Article
Biochemistry & Molecular Biology
Danyan Su, Lingxiao Yang, Xuan Shi, Xiaoya Ma, Xiaofan Zhou, S. Blair Hedges, Bojian Zhong
Summary: The study resolves the monophyly of bryophytes by improving taxon sampling of hornworts and eliminating the effect of synonymous substitutions. It estimates that land plants originated in the Precambrian, much older than widely recognized. The research emphasizes the important contribution of molecular data in the face of contentious fossil evidence and the critical scrutiny required for fossil calibrations in estimating the timescale of plant evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biology
Marie Drabkova, Kevin M. Kocot, Kenneth M. Halanych, Todd H. Oakley, Leonid L. Moroz, Johanna T. Cannon, Armand Kuris, Ana Elisa Garcia-Vedrenne, M. Sabrina Pankey, Emily A. Ellis, Rebecca Varney, Jan Stefka, Jan Zrzavy
Summary: Dicyemids and orthonectids, traditionally classified as Mesozoa, had uncertain positions within Metazoa. This study used multiple phylogenomic approaches and obtained new transcriptomes and genomes to investigate their placement. The results suggest that Mesozoa is monophyletic and closely related to Platyhelminthes or Gnathifera, but caution is needed due to potential long-branch attraction. The classic hypothesis on monophyletic Mesozoa may need further testing.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Ting Zan, Yi-Tao He, Min Zhang, Takahiro Yonezawa, Hong Ma, Qiang-Min Zhao, Wen-Ju Zhang, Chien-Hsun Huang, Wen-Yu Kuo
Summary: In this study, a detailed analysis of the phylogeny of the Camellia genus was conducted using 95 transcriptomes and 1481 low-copy genes. The results showed that the 87 species were grouped into 8 main clades and two independent species, which was different from existing classification systems. The relationships among these clades were weakly supported and did not agree with the phylogeny from chloroplast genomes. The study also revealed reticulate evolution and a rapid evolutionary history of Camellia.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Entomology
Gengyun Niu, Mahir Budak, Ertan Mahir Korkmaz, Ozgul Dogan, Andre Nel, Siying Wan, Chenyang Cai, Corentin Jouault, Min Li, Meicai Wei
Summary: In this study, genetic and morphological analyses were conducted to clarify the phylogenetic position of the Athaliidae family. The results support the taxonomic treatment of Athaliidae as a separate family and provide insights into the evolution of hymenopteran insects.
Article
Biochemistry & Molecular Biology
Rasha Shraim, Bart P. S. Nieuwenhuis
Summary: Despite limited knowledge of the natural habitats of fission yeasts, a search through a large collection of publicly available environmental metatranscriptomic datasets can help identify candidate natural habitats. Most fission yeast signatures were found in categories such as 'food' and 'terrestrial arthropods', with additional presence in various marine and freshwater habitats.
Article
Biochemistry & Molecular Biology
Anna Cho, Denis Tikhonenkov, Elisabeth Hehenberger, Anna Karnkowska, Alexander P. Mylnikov, Patrick J. Keeling
Summary: Stramenopiles are a well-studied eukaryotic supergroup, but the relationships between major subgroups, such as Bigyromonadea, remain unresolved. By analyzing transcriptomes from seven new bigyromonad species, this study reveals the diversity of Bigyromonadea and suggests that they are most likely monophyletic with oomycetes.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Entomology
Yunyun Gao, Yingqiang Ge, Liping Yan, Nikita E. Vikhrev, Qike Wang, Nathan J. Butterworth, Dong Zhang
Summary: This study establishes the phylogeny of Lispe genus and elucidates the intrageneric relationships of known species groups. It supports the monophyly of Lispe genus and clarifies the validity of 11 species groups. The study provides a better understanding of the phylogenetic relationships and evolutionary history of Lispe genus.
Article
Biochemistry & Molecular Biology
Maria Herranz, Josefin Stiller, Katrine Worsaae, Martin Sorensen
Summary: In this study, the relationships and classification of major clades within Kinorhyncha were resolved using transcriptomic data. The results provide insights into the evolution of segmentation within the group as well as the evolutionary relationships among different kinorhynch species and genera.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Elliot M. Gardner
Summary: This molecular study investigates the evolutionary history of the Neotropical Artocarpeae using phylogenomic and network analyses. The results reveal a rapid radiation, with introgression, incomplete lineage sorting, and lack of gene tree resolution causing difficulties in reconstructing a well-supported bifurcating tree. Coalescent-based species trees conflicted with morphology, while multifurcating phylogenetic network analyses recovered multiple histories that showed clearer traces of morphological alliances. The only unambiguous finding is the sister relationship between Clarisia sect. Acanthinophyllum and the rest of the Neotropical Artocarpeae, leading to the reinstatement of the genus Acanthinophyllum.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Ornithology
Gustavo A. Bravo, Bret M. Whitney, Ricardo Belmonte-Lopes, Marcos R. Bornschein, Natalia Aristizabal, Renata Beco, Jaqueline Battilana, Luciano N. Naka, Alexandre Aleixo, Marcio R. Pie, Luis F. Silveira, Elizabeth P. Derryberry, Robb T. Brumfield
Summary: Thamnophilidae is a species-rich Neotropical radiation of passerine birds, with classification based on morphology but redefined by recent studies integrating phenotypic and phylogenetic data. Results show non-monophyly of Herpsilochmus and Sakesphorus, and relationships between Herpsilochmus sellowi and Biatas, as well as Sakesphorus cristatus and a clade comprising Herpsilochmus sensu stricto and Dysithamnus. Within Herpsilochmus sensu stricto, 6 well-supported species groups were identified.
Article
Plant Sciences
Kyu Tae Park, SeonJoo Park
Summary: The study characterized the complete chloroplast genomes of Hepatica, identifying unique gene features and selection pressures. Comparative analyses revealed insights into the phylogenetic relationships of Hepatica and its relatives through multiple comparisons and gene loss events.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Wei-Tao Jin, David S. Gernandt, Christian Wehenkel, Xiao-Mei Xia, Xiao-Xin Wei, Xiao-Quan Wang
Summary: The study investigated the evolution of coniferous forests in the Northern Hemisphere, revealing that 90% of extant pine species originated in the Miocene and that the midlatitude region has served as an evolutionary museum for global pines. Additionally, it was found that topography and aridity index played crucial roles in pine diversification.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Plant Sciences
Boni Song, Changkun Liu, Dengfeng Xie, Yulin Xiao, Rongming Tian, Zixuan Li, Songdong Zhou, Xingjin He
Summary: The taxonomy of the famous folk medicinal plant Peucedanum franchetii in China has been unresolved. Through genetic and morphological studies, it was found that P. franchetii should be classified as an independent species under the genus Ligusticopsis instead of being merged with L. likiangensis.
Article
Plant Sciences
Da-Juan Chen, Jacob B. Landis, Hong-Xin Wang, Qing-Hui Sun, Qiao Wang, Hua-Feng Wang
Summary: In this study, a comprehensive analysis of the chloroplast genome of Arecaceae was conducted. It was found that the genomes possess common structural features and the phylogenetic relationships among different subfamilies are clear. Molecular dating suggests that the origin of the family can be traced back to approximately 96.60-102.40 million years ago, and ancestral traits were reconstructed.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Alicia Talavera, Ze-Long Nie, Zhi-Yao Ma, Gabriel Johnson, Stefanie M. Ickert-Bond, Elizabeth A. Zimmer, Jun Wen
Summary: This study used a set of newly designed Vitaceae baits targeting 1013 genes to explore the phylogenetic relationships among North American Vitis. The results showed that Eurasian Vitis taxa were nested within North American Vitis subgenus Vitis. North American Vitis subgenus Vitis could be divided into nine main groups. Strong cytonuclear discordances were detected in North American Vitis, with many species non-monophyletic in the plastid phylogeny but monophyletic in the nuclear phylogeny. The study also identified four distinct species in the Vitis cinerea complex in North America.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Ecology
Natalia Fraija-Fernandez, Marie-Catherine Bouquieaux, Anais Rey, Inaki Mendibil, Unai Cotano, Xabier Irigoien, Maria Santos, Naiara Rodriguez-Ezpeleta
ECOLOGY AND EVOLUTION
(2020)
Article
Immunology
Melanie T. Cushion, Parag Kumar, Ruying Lu, Alan Ashbaugh, Lilian W. Adeojo, Raul Alfaro, Raphael Mannino, Edmund Tramont, Joseph A. Kovacs
Summary: eATQ, a novel lipid-crystal nanoparticle formulation of atovaquone, showed superior activity in reducing Pneumocystis nuclei and asci in a mouse model of PCP compared to commercially available atovaquone. Combination of eATQ with anidulafungin significantly reduced nuclei better than commercial atovaquone plus anidulafungin, suggesting potential for further evaluation in PCP treatment and prevention.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Fisheries
Teunis Jansen, Einar Eg Nielsen, Naiara Rodriguez-Ezpeleta, Haritz Arrizabalaga, Soren Post, Brian R. MacKenzie
Summary: Collaborating with the Greenlandic fishing fleet, researchers have documented the presence of Atlantic bluefin tuna in Greenland waters, mainly preying on Atlantic mackerel. The tunas vary in size and age, with a wide range of individuals from different year classes migrating to the region. The summer residence of bluefin tuna in the area could be attributed to increasing sea temperatures and higher abundances of both bluefin tuna and their key prey species.
CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES
(2021)
Article
Multidisciplinary Sciences
Iraide Artetxe-Arrate, Igaratza Fraile, Jessica Farley, Audrey M. Darnaude, Naomi Clear, Naiara Rodriguez-Ezpeleta, David L. Dettman, Christophe Pecheyran, Inigo Krug, Anais Medieu, Mohamed Ahusan, Craig Proctor, Asep Priatna, Pratiwi Lestari, Campbell Davies, Francis Marsac, Hilario Murua
Summary: The study examined the potential of otolith microchemistry in understanding the spatial dynamics of skipjack tuna, a valuable commercial species in the Indian Ocean. Differences in otolith chemical signatures were observed among individuals from different nursery areas, but there was significant overlap in the signatures of the three nurseries. Cohort effects on otolith trace element signatures were detected, highlighting the importance of understanding seasonal variations in oceanographic conditions for species with multiple reproductive peaks throughout the year.
Article
Evolutionary Biology
Imanol Aguirre-Sarabia, Natalia Diaz-Arce, Iker Pereda-Agirre, Inaki Mendibil, Agurtzane Urtizberea, Hans D. Gerritsen, Finlay Burns, Ian Holmes, Jorge Landa, Ilaria Coscia, Inaki Quinconces, Marina Santurtun, Antonella Zanzi, Jann T. Martinsohn, Naiara Rodriguez-Ezpeleta
Summary: Genetics can help understand population connectivity of white anglerfish and its interaction with black anglerfish. The study found that white anglerfish is likely a single panmictic population, some specimens classified as white anglerfish are genetically identified as black anglerfish, and the two Lophius species naturally hybridize. The results set the basis for a genetics-informed white anglerfish assessment framework.
EVOLUTIONARY APPLICATIONS
(2021)
Letter
Biochemistry & Molecular Biology
Naiara Rodriguez-Ezpeleta, Olivier Morissette, Colin W. Bean, Shivakumara Manu, Pritam Banerjee, Anais Lacoursiere-Roussel, Kingsly C. Beng, S. Elizabeth Alter, Fabian Roger, Luke E. Holman, Kathryn A. Stewart, Michael T. Monaghan, Quentin Mauvisseau, Luca Mirimin, Owen S. Wangensteen, Caterina M. Antognazza, Sarah J. Helyar, Hugo de Boer, Marie-Eve Monchamp, Reindert Nijland, Cathryn L. Abbott, Hideyuki Doi, Matthew A. Barnes, Matthieu Leray, Pascal I. Hablutzel, Kristy Deiner
Summary: The term eDNA should be used to refer to the pool of DNA isolated from environmental samples. The proposed two-level terminology specifying sampling environment and targeted taxa might hinder clear communication about environmental DNA and its use in biomonitoring. It overlooks the fundamental distinction of the type of DNA from which ecological interpretations are derived.
Editorial Material
Biochemistry & Molecular Biology
Naiara Rodriguez-Ezpeleta, Lucie Zinger, Andrew Kinziger, Holly M. Bik, Aurelie Bonin, Eric Coissac, Brent C. Emerson, Carla Martins Lopes, Tara A. Pelletier, Pierre Taberlet, Shawn Narum
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Limnology
Oriol Canals, Inaki Mendibil, Maria Santos, Xabier Irigoien, Naiara Rodriguez-Ezpeleta
Summary: The use of environmental DNA (eDNA) analysis in deep-sea fish research has revealed the richness and abundance of deep-sea fish species at different depths, showing that eDNA can reflect day-night community patterns and species-specific vertical distributions. This method has the potential to improve knowledge on dark ocean ecosystems and prevent further exploitation before more damage is done.
LIMNOLOGY AND OCEANOGRAPHY LETTERS
(2021)
Article
Microbiology
Melanie T. Cushion, Alan Ashbaugh
Summary: Rezafungin, a novel echinocandin in Phase 3 development, demonstrates a favorable safety profile and pharmacokinetic properties for once-weekly dosing and antifungal activity against major pathogens. In animal studies, rezafungin showed both preventive and therapeutic effects against Pneumocystis murina pneumonia, supporting further investigation for treatment of Pneumocystis jirovecii pneumonia in humans.
Article
Microbiology
Nathan P. Wiederhold, Thomas F. Patterson, Sandra Rebholz, Connell W. C. Boal, Monika Ehrensberger, Ryan Boyle, Melanie T. Cushion
Summary: A3IS is a synthetic product that releases hydrogen peroxide at therapeutic levels. It has broad-spectrum antimicrobial effects and has shown significant efficacy against various human pathogens, including fungi. It also exhibits good inhibitory effects on Pneumocystis. These findings suggest that A3IS is a novel antifungal agent.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2022)
Article
Microbiology
Melanie T. Cushion, Alan Ashbaugh, Steven G. Sayson, Christopher Mosley, Philippe M. Hauser
Summary: The proposed life cycle of fungi in the genus Pneumocystis includes both sexual and asexual replication. Recent studies have shown that these fungi rely on the sexual cycle for survival and growth. Furthermore, treatment with echinocandins can block the sexual cycle while leaving the asexual replication unaffected.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Nikeya L. Tisdale, Alan Ashbaugh, Keeley Hendrix, Margaret S. Collins, Alexey P. Porollo, Melanie T. Cushion
Summary: This article discusses the importance of considering sex differences in disease research and suggests the inclusion of females in experimental models.
Correction
Microbiology
Nathan P. Wiederhold, Thomas F. Patterson, Sandra Rebholz, James Brennan, Thomas Patton, John Barrett, Connell W. C. Boal, Monika Ehrensberger, Ryan Boyle, Melanie T. Cushion
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Letter
Multidisciplinary Sciences
Natalia Diaz-Arce, Naiara Rodriguez-Ezpeleta
SCIENTIFIC REPORTS
(2023)
Article
Environmental Studies
John Gilbey, Gary Carvalho, Rita Castilho, Ilaria Coscia, Mark W. Coulson, Geir Dahle, Sofie Derycke, Sara M. Francisco, Sarah J. Helyar, Torild Johansen, Claudia Junge, Kara K. S. Layton, Jann Martinsohn, Iveta Matejusova, Joana I. Robalo, Naiara Rodriguez-Ezpeleta, Goncalo Silva, Ilona Strammer, Anti Vasemagi, Filip A. M. Volckaert
Summary: Effective management of marine fisheries and ecosystem monitoring require analysis of complex information, with increasing legislative demands for good environmental status. Utilizing environmental DNA for data collection presents new cost-effective methods for revolutionizing marine data collection.