Large-scale sequencing and the new animal phylogeny

Early evolution of enamel matrix proteins is reflected by pleiotropy of physiological functions

Highly specialized enamel matrix proteins (EMPs) are predominantly expressed in odontogenic tissues and diverged from common ancestral gene. They are crucial for the maturation of enamel and its extreme complexity in multiple independent lineages. However, divergence of EMPs occured already before the true enamel evolved and their conservancy in toothless species suggests that non-canonical functions are still under natural selection. To elucidate this hypothesis, we carried out an unbiased, comprehensive phenotyping and employed data from the International Mouse Phenotyping Consortium to show functional pleiotropy of amelogenin, ameloblastin, amelotin, and enamelin, genes, i.e. in sensory function, skeletal morphology, cardiovascular function, metabolism, immune system screen, behavior, reproduction, and respiratory function. Mice in all KO mutant lines, i.e. amelogenin KO, ameloblastin KO, amelotin KO, and enamelin KO, as well as mice from the lineage with monomeric form of ameloblastin were affected in multiple physiological systems. Evolutionary conserved motifs and functional pleiotropy support the hypothesis of role of EMPs as general physiological regulators. These findings illustrate how their non-canonical function can still effect the fitness of modern species by an example of influence of amelogenin and ameloblastin on the bone physiology.

Phylogenetic tree building in the genomic age

Knowing phylogenetic relationships among species is fundamental for many studies in biology. An accurate phylogenetic tree underpins our understanding of the major transitions in evolution, such as the emergence of new body plans or metabolism, and is key to inferring the origin of new genes, detecting molecular adaptation, understanding morphological character evolution and reconstructing demographic changes in recently diverged species. Although data are ever more plentiful and powerful analysis methods are available, there remain many challenges to reliable tree building. Here, we discuss the major steps of phylogenetic analysis, including identification of orthologous genes or proteins, multiple sequence alignment, and choice of substitution models and inference methodologies. Understanding the different sources of errors and the strategies to mitigate them is essential for assembling an accurate tree of life.

Inferring Ancient Relationships with Genomic Data: A Commentary on Current Practices

Contemporary phylogeneticists enjoy an embarrassment of riches, not only in the volumes of data now available, but also in the diversity of bioinformatic tools for handling these data. Here, I discuss a subset of these tools I consider well-suited to the task of inferring ancient relationships with coding sequence data in particular, encompassing data generation, orthology assignment, alignment and gene tree inference, supermatrix construction, and analysis under the best-fitting models applicable to large-scale datasets. Throughout, I compare and critique methods, considering both their theoretical principles and the details of their implementation, and offering practical tips on usage where appropriate. I also entertain different motivations for analyzing what are almost always originally DNA sequence data as codons, amino acids, and higher-order recodings. Although presented in a linear order, I see value in using the diversity of tools available to us to assess the sensitivity of clades of biological interest to different gene and taxon sets and analytical modes, which can be an indication of the presence of systematic error, of which a few forms remain poorly controlled by even the best available inference methods.

Phylogeny and reclassification of Aconitum subgenus Lycoctonum (Ranunculaceae)

Phylogenetic analyses were performed using multiple nuclear (ITS and ETS) and chloroplast regions (ndhF-trnL, psbA-trnH, psbD-trnT, and trnT-trnL) to test the monophyly of Aconitum subgen. Lycoctonum (Ranunculaceae) and reconstruct the phylogenetic relationships within the subgenus. The subgenus as currently circumscribed is revealed to be polyphyletic. To achieve its monophyly, sect. Galeata and sect. Fletcherum, both being unispecific and each having a unique array of characters (the latter even having the aberrant base chromosome number of x = 6), must be removed from the subgenus. The subgenus Lycoctonum should thus be redefined to include only two sections, the unispecific sect. Alatospermum and the relatively species-rich sect. Lycoctonum. The section Alatospermum, which is both morphologically and karyologically in the primitive condition, is resolved as the first diverging lineage of the subgenus Lycoctonum clade. The monophyly of sect. Lycoctonum is strongly supported, but all the ten series currently recognized within the section are revealed to be para- or poly-phyletic. Five major clades are recovered within the section. We propose to treat them as five series: ser. Crassiflora, ser. Scaposa, ser. Volubilia, ser. Longicassidata, and ser. Lycoctonia. Thus, a formal reclassification of subgen. Lycoctonum is presented, which involves segregating both sect. Galeata and sect. Fletcherum from the subgenus as two independent subgenera within the genus Aconitum, reinstating one series (ser. Crassiflora) and abolishing six series (ser. Laevia, ser. Longibracteolata, ser. Micrantha, ser. Ranunculoidea, ser. Reclinata, and ser. Umbrosa) within sect. Lycoctonum. The series affiliation of some species within the section is adjusted accordingly.

Phylogenomic Insights into Animal Evolution

Animals make up only a small fraction of the eukaryotic tree of life, yet, from our vantage point as members of the animal kingdom, the evolution of the bewildering diversity of animal forms is endlessly fascinating. In the century following the publication of Darwin's Origin of Species, hypotheses regarding the evolution of the major branches of the animal kingdom - their relationships to each other and the evolution of their body plans - was based on a consideration of the morphological and developmental characteristics of the different animal groups. This morphology-based approach had many successes but important aspects of the evolutionary tree remained disputed. In the past three decades, molecular data, most obviously primary sequences of DNA and proteins, have provided an estimate of animal phylogeny largely independent of the morphological evolution we would ultimately like to understand. The molecular tree that has evolved over the past three decades has drastically altered our view of animal phylogeny and many aspects of the tree are no longer contentious. The focus of molecular studies on relationships between animal groups means, however, that the discipline has become somewhat divorced from the underlying biology and from the morphological characteristics whose evolution we aim to understand. Here, we consider what we currently know of animal phylogeny; what aspects we are still uncertain about and what our improved understanding of animal phylogeny can tell us about the evolution of the great diversity of animal life.

Embracing the comparative approach: how robust phylogenies and broader developmental sampling impacts the understanding of nervous system evolution

Molecular biology has provided a rich dataset to develop hypotheses of nervous system evolution. The startling patterning similarities between distantly related animals during the development of their central nervous system (CNS) have resulted in the hypothesis that a CNS with a single centralized medullary cord and a partitioned brain is homologous across bilaterians. However, the ability to precisely reconstruct ancestral neural architectures from molecular genetic information requires that these gene networks specifically map with particular neural anatomies. A growing body of literature representing the development of a wider range of metazoan neural architectures demonstrates that patterning gene network complexity is maintained in animals with more modest levels of neural complexity. Furthermore, a robust phylogenetic framework that provides the basis for testing the congruence of these homology hypotheses has been lacking since the advent of the field of 'evo-devo'. Recent progress in molecular phylogenetics is refining the necessary framework to test previous homology statements that span large evolutionary distances. In this review, we describe recent advances in animal phylogeny and exemplify for two neural characters-the partitioned brain of arthropods and the ventral centralized nerve cords of annelids-a test for congruence using this framework. The sequential sister taxa at the base of Ecdysozoa and Spiralia comprise small, interstitial groups. This topology is not consistent with the hypothesis of homology of tripartitioned brain of arthropods and vertebrates as well as the ventral arthropod and rope-like ladder nervous system of annelids. There can be exquisite conservation of gene regulatory networks between distantly related groups with contrasting levels of nervous system centralization and complexity. Consequently, the utility of molecular characters to reconstruct ancestral neural organization in deep time is limited.

Molecular signatures that are distinctive characteristics of the vertebrates and chordates and supporting a grouping of vertebrates with the tunicates

Members of the phylum Chordata and the subphylum Vertebrata are presently distinguished solely on the basis of morphological characteristics. The relationship of the vertebrates to the two non-vertebrate chordate subphyla is also a subject of debate. Analyses of protein sequences have identified multiple conserved signature indels (CSIs) that are specific for Chordata or for Vertebrata. Five CSIs in 4 important proteins are specific for the Vertebrata, whereas two other CSIs are uniquely found in all sequenced chordate species including Ciona intestinalis and Oikapleura dioica (Tunicates) as well as Branchiostoma floridae (Cephalochordates). The shared presence of these molecular signatures by all vertebrates/chordate species, but in no other animal taxa, strongly indicates that the genetic changes represented by the identified CSIs diagnose monophyletic groups. Two other discovered CSIs are uniquely shared by different vertebrate species and by either one (Ciona intestinalis) or both tunicate (Ciona and Oikapleura) species, but they are not found in Branchiostoma or other animal species. Specific presence of these CSIs in different vertebrates and either one or both tunicate species provides strong independent evidence that the vertebrate species are more closely related to the urochordates (tunicates) than to the cephalochordates.

A higher level classification of all living organisms

We present a consensus classification of life to embrace the more than 1.6 million species already provided by more than 3,000 taxonomists' expert opinions in a unified and coherent, hierarchically ranked system known as the Catalogue of Life (CoL). The intent of this collaborative effort is to provide a hierarchical classification serving not only the needs of the CoL's database providers but also the diverse public-domain user community, most of whom are familiar with the Linnaean conceptual system of ordering taxon relationships. This classification is neither phylogenetic nor evolutionary but instead represents a consensus view that accommodates taxonomic choices and practical compromises among diverse expert opinions, public usages, and conflicting evidence about the boundaries between taxa and the ranks of major taxa, including kingdoms. Certain key issues, some not fully resolved, are addressed in particular. Beyond its immediate use as a management tool for the CoL and ITIS (Integrated Taxonomic Information System), it is immediately valuable as a reference for taxonomic and biodiversity research, as a tool for societal communication, and as a classificatory "backbone" for biodiversity databases, museum collections, libraries, and textbooks. Such a modern comprehensive hierarchy has not previously existed at this level of specificity.

BIR Pipeline for Preparation of Phylogenomic Data

SUMMARY

We present a pipeline named BIR (Blast, Identify and Realign) developed for phylogenomic analyses. BIR is intended for the identification of gene sequences applicable for phylogenomic inference. The pipeline allows users to apply their own manually curated sequence alignments (seed) in search for homologous genes in sequence databases and available genomes. BIR automatically adds the identified sequences from these databases to the seed alignments and reconstruct a phylogenetic tree from each. The BIR pipeline is an efficient tool for the identification of orthologous gene copies because it expands user-defined sequence alignments and conducts massive parallel phylogenetic reconstruction. The application is also particularly useful for large-scale sequencing projects that require management of a large number of single-gene alignments for gene comparison, functional annotation, and evolutionary analyses.

AVAILABILITY

The BIR user manual is available at http://www.bioportal.no/ and can be accessed through Lifeportal at https://lifeportal.uio.no. Access is free but requires a user account registration using the link "Register for BIR access" from the Lifeportal homepage.

Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae

Background

The green algae represent one of the most successful groups of photosynthetic eukaryotes, but compared to their land plant relatives, surprisingly little is known about their evolutionary history. This is in great part due to the difficulty of recognizing species diversity behind morphologically similar organisms. The Trebouxiophyceae is a species-rich class of the Chlorophyta that includes symbionts (e.g. lichenized algae) as well as free-living green algae. Members of this group display remarkable ecological variation, occurring in aquatic, terrestrial and aeroterrestrial environments. Because a reliable backbone phylogeny is essential to understand the evolutionary history of the Trebouxiophyceae, we sought to identify the relationships among the major trebouxiophycean lineages that have been previously recognized in nuclear-encoded 18S rRNA phylogenies. To this end, we used a chloroplast phylogenomic approach.

Results

We determined the sequences of 29 chlorophyte chloroplast genomes and assembled amino acid and nucleotide data sets derived from 79 chloroplast genes of 61 chlorophytes, including 35 trebouxiophyceans. The amino acid- and nucleotide-based phylogenies inferred using maximum likelihood and Bayesian methods and various models of sequence evolution revealed essentially the same relationships for the trebouxiophyceans. Two major groups were identified: a strongly supported clade of 29 taxa (core trebouxiophyceans) that is sister to the Chlorophyceae + Ulvophyceae and a clade comprising the Chlorellales and Pedinophyceae that represents a basal divergence relative to the former group. The core trebouxiophyceans form a grade of strongly supported clades that include a novel lineage represented by the desert crust alga Pleurastrosarcina brevispinosa. The assemblage composed of the Oocystis and Geminella clades is the deepest divergence of the core trebouxiophyceans. Like most of the chlorellaleans, early-diverging core trebouxiophyceans are predominantly planktonic species, whereas core trebouxiophyceans occupying more derived lineages are mostly terrestrial or aeroterrestrial algae.

Conclusions

Our phylogenomic study provides a solid foundation for addressing fundamental questions related to the biology and ecology of the Trebouxiophyceae. The inferred trees reveal that this class is not monophyletic; they offer new insights not only into the internal structure of the class but also into the lifestyle of its founding members and subsequent adaptations to changing environments.

New phylogenomic and comparative analyses provide corroborating evidence that Myxozoa is Cnidaria

Myxozoa, a diverse group of morphologically simplified endoparasites, are well known fish parasites causing substantial economic losses in aquaculture. Despite active research, the phylogenetic position of Myxozoa remains ambiguous. After obtaining the genome and transcriptome data of the myxozoan Thelohanellus kitauei, we examined the phylogenetic position of Myxozoa from three different perspectives. First, phylogenomic analyses with the newly sequenced genomic data strongly supported the monophyly of Myxozoa and that Myxozoa is sister to Medusozoa within Cnidaria. Second, we detected two homologs to cnidarian-specific minicollagens in the T. kitauei genome with molecular characteristics similar to cnidarian-specific minicollagens, suggesting that the minicollagen homologs in T. kitauei may have functions similar to those in Cnidaria and that Myxozoa is Cnidaria. Additionally, phylogenetic analyses revealed that the minicollagens in myxozoans and medusozoans have a common ancestor. Third, we detected 11 of the 19 proto-mesodermalgenes in the T. kitauei genome, which were also present in the cnidarian Hydra magnipapillata, indicating Myxozoa is within Cnidaria. Thus, our results robustly support Myxozoa as a derived cnidarian taxon with an affinity to Medusozoa, helping to understand the diversity of the morphology, development and life cycle of Cnidaria and its evolution.

The molecular symplesiomorphies shared by the stem groups of metazoan evolution: can sites as few as 1% have a significant impact on recognizing the phylogenetic position of myzostomida?

Although it is clear that taxon sampling, alignments, gene sampling, tree reconstruction methods and the total length of the sequences used are critical to the reconstruction of evolutionary history, weakly supported or misleading nodes exist in phylogenetic studies with no obvious flaw in those aspects. The phylogenetic studies focusing on the basal part of bilaterian evolution are such a case. During the past decade, Myzostomida has appeared in the basal part of Bilateria in several phylogenetic studies of Metazoa. However, most researchers have entertained only two competing hypotheses about the position of Myzostomida-an affinity with Annelida and an affinity with Platyhelminthes. In this study, dozens of symplesiomorphies were discovered by means of ancestral state reconstruction in the complete 18S and 28S rDNAs shared by the stem groups of Metazoa. By contrastive analysis on the datasets with or without such symplesiomorphic sites, we discovered that Myzostomida and other basal groups are basal lineages of Bilateria due to the corresponding symplesiomorphies shared with earlier lineages. As such, symplesiomorphies account for approximately 1-2% of the whole dataset have an essential impact on phylogenetic inference, and this study reminds molecular systematists of the importance of carrying out ancestral state reconstruction at each site in sequence-based phylogenetic studies. In addition, reasons should be explored for the low support of the hypothesis that Myzostomida belongs to Annelida in the results of phylogenomic studies. Future phylogenetic studies concerning Myzostomida should include all of the basal lineages of Bilateria to avoid directly neglecting the stand-alone basal position of Myzostomida as a potential hypothesis.

Phylogenetic position of Myriapoda revealed by 454 transcriptome sequencing

Myriapods had been considered closely allied to hexapods (insects and relatives). However, analyses of molecular sequence data have consistently placed Myriapoda either as a sister group of Pancrustacea, comprising crustaceans and hexapods, and thereby supporting the monophyly of Mandibulata, or retrieved Myriapoda as a sister group of Chelicerata (spiders, ticks, mites and allies). In addition, the relationships among the four myriapod groups (Pauropoda, Symphyla, Diplopoda, Chilopoda) are unclear. To resolve the phylogeny of myriapods and their relationship to other main arthropod groups, we collected transcriptome data from the symphylan Symphylella vulgaris, the centipedes Lithobius forficatus and Scolopendra dehaani, and the millipedes Polyxenus lagurus, Glomeris pustulata and Polydesmus angustus by 454 sequencing. We concatenated a multiple sequence alignment that contained 1550 orthologous single copy genes (1,109,847 amino acid positions) from 55 euarthropod and 14 outgroup taxa. The final selected alignment included 181 genes and 37,425 amino acid positions from 55 taxa, with eight myriapods and 33 other euarthropods. Bayesian analyses robustly recovered monophyletic Mandibulata, Pancrustacea and Myriapoda. Most analyses support a sister group relationship of Symphyla in respect to a clade comprising Chilopoda and Diplopoda. Inclusion of additional sequence data from nine myriapod species resulted in an alignment with poor data density, but broader taxon average. With this dataset we inferred Diplopoda+Pauropoda as closest relatives (i.e., Dignatha) and recovered monophyletic Helminthomorpha. Molecular clock calculations suggest an early Cambrian emergence of Myriapoda ∼513 million years ago and a late Cambrian divergence of myriapod classes. This implies a marine origin of the myriapods and independent terrestrialization events during myriapod evolution.

Evaluating topological conflict in centipede phylogeny using transcriptomic data sets

Relationships between the five extant orders of centipedes have been considered solved based on morphology. Phylogenies based on samples of up to a few dozen genes have largely been congruent with the morphological tree apart from an alternative placement of one order, the relictual Craterostigmomorpha, consisting of two species in Tasmania and New Zealand. To address this incongruence, novel transcriptomic data were generated to sample all five orders of centipedes and also used as a test case for studying gene-tree incongruence. Maximum likelihood and Bayesian mixture model analyses of a data set composed of 1,934 orthologs with 45% missing data, as well as the 389 orthologs in the least saturated, stationary quartile, retrieve strong support for a sister-group relationship between Craterostigmomorpha and all other pleurostigmophoran centipedes, of which the latter group is newly named Amalpighiata. The Amalpighiata hypothesis, which shows little gene-tree incongruence and is robust to the influence of among-taxon compositional heterogeneity, implies convergent evolution in several morphological and behavioral characters traditionally used in centipede phylogenetics, such as maternal brood care, but accords with patterns of first appearances in the fossil record.

Agalma: an automated phylogenomics workflow

BACKGROUND

In the past decade, transcriptome data have become an important component of many phylogenetic studies. They are a cost-effective source of protein-coding gene sequences, and have helped projects grow from a few genes to hundreds or thousands of genes. Phylogenetic studies now regularly include genes from newly sequenced transcriptomes, as well as publicly available transcriptomes and genomes. Implementing such a phylogenomic study, however, is computationally intensive, requires the coordinated use of many complex software tools, and includes multiple steps for which no published tools exist. Phylogenomic studies have therefore been manual or semiautomated. In addition to taking considerable user time, this makes phylogenomic analyses difficult to reproduce, compare, and extend. In addition, methodological improvements made in the context of one study often cannot be easily applied and evaluated in the context of other studies.

RESULTS

We present Agalma, an automated tool that constructs matrices for phylogenomic analyses. The user provides raw Illumina transcriptome data, and Agalma produces annotated assemblies, aligned gene sequence matrices, a preliminary phylogeny, and detailed diagnostics that allow the investigator to make extensive assessments of intermediate analysis steps and the final results. Sequences from other sources, such as externally assembled genomes and transcriptomes, can also be incorporated in the analyses. Agalma is built on the BioLite bioinformatics framework, which tracks provenance, profiles processor and memory use, records diagnostics, manages metadata, installs dependencies, logs version numbers and calls to external programs, and enables rich HTML reports for all stages of the analysis. Agalma includes a small test data set and a built-in test analysis of these data. In addition to describing Agalma, we here present a sample analysis of a larger seven-taxon data set. Agalma is available for download at https://bitbucket.org/caseywdunn/agalma.

CONCLUSIONS

Agalma allows complex phylogenomic analyses to be implemented and described unambiguously as a series of high-level commands. This will enable phylogenomic studies to be readily reproduced, modified, and extended. Agalma also facilitates methods development by providing a complete modular workflow, bundled with test data, that will allow further optimization of each step in the context of a full phylogenomic analysis.

Inclusion of chloroplast genes that have undergone expansion misleads phylogenetic reconstruction in the Chlorophyta

PREMISE OF THE STUDY

Chlorophytes comprise a substantial proportion of green plant diversity. However, sister-group relationships and circumscription of the classes Chlorophyceae, Trebouxiophyceae, and Ulvophyceae have been problematic to resolve. Some analyses support a sister relationship between the trebouxiophycean Leptosira and chlorophyceans, potentially altering the circumscription of two classes, also supported by a shared fragmentation in the chloroplast gene rpoB. We sought to determine whether the latter is a synapomorphy or whether the supporting analyses are vulnerable to systematic bias.

METHODS

We sequenced a portion of rpoB spanning the fragmented region in strains for which it had not previously been sampled: four Chlorophyceae, six counterclockwise (CCW) group (ulvophyceans and trebouxiophyceans) and one streptophyte. We then explored the effect of subsampling proteins and taxa on phylogenetic reconstruction from a data set of 41 chloroplast proteins.

KEY RESULTS

None of the CCW or streptophyte strains possessed the split in rpoB, including inferred near relatives of Leptosira, but it was found in all chlorophycean strains. We reconstructed alternative phylogenies (Leptosira + Chlorophyceae and Leptosira + Chlorellales) using two different protein groups (Rpo and Rps), both subject to coding-region expansion. A conserved region of RpoB remained suitable for analysis of more recent divergences.

CONCLUSIONS

The Rps sequences can explain earlier findings linking Leptosira with the Chlorophyceae and should be excluded from phylogenetic analyses attempting to resolve deep nodes because their expansion violates the assumptions of substitution models. We reaffirm that Leptosira is a trebouxiophycean and that fragmentation of rpoB has occurred at least twice in chlorophyte evolution.

A versatile and highly efficient toolkit including 102 nuclear markers for vertebrate phylogenomics, tested by resolving the higher level relationships of the caudata

Resolving difficult nodes for any part of the vertebrate tree of life often requires analyzing a large number of loci. Developing molecular markers that are workable for the groups of interest is often a bottleneck in phylogenetic research. Here, on the basis of a nested polymerase chain reaction (PCR) strategy, we present a universal toolkit including 102 nuclear protein-coding locus (NPCL) markers for vertebrate phylogenomics. The 102 NPCL markers have a broad range of evolutionary rates, which makes them useful for a wide range of time depths. The new NPCL toolkit has three important advantages compared with all previously developed NPCL sets: 1) the kit is universally applicable across vertebrates, with a PCR success rate of 94.6% in 16 widely divergent tested vertebrate species; 2) more than 90% of PCR reactions produce strong and single bands of the expected sizes that can be directly sequenced; and 3) all cleanup PCR reactions can be sequenced with only two specific universal primers. To test its actual phylogenetic utility, 30 NPCLs from this toolkit were used to address the higher level relationships of living salamanders. Of the 639 target PCR reactions performed on 19 salamanders and several outgroup species, 632 (98.9%) were successful, and 602 (94.1%) were directly sequenced. Concatenation and species-tree analyses on this 30-locus data set produced a fully resolved phylogeny and showed that Cryptobranchoidea (Cryptobranchidae + Hynobiidae) branches first within the salamander tree, followed by Sirenidae. Our experimental tests and our demonstration for a particular case show that our NPCL toolkit is a highly reliable, fast, and cost-effective approach for vertebrate phylogenomic studies and thus has the potential to accelerate the completion of many parts of the vertebrate tree of life.

Field et Al. Redux

On 12 February 1988 (by coincidence Charles Darwin's birthday), a paper published in Science by Katherine Field, Rudy Raff, and colleagues presented the first credible molecular analysis of metazoan phylogeny based on sequences from the small subunit ribosomal RNA gene (SSU). Here I examine the main conclusions reached in this manuscript. I reconstitute their dataset and, by recompiling software available in 1988, I consider how they might have achieved a more accurate tree. I show how three common methods to avoid systematic error - more data, careful taxon sampling and superior models of evolution - overcome the errors that exist in the original paper. This approach illustrates the basis of some of the major advances of the past 25 years resulting in our current understanding of animal phylogeny.

Impact of missing data on phylogenies inferred from empirical phylogenomic data sets

Progress in sequencing technology allows researchers to assemble ever-larger supermatrices for phylogenomic inference. However, current phylogenomic studies often rest on patchy data sets, with some having 80% missing (or ambiguous) data or more. Though early simulations had suggested that missing data per se do not harm phylogenetic inference when using sufficiently large data sets, Lemmon et al. (Lemmon AR, Brown JM, Stanger-Hall K, Lemmon EM. 2009. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst Biol. 58:130-145.) have recently cast doubt on this consensus in a study based on the introduction of parsimony-uninformative incomplete characters. In this work, we empirically reassess the issue of missing data in phylogenomics while exploring possible interactions with the model of sequence evolution. First, we note that parsimony-uninformative incomplete characters are actually informative in a probabilistic framework. A reanalysis of Lemmon's data set with this in mind gives a very different interpretation of their results and shows that some of their conclusions may be unfounded. Second, we investigate the effect of the progressive introduction of missing data in a complete supermatrix (126 genes × 39 species) capable of resolving animal relationships. These analyses demonstrate that missing data perturb phylogenetic inference slightly beyond the expected decrease in resolving power. In particular, they exacerbate systematic errors by reducing the number of species effectively available for the detection of multiple substitutions. Consequently, large sparse supermatrices are more sensitive to phylogenetic artifacts than smaller but less incomplete data sets, which argue for experimental designs aimed at collecting a modest number (~50) of highly covered genes. Our results further confirm that including incomplete yet short-branch taxa (i.e., slowly evolving species or close outgroups) can help to eschew artifacts, as predicted by simulations. Finally, it appears that selecting an adequate model of sequence evolution (e.g., the site-heterogeneous CAT model instead of the site-homogeneous WAG model) is more beneficial to phylogenetic accuracy than reducing the level of missing data.

Insect phylogenomics: results, problems and the impact of matrix composition

In this study, we investigated the relationships among insect orders with a main focus on Polyneoptera (lower Neoptera: roaches, mantids, earwigs, grasshoppers, etc.), and Paraneoptera (thrips, lice, bugs in the wide sense). The relationships between and within these groups of insects are difficult to resolve because only few informative molecular and morphological characters are available. Here, we provide the first phylogenomic expressed sequence tags data ('EST': short sub-sequences from a c(opy) DNA sequence encoding for proteins) for stick insects (Phasmatodea) and webspinners (Embioptera) to complete published EST data. As recent EST datasets are characterized by a heterogeneous distribution of available genes across taxa, we use different rationales to optimize the data matrix composition. Our results suggest a monophyletic origin of Polyneoptera and Eumetabola (Paraneoptera + Holometabola). However, we identified artefacts of tree reconstruction (human louse Pediculus humanus assigned to Odonata (damselflies and dragonflies) or Holometabola (insects with a complete metamorphosis); mayfly genus Baetis nested within Neoptera), which were most probably rooted in a data matrix composition bias due to the inclusion of sequence data of entire proteomes. Until entire proteomes are available for each species in phylogenomic analyses, this potential pitfall should be carefully considered.

E value cutoff and eukaryotic genome content phylogenetics

Genome content analysis has been used as a source of phylogenetic information in large prokaryotic tree of life studies. Recently the sequencing of many eukaryotic genomes has allowed for the similar use of genome content analysis for these organisms too. In this communication we examine the utility of genome content analysis for recovering phylogenetic patterns in several eukaryotic groups. By constructing multiple matrices using different e value cutoffs we examine the dynamics of altering the e value cutoff on five eukaryotic genome data sets. Our analysis indicates that the e value cutoff that is used as a criterion in the construction of the genome content matrix is a critical factor in both the accuracy and information content of the analysis. Strikingly, genome content by itself is not a reliable or accurate source of characters for phylogenetic analysis of the taxa in the five data sets we analyzed. We discuss two problems--small genome attraction and genome duplications as being involved in the rather poor performance of genome content data in recovering eukaryotic phylogeny.

Advances in insect phylogeny at the dawn of the postgenomic era

Most species on Earth are insects and thus, understanding their evolutionary relationships is key to understanding the evolution of life. Insect relationships are increasingly well supported, due largely to technological advances in molecular sequencing and phylogenetic computational analysis. In this postgenomic era, insect systematics will be furthered best by integrative methods aimed at hypothesis corroboration from molecular, morphological, and paleontological evidence. This review of the current consensus of insect relationships provides a foundation for comparative study and offers a framework to evaluate incoming genomic evidence. Notable recent phylogenetic successes include the resolution of Holometabola, including the identification of the enigmatic Strepsiptera as a beetle relative and the early divergence of Hymenoptera; the recognition of hexapods as a crustacean lineage within Pancrustacea; and the elucidation of Dictyoptera orders, with termites placed as social cockroaches. Regions of the tree that require further investigation include the earliest winged insects (Palaeoptera) and Polyneoptera (orthopteroid lineages).

The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy

Over the past two decades, there has been a long-standing debate about the impact of taxon sampling on phylogenetic inference. Studies have been based on both real and simulated data sets, within actual and theoretical contexts, and using different inference methods, to study the impact of taxon sampling. In some cases, conflicting conclusions have been drawn for the same data set. The main questions explored in studies to date have been about the effects of using sparse data, adding new taxa, including more characters from genome sequences and using different (or concatenated) locus regions. These questions can be reduced to more fundamental ones about the assessment of data quality and the design guidelines of taxon sampling in phylogenetic inference experiments. This review summarizes progress to date in understanding the impact of taxon sampling on the accuracy of phylogenetic analysis.

Deep phylogeny and evolution of sponges (phylum Porifera)

Sponges (phylum Porifera) are a diverse taxon of benthic aquatic animals of great ecological, commercial, and biopharmaceutical importance. They are arguably the earliest-branching metazoan taxon, and therefore, they have great significance in the reconstruction of early metazoan evolution. Yet, the phylogeny and systematics of sponges are to some extent still unresolved, and there is an on-going debate about the exact branching pattern of their main clades and their relationships to the other non-bilaterian animals. Here, we review the current state of the deep phylogeny of sponges. Several studies have suggested that sponges are paraphyletic. However, based on recent phylogenomic analyses, we suggest that the phylum Porifera could well be monophyletic, in accordance with cladistic analyses based on morphology. This finding has many implications for the evolutionary interpretation of early animal traits and sponge development. We further review the contribution that mitochondrial genes and genomes have made to sponge phylogenetics and explore the current state of the molecular phylogenies of the four main sponge lineages (Classes), that is, Demospongiae, Hexactinellida, Calcarea, and Homoscleromorpha, in detail. While classical systematic systems are largely congruent with molecular phylogenies in the class Hexactinellida and in certain parts of Demospongiae and Homoscleromorpha, the high degree of incongruence in the class Calcarea still represents a challenge. We highlight future areas of research to fill existing gaps in our knowledge. By reviewing sponge development in an evolutionary and phylogenetic context, we support previous suggestions that sponge larvae share traits and complexity with eumetazoans and that the simple sedentary adult lifestyle of sponges probably reflects some degree of secondary simplification. In summary, while deep sponge phylogenetics has made many advances in the past years, considerable efforts are still required to achieve a comprehensive understanding of the relationships among and within the main sponge lineages to fully appreciate the evolution of this extraordinary metazoan phylum.

MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons

Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment.

We present an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame. The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons). MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.

MACSE is distributed as an open-source java file executable with freely available source code and can be used via a web interface at: http://mbb.univ-montp2.fr/macse.

Eukaryotic systematics: a user's guide for cell biologists and parasitologists

Single-celled parasites like Entamoeba, Trypanosoma, Phytophthora and Plasmodium wreak untold havoc on human habitat and health. Understanding the position of the various protistan pathogens in the larger context of eukaryotic diversity informs our study of how these parasites operate on a cellular level, as well as how they have evolved. Here, we review the literature that has brought our understanding of eukaryotic relationships from an idea of parasites as primitive cells to a crystallized view of diversity that encompasses 6 major divisions, or supergroups, of eukaryotes. We provide an updated taxonomic scheme (for 2011), based on extensive genomic, ultrastructural and phylogenetic evidence, with three differing levels of taxonomic detail for ease of referencing and accessibility (see supplementary material at Cambridge Journals On-line). Two of the most pressing issues in cellular evolution, the root of the eukaryotic tree and the evolution of photosynthesis in complex algae, are also discussed along with ideas about what the new generation of genome sequencing technologies may contribute to the field of eukaryotic systematics. We hope that, armed with this user's guide, cell biologists and parasitologists will be encouraged about taking an increasingly evolutionary point of view in the battle against parasites representing real dangers to our livelihoods and lives.

Multigene phylogeny of the green lineage reveals the origin and diversification of land plants

The Viridiplantae (green plants) include land plants as well as the two distinct lineages of green algae, chlorophytes and charophytes. Despite their critical importance for identifying the closest living relatives of land plants, phylogenetic studies of charophytes have provided equivocal results [1-5]. In addition, many relationships remain unresolved among the land plants, such as the position of mosses, liverworts, and the enigmatic Gnetales. Phylogenomics has proven to be an insightful approach for resolving challenging phylogenetic issues, particularly concerning deep nodes [6-8]. Here we extend this approach to the green lineage by assembling a multilocus data set of 77 nuclear genes (12,149 unambiguously aligned amino acid positions) from 77 taxa of plants. We therefore provide the first multigene phylogenetic evidence that Coleochaetales represent the closest living relatives of land plants. Moreover, our data reinforce the early divergence of liverworts and the close relationship between Gnetales and Pinaceae. These results provide a new phylogenetic framework and represent a key step in the evolutionary interpretation of developmental and genomic characters in green plants.

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets

Background

The availability of many gene alignments with overlapping taxon sets raises the question of which strategy is the best to infer species phylogenies from multiple gene information. Methods and programs abound that use the gene alignment in different ways to reconstruct the species tree. In particular, different methods combine the original data at different points along the way from the underlying sequences to the final tree. Accordingly, they are classified into superalignment, supertree and medium-level approaches. Here, we present a simulation study to compare different methods from each of these three approaches.

Results

We observe that superalignment methods usually outperform the other approaches over a wide range of parameters including sparse data and gene-specific evolutionary parameters. In the presence of high incongruency among gene trees, however, other combination methods show better performance than the superalignment approach. Surprisingly, some supertree and medium-level methods exhibit, on average, worse results than a single gene phylogeny with complete taxon information.

Conclusions

For some methods, using the reconstructed gene tree as an estimation of the species tree is superior to the combination of incomplete information. Superalignment usually performs best since it is less susceptible to stochastic error. Supertree methods can outperform superalignment in the presence of gene-tree conflict.

A twist in time--the evolution of spiral cleavage in the light of animal phylogeny

Recent progress in reconstructing animal relationships enables us to draw a better picture of the evolution of important characters such as organ systems and developmental processes. By mapping these characters onto the phylogenetic framework, we can detect changes that have occurred in them during evolution. The spiral mode of development is a complex of characters that is present in many lineages, such as nemerteans, annelids, mollusks, and polyclad platyhelminthes. However, some of these lineages show variations of this general program in which sub-characters are modified without changing the overlying pattern. Recent molecular phylogenies suggest that spiral cleavage was lost, or at least has deviated from its original pattern, in more lineages than was previously thought (e.g., in rotifers, gastrotrichs, bryozoans, brachiopods, and phoronids). Here, I summarize recent progress in reconstructing the spiralian tree of life and discuss its significance for our understanding of the spiral-cleavage character complex. I conclude that more detailed knowledge of the development of spiralian taxa is necessary to understand the mechanisms behind these changes, and to understand the evolutionary changes and adaptations of spiralian embryos.

The position of gnetales among seed plants: overcoming pitfalls of chloroplast phylogenomics

The phylogenetic position of Gnetales is one of the most contentious issues in the seed plant systematics. To elucidate the Gnetales position, an improved amino acid substitution matrix was estimated based on 64 chloroplast (cp) genomes and was applied to cp genome data including all three lineages of Gnetales in maximum likelihood analyses of proteins. Although the initial analysis strongly supported the sister relation of Gnetales with Cryptomeria (Cupressophyta or non-Pinaceae conifers) (the "Gnecup" hypothesis), the support seems to be caused by a long-branch attraction (LBA) artifact. Indeed, by removing fastest evolving proteins that are most likely associated with the LBA, the support drastically declined. Furthermore, another analysis of partial genome data with dense taxon sampling of conifers showed that, in psbC, rpl2, and rps7 proteins, there are many parallel amino acid substitutions between the lineages leading to Gnetales and to Cryptomeria, and by further excluding these three genes, the sister relation of Gnetales with Pinaceae (the "Gnepine" hypothesis) became supported. Overall, our analyses indicate that the LBA and parallel substitutions cause a seriously biased inference of phylogenetic position of Gnetales with the cp genome data.

Different phylogenomic approaches to resolve the evolutionary relationships among model fish species

Comparative genomics holds the promise to magnify the information obtained from individual genome sequencing projects, revealing common features conserved across genomes and identifying lineage-specific characteristics. To implement such a comparative approach, a robust phylogenetic framework is required to accurately reconstruct evolution at the genome level. Among vertebrate taxa, teleosts represent the second best characterized group, with high-quality draft genome sequences for five model species (Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Takifugu rubripes, and Tetraodon nigroviridis), and several others are in the finishing lane. However, the relationships among the acanthomorph teleost model fishes remain an unresolved taxonomic issue. Here, a genomic region spanning over 1.2 million base pairs was sequenced in the teleost fish Dicentrarchus labrax. Together with genomic data available for the above fish models, the new sequence was used to identify unique orthologous genomic regions shared across all target taxa. Different strategies were applied to produce robust multiple gene and genomic alignments spanning from 11,802 to 186,474 amino acid/nucleotide positions. Ten data sets were analyzed according to Bayesian inference, maximum likelihood, maximum parsimony, and neighbor joining methods. Extensive analyses were performed to explore the influence of several factors (e.g., alignment methodology, substitution model, data set partitions, and long-branch attraction) on the tree topology. Although a general consensus was observed for a closer relationship between G. aculeatus (Gasterosteidae) and Di. labrax (Moronidae) with the atherinomorph O. latipes (Beloniformes) sister taxon of this clade, with the tetraodontiform group Ta. rubripes and Te. nigroviridis (Tetraodontiformes) representing a more distantly related taxon among acanthomorph model fish species, conflicting results were obtained between data sets and methods, especially with respect to the choice of alignment methodology applied to noncoding parts of the genomic region under study. This may limit the use of intergenic/noncoding sequences in phylogenomics until more robust alignment algorithms are developed.

Molecular phylogenetic insights into the evolution of Octocorallia: a review

The anthozoan sub-class Octocorallia, comprising approximately 3000 species of soft corals, gorgonians, and sea pens, remains one of the most poorly understood groups of the phylum Cnidaria. Efforts to classify the soft corals and gorgonians at the suprafamilial level have long thwarted taxonomists, and the subordinal groups in current use are widely recognized to represent grades of colony forms rather than clades. Molecular phylogenetic analyses of the sub-class do not support either the current morphologically based subordinal or familial-level taxonomy. To date, however, the resolution necessary to propose an alternative, phylogenetic classification of Octocorallia or to elucidate patterns of morphological evolution within the group is lacking. Attempts to understand boundaries between species and interspecific or intraspecific phylogenetic relationships have been hampered by the very slow rate of mitochondrial gene evolution in Octocorallia, and a consequent dearth of molecular markers with variation sufficient to distinguish species (or sometimes genera). A review of the available ITS2 sequence data for octocorals, however, reveals a yet-unexplored phylogenetic signal both at sequence and secondary-structure levels. In addition, incongruence between mitochondrial and nuclear gene trees suggests that hybrid speciation and reticulate evolution may be an important mechanism of diversification in some genera. Emerging next-generation genomic-sequencing technologies offer the best hope for a breakthrough in our understanding of phylogenetic relationships and of evolution of morphological traits in Octocorallia. Genome and transcriptome sequencing may provide enough characters to resolve relationships at the deepest levels of the octocoral tree, while simultaneously offering an efficient means to screen for new genetic markers variable enough to distinguish species and populations.

How fast is the sessile ciona?

Genomewide analyses of distances between orthologous gene pairs from the ascidian species Ciona intestinalis and Ciona savignyi were compared with those of vertebrates. Combining this data with a detailed and careful use of vertebrate fossil records, we estimated the time of divergence between the two ascidians nearly 180 My. This estimation was obtained after correcting for the different substitution rates found comparing several groups of chordates; indeed we determine here that on average Ciona species evolve 50% faster than vertebrates.