James Farris

• American Museum of Natural History

Hennig () recognized symplesiomorphies as homologies, and that view is logically correct under the concept of homology (homogeny) prevalent among evolutionists since 1870. Nelson and Platnick () instead wanted homology to exclude symplesiomorphies for reasons that they never made clear but which certainly included opposition to Hennig. They and som...

3 Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA E-mail address: msl-farr@nrm.se

Obtaining a well supported schema of phylogenetic relationships among the major groups of living organisms requires considering as much taxonomic diversity as possible, but the computational cost of calculating large phylogenies has so far been a major obstacle. We show here that the parsimony algorithms implemented in TNT can successfully process...

Grant and Kluge have recently stated that Bremer support and their own REP (“relative explanatory power”), are the only objective measures of group support. This paper discusses their claim, showing that their philosophical arguments have no basis, and that their own numerical examples actually serve to illustrate shortcomings of REP.

Abstract— Objections to my earlier demonstration, that the branch lengths of trees fitted to distance matrices have no physical interpretation, are shown to be ill-founded. In particular the contention of Felsenstein, that fitted lengths estimate expectations of amounts of change, is shown to lead to a paradox. A method is introduced for constructi...

Abstract— Felsenstein's claim of approximate additivity for sequence differences is based on an unjustified model, as is his proposed nonadditive fitting method. His advocacy of the nonnegativity restriction on fitted branch lengths rests on the false premise that distances are additive. His proposed significance test confounds sampling error with...

Parsimony can be related to explanatory power, either by noting that each additional requirement for a separate origin of a feature reduces the number of observed similarities that can be explained as inheritance from a common ancestor; or else by applying Popper’s formula for explanatory power together with the fact that parsimony yields maximum l...

The main features of the phylogeny program TNT are discussed. Windows versions have a menu interface, while Macintosh and Linux versions are command-driven. The program can analyze data sets with discrete (additive, non-additive, step-matrix) as well as continuous characters (evaluated with Farris optimization). Effective analysis of large data set...

Although promoted as a sociological history of then‐recent systematics, David L. Hull's (1988) Science as a Process was, in fact, heavily fictionalized, particularly in its treatment of debates between pheneticists and cladists. Hull routinely suppressed or modified information unfavourable to pheneticists, so presenting a misleading portrayal of s...

Peer Reviewed http://deepblue.lib.umich.edu/bitstream/2027.42/31361/1/0000273.pdf

Sequences of the small subunit (SSU) ribosomal RNA are considered useful for reconstructing the tree of life because this molecule is found in all organisms and is large enough not to have become saturated with multiple mutations. However, these data sets are large, difficult to align, and have extreme biases in base compositions which makes their...

“Relative apparent synapomorphy analysis” (RASA), a method proposed as a statistical test of hierarchic structure in data, would better be called “relative apparent similarity analysis.” The method was supposed to work by finding the regression slope relating cladistic and phenetic measures of similarity, but in fact both the indices used are measu...

Background knowledge comprises accepted (well-corroborated) theories and results. Such theories are taken to be true for the purpose of interpreting evidence when assessing the corroboration of a hypothesis currently in question. Accordingly, background knowledge does not properly include rejected theories, false assumptions, or null models. In par...

A method that allows estimating consensus trees without exhaustive searches is described. The method consists of comparing the results of different independent superficial searches. The results of the searches are then summarized through a majority rule, consensed with the strict consensus tree of the best trees found overall. This assumes that to...

Intended to support three-taxon analysis (3ta), the proposal that all character states be regarded as terminal would instead undercut that method. The same is true of the idea that cladistic methods should not account for plesiomorphies. Parsimony does not correspond to interpretation 1 for incompletely resolved cladograms. The main argument common...

Matrices of three-taxon statements (3ts) represent a transformation of original data in that they are calculated from normal data matrices. Normal matrices cannot be considered transformational (or 3ts matrices original) in that sense, because the 3ts transformation cannot be reversed. That the 3ts transformation cannot be reversed also means that...

Previous weighting methods—including compatibility weighting—have assumed that homoplasy indicates unreliability, but this assumption does not seem to hold for large molecular data matrices. Reliability can be better assessed by support weighting, which measures the degree to which the changes in a character (site) are concentrated in the supported...

Because it is based on a significance test that takes the shape of the tree as given, the Rzhetsky/Nei Confidence Probability (CP) can attribute high “confidence” to groups with little or even literally no support. CP further overestimates confidence in that it takes no account of reliability of alignment, and it shows instability in that drastic c...

Recent claims by its advocates notwithstanding, three-taxon analysis (3ta) provides no method for recognizing reversals or for applying them as apomorphies. Accordingly, 3ta could be used as a phylogenetic method only under an assumption of irreversibility. Being a method for calculating trees from character data, 3ta is not connected to any partic...

Abstract Archie (1990) prefers his “homoplasy excess ratio” HER to Farris' (1989)† ensemble retention index R. HER, he writes, lacks R's defects: R's minimum is not zero, and varies with number of terminals or characters. HER has those defects. Archie has misunderstood the permutation method on which HER rests, and mistaken the properties of R as w...

In Colless’ (1995,Syst. Biol. 44, 102–108) results, cladograms for randomly generated matrices were strongly asymmetrical, and he used this to maintain that real cladograms provide little evidence on asymmetry of phylogeny. His position, however, depended on retaining poorly supported groups as if they were well-supported. If poorly supported group...

Abstract — Contrary to the impression given by Trueman (1996), Bremer (1988) introduced what is now called Bremer support; Faith (1991) did not. Neither did Mishler and Donoghue (1991). Attaching Faith and Cranston's (1991) acronym PTP to Archie's (1989) test does not help make the authorship clear, and the same applies to Kllersjö et al.'s (1992)...

A new approach to phylogenetic analysis, parsimony jackknifing, uses simple parsimony calculations combined with resampling of characters to arrive at a tree comprising well-supported groups. This is usually much the same as the consensus of most-parsimonious trees found from extensive multiple-tree calculations, but the new method is thousands of...

The transition to a vermiform body shape is one of the most important events in animal evolution, having led to the impressive radiation of Bilateria. However, the sister group of Bilateria has remained obscure. Cladistic analyses of morphology indicate that Ctenophora is the sister group of Bilateria. Previous analyses of SSU rRNA sequences have y...

B-function MADS-box genes play crucial roles in floral development in model angiosperms. We reconstructed the structural and functional implications of B-function gene phylogeny in the earliest extant flowering plants based on analyses that include 25 new AP3 and PI sequences representing critical lineages of the basalmost angiosperms: Amborella, N...

As systematists grapple with assembling the Tree of Life, recent studies have encouraged a genomic-scale approach, obtaining DNA sequence data for entire nuclear, plastid or mitochondrial genomes for a few exemplar taxa. Some have proclaimed that this comparative genomic strategy heralds the end of incongruence in phylogeny reconstruction. Although...

A data set with 1551 fungal sequences of the small subunit ribosomal RNA has been analysed phylogenetically. Four animal sequences were used to root the tree. The parsimony ratchet algorithm in combination with tree fusion was used to find most parsimonious trees and the parsimony jackknifing method was used to establish support frequencies. The fu...

Several aspects of current resampling methods to assess group support are reviewed. When the characters have different prior weights or some state transformation costs are different, the frequencies under either bootstrapping or jackknifing can be distorted, producing either under- or overestimations of the actual group support. This is avoided by...

Phylogenetic relationships among many lineages of angiosperms have been clarified via the analysis of large molecular data sets. However, with a data set of three genes (18S rDNA, rbcL, and atpB), relationships among lineages of core eudicots (Berberidopsidales, Caryophyllales, Gunnerales, Santalales, Saxifragales, asterids, rosids) remain essentia...

Parsimony analysis provides a straightforward way of assessing homology on a tree: a state shared by two terminals comprises homologous similarity if optimization attributes that state to all the stem species lying between those terminals. Three-taxon statements (3ts), although seemingly “exact” in that each either fits a tree or does not, do not p...

A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18S rDNA (1855 bp), rbcL (1428 bp), and atpB (1450 bp) representing a total of 4733 bp is presented. Parsimony analysis was expedited by use of a new computer program, the RATCHET. Parsimony jackknifing was performed to assess the support of...

Two data sets of fungal small subunit rDNA sequences, one from the Ribosomal Database Project (RDP) with 489 sequences, and the other from the rRNA WWW Server (RNA-S) with 790 sequences, have been analyzed to estimate group support and to compare tree topologies resulting from independently aligned, large data sets. The analyses were conducted by u...

Two data sets of fungal small subunit (SSU) rDNA sequences, one from the Ribosomal Database Project (RDP) with 485 sequences, and the other from the rRNA WWW Server (RNA-S) with 785 sequences, have been analyzed to estimate group support and to compare tree topologies resulting from independently aligned, large data sets of largely the same sequenc...

Modified three-taxon analysis (m3ta), a method in which three-taxon statements are produced from a nonadditive binary coding of the original data, has been proposed as a model-free way of assessing monophyly of groups, utilizing the taxic concept of homology. In fact the taxic concept amounts to a model, and, further, one that seems to conflict dir...

Parsimony can be inconsistent, but not maximum likelihood—likelihood advocates often say. This difference and conclusions drawn from it have provided the main reasons advanced by likelihoodists against the use of parsimony. Recent statistical research, however, shows that maximum likelihood estimation of phylogenetic trees can become inconsistent i...

According to currently accepted theories, rapidly evolving nucleotide sites are phylogenetically less informative than more slowly evolving ones, especially for recognizing more ancient groupings. For this reason third codon positions are often regarded as less reliable than first and second positions as indicators of phylogeny. Analysis of the lar...

Mitochondrial protein coding genes were combined into a single matrix that included the 13 protein coding genes for 22 mammals, resulting in 11,448 characters each, or more than a quarter of a million base pairs of mitochondrial sequence. This matrix was examined for three separate a priori weighting strategies, including equal weighting, transvers...

According to currently accepted theories, rapidly evolving nucleotide sites are phylogenetically less informative than more slowly evolving ones, especially for recognizing more ancient groupings. For this reason third codon positions are often regarded as less reliable than first and second positions as indicators of phylogeny. Analysis of the lar...

The ever-larger data matrices resulting from continuing improvements in DNA sequencing techniques require faster and more efficient methods of phylogenetic analysis. Here we explore a promising new method, parsimony jackknifing, by analyzing a matrix comprising 2538 sequences of the chloroplast generbcL. The sequences included cover a broad taxonom...

Abstract — The T-PTP test for monophyly can attribute significance to entirely unsupported groups and even to both of two contradictory alternatives. The method of evaluating “support” after replacing selected groups of terminals with reconstructed ancestors has similar drawbacks. The proposed placement of Onychophora among Arthropoda is unsupporte...

The T-PTP test for monophyly can attribute significance to entirely unsupported groups and even to both of two contradictory alternatives. The method of evaluating “support” after replacing selected groups of terminals with reconstructed ancestors has similar drawbacks. The proposed placement of Onychophora among Arthropoda is unsupported by 12S da...

Intended to support three-taxon analysis (3ta), the proposal that all character states be regarded as terminal would instead undercut that method. The same is true of the idea that cladistic methods should not account for plesiomorphies. Parsimony does not correspond to interpretation 1 for incompletely resolved cladograms. The main argument common...

During only the past 4 years, two large data sets of DNA sequences have greatly clarified the broad picture of angiosperm relationships and evolution. By far the more extensive of these two data sets is that based on the chloroplast gene rbcL, with sequences representing 499 species of seed plants [1]. More recently, a smaller data set representing...

Because they are designed to produced just one tree, neighbor-joining programs can obscure ambiguities in data. Ambiguities can be uncovered by resampling, but existing neighbor-joining programs may give misleading bootstrap frequencies because they do not suppress zero-length branches and/or are sensitive to the order of terminals in the data. A n...

Abstract- Because they are designed to produced just one tree, neighbor-joining programs can obscure ambiguities in data. Ambiguities can be uncovered by resampling, but existing neighbor-joining programs may give misleading bootstrap frequencies because they do not suppress zero-length branches and/or are sensitive to the order of terminals in the...

Lefkovitch's formula for the probability of incompatibility between two binary characters can give incorrect results because it redundantly counts some possible compatibilities. The inaccuracy occurs when the characters have the same number of terminals showing the apomorphic state.

ROGERS, DS, IF GREENBAUM, SJ GUNN, AND MD ENGSTROM. 1984. Cytosystematic value of chromosomal inversion data in the genus Peromyscus (Rodentia: Cricetidae). J. Mammal. 65: 457-465. RUVOLO, M. 1992. Molecular evolutionary processes can produce ...

Peer Reviewed http://deepblue.lib.umich.edu/bitstream/2027.42/31724/1/0000662.pdf

Abstract— The skewness criterion of phylogenetic structure in data is too sensitive to character state frequencies, is not sensitive enough to number of characters (degree of corroboration) and relies on counts of arbitrarily-resolved bifurcating trees. For these reasons it can give misleading results. Permutation tests lack those drawbacks and can...

Archie (1990) prefers his "homoplasy excess ratio" HER to Farris' (1989)1 1 I had introduced the retention index at the 1988 meeting of this Society (cf. Seberg, 1989), having already implemented that measure in Hennig86. I thank W. Day for his enthusiastic interest on that occasion. ensemble retention index R. HER, he writes, lacks R's defects: R'...

https://deepblue.lib.umich.edu/bitstream/2027.42/149709/1/tax04403.pdf

Advocates of syncretistic classification have generally held that the descriptive and explanatory roles of the biological reference system should be kept separate, and that description and explanation impose conflicting goals on classification. I show that view leads to contradictions, and I summarize earlier demonstrations that the phylogenetic sy...