Phylogenetic Relationships of Basal Hexapods Reconstructed from Nearly Complete 18S and 28S rRNA Gene Sequences

Gao, Yan; Bu, Yun; Luan, Yigang

doi:10.2108/zsj.25.1139

Cited by 36 publications

(41 citation statements)

References 37 publications

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“…In addition to these coleopteran sequences, a sequence similar to the GH45 family has been identified from the Antarctic springtail Cryptopygus antarcticus [12], which belongs to one of the basal hexapodan orders, Collembola [32]. Another sequence similar to the GH45 family was reported from the water bear Hypsibius dujardini (phylum Tardigrada, a sister group of arthropods) [33].…”

Section: Resultsmentioning

confidence: 98%

Molecular Evolution of Glycoside Hydrolase Genes in the Western Corn Rootworm (Diabrotica virgifera virgifera)

et al. 2014

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Cellulose is an important nutritional resource for a number of insect herbivores. Digestion of cellulose and other polysaccharides in plant-based diets requires several types of enzymes including a number of glycoside hydrolase (GH) families. In a previous study, we showed that a single GH45 gene is present in the midgut tissue of the western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae). However, the presence of multiple enzymes was also suggested by the lack of a significant biological response when the expression of the gene was silenced by RNA interference. In order to clarify the repertoire of cellulose-degrading enzymes and related GH family proteins in D. v. virgifera, we performed next-generation sequencing and assembled transcriptomes from the tissue of three different developmental stages (eggs, neonates, and third instar larvae). Results of this study revealed the presence of seventy-eight genes that potentially encode GH enzymes belonging to eight families (GH45, GH48, GH28, GH16, GH31, GH27, GH5, and GH1). The numbers of GH45 and GH28 genes identified in D. v. virgifera are among the largest in insects where these genes have been identified. Three GH family genes (GH45, GH48, and GH28) are found almost exclusively in two coleopteran superfamilies (Chrysomeloidea and Curculionoidea) among insects, indicating the possibility of their acquisitions by horizontal gene transfer rather than simple vertical transmission from ancestral lineages of insects. Acquisition of GH genes by horizontal gene transfers and subsequent lineage-specific GH gene expansion appear to have played important roles for phytophagous beetles in specializing on particular groups of host plants and in the case of D. v. virgifera, its close association with maize.

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Section: Resultsmentioning

confidence: 98%

Molecular Evolution of Glycoside Hydrolase Genes in the Western Corn Rootworm (Diabrotica virgifera virgifera)

et al. 2014

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“…Studies encompassing representatives of Protura, Collembola, and Diplura are limited to only a few analyses (Colgan et al 1998; Carapelli et al 2000; Edgecombe et al 2000; Giribet et al 2001, 2005). Monophyletic Entognatha were recovered in all recent studies based on nuclear rRNA genes (Gao et al 2008; Dell’Ampio et al 2009; von Reumont et al 2009; Mallatt et al 2010). However, BS was low, which was either explained by character choice (Dell’Ampio et al 2009) or the influence of nonstationary processes across taxa (von Reumont et al 2009).…”

Section: Discussionmentioning

confidence: 99%

Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects

Dell'Ampio

Meusemann

Szucsich

et al. 2013

Molecular Biology and Evolution

128

126

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Phylogenetic relationships of the primarily wingless insects are still considered unresolved. Even the most comprehensive phylogenomic studies that addressed this question did not yield congruent results. To get a grip on these problems, we here analyzed the sources of incongruence in these phylogenomic studies by using an extended transcriptome data set. Our analyses showed that unevenly distributed missing data can be severely misleading by inflating node support despite the absence of phylogenetic signal. In consequence, only decisive data sets should be used which exclusively comprise data blocks containing all taxa whose relationships are addressed. Additionally, we used Four-cluster Likelihood Mapping (FcLM) to measure the degree of congruence among genes of a data set, as a measure of support alternative to bootstrap. FcLM showed incongruent signal among genes, which in our case is correlated neither with functional class assignment of these genes nor with model misspecification due to unpartitioned analyses. The herein analyzed data set is the currently largest data set covering primarily wingless insects, but failed to elucidate their interordinal phylogenetic relationships. Although this is unsatisfying from a phylogenetic perspective, we try to show that the analyses of structure and signal within phylogenomic data can protect us from biased phylogenetic inferences due to analytical artifacts.

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“…Finally, primers are well established in 28S rDNA, also for Protura. Despite the overall lack of public proturan sequences, much data is available regarding nuclear 18S rDNA and 28S rDNA [30], [67]–[69]. While 18S rDNA was previously used to resolve higher-level phylogenetic relationships within arthropods [65], [70], fragments of the 28S rDNA achieved more appropriate separation at the genus and species levels in Protura, Collembola and Diplura ([67] D3-D5, [69] D1-D11).…”

Section: Discussionmentioning

confidence: 99%

Where Taxonomy Based on Subtle Morphological Differences Is Perfectly Mirrored by Huge Genetic Distances: DNA Barcoding in Protura (Hexapoda)

et al. 2014

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BackgroundProtura is a group of tiny, primarily wingless hexapods living in soil habitats. Presently about 800 valid species are known. Diagnostic characters are very inconspicuous and difficult to recognize. Therefore taxonomic work constitutes an extraordinary challenge which requires special skills and experience. Aim of the present pilot project was to examine if DNA barcoding can be a useful additional approach for delimiting and determining proturan species.Methodology and Principal FindingsThe study was performed on 103 proturan specimens, collected primarily in Austria, with additional samples from China and Japan. The animals were examined with two markers, the DNA barcoding region of the mitochondrial COI gene and a fragment of the nuclear 28S rDNA (Divergent Domain 2 and 3). Due to the minuteness of Protura a modified non-destructive DNA-extraction method was used which enables subsequent species determination. Both markers separated the examined proturans into highly congruent well supported clusters. Species determination was performed without knowledge of the results of the molecular analyses. The investigated specimens comprise a total of 16 species belonging to 8 genera. Remarkably, morphological determination in all species exactly mirrors molecular clusters. The investigation revealed unusually huge genetic COI distances among the investigated proturans, both maximal intraspecific distances (0–21.3%), as well as maximal congeneric interspecifical distances (up to 44.7%).ConclusionsThe study clearly demonstrates that the tricky morphological taxonomy in Protura has a solid biological background and that accurate species delimitation is possible using both markers, COI and 28S rDNA. The fact that both molecular and morphological analyses can be performed on the same individual will be of great importance for the description of new species and offers a valuable new tool for biological and ecological studies, in which proturans have generally remained undetermined at species level.

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Phylogenetic Relationships of Basal Hexapods Reconstructed from Nearly Complete 18S and 28S rRNA Gene Sequences

Cited by 36 publications

References 37 publications

Molecular Evolution of Glycoside Hydrolase Genes in the Western Corn Rootworm (Diabrotica virgifera virgifera)

Molecular Evolution of Glycoside Hydrolase Genes in the Western Corn Rootworm (Diabrotica virgifera virgifera)

Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects

Where Taxonomy Based on Subtle Morphological Differences Is Perfectly Mirrored by Huge Genetic Distances: DNA Barcoding in Protura (Hexapoda)

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