Article
Multidisciplinary Sciences
Yanyou Jiang, Tianjun Cao, Yuqing Yang, Huan Zhang, Jingyu Zhang, Xiaobo Li
Summary: There is a difference in accessory chlorophyll between marine and terrestrial photosynthesis. We identified the CHLC dioxygenase from the marine diatom as the Chl c synthase, answering a long-standing question in the field.
Editorial Material
Biochemistry & Molecular Biology
Marek Elias
Summary: In recent years, the diversity of eukaryotic microbes has been greatly expanded by recognizing or discovering new major branches of the algal tree of life. A new study defines the phylogenetic home for an elusive marine planktonic lineage previously known only by plastidial rRNA genes, placing it in a new class of the phylum Haptophyta.
Article
Multidisciplinary Sciences
Yu Bai, Tianjun Cao, Oliver Dautermann, Paul Buschbeck, Michael B. Cantrell, Yinjuan Chen, Christopher D. Lein, Xiaohuo Shi, Maxwell A. Ware, Fenghua Yang, Huan Zhang, Lihan Zhang, Graham Peers, Xiaobo Li, Martin Lohr
Summary: Fucoxanthin is a major light-harvesting pigment in ecologically important algae. The biosynthetic pathway of fucoxanthin has been identified by studying knockout mutants of the diatom Phaeodactylum tricornutum. The pathway is more complex than expected and involves the metabolism of diadinoxanthin as a central regulatory hub. The study also reveals the evolution of genes for xanthophyll cycle enzymes and the alternative pathway in brown algae.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Ecology
Annie Z. Tremp, Sadia Saeed, Johannes T. Dessens
Summary: This study systematically analyzed nth genes across eukaryotic life and found that NTH is widely distributed in all major lineages, but some organisms (especially plants) completely lack nth genes. Isoform distribution and phylogenetic analysis revealed different nth gene loss scenarios in apicomplexan lineages, shedding new light on the evolution of the Piroplasmida and Eimeriidae.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Microbiology
Marianne Potvin, Milla Rautio, Connie Lovejoy
Summary: Lakes and ponds in the Arctic play a crucial role in the ecosystem, but little is known about the diversity and ecological impact of microscopic life in these water bodies. This study reveals the presence of distinct species communities and the coexistence of mixotrophic and heterotrophic bacteria in different seasons and lakes. These findings provide valuable insights into the functioning of Arctic ecosystems and biogeochemical cycles.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Ana S. P. Moreira, Joana Goncalves, Tiago A. Conde, Daniela Couto, Tania Melo, Ines B. Maia, Hugo Pereira, Joana Silva, M. Rosario Domingues, Claudia Nunes
Summary: This study unveils the polar lipidome of the haptophyte microalga Chrysotila pseudoroscoffensis, providing insights into its chemical composition and potential bioactivity. The lipid extracts of C. pseudoroscoffensis may serve as a valuable source for the development of novel microalgae-based products.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2022)
Article
Geography, Physical
Nicole R. Marshall, Anne de Vernal, Alfonso Mucci, Alexandra Filippova, Markus Kienast, Olivia Gibb, Claude Hillaire-Marcel
Summary: This study analyzed ocean sedimentary records from the northwestern Labrador Sea to examine past productivity, carbon fluxes, and carbonate preservation over the last 25,000 years. The findings show significant changes in biogenic carbonate fluxes and preservation during the last glacial interval, indicating lower productivity of calcifying organisms.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2021)
Article
Ecology
Noemi M. Fernandes, Pedro H. Campello-Nunes, Thiago S. Paiva, Carlos A. G. Soraes, Inacio D. Silva-Neto
Summary: The study investigated the diversity of ciliates in freshwater and brackish environments along the Brazilian Atlantic Forest and found differences in ciliate communities between these habitats, with highly abundant and low-abundant or rare OTUs. Additionally, a considerable fraction of ciliate diversity in the Brazilian Atlantic Forest detected through HTS was not represented in the currently available molecular databases.
Article
Multidisciplinary Sciences
Elise Parey, Alexandra Louis, Jerome Montfort, Olivier Bouchez, Celine Roques, Carole Iampietro, Jerome Lluch, Adrien Castinel, Cecile Donnadieu, Thomas Desvignes, Christabel Floi Bucao, Elodie Jouanno, Ming Wen, Sahar Mejri, Ron Dirks, Hans Jansen, Christiaan Henkel, Wei-Jen Chen, Margot Zahm, Cedric Cabau, Christophe Klopp, Andrew Thompson, Marc Robinson-Rechavi, Ingo Braasch, Guillaume Lecointre, Julien Bobe, John H. Postlethwait, Camille Berthelot, Hugues Roest Crollius, Yann Guiguen
Summary: Through the study of gene sequence and chromosomal rearrangement in teleosts, it was found that Elopomorpha and Osteoglossomorpha are sister groups to all other teleosts, resolving over 50 years of controversy on their evolutionary relationships.
Article
Multidisciplinary Sciences
Dorte H. Sogaard, Brian K. Sorrell, Mikael K. Sejr, Per Andersen, Soren Rysgaard, Per Juel Hansen, Annaliina Skytta, Signe Lemcke, Lars Chresten Lund-Hansen
Summary: The pelagic spring bloom in the Arctic Ocean is crucial for marine food webs and carbon transport. An acute under-ice algal bloom dominated by mixotrophic brackish water haptophytes was reported, suggesting that potentially toxic mixotrophic algae blooms may become more common and widespread in the future Arctic Ocean.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Anthony K. Redmond, Aoife McLysaght
Summary: This study demonstrates significant progress in partitioned phylogenomic analysis by using site-heterogeneous models and amino acid recoding to alleviate branching artefacts caused by systematic errors. The reanalysis of key datasets shows that partitioned phylogenomics does not support comb jellies as sister to other animals. Branching artefacts can confound the reconstruction of deep evolutionary relationships.
NATURE COMMUNICATIONS
(2021)
Article
Marine & Freshwater Biology
Yuri Barkhatov, Elena B. Khromechek, Vladimir V. Zykov, Denis Y. Rogozin
Summary: A monitoring study conducted on the dynamics of the cryptophyte population in Lake Shira revealed a sharp increase in cryptophyte biomass during the breakdown of stable stratification, which persisted even after the stratification was reestablished. The explosive growth in cryptophyte abundance could be attributed to a decrease in trophic pressure from zooplankton.
Article
Ecology
Qian Li, Kyle F. Edwards, Christopher R. Schvarcz, Grieg F. Steward
Summary: Small eukaryotic phytoplankton play a major role in global primary production and marine biogeochemical cycles. This study found that phototrophs that ingest bacteria come from diverse branches of the eukaryotic tree and have various functional strategies ranging from phototrophy to phagotrophy.
Article
Biotechnology & Applied Microbiology
Yanci Yang, Tao Zhou, Zengqiang Qian, Guifang Zhao
Summary: This study conducted a comprehensive phylogenetic analysis of Chinese oaks, revealing a complex evolutionary relationship where Quercus section Ilex was found to be non-monophyletic. The pattern is likely a result of incomplete lineage sorting and/or gene flow among ancestral lineages in these three sections. The current distribution, diversification, and molecular differentiation of Quercus sect. Ilex in China are likely outcomes of local adaptation to geographic and paleoclimatic changes.
Article
Genetics & Heredity
Penghao Yang, Kangning Guo, Yuqing Yang, Mingjie Lyu, Jingwen Liu, Xiaobo Li, Yanlei Feng
Summary: Haptophyte algae, including coccolithophores, play important roles in global carbon cycling and ecosystems. This study analyzed the genome variations of haptophytes and built comprehensive phylogenies, providing valuable genetic resources and insights into their evolution, especially for coccolithophores.
Article
Biochemistry & Molecular Biology
Rafael N. Leite, Rebecca T. Kimball, Edward L. Braun, Elizabeth P. Derryberry, Peter A. Hosner, Graham E. Derryberry, Marina Anciaes, Jessica S. McKay, Alexandre Aleixo, Camila C. Ribas, Robb T. Brumfield, Joel Cracraft
Summary: Target capture sequencing was used to study the phylogeny of the Pipridae family of birds, revealing that UCE data provided strong support for resolving relationships. Exon probes had limited capability and resulted in weaker support and modest topological differences. Two genera were found to be paraphyletic in all analyses, and caution is advised in interpreting relationships within the Chiroxiphia-Antilophia group. Despite some uncertainties, the analysis resulted in a robust phylogenetic hypothesis for the Pipridae family.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Rebecca T. Kimball, Peter A. Hosner, Edward L. Braun
Summary: Building taxon-rich phylogenies is crucial for macroevolutionary studies. Integrating phylogenomic studies into supermatrices can help resolve problem nodes and improve taxon sampling. However, skewed branch lengths may affect downstream macroevolutionary analyses.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Correction
Multidisciplinary Sciences
Shaohong Feng, Josefin Stiller, Yuan Deng, Joel Armstrong, Qi Fang, Andrew Hart Reeve, Duo Xie, Guangji Chen, Chunxue Guo, Brant C. Faircloth, Bent Petersen, Zongji Wang, Qi Zhou, Mark Diekhans, Wanjun Chen, Sergio Andreu-Sanchez, Ashot Margaryan, Jason Travis Howard, Carole Parent, George Pacheco, Mikkel-Holger S. Sinding, Lara Puetz, Emily Cavill, Angela M. Ribeiro, Leopold Eckhart, Jon Fjeldsa, Peter A. Hosner, Robb T. Brumfield, Les Christidis, Mads F. Bertelsen, Thomas Sicheritz-Ponten, Dieter Thomas Tietze, Bruce C. Robertson, Gang Song, Gerald Borgia, Santiago Claramunt, Irby J. Lovette, Saul J. Cowen, Peter Njoroge, John Philip Dumbacher, Oliver A. Ryder, Jerome Fuchs, Michael Bunce, David W. Burt, Joel Cracraft, Guanliang Meng, Shannon J. Hackett, Peter G. Ryan, Knud Andreas Jonsson, Ian G. Jamieson, Rute R. da Fonseca, Edward L. Braun, Peter Houde, Siavash Mirarab, Alexander Suh, Bengt Hansson, Suvi Ponnikas, Hanna Sigeman, Martin Stervander, Paul B. Frandsen, Henriette van der Zwan, Rencia van der Sluis, Carina Visser, Christopher N. Balakrishnan, Andrew G. Clark, John W. Fitzpatrick, Reed Bowman, Nancy Chen, Alison Cloutier, Timothy B. Sackton, Scott V. Edwards, Dustin J. Foote, Subir B. Shakya, Frederick H. Sheldon, Alain Vignal, Andre E. R. Soares, Beth Shapiro, Jacob Gonzalez-Solis, Joan Ferrer-Obiol, Julio Rozas, Marta Riutort, Anna Tigano, Vicki Friesen, Love Dalen, Araxi O. Urrutia, Tamas Szekely, Yang Liu, Michael G. Campana, Andre Corvelo, Robert C. Fleischer, Kim M. Rutherford, Neil J. Gemmell, Nicolas Dussex, Henrik Mouritsen, Nadine Thiele, Kira Delmore, Miriam Liedvogel, Andre Franke, Marc P. Hoeppner, Oliver Krone, Adam M. Fudickar, Borja Mila, Ellen D. Ketterson, Andrew Eric Fidler, Guillermo Friis, Angela M. Parody-Merino, Phil F. Battley, Murray P. Cox, Nicholas Costa Barroso Lima, Francisco Prosdocimi, Thomas Lee Parchman, Barney A. Schlinger, Bette A. Loiselle, John G. Blake, Haw Chuan Lim, Lainy B. Day, Matthew J. Fuxjager, Maude W. Baldwin, Michael J. Braun, Morgan Wirthlin, Rebecca B. Dikow, T. Brandt Ryder, Glauco Camenisch, Lukas F. Keller, Jeffrey M. DaCosta, Mark E. Hauber, Matthew I. M. Louder, Christopher C. Witt, Jimmy A. McGuire, Joann Mudge, Libby C. Megna, Matthew D. Carling, Biao Wang, Scott A. Taylor, Glaucia Del-Rio, Alexandre Aleixo, Ana Tereza Ribeiro Vasconcelos, Claudio V. Mello, Jason T. Weir, David Haussler, Qiye Li, Huanming Yang, Jian Wang, Fumin Lei, Carsten Rahbek, M. Thomas P. Gilbert, Gary R. Graves, Erich D. Jarvis, Benedict Paten, Guojie Zhang
Article
Evolutionary Biology
Michael Forthman, Edward L. Braun, Rebecca T. Kimball
Summary: The study found that gene tree error can affect the estimation of coalescent branch lengths, with low informative loci leading to significantly shorter CBLs. Gene tree resolution has a greater impact on UCE datasets, while it does not seem to affect exon datasets as much.
Article
Ecology
Chao Zhang, Yiming Zhao, Edward L. Braun, Siavash Mirarab
Summary: The text discusses the issue of erroneous data in sequence datasets and the need for automatic error detection methods as datasets grow larger. It introduces the TAPER method, which detects errors in species-specific stretches of sequence alignments to improve accuracy in downstream analyses.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Noor D. White, Zachary A. Batz, Edward L. Braun, Michael J. Braun, Karen L. Carleton, Rebecca T. Kimball, Anand Swaroop
Summary: The study used a probe set to capture 46 genes related to avian vision, achieving high success rates and saving sequencing resources, while avoiding the issue of chimeric assembly. By applying these data, positively selected genes in the evolution of night vision and high-speed vision were identified, providing a new perspective for evolutionary research.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Ornithology
Peter A. Hosner, Min Zhao, Rebecca T. Kimball, Edward L. Braun, J. Gordon Burleigh
Summary: Biodiversity research has been advanced by linking genetic, distributional, and trait datasets, but molecular systematics has created taxonomic instability. This study presents a method to standardize avian taxon names in NCBI GenBank with eBird/Clements taxonomy, facilitating further research on avian biodiversity.
Article
Biochemistry & Molecular Biology
Ning Wang, Edward L. Braun, Bin Liang, Joel Cracraft, Stephen A. Smith
Summary: This study focuses on the contentious parts of avian phylogenetics and reveals even greater conflicts than previously appreciated. Edge-based analysis provides insights into the impact of data type, GC content variation, and outlier genes on signal-resolution for different nodes.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Jessie F. Salter, Peter A. Hosner, Whitney L. E. Tsai, John E. McCormack, Edward L. Braun, Rebecca T. Kimball, Robb T. Brumfield, Brant C. Faircloth
Summary: Phylogenomics with historical specimen-driven analysis is becoming increasingly important in filling gaps in evolutionary history of diverse groups. Analyzing subclades can help distinguish artifactual causes of discordance introduced by historical samples.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Evolutionary Biology
Min Zhao, Sarah M. Kurtis, Noor D. White, Andre E. Moncrieff, Rafael N. Leite, Robb T. Brumfield, Edward L. Braun, Rebecca T. Kimball
Summary: This study focuses on the phylogenetic relationships between Antilophia and Chiroxiphia genera in manakins. By analyzing more than 11,000 loci from whole genomes and applying different analytical methods, the study reveals the importance of identifying factors that can affect phylogenetic signal when dealing with complex phylogenetic problems.
SYSTEMATIC BIOLOGY
(2023)
Article
Zoology
Liping Zhou, Christos Mammides, Youfang Chen, Wenyi Zhou, Wenzhang Dai, Edward L. Braun, Rebecca T. Kimball, Yang Liu, Scott K. Robinson, Eben Goodale
Summary: Participants in mixed-species bird flocks tend to associate with species that are similar in body size, diet, and evolutionary history, and they also show similarities in their plumage. The study found that body size has the strongest effect on association strength, followed by phylogeny, plumage patterns, and plumage color; diet has the weakest effect.
Article
Biology
Gabrielle E. Scolaro, Edward L. Braun
Summary: The rates of amino acid substitution during evolutionary time are influenced by the chemical properties of amino acids. Different substitution rates reflect different evolutionary models, which can be shaped by both evolutionary history and environmental factors. This study provides evidence that both history and environment contribute to model differences in protein evolution.
Article
Ornithology
George Sangster, Edward L. Braun, Ulf S. Johansson, Rebecca T. Kimball, Gerald Mayr, Alexander Suh
Summary: The knowledge of higher-level phylogenetic relationships of birds has significantly increased in the past two decades with the application of genomic data. However, the nomenclature of higher-level taxa remains unstable due to the lack of regulation by the ICZN and the use of rank-based nomenclature. Lack of regulation and instability impede effective communication among systematists. This study reviews support for avian clades using phylogenomic data sets and provides formal definitions of their names based on the rules of the PhyloCode, aiming to stabilize avian higher-level nomenclature.
Article
Ecology
De Chen, Peter A. Hosner, Donna L. Dittmann, John P. O'Neill, Sharon M. Birks, Edward L. Braun, Rebecca T. Kimball
Summary: Background Divergence time estimation is essential for understanding the evolution of organisms. While phylogenomic datasets have potential, the best ways to leverage them for divergence time estimation are not well explored. This study focused on a subset of ultraconserved elements (UCEs) for divergence time estimation in galliform taxa, suggesting partitioning and selection of tree-like partitions as effective strategies. The resulting galliform time tree is consistent with other molecular clock studies, providing a high-quality resource for further evolutionary and biogeographic studies in this group.
BMC ECOLOGY AND EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Giulio Formenti, Arang Rhie, Jennifer Balacco, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Samara Brown, Marco Rosario Capodiferro, Farooq O. Al-Ajli, Roberto Ambrosini, Peter Houde, Sergey Koren, Karen Oliver, Michelle Smith, Jason Skelton, Emma Betteridge, Jale Dolucan, Craig Corton, Iliana Bista, James Torrance, Alan Tracey, Jonathan Wood, Marcela Uliano-Silva, Kerstin Howe, Shane McCarthy, Sylke Winkler, Woori Kwak, Jonas Korlach, Arkarachai Fungtammasan, Daniel Fordham, Vania Costa, Simon Mayes, Matteo Chiara, David S. Horner, Eugene Myers, Richard Durbin, Alessandro Achilli, Edward L. Braun, Adam M. Phillippy, Erich D. Jarvis
Summary: This study developed a fully automated pipeline that successfully assembled complete mitochondrial genomes of 100 vertebrate species, and found that tissue type and library size selection significantly impact mitochondrial genome sequencing and assembly. Comparison with reference mitochondrial genomes based on short-read sequencing revealed errors, missing sequences, and incomplete genes in the references.