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Summary of Breakdowns in Attempts to Reconstruct the Tree of Life

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: “For a long time the holy grail was to build a tree of life,” says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. “We have no evidence at all that the tree of life is a reality,” says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.1 To reiterate, the basic problem is that one gene or protein yields one version of the “tree of life,” while another gene or protein yields an entirely different tree. As the New Scientist article stated: The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.2 Likewise, leading evolutionary bioinformatics specialist W. Ford Doolittle explains, “Molecular phylogenists will have failed to find the ‘true tree,’ not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.”3 Evolutionary biologists like Doolittle may claim that this problem is encountered when one tries to reconstruct the evolutionary relationships of microorganisms, such as bacteria, which can swap genes through a process called horizontal gene transfer, thereby muddying any phylogenetic signal. But this objection does not hold water, since the tree of life is challenged even among higher organisms where such gene-swapping is not observed. As the New Scientist article noted, “research suggests that the evolution of animals and plants isn't exactly tree-like either.”

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:
  • A 2009 paper in Trends in Ecology and Evolution notes that: “A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome.”5 Similarly, a paper in the journal Genome Research studied the DNA sequences in various animal groups and found that “different proteins generate different phylogenetic tree[s].”6

  • A study published in Science in 2005 tried to construct a phylogeny of animal relationships but concluded that “[d]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.” Again, the problem lies in the fact that trees based upon one gene or protein often conflict with trees based upon other genes. Their study tried to avoid this problem by using a many-gene technique, yet still found that “[a] 50-gene data matrix does not resolve relationships among most metazoan phyla.”7

  • Striking admissions of troubles in reconstructing the “tree of life” also came from a 2006 paper in the journal PLoS Biology, entitled “Bushes in the Tree of Life.” The authors acknowledge that “a large fraction of single genes produce phylogenies of poor quality,” observing that one study “omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom.” The paper suggests that “certain critical parts of the [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available.” The paper even contends that “[t]he recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics.”8 Unfortunately one assumption they were not willing to re-evaluate is that of universal common ancestry.

  • Another study published in Science found that the molecular data implied that six-legged arthropods, or hexapods (i.e. insects) are not monophyletic, a conclusion that differed strikingly from virtually all previous wisdom. The article concluded “Although this tree shows many interesting outcomes, it also contains some evidently untenable relationships, which nevertheless have strong statistical support.”9

  • A paper in the Journal of Molecular Evolution found that molecule-based phylogenies conflicted sharply with previously established phylogenies of major mammal groups, concluding that this anomalous tree “is not due to a stochastic error, but is due to convergent or parallel evolution.”10 Likewise, a study published in Proceedings of the National Academy of Sciences USA explains that when evolutionary biologists tried to construct a phylogenetic tree for the major groups of birds using mitochondrial DNA (mtDNA), their results conflicted sharply with traditional notions of bird relationships. Strikingly, they even find “convergent” similarity between some bird mtDNA and the mtDNA of distant species such as snakes and lizards. The article suggests bird mtDNA underwent “multiple independent originations,” with their study making a “finding of multiple independent origins for a particular mtDNA gene order among diverse birds.”11
  • When testifying before the TSBOE, professor Hillis also made the inaccurate claim that “there’s overwhelming correspondence between the basic structures we have about the tree of life from anatomical data, from biochemical data, molecular sequence data.” Yet many evolutionary scientists have recognized that evolutionary trees based upon morphology (physical characteristics of organisms) or fossils, commonly conflict with evolutionary trees based upon DNA or protein sequences (also called molecule-based trees).

    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.

    References Cited:

    [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).