18S rRNA alignments derived from different secondary structure models can produce alternative phylogenies

A molecular method for a qualitative analysis of potentially coding sequences of DNA

Total sequence phylogenies have low information content. Ordinary misconceptions are that character quality can be ignored and that relying on computer algorithms is enough. Despite widespread preference for a posteriori methods of character evaluation, a priori methods are necessary to produce transformation series that are independent of tree topologies. We propose a stepwise qualitative method for analyzing protein sequences. Informative codons are selected, alternative amino acid transformation series are analyzed, and most parsimonious transformations are hypothesized. We conduct four phylogenetic analyses of philodryanine snakes. The tree based on all nucleotides produces least resolution. Trees based on the exclusion of third positions, on an asymmetric step matrix, and on our protocol, produce similar results. Our method eliminates noise by hypothesizing explicit transformation series for each informative protein-coding amino acid. This approaches qualitative methods for morphological data, in which only characters successfully interpreted in a phylogenetic context are used in cladistic analyses. The method allows utilizing character information contained in the original sequence alignment and, therefore, has higher resolution in inferring a phylogenetic tree than some traditional methods (such as distance methods).

18S rDNA phylogeny of the Tubificidae (Clitellata) and its constituent taxa: dismissal of the Naididae

The phylogeny of the Tubificidae, and of most of its subfamilies and some of its genera, is revisited, on the basis of sequences of 18S ribosomal DNA in a selection of species. Forty-six new 18S sequences of Naididae (6), Tubificidae (37), Phreodrilidae (1), Lumbriculidae (1), and Enchytraeidae (1) are reported and aligned together with corresponding sequences of 21 previously studied taxa. The 18S gene of Insulodrilus bifidus provides the first molecular evidence that phreodrilids are closely related to tubificids, corroborating previous conclusions based on morphology. The data further support the monophyletic status of Tubificidae, provided that the "Naididae" is regarded a part of this family; "naidids" may not even constitute a monophyletic group. It is thus suggested that the family name Naididae is formally suppressed as a junior synonym of the Tubificidae. The 18S gene also resolves a number of relationships within the tubificids. Among the subfamilies, Tubificinae is supported, Rhyacodrilinae and Phallodrilinae are revealed as nonmonophyletic, and Limnodriloidinae remains unresolved. Most tubificid genera tested for monophyly are corroborated by the data, only one (Tubifex) is refuted, and two (Tubificoides and Limnodriloides) are unresolved from other taxa. It is concluded that it will be valuable to expand the taxonomic sampling for 18S rDNA in clitellates, and in annelids in general, as this is likely to improve the resolution at many levels. However, it will be equally important to combine the annelid 18S data with other gene sequences and nonmolecular characters, to estimate the phylogeny of these common and diverse worms with greater precision.

Molecular evolution of the small subunit ribosomal DNA in woodlice (Crustacea, Isopoda, Oniscidea) and implications for Oniscidean phylogeny

The small subunit ribosomal DNA (ssu rDNA) of 13 isopods was sequenced. The entire length of the ribosomal gene is unusually long, resulting from the presence of five expansion elements accounting for more than 40% of the gene. We found that in terrestrial isopods the length of the ssu rDNA ranges from 2414 bp (Ligidium hypnorum) to 3537 bp (Cubaris murina). This is the longest metazoan ssu rDNA reported to date. The conserved regions are highly informative for analysis of the early nodes of the tree, whereas the variable expansion elements are better suited to reconstruction of the branching pattern between closely related taxa. The suggested relationship among Synochaeta, Crinochaeta, and Diplochaeta based on the conserved regions confirms that based on previous morphological analyses. In contrast, the phylogeny within the Crinochaeta based on the entire ssu rDNA including the variable domains is in conflict with that based on most of the morphological analyses. The phylogenetic analyses of the ssu rDNA support a repeated independent evolution of the three different types of pleopodal lungs in the Crinochaeta.

Rapidly evolving lineages impede the resolution of phylogenetic relationships among Clitellata (Annelida)

The phylogenetic relationships of the Clitellata were investigated using a data set with published and new complete or partial 18S rRNA and mtCOI gene sequences of 13 and 49 taxa representing 8 and 14 families, respectively. Three different alignments were considered for 18S, and the possible influence of departures from rate constancy among sites was evaluated by analyses using a Gamma model of rate heterogeneity. Maximum-likelihood estimates of the shape parameter alpha of the Gamma distribution were very low, whatever the alignment or the gene considered, suggesting that phylogenetic reconstructions taking into account the rate heterogeneity among sites are likely to be the most reliable. Analyzed separately, the two genes did not resolve the relationships among the Clitellata, but the consensus tree was congruent with the morphology-based relationships. Our data suggest the inclusion of the Euhirudinea, Acanthobdellida, and Branchiobdellida in the Oligochaeta and suggest the Lumbriculidae as the link between both assemblages. Although separate analyses of both genes, as well as different alignments for the 18S rRNA sequences, yielded conflicting results concerning the phylogenetic position of leeches and leech-like worms vis-à-vis the Oligochaeta, subsequent analyses using the Gamma model greatly reduced the observed inconsistencies. Our analyses show that among the Clitellata, the leeches and the leech-like and gutless worms represent significantly faster evolving lineages. It is suggested that the observed higher mutation rates may be explained by the fact that these lineages contain almost exclusively commensal and/or parasitic taxa.

Molecular evidence on the evolution of the Bivalvia

Despite widespread agreement on the monophyly of several major taxa of bivalves, others remain uncertain and the relationships among them are debated. The present study compares new and published morphological phylogenies with new analyses based on 18S gene sequences.

All but one family and all superfamilies in the Bivalvia were monophyletic in all the analyses. Several higher taxa, including most subclasses and orders, were also resolved as monophyletic. Only Myoida shows strong evidence for polyphyly, with at least two origins from Veneroida. Autobranchia was supported as monophyletic in the parsimony analyses. Within Pteriomorphia, Ostreoida is the sister taxon of Pterioida, if not derived from within it, rather than closest to Pectinoida. The numerous points of agreement with morphology based analyses suggests that both types of evidence are converging on a common phylogeny; however, differences remain to be resolved by further study.

The current state of insect molecular systematics: a thriving Tower of Babel

Insect molecular systematics has undergone remarkable recent growth. Advances in methods of data generation and analysis have led to the accumulation of large amounts of DNA sequence data from most major insect groups. In addition to reviewing theoretical and methodological advances, we have compiled information on the taxa and regions sequenced from all available phylogenetic studies of insects. It is evident that investigators have not usually coordinated their efforts. The genes and regions that have been sequenced differ substantially among studies and the whole of our efforts is thus little greater than the sum of its parts. The cytochrome oxidase I, 16S, 18S, and elongation factor-1 alpha genes have been widely used and are informative across a broad range of divergences in insects. We advocate their use as standards for insect phylogenetics. Insect molecular systematics has complemented and enhanced the value of morphological and ecological data, making substantial contributions to evolutionary biology in the process. A more coordinated approach focused on gathering homologous sequence data will greatly facilitate such efforts.

Molecular systematics of the Malagasy babblers (Passeriformes: timaliidae) and warblers (Passeriformes: sylviidae), based on cytochrome b and 16S rRNA sequences

The phylogenetic relationships of the Timaliidae (babblers) and Sylviidae (warblers) have long challenged ornithologists. We focus here on three Malagasy genera currently assigned to the Timaliidae, Mystacornis, Oxylabes, and Neomixis, and on their relationships with other babblers and warblers using the sequences of two mitochondrial genes (cytochrome b and 16S rRNA). Maximum parsimony analyses show that the Malagasy "babblers" are not related to any of the other African and Asian babblers. The genus Mystacornis is neither a babbler nor a warbler. The other Malagasy "babblers" are members of warbler groups (the monophyly of the Sylviidae is not demonstrated). Oxylabes madagascariensis and Hartertula flavoviridis (we recognize Hartertula as a genus for the species flavoviridis, previously Neomixis flavoviridis) constitute, with two presumed sylviine taxa, Thamnornis chloropetoides and Cryptosylvicola randrianasoloi, a warbler radiation endemic to the island of Madagascar. The other Neomixis species (tenella, striatigula, and viridis) belong to another warbler group comprising cisticoline taxa. These results show that the Timaliidae did not disperse to Madagascar. Rather, the island has been colonized, independently, by at least two clades of warblers, probably originating from Africa, where the Sylviidae radiation has been the most extensive.

Phylogeny of the arachnid order Opiliones (Arthropoda) inferred from a combined approach of complete 18S and partial 28S ribosomal DNA sequences and morphology

The phylogenetic relationships among the main evolutionary lines of the arachnid order Opiliones were investigated by means of molecular (complete 18S rDNA and the D3 region of the 28S rDNA genes) and morphological data sets. Equally and differentially weighted parsimony analyses of independent and combined data sets provide evidence for the monophyly of the Opiliones. In all the analyses, the internal relationships of the group coincide in the monophyly of the following main groups: Cyphophthalmi, Eupnoi Palpatores, Dyspnoi Palpatores, and Laniatores. The Cyphophthalmi are monophyletic and sister to a clade that includes all the remaining opilionid taxa (=Phalangida). Within the Phalangida the most supported hypothesis suggests that Palpatores are paraphyletic, as follows: (Eupnoi (Dyspnoi + Laniatores)), but the alternative hypothesis (Laniatores (Eupnoi + Dyspnoi)) is more parsimonious in some molecular data analyses. Relationships within the four main clades are also addressed. Evolution of some morphological characters is discussed, and plesiomorphic states of these characters are evaluated using molecular data outgroup polarization. Finally, Martens' hypothesis of opilionid evolution is assessed in relation to our results.

Molecular phylogeny of microsporidians with particular reference to species that infect the muscles of fish

Ribosomal DNA from eight species of microsporidians infecting fish have been sequenced. Seven of these species infect the skeletal muscle of fish (Pleistophora spp.) and one species infects migratory mesenchyma cells (Glugea anomala). These sequences, in addition to other available microsporidian rDNA sequences from a broad range of host taxa, have been used in phylogenetic analysis. This analysis revealed that muscle-infecting microsporidians from fish are a polyphyletic group, indicating that characters supposed to be important in the classification of the genus Pleistophora have to be re-evaluated. One character that probably has a polyphyletic origin is the amorphous coat, which has been extensively used in the definition of this genus. Furthermore, our results showed that the insect parasitizing Pleistophora spp. are not related to the true pleistophorans parasitic in skeletal muscle of fish. Phylogenetic analysis of small subunit rDNA sequences revealed disagreements between the molecular phylogeny and classifications based upon ultrastructure. Many of the morphological characters claimed to be important in microsporidian classifications appeared to have arisen several times during evolution: for example, the diplokaryon and sporophorous vesicles.

Parsimony analysis as a specific kind of homology estimation and the implications for character weighting

"Remane-Hennigian systematists" still reject parsimony analysis for phylogenetics, because homology or apomorphy analyses are not included. In contrast, "pattern cladists" regard homology as a deductive concept after applying a parsimony test of character congruence. However, as in molecular phylogeny, selection of "good" characters is always done on the basis of an a priori homology analysis. The distribution criterion of homology-"homologous characters have identical or hierarchical distribution"-is the basis of parsimony analysis. Because this criterion also might fail in cases of genealogical reticulation or concerted homoplasy, character congruence is not a strict test but another probabilistic criterion of homology. A synthetic approach is proposed for phenotypic analysis with application of a priori criteria of homology. The resulting a priori probabilities of homology serve as criteria for selection and weighting of characters (very low = not selected/poor/mediocre/good/Dollo characters). After application of a parsimony algorithm the final cladogram decides homology estimations.

A priori estimation of phylogenetic information conserved in aligned sequences

A new phenomenological approach to explorative data analysis, the estimation of spectra of supporting positions, allows the search for conserved tracks left by phylogeny in DNA sequences. Spectra of supporting positions can be generated without reference to a tree topology or a model of sequence evolution and are therefore an ideal tool for a priori estimation of information content of data sets. Analysis of published 18S rDNA alignments shows that signal to noise relationship varies greatly in a way not detected by conventional tree-construction methods.