular data where criticism is due,” said Ebach, who was not involved in the new study. “Palaeoanthropology is based solely on morphology, and there is no scientific justification to favor DNA over morphological data. Yet the human-chimp relationship, generated by molecular data, has been accepted without any scrutiny.”

This is an appalling thing to say. Paleoanthropology is dependent on a wide variety of sciences in order to pursue it’s mission of understanding human variability and evolution in the past. Geology (stratigraphy, for example) and physics (in the form various dating techniques). If we stuck to morphology only we would never know that female Paranthropus may have migrated from their natal groups. Something that can’t be learned with morphology alone. One could also mention taphonomy. But, hey, by all means, lets stick our trowel in the dirt and ignore any technique that has nothing to do with morphology…

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2 Responses

  1. [...] Schwartz, Molecules, and Morphology: There Can Be Only One [...]

  2. [...] Also note that Afarnesis is now at a new site – moving from the old scienceblogs to the new wordpress. Besides getting his own real-life monster name, you can find out why your dog looks guilty and the relationships between lungfish, trout and humans. [...]

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