A combined microscopy and single-cell sequencing approach reveals the ecology, morphology, and phylogeny of uncultured lineages of zoosporic fungi by Kensuke Seto, D. Rabern Simmons, C. Alisha Quandt, Thijs Frenken, Alden C. Dirks, Rebecca A. Clemons, Katelyn M. McKindles, R. Michael L. McKay, Timothy Y. James

“…Overall, by combining photographs of parasitic fungi with phylogenetic analyses, we were able to better understand the ecological function and morphology of many of the branches on the fungal tree of life known only from DNA sequences. IMPORTANCE Much of the diversity of microbes from natural habitats, such as soil and freshwater, comprise species and lineages that have never been isolated into pure culture. …”
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Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity by Mehmet Birikmen, Katherine E. Bohnsack, Vinh Tran, Sharvari Somayaji, Markus T. Bohnsack, Markus T. Bohnsack, Ingo Ebersberger, Ingo Ebersberger, Ingo Ebersberger

“…Here, we use a comprehensive phylogenetic profiling setup, integrating targeted ortholog searches with automated scoring of protein domain architecture similarities and an assessment of when search sensitivity becomes limiting, to trace 301 curated eukaryotic ribosome biogenesis factors across 982 taxa spanning the tree of life and including 727 archaea. We show that both factor loss and lineage-specific modifications of factor function modulate ribosome biogenesis, and we highlight that limited sensitivity of the ortholog search can confound evolutionary conclusions. …”
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Foraminifera as a model of eukaryotic genome dynamism by Caitlin Timmons, Kristine Le, H. B. Rappaport, Elinor G. Sterner, Xyrus X. Maurer-Alcalá, Susan T. Goldstein, Laura A. Katz

“…The analyses here extend our understanding of the genome dynamics across the eukaryotic tree of life.IMPORTANCEIn traditional depictions of eukaryotes (i.e., cells with nuclei), life cycles alternate only between haploid and diploid phases, overlooking studies of diverse microeukaryotic lineages (e.g., amoebae, ciliates, and flagellates) that show dramatic variation in DNA content throughout their life cycles. …”
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Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton by Harriet Alexander, Sarah K. Hu, Arianna I. Krinos, Maria Pachiadaki, Benjamin J. Tully, Christopher J. Neely, Taylor Reiter

“…Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life.IMPORTANCESingle-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. …”
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DNA barcoding detects resurrected taxon Giuris laglaizei (Sauvage 1880) in Sulawesi, Indonesia: Bolano Sau Lake payangka phylogeny, phenotypic characters and implications for Giuri... by Mashening L. Rabuna, Mohamad Nasir, Abigail Mary Moore, Nur Hasanah, Muhammad Saleh Nurdin, Kasim Mansyur, Aswad Eka Putra, Samliok Ndobe

“…Homologous nucleotide sequences were obtained from public (GenBank and BOLD) databases, analysis conducted in MEGA X, and phylogenetic trees edited in the Interactive Tree of Life (iToL). Results: Within the deeply divided Giuris clade, the payangka sequence resolved into a sub-clade identified as Giuris laglaizei (Sauvage 1880), a recently resurrected taxon, based on a sequence provided by Philippe Keith. …”
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High-quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae) by Anna K. Hundsdoerfer, Tilman Schell, Franziska Patzold, Charlotte J. Wright, Atsuo Yoshido, František Marec, Hana Daneck, Sylke Winkler, Carola Greve, Lars Podsiadlowski, Michael Hiller, Martin Pippel

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Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus by Jacob L. Steenwyk, Charu Balamurugan, Huzefa A. Raja, Carla Gonçalves, Ningxiao Li, Frank Martin, Judith Berman, Nicholas H. Oberlies, John G. Gibbons, Gustavo H. Goldman, David M. Geiser, Jos Houbraken, David S. Hibbett, Antonis Rokas

“…These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the Tree of Life.IMPORTANCEIdentification of fungal species relies on the use of molecular markers. …”
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Beneficial and Detrimental Effects of Reactive Oxygen Species on Lifespan: A Comprehensive Review of Comparative and Experimental Studies by Hazel J. Shields, Hazel J. Shields, Hazel J. Shields, Annika Traa, Annika Traa, Annika Traa, Jeremy M. Van Raamsdonk, Jeremy M. Van Raamsdonk, Jeremy M. Van Raamsdonk, Jeremy M. Van Raamsdonk, Jeremy M. Van Raamsdonk

“…Accordingly, the relationship between ROS and aging is difficult to generalize across the tree of life.…”
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Aquatic Thermal Reservoirs of Microbial Life in a Remote and Extreme High Andean Hydrothermal System by Vilma Pérez, Johanna Cortés, Francisca Marchant, Cristina Dorador, Verónica Molina, Marcela Cornejo-D’Ottone, Klaudia Hernández, Wade Jeffrey, Sergio Barahona, Martha B. Hengst

“…The microbial diversity of the Lirima hydrothermal system is represented by groups from deep branches of the tree of life, suggesting this ecosystem as a reservoir of primitive life and a key system to study the processes that shaped the evolution of the biosphere.…”
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The Hypersaline Archaeal Histones HpyA and HstA Are DNA Binding Proteins That Defy Categorization According to Commonly Used Functional Criteria by Saaz Sakrikar, Rylee K. Hackley, Mar Martinez-Pastor, Cynthia L. Darnell, Angie Vreugdenhil, Amy K. Schmid

“…Here, we compare hypersaline histone function to a variety of DNA binding proteins across the tree of life, revealing histone-like behavior in some respects and specific transcriptional regulatory function in others.…”
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Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae) by Zhiyong Jiang, Wenqing Zang, Per G. P. Ericson, Gang Song, Shaoyuan Wu, Shaohong Feng, Sergei V. Drovetski, Gang Liu, Dezhi Zhang, Takema Saitoh, Per Alström, Scott V. Edwards, Fumin Lei, Yanhua Qu

“…Abstract Background Resolving the phylogeny of rapidly radiating lineages presents a challenge when building the Tree of Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that rapidly diversified at the Pliocene–Pleistocene boundary. …”
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A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera <italic toggle="yes">Aspergillus</italic> and <italic toggle="yes">Penicillium</i... by Jacob L. Steenwyk, Xing-Xing Shen, Abigail L. Lind, Gustavo H. Goldman, Antonis Rokas

“…More broadly, our approach provides a general template for phylogenomic identification of resolved and contentious branches in densely genome-sequenced lineages across the tree of life. IMPORTANCE Understanding the evolution of traits across technologically and medically significant fungi requires a robust phylogeny. …”
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Management of Epileptic Seizures in Disorders of Consciousness: An International Survey by Marie-Michèle Briand, Marie-Michèle Briand, Marie-Michèle Briand, Marie-Michèle Briand, Nicolas Lejeune, Nicolas Lejeune, Nicolas Lejeune, Nicolas Lejeune, Nathan Zasler, Nathan Zasler, Nathan Zasler, Rita Formisano, Olivier Bodart, Anna Estraneo, Anna Estraneo, Wendy L. Magee, Aurore Thibaut, Aurore Thibaut

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Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family by Wenpan Dong, Enze Li, Yanlei Liu, Chao Xu, Yushuang Wang, Kangjia Liu, Xingyong Cui, Jiahui Sun, Zhili Suo, Zhixiang Zhang, Jun Wen, Shiliang Zhou

“…Phylogenomics has been effective in providing information for resolving both deep- and shallow-scale relationships across all branches of the tree of life. The olive family (Oleaceae) is composed of 25 genera classified into five tribes with tribe Oleeae consisting of four subtribes. …”
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Microscopic and metatranscriptomic analyses revealed unique cross-domain parasitism between phylum Candidatus Patescibacteria/candidate phyla radiation and methanogenic archaea in... by Kyohei Kuroda, Meri Nakajima, Ryosuke Nakai, Yuga Hirakata, Shuka Kagemasa, Kengo Kubota, Taro Q. P. Noguchi, Kyosuke Yamamoto, Hisashi Satoh, Masaru K. Nobu, Takashi Narihiro

“…Minisyncoccaceae with methanogenic archaea are parasitisms.IMPORTANCECulture-independent DNA sequencing approaches have explored diverse yet-to-be-cultured microorganisms and have significantly expanded the tree of life in recent years. One major lineage of the domain Bacteria, Ca. …”
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Discriminating Susceptibility of Xanthine Oxidoreductase Family to Metals by Anne-Soisig Steunou, Marion Babot, Anne Durand, Marie-Line Bourbon, Sylviane Liotenberg, Guylaine Miotello, Jean Armengaud, Soufian Ouchane

“…Given the conservation of XOR structure and function across the tree of life, we anticipate that our findings could be transferable to other XORs and organisms. …”
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Density dependent environments can select for extremes of body size by Coulson, Tim, Felmy, Anja, Potter, Tomos, Passoni, Gioele, Montgomery, Robert A, Gaillard, Jean-Michel, Hudson, Peter J, Travis, Joseph, Bassar, Ronald D, Tuljapurkar, Shripad D, Marshall, Dustin, Clegg, Sonya M

“…Empirical application of the approach we develop has potential to help explain the enigma of body size variation across the tree of life.…”
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Ultrastructural and proteomic evidence for the presence of a putative nucleolus in an Archaeon by Parsifal F. Islas-Morales, Parsifal F. Islas-Morales, Parsifal F. Islas-Morales, Anny Cárdenas, Anny Cárdenas, Anny Cárdenas, María J. Mosqueira, María J. Mosqueira, Luis Felipe Jiménez-García, Luis Felipe Jiménez-García, Christian R. Voolstra, Christian R. Voolstra

“…Whereas technical limitations and further aspects remain a matter for future functional studies, our data supports the origin of nucleoli within the common ancestor of Eukarya and TACK-Archaea, based on a two-domain tree of life.…”
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Evolutionary Diversity of Dus2 Enzymes Reveals Novel Structural and Functional Features among Members of the RNA Dihydrouridine Synthases Family by Murielle Lombard, Colbie J. Reed, Ludovic Pecqueur, Bruno Faivre, Sabrine Toubdji, Claudia Sudol, Damien Brégeon, Valérie de Crécy-Lagard, Djemel Hamdane

“…Here, we combined extensive phylogenetic analysis with high-precision 3D molecular modeling of more than 30 Dus2 enzymes selected along the tree of life to determine the evolutionary molecular basis of D biosynthesis by these enzymes. …”
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Intercellular Transmission of a Synthetic Bacterial Cytotoxic Prion-Like Protein in Mammalian Cells by Aida Revilla-García, Cristina Fernández, María Moreno-del Álamo, Vivian de los Ríos, Ina M. Vorberg, Rafael Giraldo

“…Thus, a synthetic prion-like protein can be propagated to, and become cytotoxic to, cells of organisms placed at such distant branches of the tree of life as bacteria and mammalia, suggesting that mechanisms of protein aggregate spreading and toxicity follow default pathways. …”
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