Obsolete Dawkinsian evidence for evolution

For the public understanding of phylogenomics, an argument used by Richard Dawkins should be retired

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It is with hesitation that I pen a blog post that could be construed as critical of Richard Dawkins FRS. Many members of this Nature Ecology & Evolution Community may have first come to understand the Darwinian mechanism through his lucid prose. His books have sold by their millions and feature on many an undergraduate reading list. School science teachers around the globe teach what they have learned from him. In the public imagination he is our greatest living evolutionary biologist.  

But for these reasons it is important to point out where he has erred. Or at least, where scientific progress has discredited his claims. Because of his wide influence, it is in the interests of the public understanding of science that any mistakes he has made should be explicitly corrected.

In seeking to do so, I am encouraged by statements that Dawkins has often made about willingness of scientists to have their ideas disproven. With that in mind, I can have no doubt that he himself will welcome and seriously consider this post, should he happen upon it. 

My concern is that Richard Dawkins has made very public statements that, if taken to be true today, seriously misrepresent the field of phylogenetics in the era of whole genome sequencing. 

Take a look at this video hosted by the Richard Dawkins Foundation for Reason & Science YouTube Channel. In the video (8:40 minutes in), Dawkins is asked to name the single best piece of evidence for evolution. His response is to claim that phylogenetic analyses of different genes and pseudogenes each independently give us "the same family tree" for the species that carry them. This congruence between gene trees is "overwhelmingly strong evidence" for evolution - the only alternative being a deceptive creator.

Dawkins makes the same claim more fully in his book The Greatest Show on Earth: The Evidence for Evolution (2009). He writes:

"Comparative DNA (or protein) evidence can be used to decide - on the evolutionary assumption - which pairs of animals are closer cousins than which others. What turns this into extremely powerful evidence for evolution is that you can construct a tree of genetic resemblances separately for each gene in turn. And the important result is that every gene delivers approximately the same tree of life. Once again, this is exactly what you would expect if you were dealing with a true family tree. It is not what you expect if a designer had surveyed the whole of the animal kingdom and picked and chosen - or 'borrowed' - the best proteins for the job, wherever in the animal kingdom they might be found." (pp. 321-322; emphasis added)

To illustrate his point, he describes a study by David Penny et al. published in Nature in 1982 using sequence data for 5 proteins from 11 species. Dawkins claims that "All five proteins 'voted' for pretty much the same subset of trees from among the 34 million possible trees...What is more, the consensus tree that the five molecules all voted for turned out to be the same as zoologists had already worked out on anatomic and palaeontological grounds, not molecular grounds." (p. 324)

He adds that "The intervening years have seen a prolific multiplication of detailed evidence on the exact sequences of genes of lots and lots of species of animals and plants... It is the consistency of agreement among all the different genes in the genome that gives us confidence, not only in the historical accuracy of the consensus tree itself, but also in the fact that evolution has occurred." (pp. 324-325; emphasis added)

The lay-person reading this, or watching the video above, is given the clear impression that every gene or pseudogene in every living organism gives essentially the same phylogenetic tree, when analysed with its homologs from other species. This is simply not true.

If this were true, then phylogeny building in the genomic era would be a walk in the park. But, as many of my readers will know from personal experience, it is not.

If this were true, terms like horizontal gene transfer, incomplete lineage sorting, introgression, and molecular convergence would be rare curiosities in the genomic literature. But they are common (click on the links in the previous sentence to see searched for these terms on Google Scholar).

If this were true, commonly-used phylogenetic software like ASTRAL, ASTRID and BUCKy, designed to deal with gene tree incongruence, would be seldom used. But they are used often.

I hardly need to labour my point to the present audience. Dawkins' statements are simply wrong. Gloriously and utterly wrong. To promulgate this teaching is to do a disservice to the work of thousands of scientists working in the field of phylogenomics, who daily seek to make sense of incongruent gene trees.

It is time for this argument to be retired, or, even better for the public understanding of science, retracted. 

Richard Buggs

Professor, Queen Mary University of London

Comments

Go to the profile of atongsa
about 2 months ago

there is no creator, but troublemaker.

Go to the profile of yegor
about 2 months ago

University of Oregon (2020)

"In a new paper placed online April 15 ahead of print in the April 23 issue of the journal Nature, they argue that long-used approaches for reconstructing evolutionary paths are deeply flawed."

“Our finding casts serious doubts over literally thousands of studies that use phylogenetic trees of extant data to reconstruct the diversification history of taxa, especially for those taxa where fossils are rare, or that found correlations between environmental factors such as changing global temperatures and species extinction rates,” Louca said, using a term for populations of one or more organisms that form a single unit."

"I have been working with these traditional types of models for a decade now,” Pennell said. “I am one of the lead developers of a popular software package for estimating diversification rates from phylogenetic trees. And, as such, I thought I had a really good sense of how these models worked. I was wrong."


https://around.uoregon.edu/content/researchers-find-flaws-how-scientists-build-trees-life





Go to the profile of Olivier Gascuel
about 2 months ago

Reconciliation of gene and species trees is a popular topic, with plenty of publications, studies and computer programs. However, all of these do not contradict Dawkins' argument. Even if some gene trees may differ, especially with bacteria (HGT), closely related species (ILS) or simply due to reconstruction errors, the gene trees are much closer than expected by chance, with many common splits and subtrees. With a few taxa (e.g. 11 as in David Penny's study), it is still frequent to find the same tree topology (among >600 millions). All the programs you mention assume this closeness between gene trees and species trees, and among gene trees. Thus, explanations and precautions are needed, but the core of the argument is still very strong and convicing. Take care to creationists!


Olivier Gascuel

Go to the profile of Richard Buggs
about 2 months ago

Hi Olivier, thank you for a thoughtful response. However, Richard Dawkins is not just saying that most gene trees are much closer than expected by chance: he is saying that they are all "approximately the same".  This is the claim that I am disputing.

Go to the profile of Adolf Heschl
about 1 month ago

One could even go a little further and say that the fact that single genes often produce incompatible phylogenetic trees also refutes Richard Dawkins’ idea of the - selfish - gene as the relevant “unit of selection.” Referring to Douglas Futuyma’s textbook on evolution from 2013 (3rd edition), a passage from Wikipedia aptly boils it down: “One of the resolutions to reduce the implications of incomplete lineage sorting is to use multiple genes for creating species or population phylogenies. The more genes used, the more reliable the phylogeny becomes” (quoted from Wikipedia: incomplete lineage sorting/implications). In other words, entire genomes should be treated as the real units of selection because they produce the most reliable phylogenetic trees. That the molecular reconstruction of phylogeny is not as straightforward as Richard Dawkins tries to make us believe is already shown by the fact that normal sexual reproduction within a given population always involves some amount of horizontal gene transfer or hybridization between a male and a female lineage, which makes it difficult to follow the path of single genes through the population. In contrast, genomes remain relatively stable over time, even if some smaller parts of their genetic content are exchanged from time to time.

Adi Heschl

Go to the profile of Richard Buggs
about 1 month ago

Thanks for your comment, Adi. There is a big discussion to be had about levels of selection, but I agree with you that Dawkins' claim about gene tree congruence seems to be driven more by what would be predicted by a simplistic 1970s model for how evolution works than by the data.