Your browser doesn't support javascript.
Mostrar: 20 | 50 | 100
Resultados 1 - 19 de 19
Filtrar
Filtros adicionais











Tipo de estudo
País/Região como assunto
Intervalo de ano
1.
Proc Biol Sci ; 286(1895): 20182076, 2019 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-30963947

RESUMO

Phylogenetic relationships among subgroups of cockroaches and termites are still matters of debate. Their divergence times and major phenotypic transitions during evolution are also not yet settled. We addressed these points by combining the first nuclear phylogenomic study of termites and cockroaches with a thorough approach to divergence time analysis, identification of endosymbionts, and reconstruction of ancestral morphological traits and behaviour. Analyses of the phylogenetic relationships within Blattodea robustly confirm previously uncertain hypotheses such as the sister-group relationship between Blaberoidea and remaining Blattodea, and Lamproblatta being the closest relative to the social and wood-feeding Cryptocercus and termites. Consequently, we propose new names for various clades in Blattodea: Cryptocercus + termites = Tutricablattae; Lamproblattidae + Tutricablattae = Kittrickea; and Blattoidea + Corydioidea = Solumblattodea. Our inferred divergence times contradict previous studies by showing that most subgroups of Blattodea evolved in the Cretaceous, reducing the gap between molecular estimates of divergence times and the fossil record. On a phenotypic level, the blattodean ground-plan is for egg packages to be laid directly in a hole while other forms of oviposition, including ovovivipary and vivipary, arose later. Finally, other changes in egg care strategy may have allowed for the adaptation of nest building and other novelties.

2.
Proc Natl Acad Sci U S A ; 116(8): 3024-3029, 2019 02 19.
Artigo em Inglês | MEDLINE | ID: mdl-30642969

RESUMO

Polyneoptera represents one of the major lineages of winged insects, comprising around 40,000 extant species in 10 traditional orders, including grasshoppers, roaches, and stoneflies. Many important aspects of polyneopteran evolution, such as their phylogenetic relationships, changes in their external appearance, their habitat preferences, and social behavior, are unresolved and are a major enigma in entomology. These ambiguities also have direct consequences for our understanding of the evolution of winged insects in general; for example, with respect to the ancestral habitats of adults and juveniles. We addressed these issues with a large-scale phylogenomic analysis and used the reconstructed phylogenetic relationships to trace the evolution of 112 characters associated with the external appearance and the lifestyle of winged insects. Our inferences suggest that the last common ancestors of Polyneoptera and of the winged insects were terrestrial throughout their lives, implying that wings did not evolve in an aquatic environment. The appearance of the first polyneopteran insect was mainly characterized by ancestral traits such as long segmented abdominal appendages and biting mouthparts held below the head capsule. This ancestor lived in association with the ground, which led to various specializations including hardened forewings and unique tarsal attachment structures. However, within Polyneoptera, several groups switched separately to a life on plants. In contrast to a previous hypothesis, we found that social behavior was not part of the polyneopteran ground plan. In other traits, such as the biting mouthparts, Polyneoptera shows a high degree of evolutionary conservatism unique among the major lineages of winged insects.


Assuntos
Evolução Biológica , Insetos/fisiologia , Neópteros/fisiologia , Asas de Animais/fisiologia , Animais , Insetos/genética , Neópteros/genética , Filogenia
3.
Arthropod Struct Dev ; 47(4): 328-338, 2018 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-29763650

RESUMO

The phylogenetic relationships of the winged insect lineages - mayflies (Ephemeroptera), damselflies and dragonflies (Odonata), and all other winged insects (Neoptera) - are still controversial with three hypotheses supported by different datasets: Palaeoptera, Metapterygota and Chiastomyaria. Here, we reanalyze available phylogenomic data with a focus on detecting confounding and alternative signal. In this context, we provide a framework to quantitatively evaluate and assess incongruent molecular phylogenetic signal inherent in phylogenomic datasets. Despite overall support for the Palaeoptera hypothesis, we also found considerable signal for Chiastomyaria, which is not easily detectable by standardized tree inference approaches. Analyses of the accumulation of signal across gene partitions showed that signal accumulates gradually. However, even in case signal only slightly supported one over the other hypothesis, topologies inferred from large datasets switch from statistically strongly supported Palaeoptera to strongly supported Chiastomyaria. From a morphological point of view, Palaeoptera currently appears to be the best-supported hypothesis; however, recent analyses were restricted to head characters. Phylogenetic approaches covering all organ systems including analyses of potential functional or developmental convergence are still pending so that the Palaeoptera problem has to be considered an open question in insect systematics.


Assuntos
Evolução Biológica , Voo Animal , Genoma de Inseto , Paleópteros/classificação , Transcriptoma , Animais , Proteínas de Insetos/genética , Paleópteros/genética , Paleópteros/fisiologia , Filogenia
4.
Sci Rep ; 7(1): 13547, 2017 Oct 19.
Artigo em Inglês | MEDLINE | ID: mdl-29051502

RESUMO

Identifying transcriptional changes during embryogenesis is of crucial importance for unravelling evolutionary, molecular and cellular mechanisms that underpin patterning and morphogenesis. However, comparative studies focusing on early/embryonic stages during insect development are limited to a few taxa. Drosophila melanogaster is the paradigm for insect development, whereas comparative transcriptomic studies of embryonic stages of hemimetabolous insects are completely lacking. We reconstructed the first comparative transcriptome covering the daily embryonic developmental progression of the blue-tailed damselfly Ischnura elegans (Odonata), an ancient hemimetabolous representative. We identified a "core" set of 6,794 transcripts - shared by all embryonic stages - which are mainly involved in anatomical structure development and cellular nitrogen compound metabolic processes. We further used weighted gene co-expression network analysis to identify transcriptional changes during Odonata embryogenesis. Based on these analyses distinct clusters of transcriptional active sequences could be revealed, indicating that embryos at different development stages have their own transcriptomic profile according to the developmental events and leading to sequential reprogramming of metabolic and developmental genes. Interestingly, a major change in transcriptionally active sequences is correlated with katatrepsis (revolution) during mid-embryogenesis, a 180° rotation of the embryo within the egg and specific to hemimetabolous insects.

5.
Mol Phylogenet Evol ; 107: 27-38, 2017 02.
Artigo em Inglês | MEDLINE | ID: mdl-27742475

RESUMO

The study of processes driving diversification requires a fully sampled and well resolved phylogeny, although a lack of phylogenetic markers remains a limitation for many non-model groups. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole-genome sequencing data from one member of the species complex were used to identify 59 nDNA loci (32,213 base pairs), followed by Sanger sequencing of 29 individuals sampled from 13 islands of three Macaronesian archipelagos. Multispecies coalescent analyses established six putative species. Three island species formed a monophyletic clade, with one species occurring on the Azores, Europe and North America. Ancestral state reconstruction indicated at least two colonization events from the mainland (to the Canaries, respectively Azores) and one within the archipelago (between Madeira and the Canaries). Random subsets of the 59 loci showed a positive linear relationship between number of loci and node support. In contrast, node support in the multispecies coalescent tree was negatively correlated with mean number of phylogenetically informative sites per locus, suggesting a complex relationship between tree resolution and marker variability. Our approach highlights the value of combining genomics, coalescent-based phylogeography, species delimitation, and phylogenetic reconstruction to resolve recent diversification events in an archipelago species complex.


Assuntos
Insetos/classificação , Animais , Biodiversidade , Evolução Biológica , DNA/química , DNA/isolamento & purificação , DNA/metabolismo , Europa (Continente) , Loci Gênicos , Genoma , Insetos/genética , Ilhas , América do Norte , Filogenia , Filogeografia , Análise de Sequência de DNA
6.
Mol Ecol Resour ; 17(2): 257-266, 2017 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-27454666

RESUMO

High-throughput sequencing has laid the foundation for fast and cost-effective development of phylogenetic markers. Here we present the program discomark, which streamlines the development of nuclear DNA (nDNA) markers from whole-genome (or whole-transcriptome) sequencing data, combining local alignment, alignment trimming, reference mapping and primer design based on multiple sequence alignments to design primer pairs from input orthologous sequences. To demonstrate the suitability of discomark, we designed markers for two groups of species, one consisting of closely related species and one group of distantly related species. For the closely related members of the species complex of Cloeon dipterum s.l. (Insecta, Ephemeroptera), the program discovered a total of 78 markers. Among these, we selected eight markers for amplification and Sanger sequencing. The exon sequence alignments (2526 base pairs) were used to reconstruct a well-supported phylogeny and to infer clearly structured haplotype networks. For the distantly related species, we designed primers for the insect order Ephemeroptera, using available genomic data from four sequenced species. We developed primer pairs for 23 markers that are designed to amplify across several families. The discomark program will enhance the development of new nDNA markers by providing a streamlined, automated approach to perform genome-scale scans for phylogenetic markers. The program is written in Python, released under a public licence (GNU GPL version 2), and together with a manual and example data set available at: https://github.com/hdetering/discomark.


Assuntos
Biologia Computacional/métodos , Marcadores Genéticos , Genômica/métodos , Filogenia , Análise de Sequência de DNA/métodos , Software , Animais , Ephemeroptera/classificação , Ephemeroptera/genética , Sequenciamento de Nucleotídeos em Larga Escala
7.
Nat Commun ; 7: 10164, 2016 Feb 02.
Artigo em Inglês | MEDLINE | ID: mdl-26836631

RESUMO

The common bed bug (Cimex lectularius) has been a persistent pest of humans for thousands of years, yet the genetic basis of the bed bug's basic biology and adaptation to dense human environments is largely unknown. Here we report the assembly, annotation and phylogenetic mapping of the 697.9-Mb Cimex lectularius genome, with an N50 of 971 kb, using both long and short read technologies. A RNA-seq time course across all five developmental stages and male and female adults generated 36,985 coding and noncoding gene models. The most pronounced change in gene expression during the life cycle occurs after feeding on human blood and included genes from the Wolbachia endosymbiont, which shows a simultaneous and coordinated host/commensal response to haematophagous activity. These data provide a rich genetic resource for mapping activity and density of C. lectularius across human hosts and cities, which can help track, manage and control bed bug infestations.


Assuntos
Percevejos-de-Cama/genética , Regulação da Expressão Gênica no Desenvolvimento , Estágios do Ciclo de Vida/genética , Animais , Sangue , Mapeamento Cromossômico , Ingestão de Alimentos , Feminino , Perfilação da Expressão Gênica , Humanos , Masculino , Modelos Moleculares , Filogenia , Análise de Sequência de RNA
8.
Insect Mol Biol ; 24(2): 139-54, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25524309

RESUMO

Insects are the most diverse group of organisms on the planet. Variation in gene expression lies at the heart of this biodiversity and recent advances in sequencing technology have spawned a revolution in researchers' ability to survey tissue-specific transcriptional complexity across a wide range of insect taxa. Increasingly, studies are using a comparative approach (across species, sexes and life stages) that examines the transcriptional basis of phenotypic diversity within an evolutionary context. In the present review, we summarize much of this research, focusing in particular on three critical aspects of insect biology: morphological development and plasticity; physiological response to the environment; and sexual dimorphism. A common feature that is emerging from these investigations concerns the dynamic nature of transcriptome evolution as indicated by rapid changes in the overall pattern of gene expression, the differential expression of numerous genes with unknown function, and the incorporation of novel, lineage-specific genes into the transcriptional profile.


Assuntos
Insetos/genética , Transcriptoma/genética , Animais , Sequência de Bases , Evolução Biológica , Feminino , Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento , Variação Genética , Insetos/crescimento & desenvolvimento , Insetos/fisiologia , Masculino , Fenótipo , RNA/genética , Caracteres Sexuais , Estresse Fisiológico
9.
Mol Phylogenet Evol ; 69(2): 352-64, 2013 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-23684911

RESUMO

About 2800 mitochondrial genomes of Metazoa are present in NCBI RefSeq today, two thirds belonging to vertebrates. Metazoan phylogeny was recently challenged by large scale EST approaches (phylogenomics), stabilizing classical nodes while simultaneously supporting new sister group hypotheses. The use of mitochondrial data in deep phylogeny analyses was often criticized because of high substitution rates on nucleotides, large differences in amino acid substitution rate between taxa, and biases in nucleotide frequencies. Nevertheless, mitochondrial genome data might still be promising as it allows for a larger taxon sampling, while presenting a smaller amount of sequence information. We present the most comprehensive analysis of bilaterian relationships based on mitochondrial genome data. The analyzed data set comprises more than 650 mitochondrial genomes that have been chosen to represent a profound sample of the phylogenetic as well as sequence diversity. The results are based on high quality amino acid alignments obtained from a complete reannotation of the mitogenomic sequences from NCBI RefSeq database. However, the results failed to give support for many otherwise undisputed high-ranking taxa, like Mollusca, Hexapoda, Arthropoda, and suffer from extreme long branches of Nematoda, Platyhelminthes, and some other taxa. In order to identify the sources of misleading phylogenetic signals, we discuss several problems associated with mitochondrial genome data sets, e.g. the nucleotide and amino acid landscapes and a strong correlation of gene rearrangements with long branches.


Assuntos
Ordem dos Genes , Genoma Mitocondrial , Filogenia , Substituição de Aminoácidos , Aminoácidos/genética , Animais , Teorema de Bayes , Rearranjo Gênico , Funções Verossimilhança , Modelos Genéticos , Nucleotídeos/genética , Alinhamento de Sequência
10.
Mol Phylogenet Evol ; 69(2): 393-403, 2013 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-23598069

RESUMO

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.


Assuntos
Genoma Mitocondrial , Insetos/classificação , Filogenia , Animais , Evolução Molecular , Análise de Sequência de DNA
11.
Genome Biol Evol ; 4(12): 1295-309, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-23175716

RESUMO

The evolution of the diverse insect lineages is one of the most fascinating issues in evolutionary biology. Despite extensive research in this area, the resolution of insect phylogeny especially of interordinal relationships has turned out to be still a great challenge. One of the challenges for insect systematics is the radiation of the polyneopteran lineages with several contradictory and/or unresolved relationships. Here, we provide the first transcriptomic data for three enigmatic polyneopteran orders (Dermaptera, Plecoptera, and Zoraptera) to clarify one of the most debated issues among higher insect systematics. We applied different approaches to generate 3 data sets comprising 78 species and 1,579 clusters of orthologous genes. Using these three matrices, we explored several key mechanistic problems of phylogenetic reconstruction including missing data, matrix selection, gene and taxa number/choice, and the biological function of the genes. Based on the first phylogenomic approach including these three ambiguous polyneopteran orders, we provide here conclusive support for monophyletic Polyneoptera, contesting the hypothesis of Zoraptera + Paraneoptera and Plecoptera + remaining Neoptera. In addition, we employ various approaches to evaluate data quality and highlight problematic nodes within the Insect Tree that still exist despite our phylogenomic approach. We further show how the support for these nodes or alternative hypotheses might depend on the taxon- and/or gene-sampling.


Assuntos
Genoma de Inseto , Insetos/genética , Filogenia , Transcriptoma , Animais , Classificação , Evolução Molecular , Genômica , Insetos/classificação
12.
PLoS One ; 7(6): e34682, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22685537

RESUMO

Among gene families it is the Hox genes and among metazoan animals it is the insects (Hexapoda) that have attracted particular attention for studying the evolution of development. Surprisingly though, no Hox genes have been isolated from 26 out of 35 insect orders yet, and the existing sequences derive mainly from only two orders (61% from Hymenoptera and 22% from Diptera). We have designed insect specific primers and isolated 37 new partial homeobox sequences of Hox cluster genes (lab, pb, Hox3, ftz, Antp, Scr, abd-a, Abd-B, Dfd, and Ubx) from six insect orders, which are crucial to insect phylogenetics. These new gene sequences provide a first step towards comparative Hox gene studies in insects. Furthermore, comparative distance analyses of homeobox sequences reveal a correlation between gene divergence rate and species radiation success with insects showing the highest rate of homeobox sequence evolution.


Assuntos
Evolução Molecular , Genes Homeobox/genética , Insetos/genética , Família Multigênica , Sequência de Aminoácidos , Animais , Clonagem Molecular , Bases de Dados Genéticas , Proteínas de Homeodomínio/classificação , Proteínas de Homeodomínio/genética , Proteínas de Homeodomínio/isolamento & purificação , Insetos/classificação , Dados de Sequência Molecular , Filogenia , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos
13.
Mol Phylogenet Evol ; 61(3): 880-7, 2011 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-21945788

RESUMO

Molecular sequences do not only allow the reconstruction of phylogenetic relationships among species, but also provide information on the approximate divergence times. Whereas the fossil record dates the origin of most multicellular animal phyla during the Cambrian explosion less than 540 million years ago(mya), molecular clock calculations usually suggest much older dates. Here we used a large multiple sequence alignment derived from Expressed Sequence Tags and genomes comprising 129genes (37,476 amino acid positions) and 117 taxa, including 101 arthropods. We obtained consistent divergence time estimates applying relaxed Bayesian clock models with different priors and multiple calibration points. While the influence of substitution rates, missing data, and model priors were negligible, the clock model had significant effect. A log-normal autocorrelated model was selected on basis of cross-validation. We calculated that arthropods emerged ~600 mya. Onychophorans (velvet worms) and euarthropods split ~590 mya, Pancrustacea and Myriochelata ~560 mya, Myriapoda and Chelicerata ~555 mya, and 'Crustacea' and Hexapoda ~510 mya. Endopterygote insects appeared ~390 mya. These dates are considerably younger than most previous molecular clock estimates and in better agreement with the fossil record. Nevertheless, a Precambrian origin of arthropods and other metazoan phyla is still supported. Our results also demonstrate the applicability of large datasets of random nuclear sequences for approximating the timing of multicellular animal evolution.


Assuntos
Artrópodes/genética , Filogenia , Transcriptoma/genética , Animais , Teorema de Bayes , Calibragem , Evolução Molecular , Variação Genética , Modelos Genéticos , Fatores de Tempo
14.
Nucleic Acids Res ; 39(Web Server issue): W511-7, 2011 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-21609950

RESUMO

R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs.


Assuntos
Software , Eletricidade Estática , Calixarenos/química , Internet , Simulação de Dinâmica Molecular , Teoria Quântica , Interface Usuário-Computador
15.
Mol Biol Evol ; 27(11): 2451-64, 2010 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-20534705

RESUMO

Arthropods were the first animals to conquer land and air. They encompass more than three quarters of all described living species. This extraordinary evolutionary success is based on an astoundingly wide array of highly adaptive body organizations. A lack of robustly resolved phylogenetic relationships, however, currently impedes the reliable reconstruction of the underlying evolutionary processes. Here, we show that phylogenomic data can substantially advance our understanding of arthropod evolution and resolve several conflicts among existing hypotheses. We assembled a data set of 233 taxa and 775 genes from which an optimally informative data set of 117 taxa and 129 genes was finally selected using new heuristics and compared with the unreduced data set. We included novel expressed sequence tag (EST) data for 11 species and all published phylogenomic data augmented by recently published EST data on taxonomically important arthropod taxa. This thorough sampling reduces the chance of obtaining spurious results due to stochastic effects of undersampling taxa and genes. Orthology prediction of genes, alignment masking tools, and selection of most informative genes due to a balanced taxa-gene ratio using new heuristics were established. Our optimized data set robustly resolves major arthropod relationships. We received strong support for a sister group relationship of onychophorans and euarthropods and strong support for a close association of tardigrades and cycloneuralia. Within pancrustaceans, our analyses yielded paraphyletic crustaceans and monophyletic hexapods and robustly resolved monophyletic endopterygote insects. However, our analyses also showed for few deep splits that were recently thought to be resolved, for example, the position of myriapods, a remarkable sensitivity to methods of analyses.


Assuntos
Artrópodes/classificação , Artrópodes/genética , Genômica/métodos , Filogenia , Animais , Teorema de Bayes , Etiquetas de Sequências Expressas , Funções Verossimilhança , Especificidade da Espécie
16.
Mol Phylogenet Evol ; 54(2): 651-6, 2010 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-19853053

RESUMO

Pterygota are traditionally divided in two lineages, the "Palaeoptera" and Neoptera. Despite several efforts neither morphology nor molecular systematics have resolved the phylogeny of the pterygote insects. Too few markers have yet been identified for adequately tracking mesozoic-aged divergences. We tested the Elongation factor-1alpha for its phylogenetic value in pterygote insect systematics. This highly conserved nuclear protein-coding gene has previously been reported to be useful in other groups for phylogenetic analyses at the intraordinal level as well as at the interordinal level. The analyses suggest that EF-1alpha DNA sequences as well as intron positions provide informative markers for pterygote phylogenetics.


Assuntos
Insetos/genética , Íntrons , Fator 1 de Elongação de Peptídeos/genética , Filogenia , Animais , Teorema de Bayes , Genes de Insetos , Variação Genética , Insetos/classificação , Funções Verossimilhança , Modelos Genéticos , Alinhamento de Sequência , Análise de Sequência de DNA
17.
Mol Biol Evol ; 26(12): 2719-30, 2009 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-19713325

RESUMO

One of the most fascinating Bauplan transitions in the animal kingdom was the invention of insect wings, a change that also contributed to the success and enormous diversity of this animal group. However, the origin of insect flight and the relationships of basal winged insect orders are still controversial. Three hypotheses have been proposed to explain the phylogeny of winged insects: 1) the traditional Palaeoptera hypothesis (Ephemeroptera + Odonata, Neoptera), 2) the Metapterygota hypothesis (Ephemeroptera, Odonata + Neoptera), and 3) the Chiastomyaria hypothesis (Odonata, Ephemeroptera + Neoptera). Neither phylogenetic analyses of single genes nor even multiple marker systems (e.g., molecular markers + morphological characters) have yet been able to conclusively resolve basal pterygote divergences. A possible explanation for the lack of resolution is that the divergences took place in the mid-Devonian within a short period of time and attempts to solve this problem have been confounded by the major challenge of finding molecular markers to accurately track these short ancient internodes. Although phylogenomic data are available for Neoptera and some wingless (apterygote) orders, they are lacking for the crucial Odonata and Ephemeroptera orders. We adopt a multigene approach including data from two new expressed sequence tag projects-from the orders Ephemeroptera (Baetis sp.) and Odonata (Ischnura elegans)-to evaluate the potential of phylogenomic analyses in clarifying this unresolved issue. We analyzed two data sets that differed in represented taxa, genes, and overall sequence lengths: maxspe (15 taxa, 125 genes, and 31,643 amino acid positions) and maxgen (8 taxa, 150 genes, and 42,541 amino acid positions). Maximum likelihood and Bayesian inference analyses both place the Odonata at the base of the winged insects. Furthermore, statistical hypotheses testing rejected both the Palaeoptera and the Metapterygota hypotheses. The comprehensive molecular data set developed here provides conclusive support for odonates as the most basal winged insect order (Chiastomyaria hypothesis). Data quality assessment indicates that proteins involved in cellular processes and signaling harbor the most informative phylogenetic signal.


Assuntos
Variação Genética , Genômica/métodos , Insetos/anatomia & histologia , Insetos/genética , Filogenia , Asas de Animais/anatomia & histologia , Animais , DNA Concatenado/genética , Etiquetas de Sequências Expressas , Genes de Insetos/genética , Funções Verossimilhança , Modelos Genéticos , Dados de Sequência Molecular , Alinhamento de Sequência
18.
BMC Evol Biol ; 9: 119, 2009 May 27.
Artigo em Inglês | MEDLINE | ID: mdl-19473484

RESUMO

BACKGROUND: Whenever different data sets arrive at conflicting phylogenetic hypotheses, only testable causal explanations of sources of errors in at least one of the data sets allow us to critically choose among the conflicting hypotheses of relationships. The large (28S) and small (18S) subunit rRNAs are among the most popular markers for studies of deep phylogenies. However, some nodes supported by this data are suspected of being artifacts caused by peculiarities of the evolution of these molecules. Arthropod phylogeny is an especially controversial subject dotted with conflicting hypotheses which are dependent on data set and method of reconstruction. We assume that phylogenetic analyses based on these genes can be improved further i) by enlarging the taxon sample and ii) employing more realistic models of sequence evolution incorporating non-stationary substitution processes and iii) considering covariation and pairing of sites in rRNA-genes. RESULTS: We analyzed a large set of arthropod sequences, applied new tools for quality control of data prior to tree reconstruction, and increased the biological realism of substitution models. Although the split-decomposition network indicated a high noise content in the data set, our measures were able to both improve the analyses and give causal explanations for some incongruities mentioned from analyses of rRNA sequences. However, misleading effects did not completely disappear. CONCLUSION: Analyses of data sets that result in ambiguous phylogenetic hypotheses demand for methods, which do not only filter stochastic noise, but likewise allow to differentiate phylogenetic signal from systematic biases. Such methods can only rely on our findings regarding the evolution of the analyzed data. Analyses on independent data sets then are crucial to test the plausibility of the results. Our approach can easily be extended to genomic data, as well, whereby layers of quality assessment are set up applicable to phylogenetic reconstructions in general.


Assuntos
Artrópodes/genética , Evolução Molecular , Modelos Genéticos , Filogenia , Animais , Conformação de Ácido Nucleico , RNA Ribossômico 18S/genética , RNA Ribossômico 28S/genética , Alinhamento de Sequência , Análise de Sequência de RNA/métodos
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA