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Heike Hadrys - One of the best experts on this subject based on the ideXlab platform.
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a comparative analysis of complete mitochondrial genomes among Hexapoda
Molecular Phylogenetics and Evolution, 2013Co-Authors: Sabrina Simon, Heike HadrysAbstract:With respect to bauplan radiation, species and taxa richness, hexapods have an unassailable lead. But still, the phylogenetic relationships among the orders and infraorders remain a matter of discussion. The rapidly increasing mitochondrial genome sequences from diverse insect species provide the opportunity to explore miscellaneous evolutionary questions in the superclass Hexapoda. A combined primary sequence analyses of the complete available data set has not yet been performed. Until now phylogenetic analyses of subsets of selected taxa resulted to strong supported topologies showing in some instances discrepancies between morphological and nuclear data. This circumstance started the discussion about the limits of complete mitochondrial genomes for inferring deep hexapod relationships. By using the hitherto densest taxon sampling of Hexapoda our analyses resulted in discrepancies to the current phylogenetic hypotheses based on morphological and nuclear data, e.g. monophyly of hexapods and some hexapods orders, e.g. Diptera, Hemiptera and Orthoptera. Nonetheless, compared to previously published studies that strongly support systematically erroneous groups using a sparse taxon sampling, our analyses had no support for theses discrepancies. Consequently, we highly recommend interpreting mt-genome based phylogenies with incomplete representation of major orders/taxa particularly for hexapods with cautions although the inferred relationships are highly supported.
Gonzalo Giribet - One of the best experts on this subject based on the ideXlab platform.
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a phylogenomic solution to the origin of insects by resolving crustacean hexapod relationships
Current Biology, 2017Co-Authors: Martin Schwentner, David J Combosch, Joey Pakes Nelson, Gonzalo GiribetAbstract:Summary Insects, the most diverse group of organisms, are nested within crustaceans, arguably the most abundant group of marine animals. However, to date, no consensus has been reached as to which crustacean taxon is the closest relative of hexapods. A majority of studies have proposed that Branchiopoda (e.g., fairy shrimps) is the sister group of Hexapoda [1–7]. However, these investigations largely excluded two equally important taxa, Remipedia and Cephalocarida. Other studies suggested Remipedia [8–11] or Remipedia + Cephalocarida [12, 13] as potential sister groups of hexapods, but they either did not include Cephalocarida or used only Sanger sequence data and morphology [9, 12]. Here we present the first phylogenomic study specifically addressing the origins of hexapods, including transcriptomes for two species each of Cephalocarida and Remipedia. Phylogenetic analyses of selected matrices, ranging from 81 to 1,675 orthogroups and up to 510,982 amino acid positions, clearly reject a sister-group relationship between Hexapoda and Branchiopoda [1–7]. Nonetheless, support for a hexapod sister-group relationship to Remipedia or to Cephalocarida-Remipedia was highly dependent on the employed analytical methodology. Further analyses assessing the effects of gene evolutionary rate and targeted taxon exclusion support Remipedia as the sole sister taxon of Hexapoda and suggest that the prior grouping of Remipedia + Cephalocarida is an artifact, possibly due to long branch attraction and compositional heterogeneity. We further conclude that terrestrialization of Hexapoda probably occurred in the late Cambrian to early Ordovician, an estimate that is independent of their proposed sister group [4, 8, 12, 14].
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reevaluating the arthropod tree of life
Annual Review of Entomology, 2012Co-Authors: Gonzalo Giribet, Gregory D. EdgecombeAbstract:Arthropods are the most diverse group of animals and have been so since the Cambrian radiation. They belong to the protostome clade Ecdysozoa, with Onychophora (velvet worms) as their most likely sister group and tardigrades (water bears) the next closest relative. The arthropod tree of life can be interpreted as a five-taxon network, containing Pycnogonida, Euchelicerata, Myriapoda, Crustacea, and Hexapoda, the last two forming the clade Tetraconata or Pancrustacea. The unrooted relationship of Tetra- conata to the three other lineages is well established, but of three possible rooting positions the Mandibulata hypothesis receives the most support. Novel approaches to studying anatomy with noninvasive three-dimensional reconstruction techniques, the application of these techniques to new and old fossils, and the so-called next-generation sequencing techniques are at the forefront of understanding arthropod relationships. Cambrian fossils assigned to the arthropod stem group inform on the origin of arthropod characters from a lobopodian ancestry. Monophyly of Pycnogonida, Euche- licerata, Myriapoda, Tetraconata, and Hexapoda is well supported, but the interrelationships of arachnid orders and the details of crustacean paraphyly with respect to Hexapoda remain the major unsolved phylogenetic problems.
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further use of nearly complete 28s and 18s rrna genes to classify ecdysozoa 37 more arthropods and a kinorhynch
Molecular Phylogenetics and Evolution, 2006Co-Authors: Jon Mallatt, Gonzalo GiribetAbstract:This work expands on a study from 2004 by Mallatt, Garey, and Shultz [Mallatt, J.M., Garey, J.R., Shultz, J.W., 2004. Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin. Mol. Phylogenet. Evol. 31, 178-191] that evaluated the phylogenetic relationships in Ecdysozoa (molting animals), especially arthropods. Here, the number of rRNA gene-sequences was effectively doubled for each major group of arthropods, and sequences from the phylum Kinorhyncha (mud dragons) were also included, bringing the number of ecdysozoan taxa to over 80. The methods emphasized maximum likelihood, Bayesian inference and statistical testing with parametric bootstrapping, but also included parsimony and minimum evolution. Prominent findings from our combined analysis of both genes are as follows. The fundamental subdivisions of Hexapoda (insects and relatives) are Insecta and Entognatha, with the latter consisting of collembolans (springtails) and a clade of proturans plus diplurans. Our rRNA-gene data provide the strongest evidence to date that the sister group of Hexapoda is Branchiopoda (fairy shrimps, tadpole shrimps, etc.), not Malacostraca. The large, Pancrustacea clade (hexapods within a paraphyletic Crustacea) divided into a few basic subclades: hexapods plus branchiopods; cirripedes (barnacles) plus malacostracans (lobsters, crabs, true shrimps, isopods, etc.); and the basally located clades of (a) ostracods (seed shrimps) and (b) branchiurans (fish lice) plus the bizarre pentastomids (tongue worms). These findings about Pancrustacea agree with a recent study by Regier, Shultz, and Kambic that used entirely different genes [Regier, J.C., Shultz, J.W., Kambic, R.E., 2005a. Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic. Proc. R. Soc. B 272, 395-401]. In Malacostraca, the stomatopod (mantis shrimp) was not at the base of the eumalacostracans, as is widely claimed, but grouped instead with an euphausiacean (krill). Within centipedes, Craterostigmus was the sister to all other pleurostigmophorans, contrary to the consensus view. Our trees also united myriapods (millipedes and centipedes) with chelicerates (horseshoe crabs, spiders, scorpions, and relatives) and united pycnogonids (sea spiders) with chelicerates, but with much less support than in the previous rRNA-gene study. Finally, kinorhynchs joined priapulans (penis worms) at the base of Ecdysozoa.
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first molecular evidence for the existence of a tardigrada arthropoda clade
Molecular Biology and Evolution, 1996Co-Authors: Gonzalo Giribet, Salvador Carranza, Jaume Baguna, Marta Riutort, Carles RiberaAbstract:The complete 18S rDNA gene sequence of Macrobiotus group hufelandi (Tardigrada) was obtained and aligned with 18S rDNA and rRNA gene sequences of 24 metazoans (mainly protostomes). Discrete character (maximum-parsimony) and distance (neighbor-joining) methods were used to infer their phylogeny. The evolution of bootstrap proportions with sequence length (pattern of resolved nodes, PRN) was studied to test the resolution of the nodes in neighbor-joining trees. The results show that arthropods are monophyletic. Tardigrades represent the sister group of arthropods (in parsimony analyses) or they are related with crustaceans (distance analysis and PRN). Arthropoda are divided into two main evolutionary lines, the Hexapoda + Crustacea line (weakly supported), and the Myriapoda + Chelicerata line. The Hexapoda + Crustacea line includes Pentastomida, but the internal resolution is far from clear. The Insecta (Ectognatha) are monophyletic, but no evidence for the monophyly of Hexapoda is found. The Chelicerata are a monophyletic group and the Myriapoda cluster close to Arachnida. Overall, the results obtained represent the first molecular evidence for a Tardigrada + Arthropoda clade. In addition, the congruence between molecular phylogenies of the Arthropoda from other authors and this obtained here indicates the need to review those obtained solely on morphological characters.
Francesco Frati - One of the best experts on this subject based on the ideXlab platform.
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The complete mitochondrial genome of Atelura formicaria (Hexapoda: Zygentoma) and the phylogenetic relationships of basal insects.
Gene, 2009Co-Authors: Sara Comandi, Antonio Carapelli, Lars Podsiadlowski, Francesco Nardi, Francesco FratiAbstract:In this study, the complete sequence of the mitochondrial DNA (mtDNA) of Atelura formicaria (Hexapoda: Zygentoma) is described. The molecule is 15.205 bp in length and it is the third complete mt genome sequenced from the Zygentoma. The genome organization conforms with the putative ancestral insect gene arrangement. All protein coding genes use standard initiation codons (methionine and isoleucine). The exception is nad4 that starts with GTG, a codon used for this purpose in other insect species. A peculiar strand skew bias is observed, given that the PCGs encoded on the J-strand contain more thymines than adenines and more cytosines than guanines. This trend in nucleotide composition has been observed also in the "firebrat" Thermobia domestica (Zygentoma, Lepismatidae), but differs from that of the majority of hexapod species, including Tricholepidion gertschi (Zygentoma, Lepidotrichidae), where adenines and cytosines outnumber thymines and guanines. The presence of structural elements in the control region is also discussed, with emphasis on their potential implications in the regulation of replication and/or transcription of the mitochondrial genome. A mitogenomic phylogenetic analysis, centered on the internal relationships within Zygentoma and on the position of Microcoryphia and Zygentoma among Ectognatha, is performed.
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phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and crustacea
BMC Evolutionary Biology, 2007Co-Authors: Antonio Carapelli, Francesco Nardi, Pietro Lio, Elizabeth Van Der Wath, Francesco FratiAbstract:The phylogeny of Arthropoda is still a matter of harsh debate among systematists, and significant disagreement exists between morphological and molecular studies. In particular, while the taxon joining hexapods and crustaceans (the Pancrustacea) is now widely accepted among zoologists, the relationships among its basal lineages, and particularly the supposed reciprocal paraphyly of Crustacea and Hexapoda, continues to represent a challenge. Several genes, as well as different molecular markers, have been used to tackle this problem in molecular phylogenetic studies, with the mitochondrial DNA being one of the molecules of choice. In this study, we have assembled the largest data set available so far for Pancrustacea, consisting of 100 complete (or almost complete) sequences of mitochondrial genomes. After removal of unalignable sequence regions and highly rearranged genomes, we used nucleotide and inferred amino acid sequences of the 13 protein coding genes to reconstruct the phylogenetic relationships among major lineages of Pancrustacea. The analysis was performed with Bayesian inference, and for the amino acid sequences a new, Pancrustacea-specific, matrix of amino acid replacement was developed and used in this study. Two largely congruent trees were obtained from the analysis of nucleotide and amino acid datasets. In particular, the best tree obtained based on the new matrix of amino acid replacement (MtPan) was preferred over those obtained using previously available matrices (MtArt and MtRev) because of its higher likelihood score. The most remarkable result is the reciprocal paraphyly of Hexapoda and Crustacea, with some lineages of crustaceans (namely the Malacostraca, Cephalocarida and, possibly, the Branchiopoda) being more closely related to the Insecta s.s. (Ectognatha) than two orders of basal hexapods, Collembola and Diplura. Our results confirm that the mitochondrial genome, unlike analyses based on morphological data or nuclear genes, consistently supports the non monophyly of Hexapoda. The finding of the reciprocal paraphyly of Hexapoda and Crustacea suggests an evolutionary scenario in which the acquisition of the hexapod condition may have occurred several times independently in lineages descending from different crustacean-like ancestors, possibly as a consequence of the process of terrestrialization. If this hypothesis was confirmed, we should therefore re-think our interpretation of the evolution of the Arthropoda, where terrestrialization may have led to the acquisition of similar anatomical features by convergence. At the same time, the disagreement between reconstructions based on morphological, nuclear and mitochondrial data sets seems to remain, despite the use of larger data sets and more powerful analytical methods.
Antonio Carapelli - One of the best experts on this subject based on the ideXlab platform.
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The mitochondrial genome of Sinentomon erythranum (Arthropoda: Hexapoda: Protura): an example of highly divergent evolution.
BMC evolutionary biology, 2011Co-Authors: Wan-jun Chen, Antonio Carapelli, Wen-ying YinAbstract:The phylogenetic position of the Protura, traditionally considered the most basal hexapod group, is disputed because it has many unique morphological characters compared with other hexapods. Although mitochondrial genome information has been used extensively in phylogenetic studies, such information is not available for the Protura. This has impeded phylogenetic studies on this taxon, as well as the evolution of the arthropod mitochondrial genome. In this study, the mitochondrial genome of Sinentomon erythranum was sequenced, as the first proturan species to be reported. The genome contains a number of special features that differ from those of other hexapods and arthropods. As a very small arthropod mitochondrial genome, its 14,491 nucleotides encode 37 typical mitochondrial genes. Compared with other metazoan mtDNA, it has the most biased nucleotide composition with T = 52.4%, an extreme and reversed AT-skew of -0.351 and a GC-skew of 0.350. Two tandemly repeated regions occur in the A+T-rich region, and both could form stable stem-loop structures. Eighteen of the 22 tRNAs are greatly reduced in size with truncated secondary structures. The gene order is novel among available arthropod mitochondrial genomes. Rearrangements have involved in not only small tRNA genes, but also PCGs (protein-coding genes) and ribosome RNA genes. A large block of genes has experienced inversion and another nearby block has been reshuffled, which can be explained by the tandem duplication and random loss model. The most remarkable finding is that trnL2(UUR) is not located between cox1 and cox2 as observed in most hexapod and crustacean groups, but is between rrnL and nad1 as in the ancestral arthropod ground pattern. The "cox1-cox2" pattern was further confirmed in three more representative proturan species. The phylogenetic analyses based on the amino acid sequences of 13 mitochondrial PCGs suggest S. erythranum failed to group with other hexapod groups. The mitochondrial genome of S. erythranum shows many different features from other hexapod and arthropod mitochondrial genomes. It underwent highly divergent evolution. The "cox1-cox2" pattern probably represents the ancestral state for all proturan mitogenomes, and suggests a long evolutionary history for the Protura.
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The complete mitochondrial genome of Atelura formicaria (Hexapoda: Zygentoma) and the phylogenetic relationships of basal insects.
Gene, 2009Co-Authors: Sara Comandi, Antonio Carapelli, Lars Podsiadlowski, Francesco Nardi, Francesco FratiAbstract:In this study, the complete sequence of the mitochondrial DNA (mtDNA) of Atelura formicaria (Hexapoda: Zygentoma) is described. The molecule is 15.205 bp in length and it is the third complete mt genome sequenced from the Zygentoma. The genome organization conforms with the putative ancestral insect gene arrangement. All protein coding genes use standard initiation codons (methionine and isoleucine). The exception is nad4 that starts with GTG, a codon used for this purpose in other insect species. A peculiar strand skew bias is observed, given that the PCGs encoded on the J-strand contain more thymines than adenines and more cytosines than guanines. This trend in nucleotide composition has been observed also in the "firebrat" Thermobia domestica (Zygentoma, Lepismatidae), but differs from that of the majority of hexapod species, including Tricholepidion gertschi (Zygentoma, Lepidotrichidae), where adenines and cytosines outnumber thymines and guanines. The presence of structural elements in the control region is also discussed, with emphasis on their potential implications in the regulation of replication and/or transcription of the mitochondrial genome. A mitogenomic phylogenetic analysis, centered on the internal relationships within Zygentoma and on the position of Microcoryphia and Zygentoma among Ectognatha, is performed.
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phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and crustacea
BMC Evolutionary Biology, 2007Co-Authors: Antonio Carapelli, Francesco Nardi, Pietro Lio, Elizabeth Van Der Wath, Francesco FratiAbstract:The phylogeny of Arthropoda is still a matter of harsh debate among systematists, and significant disagreement exists between morphological and molecular studies. In particular, while the taxon joining hexapods and crustaceans (the Pancrustacea) is now widely accepted among zoologists, the relationships among its basal lineages, and particularly the supposed reciprocal paraphyly of Crustacea and Hexapoda, continues to represent a challenge. Several genes, as well as different molecular markers, have been used to tackle this problem in molecular phylogenetic studies, with the mitochondrial DNA being one of the molecules of choice. In this study, we have assembled the largest data set available so far for Pancrustacea, consisting of 100 complete (or almost complete) sequences of mitochondrial genomes. After removal of unalignable sequence regions and highly rearranged genomes, we used nucleotide and inferred amino acid sequences of the 13 protein coding genes to reconstruct the phylogenetic relationships among major lineages of Pancrustacea. The analysis was performed with Bayesian inference, and for the amino acid sequences a new, Pancrustacea-specific, matrix of amino acid replacement was developed and used in this study. Two largely congruent trees were obtained from the analysis of nucleotide and amino acid datasets. In particular, the best tree obtained based on the new matrix of amino acid replacement (MtPan) was preferred over those obtained using previously available matrices (MtArt and MtRev) because of its higher likelihood score. The most remarkable result is the reciprocal paraphyly of Hexapoda and Crustacea, with some lineages of crustaceans (namely the Malacostraca, Cephalocarida and, possibly, the Branchiopoda) being more closely related to the Insecta s.s. (Ectognatha) than two orders of basal hexapods, Collembola and Diplura. Our results confirm that the mitochondrial genome, unlike analyses based on morphological data or nuclear genes, consistently supports the non monophyly of Hexapoda. The finding of the reciprocal paraphyly of Hexapoda and Crustacea suggests an evolutionary scenario in which the acquisition of the hexapod condition may have occurred several times independently in lineages descending from different crustacean-like ancestors, possibly as a consequence of the process of terrestrialization. If this hypothesis was confirmed, we should therefore re-think our interpretation of the evolution of the Arthropoda, where terrestrialization may have led to the acquisition of similar anatomical features by convergence. At the same time, the disagreement between reconstructions based on morphological, nuclear and mitochondrial data sets seems to remain, despite the use of larger data sets and more powerful analytical methods.
Patrick Lafaite - One of the best experts on this subject based on the ideXlab platform.
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a complete insect from the late devonian period
Nature, 2012Co-Authors: Romain Garrouste, Pierre Gueriau, Gaël Clément, Patricial Nel, Michael S Engel, Philippe Grandcolas, Cyrille A Dhaese, Linda Lagebro, Julien Denayer, Patrick LafaiteAbstract:The fossil of a complete insect from the Late Devonian period (approximately 365 million years ago) is presented; it was terrestrial, but its features suggest that modern winged insects had already started to diversify at that early date. The early evolutionary history of the insects is obscure. Fragmentary remains of insect-like arthropods are known from the Silurian to the mid-Devonian periods, 425 million to 385 million years ago, whereas modern insects are known from the Carboniferous period, around 345 million years ago. In between lies a gap, poorly sampled by fossil specimens, during which much evolution is thought to have occurred. Here, Andre Nel and colleagues present the fossil of a complete insect that sits in that gap, about 365 million years ago in the Late Devonian. The fossil insect was terrestrial, but its features suggest that modern winged insects had already started to diversify at that early date. After terrestrialization, the diversification of arthropods and vertebrates is thought to have occurred in two distinct phases1, the first between the Silurian and the Frasnian stages (Late Devonian period) (425–385 million years (Myr) ago), and the second characterized by the emergence of numerous new major taxa, during the Late Carboniferous period (after 345 Myr ago). These two diversification periods bracket the depauperate vertebrate Romer’s gap (360–345 Myr ago) and arthropod gap (385–325 Myr ago)1, which could be due to preservational artefact2,3. Although a recent molecular dating has given an age of 390 Myr for the Holometabola4, the record of hexapods during the Early–Middle Devonian (411.5–391 Myr ago, Pragian to Givetian stages) is exceptionally sparse and based on fragmentary remains, which hinders the timing of this diversification. Indeed, although Devonian Archaeognatha are problematic5,6, the Pragian of Scotland has given some Collembola and the incomplete insect Rhyniognatha, with its diagnostic dicondylic, metapterygotan mandibles5,7. The oldest, definitively winged insects are from the Serpukhovian stage (latest Early Carboniferous period)8. Here we report the first complete Late Devonian insect, which was probably a terrestrial species. Its ‘orthopteroid’ mandibles are of an omnivorous type, clearly not modified for a solely carnivorous diet. This discovery narrows the 45-Myr gap in the fossil record of Hexapoda, and demonstrates further a first Devonian phase of diversification for the Hexapoda, as in vertebrates, and suggests that the Pterygota diversified before and during Romer’s gap.