Phylogenetics
Philogenetics studies phylogenesis, a word derived from the Greek words φῦλον 'race, tribe, classes', γένεσις 'origin, formation, genesis' thus meaning the 'formation of the classes (of biological species)'. The term was coined by Ernst Haeckel (1866, II, xx. p. 299).
Phylogenetics refers to the inference of evolutionary history from biological data, often nucleotide (DNA/RNA) or protein sequence data, and in particular, construction of phylogenetic trees or networks.
There are a number of computational methods for constructing phylogenetic trees. These include methods that are based on a distance matrix representing pair-wise distances between the data sequences such as neighbour joining and UPGMA. Other methods, such as maximum parsimony and maximum likelihood, use the actual sequences. Methods based on Bayesian statistical inference have also been proposed; see for example the MrBayes software.
In some cases, the evolutionary history can be more appropriately represented as a phylogenetic network rather than a tree. This may be due to different factors such as horizontal gene transfer. Some network methods can also be used to represent conflicting evidence in the data, even if the evolutionary history is assumed to be tree-like. Popular network construction methods include NeighborNet and MedianNetwork.
Phylogenetic methods are increasingly applied to other kinds of data, in which case they may be referred to as phylomemetics.
Amongst those applications outside the field of biology, the use of computer-assisted phylogenetic methods in stemmatology has proved to be very promising. There are indeed strong conceptual and methodological similarities between evolutionary biology and the genealogy of manuscripts, which have been noted since long (Reeve 1998 provides an interesting historical survey of the relationships between the two fields, see also Platnick and Cameron 1977, and Robins 2007). Early attempts at applying software used in biology to stemmatics are Cameron 1987, and O'Hara and Robinson 1993.
Despite clear analogies between the two approaches, there are also differences between biological phylogeny and the branching of a textual tradition. Some of them are of size and scale: a single biological species may consist of billions of slightly different individuals, and the whole process that is studied may have taken millions of years to happen, whereas very large textual traditions will be made up of a few thousand witnesses at most. Another relevant difference is that manuscripts are copied by thinking scribes who may on purpose alter the text or use more than one exemplar (contamination, to some extant this exists in biology as well, as horizontal gene-transfer).
A further problem is that the graph created by a computer is not oriented: the computer cannot say which of the manuscripts is the oldest or most original (the root), it simply shows how the manuscripts are related to each other. This must needs be so as long as the differences between witnesses are defined as commutating (thus the difference between witness A and witness B must always be equal to the difference between B and A). A scholar is required to determine how the tree should be oriented (and thus be converted to an actual stemma) and draw conclusions of it. In biology this rooting can usually be done by including a distantly related outgoup, which is usually not possible for a textual tradition, whose original is, so to speak, created "ex nihilo" by its author.
See: Cladistics.
Bibliography
– Cameron, H. Donald. 1987. “The upside-down cladogram: Problems in manuscript affiliation.” In Biological Metaphor and Cladistic Classification: An Interdisciplinary Perspective, edited by Henry M. Hoenigswald and Linda F. Wiener, 227–242. Philadelphia: University of Pennsylvania Press.
– Haeckel, Ernst. 1866. Generelle Morphologie der Organismen: allgemeine Grundzüge der organischen Formen-Wissenschaft, mechanisch begründet durch die von Charles Darwin reformirte Descendenz-Theorie. 2 vols. Berlin: Reimer.
– Huson, Daniel H., Regula Rupp and Celine Scornavacca. 2010. Phylogenetic Networks. Cambridge: Cambridge University Press.
– Lemey, Philippe, Marco Salemi, and Anne-Mieke Vandamme, eds. 2009. The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing. 2nd ed. Cambridge: Cambridge University Press.
– Morrison, David A. 2011. Introduction to Phylogenetic Networks. Uppsala: RJR Productions. – Available at http://www.rjr-productions.org/Networks. Accessed 27 October 2015.
– O'Hara, Robert, and Peter Robinson. 1993. Computer-assisted Methods of Stemmatic Analysis. In The Canterbury Tales Project Occasional Papers, edited by Norman Blake and Peter Robinson, vol. 1, 53–74. Oxford: Office for Humanities Communication.
– Platnick, Norman I., and H. Donald Cameron. 1977. “Cladistic methods in textual, linguistic and phylogenetic analysis.” Systematic Zoology 26: 380–385.
– Reeve, Michael D. 1998. “Shared innovations, dichotomies, and evolution.” In Filologia classica e filologia romanza: esperienze ecdotiche a confronto: Atti del Convegno Roma 25-27 maggio 1995, edited by Anna Ferrari, 445–505. Spoleto: Centro Italiano di Studi sull’Alto Medioevo.
– Robins, William. 2007. “Editing and Evolution.” Literature Compass 4 (1): 89–120.
In other languages
DE: Phylogenetik / Phylogenese / Phylogenie
FR: phylogénétique / phylogenèse / phylogénie
IT: filogenetica / filogenesi / filogenia