Notes on Carex (Cyperaceae) from China (VII): new synonyms and imperfectly known species

Based on literature survey, examination of type specimens and fieldwork, seven names of Carex are synonymized in the present paper: viz. Carex hypoblephara reduced to a synonym of C. glossostigma; C. dayunshanensis and C. wuyishanensis to synonyms of C. graciliflora; C. dolichogyne to a synonym of C. truncatigluma; C. kwangtoushanica to a synonym of C. tatsiensis; and C. martini to a synonym of C. rhynchophora. The holotype of Carex fokienensis is identified and confirmed at P. The putative endemic species Carex macrosandra (basionym: C. lanceolata var. macrosandra) is synonymized to C. lanceolata, whereas C. cavaleriensis, considered a synonym of the former, is here recognized as a distinct species. A lectotype is designated for C. lanceolata var. macrosandra.

Occurrence and distribution of lace bug, whitefly, and shoot fly pest species on cassava (Manihot esculenta) crops according to region in Paraná State, Brazil

The cassava (Manihot esculenta Crantz) crop is relevant for human livelihoods, particularly in poorer regions. It is consumed fresh or as industrialized flour, and the roots and aerial parts are also used to feed livestock. Pests may limit cassava production, which may endanger food security due to the socioeconomic importance of the crop. Reports of the occurrence of three insect guilds, lace bugs, shoot flies, and whiteflies have been recorded in Paraná State, Brazil, but the distinct species and their distribution are yet to be determined. This lack of information limits the development of strategies to mitigate pest damage. Surveys were conducted in 39 counties (four farms per county) distributed throughout the state that encompass the various socioeconomic regions. The collected material was properly packed and sent to the laboratory for identification, and the following species were identified: lace bugs Vatiga illudens Drake, 1922 and Vatiga manihotae Drake, 1922 (both Hemiptera: Tingidae); whiteflies Bemisia tuberculata (Bondar, 1923) and Aleurothrixus aepim (Goeldi, 1886) (both Hemiptera: Aleyrodidae), and the cassava shoot fly Neosilba perezi Romero & Ruppel, 1973 (Diptera: Lonchaeidae) in Paraná State. Lace bugs were not found in the samples in the eastern and southern portions of the state. V. illudens was more widespread than V. manihotae. The whitefly A. aepim was not observed in three counties (eastern, southern, and central regions), whereas B. tuberculata and the cassava shoot fly were found in all regions sampled in Paraná State. Suggestions for future investigations of pest management are proposed.

Hydrodroma angelieri (Acari, Hydrachnidia: Hydrodromidae) a new water mite species from Corsica based on morphological and DNA barcode evidence

In the present study we used morphological data and DNA barcodes to describe a new species, Hydrodroma angelieri sp. nov. from Corsica, France. A high genetic distance of 17.3±0.017% K2P from its molecularly most closely related European congener, H. despiciens (Müller, 1776), supports H. angelieri sp. nov. as a distinct species. Morphologically the new species can be identified on the basis of relatively small leg claws, the presence of only one swimming seta on II-L-5 and 4-6 swimming setae on the anterior surface of IV-L-5. An updated key for the European species of Hydrodroma is provided.

Phylogenetic Diversity and Mycotoxin Potential of Emergent Phytopathogens within the Fusarium tricinctum Species Complex

Recent studies on multiple continents indicate members of the Fusarium tricinctum species complex (FTSC) are emerging as prevalent pathogens of small-grain cereals, pulses, and other economically important crops. These understudied fusaria produce structurally diverse mycotoxins, among which enniatins (ENNs) and moniliformin (MON) are the most frequent and of greatest concern to food and feed safety. Herein a large survey of fusaria in the Fusarium Research Center and Agricultural Research Service culture collections was undertaken to assess species diversity and mycotoxin potential within the FTSC. A 151-strain collection originating from diverse hosts and substrates from different agroclimatic regions throughout the world was selected from 460 FTSC strains to represent the breadth of FTSC phylogenetic diversity. Evolutionary relationships inferred from a 5-locus dataset, using maximum likelihood and parsimony, resolved the 151 strains as 24 phylogenetically distinct species, including nine that are new to science. Of the five genes analyzed, nearly full-length phosphate permease sequences contained the most phylogenetically informative characters, establishing its suitability for species-level phylogenetics within the FTSC. Fifteen of the species produced ENNs, MON, the sphingosine analog 2-amino-14,16- dimethyloctadecan-3-ol (AOD), and the toxic pigment aurofusarin (AUR) on a cracked corn kernel substrate. Interestingly, the five earliest diverging species in the FTSC phylogeny (i.e., F. iranicum, F. flocciferum, F. torulosum, Fusarium spp. FTSC 8 and 24) failed to produce AOD and MON, but synthesized ENNs and/or AUR. Moreover, our reassessment of nine published phylogenetic studies on the FTSC identified 11 additional novel taxa, suggesting this complex comprises at least 36 species.

Plant speciation in the Namib Desert: origin of a widespread derivative species from a narrow endemic

Background: Parapatric (or budding) speciation is increasingly recognized as an important phenomenon in plant evolution but its role in extreme (e.g. desert) environments is poorly documented. Aims: To test this speciation model in a hypothesized sister pair, the Southwest and North African disjunct Senecio flavus and its putative progenitor, the Namibian Desert endemic S. englerianus. Methods: Phylogenetic inferences were combined with niche divergence tests, morphometrics, and experimental genetic approaches. We also evaluated the potential role of an African Dry Corridor (ADC) in promoting the hypothesized northward expansion of S. flavus (from Namibia), using palaeodistribution models. Results: Belonging to an isolated (potentially relict) clade, the two morphologically distinct species show pronounced niche divergence in Namibia and signs of digenic epistatic hybrid incompatibility (based on F2 pollen fertility). The presence of connate fluked pappus hairs in S. flavus, likely increasing dispersal ability, is controlled by a single gene locus. Conclusions: Our results provide support for a rare example of budding speciation in which a wider ranged derivative (S. flavus) originated at the periphery of a smaller ranged progenitor (S. englerianus) in the Namib Desert region. The Southwest and North African disjunction of S. flavus could have been established by dispersal across intermediate ADC areas during periods of (Late) Pleistocene aridification.

Tumor Tissue-Specific Bacterial Biomarker Panel for Colorectal Cancer: Bacteroides Massiliensis, Alistipes Species, Alistipes Onderdonkii, Bifidobacterium Pseudocatenulatum, Corynebacterium Appendicis

Human microbiome studies have shown diversity to exist among different ethnic populations. However, studies pertaining to the microbial composition of CRC among the Indian population have not been well explored. We aimed to decipher the microbial signature in tumor tissues from North Indian CRC patients. Next-generation sequencing of tumor and adjacent tissue derived bacterial 16s rRNA V3-V4 hypevariable regions was performed to investigate the abundance of specific microbes. The expression profile analysis deciphered a decreased diversity among the tumor-associated microbial communities, and at the phyla level, Proteobacteria was differentially expressed in CRC tissues than adjacent normal. Further, DESeq2 normalization identified 4 out of 79 distinct species (p<0.005) only in CRC, Bacteroides massiliensis, Alistipes onderdonkii, Bifidobacterium pseudocatenulatum, and Corynebacterium appendicis. Thus, our findings suggest the use of these microbial signatures as putative biomarkers that can distinguish CRC tissues from their adjacent normal, which may shed light on the pathogenesis of CRC.

Chromosome-Level Genome Assembly of a Human Fungal Pathogen Reveals Synteny among Geographically Distinct Species

Histoplasma species are dimorphic fungi causing significant morbidity and mortality worldwide. These fungi grow as mold in the soil and as budding yeast within the human host. Histoplasma can be isolated from soil in diverse regions, including North America, South America, Africa, and Europe.

Investigation of Inherited Chromosomally Integrated Human Herpesvirus-6A+ and -6B+ in a Patient with Ulipristal Acetate-Induced Fulminant Hepatic Failure

Inherited chromosomally integrated (ici) human herpes virus 6 (HHV-6) is estimated to occur in 0.6–2.7% of people worldwide. HHV-6 comprises two distinct species: HHV-6A and HHV-6B. Both HHV-6A and HHV-6B integration have been reported. Several drugs are capable of activating iciHHV-6 in tissues, the consequences of which are poorly understood. We report herein a case of a woman with iciHHV-6A+ and iciHHV-6B+, who developed ulipristal acetate (a selective progesterone receptor modulator)-induced fulminant hepatic failure that required liver transplantation. We confirmed the presence of ~one copy per cell of both HHV-6A and HHV-6B DNA in her hair follicles using multiplex HHV-6A/B real-time PCR and demonstrated the Mendelian inheritance of both iciHHV-6A and iciHHV-6B in her family members over three generations. Because of the rarity of this presentation, we discuss herein the possible links between reactivated HHV-6 from iciHHV-6A and/or iciHHV-6B and adverse drug reactions, suggesting that iciHHV-6 could be screened before the introduction of any hepatotoxic drugs to exclude HHV-6 active disease or combined idiosyncratic drug-induced liver injury in these patients.

Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: phylogeography of the New Zealand gecko genus Hoplodactylus.

Methodological and technological improvements are continually revolutionizing the field of ancient DNA. Most ancient DNA extraction methods require the partial (or complete) destruction of finite museum specimens, which disproportionately impacts small or fragmentary subfossil remains, and future analyses. We present a minimally destructive ancient DNA extraction method optimized for small vertebrate remains. We applied these methods to detect lost mainland genetic diversity in the large New Zealand diplodactylid gecko genus Hoplodactylus, which is presently restricted to predator-free island sanctuaries. We present the first mitochondrial genomes for New Zealand diplodactylid geckos, recovered from 19 modern, six historic/archival (1898 to 2011) and 16 Holocene Hoplodactylus duvaucelii sensu latu specimens, and one modern Woodworthia sp. specimen. No obvious damage was observed in post-extraction micro-CT reconstructions. All ‘large gecko’ specimens examined from extinct populations were found to be conspecific with extant Hoplodactylus species, suggesting their large relative size evolved only once in the New Zealand diplodactylid radiation. Phylogenetic analyses of Hoplodactylus samples recovered two genetically (and morphologically) distinct North and South Island clades, probably corresponding to distinct species. Finer phylogeographic structuring within Hoplodactylus spp. highlighted the impacts of Late-Cenozoic biogeographic barriers, including the opening and closure of Pliocene marine straits, fluctuations in size and suitability of glacial refugia, and eustatic sea-level change. Recent mainland extinction obscured these signals from the modern tissue derived data. These results highlight the utility of minimally destructive DNA extraction in genomic analyses of less well studied small vertebrate taxa, and the conservation of natural history collections.

Molecular and morphological analyses support recognition of Prostanthera volucris (Lamiaceae), a new species from the Central Tablelands of New South Wales

Research into the systematics of Prostanthera has recently revealed a close evolutionary relationship among P. phylicifolia s. str., the critically endangered P. gilesii, and a population of uncertain identity from the Central Tablelands of New South Wales, Australia. Previous analyses were unable to establish whether genetic boundaries separated these taxa. This study aimed to assess the species boundaries among these three taxa using a combination of single-nucleotide polymorphisms (SNP) sampled at the population-scale and multivariate analysis of morphological characters. Non-parametric and parametric statistics, neighbour-network analysis, phylogenetic analysis, and ancestry coefficient estimates all provided support for discrete genetic differences between the three taxa. Morphological phenetic analysis identified a suite of characters that distinguished each of these taxa. This corroboration of evidence supports the presence of three independently evolving lineages. Prostanthera gilesii and P. phylicifolia s. str. are distinct species independent from the third taxon which is described here as P. volucris R.P.O'Donnell. A detailed description, diagnostic line drawings and photographs are provided. We evaluate P. volucris as satisfying criteria to be considered Critically Endangered.