Article
Evolutionary Biology
Ryan A. Folk, Michelle L. Gaynor, Nicholas J. Engle-Wrye, Brian C. O'Meara, Pamela S. Soltis, Douglas E. Soltis, Robert P. Guralnick, Stephen A. Smith, Charles J. Grady, Yudai Okuyama
Summary: Applications of molecular phylogenetic approaches have revealed evidence of hybridization across various clades of life. This study focuses on the Heuchereae clade in Saxifragaceae and uses a combination of nuclear and chloroplast data to confirm previous hybridization events and identify a new one. The results suggest that past climate change and species' ecological strategies play important roles in shaping patterns of range contact and opportunities for hybridization.
SYSTEMATIC BIOLOGY
(2023)
Article
Microbiology
Lester J. Perez, Gavin A. Cloherty, Michael G. Berg
Summary: Picobirnaviruses (PBVs) are small double-segmented, double-stranded RNA viruses that are frequently associated with gastrointestinal and respiratory infections. The evolutionary analysis revealed that PBVs emerged simultaneously from avian Reovirus and fungal Partitivirus ancestors, indicating parallel evolution from different hosts has driven the genetic similarities among PBV species. These findings provide insights into the origins and genetic diversification of the Picobirnaviridae family.
MICROBIOLOGY SPECTRUM
(2023)
Article
Plant Sciences
Xia Liu, Zhaoshan Wang, Wei Wang, Qinqin Huang, Yanfei Zeng, Yu Jin, Honglei Li, Shuhui Du, Jianguo Zhang
Summary: This study examines the origin and biogeography of the Populus genus using phylogenetic analysis of chloroplast fragments. The results suggest that the early divergences of the Salicaceae family occurred in Eurasia after the Cretaceous-Paleogene mass extinction, with subsequent spread to other regions. Modern Populus species began to diversify during the early Oligocene, potentially facilitated by climate changes. Populus species from Eurasia colonized North America via the Bering Land Bridges. The present-day distribution of Populus can be explained by differences in extinction rates in different regions. Further research is needed to test these hypotheses. This study highlights the importance of combining phylogenetic analysis and biogeographic interpretations to understand the origin and distribution of biodiversity in temperate plant floras.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Gunnar Keppel, Francis J. Nge, Thomas Ibanez
Summary: Islands in the tropical Pacific Ocean are known for their high biodiversity and endemism, despite their relatively small landmasses. This study investigates the sources, age, number of colonizations, and diversification of 16 archipelagos in the South Pacific to understand the formation of this biodiversity. The results support the theory of the Taxon Cycle, where ongoing colonization leads to the displacement of established lineages. However, older islands such as New Caledonia and Fiji show a slower taxon cycle and lower diversification rates.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Article
Microbiology
Zhaoxue Zhang, Xinye Liu, Mengfei Tao, Xiaoyong Liu, Jiwen Xia, Xiuguo Zhang, Zhe Meng
Summary: Based on multi-locus phylogenies and morphological characteristics, three new species were discovered, namely Pseudoplagiostoma alsophilae, P. bambusae, and P. machili. Molecular clock analysis revealed that the ancestor of Pseudoplagiostomataceae and Apoharknessiaceae emerged in the Cretaceous period, with most species appearing in the Paleogene and Neogene periods. Historical biogeography reconstruction suggested that Asia, especially Southeast Asia, was likely the ancestral area for Pseudoplagiostomataceae.
Article
Biochemical Research Methods
Yu K. Mo, Robert Lanfear, Matthew W. Hahn, Bui Quang Minh
Summary: In this study, a new method for calculating site concordance factors (sCFs) is introduced. The updated version uses likelihood to generate probability distributions of ancestral states at internal nodes, thus reducing the effects of homoplasy and taxon sampling.
Article
Microbiology
Viviana Morillo-Lopez, Alexandra Sjaarda, Imon Islam, Gary G. Borisy, Jessica L. Mark Welch
Summary: The study reveals that microbial communities in different microhabitats within the human mouth vary, with the bacteria composition in corncob structures being only a subset of those present in dental plaque. Direct interactions between different bacterial species were observed, indicating complex species ensembles within these microhabitats.
Article
Multidisciplinary Sciences
Hsin Lee, Kwen-Shen Lee, Chia-Hsin Hsu, Chen-Wei Lee, Ching-En Li, Jia-Kang Wang, Chien-Chia Tseng, Wei-Jen Chen, Ching-Chang Horng, Colby T. Ford, Andreas Kroh, Omri Bronstein, Hayate Tanaka, Tatsuo Oji, Jih-Pai Lin, Daniel Janies
Summary: The classification of the Class Echinoidea is being revised based on emerging molecular phylogenetic evidence, particularly concerning the sister-group relationships within the superorder Luminacea. The placement of many families remains unresolved due to incongruent evidence from different data sources. This study investigates the phylogenetic relationships of 25 taxa, proposing three new superfamilies and revealing the importance of the tropical western Pacific and eastern Indian Oceans in the early diversification of sand dollars. The study also highlights the role of Taiwan fauna in understanding the historical migration and dispersal events in the evolutionary history of Luminacea.
SCIENTIFIC REPORTS
(2023)
Article
Forestry
Ana Posta, Zdenko Tkalcec, Ivana Kusan, Neven Matocec, Lucia Pole, Milan Cerkez, Armin Mesic
Summary: This study examined seventeen collections of the genus Parasola from Croatia using integrative taxonomic methods. A new species, Parasola papillatospora, was described based on both morphology and multigene phylogenetic analyses. The species was found growing on soil in temperate deciduous forests in two different areas of NW Croatia. The most notable features of the new species are the characteristics of its basidiospores, such as a papillate apex, central germ pore, and highly variable shape. Additionally, eight Parasola species were reported for the first time in Croatia, with P. malakandensis being a new record for Europe.
Article
Multidisciplinary Sciences
Julien Louys, Todd J. Braje, Chun-Hsiang Chang, Richard Cosgrove, Scott M. Fitzpatrick, Masaki Fujita, Stuart Hawkins, Thomas Ingicco, Ai Kawamura, Ross D. E. MacPhee, Matthew C. McDowell, Hanneke J. M. Meijer, Philip J. Piper, Patrick Roberts, Alan H. Simmons, Gerrit van den Bergh, Alexandra van der Geer, Shimona Kealy, Sue O'Conor
Summary: The impact of modern humans on previously unoccupied island ecosystems and the extinction of Pleistocene megafauna are closely linked. However, current data does not support a direct association between Pleistocene hominin arrival and global extinctions, which are difficult to separate from environmental changes. It is not until the Holocene that significant changes in technology, dispersal, demography, and human behavior visibly affect island ecosystems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Ecology
Vanessa Cutts, Dagmar M. Hanz, Martha Paola Barajas-Barbosa, Franziska Schrodt, Manuel J. Steinbauer, Carl Beierkuhnlein, Pierre Denelle, Jose Maria Fernandez-Palacios, Pierre Gauzere, Matthias Grenie, Severin D. H. Irl, Nathan Kraft, Holger Kreft, Brian Maitner, Francois Munoz, Wilfried Thuiller, Cyrille Violle, Patrick Weigelt, Richard Field, Adam C. Algar
Summary: Current models of island biogeography treat endemic and non-endemic species as if they were functionally equivalent, focussing primarily on species richness. Thus, the functional composition of island biotas in relation to island biogeographical variables remains largely unknown.
Article
Biochemistry & Molecular Biology
Eranga Wettewa, Lisa E. Wallace
Summary: Platanthera, one of the largest genera of temperate orchids, has adaptively radiated into diverse habitats in North America, Asia, Europe, North Africa, Borneo, and Sarawak. A new molecular toolkit was developed to study Platanthera, revealing the ancestry of subgenus Limnorchis originating in western North America approximately 3-4.5 million years ago. The study suggests complex biogeographic connections between Asia and North America within the genus.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Nathan M. Michielsen, Steven M. Goodman, Voahangy Soarimalala, Alexandra A. E. van der Geer, Liliana M. Davalos, Grace Saville, Nathan Upham, Luis Valente
Summary: Many unique species in Madagascar are at risk of extinction, and the long-term impact of these extinctions in terms of evolutionary history is unknown. By analyzing the phylogenetic dataset of Madagascar's non-marine mammals, researchers estimated the natural rates of extinction, colonization, and speciation. The results showed that the extinction of currently threatened species would have a much greater impact on evolution than previous extinctions since human arrival. Immediate conservation actions are needed to prevent an imminent extinction wave with significant evolutionary consequences.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Jiantao Hu, Hongjie Li, Harumi Sakai, Takahiko Mukai, Ho Young Suk, Chenhong Li
Summary: In this study, a robust phylogeny of the genus Odontobutis was built based on comprehensive molecular data collection and analysis. Divergence time estimation and ancestral range reconstruction indicated that the common ancestor of modern Odontobutis was likely distributed in Japan, southern China, or the Korean Peninsula. Geographical events in East Asia since the late Miocene, such as the opening of the Japan/East Sea and climate change, might have contributed to the diversification and current distribution pattern of Odontobutis.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Cui Li, Qi Kou, Zhen Zhang, Lisha Hu, Wen Huang, Zongmei Cui, Yumeng Liu, Peizhen Ma, Haiyan Wang
Summary: Oysters originated from the circum-Arctic region in the Early Jurassic and diversified during the Cretaceous and the Palaeogene periods due to tectonic events. Some oyster genera, such as Crassostrea and Saccostrea, have low dispersal abilities, with their major diversifications being consistent with geological changes. Environmental adaptations and reproductive patterns play key roles in the formation of oyster distribution patterns.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Genetics & Heredity
Winslow C. Johnson, Alison J. Ordway, Masayoshi Watada, Jonathan N. Pruitt, Thomas M. Williams, Mark Rebeiz
Article
Zoology
Shimpei F. Hiruta, Norio Kobayashi, Toru Katoh, Hiroshi Kajihara
ZOOLOGICAL SCIENCE
(2016)
Article
Zoology
Hiromu Suga, Wataru Hirano, Toru Katoh, Kei W. Matsubayashi, Haruo Katakura
ZOOLOGICAL SCIENCE
(2016)
Article
Marine & Freshwater Biology
Shimpei F. Hiruta, Maho Ikoma, Toru Katoh, Hiroshi Kajihara, Matthew H. Dick
Article
Multidisciplinary Sciences
Hiroyuki F. Izumitani, Yohei Kusaka, Shigeyuki Koshikawa, Masanori J. Toda, Toru Katoh
Article
Ecology
Ai-li Chen, Chuan-cheng Chen, Toru Katoh, Takehiro K. Katoh, Masayoshi Watada, Masanori J. Toda, Michael G. Ritchie, Shuo-yang Wen
JOURNAL OF EVOLUTIONARY BIOLOGY
(2019)
Article
Cell Biology
Kaori Watanabe, Yasutetsu Kanaoka, Shoko Mizutani, Hironobu Uchiyama, Shunsuke Yajima, Masayoshi Watada, Tadashi Uemura, Yukako Hattori
Article
Cell Biology
Masayoshi Watada, Yusaku Hayashi, Kaori Watanabe, Shoko Mizutani, Ayumi Mure, Yukako Hattori, Tadashi Uemura
Article
Biochemistry & Molecular Biology
William R. Conner, Emily K. Delaney, Michael J. Bronski, Paul S. Ginsberg, Timothy B. Wheeler, Kelly M. Richardson, Brooke Peckenpaugh, Kevin J. Kim, Masayoshi Watada, Ary A. Hoffmann, Michael B. Eisen, Artyom Kopp, Brandon S. Cooper, Michael Turelli
Summary: The Drosophila montium species group consists of 94 named species closely related to D. melanogaster, distributed widely across Asia, Africa, and Australasia. Genomic data from 42 species were used to estimate phylogeny, relative divergence times, and support monophyly within the group. However, age estimates for the montium crown group compared to D. melanogaster remain uncertain.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Correction
Biology
Bernard Y. Kim, Jeremy R. Wang, Danny E. Miller, Olga Barmina, Emily Delaney, Ammon Thompson, Aaron A. Comeault, David Peede, Emmanuel R. R. D'Agostino, Julianne Pelaez, Jessica M. Aguilar, Diler Haji, Teruyuki Matsunaga, Ellie Armstrong, Molly Zych, Yoshitaka Ogawa, Marina Stamenkovic-Radak, Mihailo Jelic, Marija Savic Veselinovic, Marija Tanaskovic, Pavle Eric, Jian-Jun Gao, Takehiro K. Katoh, Masanori J. Toda, Hideaki Watabe, Masayoshi Watada, Jeremy S. Davis, Leonie C. Moyle, Giulia Manoli, Enrico Bertolini, Vladimir Kostal, R. Scott Hawley, Aya Takahashi, Corbin D. Jones, Donald K. Price, Noah Whiteman, Artyom Kopp, Daniel R. Matute, Dmitri A. Petrov
Article
Multidisciplinary Sciences
Daisuke Kageyama, Toshiyuki Harumoto, Keisuke Nagamine, Akiko Fujiwara, Takafumi N. Sugimoto, Akiya Jouraku, Masaru Tamura, Takehiro K. Katoh, Masayoshi Watada
Summary: In most eukaryotes, there is a difference in evolutionary interests between biparentally inherited nuclear genomes and maternally inherited cytoplasmic genomes. Male-killing in arthropods often results from maternally inherited bacteria, but the mechanism of how viruses induce male-killing is not well understood. This study shows that a maternally inherited dsRNA virus induces male-killing in Drosophila, with a protein encoded by a gene on a specific genome segment being responsible for this phenotype. These results suggest that symbiotic viruses play a role in arthropod evolution and can be utilized for arthropod control.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Daisuke Kageyama, Kanamu Yoshimura, Takafumi N. Sugimoto, Takehiro K. Katoh, Masayoshi Watada