One wonders why both Michael Behe and Gunther Bechly accepts universal common descent, then. Not to mention essentially all of the field of evolutionary biology.
Of course there is such evidence, it’s called consilience of independent phylogenies. Even among the most divergent prokaryotic phylogenetic trees, one can still detect a central tree-like trend:
We set out to address the above question as objectively as possible, first of all dispensing with any pre-selected standard of tree-like evolution. The analyzed FOL consisted of 6,901 maximum likelihood phylogenetic trees that were built for clusters of orthologous genes from a representative set of 100 diverse bacterial and archaeal genomes [1]. The complete matrix of topological distances between these trees was analyzed using the Inconsistency Score, a measure that we defined specifically for this purpose that reflects the average topological (in)consistency of a given tree with the rest of the trees in the FOL (for the details of the methods employed in this analysis, see [21]). Although the FOL includes very few trees with exactly identical topologies, we found that the topologies of the trees were far more congruent than expected by chance. The 102 Nearly Universal Trees (NUTs; that is, the trees for genes that are represented in all or nearly all archaea and bacteria), which include primarily genes for key protein components of the translation and transcription systems, showed particularly high topological similarity to the other trees in the FOL. Although the topologies of the NUTs are not identical, apparently reflecting multiple HGT events, these transfers appeared to be distributed randomly. In other words, there seem to be no prominent ‘highways’ of HGT that would preferentially connect particular groups of archaea and bacteria. Thus, although the NUTs cannot represent the FOL completely, they appear to reflect a significant central trend, an attractor in the tree space that could be equated with the STOL (Figure (Figure11).
The central tree-like trend in the phylogenetic forest of life. The circles show genomes of extant species and the grey tree in the background shows the statistical central trend in the data. For the purpose of illustration, the figure shows an ‘FOL’ made of 16 trees with 20 deviations from the central tree-like pattern.
The set of 6,901 phylogenetic trees that comprise the FOL has become a launching pad for several new studies addressing various aspects of prokaryote evolution and general questions of evolutionary biology. In our own hands, the sequel to the original FOL study involved quantitative dissection of the evolution of prokaryotes into tree-like and web-like components [22]. We applied the approach known as quartet analysis to quantify the contributions of these two distinct modes of evolution [21] and found that, although diverse routes of net-like evolution collectively dominate the FOL, the pattern of tree-like evolution that reflects the generally consistent topologies of the NUTs is the most prominent coherent trend [22]. Thus, the ubiquity of HGT notwithstanding, this central tree-like trend reflects a major aspect of genome evolution and hence has a legitimate claim to represent the STOL.
The only good explanation for this central trend is common ancestry. The trees derived from independent genomic loci are similar because they’re constrained by a shared genealogical history. There is, a priori, no reason found in functional constraint, that explains why independent genomic loci should converge on similar phylogenetic trees. You could at best expect some degree of sequence similarity from functional constraint alone, but not such an extreme constraint on branching topology.
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