A Universal Tree of Life

Molecular homology, genes shared due to common ancestry, is a powerful tool for reconstructing the history of life. A small fraction of the research in molecular phylogeny is concerned with tracing all life to a common ancestor, or population of ancestors. Explore Evolution ignores the bulk of research in molecular evolution to focus on this narrow topic.

Even within this overly-narrow focus, the treatment is deeply inaccurate. The farther back in time a common ancestor would be, the more opportunities there have been for statistical noise to obscure the evolutionary signal. Explore Evolution emphasizes these more complicated issues, and misrepresents the views of scientists like Michael Lynch, Carl Woese, Michael Syvanen, and Michael Gordon who have addressed the shape of the early tree of life.

Whether or not there was one origin of life or several, the best available science indicates that all modern life descended from a single population of organisms. The species in this ancestral population would have shared genes so readily that the entire population can be treated as the ancestor of modern life. Explore Evolution muddles this new field of research, proposing instead a set of entirely separate trees, a vision of life tendered only by creationists, not by any active researchers in the field.

Do Different Genes Mean Different Phylogenetic Trees?

Phylogenetic trees based on single genes (or small numbers of genes) can differ from one another, but Explore Evolution overstates both the extent of the inconsistencies and their implications for phylogenetic reconstruction. Inconsistencies are most common when analyzing phylogenetic events in the very deep past (such as separation of the main animal groups in the pre-Cambrian), and occur for reasons that are well characterized and indeed predicted based on statistical and evolutionary considerations (changes in evolutionary rates, convergent evolution, etc.). In addition, the recent exponential increase in available sequence data has been shown successfully overcoming these artifacts, generating consistent trees with high confidence. Most importantly, the authors' claim that these discrepancies mean that "molecular evidence cannot be reconciled with the theory of Universal Common Descent" (p. 57) is entirely unsupported.

Yhe authors of Explore Evolution reveal a major gap in their understanding of phylogeny and of much of modern biology when they state:

… if Darwin's single Tree of Life is accurate, then we should expect that different types of biological evidence would all point to that same tree. A "family history" of organisms based on their anatomy should match the "family history" based on their molecules (such as DNA and proteins).
Explore Evolution, p. 57

Phylogenetic trees based on a specific gene (gene trees) and those based on several genetic and anatomical traits map the relationships of different entities, genes and organisms. Inconsistencies in phylogenetic tree reconstructions are a fascinating issue and research addressing these inconsistencies has led to a better understanding of complex evolutionary processes.

Phylogenetic trees reconstructed from different genes in the same organism can differ. The possible causes of such differences are understood, ranging from methodological issues (such as different parameters being applied to the algorithms used to weigh sequence similarities) to bona fide biological phenomena. The latter are more interesting and significant, and are generally due to the effects of recognized evolutionary processes on the history of individual genes: convergence, the same sequence change appearing independently in different lineages either because of similar selective pressures, or by chance; changes in evolutionary rates , certain organisms evolve faster than others; horizontal gene transfer, sequences being transfered from one species to another by mechanisms other than vertical, linear descent; and timing, two lineages radiate from a third in relatively close succession, before enough differences mayhave accumulated between them to be able to discern the order of emergence. Thus, even in the best scenarios, absolutely congruent phylogenies from the analysis of individual genes are not expected. The authors of Explore Evolution make it seem as if biologists are surprised and stumped by these inconsistencies:

Evolutionary biologist Michael Lynch has noted that creating a clear picture of evolutionary relationships is "an elusive problem." He also notes that "analyses based on different genes - and even different analyses based on the samegenes — [yield] a diversity of phylogenetic trees."
Explore Evolution, p. 57

But in the very next paragraph of the same paper, Lynch makes the main underlying issues clear:

Given the substantial evolutionary time separating the animal phyla, it is not surprising that single-gene analyses yield such discordant results. Under such circumstances, the statistical noise associated with the substitution process leads to a high probability that phylogenetic analyses based on different molecules will yield different topologies (Philippe et al. 1994; Ruvolo 1997), so that inferences based on single genes can potentially be very misleading (leaving aside for now the additional problem of orthology).[emphasis added]
Lynch M. "The Age and Relationships of the Major Animal Phyla." Evolution. 1999; 53:319-325.

In Lynch's paper the phrase "elusive problem" and the issue of multiple phylogenetic trees applied specifically to the "phylogenetic relationships of the major animal phyla", i.e. very distant evolutionary events; the Explore Evolution authors craftily presented it as if Lynch was referring to all "evolutionary relationships".

Another example of the issues encountered in phylogenetic reconstruction, and their misrepresentation in Explore Evolution, comes from the following paragraph:

A "family tree" based on anatomy may show one pattern of relationships, while a tree based on DNA or RNA may show quite another. For example, one analysis of the mitochondrial cytochrome b gene produced a "family tree" in which cats and whales wound up in the order Primates. Yet, an anatomical analysis says that cats belong to the order Carnivora, while whales belong to Cetacea – and neither of them are Primates.
Explore Evolution, p. 57

The authors are talking about a review paper by Michael Lee (Lee MSY, 1999 Trends Ecol Evol 14:177-178), in which he refers to data obtained on one of the proteins involved in the respiratory chain in mitochondria, cytochrome b. The figure below shows the tree as presented in Lee's review paper: Cytochrome b phylogenetic tree: from Lee, 1999 Trends Ecol Evol 14:177-178Cytochrome b phylogenetic tree: from Lee, (1999) Trends Ecol Evol 14:177-178

The phylogenetic inconsistency here is the misplacement of a single branch, that of tarsiers (a primitive group of primates), as if they had separated from other primates before cats and fin-back whales. Actually, the data in the original publication (see figure below, Andrews et al. 1998 "Accelerated Evolution of Cytochrome b in Simian Primates: Adaptive Evolution in Concert with Other Mitochondrial Proteins?" J Mol Evol. 47:249–257) gives a slightly different picture, namely that the analysis of cytochrome b sequence is statistically incapable of resolving the phylogenetic relationship of most of the species in the tree (the numbers in the figure represent a measure of the statistical confidence in each branch of the tree, and numbers below 30 generally indicate lower confidence; the statistically robust values are underlined). In other words, cytochrome b is simply not a good protein to choose for constructing the evolutionary tree of these species. But why is that?

Cytochrome b phylogenetic tree: from Andrews et al., 1998; adapted to match layout and nomenclature in Lee, 1999 (see prevoius figure)Cytochrome b phylogenetic tree: from Andrews et al., 1998; adapted to match layout and nomenclature in Lee, 1999 (see prevoius figure)

Both the Andrews and Lee papers suggested, based on other data, that the phylogenetic incongruence in this tree was caused by cytochrome b and other respiratory chain proteins having evolved much faster in some primate lineages compared to other mammals, possibly following unique selective pressures. As mentioned above, both accelerated and adaptive evolution can cause errors in phylogenetic tree reconstruction, masking or enhancing the similarities of related genes, depending on the circumstances. And indeed, in more recent years the accelerated adaptive evolution of respiratory chain proteins in monkeys and apes (but not tarsiers and lemurs) has been extensively confirmed (see for instance Grossman LI, et al. 2004 "Accelerated evolution of the electron transport chain in anthropoid primates." Trends Genet. 20:578-585). Thus, the inconsistency in the cytochrome b tree, rather than highlighting hopeless phylogenetic confusion as alleged in Explore Evolution, is the result of real biological and evolutionary processes. The existence of this extensive literature offers opportunities for an inquiry-based lesson on molecular evolution and evolutionary processes. Instead of offering that lesson, the supposedly inquiry-based Explore Evolution throws up its hands in confusion at any sign of difficulty.

Although molecular phylogenetic tree inconsistencies are hardly a fundamental theoretical concern for evolutionary biology, if persistent they could still cause practical problems in assessing certain evolutionary relationships. However, a number of new approaches have recently emerged that address these difficulties. These methods include the combination of large sets of sequence information from genomic databases, as well as the use of genetic features, such as large-scale structural changes or the mapping of mobile genetic elements, that are less prone to convergence and selection-related artifacts. For a thorough discussion of the potential of these approaches, see Lokas A and Carroll SB, (2006) "Bushes in the Tree of Life" PLoS Biol 4:e352.

Finally, the authors of Explore Evolution conclude:

Critics point out that the real problem may be that Universal Common Descent is wrong. In other words, maybe the reason the family trees don't agree is that the organisms in question never did share a common ancestor. Even some evolutionary biologists agree. Carl Woese of the University of Illinois, for instance, now thinks that biology must abandon what he calls Darwin's "Doctrine of Common Descent".
Explore Evolution, p. 58

Woese argues that the earliest history of life may show multiple early lineages which swapped genes extensively, making reconstruction of the early tree of life difficult. This is very different from the strictly non-overlapping trees Explore Evolution suggests as an alternative to universal common ancestry. Woese argues that these multiple lineages converged into a single population from which modern life, and would absolutely reject the claim that molecular data cannot discern the pattern of common ancestry linking all primates, or the relationship between primates, carnivores, and whales, or indeed the common ancestry of all multicellular organisms.

Phylogenetic Trees and Molecular Family Histories

The authors do not understand phylogeny, and have a very limited understanding of the biological vocabular and issues. They propose that if common descent is correct, then:

A "family history" of organisms based on their anatomy should match the "family history" based on their molecules (such as DNA and proteins).
Explore Evolution, p. 57

This is simply wrong.

Genes and organisms are very different things; gene family trees and organism family trees can, and do, differ. Contrary to the book's statements, evolutionary biology does not expect these trees to match up exactly. Rather, the relationship between genes and organisms is an issue in biology that is under active research in a wide range of fields.

The Last Universal Common Ancestor

Explore Evolution claims that certain scientists dispute the existence of a single universal ancestor, citing authors would not actually dispute universal common descent. They just disagree about the form it took, and the nature of the population of organisms from which modern living things evolved.

An Uprooted Tree of Life: From W. Ford Doolittle (2000) "Uprooting the tree of life." Scientific American, 282(2):90-5.  Note that distances are not necessarily to scale in this image.  This image reflects a view held by some practicing scientists (including Dr. Doolittle, the author of the original article) that there was a period in life's early history when genes swapped so frequently that it is impossible to treat those earlier lineages as truly distinct, nor to trace those lineages back cleanly to a single ancestor.  They do not dispute that life has some common ancestor, but they do seek to clarify how we talk about that ancestor.An Uprooted Tree of Life: From W. Ford Doolittle (2000) "Uprooting the tree of life." Scientific American, 282(2):90-5. Note that distances are not necessarily to scale in this image. This image reflects a view held by some practicing scientists (including Dr. Doolittle, the author of the original article) that there was a period in life's early history when genes swapped so frequently that it is impossible to treat those earlier lineages as truly distinct, nor to trace those lineages back cleanly to a single ancestor. They do not dispute that life has some common ancestor, but they do seek to clarify how we talk about that ancestor.

As discussed in the critique of the Introduction, there is ongoing research into the nature of the Last Universal Common Ancestor. Scientists traditionally envisioned an ancestral population of a single species which branched and gave rise to the modern diversity of life. More recently, researchers are suggesting that that ancestral population of bacteria was not composed of a single species, but of multiple species which swapped genes freely.

This is the point Michael Syvanen is making when he is quoted by Explore Evolution

Do the puzzles of conflicting phylogenetic trees or ORFans … undermine the theory of Universal Common Descent? Most evolutionary biologists say no. …Others are not so sure. Molecular evolutionist Michael Syvanen of the University of California-Davis argues that, "there is no reason to postulate that a LUCA (Last Universal Common Ancestor) ever existed."
Explore Evolution, p. 61

Once again, Explore Evolution misrepresents the views of a scientist by selecting a phrase that sounds as though evolution were on shaky ground. This 'mined' quote suggests, incorrectly, that Syvanen is arguing against Universal Common Descent. Here is what Syvanen actually wrote, in a paper indicating that genes for certain biochemical pathways had been transferred between lineages long after their divergence:

There has been recent discussion that horizontal gene transfer is so frequent that it may never be possible to reconstruct the last common ancestor. However, if biochemical unities could be achieved after speciation events by horizontal gene transfer, then there is no reason to even postulate that a LUCA ever existed. If horizontal gene transfer is as common as I am implying, the modern cell could have evolved in multiple parallel lineages. Earliest life could have been truly polyphyletic.
Michael Syvanen (2002) "On the occurrence of horizontal gene transfer among an arbitrarily chosen group of 26 genes," Journal of Molecular Evolution, 54:258-266

Syvanen is not necessarily disputing Universal Common Descent; he is disputing the existence of a Last Universal Cellular Ancestor [LUCA]. Syvanen is participating in an ongoing debate about the shape of the trunk of the tree of life. As shown in the figure above, some scientists see the evidence of extensive gene flow between ancient bacterial species as a sign that, at the base of the tree of life, lines between lineages were less clear, and that the branches didn't begin separating until a later point. Syvanen explained his views in some more depth in a post at the Panda's Thumb blog, pointing out that our increasingly detailed knowledge of the order in which certain ubiquitous genes evolved places greater and greater constraints on the composition of LUCA, and that "if we accept the existence of this LUCA there are a variety of reasons to believe that the LUCA itself was the product of an evolutionary process that employed horizontal transfer events." The full details of this debate require students to have a grasp of biological details that they will not have until after their high school biology classes, but an inquiry-based textbook might work with students to explain what sorts of research is under way to resolve some of these unresolved issues. Instead, Explore Evolution claims the existence of the discussion as proof that nothing is known, a profoundly unscientific attitude, and an unacceptable approach for a textbook to adopt. The existence of horizontal gene transfer, a major topic in discussions of the early tree of life, is not mentioned in the book's index, glossary, or relevant sections.

Malcolm Gordon

Explore Evolution claims that the common ancestry of life is disputed because:

Biologist Michael Gordon of UCLA argues that the single branching-tree picture of life's history is not accurate, but that life must have had multiple, independent starting points.
p. 61

Malcolm Gordon is an expert in the functional morphology of fish, not the origin of life. His argument in "The Concept of Monophyly: A Speculative Essay." (1999, Biology and Philosophy 14:331–348) is that there was likely to be many different environments where life could have arisen (almost certainly true), and that the mobilities of the first organisms would be limited (also likely to be true), that it is probable (note that he never says must as Explore Evolution claims) there would be sufficient time for more than one origin of life event to occur. However, he vastly underestimates the spreading capacity of even slow growing non-motile bacteria. Anyone who has had the misfortune to have a sterile solution contaminated with a few bacteria can attest to how rapidly they grow, and in the prebiotic environment there would be no competition for them. So again, unless the origin of life is astoundingly easy, the first living organism would have had the field to itself. The near universality of the genetic code is consistent with this scenario, but universal common descent does not require a single origin of life, nor have evolutionary biologists ever required only a single origin of life.

There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one …
Charles Darwin, The Origin of Species, 1859, Final paragraph

As that quotation from Darwin demonstrates, the theory of evolution does not, a priori, demand that life could not have more than one independent origin. However, there are several lines of evidence that compellingly suggest that the origin of life was limited to a very few, most probably one, initial population serving as an "organism." The strongest evidence for this idea is the nearly universal genetic code. This does not argue that the genetic code used by current organisms was found in the first life form; there are several alternative codes that would work. But if there were multiple origins for present-day life, we would expect to see significantly different genetic codes. However, all we see are minor mutational variants of the standard code.

Also, the basic biochemistry of organisms is fairly universal. If life had developed multiple times, we would expect to see at least some organisms with a radically different biochemistry, but we just don't see that.

Furthermore, unless the origin of life was exceptionally easy, it took some time for "living organisms" to develop. Hundreds of thousands to millions of years (even if they were simple self-replicating molecules) were likely required. Once the first living organism had developed, within the space of a few decades its descendants would have monopolized the prebiotic Earth, preventing the development of competitor organisms. It is unlikely, even if the origin of life were astoundingly simple, that a second form of life developed within a few years of the first one to prevent the first's monopoly. Even if a second organism had developed independently a few years after, the first organism with its head start would be much fitter, and would likely out-compete the second.