Abstract
The distance-based phylogenetic method is fast and remains the most popular one in molecular phylogenetics, especially in the big-data age when researchers often build phylogenetic trees with hundreds or even thousands of leaves. A distance-based method has two components: the evolutionary distance matrix typically derived from a substitution model, and the tree-building algorithm that constructs a tree from the distance matrix. Evolutionary distances differ not only by substitution models, but also by whether they are estimated independently (based on only information between two aligned sequences) or simultaneously (based on information from all pairwise comparisons). Simultaneous estimated distances perform much better in molecular phylogenetics than independently estimated distances. Frequently used tree-building algorithms include neighbor-joining which clusters two species by weighing two measures: how close they are to each other (which is used in a simpler method known as UPGMA) and how far they jointly are from all other species. An alternative method is based on the least-squares framework. Alternative trees first have their branches evaluated by the least-squares method, and then the best tree is chosen by either the least-square criterion or the minimum evolution criterion. Distance-based dating methods are also illustrated numerically, with both fossil-calibrated dating and tip-dating, together with the estimation of variation in the inferred dates by resampling.
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Postscript
1983 is the year when Motoo Kimura published his book entitled “The neutral theory of molecular evolution.” Molecular phylogenetics, as well as chapters on substitution models, are largely based on neutral theory. Only when an overwhelming majority of substitutions are neutral or nearly neutral will the number of substitutions between two homologous genes be roughly proportional to time, which is essential for constructing phylogenetic trees and dating speciation events. Substitutions resulting from natural selection often result in a molecular version of “punctuated equilibrium” and often not occur in a rate proportional to time. The confirmation of numerous numbers of predictions derived from neutral theory attests to the success of the theory.
1983 is also the year when Peter Medawar and Jean Medawar published a book entitled “Aristotle to zoos: a philosophical dictionary of biology” claiming that “in a sense all evolution is adaptation” (Medawar and Medawar 1983, p. 1), when the neutral theory had become so successful, so well-established, so widely accepted, and its validity so obvious. Adaptation results from natural selection, but much of evolution at the molecular level is attributable to fixation of neutral alleles. What was wrong with the Medawars failing to see this? Peter Medawar was obviously a very smart person, and he understood evolution well – his thinking on the evolution of aging is insightful. However, the claim is silly. It seems paradoxical for a person to be smart and silly at the same time.
But we are all smart and silly at the same time. We don’t see all things, just like a little chick that has scratched the surface in a corner of a vast terrain (to paraphrase Darwin), but we all have a tendency to extrapolate our fragmented observation to the whole world. Our limited interaction with a biased sample of people from a race or an ethnic group often results in racist views, and our limited understanding of other subjects often leads to academic bigotry. Think of claims such as “what is true for the colon bacillus is true for the elephant” (attributed to Jacques Monod, Jacob 1988, p. 290), or “Nothing in biology makes sense except in the light of evolution” (Dobzhansky 1973), or “All science is either physics or stamp collecting” attributed to Ernest Rutherford.
What is particularly amazing to me is that grandiosity, either racial or academic, is often much valued and treasured. Dobzhansky’s assertion has given evolutionary biologists a tremendous feeling of pride, and some of them never seem to get tired of repeating it. Rutherford’s claim is said to have inspired many young physicists. Racial or religious grandiosity had driven huge crowds of people to a narcissistic and exalted state of mind that they feel happiness beyond description.
If grandiosity blinds our views and blocks our senses, why does it often remain so captivating and delicious?
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Xia, X. (2018). Distance-Based Phylogenetic Methods. In: Bioinformatics and the Cell. Springer, Cham. https://doi.org/10.1007/978-3-319-90684-3_15
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