Phylogenetic analyses with four new Cretaceous bristletails reveal inter‐relationships of Archaeognatha and Gondwana origin of Meinertellidae

Based on fifteen Archaeognatha (=Microcoryphia) specimens from Myanmar (Burmese) amber, including males, females and immatures, two new genera and four species, Cretaceomachilis longa sp.n ., Unimeinertellus abundus gen. et sp.n. , U. bellus sp.n. and Nullmeinertellus wenxuani gen. et sp.n. , are described. Phylogenetic analyses of taxa in Archaeognatha were conducted using Maximum parsimony and Bayesian inference based on morphological characters and DNA sequence data. Our results confirm the phylogenetic position of the new genera, clarify the monophyly of Meinertellidae and indicate that the ‘paleo‐types’ excluding Ditrigoniophthalmus are nested within the Machilidae group, but suggest that the three subfamilies within Machilidae may be artificial. The diversity of meinertellids with derived characters found from the Cretaceous indicate that the divergence time of Machilidae and Meinertellidae is much earlier than the Cretaceous. We propose the possibility that Meinertellidae might have originated on Gondwana.     

Comment on Phylogenetic analyses with four new Cretaceous bristletails reveal inter-relationships of Archaeognatha and Gondwana origin of Meinertellidae

Archaeognatha (Machilida plus †Monura), with ~450 extant species worldwide, represent a key lineage for the understanding of insect evolution. In a recently published phylogenetic analysis on Archaeognatha, based on a total-evidence approach, a Machilidae key fossil (Gigamachilis triassicus) from the Middle Triassic Lagerstätte of Monte San Giorgio and a representative of †Monura (Dasyleptus triassicus) from the same fossiliferous site, were not considered. In the present study, the phylogenetic analyses performed by Zhang et al. (2018) using maximum parsimony and Bayesian inference were repeated including these two key taxa; in addition, Tricholepidion gertschi and Lepisma saccharina were included as representatives of Zygentoma. In the total-evidence Bayesian analysis, †Monura was found to be paraphyletic, whereas in the maximum parsimony analysis, performed only on morphological characters, they were monophyletic. Moreover, the attribution of G. triassicus to Machilidae is now confirmed by these analyses, indicating that members of the extant group of Machilidae were already present in the Middle Triassic, at least ~100 Myr before the previous estimate.     

The gonangulum: A reassessment of its morphology,homology, and phylogenetic significance

The gonangulum is a sclerite in the female genitalic region of insects. Its presence or full development has long been considered an apomorphy supporting Zygentoma + Pterygota. Recent studies of female genitalia in several insect orders (K.-D. Klass and co-workers) revealed many new data on the gonangulum and homologous sclerotisations (laterocoxa LC9). Herein the gonangulum area is described (including articulations, muscle attachments, sulci) and compared among Archaeognatha, Zygentoma, Odonata, Dermaptera, Dictyoptera, and Notoptera. A wider perspective is provided to the topic by addressing some novel issues: identification of LC9 sclerotisations in non-insect taxa and in insects that secondarily lack an ovipositor; occurrence of homonomous sclerotisations in other abdominal segments of both sexes; morphological interpretation of LC9; and the role of paedomorphosis in LC9 evolution. As a result, there is currently no support for any insect lineage from this character system. For gonangulum-related characters both a significant intra-ordinal variation and frequent homoplasy are demonstrated using various Odonata, Dermaptera, and Dictyoptera as examples. Divergent fates of LC9 in simplified genitalia are shown using a dermapteran and an odonatan. We view all this as a showcase of how a renewed and more detailed examination of a character system can dramatically change the phylogenetic evidence drawn from it.     

The phylogenetic interrelationships of the higher taxa of apterygote hexapods

The phylogeny of the basal hexapods, the so-called apterygote insects, was studied using parsimony analysis procedures. Most analyses took into account 47 characters mainly based on external morphology, and 19 taxa including 14 apterygote representatives, 3 pterygotes and also 2 distantly related myriapods were used as outgroups. The binary and multistate characters are discussed in detail and treated as unordered and equally weighted. Other analyses were performed using a second data set in which 28 characters, based on internal anatomy and already used in a previous work ( Bitsch & Bitsch 1998 ), were added to the first data set. This second matrix was restricted to 12 terminal taxa, the same as those of our previous work. The results of the different analyses are generally congruent. They strongly support the monophyly of several orders (Protura, Collembola, Archaeognatha) and of two groupings (Ectognatha, Dicondylia). Three other assemblages (Ellipura, Diplura, Entognatha) appear as parsimonious phylogenetic hypotheses, but they are never supported by the cladistical analyses and are based on a very small number of autapomorphies; so, the monophyly of each of them is not firmly established. Archaeognatha appears as the sister group of the Dicondylia. The three unresolved representatives of the Zygentoma are found as the sister group of the Pterygota. The results are discussed in the light of current concepts in hexapod phylogeny.     

The Complete Mitochondrial Genomes of Three Bristletails (Insecta: Archaeognatha): The Paraphyly of Machilidae and Insights into Archaeognathan Phylogeny

The order Archaeognatha was an ancient group of Hexapoda and was considered as the most primitive of living insects. Two extant families (Meinertellidae and Machilidae) consisted of approximately 500 species. This study determined 3 complete mitochondrial genomes and 2 nearly complete mitochondrial genome sequences of the bristletail. The size of the 5 mitochondrial genome sequences of bristletail were relatively modest, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. The gene orders were identical to that of Drosophila yakuba and most bristletail species suggesting a conserved genome evolution within the Archaeognatha. In order to estimate archaeognathan evolutionary relationships, phylogenetic analyses were conducted using concatenated nucleotide sequences of 13 protein-coding genes, with four different computational algorithms (NJ, MP, ML and BI). Based on the results, the monophyly of the family Machilidae was challenged by both datasets (W12 and G12 datasets). The relationships among archaeognathan subfamilies seemed to be tangled and the subfamily Machilinae was also believed to be a paraphyletic group in our study.     

A HEXAPOD FROM THE EARLY DEVONIAN WINDYFIELD CHERT, RHYNIE, SCOTLAND

Abstract: New diagnostic morphological features discovered following a re‐examination and further preparation of the holotype of Leverhulmia mariae Anderson and Trewin from the Early Devonian (Pragian) Windyfield chert are described and discussed here. The discovery of anterior (thoracic?) leg appendages with attached pretarsal elements comprising a fixed median unguis, a pair of articulated lateral ungues and possible unguitractor plate has allowed us to reclassify this enigmatic fossil as Hexapoda incertae sedis. We interpret the holotype as part of an abdomen bearing at least five pairs of segmented leglets. The condition of the ungues on the anterior appendages is strongly reminiscent of Archaeognatha and Zygentoma (= Thysanura s.s.), and the segmented leglets on the abdomen show similarities with certain fossil ‘apterygotes’ known from the Carboniferous. Leverhulmia is the third hexapod species found in the cherts at Rhynie, the other forms being the collembolan Rhyniella praecursor Hirst and Maulik, and the pterygote insect Rhyniognatha hirsti Tillyard. Showing closer affinities with Archaeognatha and Zygentoma, Leverhulmia may well represent the earliest fossil apterous insect known to date.     

Updating Carbamoylphosphate Synthase (CPS) Phylogenies: Occurrence and Phylogenetic Identity of Archaeal CPS Genes

Among Bacteria the carA and carB genes encoding the small (CarA) and large (CarB) subunits of carbamoylphosphate synthase (CPS) have been lost in certain symbionts (Haemophylus influenzae) and in most obligate intracellular parasites (Chlamydiae, Spirochaetes, Mycoplasmatales, Rickettsiae) having genome sizes in the 0.7- to 1.1-Mb range. Compared to Bacteria, Archaea exhibit a more varied pattern of CPS gene losses and an unusual propensity to incorporate CPS genes derived from both Bacteria and other Archaea. Schematically they fall into three groups. Group 1 taxa (the crenarchaeon Aeropyrum pernix and the euryarchaea Pyrococcus horikoshi and Pyrococcus abyssii) lack CPS genes altogether. Group 2 taxa (comprising Halobacteriales, Thermoplasmales, Methanococcales, Methanomicrobiales, Archaeoglobales) harbor CPS genes whose encoded CarB and CarA subunit proteins are ostensibly bacterial in origin; that is, they are intermixed with bacterial homologues on a phylogeny of concatenated CarA and CarB sequences and are not distinguishable from bacterial sequences after searching for domain-specific amino acid residue positions. Group 3 taxa (the crenarchaea Pyrobaculum aerophilum, Sulfolobus solfataricus, and Sulfolobus tokodaii and the euryarchaeon Pyrococcus furiosus) harbor CPS genes whose encoded proteins appear to be archaeal: consistent with an archaeal origin, the CarA and CarB sequences in this group possess both unique signatures and signatures affiliating them to Eukarya. Based on the topology of the clade comprising the four Group 3 taxa, we argue that CPS genes of P. furiosus (a euryarchaeon) and those of the crenarchaea P. aerophilum, S. solfataricus, and S. tokodaii are of a single type, resulting from the two genes being laterally transferred from a crenarchaeon to P. furiosus.     

Inverse dispersal patterns in a group of ant parasitoids (Hymenoptera: Eucharitidae: Oraseminae) and their ant hosts

When postulating evolutionary hypotheses for diverse groups of taxa using molecular data, there is a tradeoff between sampling large numbers of taxa with a few Sanger-sequenced genes or sampling fewer taxa with hundreds to thousands of next-generation-sequenced genes. High taxon sampling enables the testing of evolutionary hypotheses that are sensitive to sampling bias (i.e. dating, biogeography and diversification analyses), whereas high character sampling improves resolution of critical nodes. In a group of ant parasitoids (Hymenoptera: Eucharitidae: Oraseminae), we analyse both of these types of datasets independently (203 taxa with five Sanger loci, 92 taxa with 348 anchored hybrid enrichment loci) and in combination (229 taxa, 353 loci) to explore divergence dating, biogeography, host relationships and differential rates of diversification. Oraseminae specialize as parasitoids of the immature stages of ants in the subfamily Myrmicinae (Hymenoptera: Formicidae), with ants in the genus Pheidole being their most common and presumed ancestral host. A general assumption is that the distribution of the parasite must be limited by any range contraction or expansion of its host. Recent studies support a single New World to Old World dispersal pattern for Pheidole at c. 11–27 Ma. Using multiple phylogenetic inference methods (parsimony, maximum likelihood, dated Bayesian and coalescent analyses), we provide a robust phylogeny showing that Oraseminae dispersed in the opposite direction, from Old World to New World, c. 24–33 Ma, which implies that they existed in the Old World before their presumed ancestral hosts. Their dispersal into the New World appears to have promoted an increased diversification rate. Both the host and parasitoid show single unidirectional dispersals in accordance with the presence of the Beringian Land Bridge during the Oligocene, a time when the changing northern climate probably limited the dispersal ability of such tropically adapted groups.     

CHARACTERIZATION OF INVASIVE CONYZA SPECIES (ASTERACEAE) IN EUROPE: QUANTITATIVE TRAIT AND ISOZYME ANALYSIS

The genus Conyza (Asteraceae) represents one of the foremost examples of intercontinental plant invasions from the New World to the Old World that has resulted in a number of taxonomic problems owing to the dearth of knowledge concerning the biosystematics of the genus. In this study, quantitative trait and enzyme electrophoresis analysis was used to assess the pattern of variation within and among five short-lived taxa of Conyza (C. blakei, C. bonariensis, C. canadenis, C. floribunda, C. sumatrensis), introduced into Europe, and to test the hypothesis of a recent hybrid origin of C. floribunda. The five taxa exhibit marked differences in morphological and life-history characteristics that are concordant with divergence in genes encoding isozymes. In addition, a recent hybrid origin of C. floribunda is clearly not supported by either quantitative or electrophoretic data. These findings suggest that the five taxa differentiated genetically in their native range prior to their introduction in Europe. As formerly suggested by Arthur Cronquist (Bulletin of the Torrey Botanical Club 70: 629–632, 1943), C. canadensis appears to be more closely related to the genus Erigeron than the other taxa. The electrophoretic results also confirm that this particular species is diploid, while the presence of multiple bands and fixed heterozygosity demonstrates that the other Conyza taxa are all genetic allopolyploids. Both quantitative and electrophoretic data suggest the presence of two groups among the polyploid taxa: one comprising C. bonariensis and C. sumatrensis, the other C. blakei and C. floribunda. The latter grouping is supported by the observation that C. blakei and C. floribunda, both native to Argentina, exhibit a striking ability to shift from semelparous to iteroparous reproduction, while the other taxa are strictly semelparous.     

A NEW METHOD FOR OBTAINING NUCLEAR GENE SEQUENCES FROM FIELD SAMPLES AND TAXONOMIC REVISIONS OF THE PHOTOSYNTHETIC EUGLENOIDS LEPOCINCLIS (EUGLENA) HELICOIDEUS AND LEPOCINCLIS (PHACUS) HORRIDUS (EUGLENOPHYTA)1

One of the foremost issues in the field of algal taxonomy is the inability to acquire, grow, and sequence new taxa. This problem is particularly true in the study of photosynthetic euglenoids where most of the distinct taxa in culture collections have been sequenced, and many other taxa of interest have been resistant to culturing, and thus, sequencing. In an effort to address this problem, we have utilized a new technique, novel to the field of taxonomy, which allows for the sequencing of nuclear genes from a very small number of cells. Through this procedure, a DNA extraction followed by a multiple displacement amplification (MDA), taxa obtained by field collection had their genomic DNA (gDNA) amplified many fold to microgram quantities. The DNA was then used as template DNA for PCR reactions, and multiple nuclear genes were amplified successfully from several different taxa. By applying this procedure, we were able to shed new light on taxa that have been historically difficult to classify, resulting in the assignment of Euglena helicoideus (C. Bernard) M. S. Benn. et Triemer and Phacus horridus (Pochm.) M. S. Benn. et Triemer to the genus Lepocinclis.     

Biodiversity: bridging the gap between condition and conservation

The aim of this study is to create a two-tiered assessment combining restoration and conservation, both needed for biodiversity management. The first tier of this approach assesses the condition of a site using a standard bioassessment method, AUSRIVAS, to determine whether significant loss of biodiversity has occurred because of human activity. The second tier assesses the conservation value of sites that were determined to be unimpacted in the first step against a reference database. This ensures maximum complementarity without having to set a priori target areas. Using the reference database, we assign site-specific and comparable coefficients for both restoration (Observed/Expected taxa with >50% probability of occurrence) and conservation values (O/E taxa with <50%, rare taxa). In a trial on 75 sites on rivers around Sydney, NSW, Australia we were able to identify three regions: (1) an area that may need restoration; (2) an area that had a high conservation value and; (3) a region that was identified as having significant biodiversity loss but with high potential to respond to rehabilitation and become a biodiversity hotspot. These examples highlight the use of the new framework as a comprehensive system for biodiversity assessment.     

Influence of weather conditions on activity of tropical snakes

Abstract There are many anecdotal reports of massive day‐to‐day variation in activity levels of tropical reptiles and amphibians, and intuition suggests that weather conditions may be responsible for much of that variation. Our analysis of a large data set on the activity levels of tropical snakes and frogs confirms the existence of this short‐term variation in activity levels, reveals strong synchrony between sympatric taxa in this respect, but also shows that standard weather variables (temperature, humidity, precipitation, moonlight, atmospheric pressure) are surprisingly poor at predicting the numbers of individuals and species encountered during standardized surveys. We recorded the numbers of snakes and prey taxa (frogs) encountered on 349 nights over the course of one year on a 1.3‐km transect in the Adelaide River floodplain, in the wet–dry tropics of Australia. Frogs, water pythons (Liasis fuscus), slatey‐grey snakes (Stegonotus cucullatus) and keelbacks (Tropidonophis mairii) all showed strongly seasonal patterns of activity. After adjusting for seasonal differences, encounter rates were related to climatic conditions but different taxa responded to different weather variables. Water python activity was related to amount of moonlight, keelback activity was related to temperature, and frog activity was related to relative humidity, rainfall, temperature and moonlight. However, weather variables explained relatively little of the variation in activity levels. Strong synchrony was evident among encounter rates with various taxa (independent of season and weather conditions), suggesting that activity levels may be determined by other unmeasured factors.     

Jumping and the aerial behavior of aquatic mayfly larvae (Myobaetis ellenae,Baetidae)

Mayfly larvae generally are aquatic, but some madicolous taxa (i.e., living in thin water films) crawl over rocks within streams and waterfalls. When startled, these larvae can break the water film, jump, and enter an aerial phase of locomotion. Because mayfly larvae have been suggested as potential exemplars for the origin of insect wings as tracheal gills, and furthermore represent the most basal extant lineage of pterygotes, we analyzed jumping behavior and free-fall trajectories for one such species of mayfly (Myobaetis ellenae, Baetidae) in Costa Rica. Jumping was commonplace in this taxon, but was undirected and was characterized by body spinning at high angular velocities. No aerodynamic role for the tracheal gills was evident. By contrast, jumping by a sympatric species of bristletail (Meinertellus sp., Archaeognatha) consistently resulted in head-first and stable body postures during aerial translation. Although capable of intermittently jumping into the air, the mayfly larvae could neither control nor target their aerial behavior. By contrast, a stable body posture during jumps in adult bristletails, together with the demonstrated capacity for directed aerial descent in arboreal representatives of this order, support ancestrally terrestrial origins for insect flight within the behavioral context of either jumping or falling from heights.     

Cryptic diversity and female host specificity in a parasitoid where the sexes utilize hosts from separate orders

Investigating complex parasitic life cycles is important for understanding the major fitness components that drive the evolution of host–parasite systems. The rare condition of heterotrophic heteronomy, in which the sexes utilize disparate host taxa, is a poorly understood complex parasitic lifestyle. One of only two known examples occurs in the Myrmecolacidae, an unusual family of the parasitoid order Strepsiptera (Insecta), in which males parasitize ants while females parasitize grasshoppers, crickets, and praying mantids. Here, we reconstruct the evolutionary pattern and timescale of host‐use in a set of morphologically cryptic myrmecolacid taxa currently identified as Caenocholax fenyesi. We find that (i) C. fenyesi contains at least ten cryptic lineages consistent with separate species; (ii) Fossil evidence suggests a very low molecular clock rate and an ancient origin for cryptic lineages; (iii) Diversity among Caenocholax species is partitioned by geography and host association of the female; and (iv) Switches in host usage are uncoupled between the sexes, with changes in female host preference accompanying diversification. This study represents the first phylogeographical analysis of any strepsipteran, and the first molecular examination of host‐use for a heterotrophic heteronomous taxon. Our results have implications for the understanding of evolution, host usage and estimated species richness in parasitic taxa.     

Molecular Phylogenetics of <Emphasis Type="Italic">Aotus</Emphasis> (Platyrrhini,Cebidae)

The accurate identification of taxa of Aotus is essential for 1) the development of precise biomedical assays, 2) the determination of potential illegal traffic of this genus, and 3) conservation. Although many studies have contributed to what we know about the phylogenetics of Aotus, none used a sufficiently large number of samples to clarify its complexity. To address this need, we sequenced 696 base pairs of the mitochondrial cytochrome-oxidase II gene (mtCOII) in 69 specimens of 7 taxa of Aotus. We also analyzed 8 microsatellite loci in 136 individuals of 6 taxa. In contrast to previous studies, we sampled only wild individuals and have a precise geographical origin for each one. The mtDNA results showed that: 1) the northern gray-necked group of Aotus is genetically more homogeneous than the polyphyletic red-necked group of Aotus; 2) the ancestors of Aotus vociferans seem to be the original species candidate for the current Aotus; 3) Aotus azarae azarae and A. a. boliviensis are the most differentiated taxa, likely a result of extreme genetic drift during stasipatric speciation; 4) the first genetic splits found among taxa of Aotus occurred during the Pliocene (or even Miocene) while the most recent ones happened during the Pleistocene, when forest refugia may have played an important role in speciation. The mean number of microsatellite alleles was 3–5.33 alleles per locus. We found some private alleles that could be useful in helping to identify illegal trade, although a larger sample size is needed to ensure that these alleles are really private to the relevant taxa. These new findings increase our understanding of the phylogeny of Aotus and the level of genetic diversity within different taxa of Aotus.     

Tuber aestivum and Tuber uncinatum: two morphotypes or two species?

Tuber spp. are ectomycorrhizal fungi that establish symbioses with shrubs and trees. Because of their different smell and taste, Tuber uncinatum and Tuber aestivum are two truffle morphotypes with a different market value, but whether or not T. uncinatum and T. aestivum are different taxa is still an open debate among mycologists. In order to identify molecular keys characterizing both T. aestivum and T. uncinatum morphotypes, ITS/RFLPs analyses were carried out on a large collection of samples from all over Italy and from other European countries, followed by a study of the phylogenesis of ITS, beta-tubulin and EF 1-alpha genes, on representative samples. The present study provides compelling evidence that: (i) T. uncinatum and T. aestivum belong to the same species, (ii) neither morphotype presents a specific molecular fingerprint, but they may even share identical alleles at any of the loci analysed; (iii) T. aestivum is most likely under a selfing reproductive mode. Our findings suggest that ecological, rather than genetic causes may account for differences in sporal morphology, taste and smell between T. aestivum and T. uncinatum truffles.     

Seasonality of biogeochemically relevant microbial genes in a coastal ocean microbiome

Microbes drive the biogeochemical cycles of marine ecosystems through their vast metabolic diversity. While we have a fairly good understanding of the spatial distribution of these metabolic processes in various ecosystems, less is known about their seasonal dynamics. We investigated the annual patterns of 21 biogeochemical relevant functions in an oligotrophic coastal ocean site by analysing the presence of key genes, analysing high-rank gene taxonomy and the dynamics of nucleotide variants. Most genes presented seasonality: photoheterotrophic processes were enriched during spring, phosphorous-related genes were dominant during summer, coinciding with potential phosphate limitation, and assimilatory nitrate reductases appeared mostly during summer and autumn, correlating negatively with nitrate availability. Additionally, we identified the main taxa driving each function at each season and described the role of underrecognized taxa such as Litoricolaceae in carbon fixation (rbcL), urea degradation (ureC), and CO oxidation (coxL). Finally, the seasonality of single variants of some families presented a decoupling between the taxonomic abundance patterns and the functional gene patterns, implying functional specialization of the different genera. Our study unveils the seasonality of key biogeochemical functions and the main taxonomic groups that harbour these relevant functions in a coastal ocean ecosystem.     

Regulation of the kinase activity of the MIK GCK-like MAP4K by alternative splicing

Alternative splicing of introns is essential to ensure the complexity of mammalian genome functions. In particular, the generation of a high number of different isoforms by alternative splicing is an important characteristic of genes coding for signalling proteins such as mitogen activated protein kinases (MAPKs). This is thought to allow these proteins to transduce multiple stimuli in a highly regulated manner. Plant genes are also subjected to alternative splicing. Nevertheless, clear examples of the functional consequences of this phenomenon are still scarce in plants. MIK is a maize gene coding for a GCK-like MAP4K that can be activated by interaction with maize atypical receptor kinase (MARK), an atypical receptor kinase. Here we show that MIK is subjected to alternative splicing. Expression of MIK leads to, at least, 4 different mature mRNAs that accumulate with particular expression profiles during maize development. Our results show that the polypeptides encoded by the different MIK mRNAs display different kinase activity and are differentially activated by interaction with the MARK receptor. Two MIK isoforms display constitutive kinase activity, one isoform is inactive but can be activated by MARK, and the fourth MIK isoform is inactive and cannot be activated by MARK. Our results constitute a clear example of the biochemical consequences of alternative splicing in plants. The selective conservation during evolution of the intron–exon structure of the region coding for the regulator domain of MIK, as well as the maintenance in maize, rice and Arabidopsis of the alternative splicing of some of these introns, are strong indications of its functional importance.