In particular, Felsenstein pointed out that parsimony methods implicitly assume that change is improbable a priori (Felsenstein 1973b, 1979). 1977), and during the 80′s an explosion of DNA sequences started to revolutionize the incipient field of molecular phylogenetics. The major breakthroughs in DNA sequencing technologies took place in the second part of the 70′s (Maxam and Gilbert 1977 Sanger et al. During this period, Felsenstein also showed that MP could be inconsistent under certain realistic scenarios (Felsenstein 1978) where “long-branch attraction” is a concern-the so-called “Felsenstein zone” (Huelsenbeck and Hillis 1993). Also in 1973, he set the basis for his 1981 JME publication, proposing an algorithm for computing the likelihood of a tree for discrete characters advancing the “pruning” technique (see below also present in the other 1973 paper) and proposing new probabilistic models of change (see also Jukes and Cantor 1969 Felsenstein 1973b). In 1973, Felsenstein already simplified the model for quantitative characters proposed by Edwards and Cavalli-Sforza in 1964 to make it tractable (Felsenstein 1973a). thesis (Felsenstein 1968)-a current read of which tells us how much of a visionary he was in many regards. Since Edwards and Cavalli-Sforza, the development of ML in phylogenetics was clearly championed by Joe Felsenstein (but see Neyman 1971 Kashyap and Subas 1974), starting with his Ph.D. The reasons for this were several, but the most obvious was the simplicity of the former methods, a clear advantage at a time when computers were still very slow and uncommon.
Remarkably, while the LS and MP approaches rapidly became quite popular, during the 1970s the method of ML was pretty much ignored by most researchers. This was before DNA or protein sequences were even available, and their focus was on the use of blood group allele frequency data to recover the history of human populations for an account of this historical period, see Edwards ( 2009).
Over a very short period of time, they were able to develop three methods: least-squares (LS)–see also Fitch and Margoliash ( 1967), maximum parsimony (MP), and ML (Edwards and Cavalli-Sforza 1963a, b, 1964, 1965). In the early 1960s, AWF Edwards and LL Cavalli-Sforza were set on a clear mission to develop modern statistical approaches for reconstructing phylogenetic trees from genetic data, using computers. Every ‘new’ idea is like another node in a spreading network” (Edwards 2009). “In the development of scientific methodology there is no new thing under the sun. Before delving into the substance of this seminal paper, it is important to understand the historical context in which it was written.
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