These days, phylogeneticists — experts who painstakingly map the complex branches of the tree of life — suffer from an embarrassment of riches. The genomics revolution has given them mountains of DNA data that they can sift through to reconstruct the evolutionary history that connects all living beings. But the unprecedented quantity has also caused a serious problem: The trees produced by a number of well-supported studies have come to contradictory conclusions.
“It has become common for top-notch studies to report genealogies that strongly contradict each other in where certain organisms sprang from, such as the place of sponges on the animal tree or of snails on the tree of mollusks,” said Antonis Rokas, Cornelius Vanderbilt Chair in Biological Sciences at Vanderbilt University.
And the further back they go, the less reliable the genetic data becomes.
Keep this story in mind when a coworker splinters the table insisting that Darwinian evolution is supported by “mountains of evidence,” or, better yet, “mountains and mountains of evidence,”or even just plain “fact! fact! FACT!”*
What is the mountain of evidence evidence for, specifically? Nothing the next paper won’t overturn, it seems.
*Michael Ruse, Darwinism Defended: A Guide to the Evolution Controversies, (Addison-Wesley, 1982) 1983, Third Printing, p.58. Emphasis Ruse’s.
Here’s the paper’s Abstract:
To tackle incongruence, the topological conflict between different gene trees, phylogenomic studies couple concatenation with practices such as rogue taxon removal or the use of slowly evolving genes. Phylogenomic analysis of 1,070 orthologues from 23 yeast genomes identified 1,070 distinct gene trees, which were all incongruent with the phylogeny inferred from concatenation. Incongruence severity increased for shorter internodes located deeper in the phylogeny. Notably, whereas most practices had little or negative impact on the yeast phylogeny, the use of genes or internodes with high average internode support significantly improved the robustness of inference. We obtained similar results in analyses of vertebrate and metazoan phylogenomic data sets. These results question the exclusive reliance on concatenation and associated practices, and argue that selecting genes with strong phylogenetic signals and demonstrating the absence of significant incongruence are essential for accurately reconstructing ancient divergences. – Leonidas Salichos, Antonis Rokas. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature, 2013; 497 (7449): 327 DOI: 10.1038/nature12130