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Primate Phylogenetics Researchers Swinging from Tree to Tree

A recent article on ScienceDaily, titled "A New Evolutionary History of Primates," claims that by combining genetic data from 54 genes (totalling 34,927 base pairs) from a variety of primates, researchers have created "[a] robust new phylogenetic tree" which "resolves many long-standing issues in primate taxonomy." That sounds great--until you read the fine print. The paper used dozens of genes or "large-scale sequencing" to create the phylogeny--a method which is designed to smooth over conflicts between trees based upon individual genes. This method fails to test whether individual genes paint a consistent picture of common descent. Moreover, even after using this method, not everything about the tree is neat and tidy. Even when using many genes to construct the tree, the paper reports there were a variety of potential sub-trees which conflicted with one another:

However, greater frequency of phylogenetic inconsistencies or unresolved nodes occur in these subset trees, compared with the entire concatenated data set.


(Perelman et al., "A Molecular Phylogeny of Living Primates," PLoS Genetics, Vol. 7(3):e1001342 (March, 2011) (internal figure citations removed).)

Indeed, such phylogenetic inconsistencies between different phylogenetic trees are not uncommon at all, particularly in important parts of the purported primate tree. While this paper used methods that smoothed over conflicts between trees, another recent paper found primate phylogenetic data that pointed in opposite directions. A recent article on ScienceDaily, titled "Genetic Archaeology Finds Parts of Human Genome More Closely Related to Orangutans Than Chimps," stated:

In a study published online in Genome Research, in coordination with the publication of the orangutan genome sequence, scientists have presented the surprising finding that although orangutans and humans are more distantly related, some regions of our genomes are more alike than those of our closest living relative, the chimpanzee.

Of course this finding is "surprising" because it contradicts the phylogeny preferred by most evolutionists. The ScienceDaily article noted: "[I]n about 0.5% of our genome, we are closer related to orangutans than we are to chimpanzees ... and in about 0.5%, chimpanzees are closer related to orangutans than us," and the paper cited concluded:

Our analyses find that for ~0.8% of our genome, humans are more closely related to orangutans than to chimpanzees.


(Asger Hobolth et al., "Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection," Genome Research, Vol. 21:349-356 (2011).)

Since humans are typically said to be most closely related to chimps, this data conflicts with the standard supposed tree. As discussed here, the basic problem is that one gene (or portion of the genome) gives you one version of the tree, while another gene (or portion of the genome) gives you a very different version of the tree. This leads to discrepancies between molecule-based trees, wherein DNA data fails to provide a consistent picture of common ancestry. (We've discussed a number of such examples lately, such as here, here, and here. Jonathan M. also cites some discordant data pertaining to human/chimp phylogenetics here.)

0.8% of our genome might not sound like a lot, but that equates to over 20 million base pairs. That's means that over 500 times more raw genetic information than was used in the PLoS Genetics paper (to purportedly create a "robust new phylogenetic tree") is supposedly pointing in the wrong phylogenetic direction. Perelman et al.'s paper in PLoS Genetics could only find a "robust new phylogenetic tree" after using methods that are designed to avoid this problem and ignore conflicts between trees. That might sound good, but their methods are wholly assuming, rather than testing, common descent.

That brings us to the final point of this discussion. In the end, molecular trees are based upon the sheer assumption that the degree of genetic similarity reflects the degree of evolutionary relatedness. One paper makes this assumption explicit:

molecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change. Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the 'molecular assumption.' ... For historians and philosophers of science the questions that arise are how belief in the infallibility of molecular data for reconstructing evolutionary relationships emerged, and how this belief became so central ...


(Jeffrey H. Schwartz, Bruno Maresca, "Do Molecular Clocks Run at All? A Critique of Molecular Systematics," Biological Theory, Vol. 1(4):357-371, (2006).)

Clearly this assumption fails when different genes paint contradictory pictures of evolutionary relationships. But are there other mechanisms that can explain DNA similarities besides inheritance from a common ancestor? As explained here, one equally good explanation for the reason that genetic similarity is continuously being found in places both predicted, and unpredicted, by common descent, could be common design.