Microbe Profile: Buchnera aphidicola: ancient aphid accomplice and endosymbiont exemplar

Buchnera aphidicola is an obligate endosymbiont of aphids that cannot be cultured outside of hosts. It exists as diverse strains in different aphid species, and phylogenetic reconstructions show that it has been maternally transmitted in aphids for >100 million years. B. aphidicola genomes are highly reduced and show conserved gene order and no gene acquisition, but encoded proteins undergo rapid evolution. Aphids depend on B. aphidicola for biosynthesis of essential amino acids and as an integral part of embryonic development. How B. aphidicola populations are regulated within hosts remains little known.

Reconstruction of intrageneric relationships within the Indo-West Pacific littoral crab genus Metopograpsus (Decapoda, Brachyura, Grapsidae): an alternative speciation order according to a 28S rDNA molecular phylogeny

The genus Metopograpsus H. Milne Edwards, 1853 is widespread throughout the Indo-West Pacific and currently consists of seven species that can only be separated by minor morphological differences. Therefore, it represents a good example for the usefulness of genetic analyses for identification and classification. In order to obtain phylogenetic information at both lower and higher evolutionary levels, it is best to use a combination of mitochondrial and nuclear molecular markers. Here we present for the first time a molecular phylogeny based on a relative long fragment of the 28S rRNA nuclear gene for the genus Metopograpsus, after application of newly developed primers. Our data suggest an alternative intrageneric speciation order, with M. thukuhar and M. cannicci holding a basal position and a monophyletic grouping of M. frontalis, M. oceanicus and M. quadridentatus, which differs from prior phylogenetic reconstructions. Previously recognized intraspecific phylogeographic patterns in M. latifrons and M. quadridentatus could not be confirmed, due to limited variability of this conserved nuclear gene and due to an incomplete geographic coverage of the corresponding species. In contrast, the previously indicated phylogenetic subdivision within the formerly widespread species M. thukuhar, which led to the recent description of M. cannicci, is here supported.

Genomic Insights into the Distribution and Phylogeny of Glycopeptide Resistance Determinants within the Actinobacteria Phylum

The spread of antimicrobial resistance (AMR) creates a challenge for global health security, rendering many previously successful classes of antibiotics useless. Unfortunately, this also includes glycopeptide antibiotics (GPAs), such as vancomycin and teicoplanin, which are currently being considered last-resort drugs. Emerging resistance towards GPAs risks limiting the clinical use of this class of antibiotics—our ultimate line of defense against multidrug-resistant (MDR) Gram-positive pathogens. But where does this resistance come from? It is widely recognized that the GPA resistance determinants—van genes—might have originated from GPA producers, such as soil-dwelling Gram-positive actinobacteria, that use them for self-protection. In the current work, we present a comprehensive bioinformatics study on the distribution and phylogeny of GPA resistance determinants within the Actinobacteria phylum. Interestingly, van-like genes (vlgs) were found distributed in different arrangements not only among GPA-producing actinobacteria but also in the non-producers: more than 10% of the screened actinobacterial genomes contained one or multiple vlgs, while less than 1% encoded for a biosynthetic gene cluster (BGC). By phylogenetic reconstructions, our results highlight the co-evolution of the different vlgs, indicating that the most diffused are the ones coding for putative VanY carboxypeptidases, which can be found alone in the genomes or associated with a vanS/R regulatory pair.

Take a deep breath… The evolution of the respiratory system of symphytognathoid spiders (Araneae, Araneoidea)

Spiders are unique in having a dual respiratory system with book lungs and tracheae, and most araneomorph spiders breathe simultaneously via book lungs and tracheae, or tracheae alone. The respiratory organs of spiders are diverse but relatively conserved within families. The small araneoid spiders of the symphytognathoid clade exhibit a remarkably high diversity of respiratory organs and arrangements, unparalleled by any other group of ecribellate orb weavers. In the present study, we explore and review the diversity of symphytognathoid respiratory organs. Using a phylogenetic comparative approach, we reconstruct the evolution of the respiratory system of symphytognathoids based on the most comprehensive phylogenetic frameworks to date. There are no less than 22 different respiratory system configurations in symphytognathoids. The phylogenetic reconstructions suggest that the anterior tracheal system evolved from fully developed book lungs and, conversely, reduced book lungs have originated independently at least twice from its homologous tracheal conformation. Our hypothesis suggests that structurally similar book lungs might have originated through different processes of tracheal transformation in different families. In symphytognathoids, the posterior tracheal system has either evolved into a highly branched and complex system or it is completely lost. No evident morphological or behavioral features satisfactorily explains the exceptional variation of the symphytognathoid respiratory organs.

Evolution and phylogeny of the deep-sea isopod families Desmosomatidae Sars, 1897 and Nannoniscidae Hansen, 1916 (Isopoda: Asellota)

In the deep sea, the phylogeny and biogeography of only a few taxa have been well studied. Although more than 200 species in 32 genera have been described for the asellote isopod families Desmosomatidae Sars, 1897 and Nannoniscidae Hansen, 1916 from all ocean basins, their phylogenetic relationships are not completely understood. There is little doubt about the close relationship of these families, but the taxonomic position of a number of genera is so far unknown. Based on a combined morphological phylogeny using the Hennigian method with a dataset of 107 described species and a molecular phylogeny based on three markers (COI, 16S, and 18S) with 75 species (most new to science), we could separate Desmosomatidae and Nannoniscidae as separate families. However, we could not support the concept of the subfamilies Eugerdellatinae Hessler, 1970 and Desmosomatinae Hessler, 1970. Most genera of both families were well supported, but several genera appear as para- or even polyphyletic. Within both families, convergent evolution and analogies caused difficulty in defining apomorphies for phylogenetic reconstructions and this is reflected in the results of the concatenated molecular tree. There is no biogeographic pattern in the distribution as the genera occur over the entire Atlantic and Pacific Ocean, showing no specific phylogeographical pattern. Poor resolution at deep desmosomatid nodes may reflect the long evolutionary history of the family and rapid evolutionary radiations.

Observations on the population genetic structure of the leaf galling nematode, Ditylenchus gallaeformans

Ditylenchus gallaeformans is a plant parasitic nematode that induces galls on aboveground parts of Melastomataceae plants. It differs from most gall-inducing nematodes in that it is not an endoparasite, and has been considered as a possible biological control agent against invasive species of Miconia . Little is known about D. gallaeformans biology, genetic differences among populations and host preferences. This study examined the genetic differences among D. gallaeformans populations from different locations and host species and the phylogenetic relationships among them. Nematodes were collected from galls in plants from Costa Rica, Dominica, and Trinidad. The Cytochrome c oxidase 1 (cox1) region was sequenced from a total of 33 individual nematodes isolated from 33 different plant individuals, representing 21 species of Melastomataceae. Phylogenetic reconstructions, haplotype networks, and analysis of molecular variance showed that the species is monophyletic and has three major clades, which were mostly consistent with geographic location but not with host species. The first clade was composed by two subclades, one with individuals from Costa Rica and one with individuals from Dominica. The second and third clades comprised nematodes only from Trinidad. Overall, there is no evidence of host-species specialization in D. gallaeformans . Biocontrol efforts using the nematode against invasive Miconia could focus on geographical location matching but likely will not need to match host species.

Gene Flow and Diversification in Himalopsyche martynovi Species Complex (Trichoptera: Rhyacophilidae) in the Hengduan Mountains

The Hengduan Mountains are one of the most species-rich mountainous areas in the world. The origin and evolution of such a remarkable biodiversity are likely to be associated with geological or climatic dynamics, as well as taxon-specific biotic processes (e.g., hybridization, polyploidization, etc.). Here, we investigate the mechanisms fostering the diversification of the endemic Himalopsyche martynovi complex, a poorly known group of aquatic insects. We used multiple allelic datasets generated from 691 AHE loci to reconstruct species and RaxML phylogenetic trees. We selected the most reliable phylogenetic tree to perform network and gene flow analyses. The phylogenetic reconstructions and network analysis identified three clades, including H. epikur, H. martynovi sensu stricto and H. cf. martynovi. Himalopsyche martynovi sensu stricto and H. cf. martynovi present an intermediate morphology between H. epikur and H. viteceki, the closest known relative to the H. martynovi-complex. The gene flow analysis revealed extensive gene flow among these lineages. Our results suggest that H. viteceki and H. epikur are likely to have contributed to the evolution of H. martynovi sensu stricto and H. cf. martynovi via gene flow, and thus, our study provides insights in the diversification process of a lesser-known ecological group, and hints at the potential role of gene flow in the emergence of biological novelty in the Hengduan Mountains.

Gene Flow and Diversification in Himalopsyche Martynovi Species Complex (Trichoptera: Rhyacophilidae) In the Hengduan Mountains

Background: The Hengduan Mountains are one of the most species–rich mountainous areas in the world. The origin and evolution of such a remarkable biodiversity are likely to be associated with geological or climatic dynamics, as well as taxon-specific biotic processes (e.g., hybridization, polyploidization, etc.). Here, we investigate the mechanisms fostering the diversification of the endemic Himalopsyche martynovi complex, a poorly known group of aquatic insects. Methods: We used multiple allelic datasets generated from 691 AHE loci to reconstruct species and RaxML phylogenetic trees. We selected the most reliable phylogenetic tree to perform network and gene flow analyses. Results: Phylogenetic reconstructions and network analysis identified three clades, including H. epikur, H. martynovi sensu stricto and H. cf. martynovi. Himalopsyche martynovi sensu stricto and H. cf. martynovi present an intermediate morphology between H. epikur and H. viteceki, the closest known relative to the H. martynovi–complex. The gene flow analysis revealed extensive gene flow among these lineages. Conclusion: Our results suggest that H. viteceki and H. epikur are likely to have contributed to the evolution of H. martynovi sensu stricto and H. cf. martynovi via gene flow, and thus, our study provides insights in the diversification process of a lesser–known ecological group, and hints at the potential role of gene flow in the emergence of biological novelty in the Hengduan Mountains.

Checklist of fossil liverworts suitable for calibrating phylogenetic reconstructions

The number of available liverwort fossils substantially increased within the past decade, which is mainly due to new findings from Cretaceous and Cenozoic amber deposits. Many of them, however, are fragmentary and not predestined for consideration in evolutionary analyses. Here, we list those liverwort fossils that we suggest as suitable for calibrating phylogenetic reconstructions, along with brief descriptions, justification of their use, and age information. Our recommendations are based on thorough microscopic investigation of available fossils from worldwide amber collections including recent findings. We recommend that the following 42 fossil taxa can be used as confident minimum age constraints in phylogenetic reconstructions: Acrolejeunea ucrainica (35 Ma), Anastrophyllum rovnoi (35 Ma), Bazzania polyodus (34 Ma), Blepharolejeunea obovata (15 Ma), the genus Bryopteris with B. bispinosa and B. succinea (15 Ma), Calypogeia stenzeliana (34 Ma), Cephaloziella nadezhdae (35 Ma), the genus Ceratolejeunea with C. antiqua, C. palaeomexicana, and C. sublaetefusca (15 Ma), Cheilolejeunea latiloba (34 Ma), Cheirorhiza brittae (158 Ma), Cololejeunea sp. (15 Ma), Cyclolejeunea archaica (15 Ma), Dibrachiella grollei (15 Ma), Diettertia montanensis (112 Ma), Drepanolejeunea eogena (15 Ma), the genus Frullania with F. baerlocheri, F. cretacea, and F. partita (99 Ma), Frullania subgen. Frullania with F. casparyi (34 Ma) and F. riclefgrollei (35 Ma), F. subgen. Trachycolea with F. rovnoi (35 Ma) and F. schumannii (34 Ma), Gackstroemia cretacea (99 Ma), Geocalyx heinrichsii (34 Ma), the genus Lejeunea with L. hamatiloba, L. miocenica, L. resinata, and L. urbanioides (15 Ma), Lopholejeunea subnigricans (15 Ma), Marchantites cyathodoides (228 Ma), Marchesinia brachiata (15 Ma), Metzgeriothallus sharonae (383 Ma), Microlejeunea nyiahae (52 Ma), Neurolejeunea macrostipula (15 Ma), Nipponolejeunea europaea (34 Ma), Notoscyphus balticus (34 Ma), Odontoschisma (sect. Iwatsukia) dimorpha (34 Ma), Plagiochila groehnii (34 Ma), Porella subgrandiloba (34 Ma), Protolophozia kutscheri (34 Ma), Radula (subgen. Odontoradula) cretacea (99 Ma), R. (subgen. Amentuloradula) heinrichsii (99 Ma), Scapania hoffeinsiana (34 Ma), Solenostoma berendtii (34 Ma), Spruceanthus polonicus (34 Ma), Stictolejeunea squamata (15 Ma), Tetralophozia groehnii (34 Ma), Thysananthus auriculatus (15 Ma), Thysananthus contortus (34 Ma). Furthermore, we transfer Lophozia kutscheri to Protolophozia, Archilejeunea grollei to Dibrachiella, Frullania ucrainica to Acrolejeunea, and Mastigolejeunea extincta to Spruceanthus, based on new fossil evidence and morphological revisions.

Diversity of Xanthoparmelia (Parmeliaceae) species in Mexican xerophytic scrub vegetation, evidenced by molecular, morphological and chemistry data

The genus Xanthoparmelia is the largest genus of lichen- forming fungi with about 800 species worldwide. Xanthoparmelia is also common in the deserts of central Mexico, but only a few molecular studies exist on its species’ diversity in this region. In this study, we sampled 38 Xanthoparmelia species from around the world including species from the xerophytic scrubs of central Mexico to assess the diversity using an integrative approach. Molecular phylogenetic analyses were performed using a combination of the ITS, mtSSU and nuLSU genetic markers. We evaluated our phylogenetic results in a context of traditional morphological and chemical characters. The combined evidence of molecular, morphological, and chemical data identified a total of 18 Xanthoparmelia species-level lineages occurring in central Mexico. However, numerous traditionally circumscribed species did not form monophyletic groups in the molecular phylogenetic reconstructions. This conflict indicates that taxonomy and species delimitation in the genus Xanthoparmelia requires revision and emphasizes the importance of molecular evidence for more robust species delimitations in this genus.