Afarensis is a 3.5-2.8 million year old hominin from the Kada Hadar member of the Hadar formation in the Middle Awash, Ethiopia. He is approximately 41 inches tall, weighs approximately 60 pounds and has a cranial capacity of a whopping 410 cc (approximately). Afarensis is currently considered to be transitional between apes and humans and displays some traits of both. Since he spends a lot of time on the couch watching monster movies, some observers question whether he is an obligate biped (although no one has observed him climbing a tree). He also has a blog called 
Kambiz has an extensive write up of the Nature paper that examines hominid phylogeny.
Maybe I'm just getting old and set in my paleoanthropological ways, but I wasn't as impressed with the paper as Kambiz was. Before I get into that, lets look at the paper itself. The paper tries to combine morphometrics, modularity theory and cladistics to sort out hominin relationships. The main thrust of the paper is the genus Homo although the australopithecines (including Paranthropus) are mentioned as well. The study examined 17 hominid skulls plus a chimp skull, gorilla skull and the skull of an anatomically modern human from Patagonia. González-Jose´ et al use morphometrics to analyze four integrated characters, which they equate with modules, which are then used to create a phylogeny. The trees they get are pretty similar to quite a few others that have been published in the past few years (you can read Kambiz's post for more details). All in all, it sounds like a fascinating, cutting edge piece of research, fully deserving of the praise it gets. Except its not.
The idea that some traits are linked functionally or developmentally and, basically co-evolve in tandem rendering them somewhat dubious for cladistic purposes has been discussed in the literature for quite some time. Several papers in Grine's Evolutionary History of the "Robust" Australopithecines discuss this issue. The use of morphometrics to get around this problem by looking at morphological units - modules really - has been around as well. For example, a 2004 paper published in Proceedings of the National Academy of Science by Lockwood, Kimbel, and Lynch used a morphometric analysis of the temporal bone to classify apes. Lockwood et al conclude:
The use of morphological data in phylogenetic reconstruction has been criticized because of the failure to account for genetic and developmental correlations among characters. In addition, progress in using quantitative morphological data in primate phylogenetics has been limited, perhaps because of the difficulty of fitting quantitative data into a framework designed for discrete characters. In light of these concerns, the reasons why our analysis accurately recovers hominoid relationships are potentially several: (i) geometric morphometric analyses of densely sampled 3D landmarks capture shape differences among taxa more effectively than do other morphometric methods; (ii) distance-based methods of phylogenetic reconstruction may be more appropriate for continuous data than the transformation of these data into discrete character states; and (iii) the temporal bone's role in a variety of functional systems maximizes the number of independent influences on morphology and minimizes the effect of homoplasy in any one of those functional systems.
A 2006 paper in the Anatomical Record Part A, by Harvati and Weaver, followed up on Lockwood et al by examining genetic and 3D geometric morphometrics among 13 recent human populations. They end their paper by saying:
Our results support the hypothesis that cranial morphology retains a population history signal, and that different aspects of cranial morphology can preserve different kinds of information. While human temporal bone shape tracks neutral genetics well, as previously predicted for the basicranial region, so does the shape of the neurocranium, often considered too developmentally plastic and environmentally influenced to retain any signal of population history. Human facial shape appears to retain a climatic, rather than a genetic, signature, but this climatic effect may be confined to arctic populations. The relative position and orientation of the three cranial regions to each other is not informative with regards to population history. Finally, the total cranial shape is less successful than the shape of the temporal bone alone in tracking population history, suggesting that more information is not necessarily better. It is important to point out that these results may not apply when different organisms or higher taxonomic levels are considered and should be replicated with further analyses. However, our findings suggest caution and careful choice of anatomical features and regions in phylogenetic and population history reconstructions.
Yet, González-Jose´ et al do not mention either study (or Harvati's earlier geometric morphometric study of Neanderthals). Which is, to say the least, puzzling. I am, however, glad to see them give at least a token nod to modularity theory, even if it does seem somewhat ad hoc. Although the trees produced were interesting, I really don't see what the fuss was about.
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