The First Two Complete Mitochondrial Genomes of Neoephemeridae (Ephemeroptera): Comparative Analysis and Phylogenetic Implication for Furcatergalia

Mayflies of the family Neoephemeridae are widespread in the Holarctic and Oriental regions, and its phylogenetic position is still unstable in the group Furcatergalia (mayflies with fringed gills). In the present study, we determined the complete mitogenomes of two species, namely Potamanthellus edmundsi and Pulchephemera projecta, of this family. The lengths of two mitogenomes were 15,274 bp and 16,031 bp with an A + T content of 73.38% and 73.07%, respectively. Two neoephemerid mitogenomes had a similar gene size, base composition, and codon usage of protein-coding genes (PCGs), and the sequenced gene arrangements were consistent with the putative ancestral insect mitogenomes as understood today. The most variable gene of Furcatergalia mitogenomes was ND2, while the most conserved gene was COI. Meanwhile, the analysis of selection pressures showed that ND6 and ATP8 exhibited a relaxed purifying selection, and COI was under the strongest purifying selection. Phylogenetic trees reconstructed based on two concatenated nucleotide datasets using both maximum likelihood (ML) and Bayesian inference (BI) estimations yielded robust identical topologies. These results corroborated the monophyly of seven studied families and supported the family Leptophlebiidae as being of the basal lineage of Furcatergalia. Additionally, the sister-group relationship of Caenidae and Neoephemeridae was well supported. Methodologically, our present study provides a general reference for future phylogenetic studies of Ephemeroptera at the mitogenome level.

Phylogeography of Maoricicada Cambelli (Hemiptera: Cicadidae): MtDNA Evidence Interpreted Using Phylogenetics and Nested Clade Analysis

<p>New Zealand, because of its wide range of habitats and rapidly changing, well-studied palaeohistory provides an excellent opportunity to investigate the impact of earth processes on the distribution of taxa. There are now a variety of studies on plants that investigate such patterns, and a growing number of studies on animal taxa. Most studies have supported the hypothesis that current patterns of distribution of New Zealand taxa were created by dispersal, mediated by landscape and climatic conditions over time, and have contradicted the panbiogeographic hypothesis that explained distributions via vicariant landscape changes such as lateral displacement along the Alpine Fault. This thesis presents a detailed phylogeographic history of a widespread, endemic New Zealand cicada, Maoricicada campbelli, that is abundant throughout much of the South Island and is also found in the central volcanic plateau of the North Island. Mitochondrial DNA sequences of 223 individuals from 70 populations of M. campbelli were studied using both traditional phylogenetic methods and nested clade analysis (NCA). As found in a previous study of 35 M. campbelli individuals, geographic structuring was strong, with two main clades (North Island+northern South Island versus Otago) representing diverse lineages that may in fact be different species. Population structuring within the northern South Island clade suggested that the central South Island was mostly uninhabitable during glacial periods and demonstrated a sister-group relationship between northern and southern Southern Alps populations to the exclusion of the more central Southern Alps populations. Population histories estimated from NCA support the hypothesis that most M. campbelli populations were formed through dispersal rather than via fragmentation or Alpine Fault vicariance. Three areas of ring-species-like secondary contact were found between the Otago and northern South Island clades, between lineages that had been isolated for approximately 2.3my. Further study is predicted to confirm the presence of additional suspected contact zones, and will demonstrate whether the different lineages are reproductively isolated or hybridising at these areas of secondary contact.</p>

Phylogeography of Maoricicada Cambelli (Hemiptera: Cicadidae): MtDNA Evidence Interpreted Using Phylogenetics and Nested Clade Analysis

<p>New Zealand, because of its wide range of habitats and rapidly changing, well-studied palaeohistory provides an excellent opportunity to investigate the impact of earth processes on the distribution of taxa. There are now a variety of studies on plants that investigate such patterns, and a growing number of studies on animal taxa. Most studies have supported the hypothesis that current patterns of distribution of New Zealand taxa were created by dispersal, mediated by landscape and climatic conditions over time, and have contradicted the panbiogeographic hypothesis that explained distributions via vicariant landscape changes such as lateral displacement along the Alpine Fault. This thesis presents a detailed phylogeographic history of a widespread, endemic New Zealand cicada, Maoricicada campbelli, that is abundant throughout much of the South Island and is also found in the central volcanic plateau of the North Island. Mitochondrial DNA sequences of 223 individuals from 70 populations of M. campbelli were studied using both traditional phylogenetic methods and nested clade analysis (NCA). As found in a previous study of 35 M. campbelli individuals, geographic structuring was strong, with two main clades (North Island+northern South Island versus Otago) representing diverse lineages that may in fact be different species. Population structuring within the northern South Island clade suggested that the central South Island was mostly uninhabitable during glacial periods and demonstrated a sister-group relationship between northern and southern Southern Alps populations to the exclusion of the more central Southern Alps populations. Population histories estimated from NCA support the hypothesis that most M. campbelli populations were formed through dispersal rather than via fragmentation or Alpine Fault vicariance. Three areas of ring-species-like secondary contact were found between the Otago and northern South Island clades, between lineages that had been isolated for approximately 2.3my. Further study is predicted to confirm the presence of additional suspected contact zones, and will demonstrate whether the different lineages are reproductively isolated or hybridising at these areas of secondary contact.</p>

A new species of the southern Central American genus Linoderus Sharp (Coleoptera: Staphylinidae: Staphylininae) with a revised key and an updated phylogeny

Linoderus smetanai sp. nov. is described from Costa Rica. This is the third species in the southern Central American genus Linoderus of the subtribe Philonthina (tribe Staphylinini). The new species was included in a previous dataset of 52 morphological characters scored for the genus and representatives of its allied genera (Neopescolinus Chani-Posse, Paederomimus Sharp, Pescolinus Sharp) and its phylogenetic position analysed by Maximum Parsimony and Bayesian Inference. The analyses unambiguously placed L. smetanai within Linoderus in a sister-group relationship with L. alajuelensis Chani-Posse & Solodovnikov and L. gracilipes Sharp. A revised key to species and an updated phylogeny of Linoderus are also provided.

Proposal of Arktourella gen. nov., a new genus of the family Normanellidae Lang 1944 (Copepoda: Harpacticoida) from the Province of Cortez

A new genus, Arktourella gen. nov., is proposed to accommodate a new member of the harpacticoid family Normanellidae, A. margarethae gen. et sp. nov., from a polluted estuary in north-western Mexico. The new genus was attributed to the laophontoidean family Normanellidae on account of the lack of outer spinous processes on the second antennulary segment, one abexopodal seta on the antennary allobasis, four setae on the one-segmented antennary exopod, endopod of first swimming leg two-segmented with first segment elongated and with two distal elements on second segment, endopods of second to fourth legs two-segmented, distal setae on the male second endopodal segment of second and third legs reduced, and outer spine of the male second endopodal segment of third leg fused to segment. The new, so far monotypic genus, differs from the other normanellid genera in the presence of four elements on the third exopodal segment of the first leg, and two outer spines on the third exopodal segment of second to fourth legs. No synapomorphies were observed for Arktourella gen. nov. and Normanella, but they are unique within the Normanellidae in that the mandibular basis and endopod are not fused. Maximum parsimony analysis and Bayesian inference using 59 morphological characters to assess the relationships between the genera of the family Normanellidae confirmed the affinity of Arktourella gen. nov. and Normanella, and their sister group relationship with Sagamiella. Paranaiara and Pseudocletodes were shown consistently to be closely related and are the sister taxa of Normanella-Arktourella gen. nov.-Sagamiella. Arktourella gen. nov., Paranaiara and Pseudocletodes share the presence of a large spinulose spine on the fifth and sixth segments of the female antennule, but its significance is not clear. Additionally, we propose a key to the genera of the Normanellidae.

Three Complete Mitochondrial Genomes of Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis (Insecta: Phasmatodea) and Their Phylogeny

Insects of the order Phasmatodea are mainly distributed in the tropics and subtropics and are best known for their remarkable camouflage as plants. In this study, we sequenced three complete mitochondrial genomes from three different families: Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis. The lengths of the three mitochondrial genomes were 15,896 bp, 16,869 bp, and 17,005 bp, respectively, and the gene composition and structure of the three stick insects were identical to those of the most recent common ancestor of insects. The phylogenetic relationships among stick insects have been chaotic for a long time. In order to discuss the intra- and inter-ordinal relationship of Phasmatodea, we used the 13 protein-coding genes (PCGs) of 85 species for maximum likelihood (ML) and Bayesian inference (BI) analyses. Results showed that the internal topological structure of Phasmatodea had a few differences in both ML and BI trees and long-branch attraction (LBA) appeared between Embioptera and Zoraptera, which led to a non-monophyletic Phasmatodea. Consequently, after removal of the Embioptera and Zoraptera species, we re-performed ML and BI analyses with the remaining 81 species, which showed identical topology except for the position of Tectarchus ovobessus (Phasmatodea). We recovered the monophyly of Phasmatodea and the sister-group relationship between Phasmatodea and Mantophasmatodea. Our analyses also recovered the monophyly of Heteropterygidae and the paraphyly of Diapheromeridae, Phasmatidae, Lonchodidae, Lonchodinae, and Clitumninae. In this study, Peruphasma schultei (Pseudophasmatidae), Phraortes sp. YW-2014 (Lonchodidae), and species of Diapheromeridae clustered into the clade of Phasmatidae. Within Heteropterygidae, O. guangxiensis was the sister clade to O. mouhotii belonging to Dataminae, and the relationship of (Heteropteryginae + (Dataminae + Obriminae)) was recovered.

Comparative morphology of extant raptorial Mantispoidea (Neuroptera: Mantispidae, Rhachiberothidae) suggests a non-monophyletic Mantispidae and a single origin of the raptorial condition within the superfamily

Adult external morphology of the extant raptorial Mantispoidea (Insecta: Neuroptera: Mantispidae and Rhachiberothidae) is compared emphasizing the morphology of the subfamily Symphrasinae as a key group to understand the phylogenetic relationships among the members of the superfamily. Plega dactylota Rehn, 1939 is thoroughly characterized in order to exemplify the morphology of the Symphrasinae. Additionally, following a review of the literature and examination of comparative material of Dilaridae, Berothidae, Rhachiberothidae and all Mantispidae subfamilies, a new interpretation of the components of the raptorial apparatus (i.e., head, prothorax, grasping forelegs, as well as integumentary specializations) is presented. Also, wing venation for these groups is reinterpreted, and new homology hypotheses for wing venation are proposed based on tracheation and comparative analyses. Given the high morphological divergence on the genital sclerites within the Mantispoidea, plus the confusing previous usage of neutral terminology and terms referring to appendages across taxonomic and morphological studies, we attempt to standardize, simplify, and situate terminology in an evolutionary context under the “gonocoxite concept” (multi-coxopod hypothesis). The remarkable morphological similarity of the genital sclerites of Symphrasinae and Rhachiberothidae (sensu U. Aspöck & Mansell 1994) with the Nallachinae (Dilaridae) was taken as a starting point to understand the morphology of other Mantispidae subfamilies. Based on these morphological comparisons, we provide a revised phylogenetic analysis of Mantispoidea. This new phylogenetic analysis supports a sister group relationship between the family Rhachiberothidae, comprising Rhachiberothinae and Symphrasinae, and the family Mantispidae, including the subfamily Mantispinae and its sister taxa Drepanicinae and Calomantispinae, which may represent a single subfamily. Based on these analyses, raptorial condition probably evolved a single time in these insects and subsequently became diversified in the two sister clades of the raptorial Mantispoidea.

The First Mitogenomes of the Subfamily Odontiinae (Lepidoptera, Crambidae) and Phylogenetic Analysis of Pyraloidea

The complete mitochondrial genomes of three species of Odontiinae were newly sequenced: Dausara latiterminalis Yoshiyasu, Heortia vitessoides (Moore), and Pseudonoorda nigropunctalis (Hampson). These circular and double-stranded mitogenomes vary from 15,084 bp to 15,237 bp in size, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs) and an A + T-rich region. The nucleotide composition indicated a strong A/T bias. Most PCGs are initiated with an ATN codon and terminated by a codon of TAR. All tRNAs could be folded into the clover-leaf structure with the exception of trnS1 (AGN), in which the dihydrouridine (DHU) arm formed a simple loop, and the motif ‘ATAG’ and ‘ATTTA’ in the A + T-rich region was also founded. The phylogenomic analyses covering Odontiinae + 11 subfamilies of Pyraloidea were conducted. Similar topologies were generated from both Bayesian inference (BI) and maximum likelihood (ML) analyses based on the nucleotide and amino acid sequence data. There was some discrepancy in the sister-group relationship of Odontiinae and Glaphyriinae, and the relationships among the subfamilies in the ‘CAMMSS clade’ of the Crambidae. The results of this study suggest that mitogenomic data are useful for resolving the deep-level relationships of Pyraloidea and the topologies generated from amino acid data might be more realistic and reliable. Moreover, more mitogenomic taxon sampling and larger scale analyses with more genes or a combination of mitogenomic and nuclear genes are needed to reconstruct a comprehensive framework of the pyraloid phylogeny.

Paleogenomics illuminates the evolutionary history of the extinct Holocene “horned” crocodile of Madagascar, Voay robustus

Ancient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300–1400 year old specimens (n = 2) of the extinct “horned” crocodile, Voay robustus, collected from Holocene deposits in southwestern Madagascar. Phylogenetic analyses of partial mt genomes and tip-dated timetrees based on molecular, fossil, and stratigraphic data favor a sister group relationship between Voay and Crocodylus (true crocodiles). These well supported trees conflict with recent morphological systematic work that has consistently placed Voay within Osteolaeminae (dwarf crocodiles and kin) and provide evidence for likely homoplasy in crocodylian cranial anatomy and snout shape. The close relationship between Voay and Crocodylus lends additional context for understanding the biogeographic origins of these genera and refines competing hypotheses for the recent extinction of Voay from Madagascar.

Inferring the deep past from molecular data

There is an expectation that analyses of molecular sequences might be able to distinguish between alternative hypotheses for ancient relationships, but the phylogenetic methods used and types of data analyzed are of critical importance in any attempt to recover historical signal. Here we discuss some common issues that can influence the topology of trees obtained when using overly-simple models to analyze molecular data that often display complicated patterns of sequence heterogeneity. To illustrate our discussion, we have used three examples of inferred relationships which have changed radically as models and methods of analysis have improved. In two of these examples, the sister-group relationship between thermophilic Thermus and mesophilic Deinococcus, and the position of long-branch Microsporidia among eukaryotes, we show that recovering what is now generally considered to be the correct tree is critically dependent on the fit between model and data. In the third example, the position of eukaryotes in the tree of life, the hypothesis that is currently supported by the best available methods is fundamentally different from the classical view of relationships between major cellular domains. Since heterogeneity appears to be pervasive and varied among all molecular sequence data, and even the best available models can still struggle to deal with some problems, the issues we discuss are generally relevant to phylogenetic analyses. It remains essential to maintain a critical attitude to all trees as hypotheses of relationship that may change with more data and better methods.