Putative Origin Research Articles

Chromatic Acclimation Processes and Their Relationships with Phycobiliprotein Complexes.

Chromatic acclimation (CA) is a widespread mechanism for optimizing the composition of phycobiliprotein complexes to maximize the cyanobacterial light capture efficiency. There are seven CA types, CA1-CA7, classified according to various photoregulatory pathways. Here, we use sequence analyses and bioinformatics to predict the presence of CA types according to three GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA)-containing photoreceptors, CcaS (cyanobacterial chromatic acclimation sensor), RcaE (regulator of chromatic adaptation), and RfpA (regulator for far-red photoacclimation). These photoreceptors were classified into three different phylogenetic groups leading different CA types in a diverse range of cyanobacteria. Combining with genomic information of phycobilisome compositions, the CA capabilities of various cyanobacteria were conjectured. Screening 65 accessible cyanobacterial genomes, we defined 19 cyanobacteria that have the capability to perform far-red light photoacclimation (FaRLiP) under the control of RfpA. Forty out of sixty-five cyanobacteria have the capability to perform green/red light photoacclimation, although they use different photoreceptors (RcaE and/or CcaS) and photoregulatory pathways. The reversible response of photoreceptors in CA regulation pathways trigged by changed light conditions reflects the flexibility of photoregulatory mechanisms in cyanobacteria and the putative independent evolutionary origin of photoacclimation types.

The Significance of Pain Drawing as a Screening Tool for Cervicogenic Headache and Associated Symptoms in Chronic Fatigue.

PurposePatients with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) present with a broad spectrum of symptoms, including headache. A simple, yet powerful tool – the pain drawing identifies essential aspects such as pain distribution. The aim with this study was to 1) evaluate the significance of pain drawing as a screening tool for cervicogenic headache using a predefined C2 pain pattern, 2) assess whether there was an association between dizziness/imbalance and a C2 pain pattern, and 3) compare subgroups according to the pain drawing with respect to pain characteristics and quality of life.Patients and MethodsPain drawings and clinical data from 275 patients investigated for ME/CFS were stratified into: 1) cervicogenic headache as determined by a C2 pain pattern, 2) headache with no C2 pain pattern, and 3) no headache. For inference logistic regression presented with odds ratios (OR) and 95% confidence intervals (95% CI) and Kruskal–Wallis test were applied.ResultsOne hundred sixteen participants (42%) were stratified to the group for which the pain drawing corresponded to the C2 pain pattern, thus indicating putative cervicogenic origin of the headache. Dizziness/imbalance was strongly associated with a C2 pain pattern; OR 6.50 ([95% CI 2.42–17.40] p ˂ 0.00), whereas this association was non-significant for patients with headache and no C2 pain pattern. Those demonstrating a C2 pain pattern reported significantly higher pain intensity (p = 0.00) and greater pain extent (p = 0.00) than the other groups, and lower health-related quality of life (p = 0.00) than the group with no headache.ConclusionFor patients with chronic fatigue who present with a C2 pain pattern (interpreted as cervicogenic headache) the pain drawing seems applicable as a screening tool for signs associated with neuropathic and more severe pain, dizziness and reduced quality of life as detection of these symptoms is essential for targeted treatment.

Molecular Assessments, Statistical Effectiveness Parameters and Genetic Structure of Captive Populations of Tursiops truncatus Using 15 STRs.

Simple SummaryThe bottlenose dolphins are one of the most used species in entertainment, assisted therapy, education, and research on welfare. However, their maintenance in captivity requires powerful and sensitive tools for preserving their diversity. The number of genetic markers for this purpose remains controversial, restraining the marine species’ genetic diversity determination. We aimed to select 15 hypervariable molecular markers whose statistical parameters were made in 210 captive dolphins from 18 Mexican centers to support their usefulness. The proposed set of markers allowed us to obtain a genetic fingerprint of each dolphin. Additionally, we identified the structure of the captive population, analyzing the groups according to the capture location. Such characterization is key for maintaining the captive species’ biodiversity rates within conservation and reintroduction programs. However, these 15 genetic markers can also be helpful for small- isolated populations, subspecies and other genera of endangered and vulnerable species. Genetic analysis is a conventional way of identifying and monitoring captive and wildlife species. Knowledge of statistical parameters reinforcing their usefulness and effectiveness as powerful tools for preserving diversity is crucial. Although several studies have reported the diversity of cetaceans such as Tursiops truncatus using microsatellites, its informative degree has been poorly reported. Furthermore, the genetic structure of this cetacean has not been fully studied. In the present study, we selected 15 microsatellites with which 210 dolphins were genetically characterized using capillary electrophoresis. The genetic assertiveness of this set of hypervariable markers identified one individual in the range of 6.927e13 to 1.806e16, demonstrating its substantial capability in kinship relationships. The genetic structure of these 210 dolphins was also determined regarding the putative capture origin; a genetic stratification (k = 2) was found. An additional dolphin group of undetermined origin was also characterized to challenge the proficiency of our chosen markers. The set of markers proposed herein could be a helpful tool to guarantee the maintenance of the genetic diversity rates in conservation programs both in Tursiops truncatus and across other odontocetes, Mysticeti and several genera of endangered and vulnerable species.

On the origin of the two putative allopolyploids, Opuntia curvispina and O. martiniana (Cactaceae): A case of cryptic speciation in prickly pear cacti

The putative allopolyploid taxon, Opuntia curvispina, is distributed from northeastern Arizona and southern Nevada to southeastern California, where it often grows in close proximity to, or sympatric with, O. chlorotica, O. engelmannii and O. phaeacantha. Another putative allopolyploid, O. martiniana, grows sympatrically with O. curvispina in only one area north of the Hualapai Mts., northwestern Arizona. Both of these taxa have previously been treated as either nothospecies or mere spontaneous hybrids by previous researchers. My objectives were to determine the origins of both O. curvispina and O. martiniana to test previous hypotheses of hybrid origin, with O. curvispina putatively derived from O. chlorotica and O. phaeacantha and O. martiniana putatively derived from O. chlorotica and O. engelmannii. I also wanted to determine the overall extent of the ranges of the two taxa by expanding collections and verifying existing herbarium collections, as numerous specimens identified as O. martiniana and O. curvispina have been reported from outside of their expected ranges. My data indicate that O. curvispina indeed is partially derived from O. chlorotica, as well as another putative parent, likely O. phaeacantha, while O. martiniana appears to be most likely derived from O. curvispina and O. macrorhiza, two taxa not before implicated in the origin of O. martiniana. The hexaploid O. phaeacantha also appears to be non-monophyletic and may have been derived several times from different hybridization events. Careful morphological study of O. martiniana clearly separates that species from O. curvispina, although it may be considered cryptically different, a likely result of its partial putative origin from O. curvispina. Given the very broad distribution and dominance of O. curvispina in parts of its range, it is most appropriate to recognize this allopolyploid as a species, rather than as a nothotaxon, as previously designated. The unique feature of an obovate or urceolate style in Opuntia martiniana appears to be a transgressive trait rather than a synapomorphy, given that the taxon is derived from reticulation, and neither putative parent exhibits that character state. This work provides a framework for species recognition using DNA sequence data, morphological characters, geography and cytological information—a total evidence approach clearly needed for taxonomically difficult taxa, such as many within the genus Opuntia. A treatment of O. curvispina and O. martiniana is given with updated descriptions, and O. martiniana is neotypified.

Unprecedented frequency of mitochondrial introns in colonial bilaterians

Animal mitogenomes are typically devoid of introns. Here, we report the largest number of mitochondrial introns ever recorded from bilaterian animals. Mitochondrial introns were identified for the first time from the phylum Bryozoa. They were found in four species from three families (Order Cheilostomatida). A total of eight introns were found in the complete mitogenome of Exechonella vieirai, and five, 17 and 18 introns were found in the partial mitogenomes of Parantropora penelope, Discoporella cookae and Cupuladria biporosa, respectively. Intron-encoded protein domains reverse transcriptase and intron maturase (RVT-IM) were identified in all species. Introns in E. vieirai and P. penelope had conserved Group II intron ribozyme domains V and VI. Conserved domains were lacking from introns in D. cookae and C. biporosa, preventing their further categorization. Putative origins of metazoan introns were explored in a phylogenetic context, using an up-to-date alignment of mitochondrial RVT-IM domains. Results confirmed previous findings of multiple origins of annelid, placozoan and sponge RVT-IM domains and provided evidence for common intron donor sources across metazoan phyla. Our results corroborate growing evidence that some metazoans with regenerative abilities (i.e. placozoans, sponges, annelids and bryozoans) are susceptible to intron integration, most likely via horizontal gene transfer.

Recurrent bacteremia with a hypermucoviscous Escherichia coli isolated from a patient with perihilar cholangiocarcinoma: insights from a comprehensive genome-based analysis

BackgroundEscherichia coli (E. coli) is a common human pathogen, responsible for a broad spectrum of infections. Sites of infection can vary, but the hepato-biliary system is of particular concern due to the infection-associated formation of gallstones and the spread of pathogens from the bile ducts into the bloodstream.Case presentationThe presented case is striking, as the detected isolate showed a positive string test. This hypermucoviscous phenotype is atypical for E. coli and a particular feature of hypervirulent Klebsiella pneumoniae (K. pneumoniae) variants.ObjectivesTo provide new insights into the genomic background of an E. coli strain with an unusual hypermucoviscous phenotype using hybrid short- and long-read sequencing approaches.ResultsComplete hybrid assemblies of the E. coli genome and plasmids were done and used for genome based typing. Isolate 537–20 was assigned to the multilocus sequence type ST88 and serotype O8:H4. The strain showed a close relationship to avian pathogenic strains. Analysis of the chromosome and plasmids revealed the presence of several virulence factors, such as the Conserved Virulence Plasmidic (CVP) region on plasmid 537-20_1, including several iron acquisition genes (sitABCD, iroABCDEN, iucABCD, hbd) and the iutA gene encoding the receptor of the siderophore aerobactin. The hypermucoviscous phenotype could be caused by encapsulation of putative K. pneumoniae origin.ConclusionsHybrid sequencing enabled detailed genomic characterization of the hypermucoviscous E. coli strain, revealing virulence factors that have their putative origin in K. pneumoniae.

Identifying SARS-CoV-2 regional introductions and transmission clusters in real time.

The unprecedented severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) global sequencing effort has suffered from an analytical bottleneck. Many existing methods for phylogenetic analysis are designed for sparse, static datasets and are too computationally expensive to apply to densely sampled, rapidly expanding datasets when results are needed immediately to inform public health action. For example, public health is often concerned with identifying clusters of closely related samples, but the sheer scale of the data prevents manual inspection and the current computational models are often too expensive in time and resources. Even when results are available, intuitive data exploration tools are of critical importance to effective public health interpretation and action. To help address this need, we present a phylogenetic heuristic that quickly and efficiently identifies newly introduced strains in a region, resulting in clusters of infected individuals, and their putative geographic origins. We show that this approach performs well on simulated data and yields results largely congruent with more sophisticated Bayesian phylogeographic modeling approaches. We also introduce Cluster-Tracker (https://clustertracker.gi.ucsc.edu/), a novel interactive web-based tool to facilitate effective and intuitive SARS-CoV-2 geographic data exploration and visualization across the USA. Cluster-Tracker is updated daily and automatically identifies and highlights groups of closely related SARS-CoV-2 infections resulting from the transmission of the virus between two geographic areas by travelers, streamlining public health tracking of local viral diversity and emerging infection clusters. The site is open-source and designed to be easily configured to analyze any chosen region, making it a useful resource globally. The combination of these open-source tools will empower detailed investigations of the geographic origins and spread of SARS-CoV-2 and other densely sampled pathogens.

Neural network learning defines glioblastoma features to be of neural crest perivascular or radial glia lineages.

Glioblastoma is believed to originate from nervous system cells; however, a putative origin from vessel-associated progenitor cells has not been considered. We deeply single-cell RNA–sequenced glioblastoma progenitor cells of 18 patients and integrated 710 bulk tumors and 73,495 glioma single cells of 100 patients to determine the relation of glioblastoma cells to normal brain cell types. A novel neural network–based projection of the developmental trajectory of normal brain cells uncovered two principal cell-lineage features of glioblastoma, neural crest perivascular and radial glia, carrying defining methylation patterns and survival differences. Consistently, introducing tumorigenic alterations in naïve human brain perivascular cells resulted in brain tumors. Thus, our results suggest that glioblastoma can arise from the brains’ vasculature, and patients with such glioblastoma have a significantly poorer outcome.

Widespread phages of endosymbionts: Phage WO genomics and the proposed taxonomic classification of Symbioviridae.

Wolbachia are the most common obligate, intracellular bacteria in animals. They exist worldwide in arthropod and nematode hosts in which they commonly act as reproductive parasites or mutualists, respectively. Bacteriophage WO, the largest of Wolbachia’s mobile elements, includes reproductive parasitism genes, serves as a hotspot for genetic divergence and genomic rearrangement of the bacterial chromosome, and uniquely encodes a Eukaryotic Association Module with eukaryotic-like genes and an ensemble of putative host interaction genes. Despite WO’s relevance to genome evolution, selfish genetics, and symbiotic applications, relatively little is known about its origin, host range, diversification, and taxonomic classification. Here we analyze the most comprehensive set of 150 Wolbachia and phage WO assemblies to provide a framework for discretely organizing and naming integrated phage WO genomes. We demonstrate that WO is principally in arthropod Wolbachia with relatives in diverse endosymbionts and metagenomes, organized into four variants related by gene synteny, often oriented opposite the putative origin of replication in the Wolbachia chromosome, and the large serine recombinase is an ideal typing tool to distinguish the four variants. We identify a novel, putative lytic cassette and WO’s association with a conserved eleven gene island, termed Undecim Cluster, that is enriched with virulence-like genes. Finally, we evaluate WO-like Islands in the Wolbachia genome and discuss a new model in which Octomom, a notable WO-like Island, arose from a split with WO. Together, these findings establish the first comprehensive Linnaean taxonomic classification of endosymbiont phages, including non-Wolbachia phages from aquatic environments, that includes a new family and two new genera to capture the collective relatedness of these viruses.

INSP-03. Neuronal regulation of glioma progression

The nervous system regulates stem and precursor cell behavior across a range of tissues. In the central nervous system, neuronal activity is a critical regulator of development and plasticity. Activity-dependent proliferation of healthy glial progenitors, oligodendrocyte precursor cells (OPCs), and the consequent generation of new oligodendrocytes contributes to adaptive myelination. This plasticity of myelin tunes neural circuit function and contributes to healthy cognition. The robust mitogenic effect of neuronal activity on normal oligodendroglial precursor cells, a putative cellular origin for many forms of glioma, suggests that dysregulated or “hijacked” mechanisms of myelin plasticity might similarly promote malignant cell proliferation in this devastating group of brain cancers. Indeed, neuronal activity regulates initiation and promotes progression of gliomas in preclinical models. Crucial mechanisms mediating activity-regulated glioma progression include secretion of BDNF and the synaptic protein neuroligin-3 (NLGN3). NLGN3 induces multiple oncogenic signaling pathways in the cancer cell, and also promotes glutamatergic synapse formation between neurons and glioma cells. This synaptic and electrical integration of glioma into neural circuits is central to tumor progression in preclinical models. NLGN3 is necessary for the growth of gliomas in a range of preclinical models, and therapeutic targeting of NLGN3 is presently under clinical investigation. Thus, neuron-glial interactions not only modulate neural circuit structure and function in the healthy brain, but paracrine and synaptic neuron-glioma interactions also play important roles in the pathogenesis of glial cancers. The mechanistic parallels between normal and malignant neuron-glial interactions underscores the extent to which mechanisms of neurodevelopment and plasticity are subverted by malignant gliomas, and the importance of understanding the neuroscience of cancer.

MEDB-55. Single-cell transcriptomics reveals progenitor cells expressing a photoreceptor program as putative cells origin of MYC-driven Group 3 Medulloblastoma

Brain tumors are the leading cause of childhood cancer-related death. Medulloblastoma is the most common malignant pediatric brain tumor with about 70% survival. Medulloblastoma comprises four distinct subgroups respective of genomic and molecular drivers influencing tumorigenesis. It has been established that despite being considered a single disease entity, each subgroup arises from a distinct population of cells found within unique compartments of the developing brain. The cell of origin of Group 3 medulloblastoma, the most malignant medulloblastoma subgroups, is currently unknown and remains controversial. Transcriptional profiling has revealed that Group 3 medulloblastomas are characterized by elevated expression of a photoreceptor program, which has not been described in the normal cerebellar development but is well characterized in the developing pineal gland and retinal. By investigating and comparing brain and tumor development between our previously developed medulloblastoma mice model (GMYC), where mice spontaneously develop Group 3 medulloblastoma after 4-6 months of age, and their control counterparts, we found that tumor cells emerged from progenitor cells where MYC overexpression drove the transformation of immature progenitor cells expressing a photoreceptor program. Our data suggest that MYC-driven Group 3 medulloblastoma originates from progenitor cells expressing a photoreceptor program, which has implications for future research and the development of novel treatments targeting this devastating childhood malignancy.

Draft mitogenomes of the invasive ant Lepisiota frauenfeldi (Mayr 1855) (Hymenoptera: Formicidae)

We present the draft mitochondrial genomes (mitogenomes) of two Lepisiota frauenfeldi (Mayr 1855) workers from two separate invasive populations detected in Western Australia (Perth OK569858) and Queensland (Brisbane OK5569859), Australia. The draft mitogenomes ranged between 16,657 and 17,090 bp and contained 37 genes (13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNA (rRNA) genes). As with other arthropod mitogenomes, we observed high A + T content (A: 39.4–39.8%, T: 40.55–41.5%). We confirmed the species identity by molecular diagnostics based on the partial mtCOI gene that showed >99% similarity between the Australian populations and other L. frauenfeldi sequences reported to date, and in the process identified putative origins of the invasive populations as Pakistan and India for the WA and Qld incursions respectively that suggested separate introductions.

Intra- and Inter-Population Genetic Diversity of “Russello” and “Timilia” Landraces from Sicily: A Proxy towards the Identification of Favorable Alleles in Durum Wheat

Climate change and global population growth call for urgent recovery of genetic variation from underexploited or unexplored durum wheat (Triticum turgidum ssp. durum) landraces. Indeed, these untapped genetic resources can be a valuable source of favorable alleles for environmental adaptation and tolerance or resistance to (a)biotic stress. In southern Italy, in addition to the widespread modern and highly productive durum wheat cultivars, various landraces have been rediscovered and reused for their adaptation to sustainable and low-input cropping systems and for their peculiar qualitative characteristics. Sicily is a semiarid area rich in landraces, some of which are independently reproduced by many farmers. Among these, “Timilia” and “Russello” have been independently grown in various areas and are now cultivated, mostly under organic systems, for their hypothetical greater benefits and height, which give them a high level of competitiveness against weeds despite their low yield potential. So far, there is little information on the genetic variations of “Timilia” and “Russello” despite their putative origin from a common funder. This work aims to dissect the genetic variation patterns of two large germplasm collections of “Timilia” and “Russello” using SNP genotyping. The analysis of intra- and inter-population genetic variation and the identification of divergent loci between genetic groups showed that (i) there are two “Russello” genetic groups associated with different Sicilian geographical areas, which differ in important traits related to gluten quality and adaptation, and (ii) the individuals of “Timilia”, although presenting wide genetic variation, have undergone a conservative selection, likely associated with their distinctive traits. This work paves the way for a deeper exploration of the wide genetic diversity in Sicilian landraces, which could be conveniently exploited in future breeding programs, and points out that intra-population genetic diversity should be taken into account when ‘conservation varieties’ are to be registered in national registers of crops.

Substantial Biogeochemical and Biomolecular Processing of Dissolved Organic Matter in an Anticyclonic Eddy in the Northern South China Sea Down to Bathypelagic Depths

Solid-phase extracted dissolved organic matter (SPE-DOM) was isolated from two depth profiles at the core and at the edge of an anticyclonic eddy (ACE) in the northern South China Sea. Non-target nuclear magnetic resonance (NMR) spectroscopy and Fourier transform ion cyclotron mass spectrometry (FTICR/MS) of SPE-DOM revealed a higher uniformity of DOM molecules within the ACE than at the edge of the ACE. Small-scale upwelling of external nutrients may have contributed to higher productivity and production of fresher DOM, with higher proportions of CHNO and CHNOS compounds and low molecular weight species at the edge of the eddy. Common SPE-DOM molecules of supposedly biological origin such as carbohydrates and olefins were most abundant in the chlorophyll maximum layer in both stations. An unusual suite of ~10 abundant and ~35 less abundant tert-butyl benzene derivatives with potential to act as endocrine disruptors within a marine food chain and ~two dozen ketones of putative bacterial origin was recognized at meso- and bathypelagic depths in single-digit micromolar concentrations, with a distinct maximum at 1000 m depth at the edge of ACE. Downwelling might bring temporary large volumes of productive marine waters into deep waters, with micromolar concentration of abundant, microbial food web-specific metabolites (e.g. 2,4-di-tert-butylphenol et al.). In our study, these eventually added up to one quarter of common background biogeochemical marine organic matter even at bathypelagic depths and beneath and are significant food and energy sources for marine biota. Mesoscale chemical heterogeneity of marine water columns might extend to larger depths than currently anticipated and may create activity hotspots influencing biota, processing of DOM, and cycling of nutrients and trace elements.

GJB2 Is a Major Cause of Non-Syndromic Hearing Impairment in Senegal.

Simple SummaryThe prevalence of GJB2-related (MIM: 121011) congenital non-syndromic hearing impairment (NSHI) accounts for close to 50% in populations of Asian and European ancestry. However, in sub-Saharan Africa, except for Ghana, previous data showed that the prevalence of GJB2-associated NSHI is close to zero. To investigate the contribution of GJB2 mutations in autosomal recessive NSHI in Senegal, we screened 129 affected and 143 unaffected individuals from 44 multiplex families, 9 sporadic cases, and 148 hearing controls with no personal or family history of hearing impairment, by targeted gene sequencing. We identified three pathogenic GJB2 variants in 34% (n = 15/44) of multiplex families, of which 80% (n = 12/15) were consanguineous. The most common variant, GJB2: c.94C>T: p.(Arg32Cys), accounted for 27.3% (n = 12/44) of familial cases. We also identified the previously reported “Ghanaian” founder variant, GJB2: c.427C>T: p.(Arg143Trp), in four multiplex Senegalese families. Relatively high allele frequencies of c.94C>T. and c.427C>T variants were observed among the screened hearing controls: 1% (n = 2/148 ∗ 2), and 2% (n = 4/148 ∗ 2), respectively. No GJB6-D13S18 deletion was identified in any of the hearing-impaired participants. The data suggest that GJB2: c.94C>T: p.(Arg32Cys) should be routinely tested in NSHI in Senegal.This study aimed to investigate GJB2 (MIM: 121011) and GJB6 (MIM: 604418) variants associated with familial non-syndromic hearing impairment (HI) in Senegal. We investigated a total of 129 affected and 143 unaffected individuals from 44 multiplex families by segregating autosomal recessive non-syndromic HI, 9 sporadic HI cases of putative genetic origin, and 148 control individuals without personal or family history of HI. The DNA samples were screened for GJB2 coding-region variants and GJB6-D3S1830 deletions. The mean age at the medical diagnosis of the affected individuals was 2.93 ± 2.53 years [range: 1–15 years]. Consanguinity was present in 40 out of 53 families (75.47%). Variants in GJB2 explained HI in 34.1% (n = 15/44) of multiplex families. A bi-allelic pathogenic variant, GJB2: c.94C>T: p.(Arg32Cys) accounted for 25% (n = 11/44 families) of familial cases, of which 80% (n = 12/15) were consanguineous. Interestingly, the previously reported “Ghanaian” founder variant, GJB2: c.427C>T: p.(Arg143Trp), accounted for 4.5% (n = 2/44 families) of the families investigated. Among the normal controls, the allele frequency of GJB2: c.94C>T and GJB2: c.427C>T was estimated at 1% (2/148 ∗ 2) and 2% (4/148 ∗ 2), respectively. No GJB6-D3S1830 deletion was identified in any of the HI patients. This is the first report of a genetic investigation of HI in Senegal, and suggests that GJB2: c.94C>T: p.(Arg32Cys) and GJB2: c.427C>T: p.(Arg143Trp) should be tested in clinical practice for congenital HI in Senegal.

Resurrection of Stipatremula and taxonomy of the high-alpine species from the Stipapurpurea complex (Poaceae, Pooideae).

Stipapurpurea is a high-alpine species that occurs in cryophilous steppes, semi-deserts and stony slopes, from the Tian Shan and Pamirian Plateau through Qinghai-Xizang Plateau to the Himalayas and is characterised by a great morphological variability. During the revision of specimens of the taxon, we observed that the pattern of this variability is linked to the geographical distribution of the specimens. Numerical analyses (PCA and UPGMA) revealed three groups of OTUs corresponding to three morphotypes within the S.purpurea complex. A set of macro- and micromorphological characters, supported by a map of general distributional ranges, are presented to distinguish each of the three taxa within the complex and we reassess the status of Lasiagrostistremula described by Ruprecht in 1869. As a result, Stipatremula, S.purpurea and S.arenosa were distinguished within the complex. The intermediate characters of S.arenosa may suggest its putative hybrid origin (S.tremula × S.purpurea), whereas the presence of extremely long florets may be an expression of the gigas effect. We propose two new combinations (S.tremula and S.arenosa), describe a new nothospecies (S.×ladakhensis) that originated from hybridisation between S.klimesii and S.purpurea s.l. and designate the lectotype for Ptilagrostissemenovii. An identification key and detailed morphological description of species from the S.purpurea complex are also presented.

Cryptic Triploids and Leaky Premating Isolation in an Odontophrynus Hybrid Zone

The diploid Odontophrynus cordobae and its autopolyploid counterpart O. americanus (4n) co-occur in a small-sized contact zone in Central Argentina, together with numerous specimens of a cryptic triploid taxon. Additionally, we monitor another five localities inhabited by taxa of this species complex within a radius of 76 km north and south of the contact zone to look for possible co-occurrence of taxa. In this study, we analyze the reproductive interactions in this breeding assemblage covering three levels of ploidy. We focus on the advertisement call structure as a powerful mechanism of premating isolation and on the mating preferences of males and females in the natural habitat. Advertisement calls of triploids were indistinguishable from those of tetraploids, and both differed significantly in pulse rate from diploids. Analyses of 21 amplexi demonstrated that heterospecific matings dominated breeding: one between a diploid female and tetraploid male, and ten between triploids and tetraploids. At three localities with syntopic diploids and tetraploids, premating isolation was almost perfect, preventing the formation of triploids. Therefore, we question the putative origin of triploids from hybridization and discuss alternatives. This unique system, including three bisexual taxa of distinct ploidy, which interact reproductively, remains to be investigated in more detail to fully understand the mechanism stabilizing its persistence.

On the hybrid origin of the C2 Salsola divaricata agg. (Amaranthaceae) from C3 and C4 parental lineages.

C2 photosynthesis is characterised using recapturing photorespiratory CO2 by RuBisCo in Kranz-like cells and is therefore physiologically intermediate between C3 and C4 photosynthesis. C2 can be interpreted as an evolutionary precursor of C4 and/or as the result of hybridisation between a C3 and C4 lineage. We compared the expression of photosynthetic traits among populations of the Salsola divaricata agg. (C2 ) from humid subtropical to arid habitats on the coasts of the Canary Islands and Morocco and subjected them to salt and drought treatments. We screened for enhanced C4 -like expression of traits related to habitat or treatment. We estimated species trees with a transcriptome dataset of Salsoleae and explored patterns of gene tree discordance. With phylogenetic networks and hybridisation analyses we tested for the hybrid origin of the Salsola divaricata agg. We observed distinct independent variation of photosynthetic traits within and among populations and no clear evidence for selection towards C4 -like trait expression in more stressful habitats or treatments. We found reticulation and gene tree incongruence in Salsoleae supporting a putative hybrid origin of the Salsola divaricata agg. C2 photosynthesis in the Salsola divaricata agg. combines traits inherited from its C3 and C4 parental lineages and seems evolutionarily stable, possibly well adapted to a wide climatic amplitude.

Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal.

The Zika virus (ZIKV) disease caused a public health emergency of international concern that started in February 2016. The overall number of ZIKV-related cases increased until November 2016, after which it declined sharply. While the evaluation of the potential risk and impact of future arbovirus epidemics remains challenging, intensified surveillance efforts along with a scale-up of ZIKV whole-genome sequencing provide an opportunity to understand the patterns of genetic diversity, evolution, and spread of ZIKV. However, a classification system that reflects the true extent of ZIKV genetic variation is lacking. Our objective was to characterize ZIKV genetic diversity and phylodynamics, identify genomic footprints of differentiation patterns, and propose a dynamic classification system that reflects its divergence levels. We analysed a curated dataset of 762 publicly available sequences spanning the full-length coding region of ZIKV from across its geographical span and collected between 1947 and 2021. The definition of genetic groups was based on comprehensive evolutionary dynamics analyses, which included recombination and phylogenetic analyses, within- and between-group pairwise genetic distances comparison, detection of selective pressure, and clustering analyses. Evidence for potential recombination events was detected in a few sequences. However, we argue that these events are likely due to sequencing errors as proposed in previous studies. There was evidence of strong purifying selection, widespread across the genome, as also detected for other arboviruses. A total of 50 sites showed evidence of positive selection, and for a few of these sites, there was amino acid (AA) differentiation between genetic clusters. Two main genetic clusters were defined, ZA and ZB, which correspond to the already characterized ‘African’ and ‘Asian’ genotypes, respectively. Within ZB, two subgroups, ZB.1 and ZB.2, represent the Asiatic and the American (and Oceania) lineages, respectively. ZB.1 is further subdivided into ZB.1.0 (a basal Malaysia sequence sampled in the 1960s and a recent Indian sequence), ZB.1.1 (South-Eastern Asia, Southern Asia, and Micronesia sequences), and ZB.1.2 (very similar sequences from the outbreak in Singapore). ZB.2 is subdivided into ZB.2.0 (basal American sequences and the sequences from French Polynesia, the putative origin of South America introduction), ZB.2.1 (Central America), and ZB.2.2 (Caribbean and North America). This classification system does not use geographical references and is flexible to accommodate potential future lineages. It will be a helpful tool for studies that involve analyses of ZIKV genomic variation and its association with pathogenicity and serve as a starting point for the public health surveillance and response to on-going and future epidemics and to outbreaks that lead to the emergence of new variants.

Generalized infections of putative oral origin in Helsinki University Hospital in 2012 to 2017.

Bacteria entering the bloodstream through oral mucosa cause bacteremia, which can lead to septic or distant infections. The underlying factors and need for dental treatment in patients referred for oral examination because of septic infection were investigated. It was expected that general diseases and poor socioeconomic status of patients would increase the risk of bacteremia. This descriptive retrospective study included patients (N = 128) referred from medical clinics of the Helsinki University Hospital (HUH), during 2012 to 2017, to the Department of Oral and Maxillofacial Diseases due to bacteremia suspected to be of oral origin. Data were extracted from medical and dental records according to the World Health Organization International Classification of Diseases (ICD-10) for systemic or remote infections. Different groups were formed using modified Skapinakis classification for socioeconomic status (SES), from I (high) to V (low). Underlying medical conditions were retrieved according to McCabe classification: healthy, nonfatal, ultimately fatal, and rapidly fatal diseases. The data were analyzed using the statistical software package SPSS (IBM). Patients were referred most often from the Departments of Infectious Diseases and Internal Medicine. Because of infection, 12 patients needed aortic or mitral valve operations. Many of the patients were intravenous drug users. However, the majority of patients presented McCabe class I, indicating no systemic disease. The main SES was intermediate III. Tooth extraction was the principal mode of treatment. No demographic background variables were identified to explain increase of the risk for bacteremia except that most patients were men with untreated dental problems. Contrary to the authors' expectation, poor SES and underlying diseases did not seem to link to the outcome. However, untreated dental infections present an evident risk for life-threatening septic complications also in generally healthy individuals.