An algebraic analysis of cladistic characters

Cladistic characters are used by many numerical axonomists in the estimation of evolutionary history. We make use of semilattice theory to give an algebraic formulation of the ideas involved in this process and to give rigorous proofs of theorems which justify certain operational procedures in current use. In particular, we discuss certain compatibility tests for a collection of charactersPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/21663/1/0000050.pd

Unique perfect phylogeny is NP-hard

We answer, in the affirmative, the following question proposed by Mike Steel as a $100 challenge: "Is the following problem NP-hard? Given a ternary phylogenetic X-tree T and a collection Q of quartet subtrees on X, is T the only tree that displays Q ?

A mathematical foundation for the analysis of cladistic character compatibility

Using formal algebraic definitions of "cladistic character" and "character compatibility", the concept of "binary factors of a cladistic character" is formalized and used to describe and justify an algorithm for checking the compatibility of a set of characters. The algorithm lends itself to the selection of maximal compatible subsets when compatibility fails.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/21887/1/0000294.pd

When is one estimate of evolutionary relationships a refinement of another?

A new way to view a certain type of taxonomic character is presented and several fundamental results are rederived using this approach.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46940/1/285_2004_Article_BF00276095.pd

The phylogeny of the Charadriiformes (Aves): a new estimate using the method of character compatibility analysis

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72525/1/j.1096-3642.1978.tb00375.x.pd

Phylogenetic reanalysis of Strauch\u27s osteological data set for the Charadriiformes

Strauch\u27s (1978) compatibility analysis of relationships among the shorebirds (Charadriiformes) was the first study to examine the full range of charadriiform taxa in a reproducible way. Subsequently Mickevich and Parenti (1980) leveled serious charges against Strauch\u27s characters, method of phylogenetic inference, and results. To account for these charges, Strauch\u27s characters were re-examined and recoded, and parsimony analyses were performed on the revised matrix. A parsimony analysis on 74 taxa from the revised matrix yielded 855 shortest trees, each length = 286 and consistency index = 0.385. In each shortest tree there were two major lineages, a lineage of sandpiper-like birds and a lineage of plover-like birds; the two formed a monophyletic group, with the auks (Alcidae) being that group’s sister taxon. The shortest trees were then compared with other estimates of shorebird relationships, comparison suggesting that the charges against Strauch\u27s results may have resulted from the Mickevich and Parenti decisions to exclude much of Strauch\u27s character evidence

Phylogenetic stability, tree shape, and character compatibility: a case study using early tetrapods

Phylogenetic tree shape varies as the evolutionary processes affecting a clade change over time. In this study, we examined an empirical phylogeny of fossil tetrapods during several time intervals, and studied how temporal constraints manifested in patterns of tree imbalance and character change. The results indicate that the impact of temporal constraints on tree shape is minimal and highlights the stability through time of the reference tetrapod phylogeny. Unexpected values of imbalance for Mississippian and Pennsylvanian time slices strongly support the hypothesis that the Carboniferous was a period of explosive tetrapod radiation. Several significant diversification shifts take place in the Mississippian and underpin increased terrestrialization among the earliest limbed vertebrates. Character incompatibility is relatively high at the beginning of tetrapod history, but quickly decreases to a relatively stable lower level, relative to a null distribution based on constant rates of character change. This implies that basal tetrapods had high, but declining, rates of homoplasy early in their evolutionary history, although the origin of Lissamphibia is an exception to this trend. The time slice approach is a powerful method of phylogenetic analysis and a useful tool for assessing the impact of combining extinct and extant taxa in phylogenetic analyses of large and speciose clades

When are two qualitative taxonomic characters compatible?

A proof is given of a procedure that has previously appeared claiming to determine when two amino acid positions on a protein could both possibly be divergent taxonomic characters. An algorithm for executing this procedure is described.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46948/1/285_2004_Article_BF00275985.pd

Historical Examination Of Delayed Plumage Maturation In The Shorebirds (Aves: Charadriiformes)

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/137446/1/evo01315.pd