Recently in Phylogenetics Category

Word has reached me that Peter Sneath died last Friday at his home in Leicestershire. He was 87 or 88. For a more complete and entertaining autobiographical account see page 77 of this Bulletin of Bergeys International Society for Microbial Systematics.

Peter was a medical microbiologist, who, in the late 1950s, began to work on numerical methods for classifying bacteria. He developed numerical clustering methods. He soon came into contact with Robert Sokal, who was doing the same. Together they wrote Principles of Numerical Taxonomy, a widely-noticed textbook advocating taking a phenetic approach to classification, basing it on measures of overall similarity rather than any inference of phylogeny. The smartest thing Sokal and Sneath did was to not fight over who invented numerical taxonomy, but to join together to promote it (Sneath was first author on the 1973 revision Numerical Taxonomy).

                 Peter Sneath with his children, about 1960. Photo by Joan Sneath, courtesy of the late Peter Sneath

Numerical taxonomy rattled the systematic establishment, then dominated by followers of Ernst Mayr and George Gaylord Simpson’s school of “evolutionary systematics”. It encouraged and stimulated many younger people to look into numerical approaches. By about 1980 phenetic approaches had been pushed aside by phylogenetic systematics, but Sneath and Sokal’s work is still regarded by mathematical clusterers as the most important founding work in their field. The most widely-used of Sneath’s methods is the UPGMA clustering method (independently also invented by F. J. Rohlf). [See comment of September 30 below for correction of this statement].

I always enjoyed meeting Peter and Joan Sneath. Peter was intrigued by any and all uses of numerical and computer methods in science, and was even willing on occasion to violate his own precepts and come up with methods for analyzing phylogenies. He wrote a pioneering 1975 paper (with Sackin and Ambler) on detecting recombination between lineages, for example. I remember Peter telling me that as he traveled around he collected soil samples to study their bacteria. He carried no sterile vials for that – he simply went out and bought a ream of typing paper, as it was sterile, then used some to scoop up the sample and fold it into an envelope. It was a brilliant common-sense improvisation typical of the best of his generation of English scientists.

One of the goals of the intelligent design (ID) movement is to show that evolution cannot be random and/or unguided, and one way to demonstrate this is to show that an evolutionary transition is impossibly unlikely without guidance or intervention. Michael Behe has attempted to do this, without success. And Doug Axe, the director of Biologic Institute, is working on a similar problem. Axe’s work (most recently with a colleague, Ann Gauger) aims (in part, at least) to show that evolutionary transitions at the level of protein structure and function are so fantastically improbable that they could not have occurred "randomly."

Recently, Axe has been writing on this issue. First, he and Gauger just published some experimental results in the ID journal BIO-Complexity. Second, Axe wrote a blog post at the Biologic site in which he defends his approach against critics like Art Hunt and me. Here are some comments on both.

Read the rest at Quintessence of Dust.

Phylogenetic trees are essential tools for representing evolutionary relationships. Unfortunately, they are also a major conceptual stumbling block for budding biologists. Anyone who has taught basic evolutionary concepts to college undergrads (and probably high school students as well) has most likely dealt with students struggling to properly read and draw phylogenies.

Lucky for us, there is also a growing body of literature on the most effective ways to teach what has been dubbed “tree-thinking”. I have summarized this literature in a review due to be published in the journal Evolution: Education and Outreach (doi:10.1007/s12052-010-0254-9). The full text of the article is available at that link, and I have reproduced the abstract below.

Evolution is the unifying principle of all biology, and understanding how evolutionary relationships are represented is critical for a complete understanding of evolution. Phylogenetic trees are the most conventional tool for displaying evolutionary relationships, and “tree-thinking” has been coined as a term to describe the ability to conceptualize evolutionary relationships. Students often lack tree-thinking skills, and developing those skills should be a priority of biology curricula. Many common student misconceptions have been described, and a successful instructor needs a suite of tools for correcting those misconceptions. I review the literature on teaching tree-thinking to undergraduate students and suggest how this material can be presented within an inquiry-based framework.