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Why Scientists Can’t Reconstruct Darwin's "Tree of Life"

In 2009, the elites at London's Natural History Museum decided to observe Darwin's 200th birthday by commissioning a piece of artwork for the ceiling of an exhibit room. Titled "TREE," the work was inspired by Darwin's famous vision of a grand tree of life. Though BBC radio called the TREE exhibit "The Darwinian Sistine Chapel,"¹ it was no religious icon. According an article in Archives of Natural History, TREE "celebrates Darwinian evolutionism" and "secular science and reason."²

The "tree of life" has become the most famous icon representing Darwin's theory of evolution. In fact, it was his only illustration in On the Origin of Species (see page 51). But does the tree of life exist?

In Salvos 25 and 26 we saw that the evidence from both living and dead organisms (i.e., biogeography and fossils) has failed to confirm a Darwinian view of life, according to which all species evolved through common descent with modification. Instead, the record shows that major groups of animals appeared abruptly, without direct evolutionary precursors.

Because biogeography and fossils have failed to bolster common descent, many evolutionary scientists have turned to molecules—the nucleotide and amino acid sequences of genes and proteins—to establish a phylogenetic tree of life showing the evolutionary relationships between all living organisms.

The Best Proof of Macroevolution?

The project was first conceived in the 1960s, soon after the genetic code was uncovered. Two pioneering scientists, Linus Pauling and Emile Zuckerkandl, boldly predicted that phylogenetic trees based upon molecular data would confirm expectations of common descent already held by evolutionary biologists who studied morphology (i.e., the physical traits of organisms). They declared, "If the two phylogenic trees are mostly in agreement with respect to the topology of branching, the best available single proof of the reality of macro-evolution would be furnished."³

Hoping to validate Pauling and Zuckerkandl's prediction, biologists set themselves to the task of sequencing genes from all manner of living organisms. Technologies were refined, genomes were sequenced, and new discoveries were made. One revolutionary discovery was made in the 1990s, when it was realized that the "five kingdoms" view of life, taught to many previous generations of students, was incomplete. Examination of the gene sequences of living organisms revealed instead that they fell into three basic domains: Archaea, Bacteria, and Eukarya.

About the same time, another discovery was made that confounded evolutionary biologists who studied genes: they found that the three domains of life could not be resolved into a tree-like pattern. This led the prominent biochemist W. Ford Doolittle to famously lament: "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."⁴ He later acknowledged, "It is as if we have failed at the task that Darwin set for us: delineating the unique structure of the tree of life."⁵

Conflicts in the Trees

The basic problem is that, while one gene leads to one version of the tree of life, another gene leads to an entirely different tree. What seems to imply a close evolutionary relationship in one case (i.e., two similar genes) doesn't do so in another. To put it another way, biological similarity is constantly being found in places where it wasn't predicted by common descent, leading to conflicts between phylogenetic trees. When two trees conflict, at least one must be wrong. How do we know that both aren't?

Many papers have noted the prevalence of contradictory molecule-based phylogenetic trees. For instance:

• A 1998 paper in Genome Research observed that "different proteins generate different phylogenetic tree[s]."⁶
• A 2009 paper in Trends in Ecology and Evolution acknowledged that "evolutionary trees from different genes often have conflicting branching patterns."⁷
• A 2013 paper in Trends in Genetics reported that "the more we learn about genomes the less tree-like we find their evolutionary history to be."⁸

Perhaps the most candid discussion of the problem came in a 2009 review article in New Scientist titled "Why Darwin Was Wrong about the Tree of Life."9 The author quoted researcher Eric Bapteste explaining that "the holy grail was to build a tree of life," but "today that project lies in tatters, torn to pieces by an onslaught of negative evidence." According to the article, "many biologists now argue that the tree concept is obsolete and needs to be discarded."

The paper also recounted the results of a study by Michael Syvanen that compared 2,000 genes across six diverse animal phyla: "In theory, [Syvanen] should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories."

Syvanen succinctly summarized the problem: "We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely. What would Darwin have made of that?"

Molecules vs. Morphology

Clearly molecule-based trees often conflict with one another. But what about Pauling and Zuckerkandl's prediction that molecule-based trees should match those constructed by morphology? A review article in Nature titled "Bones, Molecules, or Both?" explains that they often don't.

"When biologists talk of the 'evolution wars'," the article opened, "they usually mean the ongoing battle for supremacy in American schoolrooms between Darwinists and their creationist opponents." But the warfare metaphor could also be applied to a debate raging within evolutionary biology:

On one side stand traditionalists who have built evolutionary trees from decades of work on species' morphological characteristics. On the other lie molecular systematists, who are convinced that comparisons of DNA and other biological molecules are the best way to unravel the secrets of evolutionary history.

The article observed that "battles between molecules and morphology are being fought across the entire tree of life," leaving readers with a stark assessment: "Evolutionary trees constructed by studying biological molecules often don't resemble those drawn up from morphology."¹⁰

For example, consider the tree of placental mammals. A 2013 paper comically acknowledged the problems encountered when trying to reconcile the conflicting versions of the mammalian tree provided by molecules and morphology:

Untangling the root of the evolutionary tree of placental mammals has been nearly an impossible task. The good news is that only three possibilities are seriously considered. The bad news is that all three possibilities are seriously considered. Paleontologists favor a root anchored by Xenarthra (e.g., sloths and anteater), whereas molecular evolutionists have favored the two other possible roots: Afrotheria (e.g., elephants, hyraxes, and tenrecs) and Atlantogenata (Afrotheria + Xenarthra). Now, two groups of researchers have scrutinized the largest available genomic data sets bearing on the question and have come to opposite conclusions, as reported in this issue of Molecular Biology and Evolution. Needless to say, more research is needed.¹¹

But is "more research" going to solve these problems? A 2012 paper noted that "phylogenetic conflict is common, and [is] frequently the norm rather than the exception," since "incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species."¹²

Epic Fall

The creator of the TREE exhibit at the London museum stated she was inspired by Darwin's "bravery to profoundly challenge orthodoxy."¹³ But the tree of life itself has now become orthodoxy—orthodoxy that needs to be challenged because it's no longer supported by the evidence.

Nonetheless, the frequent discrepancies between molecular and morphology-based trees, and between various molecule-based trees, have led some dissenters to conclude that the prediction made by Zuckerkandl and Pauling was fundamentally wrong. A paper in the journal Biological Theory explained:

[M]olecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling, that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change. Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the "molecular assumption."¹⁴

With the failure of Zuckerkandl and Pauling's "best available single proof of the reality of macro-evolution," it would seem evolutionary biology needs a new icon to replace the tree of life. •

Endnotes
1. www.bbc.co.uk/darwin/?tab=21.
2. "The tree as evolutionary icon," Archives of Natural History (2011), 38:1–17.
3. Zuckerkandl and Pauling, "Evolutionary Divergence and Convergence in Proteins," in Evolving Genes and Proteins, Bryson and Vogel, eds. (Academic, 1965), 101.
4. Doolittle, "Phylogenetic Classification and the Universal Tree," Science, 284:2124-28 (1999).
5. Doolittle, "Uprooting the Tree of Life," Scientific American (2000).
6. "Large-Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes," Genome Research (1998), 8:590–598. 
7. "Gene tree discordance, phylogenetic inference and the multispecies coalescent," Trends in Ecology and Evolution (2009), 24:332–340.
8. Bapteste et al., "Networks: expanding evolutionary thinking," Trends in Genetics (2013), 29:439–441.
9. "Why Darwin was wrong about the tree of life," New Scientist (2009).
10. "Bones, Molecules, or Both?" Nature (2000), 406:230–233.
11. "Making the Impossible Possible: Rooting the Tree of Placental Mammals," Molecular Biology and Evolution (2013).
12. "Understanding phylogenetic incongruence: lessons from phyllostomid bats," Biological Reviews of the Cambridge Philosophical Society (2012), 87:991–1024.
13. www.nhm.ac.uk/resources-rx/files/tree-leaflet-1-30586.pdf.
14. "Do Molecular Clocks Run at All? A Critique of Molecular Systematics,"Biological Theory (2006), 1:357–371.

From Salvo 27 (Winter 2013)
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