Three-taxon analysis
{{short description|Cladistic based method of phylogenetic reconstruction}}
File:Grand et al. Fig. 1 col.tif
Three-taxon analysis (or TTS, three-item analysis, 3ia) is a cladistic based method of phylogenetic reconstruction. Introduced by Nelson and Platnick in 1991{{Cite journal | last1 = Nelson | first1 = G. | last2 = Platnick | first2 = N. I. | title = Three-Taxon Statements: A More Precise Use of Parsimony? | journal = Cladistics | volume = 7 | issue = 4 | pages = 351 | year = 1991 | doi = 10.1111/j.1096-0031.1991.tb00044.x | s2cid = 86270478 | doi-access = free }} to reconstruct organisms' phylogeny, this method can also be applied to biogeographic areas. It attempts to reconstruct complex phylogenetic trees by breaking the problem down into simpler chunks. Rather than try to resolve the relationships of all X taxa at once, it considers taxa 3 at a time. It is relatively easy to generate three-taxon statements (3is); that is, statements of the form "A and B are more closely related to one another than to C".{{Cite journal | last1 = Zaragueta-Bagils | first1 = R. | last2 = Bourdon | first2 = E. | title = Three-item analysis: Hierarchical representation and treatment of missing and inapplicable data | journal = Comptes Rendus Palevol | volume = 6 | issue = 6–7 | pages = 527 | year = 2007 | doi = 10.1016/j.crpv.2007.09.013 }} Once each group of three taxa has been considered, the method constructs a tree that is consistent with as many three-item statements as possible.
From a theoretical point of view, the method has three main problems: (1) character evolution is a priori assumed to be irreversible; (2) 3is that are not logically independent are treated as if they are; (3) 3is that are considered as independent support for a given tree may be mutually exclusive on that tree. {{Cite journal | last1 = De Laet | first1 = J. | last2 = Smets | first2 = E. | title = On the three-taxon approach to parsimony analysis | journal = Cladistics | volume = 14 | issue = 4 | pages = 363–381 | year = 1998 | doi = 10.1111/j.1096-0031.1998.tb00344.x | pmid = 34929915 | s2cid = 221583681 | doi-access = free }}
A computer program that implement three-taxon analysis is LisBeth{{Cite journal | last1 = Bagils | first1 = R. Z. E. | last2 = Ung | first2 = V. | last3 = Grand | first3 = A. S. | last4 = Vignes-Lebbe | first4 = R. G. | last5 = Cao | first5 = N. L. | last6 = Ducasse | first6 = J. | doi = 10.1016/j.crpv.2012.07.002 | title = LisBeth: New cladistics for phylogenetics and biogeography | journal = Comptes Rendus Palevol | volume = 11 | issue = 8 | pages = 563 | year = 2012 }} (for systematic and biogeographic studies). LisBeth have been freely released.{{Cite web|url = http://infosyslab.fr/lis/?q=en/resources/software/lisbeth|title = LisBeth package}} A recent simulation-based study found that Three-taxon analysis yields good power and an error rate intermediate between parsimony with ordered states and parsimony with unordered states.{{Cite journal | doi=10.1111/bij.12159|title = Phylogenetic inference using discrete characters: Performance of ordered and unordered parsimony and of three-item statements| journal=Biological Journal of the Linnean Society| volume=110| issue=4| pages=914–930|year = 2013|last1 = Grand|first1 = Anaïs| last2=Corvez| first2=Adèle| last3=Duque Velez| first3=Lina Maria| last4=Laurin| first4=Michel| doi-access=free}}