SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics

BACKGROUND: Phylogenetic analyses based on datasets rich in both genes and species (phylogenomics) are becoming a standard approach to resolve evolutionary questions. However, several difficulties are associated with the assembly of large datasets, such as multiple copies of a gene per species (paralogous or xenologous genes), lack of some genes for a given species, or partial sequences. The use of undetected paralogous or xenologous genes in phylogenetic inference can lead to inaccurate results, and the use of partial sequences to a lack of resolution. A tool that selects sequences, species, and genes, while dealing with these issues, is needed in a phylogenomics context. RESULTS: Here, we present SCaFoS, a tool that quickly assembles phylogenomic datasets containing maximal phylogenetic information while adjusting the amount of missing data in the selection of species, sequences and genes. Starting from individual sequence alignments, and using monophyletic groups defined by the user, SCaFoS creates chimeras with partial sequences, or selects, among multiple sequences, the orthologous and/or slowest evolving sequences. Once sequences representing each predefined monophyletic group have been selected, SCaFos retains genes according to the user's allowed level of missing data and generates files for super-matrix and super-tree analyses in several formats compatible with standard phylogenetic inference software. Because no clear-cut criteria exist for the sequence selection, a semi-automatic mode is available to accommodate user's expertise. CONCLUSION: SCaFos is able to deal with datasets of hundreds of species and genes, both at the amino acid or nucleotide level. It has a graphical interface and can be integrated in an automatic workflow. Moreover, SCaFoS is the first tool that integrates user's knowledge to select orthologous sequences, creates chimerical sequences to reduce missing data and selects genes according to their level of missing data. Finally, applying SCaFoS to different datasets, we show that the judicious selection of genes, species and sequences reduces tree reconstruction artefacts, especially if the dataset includes fast evolving species

Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics

Phylemon is an online platform for phylogenetic and evolutionary analyses of molecular sequence data. It has been developed as a web server that integrates a suite of different tools selected among the most popular stand-alone programs in phylogenetic and evolutionary analysis. It has been conceived as a natural response to the increasing demand of data analysis of many experimental scientists wishing to add a molecular evolution and phylogenetics insight into their research. Tools included in Phylemon cover a wide yet selected range of programs: from the most basic for multiple sequence alignment to elaborate statistical methods of phylogenetic reconstruction including methods for evolutionary rates analyses and molecular adaptation. Phylemon has several features that differentiates it from other resources: (i) It offers an integrated environment that enables the direct concatenation of evolutionary analyses, the storage of results and handles required data format conversions, (ii) Once an outfile is produced, Phylemon suggests the next possible analyses, thus guiding the user and facilitating the integration of multi-step analyses, and (iii) users can define and save complete pipelines for specific phylogenetic analysis to be automatically used on many genes in subsequent sessions or multiple genes in a single session (phylogenomics). The Phylemon web server is available at http://phylemon.bioinfo.cipf.es

Phylogeny and evolutionary perspective of Opisthokonta protists

[cat] Per entendre l’origen dels Opistoconts (grup taxonòmic que conté animals, fongs i diversos llinatges protists emparentats) o inferir les seves transicions evolutives, és fonamental primer entendre les relacions filogenètiques entre les espècies existents en l’actualitat. La filogènia, particularment la filogenòmica, és el procediment vàlid per inferir relacions evolutives entre espècies, ja que la morfologia, les sinapomorfies moleculars o els canvis genètics singulars són arguments cíclics dependents del mostreig taxonòmic. Per aquesta raó hem fet servir dades genòmiques i transcriptòmiques per a construir un nou conjunt de dades format per dominis proteics de còpia única i els hem analitzat mitjançat diversos mètodes per prevenir errors sistemàtics. Hem pogut així confirmar la divisió entre Holomycota (Nucleariids, Opisthosporidia, quitridiomiciets i fongs) i Holozoa (Ichthyosporea, Filasterea, Choanomonada i Metazoa). També hem obtingut dades de RNAseq per situar espècies particularment ambigües com: Corallochytrium limacisporum la qual hem situat com a grup germà de Ichthyosporea, un altre grup holozou osmotròfic. Partint d’aquesta base filogenètica es pot començar a especular sobre les transicions evolutives entre els grups. No obstant, abans cal reconstruir els ancestres dels llinatges dels Opistoconts com també dels seus grups externs actuals: Apusomonadida i Breviatea. Els resultats indiquen que no existeix cap lligam definit entre els bacterívors ancestrals biflagelats (grup extern) i cap dels llinatges Opistoconts (grup d’interès). També que el darrer avantpassat comú dels Opistoconts probablement conservaria quasi tots els caràcters ancestrals com el moviment ameboide, filopodis, la fagotrofia, etc.; però seria uniflagel·lat, amb una forma cel·lular menys restringida pel tipus d’alimentació. Mitjançant la genòmica comparada hem estudiat les similituds entre grups no emparentats d’Opistoconts com els osmòtrofs amb paret cel·lular o les amebes filopodials nues. Per exemple, hem trobat que Ministeria vibrans (Filasterea) i C. limacisporum (Ichthyosporea) presenten un aparell flagel·lar fins ara desconegut amb un patró similar al que formen fongs i altres eucariotes. També que Ichthyosporea fa servir un material semblant a la quitina per construir la seva paret cel·lular. Aquestes similituds plantegen hipòtesis de convergència evolutiva o paral·lelisme entre llinatges propers que s’hauran de comprovar en un futur.[eng] To understand the origin of opisthokonts or infer evolutionary transitions within the group that contains two multicellular lineages (animals and fungi), it is first fundamental to understand the phylogenetic relationships between extant living species. Phylogeny and particularly phylogenomics (such the supermatrix approach) is the only valid procedure to infer evolutionary relationships between species, as morphological or molecular synapomorphies or rare genomic changes are cyclic arguments and really taxon dependent. This is why we have used genomic and transcriptomic data to build a novel dataset of Single Copy Protein Domains and test phylogenetic hypotheses with multiple methods to discard problems of systematic error. We have confirmed the division between Holomycota (Nucleariids, Opisthosporidia, chytrid fungi and fungi) and Holozoa (Ichthyosporea, Filasterea, Choanomonada and Metazoa). We also have generated RNAseq data to place a specially elusive species: Corallochytrium limacisporum and found it placed as sister group to Ichthyosporea, another osmotrophic holozoan group. With this solid phylogenetic background we can start to speculate on evolutionary transitions between groups, but not before reconstructing ancestral character states in different opisthokont lineages and also the extant living outgroups: Apusomonadida and Breviatea. So we conclude that there is no clear link between biflagellated free-living gliding bacterivores (outgroup) and any opisthokont lineage (ingroup). The Last Opisthokont Common Ancestor was probably uniflagellated but retained all other ancestral characters such amoeboid movement, filopodia, phagotrophy, etc. but had a less constrained cell shape or feeding mode. Then, we studied the similarities found between non-related groups of opisthokonts, such the walled osmotrophs or the naked filose amoebae through comparative genomics. For example, we found that Ministeria vibrans (Filasterea) and C. limacisporum (Ichthyosporea) have a flagellar apparatus previously unnoticed, and with a molecular pattern of flagellum reduction also seen in fungi and other eukaryotes. Also, Ichthyosporea probably use a chitin-like substance to build their cell wall (similar to fungi) but with an independently diversified pathway

Unravelling body plan and axial evolution in the Bilateria with molecular phylogenetic markers

SETTING THE PROBLEM The emergence of dramatic morphological differences (disparity) and the ensuing bewildering increase in the number of species (diversity) documented in the fossil record at key stages of animal and plant evolution have defied, and still defy, the explanatory powers of Darwin’s theory of evolution by natural selection. Among the best examples that have captured the imagination of the layman and the interest of scores of scientists for 150 years are the origins of land plants from aquatic green plants, of flowering plants from seed plants, of chordates from non-chordates and of tetrapod vertebrates from non-tetrapods; and the conquest of the land by amphibians; the emergence of endotherms from ectotherm animals; the recurrent invention of flight (e.g. in arthropods, birds and mammals) from non-flying ancestors; and the origin of aquatic mammals from four-legged terrestrial ancestors. Key morphological transitions pose a basic difficulty: reconstruction of ancestral traits of derived clades is problematic because of a lack of transitional forms in the fossil record and obscure homologies between ‘ancestral’ and derived groups. Lack of transitional forms, in other words gaps in the fossil record, brought into question one of the basic tenets of Darwin’s theory, namely gradualism, as Darwin himself acknowledged. Since Darwin, however, and especially in the past 50 years, numerous examples that may reflect transitional stages between major groups of organisms have accumulated

Deep Genomic-Scale Analyses of the Metazoa Reject Coelomata: Evidence from Single- and Multigene Families Analyzed Under a Supertree and Supermatrix Paradigm

Solving the phylogeny of the animals with bilateral symmetry has proven difficult. Morphological studies have suggested a variety of alternative hypotheses, of which, Hyman’s Coelomata hypothesis has become the most established. Studies based on 18S rRNA have failed to endorse Coelomata, supporting instead the rearrangement of the protostomes into two new clades: the Lophotrochozoa (including, e.g., the molluscs and the annelids) and the Ecdysozoa (including the Panarthropoda and most pseudocoelomates, such as the nematodes and priapulids). Support for this new animal phylogeny has been attained from expressed sequence tag studies, although these generally have a limited gene sampling. In contrast, deep genomic-scale analyses have often supported Coelomata. However, these studies are problematic due to their limited taxonomic sampling, which could exacerbate tree reconstruction artifacts

Phylogenetic support values are not necessarily informative: the case of the Serialia hypothesis (a mollusk phylogeny)

Background: Molecular phylogenies are being published increasingly and many biologists rely on the most recent topologies. However, different phylogenetic trees often contain conflicting results and contradict significant background data. Not knowing how reliable traditional knowledge is, a crucial question concerns the quality of newly produced molecular data. The information content of DNA alignments is rarely discussed, as quality statements are mostly restricted to the statistical support of clades. Here we present a case study of a recently published mollusk phylogeny that contains surprising groupings, based on five genes and 108 species, and we apply new or rarely used tools for the analysis of the information content of alignments and for the filtering of noise (masking of random-like alignment regions, split decomposition, phylogenetic networks, quartet mapping). Results: The data are very fragmentary and contain contaminations. We show that that signal-like patterns in the data set are conflicting and partly not distinct and that the reported strong support for a "rather surprising result" (monoplacophorans and chitons form a monophylum Serialia) does not exist at the level of primary homologies. Split-decomposition, quartet mapping and neighbornet analyses reveal conflicting nucleotide patterns and lack of distinct phylogenetic signal for the deeper phylogeny of mollusks. Conclusion: Even though currently a majority of molecular phylogenies are being justified with reference to the 'statistical' support of clades in tree topologies, this confidence seems to be unfounded. Contradictions between phylogenies based on different analyses are already a strong indication of unnoticed pitfalls. The use of tree-independent tools for exploratory analyses of data quality are highly recommended. Concerning the new mollusk phylogeny more convincing evidence is needed

A Consistent Phylogenetic Backbone for the Fungi

The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data—a common practice in phylogenomic analyses—introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses