Kelly et al.
Abstract.Phylogenetic relationships of advanced snakes (Acrochordus + Colubroidea = Caenophidia), and the position of the genus Acrochordus relative to colubroid taxa, are contentious. These concerns were investigated by phylogenetic analysis of fragments from four mitochondrial genes representing sixty-two caenophidian genera and five non-caenophidian taxa. Four methods of phylogeny reconstruction were applied: Matrix Representation with Parsimony (MRP) supertree consensus, maximum parsimony, maximum likelihood and Bayesian analysis. Due to incomplete sampling, extensive missing data were inherent in this study. Analyses of individual genes retrieved roughly the same clades, but branching order varied greatly between gene trees, and nodal support was poor. Trees generated from combined datasets using maximum parsimony, maximum likelihood, and Bayesian analysis had medium to low nodal support, but were largely congruent with each other and with MRP supertrees. Conclusions about caenophidian relationships were based on these combined analyses. The Xenoderminae, Viperidae, Pareatinae, Psammophiinae, Pseudoxyrophiinae, Homalopsinae, Natricinae, Xenodontinae, and Colubrinae (redefined) emerged monophyletic, whilst Lamprophiinae, Atractaspididae, and Elapidae were non-monophyletic in one or more topologies. A clade comprising Acrochordus and Xenoderminae branched closest to the root, and when Acrochordus was assessed in relation to a colubroid subsample and all five non-caenophidians, it remained associated with the Colubroidea. Thus Acrochordus + Xenoderminae appear to be sister to the Colubroidea, and Xenoderminae should be excluded from Colubroidea. Within Colubroidea, Viperidae was the most basal clade. Other relationships appearing in all final topologies were: 1) a clade comprising Psammophiinae, Lamprophiinae, Atractaspididae, Pseudoxyrophiinae, and Elapidae, within which the latter four taxa formed a subclade; 2) a clade comprising Colubrinae, Natricinae, and Xenodontinae, within which the latter two taxa formed a subclade. Pareatinae and Homalopsinae were the most unstable clades.
Abstract.An intraspecific phylogeny was established for the New Zealand short-tailed bat Mystacina tuberculata using a 2878 bp sequence alignment from multiple mitochondrial genes (control region, ND2, 12S rRNA, 16S rRNA, and tRNA). The inferred phylogeny comprises six lineages with estimated divergences extending back between 0.93 and 0.68 My to the middle Pleistocene. The lineages do not correspond to the existing subspecific taxonomy. Although multiple lineages occur sympatrically in many populations, the lineages are geographically structured. This structure has persisted despite repeated cycles of range expansion and contraction in response to climatic oscillations and catastrophic volcanic eruptions. The distribution of lineages among populations in central North Island indicates a hybrid zone was formed by simultaneous colonization from single-lineage source populations inhabiting remote forest refugia. The observed pattern is not typical of microbats, which because of their high mobility generally exhibit low levels of genetic differentiation and geographic structure over continental ranges. Although lineages of M. tuberculata occur sympatrically in many populations, genetic distances between them are sufficiently large to suggest that they may be considered as evolutionary significant units or taxonomic subspecies.
Cummings et al.
Abstract.Assessment of the reliability of a given phylogenetic hypothesis is an important step in phylogenetic analysis. Historically, the application of a non-parametric bootstrap procedure has been the most frequently used method for assessing the support for specific phylogenetic relationships. The recent employment of Bayesian methods for phylogenetic inference problems has resulted in clade support being expressed in terms of posterior probabilities. Here, we used simulated data and the four-taxon case to explore the relationship between non-parametric bootstrap values (as inferred by maximum likelihood) and posterior probabilities (as inferred by Bayesian analysis). The results suggest a complex association between the two measures. Three general regions of tree space can be identified. These are: (A) the neutral zone, where differences between mean bootstrap and mean posterior probability values are not statistically significant, (B) near the two-branch corner, and (C) deep in the two-branch corner. In the last two regions, statistically significant differences are observed between mean bootstrap and mean posterior probability values. Whether bootstrap or posterior probability values are higher depends on the data in support of alternative topologies. Examination of star-topologies showed that both bootstrap and posterior probability values differ significantly from theoretical expectations, and in particular there are more posterior probability values in the range 0.85 -- 1 than expected by theory. Therefore our results corroborate the finding by others that posterior probability values are excessively high. Our results also suggest that extrapolations from single topology-branch length studies are unlikely to provide any general conclusions regarding the relationship between bootstrap and posterior probability values.
Guill et al.
Abstract.We conducted a geometric morphometric analysis of interspecific body shape variation among representatives of 31 species of darters (Pisces: Percidae) to determine whether there is evidence of a phylogenetic effect in body shape variation. Cartesian transformation grids representing relative shape differences of individual species and subspecies revealed qualita-tive similarities within most traditionally recognized taxonomic groups (genera and subgenera). Canonical variates analysis and a UPGMA cluster analysis were conducted to explore further the relationships among body shapes of species; both analyses revealed patterns of variation consistent with the interpretation that shape is associated with taxonomic affinities. Normalized Mantel statistics revealed a significant positive association between body shape differences and phylogenetic interrelatedness for each of four recent phylogenetic hypotheses, providing evidence of a phylogenetic effect. This result is somewhat surprising, however, given the largely incompatible nature of these four phylogenies. We provide evidence that this result may be due to (1) the inclusion of multiple sets of closely related species to represent the traditionally recognized genera and subgenera within each phylogeny and/or (2) the inclusion of several species with relatively divergent shapes and their particular positions within the phylogenies relative to one another or to the other species of darters.
Wiens et al.
Abstract.Convergence, 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 paper, 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 mtDNA 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 (like 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.
Abstract.Haeckel created much of our current vocabulary in evolutionary biology, such as the term 'phylogeny' that is currently used to designate trees. Assuming that Haeckel gave the same meaning to this term, one often reproduces Haeckel's trees as the first illustrations of phylogenetic trees. Based on a detailed analysis of Haeckel's own evolutionary vocabulary and theory, I shall demonstrate that Haeckel's trees were genealogical trees and that Haeckel's phylogeny was a morphological concept. However, phylogeny was actually the core of Haeckel's tree reconstruction, and understanding the exact meaning Haeckel gave to phylogeny is crucial to understanding the information Haeckel wanted to convey in his famous trees. Haeckel's phylogeny was a linear series of main morphological stages along the lines of descent of a given species. The phylogeny of a single species would provide a trunk around which lateral branches were added as mere ornament; the phylogeny selected for drawing a tree of a given group was considered the most complete line of progress from lower to higher forms of this group, such as the phylogeny of Man for the genealogical tree of Vertebrates. Haeckel's phylogeny was mainly inspired by the idea of Scala naturae, or scale of beings. Therefore, Haeckel's genealogical trees, which were only branched on the surface, mainly represented the old idea of scale of beings. Even though Haeckel decided to draw genealogical trees after reading The Origin of Species and was called the 'German Darwin,' he did not draw Darwinian branching diagrams. Although Haeckel always saw Lamarck, Goethe and Darwin as the three 'fathers' of the theory of evolution, he was mainly influenced by Lamarck and Goethe for his approach to tree reconstruction.
Abstract.The problem of missing data is often considered to be the most important obstacle in reconstructing the phylogeny of fossil taxa and in combining data from diverse characters and taxa for phylogenetic analysis. Empirical and theoretical studies show that including highly incomplete taxa can lead to multiple equally parsimonious trees, poorly resolved consensus trees, and decreased phylogenetic accuracy. However, the mechanisms that cause incomplete taxa to be problematic have remained unclear. It has been widely assumed that incomplete taxa are problematic because of the proportion or amount of missing data that they bear. In this study, I use simulations to show that the reduced accuracy associated with including incomplete taxa is caused by these taxa bearing too few complete characters rather than too many missing data cells. This seemingly subtle distinction has a number of important implications. First, the so-called missing data problem for incomplete taxa is, paradoxically, not directly related to their amount or proportion of missing data. Thus, the level of completeness alone should not guide the exclusion of taxa (contrary to common practice), and these results may explain why empirical studies have sometimes found little relationship between the completeness of a taxon and its impact on an analysis. Furthermore, these results (a) suggest a more effective strategy for dealing with incomplete taxa, (b) call into question a justification of the controversial phylogenetic supertree approach, and (c) show the potential for the accurate phylogenetic placement of highly incomplete taxa, both when combining diverse data sets and when analyzing relationships of fossil taxa.