Background
We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacrificing scalability.

/pdf/fasttree-2-approximately-maximum-likelihood-trees-for-large-1monmwsbs8.pdf

FastTree 2--approximately maximum-likelihood trees for large alignments.

http://amborella.net/2010PlantSystematics/DATA/3-24-APG%202003%20Bot%20J%20Linn%20Soc%20APGII.pdf

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II

http://aracnologia.macn.gov.ar/st/biblio/Goloboff%20et%20al%202008%20TNT.pdf

TNT, a free program for phylogenetic analysis

Perp. punya vol. X. Flowering plant, eudicots : sapindales, cucurbitales, myrtaceae. Perp.punya: 1eks.

The Families And Genera Of Vascular Plants

The issue of species delimitation has long been confused with that of species conceptualization, leading to a half century of controversy concerning both the definition of the species category and methods for inferring the boundaries and numbers of species. Alternative species concepts agree in treating existence as a separately evolving metapopulation lineage as the primary defining property of the species category, but they disagree in adopting different properties acquired by lineages during the course of divergence (e.g., intrinsic reproductive isolation, diagnosability, monophyly) as secondary defining properties (secondary species criteria). A unified species concept can be achieved by treating existence as a separately evolving metapopulation lineage as the only necessary property of species and the former secondary species criteria as different lines of evidence (operational criteria) relevant to assessing lineage separation. This unified concept of species has several consequences for species delimitation, including the following: First, the issues of species conceptualization and species delimitation are clearly separated; the former secondary species criteria are no longer considered relevant to species conceptualization but only to species delimitation. Second, all of the properties formerly treated as secondary species criteria are relevant to species delimitation to the extent that they provide evidence of lineage separation. Third, the presence of any one of the properties (if appropriately interpreted) is evidence for the existence of a species, though more properties and thus more lines of evidence are associated with a higher degree of corroboration. Fourth, and perhaps most significantly, a unified species concept shifts emphasis away from the traditional species criteria, encouraging biologists to develop new methods of species delimitation that are not tied to those properties.

/pdf/species-concepts-and-species-delimitation-4we3sl6pvr.pdf

Species Concepts and Species Delimitation

The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis

Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences

An amplification of the phylogenetic species concept

Systematists should distinguish between cladistic analysis, i.e., a numerical procedure, and phylogenetic analysis, i.e., the reconstruction of hierarchic descent relationships. Modern cladistic analysis uses parsimony to construct hierarchic arrangements (trees) of terminal units (terminals) that have been scored for a series of attributes. The interpretation of cladistic relationships as representative of phylogenetic relationships requires two conditions, both of which were identified by Hennig (1966, Phylogenetic systematics, Univ. Illinois Press, Urbana). First, descent relationships among the terminals must be hierarchic; that is, all terminals must have been generated by the subdivision or replication of previously existing ancestors

Kevin C. Nixon

Papers

TNT, a free program for phylogenetic analysis

The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis

Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences

An amplification of the phylogenetic species concept

Populations, Genetic Variation, and the Delimitation of Phylogenetic Species