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Top Scientific Problems with Evolution: Molecular Phylogeny

Jonathan Wells
Image credit: Arek Socha, via Pixabay.

Editor’s note: We are delighted to present a series by biologist Jonathan Wells on the top scientific problems with evolution. This is the fourth entry in the series, excerpted from the new book The Comprehensive Guide to Science and Faith: Exploring the Ultimate Questions About Life and the CosmosFind the full series so far here.

The word phylogeny refers to the evolutionary history of an organism.1 The word was coined by German Darwinian biologist Ernst Haeckel several years after the publication of On the Origin of Species. Evolutionary biologists have proposed phylogenies based on homologies in fossils, but as we have seen, there are problems with both fossils and homology. With the rise of modern molecular biology, evolutionary biologists have increasingly sought to base phylogenies on molecules such as proteins and DNA. 

Proteins consist of sequences of subunits called amino acids, and DNA consists of subunits called nucleotides. Different species may contain similar proteins or DNA molecules that exhibit slight differences in the sequences of their subunits. If three different species contain a similar DNA molecule, and its sequence in species A is more similar to its sequence in species B than in species C, then an evolutionary biologist might infer that A is more closely related to B than it is to C. 

Defining “Related”

But the meaning of related is ambiguous. In one sense it can refer to genealogy, as in “Charles Darwin was more closely related to Erasmus Darwin (his grandfather) than either was to Geronimo.” In another sense it can refer to similarity, as in “iron is more closely related to aluminum than either is to a daffodil.”2 Phylogenetic inferences assume that molecular relatedness (the second sense) is equivalent to genealogical relatedness (the first sense). This premise is based on the assumption of common ancestry. 

Molecular comparisons are complicated by the problem of alignment. DNA sequences in living things typically contain repeated and/or deleted segments, so it is often unclear where to line them up. If two sequences can be aligned in more than one way, then any comparison will depend heavily on what alignment the investigator chooses. And when many sequences are compared, as they are in molecular phylogenies, the problem becomes much worse.3

Evolution’s Tree of Life

Darwin thought that the history of living things could be represented as a “great Tree of Life,” with common ancestors as the trunk and modern organisms as the tips of the branches.4 If the history of life is treelike, one would expect that the data from molecular phylogeny would eventually converge on a single tree, and that as more data were found, the fit would improve. Yet from the very beginning, molecular phylogenetics has been plagued with discrepancies among trees based on different sequences and different alignments. 

And the problem has only grown worse as more data have accumulated. In 2005, three biologists who compared 50 DNA sequences from 17 animal groups concluded that “different phylogenetic analyses can reach contradicting inferences with [seemingly] absolute support.”5 In 2012, four evolutionary biologists reported “incongruence between phylogenies derived from…different subsets of molecular sequences has become pervasive.”6

So the idea of common ancestry remains an assumption. It does not follow from homology, except by circular reasoning. The fossil record remains (as Darwin acknowledged) a serious problem. And common ancestry does not emerge from the inconsistent findings of molecular phylogenetics.

Tomorrow, natural selection.


  1. Merriam-Webster’s definition of “phylogeny,” https://www.merriam-webster.com/dictionary/phylogeny (accessed August 23, 2020). 
  2. Wells, Zombie Science, 32-33.
  3. James A. Lake, “The order of sequence alignment can bias the selection of tree topology,” Molecular Biology and Evolution 8 (1991), 378–385; Wells, Zombie Science, 35-36.
  4. Charles Darwin, Origin of Species, 1st ed., 130, http://darwin-online.org.uk/content/frameset?pageseq=148&itemID=F373&viewtype=side (accessed August 23, 2020).
  5. Antonis Rokas, Dirk Krüger, and Sean B. Carroll, “Animal evolution and the molecular signature of radiations compressed in time,” Science 310 (2005), 1933-1938.
  6. Liliana Dávalos, Andrea Cirranello, Jonathan Geisler, and Nancy Simmons, “Understanding phylogenetic incongruence: Lessons from phyllostomid bats,” Biological Reviews of the Cambridge Philosophical Society 87 (2012), 991-1024.