Is It Scaly Anteater or Bat A Real Origin of The 2019-Novel CoV: A Probable Hypothesis? by Salar Ali, Taib Hama-Soor, Muhammed Babakir-Mina, Salvatore Dimonte, Francesco Greco

“…The phylogenetic trees analysis illustrated that 2019nCoV in all four proteins are very closely related with coronaviruses isolated from Pangolin (scaly anteater) and Bat-SARS-like-coronavirses because all of them are clustered in the same clade. …”
Get full text

Phylobook: a tool for display, clade annotation and extraction of sequences from molecular phylogenies by Jeffrey C Furlong, Peter D Darley, Wenjie Deng, James I Mullins, Roger E Bumgarner

“…Starting with a sequence alignment file, Phylobook generates and displays phylogenetic trees adjacent to highlighter plots showing the position of mutations, and allows the user to identify lineages and recombinants, annotate and export selected subsets of sequences for downstream analysis. …”
Get full text

multistrap: boosting phylogenetic analyses with structural information by Athanasios Baltzis, Luisa Santus, Björn E. Langer, Cedrik Magis, Damien M. de Vienne, Olivier Gascuel, Leila Mansouri, Cedric Notredame

“…These variations exhibit less saturation than sequence-based Hamming distances and support the computation of tree-like distance matrices resolvable into phylogenetic trees using distance-based methods such as minimum evolution. …”
Get full text

Five New Species of Pezizales from Northeastern China by Zhengqing Chen, Tolgor Bau

“…Maximum likelihood and Bayesian analyses were performed using a combined nuc rDNA internal transcribed spacer region (ITS) and nuc 28S rDNA (nrLSU) dataset for the construction of phylogenetic trees. Morphological descriptions, line illustrations, and photographs of the ascocarps of these new species are provided, along with lists of the salient attributes exhibited by the species in the three genera under consideration.…”
Get full text

Two new species of Micropsalliota (Agaricales, Agaricaceae) from subtropical regions of China by Jun-Qing Yan, Zhi-Heng Zeng, Ya-Ping Hu, Cheng-Feng Nie, Bin-Rong Ke, Sheng-Nan Wang, Hui Zeng

“…Their distinct taxonomic status is confirmed by the positions of the two new species in 4-locus (ITS, LSU, rpb2, tef-1α) phylogenetic trees. Detailed descriptions and morphological photographs of two new species are presented. …”
Get full text

New insights into the phylogeny and infrageneric taxonomy of Saussurea based on hybrid capture phylogenomics (Hyb-Seq) by Liansheng Xu, Zhuqiu Song, Tian Li, Zichao Jin, Buyun Zhang, Siyi Du, Shuyuan Liao, Xingjie Zhong, Yousheng Chen

“…A comprehensive infrageneric classification, supported by robust phylogenetic trees and corroborated by morphological and other data, has not yet been published. …”
Get full text

Movements of the Glandirana Frogs in Japan and South Korea: A Strategy for Defining Geographical Movements of Amphibians by Akira Oike, Koji Tojo, Yoriko Nakamura, Etsuro Ito, Masahisa Nakamura

“…Then, we constructed time-calibrated and RAxML phylogenetic trees based on nucleotide sequences of the mitochondrial genes of the Glandirana frogs in Japan and South Korea. …”
Get full text

Sinistroporomonorchis bolini n. sp. (Trematoda: Monorchiidae) from the Ocellated killifish, Floridichthys polyommus (Cyprinodontidae) in the Yucatán Peninsula, Mexico based on an i... by Leopoldo Andrade-Gómez, Juan F. Espínola-Novelo, Brenda Solórzano-García, Gerardo Pérez-Ponce de León

“…In addition, sequences of the 28S of large subunit of nuclear ribosomal RNA and cox1 of the mitochondrial DNA were obtained. Phylogenetic trees inferred from each dataset, placed all the specimens in a monophyletic clade, confirming that the isolates belonged to the same species. …”
Get full text

Molecular phylogeny and comparative chloroplast genome analysis of the type species Crucigenia quadrata by Ting Wang, Huan Feng, Huan Zhu, Bojian Zhong

“…The Bayesian and maximum likelihood (ML) phylogenetic trees support a monophyletic group of C. quadrata and Scenedesmaceae (Chlorophyceae) species. …”
Get full text

Phylogenetic Relationships in the Miracle Berry Genus, <i>Synsepalum</i>, Sensu Lato, and Relatives (Sapotaceae) by Daniel Potter, Mark Uleh

“…Bayesian analyses and Maximum likelihood of nuclear internal transcribed spacer (<i>ITS</i>) and plastid (<i>trnH-psbA</i>) sequences were used to reconstruct the phylogeny of the two genera. Phylogenetic trees generated for both regions (nuclear and plastid) resulted in the resolution of six clades. …”
Get full text

Coalgebraic Structure of Genetic Inheritance by Jianjun Tian, Bai-Lian Li

“…It isnot the dual coalgebraic structure and can be used in theconstruction of phylogenetic trees. Mathematically, to constructphylogenetic trees means we need to solve equations x[n]=a, or x(n)=b. …”
Get full text

Identification of Legionella by MALDI Biotyper through three preparation methods and an in-house library comparing phylogenetic and hierarchical cluster results by Luna Girolamini, Paolo Caiazza, Federica Marino, Maria Rosaria Pascale, Laura Caligaris, Simona Spiteri, Carlo Derelitto, Maria Luisa Simone, Antonella Grottola, Sandra Cristino

“…The HCA confirmed the relationship among the isolates reported in the phylogenetic trees. An improvement in sensitivity was obtained using an in-house library. …”
Get full text

Subfamily evolution analysis using nuclear and chloroplast data from the same reads by Eranga Pawani Witharana, Takaya Iwasaki, Myat Htoo San, Nadeeka U. Jayawardana, Nobuhiro Kotoda, Masashi Yamamoto, Yukio Nagano

“…In response, we employed the same raw read sequencing data to construct cp genome-based trees and nuclear DNA phylogenetic trees using Read2Tree, a cost-efficient method for extracting conserved nuclear gene sequences from raw read data, focusing on the Aurantioideae subfamily, which includes Citrus and its relatives. …”
Get full text

First two mitochondrial genomes for the order Filobasidiales reveal novel gene rearrangements and intron dynamics of Tremellomycetes by Qiang Li, Zhijie Bao, Ke Tang, Huiyu Feng, Wenying Tu, Lijiao Li, Yunlei Han, Mei Cao, Changsong Zhao

“…Phylogenetic analyses based on Bayesian inference and the maximum likelihood methods using a combined mitochondrial gene set generated identical and well-supported phylogenetic trees, wherein Filobasidium species had close relationships with Trichosporonales species. …”
Get full text

Analysis of the Complete Genomes of Enterovirus 71 Subtypes in China by Lei Wang, Yuzhu Dai, Jun Cheng, Changgui Sun, Yu Chen, Dawei Cui

“…Here, the complete genomes of EV-A71 from China between 1998 and 2019 were downloaded from GenBank. The phylogenetic trees were developed by MEGA7.0 software, and the complete genetic epidemiological characteristics and amino acid mutations of EV-A71 from China were also analysed. …”
Get full text

Species delimitation in the Populus laurifolia complex (Salicaceae) based on phylogenetic and morphometric evidence by Xueya Wei, Xingyong Cui, Fulin Yuan, Kerou Zhou, Liwei Zhou, Changli Zhao, Shaoyu Guo, Ce Shang, Zhixiang Zhang

“…The results revealed that this complex, based on a series of significant character states, could be morphologically distinguished into three species—P. laurifolia (Populus pilosa considered a synonym of P. laurifolia), Populus talassica, and Populus pamirica—which also correspond to three well-supported clades in the phylogenetic trees. P. pamirica exhibits some degree of ecological niche differentiation from P. talassica and P. laurifolia, whereas the latter two show minimal differentiation. …”
Get full text

Bithyniid snails (Gastropoda: Bithyniidae) infected with Xiphidiocercariae in Thailand include a new record of Bithynia siamensis siamensis as the intermediate host of Plagiorchis... by Abdulhakam Dumidae, Jiranun Ardpairin, Supawan Pansri, Chanatinat Homkaew, Mayura Nichitcharoen, Aunchalee Thanwisai, Apichat Vitta

“…BLASTn searches in GenBank and phylogenetic trees based on xiphidiocercariae were used to classify the samples into four different families spanning two superfamilies of digenean trematodes. …”
Get full text

Integrating taxonomic, genetic and ecological data to explore the species richness of wild bees (Hymenoptera, Apoidea, Anthophila) of the Culuccia Peninsula (NE Sardinia, Italy) by Matteo Annessi, Alessandra Riccieri, Marilena Marconi, Sabrina Rossi, Andrea Di Giulio

“…DNA was extracted to amplify sequences of the mitochondrial gene Cyotochrome oxydase I, which were then compared with those in BOLD using the identification tool and by constructing neighbor-joining phylogenetic trees. Seventy-six different species belonging to 29 genera and six families were collected and identified. …”
Get full text

Variation in nuclear genome size within the Eisenia nordenskioldi complex (Lumbricidae, Annelida) by S. V. Shekhovtsov, Ya. R. Efremov, T. V. Poluboyarova, S. E. Peltek

“…We compared the obtained data to phylogenetic trees based on transcriptome data. Genome size in ancestral population was more likely to be big. …”
Get full text

Diagnosis of the mechanisms of different types of discordances between phylogenies inferred from nuclear and mitochondrial markers by A. A. Poroshina, D. Y. Sherbakov, T. E. Peretolchina

“…All these phenomena are diagnosed by comparing the topologies of phylogenetic trees inferred from molecular markers of evolution located in mitochondria and nuclei. …”
Get full text