Army Ants Trapped by Their Evolutionary History

A phylogenetic study of army ants has completely changed our view of their evolutionary history, including the origin of the curious and fatal phenomenon known as circular mill formatio

Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans

BACKGROUND: Comparative genomic data among organisms allow the reconstruction of their phylogenies and evolutionary time scales. Molecular timings have been recently used to suggest that environmental global change have shaped the evolutionary history of diverse terrestrial organisms. Living xenarthrans (armadillos, anteaters and sloths) constitute an ideal model for studying the influence of past environmental changes on species diversification. Indeed, extant xenarthran species are relicts from an evolutionary radiation enhanced by their isolation in South America during the Tertiary era, a period for which major climate variations and tectonic events are relatively well documented. RESULTS: We applied a Bayesian approach to three nuclear genes in order to relax the molecular clock assumption while accounting for differences in evolutionary dynamics among genes and incorporating paleontological uncertainties. We obtained a molecular time scale for the evolution of extant xenarthrans and other placental mammals. Divergence time estimates provide substantial evidence for contemporaneous diversification events among independent xenarthran lineages. This correlated pattern of diversification might possibly relate to major environmental changes that occurred in South America during the Cenozoic. CONCLUSIONS: The observed synchronicity between planetary and biological events suggests that global change played a crucial role in shaping the evolutionary history of extant xenarthrans. Our findings open ways to test this hypothesis further in other South American mammalian endemics like hystricognath rodents, platyrrhine primates, and didelphid marsupials

Heterotachy and long-branch attraction in phylogenetics

BACKGROUND: Probabilistic methods have progressively supplanted the Maximum Parsimony (MP) method for inferring phylogenetic trees. One of the major reasons for this shift was that MP is much more sensitive to the Long Branch Attraction (LBA) artefact than is Maximum Likelihood (ML). However, recent work by Kolaczkowski and Thornton suggested, on the basis of simulations, that MP is less sensitive than ML to tree reconstruction artefacts generated by heterotachy, a phenomenon that corresponds to shifts in site-specific evolutionary rates over time. These results led these authors to recommend that the results of ML and MP analyses should be both reported and interpreted with the same caution. This specific conclusion revived the debate on the choice of the most accurate phylogenetic method for analysing real data in which various types of heterogeneities occur. However, variation of evolutionary rates across species was not explicitly incorporated in the original study of Kolaczkowski and Thornton, and in most of the subsequent heterotachous simulations published to date, where all terminal branch lengths were kept equal, an assumption that is biologically unrealistic. RESULTS: In this report, we performed more realistic simulations to evaluate the relative performance of MP and ML methods when two kinds of heterogeneities are considered: (i) within-site rate variation (heterotachy), and (ii) rate variation across lineages. Using a similar protocol as Kolaczkowski and Thornton to generate heterotachous datasets, we found that heterotachy, which constitutes a serious violation of existing models, decreases the accuracy of ML whatever the level of rate variation across lineages. In contrast, the accuracy of MP can either increase or decrease when the level of heterotachy increases, depending on the relative branch lengths. This result demonstrates that MP is not insensitive to heterotachy, contrary to the report of Kolaczkowski and Thornton. Finally, in the case of LBA (i.e. when two non-sister lineages evolved faster than the others), ML outperforms MP over a wide range of conditions, except for unrealistic levels of heterotachy. CONCLUSION: For realistic combinations of both heterotachy and variation of evolutionary rates across lineages, ML is always more accurate than MP. Therefore, ML should be preferred over MP for analysing real data, all the more so since parametric methods also allow one to handle other types of biological heterogeneities much better, such as among sites rate variation. The confounding effects of heterotachy on tree reconstruction methods do exist, but can be eschewed by the development of mixture models in a probabilistic framework, as proposed by Kolaczkowski and Thornton themselves

PhyloExplorer: a web server to validate, explore and query phylogenetic trees

<p>Abstract</p> <p>Background</p> <p>Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in publications or analyses such as supertree inference and tree comparisons. However, no tool is currently available to facilitate the management of tree collections providing, for instance: standardisation of taxon names among trees with respect to a reference taxonomy; selection of relevant subsets of trees or sub-trees according to a taxonomic query; or simply computation of descriptive statistics on the collection. Moreover, although several databases of phylogenetic trees exist, there is currently no easy way to find trees that are both relevant and complementary to a given collection of trees.</p> <p>Results</p> <p>We propose a tool to facilitate assessment and management of phylogenetic tree collections. Given an input collection of rooted trees, PhyloExplorer provides facilities for obtaining statistics describing the collection, correcting invalid taxon names, extracting taxonomically relevant parts of the collection using a dedicated query language, and identifying related trees in the TreeBASE database.</p> <p>Conclusion</p> <p>PhyloExplorer is a simple and interactive website implemented through underlying Python libraries and MySQL databases. It is available at: <url>http://www.ncbi.orthomam.univ-montp2.fr/phyloexplorer/</url> and the source code can be downloaded from: <url>http://code.google.com/p/taxomanie/</url>.</p

OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics

<p>Abstract</p> <p>Background</p> <p>Molecular sequence data have become the standard in modern day phylogenetics. In particular, several long-standing questions of mammalian evolutionary history have been recently resolved thanks to the use of molecular characters. Yet, most studies have focused on only a handful of standard markers. The availability of an ever increasing number of whole genome sequences is a golden mine for modern systematics. Genomic data now provide the opportunity to select new markers that are potentially relevant for further resolving branches of the mammalian phylogenetic tree at various taxonomic levels.</p> <p>Description</p> <p>The EnsEMBL database was used to determine a set of orthologous genes from 12 available complete mammalian genomes. As targets for possible amplification and sequencing in additional taxa, more than 3,000 exons of length > 400 bp have been selected, among which 118, 368, 608, and 674 are respectively retrieved for 12, 11, 10, and 9 species. A bioinformatic pipeline has been developed to provide evolutionary descriptors for these candidate markers in order to assess their potential phylogenetic utility. The resulting OrthoMaM (Orthologous Mammalian Markers) database can be queried and alignments can be downloaded through a dedicated web interface <url>http://kimura.univ-montp2.fr/orthomam</url>.</p> <p>Conclusion</p> <p>The importance of marker choice in phylogenetic studies has long been stressed. Our database centered on complete genome information now makes possible to select promising markers to a given phylogenetic question or a systematic framework by querying a number of evolutionary descriptors. The usefulness of the database is illustrated with two biological examples. First, two potentially useful markers were identified for rodent systematics based on relevant evolutionary parameters and sequenced in additional species. Second, a complete, gapless 94 kb supermatrix of 118 orthologous exons was assembled for 12 mammals. Phylogenetic analyses using probabilistic methods unambiguously supported the new placental phylogeny by retrieving the monophyly of Glires, Euarchontoglires, Laurasiatheria, and Boreoeutheria. Muroid rodents thus do not represent a basal placental lineage as it was mistakenly reasserted in some recent phylogenomic analyses based on fewer taxa. We expect the OrthoMaM database to be useful for further resolving the phylogenetic tree of placental mammals and for better understanding the evolutionary dynamics of their genomes, i.e., the forces that shaped coding sequences in terms of selective constraints.</p

Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny

International audienceBACKGROUND: Tunicates represent a key metazoan group as the sister-group of vertebrates within chordates. The six complete mitochondrial genomes available so far for tunicates have revealed distinctive features. Extensive gene rearrangements and particularly high evolutionary rates have been evidenced with regard to other chordates. This peculiar evolutionary dynamics has hampered the reconstruction of tunicate phylogenetic relationships within chordates based on mitogenomic data. RESULTS: In order to further understand the atypical evolutionary dynamics of the mitochondrial genome of tunicates, we determined the complete sequence of the solitary ascidian Herdmania momus. This genome from a stolidobranch ascidian presents the typical tunicate gene content with 13 protein-coding genes, 2 rRNAs and 24 tRNAs which are all encoded on the same strand. However, it also presents a novel gene arrangement, highlighting the extreme plasticity of gene order observed in tunicate mitochondrial genomes. Probabilistic phylogenetic inferences were conducted on the concatenation of the 13 mitochondrial protein-coding genes from representatives of major metazoan phyla. We show that whereas standard homogeneous amino acid models support an artefactual sister position of tunicates relative to all other bilaterians, the CAT and CAT+BP site- and time-heterogeneous mixture models place tunicates as the sister-group of vertebrates within monophyletic chordates. Moreover, the reference phylogeny indicates that tunicate mitochondrial genomes have experienced a drastic acceleration in their evolutionary rate that equally affects protein-coding and ribosomal-RNA genes. CONCLUSION: This is the first mitogenomic study supporting the new chordate phylogeny revealed by recent phylogenomic analyses. It illustrates the beneficial effects of an increased taxon sampling coupled with the use of more realistic amino acid substitution models for the reconstruction of animal phylogeny

Systematics of hairy armadillos and the taxonomic status of the Andean hairy armadillo (<i>Chaetophractus nationi</i>)

Hairy armadillos constitute an ecologically homogeneous and morphologically similar group with currently 5 species classified in the subfamily Euphractinae. Among them, the Andean hairy armadillo Chaetophractus nationi (Xenarthra, Cingulata, Dasypodidae) is a small, endangered armadillo that has long been suspected to represent a high-altitude variant of Chaetophractus vellerosus. Here, we report the 1st phylogenetic systematics assessment of hairy armadillos using morphological and molecular analyses of all described species with focus on the status of the Andean hairy armadillo. Multivariate analyses of shape variation based on 3-dimensional landmark coordinates of skulls allowed a clear differentiation of each species with the exception of C. vellerosus and C. nationi, within which only a latitudinal and/or altitudinal gradient in size was apparent. Moreover, analyses of mitochondrial DNA control region (D-loop) revealed a single C. nationi haplotype that appeared to be identical with a C. vellerosus haplotype from Argentina. Identical sequences in C. vellerosus and C. nationi were also observed for 3 of the 5 non-coding nuclear markers investigated. Based on these data, we propose that C. nationi should be considered as a synonym of C. vellerosus. However, this taxonomic change should not preclude the protection of the high-altitude Bolivian populations that are steadily declining because of their overexploitation for traditional purposes. Finally, phylogenetic analyses of euphractine armadillos based on a combination of 6 non-coding nuclear markers and 2 nuclear exons suggest the paraphyly of the genus Chaetophractus, with C. vellerosus being more closely related to Zaedyus pichiy than to C. villosus.Los armadillos peludos constituyen un grupo ecológicamente homogéneo y morfológicamente similar que actualmente consiste de 5 especies clasificadas en la subfamilia Euphractinae. Una de ellas, el quirquincho Andino Chaetophractus nationi (Xenarthra, Cingulata, Dasypodidae), es un pequeño armadillo amenazado de extinción del cual se ha sospechado durante mucho tiempo que representa una variedad de altitud de Chaetophractus vellerosus. Aquí reportamos la primera evaluación sistemática filogenética de armadillos peludos utilizando análisis morfológicos y moleculares de todas las especies descritas, poniendo un especial enfoque en el estado del quirquincho Andino. Los análisis multivariados de la forma basados en landmarks tridimensionales de cráneos, permitieron distinguir claramente las especies, con la excepción de C. vellerosus y C. nationi en los cuales sólo se halló un gradiente latitudinal y/o altitudinal en el tamaño. Además, los análisis de la región control del ADN mitocondrial (D-loop) mostraron un solo haplotipo de C. nationi, que fue idéntico a un haplotipo de C. vellerosus de Argentina. También se observaron secuencias idénticas para C. vellerosus y C. nationi en 3 de los 5 marcadores nucleares no codificantes analizados. A partir de estos resultados proponemos que C. nationi sea considerado sinónimo de C. vellerosus. Sin embargo, este cambio taxonómico no debe excluir la protección de las poblaciones altoandinas de Bolivia que están sufriendo una reducción continua debido a su sobreexplotación para fines tradicionales. Finalmente, los análisis filogenéticos de los armadillos eufractinos basados en una combinación de 6 marcadores nucleares no codificantes y 2 exones nucleares sugieren la parafilia del género Chaetophractus, Siendo C. vellerosus relacionado mas estrechamente con Zaedyus pichiy que con C. villosus.Facultad de Ciencias Naturales y Muse

Quand l’Évolution se prête au jeu…

Créé par l’École de l’ADN et ses partenaires, « Trivial Évolution » est un jeu éducatif qui a pour objectifs de faire découvrir les concepts de base de l’Évolution des espèces et de combattre les idées reçues sur la théorie de l’Évolution : les concepteurs présentent ici une première évaluation de cet outil ludique de vulgarisation scientifique.Developed by the ADN school and its partners, « Trivial Evolution » is an educational board game which aims at helping players to grasp the basic concepts of species evolution, and to combat preconceived ideas concerning the Evolution theory: the designers present a first-time assessment of this educative and fun tool for the general public interested in Science

Deep Sequencing of Mixed Total DNA without Barcodes Allows Efficient Assembly of Highly Plastic Ascidian Mitochondrial Genomes

Ascidians or sea squirts form a diverse group within chordates, which includes a few thousand members of marine sessile filter-feeding animals. Their mitochondrial genomes are characterized by particularly high evolutionary rates and rampant gene rearrangements. This extreme variability complicates standard polymerase chain reaction (PCR) based techniques for molecular characterization studies, and consequently only a few complete Ascidian mitochondrial genome sequences are available. Using the standard PCR and Sanger sequencing approach, we produced the mitochondrial genome of Ascidiella aspersa only after a great effort. In contrast, we produced five additional mitogenomes (Botrylloides aff. leachii, Halocynthia spinosa, Polycarpa mytiligera, Pyura gangelion, and Rhodosoma turcicum) with a novel strategy, consisting in sequencing the pooled total DNA samples of these five species using one Illumina HiSeq 2000 flow cell lane. Each mitogenome was efficiently assembled in a single contig using de novo transcriptome assembly, as de novo genome assembly generally performed poorly for this task. Each of the new six mitogenomes presents a different and novel gene order, showing that no syntenic block has been conserved at the ordinal level (in Stolidobranchia and in Phlebobranchia). Phylogenetic analyses support the paraphyly of both Ascidiacea and Phlebobranchia, with Thaliacea nested inside Phlebobranchia, although the deepest nodes of the Phlebobranchia–Thaliacea clade are not well resolved. The strategy described here thus provides a cost-effective approach to obtain complete mitogenomes characterized by a highly plastic gene order and a fast nucleotide/amino acid substitution rate

An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

<p>Abstract</p> <p>Background</p> <p>Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea.</p> <p>Results</p> <p>Thirty new complete 18S rRNA sequences were acquired from previously unsampled tunicate species, with special focus on groups presenting high evolutionary rate. The updated 18S rRNA dataset has been aligned with respect to the constraint on homology imposed by the rRNA secondary structure. A probabilistic framework of phylogenetic reconstruction was adopted to accommodate the particular evolutionary dynamics of this ribosomal marker. Detailed Bayesian analyses were conducted under the non-parametric CAT mixture model accounting for site-specific heterogeneity of the evolutionary process, and under RNA-specific doublet models accommodating the occurrence of compensatory substitutions in stem regions. Our results support the division of tunicates into three major clades: 1) Phlebobranchia + Thaliacea + Aplousobranchia, 2) Appendicularia, and 3) Stolidobranchia, but the position of Appendicularia could not be firmly resolved. Our study additionally reveals that most Aplousobranchia evolve at extremely high rates involving changes in secondary structure of their 18S rRNA, with the exception of the family Clavelinidae, which appears to be slowly evolving. This extreme rate heterogeneity precluded resolving with certainty the exact phylogenetic placement of Aplousobranchia. Finally, the best fitting secondary-structure and CAT-mixture models suggest a sister-group relationship between Salpida and Pyrosomatida within Thaliacea.</p> <p>Conclusion</p> <p>An updated phylogenetic framework for tunicates is provided based on phylogenetic analyses using the most realistic evolutionary models currently available for ribosomal molecules and an unprecedented taxonomic sampling. Detailed analyses of the 18S rRNA gene allowed a clear definition of the major tunicate groups and revealed contrasting evolutionary dynamics among major lineages. The resolving power of this gene nevertheless appears limited within the clades composed of Phlebobranchia + Thaliacea + Aplousobranchia and Pyuridae + Styelidae, which were delineated as spots of low resolution. These limitations underline the need to develop new nuclear markers in order to further resolve the phylogeny of this keystone group in chordate evolution.</p