Sennblad and Bremer
Abstract.A new approach to a nomenclatural system, including elements from both Linnaean and phylogenetic nomenclature, is proposed. It is compatible with the existing Linnaean system, including "standard names" corresponding to principal and secondary ranks, and uses a variant of the definitions from the Phylocode system. A new infrafamilial classification, using this nomenclatural approach, of the Apocynaceae s.l. (i.e., including the Asclepiadaceae) based mainly on analyses of rbcL and ndhF data is discussed. Twenty-one tribes and four rankles taxa are defined.
Lundrigan et al.
Abstract.Several species in the rodent genus Mus are used as model research organisms, but comparative studies of these mice have been hampered by the lack of a well-supported phylogeny. We used DNA sequences from six genes representing paternally, maternally, and biparentally inherited regions of the genome to infer phylogenetic relationships among 10 species of Mus commonly used in laboratory research. Our sample included seven species from the subgenus Mus; one species each from the subgenera Pyromys, Coelomys, and Nannomys; and representatives from three additional murine genera, which served as outgroups in the phylogenetic analyses. Although each of the six genes yielded a unique phylogeny, several clades were supported by four or more gene trees. Nodes that conflicted between trees were generally characterized by weak support for one or both of the alternative topologies, thus providing no compelling evidence that any individual gene, or part of the genome, was misleading with respect to the evolutionary history of these mice. Analysis of the combined data resulted in a fully resolved tree that strongly supports monophyly of the genus Mus, monophyly of the subgenus Mus, division of the subgenus Mus into Palearctic (M. musculus, M. macedonicus, M. spicilegus, and M. spretus) and Asian (M. cervicolor, M. cookii, and M. caroli) clades, monophyly of the house mice (M. m. musculus, "M. m. molossinus," M. m. castaneus, and M. m. domesticus), and a sister-group relationship between M. macedonicus and M. spicilegus. Other clades that were strongly supported by one or more gene partitions were not strongly supported by the combined data. This appears to reflect a localized homoplasy in one partition obscuring the phylogenetic signal from another, rather than differences in gene or genome histories.
Waters et al.
Abstract.We used mitochondrial DNA sequences to determine the phylogenetic placement of southern smelts (Retropinnidae), a group of diadromous fishes endemic to New Zealand and Australia. Our genetic data strongly support a sister group relationship between retropinnids and northern hemisphere smelts (Osmeridae), a relationship that seems consistent with the similar appearance and life-history strategies of these two groups. Our analysis indicates that Retropinnidae and Osmeridae together represent the sister group to the southern hemisphere galaxiid fishes (Galaxiidae). However, this finding conflicts with several recent osteological analyses which supported a sister relationship for Retropinnidae and Galaxiidae, giving a monophyletic southern hemisphere assemblage (Galaxioidea). We review cases of incongruence and discuss factors that might explain significant disagreement between molecular and morphological data matrices. We suggest that repeated evolutionary simplification may have undermined the accuracy of morphological hypotheses of osmeroid relationships. Although equally weighted parsimony analysis of morphological data rejects the molecular hypothesis (Osmeridae + Retropinnidae), implementation of a range of weighting schemes suggests that incongruence is non-significant under asymmetric character transformation models. We propose that simple 'equal transformation cost' parsimony analysis may be biologically unrealistic, especially when reductive homoplasy is widespread. It is increasingly accepted that complex character states are more readily lost than gained. Therefore, we recommend that morphological systematists routinely implement a range of character transformation models to assess the sensitivity of their phylogenetic reconstructions. We discuss the antitropical biogeography of osmeroid fishes in the context of vicariance and trans-equatorial dispersal.
Belshaw and Quicke
Abstract.We test hypotheses for the evolution of a life history trait among a group of parasitoid wasps (Hymenoptera: Ichneumonoidea), namely the transition among koinobiont parasitoids (= parasitoids whose hosts continue development after oviposition) between attacking exposed hosts and attacking hosts that are concealed within plant tissue. Using a range of phylogeny estimates based on 28S rDNA sequences, we use maximum parsimony (MP) and maximum likelihood (ML) methods to estimate the ancestral life history traits for the main clades in which both traits occur (using the programs MacClade and Discrete respectively). We also assess the robustness of these estimates, for MP using step matrices in PAUP* to find the minimum weight necessary to reverse estimates or make them ambiguous, and for ML measuring the differences in likelihood after fixing the ancestral nodes at the alternate states. We also measure the robustness of the MP ancestral state estimate to uncertainties in the phylogeny estimate, manipulating the most parsimonious tree in MacClade in order to find the shortest sub-optimal tree in which the ancestral state estimate is reversed or made ambiguous. Using these methods we find strong evidence supporting two transitions among koinobiont Ichneumonoidea: (1) to attacking exposed hosts in a clade consisting of the Helconinae and related subfamilies, and (2) for the reverse transition in a clade consisting of the Euphorinae and related subfamilies. In exploring different methods of analysing variable length DNA sequences we found that direct optimisation using POY gave some clearly erroneous results that had a profound effect on the overall phylogeny estimate. We also discuss relationships within the superfamily, and expand the Mesostoinae to include all the gall-associated braconids that form the sister group of the Aphidiinae.
Jeffery et al.
Abstract.Heterochrony is important as a potential mechanism of evolutionary change. However, the analysis of developmental timing data within a phylogenetic framework to identify important shifts has proven difficult. In particular, analytical problems with sequence (event) heterochrony, revolve around the lack of an absolute time frame in development to allow standardization of timing data across species. An important breakthrough in this regard is the method of "event-pairing" which compares the relative timing of developmental events in a pairwise fashion. The resulting event-pair encoded data can be mapped onto a phylogeny, which can provide important biological information. However, event-paired data are cumbersome to work with and lack a rigorous quantitative framework under which to analyze them. Critically, the otherwise advantageous relativity of event-pairing prevents an assessment of whether one or both events in a single event-pair have changed position during evolutionary history. Building on the method of event-pairing, we describe a protocol whereby event-pair transformations along a given branch are analyzed en bloc. Our method of "event-pair cracking" thereby allows developmental timing data to be quantitatively analyzed within a phylogenetic framework to infer key heterochronic shifts. We demonstrate the utility of event-pair cracking through a worked example and show how it provides a set of desired features identified by previous authors.
Abstract.An approximately unbiased (AU) test that uses a newly devised multiscale bootstrap technique was developed for general hypothesis testing of regions in an attempt to reduce test bias, and it was applied to maximum-likelihood tree selection for obtaining the confidence set of trees. The AU test is based on the theory of Efron, Halloran, and Holmes (1996), but the new method provides higher-order accuracy yet simpler implementation. The AU test, as well as the Shimodaira-Hasegawa (SH) test, adjusts the selection bias overlooked in the standard use of the bootstrap probability (BP) and Kishino-Hasegawa (KH) tests. The selection bias comes from comparing many trees at the same time, and it often leads to overconfidence in the wrong trees. The SH test, though safe to use, may suffer from another type of bias such that it appears conservative. We show that the AU test is less biased than other methods in typical cases of tree selection. These points are illustrated in a simulation study as well as in the analysis of mammalian mitochondrial protein sequences. The theoretical argument provides a simple formula that covers the BP, the KH test, the AU test, and the Zharkikh-Li (ZL) test. A practical suggestion is provided as to which test should be used under particular circumstances.
Abstract.Probabilistic tests of topology offer a powerful means to evaluate competing phylogenetic hypotheses. The performance of the nonparametric Shimodaira-Hasegawa (SH) test, the parametric Swofford-Olsen-Waddell-Hillis (SOWH) test, and Bayesian posterior probabilities were explored for five data sets for which all the phylogenetic relationships are known with a very high degree of certainty. These results are consistent with previous simulation studies that have indicated a tendency for the SOWH test to be prone to generating Type I errors due to model misspecification coupled with branch length heterogeneity. These results also suggest that the SOWH test may accord overconfidence in the true topology when the null hypothesis is in fact correct. In contrast, the SH test was observed to be much more conservative, even under high substitution rates and branch length heterogeneity. For some of those data sets where the SOWH test proved misleading, it was also observed that Bayesian posterior probabilities were misleading. The results of all tests were strongly influenced by the exact substitution model assumptions. Simple models, especially those that assume rate homogeneity among sites, had a higher Type I error rate and were more likely to generate misleading posterior probabilities. For some of these data sets, the commonly used substitution models appear to be inadequate for estimating appropriate levels of uncertainty using the SOWH test and Bayesian methods. Reasons for the differences in statistical power between the two maximum likelihood tests are discussed, and are contrasted with the Bayesian approach.