Kevin C. Nixon

TNT, a free program for phylogenetic analysis

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 sets can be carried out in reasonable times, and a number of methods to help identifying wildcard taxa in the case of ambiguous data sets are implemented. A variety of methods for diagnosing trees and exploring character evolution is available in TNT, and publication‐quality tree‐diagrams can be saved as metafiles. 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.

The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis☆

The Parsimony Ratchet1 is presented as a new method for analysis of large data sets. The method can be easily implemented with existing phylogenetic software by generating batch command files. Such an approach has been implemented in the programs DADA (Nixon, 1998) and Winclada (Nixon, 1999). The Parsimony Ratchet has also been implemented in the most recent versions of NONA (Goloboff, 1998). These implementations of the ratchet use the following steps: (1) Generate a starting tree (e.g., a “Wagner” tree followed by some level of branch swapping or not). (2) Randomly select a subset of characters, each of which is given additional weight (e.g., add 1 to the weight of each selected character). (3) Perform branch swapping (e.g., “branch-breaking” or TBR) on the current tree using the reweighted matrix, keeping only one (or few) tree. (4) Set all weights for the characters to the “original” weights (typically, equal weights). (5) Perform branch swapping (e.g., branch-breaking or TBR) on the current tree (from step 3) holding one (or few) tree. (6) Return to step 2. Steps 2–6 are considered to be one iteration, and typically, 50–200 or more iterations are performed. The number of characters to be sampled for reweighting in step 2 is determined by the user; I have found that between 5 and 25% of the characters provide good results in most cases. The performance of the ratchet for large data sets is outstanding, and the results of analyses of the 500 taxon seed plant rbcL data set (Chase et al., 1993) are presented here. A separate analysis of a three-gene data set for 567 taxa will be presented elsewhere (Soltis et al., in preparation) demonstrating the same extraordinary power. With the 500-taxon data set, shortest trees are typically found within 22 h (four runs of 200 iterations) on a 200-MHz Pentium Pro. These analyses indicate efficiency increases of 20×–80× over “traditional methods” such as varying taxon order randomly and holding few trees, followed by more complete analyses of the best trees found, and thousands of times faster than nonstrategic searches with PAUP. Because the ratchet samples many tree islands with fewer trees from each island, it provides much more accurate estimates of the “true” consensus than collecting many trees from few islands. With the ratchet, Goloboffs 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.

AN AMPLIFICATION OF THE PHYLOGENETIC SPECIES CONCEPT

Abstract— The goal of a phylogenetic species concept is to reveal the smallest units that are analysable by cladistic methods and interpretable as the result of phylogenctic history. We define species as the smallest aggregation of populations (sexual) or lineagcs (asexual) diagnosable by a unique combination of character states in comparable individuals (semaphoronts). A character state is an inherited attribute distributed among all comparable individuals (semaphoronts) of the same historical population, clade, or terminal lineage. This definition of species is character‐based and pattern oriented. Evolutionary explanations of phylogenetic species are consistent with contemporary explanations of processes of speciation, but require only the assumption of nested hierarchical pattern. We discuss the compatibility of the phylogenetic species concept with various biological needs for species and justify its use at the exclusion of alternative species concepts.

ON SIMULTANEOUS ANALYSIS

Arguments for and against combined analysis of multiple data sets in phylogenetic inference are reviewed. Simultaneous analysis of combined data better maximizes cladistic parsimony than separate analyses, hence is to be preferred. Simultaneous analysis can allow “secondary signals” to emerge because it measures strength of evidence supporting disparate results. Separate analyses are useful and of interest to understanding the differences among data sets, but simultaneous analysis provides the greatest possible explanatory power, and should always be evaluated when possible. The mechanics of simultaneous analysis are discussed.  1996 The Willi Hennig Society “Yes, yes, I know that, Sidney . . . everybody knows that! . . . But look: Four wrongs squared, minus two wrongs to the fourth power, divided by this formula, do make a right.” Gary Larson, The Far Side

A reevaluation of seed plant phylogeny

Seed plant phylogeny is evaluated using a data set of 46 terminals (taxa) and 103 morphological and anatomical characters. Cladistic analyses using the criterion of parsimony were performed on the complete data set as well as on subsets of the data, e.g., excluding fossils and/or combining various complex taxa into single terminals. 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. When fossils were included, Bennettitales (cycadeoids) were part of an «anthophyte» clade that included gnetopsids and angiosperms. Pentoxylon was a sister taxon to the core anthophyte clade, in some, but not all, of the most parsimonious trees

Fossil evidence and phylogeny: the age of major angiosperm clades based on mesofossil and macrofossil evidence from Cretaceous deposits.

The fossil record has played an important role in the history of evolutionary thought, has aided the determination of key relationships through mosaics, and has allowed an assessment of a number of ecological hypotheses. Nonetheless, expectations that it might accurately and precisely mirror the progression of taxa through time seem optimistic in light of the many factors potentially interfering with uniform preservation. In view of these limitations, attempts to use the fossil record to corroborate phylogenetic hypotheses based on extensive comparisons among extant taxa may be misplaced. Instead we suggest a method-minimum age node mapping-for combining reliable fossil evidence with hypotheses of phylogeny. We use this methodology in conjunction with a phylogeny for angiosperms to assess timing in the history of major angiosperm clades. This method places many clades both with and without fossil records in temporal perspective, reveals discrepancies among clades in propensities for preservation, and raises some interesting questions about angiosperm evolution. By providing a context for understanding the gaps in the angiosperm fossil record this technique lends credibility and support to the remainder of the angiosperm record and to its applications in understanding a variety of aspects of angiosperm history. In effect, this methodology empowers the fossil record.

Polymorphic taxa, missing values and cladistic analysis

Abstract Missing values have been used in cladistic analyses when data are unavailable, inapplicable or sometimes when character states are variable within terminal taxa. The practice of scoring taxa as having “missing values” for polymorphic characters introduces errors into the calculation of cladogram lengths and consistency indices because some character change is hidden within terminals. Because these hidden character steps are not counted, the set of most parsimonious cladograms may differ from those that would be found if polymorphic taxa had been broken into monomorphic subunits. In some cases, the trees found when polymorphisms are scored as missing values may not include any of the most parsimonious trees found when the data are scored properly. Additionally, in some cases, polymorphic taxa may be found to be polyphyletic when broken into monomorphic subunits; this is undetected when polymorphisms are treated as missing. Because of these problems, terminal units in cladistic analysis should be based on unique, fixed combinations of characters. Polymorphic taxa should be subdivided into subunits that are monomorphic for each character used in the analysis. Disregarding errors in topology, the additional hidden steps in a cladogram in which polymorphisms are scored as missing can be calculated by a simple formula, based on the observation that if it is assumed that polymorphic terminals include all combinations of character states, 2p− 1 additional steps are required for each taxon in which p polymorphic binary characters are scored as missing values. Thus, when several polymorphisms are scored as missing in the same taxon, very large errors can be introduced into the calculation of tree length.

Functional Constraints and rbcL Evidence for Land Plant Phylogeny

Although the proportion of «functional» DNA in eukaryotic genomes is both debatable and subject to definition, most sequences gathered for phylogenetic purposes are indisputably functional. For example, patterns of variation are likely to be strongly constrained in ribosomal RNAs because of their structural and catalytic roles in protein translation, and in protein-coding genes, because of protein function itself. Although seemingly obvious, these concerns are usually ignored by workers producing gene trees. We have examined the extent of functional constraints in land-plant rbcL sequences. Not only do rbcL sequences appear to change with essentially clocklike regularity, but nucleotide-based cladograms imply tbat approximately 97.5% of codon changes on internal branches are functionally neutral (i.e., synonymous or functionally labile)

ON CONSENSUS, COLLAPSIBILITY, AND CLADE CONCORDANCE

Abstract — Consensus in cladistics is reviewed. Consensus trees, which summarize the agreement in grouping among a set of cladograms, are distinguished from compromise trees, which may contain groups that do not appear in all the cladograms being compared. Only a strict or Nelson tree is an actual consensus. This distinction has implications for the concept of support for cladograms: only those branches supported under all possible optimizations are unambiguously supported. We refer to such cladograms as strictly supported, in contrast to the semistrictly (ambiguously) supported cladograms output by various current microcomputer programs for cladistic analysis. Such semistrictly supported cladograms may be collapsed, however, by a variety of options in various programs. Consideration of collapsibility and optimization on multifurcations leads to some conclusions on the use of consensus. Consensus tree length provides information about character conflict that occurs between, not within, cladograms. We propose the clade concordance index, which employs the consensus tree length to measure inter‐cladogram character conflict for all characters among a set of cladograms.

Fossil Clusiaceae from the late Cretaceous (Turonian) of New Jersey and implications regarding the history of bee pollination.

The Turonian flora from Sayreville New Jersey includes one of the worlds most diverse assemblages of Cretaceous angiosperm flowers. This flora is made even more interesting by its association with a large insect fauna that is preserved by charcoalification as well as in amber. Floral diversity includes numerous representatives of Magnoliidae, Hamamelididae, Rosidae, Dilleniidae, and Asteridae (Ericales sensu lato). Included are hypogynous, five-merous flowers with uniseriate hairs on the pedicels and stamens in bundles most frequently borne opposite the petals. There is considerable variation in filament length, and some filaments are branched. On some anthers, strands of residue, suggesting the former presence of a liquid of unknown nature, partially occlude the apparent zone of dehiscence. In other cases, open anthers are fully occluded by an amorphous substance. Pollen is rarely found associated with anthers, but is common on stigmatic surfaces. Pollen is prolate and tricolporate with reticulate micromorphology. The superior syncarpous ovary is five-carpellate with axile/intruded parietal placentation and numerous anatropous ovules/carpel. Ovary partitions have closely spaced, parallel ascending channels (secretory canals?), and there are apparent secretory canals/cavities in receptacles, sepals, and petals. Individual stigmas are cuneiform with a central groove and eccentrically peltate. Styles are short and fused. In aggregate, the stigmas form a secondarily peltate stigma. Seeds have a reticulate sculpture pattern, a pronounced raphe, and funicular arils with sculpture similar to the seeds. Phylogenetic analyses of several data matrices of extant taxa place this fossil in a monophyletic group with the modern genera Garcinia and Clusia within the Clusiaceae. As such, these fossils represent the earliest fossil evidence of the family Clusiaceae. Some modern Clusiaceae are notable, in particular, for their close relationship with meliponine and other highly derived bee pollinators; the fossil flowers share several characters that suggest a similar mode of pollination. This possibility is consistent with other floral and insect data from the same locality.