Phylogeny of the Rosidae: A dense taxon sampling analysis

Rosidae, a clade of approximately 90 000 species of angiosperms, exhibits remarkable morphological diversity and extraordinary heterogeneity in habitats and life forms. Resolving phylogenetic relationships within Rosidae has been difficult, in large part due to nested radiations and the enormous size of the clade. Current estimates of phylogeny contain areas of poor resolution and/or support, and there have been few attempts to synthesize the available data into a comprehensive view of Rosidae phylogeny. We aim to improve understanding of the phylogeny of Rosidae with a dense sampling scheme using both newly generated sequences and data from GenBank of the chloroplast rbcL, atpB, and matK genes and the mitochondrial matR gene. We combined sequences from 9300 species, representing 2775 genera, 138 families, and 17 orders into a supermatrix. Although 59.26% of the cells in the supermatrix have no data, our results generally agree with previous estimates of Rosidae phylogeny and provide greater resolution and support in several areas of the topology. Several noteworthy phylogenetic relationships are recovered, including some novel relationships. Two families (Euphorbiaceae and Salvadoraceae) and 467 genera are recovered as non-monophyletic in our sampling, suggesting the need for future systematic studies of these groups. Our study shows the value of a botanically informed bioinformatics approach and dense taxonomic sampling for resolving rosid relationships. The resulting tree provides a starting point for large-scale analyses of the evolutionary patterns within Rosidae.     

Aligned 18S and insect phylogeny

The nuclear small subunit rRNA (18S) has played a dominant role in the estimation of relationships among insect orders from molecular data. In previous studies, 18S sequences have been aligned by unadjusted automated approaches (computer alignments that are not manually readjusted), most recently with direct optimization (simultaneous alignment and tree building using a program called "POY"). Parsimony has been the principal optimality criterion. Given the problems associated with the alignment of rRNA, and the recent availability of the doublet model for the analysis of covarying sites using Bayesian MCMC analysis, a different approach is called for in the analysis of these data. In this paper, nucleotide sequence data from the 18S small subunit rRNA gene of insects are aligned manually with reference to secondary structure, and analyzed under Bayesian phylogenetic methods with both GTR+I+G and doublet models in MrBayes. A credible phylogeny of Insecta is recovered that is independent of the morphological data and (unlike many other analyses of 18S in insects) not contradictory to traditional ideas of insect ordinal relationships based on morphology. Hexapoda, including Collembola, are monophyletic. Paraneoptera are the sister taxon to a monophyletic Holometabola but weakly supported. Ephemeroptera are supported as the sister taxon of Neoptera, and this result is interpreted with respect to the evolution of direct sperm transfer and the evolution of flight. Many other relationships are well-supported but several taxa remain problematic, e.g., there is virtually no support for relationships among orthopteroid orders. A website is made available that provides aligned 18S data in formats that include structural symbols and Nexus formats.     

Insufficient resolving power of mitogenome data in deciphering deep phylogeny of Holometabola

The mitochondrial genome (mitogenome) is one of the most widely used markers for phylogenetic analysis. Compared with whole-genome data, mitogenome data are less expensive to obtain and easier to manipulate. However, compositional bias and accelerated evolutionary rate reduce the effectiveness of the mitogenome in determining insect phylogeny. This study shows that mitogenome data are not suitable to reconstruct deep holometabolan evolution, even with a most comprehensive data coding scheme and the more realistic CAT model. For the deep levels of divergence within Holometabola, protein-coding genes only retain weak phylogenetic signals, leading to peculiar interordinal relationships. Consensus relationships in the Holometabola phylogeny, such as the monophyly of Holometabola, the most basal position of Hymenoptera, and the sister group relationship between the Strepsiptera and Coleoptera were rarely resolved in our analyses. The relationships of the holometabolan groups as inferred by mitogenomes are highly vulnerable to gene types, data coding regimes, model choice, and optimality criteria, and no consistent alternative hypothesis of Holometabola's relationships is supported. Thus, we suggest that the slowly evolving nuclear genes or genome-scale approaches may be better options for resolving deep-level phylogeny of Holometabola.     

Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes)

Sharks are a diverse and ecologically important group, including some of the ocean's largest predatory animals. Sharks are also commercially important, with many species suffering overexploitation and facing extinction. However, despite a long evolutionary history, commercial, and conservation importance, phylogenetic relationships within the sharks are poorly understood. To date, most studies have either focused on smaller clades within sharks, or sampled taxa sparsely across the group. A more detailed species-level phylogeny will offer further insights into shark taxonomy, provide a tool for comparative analyses, as well as facilitating phylogenetic estimates of conservation priorities. We used four mitochondrial and one nuclear gene to investigate the phylogenetic relationships of 229 species (all eight Orders and 31 families) of sharks, more than quadrupling the number of taxon sampled in any prior study. The resulting Bayesian phylogenetic hypothesis agrees with prior studies on the major relationships of the sharks phylogeny; however, on those relationships that have proven more controversial, it differs in several aspects from the most recent molecular studies. The phylogeny supports the division of sharks into two major groups, the Galeomorphii and Squalimorphii, rejecting the hypnosqualean hypothesis that places batoids within sharks. Within the squalimorphs the orders Hexanchiformes, Squatiniformes, Squaliformes, and Pristiophoriformes are broadly monophyletic, with minor exceptions apparently due to missing data. Similarly, within Galeomorphs, the orders Heterodontiformes, Lamniformes, Carcharhiniformes, and Orectolobiformes are broadly monophyletic, with a couple of species 'misplaced'. In contrast, many of the currently recognized shark families are not monophyletic according to our results. Our phylogeny offers some of the first clarification of the relationships among families of the order Squaliformes, a group that has thus far received relatively little phylogenetic attention. Our results suggest that the genus Echinorhinus is not a squaliform, but rather related to the saw sharks, a hypothesis that might be supported by both groups sharing 'spiny' snouts. In sum, our results offer the most detailed species-level phylogeny of sharks to date and a tool for comparative analyses.     

The Evolution of Hexamerins and the Phylogeny of Insects

The evolutionary relationships among arthropod hemocyanins and insect hexamerins were investigated. A multiple sequence alignment of 12 hemocyanin and 31 hexamerin subunits was constructed and used for studying sequence conservation and protein phylogeny. Although hexamerins and hemocyanins belong to a highly divergent protein superfamily and only 18 amino acid positions are identical in all the sequences, the core structures of the three protein domains are well conserved. Under the assumption of maximum parsimony, a phylogenetic tree was obtained that matches perfectly the assumed phylogeny of the insect orders. An interesting common clade of the hymenopteran and coleopteran hexamerins was observed. In most insect orders, several paralogous hexamerin subclasses were identified that diversified after the splitting of the major insect orders. The dipteran arylphorin/LSP-1-like hexamerins were subject to closer examination, demonstrating hexamerin gene amplification and gene loss in the brachyceran Diptera. The hexamerin receptors, which belong to the hexamerin/hemocyanin superfamily, diverged early in insect evolution, before the radiation of the winged insects. After the elimination of some rapidly or slowly evolving sequences, a linearized phylogenetic tree of the hexamerins was constructed under the assumption of a molecular clock. The inferred time scale of hexamerin evolution, which dates back to the Carboniferous, agrees with the available paleontological data and reveals some previously unknown divergence times among and within the insect orders. Received: 4 August 1997 / Accepted: 29 October 1997     

Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies

Background  

Taxon sampling is a major concern in phylogenetic studies. Incomplete, biased, or improper taxon sampling can lead to misleading results in reconstructing evolutionary relationships. Several theoretical methods are available to optimize taxon choice in phylogenetic analyses. However, most involve some knowledge about the genetic relationships of the group of interest (i.e., the ingroup), or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications.     

A mitochondrial genome phylogeny of the Neuropterida (lace-wings, alderflies and snakeflies) and their relationship to the other holometabolous insect orders

We present a mitochondrial (mt) genome phylogeny inferring relationships within Neuropterida (lacewings, alderflies and camel flies) and between Neuropterida and other holometabolous insect orders. Whole mt genomes were sequenced for Sialis hamata (Megaloptera: Sialidae), Ditaxis latistyla (Neuroptera: Mantispidae), Mongoloraphidia harmandi (Raphidioptera: Raphidiidae), Macrogyrus oblongus (Coleoptera: Gyrinidae), Rhopaea magnicornis (Coleoptera: Scarabaeidae), and Mordella atrata (Coleoptera: Mordellidae) and compared against representatives of other holometabolous orders in phylogenetic analyses. Additionally, we test the sensitivity of phylogenetic inferences to four analytical approaches: inclusion vs. exclusion of RNA genes, manual vs. algorithmic alignments, arbitrary vs. algorithmic approaches to excluding variable gene regions and how each approach interacts with phylogenetic inference methods (parsimony vs. Bayesian inference). Of these factors, phylogenetic inference method had the most influence on interordinal relationships. Bayesian analyses inferred topologies largely congruent with morphologically‐based hypotheses of neuropterid relationships, a monophyletic Neuropterida whose sister group is Coleoptera. In contrast, parsimony analyses failed to support a monophyletic Neuropterida as Raphidioptera was the sister group of the entire Holometabola excluding Hymenoptera, and Neuroptera + Megaloptera is the sister group of Diptera, a relationship which has not previously been proposed based on either molecular or morphological data sets. These differences between analytical methods are due to the high among site rate heterogeneity found in insect mt genomes which is properly modelled by Bayesian methods but results in artifactual relationships under parsimony. Properly analysed, the mt genomic data set presented here is among the first molecular data to support traditional, morphology‐based interpretations of relationships between the three neuropterid orders and their grouping with Coleoptera.     

Towards an 18S phylogeny of hexapods: accounting for group-specific character covariance in optimized mixed nucleotide/doublet models

The phylogenetic diversification of Hexapoda is still not fully understood. Morphological and molecular analyses have resulted in partly contradicting hypotheses. In molecular analyses, 18S sequences are the most frequently employed, but it appears that 18S sequences do not contain enough phylogenetic signals to resolve basal relationships of hexapod lineages. Until recently, character interdependence in these data has never been treated seriously, though possibly accounting for the occurrence of biased results. However, software packages are readily available which can incorporate information on character interdependence within a Bayesian approach. Accounting for character covariation derived from a hexapod consensus secondary structure model and applying mixed DNA/RNA substitution models, our Bayesian analysis of 321 hexapod sequences yielded a partly robust tree that depicts many hexapod relationships congruent with morphological considerations. It appears that the application of mixed DNA/RNA models removes many of the anomalies seen in previous studies. We focus on basal hexapod relationships for which unambiguous results are missing. In particular, the strong support for a “Chiastomyaria” clade (Ephemeroptera+Neoptera) obtained in Kjer's [2004. Aligned 18S and insect phylogeny. Syst. Biol. 53, 1–9] study of 18S sequences could not be confirmed by our analysis. The hexapod tree can be rooted with monophyletic Entognatha but not with a clade Ellipura (Collembola+Protura). Compared to previously published contributions, accounting for character interdependence in analyses of rRNA data presents an improvement of phylogenetic resolution. We suggest that an integration of explicit clade-specific rRNA structural refinements is not only possible but an important step in the optimization of substitution models dealing with rRNA data.     

Phylogeny of the holometabolous insect orders: molecular evidence

Phylogenetic relationships among the holometabolous insect orders were reconstructed using 18S ribosomal DNA data drawn from a sample of 182 taxa representing all holometabolous insect orders and multiple outgroups. Parsimony analysis supports the monophyly of all holometabolous insect orders except for Coleoptera and Mecoptera. Mecoptera is paraphyletic with respect to Siphonaptera, which is nested within Mecoptera. Coleoptera is scattered as a paraphyletic assemblage across the tree topology. These data support a monophyletic Halteria (Strepsiptera + Diptera), Amphiesmenoptera (Trichoptera + Lepidoptera), Neuropterida (Neuroptera + (Megaloptera + Raphidioptera)), but Antliophora (Halteria + Mecoptera + Siphonaptera) and Mecopterida (Antliophora + Amphiesmenoptera) are paraphyletic. The limitations of using 18S ribosomal DNA as the sole phylogenetic marker for reconstructing insect ordinal relationships are discussed.     

Phylogeny of Oedogoniales, Chaetophorales and Chaetopeltidales (Chlorophyceae): inferences from sequence-structure analysis of ITS2

Background and Aims

The green algal class Chlorophyceae comprises five orders (Chlamydomonadales, Sphaeropleales, Chaetophorales, Chaetopeltidales and Oedogoniales). Attempts to resolve the relationships among these groups have met with limited success. Studies of single genes (18S rRNA, 26S rRNA, rbcL or atpB) have largely failed to unambiguously resolve the relative positions of Oedogoniales, Chaetophorales and Chaetopeltidales (the OCC taxa). In contrast, recent genomics analyses of plastid data from OCC exemplars provided a robust phylogenetic analysis that supports a monophyletic OCC alliance.

Methods

An ITS2 data set was assembled to independently test the OCC hypothesis and to evaluate the performance of these data in assessing green algal phylogeny at the ordinal or class level. Sequence-structure analysis designed for use with ITS2 data was employed for phylogenetic reconstruction.

Key Results

Results of this study yielded trees that were, in general, topologically congruent with the results from the genomic analyses, including support for the monophyly of the OCC alliance.

Conclusions

Not all nodes from the ITS2 analyses exhibited robust support, but our investigation demonstrates that sequence-structure analyses of ITS2 provide a taxon-rich means of testing phylogenetic hypotheses at high taxonomic levels. Thus, the ITS2 data, in the context of sequence-structure analysis, provide an economical supplement or alternative to the single-marker approaches used in green algal phylogeny.     

New nuclear evidence for the oldest divergence among neognath birds: the phylogenetic utility of ZENK (i)

To date, there is little consensus concerning the phylogenetic relationships among neognath orders, which include all extant birds except ratites and tinamous. Different data sets, both molecular and morphologic, have yielded radically different and often unresolved ordinal topologies, especially within the neoaves clade. This lack of resolution and ongoing conflict indicates a need for additional phylogenetic characters to be applied to the question of higher-level avian phylogeny. In this study, sequences of a single-copy nuclear gene, ZENK, were used to reconstruct an ordinal-level phylogeny of neognath birds. Strong support was indicated for the oldest divergence within Neognathae; the chicken- and duck-like birds formed a clade that was sister to all other modern birds. In addition, many families of traditional taxonomic orders clustered together in the ZENK tree, indicating the gene's general phylogenetic reliability. However, within the neoaves clade, there was little support for relationships among orders, which is a result similar to all other recent molecular studies of higher-level avian phylogeny. This similarity among studies suggests the possibility of a rapid radiation of the major neoaves lineages. Despite the ongoing lack of neoaves resolution, ZENK's sequence divergence and base composition patterns indicate its general utility as a new phylogenetic marker for higher-level avian systematics.     

Novel Relationships Among Ten Fish Model Species Revealed Based on a Phylogenomic Analysis Using ESTs

The power of comparative phylogenomic analyses also depends on the amount of data that are included in such studies. We used expressed sequence tags (ESTs) from fish model species as a proof of principle approach in order to test the reliability of using ESTs for phylogenetic inference. As expected, the robustness increases with the amount of sequences. Although some progress has been made in the elucidation of the phylogeny of teleosts, relationships among the main lineages of the derived fish (Euteleostei) remain poorly defined and are still debated. We performed a phylogenomic analysis of a set of 42 of orthologous genes from 10 available fish model systems from seven different orders (Salmoniformes, Siluriformes, Cypriniformes, Tetraodontiformes, Cyprinodontiformes, Beloniformes, and Perciformes) of euteleostean fish to estimate divergence times and evolutionary relationships among those lineages. All 10 fish species serve as models for developmental, aquaculture, genomic, and comparative genetic studies. The phylogenetic signal and the strength of the contribution of each of the 42 orthologous genes were estimated with randomly chosen data subsets. Our study revealed a molecular phylogeny of higher-level relationships of derived teleosts, which indicates that the use of multiple genes produces robust phylogenies, a finding that is expected to apply to other phylogenetic issues among distantly related taxa. Our phylogenomic analyses confirm that the euteleostean superorders Ostariophysi and Acanthopterygii are monophyletic and the Protacanthopterygii and Ostariophysi are sister clades. In addition, and contrary to the traditional phylogenetic hypothesis, our analyses determine that killifish (Cyprinodontiformes), medaka (Beloniformes), and cichlids (Perciformes) appear to be more closely related to each other than either of them is to pufferfish (Tetraodontiformes). All 10 lineages split before or during the fragmentation of the supercontinent Pangea in the Jurassic. [Reviewing Editor: Dr. Rafael Zardoya]     

Phylogenetic utility of the major opsin in bees (Hymenoptera: Apoidea): a reassessment

Major opsin (LW Rh) DNA sequence has been reported to provide useful data for resolving phylogenetic relationships among tribes of corbiculate bees based on analyses of 502 bp of coding sequence. However, the corbiculate tribes are believed to be of Cretaceous age, and strong support for insect clades of this age from small data sets of nucleotide sequence data has rarely been demonstrated. To more critically assess opsin's phylogenetic utility we generated an expanded LW Rh data set by sequencing the same gene fragment from 52 additional bee species from 24 tribes and all six extant bee families. Analyses of this data set failed to provide substantial support for monophyly of corbiculate bees, for relationships among corbiculate tribes, or for most other well-established higher-level relationships among long-tongued bees. However, monophyly of nearly all genera and tribes is strongly supported, indicating that LW Rh provides useful phylogenetic signal at lower taxonomic levels. When our expanded LW Rh data set is combined with a morphological and behavioral data set for corbiculate bees, the results unambiguously support the traditional phylogeny of the corbiculate bee tribes: (Euglossini + (Bombini + (Meliponini + Apini))). This implies a single origin of advanced eusocial behavior among bees rather than dual origins, as proposed by several recent studies.     

Phylogeny of the cricket subfamily Eneopterinae (Orthoptera, Grylloidea, Eneopteridae) based on four molecular loci and morphology

The phylogenetic relationships of 39 species of Eneopterinae crickets are reconstructed using four molecular markers (16S rRNA, 12S rRNA, cytochrome b, 18S rRNA) and a large morphological data set. Phylogenetic analysis via direct optimisation of DNA sequence data using parsimony as optimality criterion is done for six combinations of weighting parameter sets in a sensitivity analysis. The results are discussed in a twofold purpose: first, in term of significance of the molecular markers for phylogeny reconstruction in Ensifera, as our study represents the first molecular phylogeny performed for this insect suborder at this level of diversity; second, in term of corroboration of a previous phylogeny of Eneopterinae, built on morphological data alone. The four molecular markers all convey phylogenetic signal, although variously distributed on the tree. The monophyly of the subfamily, that of three over five tribes, and of 10 over 13 genera, are recovered. Finally, previous hypotheses on the evolution of acoustic devices and signals in the Eneopterinae clade are briefly tested, and supported, by our new data set.     

Mitochondrial DNA,morphology, and the phylogenetic relationships of Antarctic icefishes (Notothenioidei: Channichthyidae)

The Channichthyidae is a lineage of 16 species in the Notothenioidei, a clade of fishes that dominate Antarctic near-shore marine ecosystems with respect to both diversity and biomass. Among four published studies investigating channichthyid phylogeny, no two have produced the same tree topology, and no published study has investigated the degree of phylogenetic incongruence between existing molecular and morphological datasets. In this investigation we present an analysis of channichthyid phylogeny using complete gene sequences from two mitochondrial genes (ND2 and 16S) sampled from all recognized species in the clade. In addition, we have scored all 58 unique morphological characters used in three previous analyses of channichthyid phylogenetic relationships. Data partitions were analyzed separately to assess the amount of phylogenetic resolution provided by each dataset, and phylogenetic incongruence among data partitions was investigated using incongruence length difference (ILD) tests. We utilized a parsimony-based version of the Shimodaira-Hasegawa test to determine if alternative tree topologies are significantly different from trees resulting from maximum parsimony analysis of the combined partition dataset. Our results demonstrate that the greatest phylogenetic resolution is achieved when all molecular and morphological data partitions are combined into a single maximum parsimony analysis. Also, marginal to insignificant incongruence was detected among data partitions using the ILD. Maximum parsimony analysis of all data partitions combined results in a single tree, and is a unique hypothesis of phylogenetic relationships in the Channichthyidae. In particular, this hypothesis resolves the phylogenetic relationships of at least two species (Channichthys rhinoceratus and Chaenocephalus aceratus), for which there was no consensus among the previous phylogenetic hypotheses. The combined data partition dataset provides substantial statistical power to discriminate among alternative hypotheses of channichthyid relationships. These findings suggest the optimal strategy for investigating the phylogenetic relationships of channichthyids is one that uses all available phylogenetic data in analyses of combined data partitions.     

Phylogenetic analyses of marine sponges within the order Verongida: a comparison of morphological and molecular data

Abstract. Because the taxonomy of marine sponges is based primarily on morphological characters that can display a high degree of phenotypic plasticity, current classifications may not always reflect evolutionary relationships. To assess phylogenetic relationships among sponges in the order Verongida, we examined 11 verongid species, representing six genera and four families. We compared the utility of morphological and molecular data in verongid sponge systematics by comparing a phylogeny constructed from a morphological character matrix with a phylogeny based on nuclear ribosomal DNA sequences. The morphological phylogeny was not well resolved below the ordinal level, likely hindered by the paucity of characters available for analysis, and the potential plasticity of these characters. The molecular phylogeny was well resolved and robust from the ordinal to the species level. We also examined the morphology of spongin fibers to assess their reliability in verongid sponge taxonomy. Fiber diameter and pith content were highly variable within and among species. Despite this variability, spongin fiber comparisons were useful at lower taxonomic levels (i.e., among congeneric species); however, these characters are potentially homoplasic at higher taxonomic levels (i.e., between families). Our molecular data provide good support for the current classification of verongid sponges, but suggest a re-examination and potential reclassification of the genera Aiolochroia and Pseudoceratina . The placements of these genera highlight two current issues in morphology-based sponge taxonomy: intermediate character states and undetermined character polarity.     

Networks in a Large-Scale Phylogenetic Analysis: Reconstructing Evolutionary History of Asparagales (Lilianae) Based on Four Plastid Genes

Phylogenetic analysis aims to produce a bifurcating tree, which disregards conflicting signals and displays only those that are present in a large proportion of the data. However, any character (or tree) conflict in a dataset allows the exploration of support for various evolutionary hypotheses. Although data-display network approaches exist, biologists cannot easily and routinely use them to compute rooted phylogenetic networks on real datasets containing hundreds of taxa. Here, we constructed an original neighbour-net for a large dataset of Asparagales to highlight the aspects of the resulting network that will be important for interpreting phylogeny. The analyses were largely conducted with new data collected for the same loci as in previous studies, but from different species accessions and greater sampling in many cases than in published analyses. The network tree summarised the majority data pattern in the characters of plastid sequences before tree building, which largely confirmed the currently recognised phylogenetic relationships. Most conflicting signals are at the base of each group along the Asparagales backbone, which helps us to establish the expectancy and advance our understanding of some difficult taxa relationships and their phylogeny. The network method should play a greater role in phylogenetic analyses than it has in the past. To advance the understanding of evolutionary history of the largest order of monocots Asparagales, absolute diversification times were estimated for family-level clades using relaxed molecular clock analyses.     

A phylogenomic study of human, dog, and mouse

In recent years the phylogenetic relationship of mammalian orders has been addressed in a number of molecular studies. These analyses have frequently yielded inconsistent results with respect to some basal ordinal relationships. For example, the relative placement of primates, rodents, and carnivores has differed in various studies. Here, we attempt to resolve this phylogenetic problem by using data from completely sequenced nuclear genomes to base the analyses on the largest possible amount of data. To minimize the risk of reconstruction artifacts, the trees were reconstructed under different criteria-distance, parsimony, and likelihood. For the distance trees, distance metrics that measure independent phenomena (amino acid replacement, synonymous substitution, and gene reordering) were used, as it is highly improbable that all of the trees would be affected the same way by any reconstruction artifact. In contradiction to the currently favored classification, our results based on full-genome analysis of the phylogenetic relationship between human, dog, and mouse yielded overwhelming support for a primate-carnivore clade with the exclusion of rodents.