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TNT, a free program for phylogenetic analysis
Through the use of a number of native commands and a simple but powerful scripting language, TNT allows the user an enormous flexibility in phylogenetic analyses or simulations.
Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences
A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18S rDNA, rbcL, and atpB representing a total of 4733 bp is presented, resulting in the most highly resolved and strongly supported topology yet obtained for angiosPerms.
The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis
- K. Nixon
- Computer Science
- 1 December 1999
With the ratchet, Goloboff's NONA, and existing computer hardware, data sets that were previously intractable or required months or years of analysis with PAUP* can now be adequately analyzed in a few hours or days.
Populations, Genetic Variation, and the Delimitation of Phylogenetic Species
Cl cladistic relationships as representative of phylogenetic relationships requires two conditions, both of which were identified by Hennig (1966, Phylogenetic systematics, Univ. Illinois Press, Urbana).
ON SIMULTANEOUS ANALYSIS
Arguments for and against combined analysis of multiple data sets in phylogenetic inference are reviewed and simultaneous analysis is to be preferred because it better maximizes cladistic parsimony than separate analyses.
Phylogeny, biogeography, and processes of molecular differentiation in Quercus subgenus Quercus (Fagaceae).
The biogeographic hypothesis that all major oak lineages evolved locally at middle latitudes within the general distribution of their fossil ancestors was fully supported and a New World origin for the widespread white oaks of the Northern Hemisphere was suggested.
Archaefructaceae, a New Basal Angiosperm Family
Archaefructaceae is proposed as a new basal angiosperm family of herbaceous aquatic plants and is a sister clade to all angiosperms when their characters are included in a combined three-gene molecular and morphological analysis.
Infrageneric classification of Quercus (Fagaceae) and typification of sectional names
- K. Nixon
- Environmental Science
Summary — The genus Quercus L (the true oaks) is widespread in the Northern hemisphere, in habitats ranging from temperate and tropical forests to dry thorn scrub and semi-desert. As far as is…
AN AMPLIFICATION OF THE PHYLOGENETIC SPECIES CONCEPT
The compatibility of the phylogenetic species concept with various biological needs for species and its use at the exclusion of alternative species concepts are discussed.
A Reevaluation of Seed Plant Phylogeny
The results support the placement of the cycads as the sister group of a monophyletic group that includes several fossil «seed ferns» as well as extant Ginkgo, conifers, gnetopsids, and angiosperms.