Morphological and molecular evidence reveals three new species of Lithocarpus (Fagaceae) from Bidoup-Nui Ba National Park, Vietnam

Three new species, Lithocarpus bidoupensis Ngoc & Tagane, L. congtroiensis Ngoc & Yahara, and L. hongiaoensis Ngoc & Binh are described from Bidoup-Nui Ba National Park, Central Highland of Vietnam. Morphological analyses and Maximum likelihood tree based on genome-wide SNPs support the distinction of those species from the previously known taxa in the region. The three new species are considered to be endemic to the Bidoup-Nui Ba National Park and the preliminary conservation status for each species is evaluated as Critically Endangered.

Genetic Variation Among Certain Fish Species in Terms of Evolution and Lineages

Three tests of phylogenetic including likelihood-joining tree, neighbour-joining tree, and minimum evolution tree have been used based on sox3 gene. Phylogenetic analysis was used to detect the genetic affinity and common ancestors for selected species that belong to the same or different families. This study showed the most appropriate methods for testing the genetic affinity among species and the methodology of each test according to the requirement of molecular applications. Secondary RNA predicted structure and minimum free energy were also included in this study because of their contribution to the detection of the orthologous gene and variance in RNA folding among species related to the different families. The genetic distance in the studied populations was calculated to know the most appropriate way to find out the genetic similarity among the studied species. The low distance-variance value of each group indicated significant genetic affinity among the species of the same family, this result is more consistent with the test of maximum-likelihood tree indicating the validity of this test to measure the genetic affinity among species that have common ancestors.

Phylogenetic study of thermophilic genera Anoxybacillus, Geobacillus, Parageobacillus, and proposal of a new classification Quasigeobacillus gen. nov.

A phylogenetic study of Anoxybacillus, Geobacillus and Parageobacillus was performed using publicly available whole genome sequences. A total of 113 genomes were selected for phylogenomic metrics including calculation of Average Nucleotide Identity (ANI) and Average Amino acid Identity (AAI), and a maximum likelihood tree was built from alignment of a set of 662 orthologous core genes. The combined results from the core gene tree and ANI and AAI dendrograms show that the genomes split into two main clades, clade I containing all Geobacillus, all Parageobacillus and some species of Anoxybacillus, and clade II, containing the majority of Anoxybacillus species. Clade I is further partitioned into three clades, consisting separately of Geobacillus, Parageobacillus, and a third clade which we suggest should be elevated to a new genus Quasigeobacillus gen. nov. Two species of Anoxybacillus showed inconsistent positioning among the trees produced by differing methods and could not be clearly resolved into any of the three existing genera or the new genus. This research shows the importance of considering closely related genera together when studying phylogeny or assigning genomic affinities.

Early and ongoing importations of SARS-CoV-2 in Canada

Tracking the emergence and spread of SARS–CoV–2 is critical to inform public health interventions. Phylodynamic analyses have quantified SARS–CoV–2 migration on global and local scales, yet they have not been applied to determine transmission dynamics in Canada. We quantified SARS-CoV-2 migration into, within, and out of Canada in the context of COVID-19 travel restrictions. To minimize sampling bias, global sequences were subsampled with probabilities corrected for their countries' monthly contribution to global new diagnoses. A time–scaled maximum likelihood tree was used to estimate most likely ancestral geographic locations (country or Canadian province), enabling identification of sublineages, defined as introduction events into Canada resulting in domestic transmission. Of 402 Canadian sublineages identified, the majority likely originated from the USA (54%), followed by Russia (7%), India (6%), Italy (6%), and the UK (5%). International introductions were mostly into Ontario (39%) and Quebec (38%). Among Pango lineages, B.1 was imported at least 191 separate times from 11 different countries. Introduction rates peaked in late March then diminished but were not eliminated following national interventions including restrictions on non–essential travel. We further identified 1,380 singleton importations, international importations that did not result in further sampled transmission, whereby representation of lineages and location were comparable to sublineages. Although proportion of international transmission decreased over time, this coincided with exponential growth of within–province transmission – in fact, total number of sampled transmission events from international or interprovincial sources increased from winter 2020 into spring 2020 in many provinces. Ontario, Quebec, and British Columbia acted as sources of transmission more than recipients, within the caveat of higher sequence representation. We present strong evidence that international introductions and interprovincial transmission of SARS–CoV–2 contributed to the Canadian COVID–19 burden throughout 2020, despite initial reductions mediated by travel restrictions in 2020. More stringent border controls and quarantine measures may have curtailed introductions of SARS–CoV–2 into Canada and may still be warranted.

First report of the leaf-mining genus Parornix Spuler from China, with descriptions of two new species (Lepidoptera, Gracillariidae, Parornichinae)

The subfamily Parornichinae and thus the genus Parornix Spuler, 1910 are reported for the first time in China. Two new species, P. sinensis Liu, sp. n. feeding on Amygdalus davidiana and P. yuliella Liu & Teng, sp. n. on Cerasus japonica, are described herein. Both host plant species belong to Rosaceae. Adult, genitalia of both sexes, and leaf mines are described and illustrated for both species. A Maximum Likelihood tree based on DNA barcodes available for Parornix is also provided for species separation. Reference barcodes for both new species are generated.

CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes

We present CoronaHiT, a platform and throughput flexible method for sequencing SARS-CoV-2 genomes (≤ 96 on MinION or > 96 on Illumina NextSeq) depending on changing requirements experienced during the pandemic. CoronaHiT uses transposase-based library preparation of ARTIC PCR products. Method performance was demonstrated by sequencing 2 plates containing 95 and 59 SARS-CoV-2 genomes on nanopore and Illumina platforms and comparing to the ARTIC LoCost nanopore method. Of the 154 samples sequenced using all 3 methods, ≥ 90% genome coverage was obtained for 64.3% using ARTIC LoCost, 71.4% using CoronaHiT-ONT and 76.6% using CoronaHiT-Illumina, with almost identical clustering on a maximum likelihood tree. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally.

Figs S1-S3

Fig. S1. Maximum likelihood tree based on ITS dataset. Branch support values >75 % and Bayesian posterior probabilities > 0.90 are indicated. Symbols with closed circles represent gasteroid taxa, symbols with half circles represent secotoid taxa, and all other taxa are agaricoid. Limacella glioderma was used as an outgroup.Fig. S2. Maximum likelihood tree based on LSU dataset. Branch support values >75 % and Bayesian posterior probabilities > 0.90 are indicated. Symbols with closed circles represent gasteroid taxa, symbols with half circles represent secotoid taxa, and all other taxa are agaricoid. Limacella glioderma was used as an outgroup. Fig. S3. Maximum likelihood tree based on concatenated LSU, rpb2, and tef1 dataset with ambiguously aligned regions excluded. Branch bootstrap support values >75 % and Bayesian posterior probabilities > 0.90 are indicated. Limacella delicata, Limacella glioderma and Limacella guttata were used as an outgroup.

Two Complete Mitochondrial Genomes From Leuctridae (Plecoptera: Nemouroidea): Implications for the Phylogenetic Relationships Among Stoneflies

The family-level relationships within Plecoptera have been a focused area of research for a long time. Its higher classification remains unstable, and the phylogenetic relationships within Plecoptera should be re-examined. Here, we sequenced and analyzed two complete mitochondrial genomes (mitogenomes) of Paraleuctra cercia and Perlomyia isobeae of the family Leuctridae. We reconstructed the phylogeny of Plecoptera based on 13 protein-coding genes (PCGs) from published stoneflies. Our results showed that the Bayesian inference and maximum-likelihood tree had similar topological structures except for the positions of two families, Peltoperlidae and Scopuridae. The Plecoptera is divided into two clades, the suborder Antarctoperlaria and the suborder Arctoperlaria. The two suborders subsequently formed two groups, Eusthenioidea and Gripopterygoidea, and Euholognatha and Systellognatha, which is consistent with the results of morphological studies. In addition, the Leuctridae is the earliest branch within the superfamily Nemouroidea. But the monophyly of Perloidea and Pteronarcyoidea are still not well supported.

First record of a reticulated toadfish, Arothron reticularis (Tetraodontiformes: Tetraodontidae), in Korea

A single specimen of Arothron reticularis (398 mm in total length), belonging to the family Tetraodontidae, was collected in the coastal waters off Hansan island using a set net in May 2019. The morphological characteristics of the specimen are as follows: large eyes and mouth, white spots on the body, and a white line surrounding the eyes in an annular shape. A result of maximum likelihood tree showed that A. reticularis is related to A. hispidus (93.6%). We proposed the Korean name “Geu-murl-mu-nui-kkeo-kkeurl-bok,” in accordance with the characteristics of the specimen.