Culture and genomic analysis of Symbiopectobacterium purcellii, gen.nov. sp. nov., isolated from the leafhopper Empoasca decipiens

Bacterial endosymbionts are found in multiple arthropod species, where they play crucial roles as nutritional symbionts, defensive symbionts or reproductive parasites. Recent work has highlighted a new clade of heritable microbes within the gammaproteobacteria that enter into both obligate and facultative symbioses, with an obligately required unculturable symbiont recently given the name Cand. Symbiopectobacterium. In this study, we describe a culturable rod shaped non-flagellated bacterial symbiont from this clade isolated from the leafhopper Empoasca decipiens. The symbiont is related to the transovarially-transmitted 'BEV' bacterium that was first isolated from the leafhopper Euscelidius variegatus by Alexander Purcell, and we therefore name the symbiont Symbiopectobacterium purcellii sp. nov. gen. nov. We further report the closed genome sequence for S. purcellii. The genome is atypical for a heritable microbe, being large in size, without profound AT bias and with little evidence of pseudogenization. The genome is predicted to encode Type II, III and VI secretion systems and associated effectors and a non-ribosomal peptide synthase array likely to produce bioactive small molecules. Predicted metabolism is more complete than for other symbionts in the Symbiopectobacterium clade, and the microbe is predicted to synthesize a range of B vitamins. However, Biolog plate analysis indicate metabolism is depauperate compared to the sister clade, represented by Pectobacterium carotovorum. A quorum-sensing pathway related to that of Pectobacterium spp. (containing an overlapping expI-expR1 pair in opposite directions and a "solo" expR2) is evidenced, and LC-MS/MS analysis reveals the presence of 3-hydroxy-C10-HSL as the sole N-acylhomoserine lactone (AHL) in our strain. This AHL profile is profoundly divergent from that of other Erwinia and Pectobacterium spp., which produce mostly 3-oxo-C6- and 3-oxo-C8-HSL and could aid group identification. Thus, this microbe denotes one that has lost certain pathways associated with a saprophytic lifestyle but represents an important baseline against which to compare other members of the genus Symbiopectobacterium that show more profound integration into host biology.

Crassoascoma gen. nov. (Lentitheciaceae, Pleosporales): Unrevealing Microfungi from the Qinghai-Tibet Plateau in China

Microfungi associated with woody plants on the Qinghai–Tibet Plateau (QTP) were investigated, and four collections associated with Potentilla fruticosa were obtained from Gansu and Qinghai provinces in China. Morphologically, they line well with Lentitheciaceae in having subglobose to globose ascomata with brown setae on the papilla but can be distinguished from other genera by its superficial, globose, black, thick-walled ascomata, and fusiform, hyaline (rarely pale brown), one-septate ascospores, surrounded by an entire mucilaginous sheath. The phylogenetic analyses based on a combined SSU, ITS, LSU and TEF1-α sequence data showed that four isolates formed a monophyletic clade among the genera of Lentitheciaceae, and present as a distinct lineage (sister clade to Darksidea). Therefore, we introduce a new genus Crassoascoma, with C. potentillae as the type to accommodate these taxa. Detailed description and illustration are provided, and the establishment of new taxa is justified with morphology and phylogenetic evidence.

The Occurrence of Quill Mites (Arachnida: Acariformes: Syringophilidae) on Bee-Eaters (Aves: Coraciiformes: Meropidae: Merops) of Two Sister Clades

We studied the quill mite fauna of the family Syringophilidae, associated with bee-eaters. We examined 273 bird specimens belonging to nine closely related species of the genus Merops, representing two phylogenetic sister clades of a monophyletic group. Our examination reveals the presence of two species of the genus Peristerophila, as follows: (1) a new species Peristerophila mayri sp. n. from Merops viridis in the Philippines, M. leschenaulti in Nepal and Sri Lanka, and M. orientalis in Sri Lanka; and (2) P. meropis from M. superciliosus in Tanzania and Egypt, M. persicus in Sudan, Tanzania, Liberia, Senegal, Kenya, and D.R. Congo, M. ornatus in Papua New Guinea, M. philippinus in Thailand, Indonesia and Sri Lanka, and M. americanus in the Philippines. The prevalence of host infestations by syringophilid mites varied from 3.1 to 38.2%. The distribution of syringophilid mites corresponds with the sister clade phylogenetic relationships of the hosts, except for P. meropis associated with Merops americanus. Possible hypotheses for the host lineage shift are proposed.

In search for the unlikely: Leaf-mining caterpillars (Gracillariidae, Lepidoptera) from Upper Cretaceous and Eocene ambers

Fossil leaf-mining caterpillars from amber are firstly described as the new species Phyllocnistis cretacea from Upper Cretaceous Myanmar amber and Phyllonorycter inopinata from Eocene Baltic amber. Both show typical traits of leaf-miners, and specifically, of later instars of caterpillars of their respective genera. The findings give further evidence for these being quite old and conservative genera of Gracillariidae. These are basal Ditrysia which retained the larval feeding and mining live mode. The findings also represent direct fossil evidence of individual stages of hypermetamorphosis known from extant Gracillariidae. The finds from the Upper Cretaceous and their putative identifications give direct evidence for a minimal geological age for the genus Phyllocnistis (Phyllocnistinae) and, by indirect conclusion based on their divergence, also for the genus Phyllonorycter in a sister clade (Lithocolletinae). It also predates mining habit closer to the time of radiation of their angiospermous host plants.

Rhythmic Clock Gene Expression in Atlantic Salmon Parr Brain

To better understand the complexity of clock genes in salmonids, a taxon with an additional whole genome duplication, an analysis was performed to identify and classify gene family members (clock, arntl, period, cryptochrome, nr1d, ror, and csnk1). The majority of clock genes, in zebrafish and Northern pike, appeared to be duplicated. In comparison to the 29 clock genes described in zebrafish, 48 clock genes were discovered in salmonid species. There was also evidence of species-specific reciprocal gene losses conserved to the Oncorhynchus sister clade. From the six period genes identified three were highly significantly rhythmic, and circadian in their expression patterns (per1a.1, per1a.2, per1b) and two was significantly rhythmically expressed (per2a, per2b). The transcriptomic study of juvenile Atlantic salmon (parr) brain tissues confirmed gene identification and revealed that there were 2,864 rhythmically expressed genes (p < 0.001), including 1,215 genes with a circadian expression pattern, of which 11 were clock genes. The majority of circadian expressed genes peaked 2 h before and after daylight. These findings provide a foundation for further research into the function of clock genes circadian rhythmicity and the role of an enriched number of clock genes relating to seasonal driven life history in salmonids.

Issi saaneq gen. et sp. nov.—A New Sauropodomorph Dinosaur from the Late Triassic (Norian) of Jameson Land, Central East Greenland

The Late Triassic (Norian) outcrops of the Malmros Klint Formation, Jameson Land (Greenland) have yielded numerous specimens of non-sauropod sauropodomorphs. Relevant fossils were briefly reported in 1994 and were assigned to Plateosaurus trossingensis. However, continuous new findings of early non-sauropod sauropodomorphs around the globe facilitate comparisons and allow us to now revise this material. Here, the non-sauropod sauropodomorph Issi saaneq gen. et sp. nov. is described based on two almost complete and articulated skulls. The two skulls represent a middle-stage juvenile and a late-stage juvenile or subadult. Issi saaneq differs from all other sauropodomorphs by several unique traits: (1) a small foramen at the medial surface of the premaxilla; (2) an anteroposteriorly elongated dorsoposterior process of the squamosal; (3) a relatively high quadrate relative to rostrum height; (4) a well-developed posterodorsal process of the articular. These features cannot be explained by taphonomy, ontogeny, or intraspecific variation. Issi saaneq shows affinities to Brazilian plateosaurids and the European Plateosaurus, being recovered as the sister clade of the latter in our phylogenetic analysis. It is the northernmost record of a Late Triassic sauropodomorph, and a new dinosaur species erected for Greenland. Issi saaneq broadens our knowledge about the evolution of plateosaurid sauropodomorphs.

The role of vicariance and dispersal on the temporal range dynamics of forest vipers in the Neotropical region

The emergence of the diagonal of open/dry vegetations, including Chaco, Cerrado and Caatinga, is suggested to have acted as a dispersal barrier for terrestrial organisms by fragmenting a single large forest that existed in South America into the present Atlantic and Amazon forests. Here we tested the hypothesis that the expansion of the South American diagonal of open/dry landscapes acted as a vicariant process for forest lanceheads of the genus Bothrops, by analyzing the temporal range dynamics of those snakes. We estimated ancestral geographic ranges of the focal lancehead clade and its sister clade using a Bayesian dated phylogeny and the BioGeoBEARS package. We compared nine Maximum Likelihood models to infer ancestral range probabilities and their related biogeographic processes. The best fitting models (DECTS and DIVALIKETS) recovered the ancestor of our focal clade in the Amazon biogeographic region of northwestern South America. Vicariant processes in two different subclades resulted in disjunct geographic distributions in the Amazon and the Atlantic Forest. Dispersal processes must have occurred mostly within the Amazon and the Atlantic Forest and not between them. Our results suggest the fragmentation of a single ancient large forest into the Atlantic and Amazon forests acting as a driver of vicariant processes for the snake lineage studied, highlighting the importance of the diagonal of open/dry landscapes in shaping distribution patterns of terrestrial biota in South America.

Karyotype structure and cytogenetic markers of Amoimyrmex bruchi and Amoimyrmex silvestrii: the contribution to understanding leafcutting ant relationships

Leafcutting ants are considered the most important herbivores in terrestrial environments throughout the Neotropics. <i>Amoimyrmex</i> is the sister clade of the remaining leafcutter ants from the genera <i>Atta</i> and <i>Acromyrmex</i>. <i>Amoimyrmex striatus</i> was the only species cytogenetically studied within the genus and shares the same chromosomal number with <i>Atta</i>, bearing 22 chromosomes, whereas <i>Acromyrmex</i> bears 38 chromosomes, with the exception of the social parasite <i>Acromyrmex ameliae</i> (2n=36). Our objective here was to analyze cytogenetically the species of <i>Amoimyrmex bruchi</i> and <i>Amoimyrmex silvestrii</i>, as well as to describe the karyotype of these sister species, by means of an integrative approach using classical and molecular cytogenetics. We aimed to characterize cytogenetic markers that contribute to the systematics and taxonomy of the genus. Our results showed that the karyotypes of these two species are very similar, with an identical chromosome number (2n=22), chromosome morphology (2K=20m+2sm), and location of 18S rDNA and the telomeric repeat TTAGG on the chromosomes. Yet, the microsatellite probe GA(15) showed variation across the species and populations studied. We suggest that both species diverged relatively recently and are unmistakably sisters because of the many shared characteristics, including the highly conserved karyotypes.

Comparative Mitogenomes of Two Coreamachilis Species (Microcoryphia: Machilidae) along with Phylogenetic Analyses of Microcoryphia

The order Microcoryphia, commonly known as bristletails, is considered as the most primitive one among living insects. Within this order, two species, Coreamachilis coreanus and C. songi (Machilidae: Machilinae), display the following contrasting reproductive strategies: parthenogenesis occurs in C. coreanus, whereas sexual reproduction is found in C. songi. In the present study, the complete mitogenomes of C. coreanus and C. songi were sequenced to compare their mitogenome structure, analyze relationships within the Microcoryphia, and assess adaptive evolution. The length of the mitogenomes of C. coreanus and C. songi were 15,578 bp and 15,570 bp, respectively, and the gene orders were those of typical insects. A long hairpin structure was found between the ND1 and 16S rRNA genes of both species that seem to be characteristic of Machilinae and Petrobiinae species. Phylogenetic assessment of Coreamachilis was conducted using BI and ML analyses with concatenated nucleotide sequences of the 13 protein-coding genes. The results showed that the monophyly of Machilidae, Machilinae, and Petrobiinae was not supported. The genus Coreamachilis (C. coreanus and C. songi) was a sister clade to Allopsontus helanensis, and then the clade of ((C. coreanus + C. songi) + A. helanensis) was a sister clade to A. baii, which suggests that the monophyly of Allopsontus was not supported. Positive selection analysis of the 13 protein-coding genes failed to reveal any positive selection in C. coreanus or C. songi. The long hairpin structures found in Machilinae and Petrobiinae were highly consistent with the phylogenetic results and could potentially be used as an additional molecular characteristic to further discuss relationships within the Microcoryphia.

Rhythmic clock gene expression in Atlantic salmon parr brain

To better understand the complexity of clock genes in salmonids, a taxon with an additional whole genome duplication, an analysis was performed to identify and classify gene family members (clock, arntl, period, cryptochrome, nr1d, ror, and csnk1). The majority of clock genes in zebrafish and Northern pike, appeared to be duplicated. In comparison to the 29 clock genes described in zebrafish, 48 clock genes were discovered in salmonid species. There was also evidence of species-specific reciprocal gene losses conserved to the Oncorhynchus sister clade. From the six period genes identified four were highly significantly rhythmically expressed (per1a.1, per1a.2, per1b, per2b) and one was marginally significantly rhythmically expressed (per2a). The transcriptomic study of juvenile Atlantic salmon (parr) brain tissues confirmed gene identification and revealed that there were 1,642 rhythmically expressed genes (p < 0.001), of which 12 were clock genes. The majority of rhythmically expressed genes peaked two hours before and after daylight. These findings provide a foundation for further research into the function of clock genes circadian rhythmicity and the role of an enriched number of clock genes relating to seasonal driven life history in salmonids.