The Experts below are selected from a list of 5919 Experts worldwide ranked by ideXlab platform
Yunxia Luan - One of the best experts on this subject based on the ideXlab platform.
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microrna evolution provides new evidence for a close relationship of diplura to insecta
Systematic Entomology, 2020Co-Authors: Yunxia Luan, Wan-jun Chen, Aimin Liu, Chengwang Huang, Changyuan Qian, Yan Liang, Shuai ZhanAbstract:The phylogenetic interrelationships among four Hexapod lineages (Protura, Collembola, Diplura and Insecta) are pivotal to understanding the origin of insects and the early diversification of Hexapoda, but they have been difficult to clarify based on the available data. In this study, we identified 91 conserved microRNA (miRNA) families from 36 panarthropod taxa, including seven newly sequenced non‐insect Hexapods. We found major clade differentiation accompanied by the origin of novel miRNA families, and most miRNA clusters are conserved with a high degree of microsynteny. Importantly, we were able to identify two miRNA families unique to Hexapoda, and four miRNA families and a miRNA cluster that exist exclusively in Diplura and Insecta, suggesting a close relationship between Diplura and Insecta as well as the monophyly of Hexapoda. Combined with a phylogenetic analysis based on the presence/absence matrix of miRNA families, our study demonstrates the effectiveness of miRNA in resolving deep phylogenetic problems.
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Evolutionary implications of dipluran hexamerins.
Insect biochemistry and molecular biology, 2014Co-Authors: Wei Xie, Yunxia LuanAbstract:Hexamerin, as a member of the highly conserved arthropod hemocyanin superfamily, has been shown to be a good marker for the phylogenetic study of insects. However, few studies have been conducted on hexamerins in basal Hexapods. The first Diplura hexamerin CspHex1 was reported only recently (Pick and Burmester, 2009). Remarkably, CspHex1 was suggested to have evolved from Hexapod hemocyanin subunit type 2, which is very different from all insect hexamerins originated from Hexapod hemocyanin subunit type 1. Does this finding suggest double or even multiple origins of hexamerins in Hexapoda? To find more evidence on the evolution of dipluran hexamerins, eight putative hexamerin gene sequences were obtained from three dipluran species, as were three hemocyanin genes from two collembolan species. Unexpectedly, after adding the new sequences into the phylogenetic analyses, all dipluran hexamerins including CspHex1 grouped together and as sister to the insect hexamerins, with high likelihood and Bayesian support. Our analysis supports a single origin of the hexamerins in Hexapoda, and suggests the close relationship between Diplura and Insecta. In addition, our study indicates that a relatively comprehensive taxa sampling is essential to solve some problems in phylogenetic reconstruction.
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ribosomal dna gene and phylogenetic relationships of diplura and lower Hexapods
Science China-life Sciences, 2003Co-Authors: Yunxia Luan, Yaping Zhang, Rongdong Xie, Qiaoyun Yue, Junfeng Pang, Wen-ying YinAbstract:The monophyly of Diplura and its phylogenetic relationship with other Hexapods are important for understanding the phylogeny of Hexapoda. The complete 18SrRNAgene and partial 28SrRNA gene (D3-D5 region) from 2 dipluran species (Campodeidae and Japygidae), 2 proturan species, 3 collembolan species, and 1 locust species were sequenced. Combining related sequences in GenBank, phylogenetic trees of Hexapoda were constructed by MP method using a crustaceanArtemia salina as an outgroup. The results indicated that: (i) the integrated data of 18SrDNA and 28SrDNA could provide better phylogenetic information, which well supported the monophyly of Diplura; (ii) Diplura had a close phylogenetic relationship to Protura with high bootstrap support.
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.
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A review of molecular data for the phylogeny of basal Hexapods
Pedobiologia, 2006Co-Authors: Antonio Carapelli, Francesco Nardi, Romano Dallai, Francesco FratiAbstract:Summary Molecular data have been increasingly used to study the phylogenetic relationships among many animal taxa, including arthropods. Sometimes they have provided phylogenetic reconstructions that are in conflict with morphological data leading to a re-evaluation of long-standing evolutionary hypotheses. In this paper, we review the major contributions to the phylogeny of Hexapods based on molecular data, with emphasis on the relationships of basal Hexapod taxa. The placement and the monophyly of the five basal Hexapod lineages (the “apterygotes”: Protura, Collembola, Diplura, Microcoryphia and Zygentoma) are one of the hottest issues in arthropod phylogeny. We discuss methods of data collection and analysis, and we describe the areas of conflict and agreement between molecular phylogenies and the evidence provided by morphological characters.
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.
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.
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A review of molecular data for the phylogeny of basal Hexapods
Pedobiologia, 2006Co-Authors: Antonio Carapelli, Francesco Nardi, Romano Dallai, Francesco FratiAbstract:Summary Molecular data have been increasingly used to study the phylogenetic relationships among many animal taxa, including arthropods. Sometimes they have provided phylogenetic reconstructions that are in conflict with morphological data leading to a re-evaluation of long-standing evolutionary hypotheses. In this paper, we review the major contributions to the phylogeny of Hexapods based on molecular data, with emphasis on the relationships of basal Hexapod taxa. The placement and the monophyly of the five basal Hexapod lineages (the “apterygotes”: Protura, Collembola, Diplura, Microcoryphia and Zygentoma) are one of the hottest issues in arthropod phylogeny. We discuss methods of data collection and analysis, and we describe the areas of conflict and agreement between molecular phylogenies and the evidence provided by morphological characters.
Takashi Miyata - One of the best experts on this subject based on the ideXlab platform.
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molecular phylogenetic analyses support the monophyly of Hexapoda and suggest the paraphyly of entognatha
BMC Evolutionary Biology, 2013Co-Authors: Go Sasaki, Ryuichiro Machida, Keisuke Ishiwata, Takashi MiyataAbstract:Molecular phylogenetic analyses have revealed that Hexapoda and Crustacea form a common clade (the Pancrustacea), which is now widely accepted among zoologists; however, the origin of Hexapoda remains unresolved. The main problems are the unclear relationships among the basal Hexapod lineages, Protura (proturans), Collembola (springtails), Diplura (diplurans), and Ectognatha (bristletails, silverfishes, and all winged insects). Mitogenomic analyses have challenged Hexapod monophyly and suggested the reciprocal paraphyly of Hexapoda and Crustacea, whereas studies based on nuclear molecular data support the monophyletic origin of Hexapods. Additionally, there are significant discrepancies with respect to these issues between the results of morphological and molecular studies. To investigate these problems, we performed phylogenetic analyses of Pancrustacea based on the protein sequences of three orthologous nuclear genes encoding the catalytic subunit of DNA polymerase delta and the largest and second largest subunits of RNA polymerase II from 64 species of arthropods, including representatives of all Hexapod orders. Phylogenetic analyses were conducted based on the inferred amino acid (aa) sequences (~3400 aa in total) of the three genes using the maximum likelihood (ML) method and Bayesian inference. Analyses were also performed with additional datasets generated by excluding long-branch taxa or by using different outgroups. These analyses all yielded essentially the same results. All Hexapods were clustered into a common clade, with Branchiopoda as its sister lineage, whereas Crustacea was paraphyletic. Within Hexapoda, the lineages Ectognatha, Palaeoptera, Neoptera, Polyneoptera, and Holometabola were each confirmed to be monophyletic with robust support, but monophyly was not supported for Entognatha (Protura + Collembola + Diplura), Ellipura (Protura + Collembola), or Nonoculata (Protura + Diplura). Instead, our results showed that Protura is the sister lineage to all other Hexapods and that Diplura or Diplura + Collembola is closely related to Ectognatha. This is the first study to include all Hexapod orders in a phylogenetic analysis using multiple nuclear protein-coding genes to investigate the phylogeny of Hexapoda, with an emphasis on Entognatha. The results strongly support the monophyletic origin of Hexapods but reject the monophyly of Entognatha, Ellipura, and Nonoculata. Our results provided the first molecular evidence in support of Protura as the sister group to other Hexapods. These findings are expected to provide additional insights into the origin of Hexapods and the processes involved in the adaptation of insects to life on land.
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Molecular phylogenetic analyses support the monophyly of Hexapoda and suggest the paraphyly of Entognatha
BMC Evolutionary Biology, 2013Co-Authors: Go Sasaki, Ryuichiro Machida, Keisuke Ishiwata, Takashi Miyata, Zhi-hui SuAbstract:Background: Molecular phylogenetic analyses have revealed that Hexapoda and Crustacea form a common clade (the Pancrustacea), which is now widely accepted among zoologists; however, the origin of Hexapoda remains unresolved. The main problems are the unclear relationships among the basal Hexapod lineages, Protura (proturans), Collembola (springtails), Diplura (diplurans), and Ectognatha (bristletails, silverfishes, and all winged insects). Mitogenomic analyses have challenged Hexapod monophyly and suggested the reciprocal paraphyly of Hexapoda and Crustacea, whereas studies based on nuclear molecular data support the monophyletic origin of Hexapods. Additionally, there are significant discrepancies with respect to these issues between the results of morphological and molecular studies. To investigate these problems, we performed phylogenetic analyses of Pancrustacea based on the protein sequences of three orthologous nuclear genes encoding the catalytic subunit of DNA polymerase delta and the largest and second largest subunits of RNA polymerase II from 64 species of arthropods, including representatives of all Hexapod orders. Results: Phylogenetic analyses were conducted based on the inferred amino acid (aa) sequences (~3400 aa in total) of the three genes using the maximum likelihood (ML) method and Bayesian inference. Analyses were also performed with additional datasets generated by excluding long-branch taxa or by using different outgroups. These analyses all yielded essentially the same results. All Hexapods were clustered into a common clade, with Branchiopoda as its sister lineage, whereas Crustacea was paraphyletic. Within Hexapoda, the lineages Ectognatha, Palaeoptera, Neoptera, Polyneoptera, and Holometabola were each confirmed to be monophyletic with robust support, but monophyly was not supported for Entognatha (Protura+Collembola+Diplura), Ellipura (Protura+Collembola), or Nonoculata (Protura+ Diplura). Instead, our results showed that Protura is the sister lineage to all other Hexapods and that Diplura or Diplura+ Collembola is closely related to Ectognatha. Conclusion: This is the first study to include all Hexapod orders in a phylogenetic analysis using multiple nuclear protein-coding genes to investigate the phylogeny of Hexapoda, with an emphasis on Entognatha. The results strongly support the monophyletic origin of Hexapods but reject the monophyly of Entognatha, Ellipura, and Nonoculata. Our results provided the first molecular evidence in support of Protura as the sister group to other Hexapods. These findings are expected to provide additional insights into the origin of Hexapods and the processes involved in the adaptation of insects to life on land.