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SUMMARY Termites are highly eusocial insects with a caste polyphenism (i.e., discontinuous morphological differences between castes) and elaborated behaviors. While the developmental pathways leading to caste occurrence are well-known in many species, the evolutionary origin of these pathways is still obscure. Recent molecular phylogenetic studies suggest multiple independent origins of sterile castes in termites, reviving a 30 years old debate. We demonstrate here that diploid sterile castes ('true' workers) evolved several times independently in this group and that this caste was lost at least once in a lineage with developmentally more flexible workers called pseudergates or 'false' workers. We also infer that flexibility in post-embryonic development was acquired multiple times independently during termite evolution. We suggest that focusing on detailed developmental pathways in phylogenetic analyses is essential for elucidating the origin of caste polyphenism in termites. [ABSTRACT FROM AUTHOR]

A comprehensive taxonomic sampling of Mantodea (praying mantises), covering virtually all higher-level groups, was assembled to reconstruct the phylogeny of the order. Sequence data were generated from five mitochondrial and four nuclear loci (12S rRNA, 16S rRNA, 18S rRNA, 28S rRNA, Histone III, Cytochrome Oxidase I & II, NADH dehydrogenase subunit 4, and Wingless) for 329 mantis exemplars along with seven cockroach and eight termite species. Only seven of 14 families, 14 of 33 subfamilies, and seven of 14 tribes were recovered as monophyletic, indicating that phylogeny is largely incongruent with classification. Mapping biogeographical regions on the phylogeny demonstrated that our results adhere closer to biogeographical distributions than to classification. Specific patterns in distribution suggest that major morphological convergences have confounded taxonomists’ ability to reconstruct natural groups. A major revision of higher-level relationships is in order through a comprehensive investigation of morphology and molecular data. We found that major mantis lineages diverged prior to and during the isolation of geographical regions and subsequent ecomorphic specializations within these regions may have led to convergences in morphology. Divergence time estimation places the origin of Mantodea at the beginning of the Jurassic with most modern mantises originating on Gondwana in the Cretaceous. The first major divergence among modern mantises occurred as a result of the north–south splitting of South America and Africa. Subsequent divergences resulted from the breakup of Gondwana. The position of the Indian subcontinent appears to be central to the diversification of Afrotropical and Indomalayan mantises while Antarctica may have served as the conduit for the mantis invasions into South America and Australasia. When India separated from Antarctica and drifted north it distributed mantis lineages back into the Afrotropics and carried a diverse taxonomic assemblage to Asia. [ABSTRACT FROM AUTHOR]

Siphonaptera (fleas) is a highly specialized order of holometabolous insects comprising ∼2500 species placed in 16 families. Despite a long history of extensive work on flea classification and biology, phylogenetic relationships among fleas are virtually unknown. We present the first formal analysis of flea relationships based on a molecular matrix of four loci (18S ribosomal DNA, 28S ribosomal DNA, Cytochrome Oxidase II, and Elongation Factor 1-alpha) for 128 flea taxa from around the world representing 16 families, 25 subfamilies, 26 tribes, and 83 flea genera with eight outgroups. Trees were reconstructed using direct optimization and maximum likelihood techniques. Our analysis supports Tungidae as the most basal flea lineage, sister group to the remainder of the extant fleas. Pygiopsyllomorpha is monophyletic, as are the constituent families Lycopsyllidae, Pygiopsyllidae, and Stivaliidae, with a sister group relationship between the latter two families. Macropsyllidae is resolved as sister group to Coptopsyllidae with moderate nodal support. Stephanociricidae is monophyletic, as are the two constituent subfamilies Stephanocircinae and Craneopsyllinae. Vermipsyllidae is placed as sister group to Jordanopsylla. Rhopalopsyllidae is monophyletic as are the two constituent subfamilies Rhopalopsyllinae and Parapsyllinae. Hystrichopsyllidae is paraphyletic with Hystrichopsyllini placed as sister to some species of Anomiopsyllini and Ctenopariini placed as sister to Carterettini. Ctenophthalmidae is grossly paraphyletic with the family broken into seven lineages dispersed on the tree. Most notably, Anomiopsyllini is paraphyletic. Pulicidae and Chimaeropsyllidae are both monophyletic and these families are sister groups. Ceratophyllomorpha is monophyletic and includes Ischnopsyllidae, Ceratophyllidae, and Leptopsyllidae. Leptopsyllidae is paraphyletic as are its constituent subfamilies Amphipsyllinae and Leptopsyllinae and the tribes Amphipsyllini and Leptopsyllini. Ischnopsyllidae is monophyletic. Ceratophyllidae is monophyletic, with a monophyletic Dactypsyllinae nested within Ceratophyllinae, rendering the latter group paraphyletic. Mapping of general host associations on our topology reveals an early association with mammals with four independent shifts to birds. © The Willi Hennig Society 2008. [ABSTRACT FROM AUTHOR]

Abstract: A phylogenetic hypothesis of termite relationships was inferred from DNA sequence data. Seven gene fragments (12S rDNA, 16S rDNA, 18S rDNA, 28S rDNA, cytochrome oxidase I, cytochrome oxidase II and cytochrome b) were sequenced for 40 termite exemplars, representing all termite families and 14 outgroups. Termites were found to be monophyletic with Mastotermes darwiniensis (Mastotermitidae) as sister group to the remainder of the termites. In this remainder, the family Kalotermitidae was sister group to other families. The families Kalotermitidae, Hodotermitidae and Termitidae were retrieved as monophyletic whereas the Termopsidae and Rhinotermitidae appeared paraphyletic. All of these results were very stable and supported with high bootstrap and Bremer values. The evolution of worker caste and foraging behavior were discussed according to the phylogenetic hypothesis. Our analyses suggested that both true workers and pseudergates (“false workers”) were the result of at least two different origins. Our data support a traditional hypothesis of foraging behavior, in which the evolutionary transition from a one-piece type to a separate life type occurred through an intermediate behavioral form. [Copyright &y& Elsevier]

Abstract: The entire mitochondrial genome of the tobacco hornworm, Manduca sexta (Lepidoptera: Spinghidae) was sequenced — a circular molecular 15516 bp in size. The arrangement of the protein coding genes (PCGs) was the same as that found in the ancestral insect, however Manduca possessed the derived tRNA arrangement of CR-M-I-Q which has been found in all Lepidoptera sequenced to date. Additionally, Manduca, like all lepidopteran mt genomes, has numerous large intergenic spacer regions and microsatellite-like repeat regions. Nucleotide composition is highly A+T biased, and the lepidopterans have the second most biased nucleotide composition of the insect orders after Hymenoptera. Secondary structural features of the PCGs identified in other Lepidoptera were present but highly modified by the presence of microsatellite-like repeat regions which may significantly alter their function in the post-transcriptional modification of pre-mRNAs. Secondary structure models of the ribosomal RNA genes of Manduca are presented and are similar to those proposed for other insect orders. Conserved regions were identified within non-translated spacer regions which correspond to sites for the origin and termination of replication and transcription. Comparisons of gene variability across the order suggest that the mitochondrial genes most frequently used in phylogenetic analysis of the Lepidoptera, cox1 and cox2, are amongst the least variable genes in the genome and phylogenetic resolution could be improved by using alternative, higher variability genes such as nad2, nad3, nad4 and nad5. [Copyright &y& Elsevier]

Abstract: Phylogenetic relationships within the diverse beetle superfamily Cucujoidea are poorly known. The Cerylonid Series (C.S.) is the largest of all proposed superfamilial cucujoid groups, comprising eight families and representing most of the known cucujoid species diversity. The monophyly of the C.S., however, has never been formally tested and the higher-level relationships among and within the constituent families remain equivocal. Here we present a phylogenetic study based on 18S and 28S rDNA for 16 outgroup taxa and 61 C.S. ingroup taxa, representing seven of the eight C.S. families and 20 of 39 subfamilies. We test the monophyly of the C.S., investigate the relationships among the C.S. families, and test the monophyly of the constituent families and subfamilies. Phylogenetic reconstruction of the combined data was achieved via standard static alignment parsimony analyses, Direct Optimization using parsimony, and partitioned Bayesian analysis. All three analyses support the paraphyly of Cucujoidea with respect to Tenebrionoidea and confirm the monophyly of the C.S. The C.S. families Bothrideridae, Cerylonidae, Discolomatidae, Coccinellidae and Corylophidae are supported as monophyletic in all analyses. Only the Bayesian analysis recovers a monophyletic Latridiidae. Endomychidae is recovered as polyphyletic in all analyses. Of the 14 subfamilies with multiple terminals in this study, 11 were supported as monophyletic. The corylophid subfamily Corylophinae and the coccinellid subfamilies Chilocorinae and Scymninae are recovered as paraphyletic. A sister grouping of Anamorphinae+Corylophidae is supported in all analyses. Other taxonomic implications are discussed in light of our results. [Copyright &y& Elsevier]

Termites of the genus Reticulitermes are some of the most significant pests of structural timber and tree farming in the northern hemisphere, causing losses in the billions of dollars annually because of direct damage and termite control costs. This group has been frequently targeted for population genetic, phylogenetic, and species limit studies, most of which use mitochondrial (mt) genes; however, only a small fraction of the genome has been sequenced. The entire mt genome was sequenced for the eastern North American members of Reticulitermes: R. flavipes, R. santonensis, R. virginicus, and R. hageni. The mt genome has the same gene content and organization as that found in most insect species; however, the nucleotide composition and skew are highly biased (AT% low, strong A- and C-skew). Both the protein-coding and transfer RNA genes show high absolute levels of nucleotide substitution, suggesting that the high rates of mutation within Reticulitermes inferred from analyses of single mt genes are a general characteristic of the entire mt genome. The AT-rich or control region has a remarkable structure not previously observed in insect mt genomes. The majority of the control region is made up of 2 sets of repeat units, typically with 2 full and 1 partial copies of both the A (or small; 186 bp) and B (or large; 552 bp) repeats. The partial repeat units overlap by 36 bp. The size, location, and degree of overlap for the partial repeat units correspond to highly conserved stem/loop structures within the repeat units, suggesting that these structures are involved in the replication-mediated processes that govern repeat-unit evolution within mt genomes. Finally, molecular variation within the mt gene regions was compared with previous regions used in molecular diagnostics or phylogenetics of Reticulitermes. High numbers of single nucleotide polymorphisms were found in each of the mt genes, and some of the highest variability was found in gene regions that have not previously been investigated in this group. The whole mt genome sequence can thus be used to predict useful regions for future investigation. [ABSTRACT FROM AUTHOR]

Abstract: Ice crawlers (Insecta: Grylloblattodea) are rarely encountered insects that consist of five genera representing 26 species from North America and Asia. Asian grylloblattids are the most diverse, but North American ice crawlers (genus Grylloblatta) are known for their adaptation to cold conditions. Phylogenetic relationships among grylloblattid species and genera are not known. Six genes were sampled in 35 individuals for 18S rRNA, 28S rRNA, histone 3, 12S rRNA, 16S rRNA, and cytochrome oxidase II from 21 populations of Grylloblatta, three populations from Japan (genus Galloisiana), and three populations from Russia (genus Grylloblattina). Phylogenetic analysis of these data with two mantophasmid outgroups in POY supported monophyletic genera, with Grylloblatta as sister to Grylloblattina. Grylloblatta was shown to contain two major lineages: a clade in Northern California and Oregon and a clade in Washington and Oregon. One new species and six candidate species are proposed. IUCN Red List Conservation Criteria were implemented to designate conservation status for each lineage. [Copyright &y& Elsevier]

Abstract: This study represents the first molecular phylogeny for the Order Ephemeroptera. The analyses included 31 of the 37 families, representing ∼24% of the genera. Fifteen families were supported as being monophyletic, five families were supported as nonmonophyletic, and 11 families were only represented by one species, and monophyly was not testable. The suborders Furcatergalia and Carapacea were supported as monophyletic while Setisura and Pisciforma were not supported as monophyletic. The superfamilies Ephemerelloidea and Caenoidea were supported as monophyletic while Baetoidea, Siphlonuroidea, Ephemeroidea, and Heptagenioidea were not. Baetidae was recovered as sister to the remaining clades. The mayfly gill to wing origin hypothesis was not supported nor refuted by these data. Mandibular tusks were supported as having at least one loss in Behningiidae and, together with the burrowing lifestyle, possibly two origins. The fishlike body form was supported as plesiomorphic for mayflies with multiple secondary losses. Topological sensitivity analysis was used as a tool to examine patterns concerning the stability of relationships across a parameter landscape, providing additional information that may not have been acquired otherwise. [Copyright &y& Elsevier]

The wealth of data available for phylogenetic analysis of the insect orders, from both morphological and molecular sources, is steadily increasing. However, controversy exists among the methodologies one can use to reconstruct ordinal relationships. Recently, ) presented an analysis of insect ordinal relationships based exclusively on a single source of information: 18S rDNA sequence data. Kjer claims that his analysis resulted in a more “credible” phylogeny for the insect orders and strongly criticized our previous phylogenetic results. However, Kjer only used a subset of the data that are currently available for insect ordinal phylogeny, misrepresented our analyses, and omitted other analyses we have published on insect ordinal phylogeny. In our estimation, Kjer did a poor job of representing the current state of affairs in insect ordinal phylogenetics. Furthermore, we examine a number of analytical issues that are relevant not only for insect phylogeny, but systematics as a science, such as: repeatability and objectivity, locating alignment boundaries, secondary structure, goodness of fit measure, epistemological coherence, practicality and homology. © The Willi Hennig Society 2005. [ABSTRACT FROM AUTHOR]

Sensitivity analyses can be performed with respect to different methodologies, differential analytical parameters or models within a single methodology, or alignment parameters. The latter investigations are particularly relevant when divergence and/or the size of molecular data sets make alignment of sequences difficult. Sensitivity analyses are often performed for analyses incorporating Direct Optimization (via POY), either to select optimal alignment parameters or to investigate the stability of topology across parameter sets. Such investigations are rarely, if ever, performed for Clustal alignments as some manual adjustments are nearly always incorporated in the final alignment. Exploration of the performance of both POY and Clustal for a large insect data set incorporating three genes (18S, 28S, H3) and morphology reveals that the performance of POY, as measured by and ILD metric, is predictable across the landscape topology with minimal incongruence when all parameters are treated equally. In contrast, Clustal alignment followed by parsimony analysis yields a landscape with less overall variance, but less predictable behaviour across the parameter topology. © The Willi Hennig Society 2005. [ABSTRACT FROM AUTHOR]

Polyneoptera is a name sometimes applied to an assemblage of 11 insect orders comprising the lower neopterous or “orthopteroid” insects. These orders include familiar insects such as Orthoptera (grasshoppers), Blattodea (roaches), Isoptera (termites) (Mantodea) praying mantises, Dermaptera (earwigs), Phasmatodea (stick insects), Plecoptera (stoneflies), as well as the more obscure, Embiidina (web-spinners), Zoraptera (angel insects) and Grylloblattodea (ice-crawlers). Many of these insect orders exhibit a high degree of morphological specialization, a condition that has led to multiple phylogenetic hypotheses and little consensus among investigators. We present a phylogenetic analysis of the polyneopteran orders representing a broad range of their phylogenetic diversity and including the recently described Mantophasmatodea. These analyses are based on complete 18S rDNA, 28S rDNA, Histone 3 DNA sequences, and a previously published morphology matrix coded at the ordinal level. Extensive analyses utilizing different alignment methodologies and parameter values across a majority of possible ranges were employed to test for sensitivity of the results to ribosomal alignment and to explore patterns across the theoretical alignment landscape. Multiple methodologies support the paraphyly of Polyneoptera, the monophyly of Dictyoptera, Orthopteroidea ( sensu Kukalova-Peck; i.e. Orthoptera + Phasmatodea + Embiidina), and a group composed of Plecoptera + Dermaptera + Zoraptera. Sister taxon relationships between Embiidina + Phasmatodea in a group called “Eukinolabia”, and Dermaptera + Zoraptera (“Haplocercata”) are also supported by multiple analyses. This analysis also supports a sister taxon relationship between the newly described Mantophasmatodea, which are endemic to arid portions of southern Africa, and Grylloblattodea, a small order of cryophilic insects confined to the north-western Americas and north-eastern Asia, in a group termed “Xenonomia”. This placement, coupled with the morphological disparity of the two groups, validates the ordinal status of Mantophasmatodea. © The Willi Hennig Society 2005. [ABSTRACT FROM AUTHOR]

The previously unknown phylogenetic relationships among Mantodea (praying mantids) were inferred from DNA sequence data. Five genes (16S rDNA, 18S rDNA, 28S rDNA, cytochrome oxidase II and histone 3) were sequenced for sixty-three taxa representing major mantid lineages and outgroups. The monophyly of mantid families and subfamilies was tested under varying parameter settings using parsimony and Bayesian analyses. The analyses revealed the paraphyly of Hymenopodidae, Iridopterygidae, Mantidae, and Thespidae and the monophyly of the Amorphoscelidae subfamily Paraoxypilinae. All represented subfamilies of Iridopterygidae and Mantidae appear paraphyletic. Mantoididae is sister group to the rest of the sampled mantid taxa. Lineages congruent with current subfamilial taxonomy include Paraoxypilinae, Hoplocoryphinae, Hymenopodinae, Acromantinae and Oligonicinae. The mantid hunting strategy is defined as either generalist, cursorial or ambush predators. By mapping hunting strategy onto our phylogeny, we reconstructed the ancestral predatory condition as generalist hunting, with three independent shifts to cursorial hunting and one shift to ambush hunting, associated with the largest radiation of mantid species. [ABSTRACT FROM AUTHOR]

While the monophyly of winged insects (Pterygota) is well supported, phylogenetic relationships among the most basal extant pterygote lineages are problematic. Ephemeroptera (mayflies) and Odonata (dragonflies) represent the two most basal extant lineages of winged insects, and determining their relationship with regard to Neoptera (remaining winged insects) is a critical step toward understanding insect diversification. A recent molecular analysis concluded that Paleoptera (Odonata + Ephemeroptera) is monophyletic. However, we demonstrate that this result is supported only under a narrow range of alignment parameters. We have further tested the monophyly of Paleoptera using additional sequence data from 18SrDNA, 28S rDNA, and Histone 3 for a broader selection of taxa and a wider range of analytical methodologies. Our results suggest that the current suite of molecular data ambiguously resolve the three basal winged insect lineages and do not provide independent confirmation of Odonata + Neoptera as supported via morphological data. [Copyright &y& Elsevier]

The evolution of wings was the central adaptation allowing insects to escape predators, exploit scattered resources, and disperse into new niches, resulting in radiations into vast numbers of species[SUP1]. Despite the presumed evolutionary advantages associated with full-sized wings (macroptery), nearly all pterygote (winged) orders have many partially winged (brachypterous) or wingless (apterous) lineages, and some entire orders are secondarily wingless (for example, fleas, lice, grylloblattids and mantophasmatids), with about 5% of extant pterygote species being flightless[SUP2,3]. Thousands of independent transitions from a winged form to winglessness have occurred during the course of insect evolution; however, an evolutionary reversal from a flight-less to a volant form has never been demonstrated clearly for any pterygote lineage. Such a reversal is considered highly unlikely because complex interactions between nerves, muscles, sclerites and wing foils are required to accommodate flight[SUP4]. Here we show that stick insects (order Phasmatodea) diversified as wingless insects and that wings were derived secondarily, perhaps on many occasions. These results suggest that wing developmental pathways are conserved in wingless phasmids, and that `re-evolution' of wings has had an unrecognized role in insect diversification. [ABSTRACT FROM AUTHOR]

Phylogenetic relationships among the holometabolous insect orders were reconstructed using 18S ribosomal DNA data drawn from a sample of 182 taxa representing all holometabolous insect orders and multiple outgroups. Parsimony analysis supports the monophyly of all holometabolous insect orders except for Coleoptera and Mecoptera. Mecoptera is paraphyletic with respect to Siphonaptera, which is nested within Mecoptera. Coleoptera is scattered as a paraphyletic assemblage across the tree topology. These data support a monophyletic Halteria (Strepsiptera + Diptera), Amphiesmenoptera (Trichoptera + Lepidoptera), Neuropterida (Neuroptera + (Megaloptera + Raphidioptera)), but Antliophora (Halteria + Mecoptera + Siphonaptera) and Mecopterida (Antliophora + Amphiesmenoptera) are paraphyletic. The limitations of using 18S ribosomal DNA as the sole phylogenetic marker for reconstructing insect ordinal relationships are discussed. [ABSTRACT FROM AUTHOR]

Phylogenetic relationships among members of the Mecoptera and Siphonaptera were inferred from DNA sequence data. Four loci (18S and 28S ribosomal DNA, cytochrome oxidase II and elongation factor-1α) were sequenced for 69 taxa selected to represent major flea and mecopteran lineages. Phylogenetic analyses of these data support a paraphyletic Mecoptera with two major lineages: Nannochoristidae + (Siphonaptera + Boreidae) and Meropidae + ((Choristidae + Apteropanorpidae) (Panorpidae + (Panorpidae + Bittacidae))). The flea family Ctenophthalmidae is paraphyletic, and the Ceratophylloidea is monophyletic. Morphological evidence is discussed which is congruent with the placement of Siphonaptera as sister group to Boreidae. [ABSTRACT FROM AUTHOR]

Whereas most traditional classifications identify Ischnocera as a major suborder of lice in the order Phthiraptera, a recent molecular study based on one gene did not recover monophyly of Ischnocera. In this study we test the monophyly of Ischnocera using sequences of portions of three different genes: two nuclear (EF1α and 18S) and one mitochondrial (COI). Analysis of EF1α and COI sequences did not recover monophyly of Ischnocera, but these genes provided little support for ischnoceran paraphyly because homoplasy is high among the divergent taxa included in this study. Analysis of 18S sequences recovered ischnoceran monophyly with strong support. Sequences from these three gene regions showed significant conflict with the partition homogeneity test, but this heterogeneity probably arises from the dramatic differences in substitution rates. In support of this conclusion, Kishino–Hasegawa tests of the EF1α and COI genes did not reject several trees containing ischnoceran monophyly. Combined analysis of all three gene regions supported monophyly of Ischnocera, although not as strongly as analysis of 18S by itself. In sum, although rapidly evolving genes can retain some phylogenetic signal for deep phylogenetic relationships, strong support for such relationships is likely to come from more slowly evolving genes. [Copyright &y& Elsevier]

Discusses the controversy arising from Whitting and Wheeler's proposal that Strepsiptera + Diptera were sister groups based on molecular and morphological data. Findings of the original phylogenetic analysis; Sequencing of multiple representatives of all holometabolous insect orders and multiple outgroups; Morphological characters that argue against the placement of Strepsiptera as sister group to Coleoptera.

Ramp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented. Ramp sequences were compared from 247 vertebrates (114 Mammalian and 133 non-mammalian), where the presence and absence of ramp sequences was analyzed as a binary character in a parsimony and maximum likelihood framework. Additionally, ramp sequences were mapped to the Open Tree of Life synthetic tree to determine the number of parallelisms and reversals that occurred, and those results were compared to random permutations. Parsimony and maximum likelihood analyses of the presence and absence of ramp sequences recovered phylogenies that are highly congruent with established phylogenies. Additionally, 81% of vertebrate mammalian ramps and 81.2% of other vertebrate ramps had less parallelisms and reversals than the mean from 1000 randomly permuted trees. A chi-square analysis of completely orthologous ramp sequences resulted in a p-value < 0.001 as compared to random chance. Ramp sequences recover comparable phylogenies as other phylogenomic methods. Although not all ramp sequences appear to have a phylogenetic signal, more ramp sequences track speciation than expected by random chance. Therefore, ramp sequences may be used in conjunction with other phylogenomic approaches if many orthologs are taken into account. However, phylogenomic methods utilizing few orthologs should be cautious in incorporating ramp sequences because individual ramp sequences may provide conflicting signals. [ABSTRACT FROM AUTHOR]

Identical codon pairing and co-tRNA codon pairing increase translational efficiency within genes when two codons that encode the same amino acid are translated by the same tRNA before it diffuses from the ribosome. We examine the phylogenetic signal in both identical and co-tRNA codon pairing across 23 428 species using alignment-free and parsimony methods. We determined that conserved codon pairing typically has a smaller window size than the length of a ribosome, and codon pairing tracks phylogenies across various taxonomic groups. We report a comprehensive analysis of codon pairing, including the extent to which each codon pairs. Our parsimony method generally recovers phylogenies that are more congruent with the established phylogenies than our alignment-free method. However, four of the ten taxonomic groups did not have sufficient orthologous codon pairings and were therefore analyzed using only the alignment-free methods. Since the recovered phylogenies using only codon pairing largely match phylogenies from the Open Tree of Life and the NCBI taxonomy, and are comparable to trees recovered by other algorithms, we propose that codon pairing biases are phylogenetically conserved and should be considered in conjunction with other phylogenomic techniques. [ABSTRACT FROM AUTHOR]

Recurrence is an under-appreciated but potentially wide-spread evolutionary phenomenon. Recurrence has been suggested for the re-evolution of eyes in ostracods, ocelli in cave crickets, wings in water striders and other complex features in a wide variety of taxa. The study in this article received such widespread attention because it stands as the most compelling case of recurrence to date. The placement of multiple lineages of wingless taxa at the base of the phasmid topology was a pattern which unexpectedly emerged from the phylogenetic reconstruction.

Presents highlights of the XXI International Congress of Entomology held in August 2000 in Brazil. Discussion on the phylogeny of holometabola.

With the recent advance in molecular phylogenetics focused on the leaf insects (Phasmatodea, Phylliidae), gaps in knowledge are beginning to be filled. Yet, shortcomings are also being highlighted, for instance, the unveiling of numerous undescribed phylliid species. Here, some of these taxa are described, including Phyllium iyadaon sp. nov. from Mindoro Island, Philippines; Phyllium samarense sp. nov. from Samar Island, Philippines; Phyllium ortizi sp. nov. from Mindanao Island, Philippines; Pulchriphyllium heracles sp. nov. from Vietnam; Pulchriphyllium delislei sp. nov. from South Kalimantan, Indonesia; and Pulchriphyllium bhaskarai sp. nov. from Java, Indonesia. Several additional specimens of these species together with a seventh species described herein, Pulchriphyllium anangu sp. nov. from southwestern India, were incorporated into a newly constructed phylogenetic tree. Additionally, two taxa that were originally described as species, but in recent decades have been treated as subspecies, are elevated back to species status to reflect their unique morphology and geographic isolation, creating the following new combinations: Pulchriphyllium scythe (Gray, 1843) stat. rev., comb. nov. from Bangladesh and northeastern India, and Pulchriphyllium crurifolium (Audinet-Serville, 1838) stat. rev., comb. nov. from the Seychelles islands. Lectotype specimens are also designated for Pulchriphyllium scythe (Gray, 1843) stat. rev., comb. nov. and Pulchriphyllium crurifolium (Audinet-Serville, 1838) stat. rev., comb. nov. from original type material. [ABSTRACT FROM AUTHOR]

Fireflies are some of the most captivating organisms on the planet. They have a rich history as subjects of scientific study, especially in relation to their bioluminescent behavior. Yet, the phylogenetic relationships of fireflies are still poorly understood. Here, we present the first total evidence approach to reconstruct lampyrid phylogeny using both a molecular matrix from six loci and an extensive morphological matrix. Using this phylogeny we test the hypothesis that adult bioluminescence evolved after the origin of the firefly clade. The ancestral state of adult bioluminescence is recovered as non-bioluminescent with one to six gains and five to ten subsequent losses. The monophyly of the family, as well as the subfamilies is also tested. Ototretinae, Cyphonocerinae, Luciolinae (incl. Pristolycus ), Amydetinae, “ cheguevarinae ” sensu Jeng 2008, and Photurinae are highly supported as monophyletic. With the exception of four taxa, Lampyrinae is also recovered as monophyletic with high support. Based on phylogenetic and morphological data Lamprohiza , Phausis , and Lamprigera are transferred to Lampyridae incertae sedis. [ABSTRACT FROM AUTHOR]

Fleas (order Siphonaptera) are highly-specialized, diverse blood-feeding ectoparasites of mammals and birds with an enigmatic evolutionary history and obscure origin. We here present a molecular phylogenetic study based on a comprehensive taxon sampling of 259 flea taxa, representing 16 of the 18 extant families of this order. A Bayesian phylogenetic tree with strong nodal support was recovered, consisting of seven sequentially derived lineages with Macropsyllidae as the earliest divergence, followed by Stephanocircidae. Divergence times of flea lineages were estimated based on fossil records and host specific associations to bats (Chiroptera), suggesting that the common ancestor of extant Siphonaptera diversified during the Cretaceous. However, most of the intraordinal divergence into extant lineages took place after the K-Pg boundary. Ancestral states of host association and biogeographical distribution were reconstructed, suggesting with high likelihood that fleas originated in the southern continents (Gondwana) and migrated from South America to their extant distributions in a relatively short time frame. Theria (placental mammals and marsupials) represent the most likely ancestral host group of extant Siphonaptera, with marsupials occupying a more important role than previously assumed. Major extant flea families evolved in connection to post K-Pg diversification of Placentalia. The association of fleas with monotremes and birds is likely due to later secondary host association. These results suggest caution in casually interpreting recently discovered Mesozoic fossil “dinosaur fleas” of Northeast Asia as part of what we currently consider Siphonaptera. [ABSTRACT FROM AUTHOR]

Introgression is an important biological process affecting at least 10% of the extant species in the animal kingdom. Introgression significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here, we use phylogenomic approaches to understand patterns of introgression along the evolutionary history of a unique, nonmodel insect system: dragonflies and damselflies (Odonata). We demonstrate that introgression is a pervasive evolutionary force across various taxonomic levels within Odonata. In particular, we show that the morphologically "intermediate" species of Anisozygoptera (one of the three primary suborders within Odonata besides Zygoptera and Anisoptera), which retain phenotypic characteristics of the other two suborders, experienced high levels of introgression likely coming from zygopteran genomes. Additionally, we find evidence for multiple cases of deep inter-superfamilial ancestral introgression. [Gene flow; Odonata; phylogenomics; reticulate evolution.] [ABSTRACT FROM AUTHOR]

Nuclear mitochondrial pseudogenes (numts) are non-functional fragments of mtDNA inserted into the nuclear genome. Numts are prevalent across eukaryotes and a positive correlation is known to exist between the number of numts and the genome size. Most numt surveys have relied on model organisms with fully sequenced nuclear genomes, but such analyses have limited utilities for making a generalization about the patterns of numt accumulation for any given clade. Among insects, the order Orthoptera is known to have the largest nuclear genome and it is also reported to include several species with a large number of numts. In this study, we use Orthoptera as a case study to document the diversity and abundance of numts by generating numts of three mitochondrial loci across 28 orthopteran families, representing the phylogenetic diversity of the order. We discover that numts are rampant in all lineages, but there is no discernable and consistent pattern of numt accumulation among different lineages. Likewise, we do not find any evidence that a certain mitochondrial gene is more prone to nuclear insertion than others. We also find that numt insertion must have occurred continuously and frequently throughout the diversification of Orthoptera. Although most numts are the result of recent nuclear insertion, we find evidence of very ancient numt insertion shared by highly divergent families dating back to the Jurassic period. Finally, we discuss several factors contributing to the extreme prevalence of numts in Orthoptera and highlight the importance of exploring the utility of numts in evolutionary studies. [ABSTRACT FROM AUTHOR]

The phasmatodeans or stick and leaf insects are considered to be a mesodiverse insect order with more than 3000 species reported mainly from the tropics. The stick insect subfamily Necrosciinae comprises approximately 700 described species in more than 60 genera from the Oriental and Australian region, forming the most species-rich subfamily traditionally recognized within Phasmatodea. However, the monophyly of this taxon has never been thoroughly tested and the evolutionary relationships among its members are unknown. We analyse three nuclear ( 18S and 28S r DNA, histone 3) and three mitochondrial ( CO II, 12S and 16S r DNA) genes to infer the phylogeny of 60 species of stick insects that represent all recognized families and major subfamilies sensu Günther and the remarkable diversity within Necrosciinae. Maximum parsimony, maximum likelihood and Bayesian techniques largely recover the same substantial clades, albeit with highly discordant relationships between them. Most members of the subfamily Necrosciinae form a clade. However, the genus Neohirasea - currently classified within Lonchodinae - is strongly supported as subordinate to Necrosciinae, whereas Baculofractum, currently classified within Necrosciinae, is strongly supported within Lonchodinae. Accordingly, we formally transfer Neohirasea and allied taxa (namely Neohiraseini) to Necrosciinae sensu nova (s.n.) and Baculofractum to Lonchodinae s.n. We also provide further evidence that Leprocaulinus, until recently recognized as Necrosciinae, belongs to Lonchodinae, and forms the sister taxon of Baculofractum. Furthermore, Lonchodinae is paraphyletic under exclusion of Eurycantha and Neopromachus. We reinstate the traditional view that Neopromachus and related taxa ( Neopromachini sensu Günther) are a subgroup of Lonchodinae and transfer those taxa + the New Guinean Eurycanthinae accordingly. Morphological evidence largely corroborates our molecular-based findings and also reveals that Menexenus fruhstorferi is a member of the genus Neohirasea and is thus transferred from Menexenus ( Lonchodinae) to Neohirasea, as Neohirasea fruhstorferi comb.n. ( Necrosciinae s.n.). Other phylogenetic results include Areolatae and Anareolatae each supported as polyphyletic, Heteropteryginae and Lanceocercata ( Bayesian analysis) are monophyletic, albeit with low support, and Necrosciinae s.n. and Lonchodinae s.n. are recovered as sister taxa ( Bayesian analysis). [ABSTRACT FROM AUTHOR]

Highlights: [•] The phylogeny of katydids (Orthoptera: Tettigoniidae) was inferred using 6 molecular markers. [•] Five subfamilies were paraphyletic under various reconstruction methods. [•] Seven subfamilies were found to be monophyletic. [•] The thoracic auditory spiracle, a diagnostic character for Pseudophyllinae, is homoplasious. [•] Leaf-like wings have been derived independently in at least six lineages with secondary losses in at least four lineages. [ABSTRACT FROM AUTHOR]

Abstract: One of the main challenges in analyzing multi-locus phylogenomic data is to find an optimal data partitioning strategy to account for variable evolutionary histories of different loci for any given dataset. Although a number of studies have addressed the issue of data partitioning in a Bayesian phylogenetic framework, such studies in a maximum likelihood framework are comparatively lacking. Furthermore, a rigorous statistical exploration of possible data partitioning schemes has not been applied to mitochondrial genome (mtgenome) data, which provide a complex, but manageable platform for addressing various challenges in analyzing phylogenomic data. In this study, we investigate the issue of data partitioning in the maximum likelihood framework in the context of the mitochondrial phylogenomics of an orthopteran superfamily Acridoidea (Orthoptera: Caelifera). The present study analyzes 34 terminals representing all 8 superfamilies within Caelifera, which includes newly sequenced partial or complete mtgenomes for 11 families. Using a new partition-selection method implemented in the software PartitionFinder, we compare a large number of data partitioning schemes in an attempt to identify the most effective method of analyzing the mtgenome data. We find that the best-fit partitioning scheme selected by PartitionFinder is superior to any a priori schemes commonly utilized in mitochondrial phylogenomics. We also show that over-partitioning is often detrimental to phylogenetic reconstruction. A comparative analysis of mtgenome structures finds that the tRNA gene rearrangement between cytochrome c oxidase subunit II and ATP synthase protein 8 does not occur in the most basal caeliferan lineage Tridactyloidea, suggesting that this gene rearrangement must have evolved at least in the common ancestor of Tetrigoidea and Acridomorpha. We find that mtgenome data contain sufficient phylogenetic information to broadly resolve the relationships across Acridomorpha and Acridoidea. [Copyright &y& Elsevier]

The order Thysanoptera (Paraneoptera), commonly known as thrips, displays a wide range of behaviours, and includes several pest species. The classification and suggested relationships among these insects remain morphologically based, and have never been evaluated formally with a comprehensive molecular phylogenetic analysis. We tested the monophyly of the suborders, included families and the recognized subfamilies, and investigated their relationships. Phylogenies were reconstructed based upon 5299 bp from five genetic loci: 18S ribosomal DNA, 28S ribosomal DNA, Histone 3, Tubulin-alpha I and cytochrome oxidase c subunit I. Ninety-nine thrips species from seven of the nine families, all six subfamilies and 70 genera were sequenced. Maximum parsimony, maximum likelihood and Bayesian analyses all strongly support a monophyletic Tubulifera and Terebrantia. The families Phlaeothripidae, Aeolothripidae, Melanthripidae and Thripidae are recovered as monophyletic. The relationship of Aeolothripidae and Merothripidae to the rest of Terebrantia is equivocal. Molecular data support previous suggestions that Aeolothripidae or Merothripidae could be a sister to the rest of Terebrantia. Four of the six subfamilies are recovered as monophyletic. The two largest subfamilies, Phlaeothripinae and Thripinae, are paraphyletic and require further study to understand their internal relationships. [ABSTRACT FROM AUTHOR]

A phylogenetic analysis of the order Embioptera is presented with a revised classification based on results of the analysis. Eighty-two species of Embioptera are included from all families except Paedembiidae Ross and Embonychidae Navás. Monophyly of each of the eight remaining currently recognized families is tested except Andesembiidae Ross, for which only a single species was included. Nine outgroup taxa are included from Blattaria, Grylloblattaria, Mantodea, Mantophasmatodea, Orthoptera, Phasmida and Plecoptera. Ninety-six morphological characters were analysed along with DNA sequence data from the five genes 16S rRNA, 18S rRNA, 28S rRNA, cytochrome c oxidase I and histone III. Data were analysed in combined analyses of all data using parsimony and Bayesian optimality criteria, and combined molecular data were analysed using maximum likelihood. Several major conclusions about Embioptera relationships and classification are based on interpretation of these analyses. Of eight families for which monophyly was tested, four were found to be monophyletic under each optimality criterion: Clothodidae Davis, Anisembiidae Davis, Oligotomidae Enderlein and Teratembiidae Krauss. Australembiidae Ross was not recovered as monophyletic in the likelihood analysis in which one Australembia Ross species was recovered in a position distant from other australembiids. This analysis included only molecular data and the topology was not strongly supported. Given this, and because parsimony and the Bayesian analyses recovered a strongly supported clade including all Australembiidae, we regard this family also as monophyletic. Three other families - Notoligotomidae Davis, Archembiidae Ross and Embiidae Burmeister, as historically delimited - were not found to be monophyletic under any optimality criterion. Notoligotomidae is restricted here to include only the genus Notoligotoma Davis with a new family, Ptilocerembiidae Miller and Edgerly, new family, erected to include the genus Ptilocerembia Friederichs. Archembiidae is restricted here to include only the genera Archembia Ross and Calamoclostes Enderlein. The family group name Scelembiidae Ross is resurrected from synonymy with Archembiidae (new status) to include all other genera recently placed in Archembiidae. Embiidae is not demonstrably monophyletic with species currently placed in the family resolved in three separate clades under each optimality criterion. Because taxon sampling is not extensive within this family in this analysis, no changes are made to Embiidae classification. Relationships between families delimited herein are not strongly supported under any optimality criterion with a few exceptions. Either Clothodidae Davis (parsimony) or Australembiidae Ross (Bayesian) is the sister to the remaining Embioptera taxa. The Bayesian analysis includes Australembiidae as the sister to all other Embioptera except Clothididae, suggesting that each of these taxa is a relatively plesiomorphic representatative of the order. Oligotomidae and Teratembiidae are sister groups, and Archembiidae ( sensu novum), Ptilocerembiidae, Andesembiidae and Anisembiidae form a monophyletic group under each optimality criterion. Each family is discussed in reference to this analysis, diagnostic combinations and taxon compositions are provided, and a key to families of Embioptera is included. [ABSTRACT FROM AUTHOR]

DNA barcoding is a diagnostic method of species identification based on sequencing a short mitochondrial DNA fragment of cytochrome oxidase I (COI), but its ability to correctly diagnose species is limited by the presence of nuclear mitochondrial pseudogenes (numts). Numts can be coamplified with the mitochondrial orthologue when using universal primers, which can lead to incorrect species identification and an overestimation of the number of species. Some researchers have proposed that using more specific primers may help eliminate numt coamplification, but the efficacy of this method has not been thoroughly tested. In this study, we investigate the taxonomic distribution of numts in 11 lineages within the insect order Orthoptera, by analysing cloned COI sequences and further test the effects of primer specificity on eliminating numt coamplification in four lineages. We find that numts are coamplified in all 11 taxa using universal (barcoding) primers, which suggests that numts may be widespread in other taxonomic groups as well. Increased primer specificity is only effective at reducing numt coamplification in some species tested, and only eliminates it in one species tested. Furthermore, we find that a number of numts do not have stop codons or indels, making it difficult to distinguish them from mitochondrial orthologues, thus putting the efficacy of barcoding quality control measures under question. Our findings suggest that numt coamplification is a serious problem for DNA barcoding and more quality control measures should be implemented to identify and eliminate numts prior to using mitochondrial barcodes for species diagnoses. [ABSTRACT FROM AUTHOR]

A phylogenetic analysis of the diving beetle tribe Hydaticini Sharp (Coleoptera: Dytiscidae: Dytiscinae) is presented based on data from adult morphology, two nuclear (histone III and wingless) and two mitochondrial (cytochrome c oxidase I and II) protein-coding genes. We explore how to best partition a data set of multiple nuclear and mitochondrial protein-coding genes by using Bayes factor and a penalized modification of Bayes Factor. Ten biologically relevant partitioning strategies were identified ranging from all DNA analysed under a single model to each codon position of each gene treated with a separate model. Model selection criteria AIC, AICc, BIC and four ways of traversing parameter space in a hierarchical likelihood ratio test were applied to each partition. All unique partitioning and model combinations were analysed with Bayesian methods. Results show that partitioning by codon position and genome source (nuclear vs. mitochondrial) is strongly favoured over partitioning by gene. We also find evidence that Bayes Factor can penalize overparameterization even when comparing nested models. Species groups showing a strong geographical pattern were generally highly supported, however, the sister group relationship of an isolated Madagascan and Australian species were shown to be artefactual with a long-branch extraction test. The following conclusions were supported in both the selected method of partitioning the Bayesian analysis and combined parsimony analyses: (i) the tribe Hydaticini is monophyletic (ii) the genus Hydaticus Leach is paraphyletic with respect to Prodaticus Sharp (iii) the subgenus Hydaticus ( Hydaticus) is monophyletic, and (iv) the subgenus H. ( Guignotites) Brinck is paraphyletic with respect to Prodaticus and the subgenera H. ( Pleurodytes) Régimbart and H. ( Hydaticinus) Guignot. Based on these results, Hydaticus and Prodaticus are each recognized as valid genera and Guignotites, Hydaticinus and Pleurodytes are each placed as junior synonyms of Prodaticus (new synonymies). [ABSTRACT FROM AUTHOR]

Nuclear mitochondrial pseudogenes (numts) are nonfunctional copies of mtDNA in the nucleus that have been found in major clacles of eukaryotic organisms. They can be easily coamplified with orthologous mtDNA by using conserved universal primers; however, this is especially problematic for DNA barcoding, which attempts to characterize all living organisms by using a short fragment of the mitochondrial cytochrome c oxidase I (COl) gene. Here, we study the effect of numts on DNA barcoding based on phylogenetic and barcoding analyses of numt and mtDNA sequences in two divergent lineages of arthropods: grasshoppers and crayfish. Single individuals from both organisms have numts of the COl gene, many of which are highly divergent from orthologous mtDNA sequences, and DNA barcoding analysis incorrectly overestimates the number of unique species based on the standard metric of 3% sequence divergence. Removal of numts based on a careful examination of sequence characteristics, including indels, in-frame stop codons, and nucleotide composition, drastically reduces the incorrect inferences of the number of unique species, but even such rigorous quality control measures fail to identify certain numts. We also show that the distribution of numts is lineagespecific and the presence of numts cannot be known a priori. Whereas DNA barcoding strives for rapid and inexpensive generation of molecular species tags, we demonstrate that the presence of COl numts makes this goal difficult to achieve when numts are prevalent and can introduce serious ambiguity into DNA barcoding. [ABSTRACT FROM AUTHOR]

Abstract: External and internal head structures of Caurinus dectes were examined and described in detail. The features are compared to conditions found in other groups of Antliophora. Caurinus is obviously crucial for the reconstruction of the mecopteran and antliophoran groundplan. It displays a remarkable series of plesiomorphic character states such as a complete clypeolabral suture, the presence of M. hypopharyngomandibularis (M. 13) and M. frontohypopharyngalis (M. 41), a subdivided clypeus, a short head without rostrum, a dorsal tentorial arm attached to the head capsule, the absence of a cranial dilator of the antenna, and large mandibles with a well developed apical tooth, two distinct subapical teeth, and a basal molar part. The first three plesiomorphic features render potential autapomorphies of Mecoptera in the traditional sense invalid. Autapomorphies of Caurinus are the distinctly flattened labrum, the absence of the labroepipharyngeal muscle, the very large size of M. 13, the strongly enlarged penultimate palpomeres, the partition of M. 41, the very strongly developed precerebral sucking chamber, strongly curved optic lobes, the presence of a large protocerebral extension in the genal region and deep posterior excavations of the protocerebrum. The maxillolabial plate, the absence of cardines as separate structures, the reduction of ocelli, and the origin of maxillary palp muscles on a median ridge or area of the maxillolabial plate are likely autapomorphies of Boreidae. Another potential autapomorphy of the family is the presence of longitudinal furrows on the mandibles. However, they are absent in Boreus. The thick strongly sclerotised, median ridge of the maxillolabial plate, the missing retractibility of the prementum, the absence of extrinsic labial muscles, and the presence of a median ridge on the prepharyngeal roof suggest a clade Boreus + Hesperoboreus. The origin of extrinsic maxillary muscles from the clypeus has probably evolved independently in Boreus and Hesperoboreus, and in Panorpa, respectively. The absence of M. craniolacinialis and the presence of a row of several subapical mandibular teeth are autapomorphies of Boreus. The presence of a specific intrinsic muscle of the salivary duct and a membranous galea enclosing the labrum and mandibular base are derived features shared by Boreidae and Pistillifera (galea absent in Nannochorista, Siphonaptera and Diptera). The loss of M. frontolabralis (M. 8) is a potential apomorphy of Mecoptera incl. Siphonaptera. A sister group relationship between Boreidae and Siphonaptera is not supported by characters of the adult head. Head structures of Siphonaptera are extremely modified in correlation with ectoparasitic habits. [Copyright &y& Elsevier]

A letter to the editor is presented in response to an article about an analysis of phylogenetic relationships of the major lineages of mayflies (Ephemeroptera).

Third instars of the diving beetle Notaticus fasciatus Zimmermann (Coleoptera: Dytiscidae) are described for tile first time, representing the first description of larvae from Aubehydrini, the only remaining tribe of Dytiscinae unknown as larvae. The description is based on larvae suspected to be N. fasciatus collected in French Guiana. The specimens were associated with adults by analyzing an 806-bp fragment of cytochrome c oxidase I. Adults of N. fasciatus mid 19 other species were included representing all tribes and most species of Dytiscinae found in northern South America with multiple representatives of some for a total of 33 terminals. Data were analyzed using parsimony and p-distances. Tim parsimony analysis resulted in a single tree. The unknown larva grouped with adult specimens of N. fasciatus (bootstrap 100%). Distance between them averaged 0.01 (0.01-0.02) compared with 0.02 (0-0.06) between other conspecifics and 0.13 (0.05-0.17) between different species. N. fasciatus larvae differ from other Dytiscinae in the following characters: 1) head capsule subtriangular; 2) occipital suture absent; 3) anterior margin of frontoclypeus convex: 4) dorsal margin of foramen magnum straight; 5) dorsal pair of stemmata unmodified; 6) antennomere I, maxillary palpomere I, and labial palpomeres I and II not subdivided: 7) maxillary palpomere II subdivided; 8) ligula absent; 9) galea well developed: 10) natatory setae present on dorsal margin of coxae, absent along ventral margin of trochanters mid tarsi; 11) tarsal claws not serrate; 12) abdominal tergites fully developed; and 13) urogomphus well developed, shorter than last abdominal segment, and without natatory setae. [ABSTRACT FROM AUTHOR]

Mitochondrial (mt) genome rearrangement has generally been studied with respect to the phenomenon itself, focusing on their phylogenetic distribution and causal mechanisms. Rearrangements have additional significance through effects on substitution, transcription, and mRNA processing. Lice are an ideal group in which to study the interactions between rearrangements and these factors due to the heightened rearrangement rate within this group. The entire mt genome of the screamer louse Bothriometopus was sequenced and compared to previously sequenced louse genomes. The mt genome is 15,564 bp, circular, and all genes are encoded on the same strand. The gene arrangement differs radically from both other louse species and the ancestral insect. Nucleotide composition is A+T biased, but there is no skew which may be due to reversal of replication direction or a transcriptional effect. Bothriometopus has both tRNA duplication and concerted evolution which has not been observed previously. Eleven of the 13 protein-coding genes have 3′ end stem-loop structures which may allow mRNA processing without flanking tRNAs and so facilitate gene rearrangements. There are five candidate control regions capable of forming stem-loop structures. Two are structurally more similar to the control regions of other insect species than those of other lice. Analyses of Bothriometopus demonstrate that louse mt genomes, in addition to being extensively rearranged, differ significantly from most insect species in nucleotide composition biases, tRNA evolution, protein-coding gene structures and putative signaling sites such as the control region. These may be either a cause or a consequence of gene rearrangements. [ABSTRACT FROM AUTHOR]

Phylogenetic relationships among members of the diving beetle tribe Cybistrini (Coleoptera: Dytiscidae) were inferred from analysis of 47 adult and larval morphological characters and sequences from portions of the genes cytochrome oxidase I (COI) and II (COII), histone III (H3) and wingless. Thirty-three species of Cybistrini were included, representing all genus-groups except Regimbartina Chatanay and Megadytes ( Bifurcitus) Brinck, and most historically recognized species groups and subgenera used in the tribe. Outgroups include six species from other tribes within Dytiscinae and Lancetinae. Analyses included parsimony analysis of the combined data, likelihood analysis of combined molecular data and partitioned Bayesian analysis of the combined data. Results indicate that Cybistrini is well supported as a monophyletic group. Within the tribe, all currently recognized genus groups were found to be monophyletic with the exception of Onychohydrus Schaum, which is paraphyletic with respect to Austrodytes Watts in the parsimony analysis, but monophyletic in the likelihood and Bayesian analyses, and Cybister sensu stricto, which is paraphyletic with respect to C. ( Melanectes) Brinck and C. ( Scaphinectes) Ádám in the parsimony analysis or only the latter in the likelihood and Bayesian analyses. Results also suggest that some, but not all, historically recognized species groups or subgenera in the large genus Cybister Curtis are monophyletic, and this is discussed and compared. To improve the classification, the name Sternhydrus Brinck is elevated from subgenus to genus rank ( new status). Four subgenera in the genus Cybister are recognized: C. ( Melanectes) Brinck, C. ( Megadytoides) Brinck ( resurrected), C. ( Neocybister) Miller, Bergsten and Whiting ( new subgenus) and C. ( Cybister) Curtis. The following new synonyms are established: Trochalus Dejean ( new synonym), and ScaphinectesÁdám =  Cybister ( Cybister) ( new synonym). The Neotropical species Cybister parvus Trémouilles (not examined) apparently does not fit any historical or currently recognized genus-group diagnosis in Cybistrini, so it is retained in Cybister but incertae sedis with respect to subgenus. In addition to classification, the evolution of the unique character combinations present in cybistrines are discussed. A key to the adults of genera and subgenera is presented. [ABSTRACT FROM AUTHOR]

Abstract: This is the first report of Arsenophonus- and Photorhabdus-type bacteria from Streblidae (bat flies) and Hippoboscidae (louse flies, keds). Strains were detected by means of polymerase chain reaction of 16S rDNA, and phylogenetic analysis determined the relationship of the obtained sequences to previously reported sequences in GenBank. Phylogenetic analysis by means of maximum parsimony revealed that all isolated Arsenophonus spp. 16S rDNA sequences formed a monophyletic sub-clade within other insect Arsenophonus spp., while the Photorhabdus spp. sequences are part of a monophyletic clade including Photorhabdus spp., Xenorhabdus spp. and Proteus spp. [Copyright &y& Elsevier]

Dermaptera (earwigs) is a cosmopolitan order of insects, the phylogenetic relationships of which are poorly understood. The phylogeny of Dermaptera was inferred from large subunit ribosomal (28S), small subunit ribosomal (18S), histone-3 (H3) nuclear DNA sequences, and forty-three morphological characters. Sequence data were collected for thirty-two earwig exemplar taxa representing eight families in two suborders: Hemimeridae (suborder Hemimerina); Pygidicranidae, Anisolabididae, Labiduridae, Apachyidae, Spongiphoridae, Chelisochidae and Forficulidae (suborder Forficulina). Eighteen taxa from ten additional orders were also included, representing Ephemeroptera, Odonata, Orthoptera, Phasmida, Embiidina, Mantodea, Isoptera, Blattaria, Grylloblattodea and Zoraptera. These data were analysed via direct optimization in poy under a range of gap and substitution values to test the sensitivity of the data to variations in parameter values. These results indicate that the epizoic Hemimerus is not sister to the remaining Dermaptera, but rather nested as sister to Forficulidae + Chelisochidae. These analyses support the paraphyly of Pygidicranidae and Spongiphoridae and the monophyly of Chelisochidae, Forficulidae, Anisolabididae and Labiduridae. [ABSTRACT FROM AUTHOR]

Phylogenetic relationships of Erotylidae (pleasing fungus beetles) were inferred based on DNA sequence data. Relationships of clades within Erotylidae were examined, as was the relationship of the entire family to Languriidae (lizard beetles). 18S and 28S ribosomal DNA were sequenced for sixty-one taxa representing major erotylid lineages and outgroups. Phylogenetic analyses under varying parameter settings using standard parsimony and likelihood techniques were performed. These data indicate a paraphyletic Erotylidae and Languriidae. Encaustinae (including Coptengis), Megalodacninae and Erotylinae are supported as monophyletic, whereas Dacninae and Tritominae are paraphyletic. Taxonomic and biological implications are discussed. Gregariousness has arisen at least three times in Erotylidae. The erotylid clade has experienced at least one evolutionary transition from mycophagy (on Aphyllophorales) to phytophagy, three transitions from Aphyllophorales hosts to Euagarics, and one transition from Euagarics hosts to Mucorales (Zygomycetes). There are no recognizable phylogenetic trends in coloration across higher-level erotylid lineages. [ABSTRACT FROM AUTHOR]

• Codon usages are 1109× more likely than random to follow the Open Tree of Life. • We analyzed 890,814 codons from 12,337 species across all kingdoms of life. • We confirm turtles as sister taxa to archosaurs. • We provide a framework to analyze codon usages against any phylogeny. Using parsimony, we analyzed codon usages across 12,337 species and 25,727 orthologous genes to rank specific genes and codons according to their phylogenetic signal. We examined each codon within each ortholog to determine the codon usage for each species. In total, 890,814 codons were parsimony informative. Next, we compared species that used a codon with species that did not use the codon. We assessed each codon's congruence with species relationships provided in the Open Tree of Life (OTL) and determined the statistical probability of observing these results by random chance. We determined that 25,771 codons had no parallelisms or reversals when mapped to the OTL. Codon usages from orthologous genes spanning many species were 1109× more likely to be congruent with species relationships in the OTL than would be expected by random chance. Using the OTL as a reference, we show that codon usage is phylogenetically conserved within orthologous genes in archaea, bacteria, plants, mammals, and other vertebrates. We also show how to use our provided framework to test different tree hypotheses by confirming the placement of turtles as sister taxa to archosaurs. [ABSTRACT FROM AUTHOR]

Although many studies have documented codon usage bias in different species, the importance of codon usage in a phylogenetic framework remains largely unknown. We demonstrate that a phylogenetic signal is present in the codon usage and non-usage biases of 17 717 orthologues evaluated across 72 tetrapod species using a simple parsimony analysis of a binary matrix of codon characters. Phylogenies estimated using stop codons were more congruent with previous hypotheses than phylogenies based on any other single codon or a combination of codons. Although each codon is present in every species, specific genes have different codon preferences and may or may not use every possible codon. This observation allowed us to map the pattern of codon usage and non-usage across the topology. These results suggest that codon usage is phylogenetically conserved across shallow and deep levels within tetrapods. [ABSTRACT FROM AUTHOR]

Insects have developed incredible means to avoid detection by predators. At least five insect orders have species that resemble leaves. Katydids (Orthoptera : Tettigoniidae) are the most diverse and wide-ranging of the leaf-like insects. At least 14 of the 20 extant katydid subfamilies contain species with leaf-like wings. Although it is undisputed that many katydids resemble leaves, methods for delineating the leaf-like from non-leaf-like forms have varied by author and in many cases are not explicitly stated. We provide a simple ratio method that can be used to differentiate the leaf-like and nonleaf- like forms. Geometric morphometrics were used to validate the ratio method. Leaf-like wings have been independently derived in at least 15 katydid lineages. Relative rates of speciation were found to be greater in the non-leaf-like forms, suggesting that leaf-like wings within Tettigoniidae are not a driver of diversification. Likewise, throughout Tettigoniidae, selection seems to be favouring the transition away from leaf-like wings. However, within the large Phaneropterinae subclade, relative speciation and transition rates between the leaf-like and non-leaf-like forms do not differ significantly. [ABSTRACT FROM AUTHOR]

Dermaptera is a relatively small order of free-living insects that typically feed on detritus and other plant material. However, two earwig lineages – Arixeniidae and Hemimeridae – are epizoic on Cheiromeles bats and Beamys and Cricetomys rats respectively. Both of these epizoic families are comprised of viviparous species. The monophyly of these epizoic lineages and their placement within dermapteran phylogeny has remained unclear. A phylogenetic analyses was performed on a diverse sample of 47 earwig taxa for five loci (18S rDNA, 28S rDNA, COI, Histone 3, and Tubulin Alpha I). Our results support two independent origins of the epizoic lifestyle within Dermaptera, with Hemimeridae and Arixeniidae each derived from a different lineage of Spongiphoridae. Our analyses places Marava , a genus of spongiphorids that includes free-living but viviparous earwigs, as sister group to Arixeniidae, suggesting that viviparity evolved prior to the shift to the epizoic lifestyle. Additionally, our results support the monophyly of Forficulidae and Chelisochidae and the paraphyly of Labiduridae, Pygidicranidae, Spongiphoridae, and Anisolabididae. [ABSTRACT FROM AUTHOR]

Recently, a set of publications described flea fossils from Jurassic and Early Cretaceous geological strata in northeastern China, which were suggested to have parasitized feathered dinosaurs, pterosaurs, and early birds or mammals. In support of these fossils being fleas, a recent publication in BMC Evolutionary Biology described the extended abdomen of a female fossil specimen as due to blood feeding. We here comment on these findings, and conclude that the current interpretation of the evolutionary trajectory and ecology of these putative dinosaur fleas is based on appeal to probability, rather than evidence. Hence, their taxonomic positioning as fleas, or stem fleas, as well as their ecological classification as ectoparasites and blood feeders is not supported by currently available data. [ABSTRACT FROM AUTHOR]