Properties of some methylellagic acids and their glycosides

Methylellagic acids and their glycosides have been isolated from or detected in different tissues of eucalypts. These compounds appear to constitute a taxonomic character and to facilitate their detection a number of their properties are reported.     

Species names in phylogenetic nomenclature

Linnaean binomial nomenclature is logically incompatible with the phylogenetic nomenclature of de Queiroz and Gauthier (1992, Annu. Rev. Ecol. Syst. 23:449-480): The former is based on the concept of genus, thus making this rank mandatory, while the latter is based on phylogenetic definitions and requires the abandonment of mandatory ranks. Thus, if species are to receive names under phylogenetic nomenclature, a different method must be devised to name them. Here, 13 methods for naming species in the context of phylogenetic nomenclature are contrasted with each other and with Linnaean binomials. A fundamental dichotomy among the proposed methods distinguishes those that retain the entire binomial of a preexisting species name from those that retain only the specific epithet. Other relevant issues include the stability, uniqueness, and ease of pronunciation of species names; their capacity to convey phylogenetic information; and the distinguishability of species names that are governed by a code of phylogenetic nomenclature both from clade names and from species names governed by the current codes. No method is ideal. Each has advantages and drawbacks, and preference for one option over another will be influenced by one's evaluation of the relative importance of the pros and cons for each. Moreover, sometimes the same feature is viewed as an advantage by some and a drawback by others. Nevertheless, all of the proposed methods for naming species in the context of phylogenetic nomenclature provide names that are more stable than Linnaean binomials.     

When are phylogenetic analyses misled by convergence? A case study in Texas cave salamanders

Convergence, i.e., similarity between organisms that is not the direct result of shared phylogenetic history (and that may instead result from independent adaptations to similar environments), is a fundamental issue that lies at the interface of systematics and evolutionary biology. Although convergence is often cited as an important problem in morphological phylogenetics, there have been few well-documented examples of strongly supported and misleading phylogenetic estimates that result from adaptive convergence in morphology. In this article, we propose criteria that can be used to infer whether or not a phylogenetic analysis has been misled by convergence. We then apply these criteria in a study of central Texas cave salamanders (genus Eurycea). Morphological characters (apparently related to cave-dwelling habitat use) support a clade uniting the species E. rathbuni and E. tridentifera, whereas mitochondrial DNA sequences and allozyme data show that these two species are not closely related. We suggest that a likely explanation for the paucity of examples of strongly misleading morphological convergence is that the conditions under which adaptive convergence is most likely to produce strongly misleading results are limited. Specifically, convergence is most likely to be problematic in groups (such as the central Texas Eurycea) in which most species are morphologically very similar and some of the species have invaded and adapted to a novel selective environment.     

Increased taxon sampling greatly reduces phylogenetic error

Several authors have argued recently that extensive taxon sampling has a positive and important effect on the accuracy of phylogenetic estimates. However, other authors have argued that there is little benefit of extensive taxon sampling, and so phylogenetic problems can or should be reduced to a few exemplar taxa as a means of reducing the computational complexity of the phylogenetic analysis. In this paper we examined five aspects of study design that may have led to these different perspectives. First, we considered the measurement of phylogenetic error across a wide range of taxon sample sizes, and conclude that the expected error based on randomly selecting trees (which varies by taxon sample size) must be considered in evaluating error in studies of the effects of taxon sampling. Second, we addressed the scope of the phylogenetic problems defined by different samples of taxa, and argue that phylogenetic scope needs to be considered in evaluating the importance of taxon-sampling strategies. Third, we examined the claim that fast and simple tree searches are as effective as more thorough searches at finding near-optimal trees that minimize error. We show that a more complete search of tree space reduces phylogenetic error, especially as the taxon sample size increases. Fourth, we examined the effects of simple versus complex simulation models on taxonomic sampling studies. Although benefits of taxon sampling are apparent for all models, data generated under more complex models of evolution produce higher overall levels of error and show greater positive effects of increased taxon sampling. Fifth, we asked if different phylogenetic optimality criteria show different effects of taxon sampling. Although we found strong differences in effectiveness of different optimality criteria as a function of taxon sample size, increased taxon sampling improved the results from all the common optimality criteria. Nonetheless, the method that showed the lowest overall performance (minimum evolution) also showed the least improvement from increased taxon sampling. Taking each of these results into account re-enforces the conclusion that increased sampling of taxa is one of the most important ways to increase overall phylogenetic accuracy.     

Convergence among cave catfishes: long-branch attraction and a Bayesian relative rates test

Convergence has long been of interest to evolutionary biologists. Cave organisms appear to be ideal candidates for studying convergence in morphological, physiological, and developmental traits. Here we report apparent convergence in two cave-catfishes that were described on morphological grounds as congeners: Prietella phreatophila and Prietella lundbergi. We collected mitochondrial DNA sequence data from 10 species of catfishes, representing five of the seven genera in Ictaluridae, as well as seven species from a broad range of siluriform outgroups. Analysis of the sequence data under parsimony supports a monophyletic Prietella. However, both maximum-likelihood and Bayesian analyses support polyphyly of the genus, with P. lundbergi sister to Ictalurus and P. phreatophila sister to Ameiurus. The topological difference between parsimony and the other methods appears to result from long-branch attraction between the Prietella species. Similarly, the sequence data do not support several other relationships within Ictaluridae supported by morphology. We develop a new Bayesian method for examining variation in molecular rates of evolution across a phylogeny.     

The validation of a bioanalytical method for the determination of clopidogrel in human plasma

A fast, sensitive and specific LC-MS/MS bioanalytical method for the determination of unchanged clopidogrel in human plasma has been developed and validated over the range of 10-12,000 pg mL(-1) (r2 0.9993) by the Contract Research group at HFL. Samples (0.3 mL) were buffered (pH 6.8), extracted using diethyl ether and 10 microL of the sample extract was injected onto the LC-MS/MS system. Analysis was performed using a C8 column (temperature controlled to 50 degrees C) by gradient elution at a flow rate of 0.9 mL min(-1) over a 3 min run time. Retention times of 1.61 and 1.59 min were observed for clopidogrel and 2H3-clopidogrel (I.S.), respectively. Detection was achieved using a Sciex API 4000, triple quadrupole mass spectrometer, in positive TurboIonspray (electrospray) ionisation mode. Ion transitions were monitored using MRM (multiple reaction monitoring) for clopidogrel (m/z 322-212) and for 2H3-clopidogrel (m/z 327-217). This validated method was used to support a pharmacokinetic study in healthy volunteers.