When arguing for common descent, evolutionary scientists typically assert that the degree of genetic (or anatomical) similarity between two species indicates how closely they are related. But there are numerous cases where this assumption fails, and anatomical or molecular data yield evolutionary trees (called ‘phylogenies’) that conflict with conventional views of organismal relationships. The basic problem is that evolutionary trees based on one gene commonly differ strikingly from a phylogeny based on a different gene.
Leading evolutionists are loath to admit this fact during public debate. During the 2009 Texas State Board of Education (TSBOE) hearings on evolution-education, University of Texas Austin evolutionary scientist David Hillis cited himself as a “world’s leading exper[t] on the tree of life” and told the TSBOE that there is “overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence” when reconstructing evolutionary history using biological molecules. Hillis’s self-proclaimed expertise makes it all the more disconcerting that he tried to mislead the TSBOE about the widespread prevalence of incongruencies between various molecular phylogenies within his own field.
Indeed, the very day that Hillis testified before the TSBOE, the journal New Scientist published a cover story titled “Why Darwin was wrong about the tree of life.” Directly contradicting Hillis’s gross oversimplification of the case for common ancestry, the article reported that “The problem was that different genes told contradictory evolutionary stories.” The article observed that with the sequencing of the genes and proteins of various living organisms, the tree of life fell apart:
Authority Carl Woese has also observed that these problems extend well beyond the base of the tree of life, stating: “Phylogenetic incongruities [conflicts] can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.”4 To reiterate, even among higher organisms, as the New Scientist article explains that “The problem was that different genes told contradictory evolutionary stories,” therefore leading one scientist to say regarding the relationships of these higher groups, “We’ve just annihilated the tree of life.” Many studies have reported such problems:
For example, a review paper by Darwinian leaders in this field stated, “As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened. Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology.”12 Another set of pro-evolution experts wrote, “That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists. Most of the latter know that the two lines of evidence may often be incongruent.”13
The widespread prevalence of disagreement and non-correspondence between molecule-based evolutionary trees and anatomy-based evolutionary trees led a review article in Nature to report that “disparities between molecular and morphological trees” cause “evolution wars” because “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.”14
As one specific example, textbooks often cite the phylogenetic tree based upon cytochrome c as purportedly matching and confirming the standard anatomy-based phylogenetic tree of many vertebrates. But one paper in Trends in Ecology and Evolution noted that the cytochrome b tree yielded “an absurd phylogeny of mammals, regardless of the method of tree construction” where “[c]ats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers.” The paper concluded that “Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting.”15
This problem also exists among higher primates as molecular data often conflicts with the prevalent phylogenetic tree which claims humans are most closely related to chimpanzees.16 As one article in the journal Molecular Biology and Evolution found, “[f]or about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee.”17
The common textbook claim that a universal “tree of life” has been established by congruent molecular and morphological phylogenetic trees is contradicted by much data and scientific opinion – but this information is almost always omitted from textbook instruction given to students.
[1.] Graham Lawton, “Why Darwin was wrong about the tree of life,” New Scientist (January 21, 2009) (emphasis added).
[2.] Graham Lawton, “Why Darwin was wrong about the tree of life,” New Scientist (January 21, 2009).
[3.] W. Ford Doolittle, “Phylogenetic Classification and the Universal Tree,” Science, Vol. 284:2124-2128 (June 25, 1999).
[4.] Carl Woese “The Universal Ancestor,” Proceedings of the National Academy of Sciences USA, Vol. 95:6854-9859 (June, 1998) (emphasis added).
[5.] James H. Degnan and Noah A. Rosenberg, “Gene tree discordance, phylogenetic inference and the multispecies coalescent,” Trends in Ecology and Evolution, Vol. 24(6) (March, 2009).
[6.] Mushegian et al., “Large-Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes,” Genome Research, Vol. 8:590-598 (1998).
[7.] Antonis Rokas, Dirk Krueger, and Sean B. Carroll, “Animal Evolution and the Molecular Signature of Radiations Compressed in Time,” Science, Vol. 310:1933-1938 (Dec. 23, 2005).
[8.] Antonis Rokas and Sean B. Carroll, “Bushes in the Tree of Life,” PLoS Biology, Vol. 4(11): 1899-1904 (Nov., 2006) (internal citations and figures omitted).
[9.] Nardi et al., “Hexapod Origins: Monophyletic or Paraphyletic?,” Science, Vol. 299:1887-1889 (March 21, 2003)
[10.] Cao et al., “Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders,” Journal of Molecular Evolution, Vol. 47:307-322 (1998).
[11.] Mindell et al., “Multiple independent origins of mitochondrial gene order in birds,” Proceedings of the National Academy of Sciences USA, Vol. 95: 10693-10697 (Sept. 1998).
[12.] Colin Patterson et al., “Congruence between Molecular and Morphological Phylogenies,” Annual Review of Ecology and Systematics, Vol. 24, pg. 179 (1993) (emphasis added).
[13.] Masami Hasegawa, Jun Adachi, Michel C. Milinkovitch, “Novel Phylogeny of Whales Supported by Total Molecular Evidence,” Journal of Molecular Evolution, Vol. 44, pgs. S117-S120 (Supplement 1, 1997) (emphasis added).
[14.] Trisha Gura, “Bones, Molecules or Both?,” Nature, Vol. 406:230-233 (July 20, 2000) (emphasis added).
[15.] Michael S. Y. Lee, “Molecular phylogenies become functional,” Trends in Ecology and Evolution, Vol. 14(5): 177-178 (May, 1999).
[16.] See for example, 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); Ingo Ebersberger et al., “Mapping Human Genetic Ancestry,” Molecular Biology and Evolution, Vol. 24(10):2266–2276 (2007); Trisha Gura, “Bones, Molecules or Both?,” Nature, Vol. 406:230-233 (July 20, 2000).
[17.] Ingo Ebersberger et al., “Mapping Human Genetic Ancestry,” Molecular Biology and Evolution, Vol. 24(10):2266–2276 (2007).