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DNA Scrambles Darwin's Tree

Darwin's tree of life might be visible in DNA, if DNA didn't conspire to scramble the signal.

Now that quite a few genomes have been published, a team from Australia and France went on a Darwin fishing trip in the gene pool. In the largest study of its kind to date, they examined microsatellite markers (tandem-repeated DNA motifs of 1-6 base pairs) that are widespread in eukaryotic genomes. If neo-Darwinism is correct, these non-coding stretches of DNA should reflect the tree of common ancestry by showing similar mutational patterns in related groups.

Well, they don't. The paper by Meglecz, Neve, Biffin and Gardner in PLoS ONE is titled, "Breakdown of Phylogenetic Signal: A Survey of Microsatellite Densities in 454 Shotgun Sequences from 154 Non Model Eukaryote Species." What went wrong?

As the title implies, the team checked 154 "non-model" species. Darwinian evolutionists tend to focus on the model species, like a particular roundworm, the fruit fly Drosophila melanogaster, and a species of watercress, because their genomes are complete and most researchers use them in experiments. Problem: they may or may not be representative:

Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within groups has been conducted. In this study, we examined microsatellite coverage and motif patterns from 454 shotgun sequences of 154 Eukaryote species from eight distantly related phyla (Cnidaria, Arthropoda, Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and Streptophyta) to test if a consistent phylogenetic pattern emerges from the microsatellite composition of these species.
Sounds like a good test. After all, scientists shouldn't generalize on overinflated signals, right? The team expected to find nicely behaved data interpolated between the model species. It wasn't to be:
It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.
There are two ways to interpret this anomaly. One is that microsatellites mutate too fast to maintain the phylogenetic signal. (This is known as a "post hoc rationalization.")

The other is that Darwin was wrong. Data do not show a phylogenetic pattern; they show common design with some variation.

Well, Darwinists are not ones to allow a little data to get in the way of their grand scenario. "The origin and spread of microsatellites within a genome is a puzzling question," the researchers say, couching solutions in a nebulous future: someday, someone may figure out how they evolve. "A more thorough understanding of factors influencing the genomic distribution of microsatellites would facilitate their continued use as a molecular marker and contribute to a general understanding of microsatellite evolution in genomes," they rationalize. Maybe they arise de novo by point mutations then elongate. Maybe they spread by transposable elements.

For one thing, chance is out: "Microsatellite formation cannot be explained by chance alone, since the expected density of microsatellites, assuming random association of DNA bases, is far lower than their observed genome wide density," they confess. Does this suggest some functional principle in microsatellites? (Remember, this paper preceded the publication of the ENCODE project.)

They do claim partial success. Most of the vertebrate class data was not as "heterogeneous" (scrambled) as in other taxa. They claim that this shows scrambling increases with time; the data were less scrambled for species evolving within the last 200 million years, they say. However, it was very scrambled for arthropods over the same time frame. And even the "conserved phylogenetic pattern" for vertebrates could be a false positive. Why? Because earlier surveys using fewer species produced patterns that evaporated in their survey with more species:

Thus, by increasing the number of species studied for each phylogenetic group, considerable heterogeneity is observed in microsatellite composition and coverage. This is a very important take home message from this study.
So no clear pattern can be claimed in their study either. Even within certain vertebrate classes (e.g., birds), some outlier species had very different microsatellite compositions. Overall, "no general pattern emerged," they say. "Just as total microsatellite coverage varied within classes and orders, motif length proportions can be markedly different between even closely related species."

This is hard to explain in either a design paradigm or a Darwinian one. Why would a designer make closely related species so completely different in their microsatellite composition? More on that in a minute.

How's this for covering your bases:

Both the presence and absence of such a phylogenetic signal are likely to throw light on the evolution of microsatellites. For example, evidence for the maintenance of inherent differences between major evolutionary groups invokes a varied yet functional contribution of these repetitive elements within disparate genomes. Alternatively, inconsistencies within lineages call for a greater role of random processes for explaining microsatellite distributions.
Darwinian evolution can't lose. If the signal is there, it evolved! If it's not there, it evolved!

Aren't Darwin skeptics permitted to call foul here? Darwinian theory predicts phylogenetic patterns. What better place to look than in DNA? If mutations spread in the gene pool over time, and nature selects any beneficial mutations, or doesn't eliminate neutral genetic drift, why wouldn't there be a phylogenetic signal in both genes and non-coding regions? It's a little late to make excuses after the data are in.

Design researchers, by contrast, might be surprised at the variations, but not worried. They had no need to predict a phylogenetic pattern. ID advocates could accept quite a bit of variation by epigenetic coding algorithms that respond to environmental cues. It's not a showstopper, as it should be for neo-Darwinism. In fact, it might be a motivator instead: let's explore the functional significance of the variations.

In their conclusion, the authors warn fellow Darwinists about sample bias: "Sampling of the rest of the Eukaryotes was insufficient to reveal a phylogenetic pattern, but even with limited information, we could clearly point out that generalizing information of microsatellite content from few species to a whole group can only be justified if they are from a very recent clade."

The authors are very adept at listing all the possible reasons (excuses) for their failed prediction. Readers can explore these at their leisure in the Discussion section of this open-access paper. What's clear, though, is that the Darwin fishing expedition came back empty, with a lot of fish stories about the one that got away.