Body mass and temperature influence rates of mitochondrial DNA evolution in North American cyprinid fish.

The mass-specific metabolic rate hypothesis of Gillooly and others predicts that DNA mutation and substitution rates are a function of body mass and temperature. We tested this hypothesis with sequence divergences estimated from mtDNA cytochrome b sequences of 54 taxa of cyprinid fish. Branch lengths estimated from a likelihood tree were compared with metabolic rates calculated from body mass and environmental temperatures experienced by those taxa. The problem of unknown age estimates of lineage splitting was avoided by comparing estimated amounts of metabolic activity along phyletic lines leading to pairs of modern taxa from their most recent common ancestor with sequence divergences along those same pairs of phyletic lines. There were significantly more pairs for which the phyletic line with greater genetic change also had the higher metabolic activity, when compared to the prediction of a hypothesis that body mass and temperature are not related to substitution rate.

Wilkinson support calculated with exact probabilities: an example using Floricaula/LEAFY amino acid sequences that compares three hypotheses involving gene gain/loss in seed plants.

This paper describes a method for quantifying the extent to which a character supports a hypothesized monophyletic group. The basic idea was first proposed by Wilkinson in 1998; hence, we call it Wilkinson support. A character provides Wilkinson support if it could have changed state on the branch leading to the hypothesized monophyletic group without requiring any extra steps in an evolutionary tree. We describe a method to determine the exact probability that a character would provide Wilkinson support for a random group of the same size as the hypothesized monophyletic group. A character's weight is defined as the negative natural log of this probability. The sum over all characters of these weights in a data set is a measure of total weighted support. We exemplify this method using 30 Floricaula/LEAFY amino acid sequences. One copy of this gene occurs in angiosperms, but two copies occur in the other four seed plant groups. Angiosperms could have been primitively single-copy or could have lost either of the two paralogs. These possibilities correspond to three hypotheses of monophyly. We use total weighted Wilkinson support to evaluate these three hypotheses, and all three are shown to be significantly different from random as individual hypothesized monophyletic groups. Comparing these three hypotheses for total weighted support reveals that one has much more support than do the other two. This hypothesis favors the "mostly-male" theory of flowering-plant origins.

Measuring the phylogenetic randomness of biological data sets.

Two qualitative taxonomic characters are potentially compatible if the states of each can be ordered into a character state tree in such a way that the two resulting character state trees are compatible. The number of potentially compatible pairs (NPCP) of qualitative characters from a data set may be considered to be a measure of its phylogenetic randomness. The value of NPCP depends on the number of evolutionary units (EUs), the number of characters, the number of states in the characters, the distributions of EUs among these states, and the amount and distribution of missing information and so does not directly indicate degree of phylogenetic randomness. Thus, for an observed data set, we used Monte Carlo methods to estimate the probability that a data set chosen equiprobably from among those identical (with respect to all the other above determining features) to the observed data set would have as high (or low) an NPCP as the observed data set. This probability, the realized significance of the observed NPCP, is attractive as an indication of phylogenetic randomness because it does not require the assumptions made by other such methods: No character state trees are assumed and consequently, only potential compatibility can be determined; no particular method of phylogenetic estimation is assumed; and no phylogenetic trees are constructed. We determined the values and significances of NPCP for analyses of 57 data sets taken from 53 published sources. All data sets from 37 of those sources exhibited realized significances of < 0.01, indicating high levels of phylogenetic nonrandomness. From each of the remaining 16 sources, at least one data set was more phylogenetically random. Inclusion of outgroups changed significance in some cases, but not always in the same direction. Data sets with significantly low NPCP may be consistent with an ancient hybrid origin (or other ancient polyphyletic gene exchange, crossing over, viral transfer, etc.) of the study group.

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.