title: Towards a higher-level Ensifera phylogeny inferred from mitogenome sequences.
abstract: Although mitogenomes are useful tools for inferring evolutionary history, only a few representative ones can be used for most Ensifera lineages. Thirty-two ensiferan mitogenomes were determined using ABI Sanger sequencing and standard primer walking of 2-3 overlapping Long-PCR fragments, or Illumina® HiSeq2000 for "shotgun" sequenced long-PCR-amplified mitochondrial or total genomic DNA. Six patterns of gene arrangements, including the novel trnR-trnSAGN-trnA-trnN-trnG-nad3 in Lipotactes tripyrga (Lipotactinae), were identified from 59 ensiferan mitogenomes. The results suggest that trnM-trnI-trnQ and trnA-trnR-trnE-trnSAGN-trnN-trnF rearrangements might be a shared derived character in Pseudophyllinae and Gryllidae, respectively. We found base composition biases in our dataset, which potentially complicate the inference of higher-level ensiferan phylogeny. Site-heterogeneous Bayesian inference (BI) and site-homogeneous maximum likelihood (ML) analyses recovered all ensiferan superfamilies as monophyletic. The site-homogeneous BI analysis failed to recover the monophyly of Stenopelmatoidea. As Schizodactyloidea was only represented by Comicus campestris, its monophyly could not be tested. In the Triassic/Jurassic boundary, Ensifera diverged into grylloid and non-grylloid clades. All analyses confirmed Grylloidea and Gryllotalpoidea as sister groups. Site-heterogeneous BI analysis found Schizodactyloidea as the most basal lineage and sister to the clade formed by Grylloidea and Gryllotalpoidea, but the site-homogeneous analyses placed it basally to the non-grylloid clade and recovered a sister relationship between Tettigonioidea and (Hagloidea, Rhaphidophoroidea, Stenopelmatoidea), although this clade had a low support. The site-heterogeneous BI analysis found Tettigonioidea and Hagloidea were sister groups (posterior probability (PP)=0.99), Stenopelmatoidea was sister to (Tettigonioidea, Hagloidea) (PP>0.91), and Rhaphidophoroidea was basal to the non-grylloid clade. At a lower level, all analyses divided Tettigonioidea into Phaneropteridae and Tettigoniidae.
authors.affiliation: Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China. Electronic address: zhijunzhou@163.com.
authors.forename: Zhijun
authors.initials: Z
authors.lastname: Zhou
authors.affiliation: College of Life Sciences and Biotechnology, Mianyang Normal University, Mianyang, Sichuan 621000, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Zhao
authors.affiliation: College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710062, China.
authors.forename: Nian
authors.initials: N
authors.lastname: Liu
authors.affiliation: Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China.
authors.forename: Huifang
authors.initials: H
authors.lastname: Guo
authors.affiliation: Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China.
authors.forename: Bei
authors.initials: B
authors.lastname: Guan
authors.affiliation: Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China.
authors.forename: Juanxia
authors.initials: J
authors.lastname: Di
authors.affiliation: Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China. Electronic address: shif_m@126.com.
authors.forename: Fuming
authors.initials: F
authors.lastname: Shi
mesh_terms: D000818:Animals; D001482:Base Composition / Q000235:genetics; D001483:Base Sequence; D001499:Bayes Theorem; D023061:Gene Order; D014644:Genetic Variation; D054629:Genome, Mitochondrial; D016013:Likelihood Functions; D009987:Orthoptera / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D013997:Time Factors
keywords: Ensifera; Gene rearrangement; Mitogenome; Next generation sequencing; Phylogeny