Publications

2023
Daniel S Park, Xiao Feng, Shinobu Akiyama, Marlina Ardiyani, Neida Avendaño, Zoltan Barina, Blandine Bärtschi, Manuel Belgrano, Julio Betancur, Roxali Bijmoer, Ann Bogaerts, Asunción Cano, Jiří Danihelka, Arti Garg, David E Giblin, Rajib Gogoi, Ramagwai J Sebola, Tomoyuki Katagiri, Jonathan A. Kennedy, Tojibaev Sh. Komil, Byoungyoon Lee, Serena ML Lee, Donatella Magri, Rossella Marcucci, Siro Masinde, Denis Melnikov, Patrik Mráz, Wieslaw Mulenko, Paul Musili, Geoffrey Mwachala, Burrell E Nelson, Christine Niezgoda, Carla Novoa Sepúlveda, Sylvia Orli, Alan Paton, Serge Payette, Kent D Perkins, Maria Jimena Ponce, Heimo Rainer, L. Rasingam, Himmah Rustiami, Natalia M Shiyan, Charlotte Sletten Bjorå, James Solomon, Fred Stauffer, Alex Sumadijaya, Mélanie Thiébaut, Barbara M Thiers, Hiromi Tsubota, Alison Vaughan, Risto Virtanen, Timothy JS Whitfeld, Dianxiang Zhang, Fernando O Zuloaga, and Charles C. Davis. 6/12/2023. “The colonial legacy of herbaria.” Nature Human Behavior. parketal_2023_coloniallegacy
2022
Charles C. Davis, Goia M. Lyra, Daniel S. Park, Renata Asprino, Rogério Maruyama, Débora Torquato, Benjamin I. Cook, and Aaron M. Ellison. 8/2022. “New directions in tropical phenology.” Trends in Ecology and Evolution, 37, 8, Pp. 683-693. Publisher's Version PDF
Liming Cai, Hongrui Zhang, and Charles C. Davis. 5/2022. “PhyloHerb: A high-throughput phylogenomic pipeline for processing genome skimming data.” Applications in Plant Sciences, 10, 3. PDF
Giulia Albani Rochetti, Charles C. Davis, Giulia Caneva, Gianluigi Bacchetta, Guiseppe Fabrini, Guiseppe Fenu, Bruno Foggi, Gabriele Galasso, Domenico Gargano, Gianpietro Giusso del Galdo, Mauro Iberite, Sara Magrini, Alfred Mayer, Andrea Mondoni, Chiara Nepi, Simone Orsenigo, Lorenzo Peruzzi, and Thomas Abeli. 2/2022. “A pragmatic and prudent consensus on the resurrection of extinct plant species using herbarium specimens.” Taxon, 71, 1, Pp. 168-177. Publisher's Version PDF
2021
Barnabas H. Daru, T. Jonathan Davies, Charles G. Willis, Emily K. Meineke, Argo Ronk, Martin Zobel, Meelis Pärtel, Alexandre Antonelli, and Charles C. Davis. 12/6/2021. “Widespread homogenization of plant communities in the Anthropocene.” Nature Communications, 12. Publisher's Version PDF
Goia M. de Lyra, Cintia Iha, Christopher J. Grassa, Liming Cai, Hongrui Zhang, Christopher Lane, Nicolas Blouin, Mariana C. Oliveira, José Marcos Castro de Nunes, and Charles C. Davis. 12/2021. “Phylogenomics, divergence time estimation and trait evolution provide a new look into the Gracilariales (Rhodophyta).” Molecular Phylogenetics and Evolution, 165. Publisher's Version PDF
Yujing Yan, Charles C. Davis, Dimitar Dimitrov, Zhiheng Wang, Carsten Rahbek, and Michael Krabbe Borregaard. 6/9/2021. “Phytogeographic history of the Tea family inferred through high-resolution phylogeny and fossils.” Systematic Biology, 042. Publisher's Version PDF
Luiza Teixeira-Costa, Charles C. Davis, and Gregorio Ceccantini. 5/14/2021. “Striking developmental convergence in angiosperm endoparasites.” American Journal of Botany , 108, 5, Pp. 1-13. Publisher's Version PDF
Lucas C. Marinho, Pedro Fiaschi, Moabe F. Fernandes, Liming Cai, Xiaoshan Duan, André M. Amorim, and Charles C. Davis. 3/29/2021. “Phylogenetic Relationships of Tovomita (Clusiaceae): Carpel Number and Geographic Distribution Speak Louder than Venation Pattern.” Systematic Botany, 41, 1, Pp. 102-108. Publisher's Version PDF
Emily K. Meineke, Charles C. Davis, and T. Jonathan Davies. 3/18/2021. “Phenological sensitivity to temperature mediates herbivory.” Global Change Biology. Publisher's Version PDF
Charles C. Davis, Jonathan A. Kennedy, and Christopher J. Grassa. 3/16/2021. “Back to the future: A refined single-user photostation for massively scaling herbarium digitization.” Taxon, 00, 00, Pp. 1-9. Publisher's Version PDF
Liming Cai, Brian J Arnold, Zhenxiang Xi, Danielle E Khost, Niki Patel, Claire B Hartmann, Sugumaran Manickam, Sawitree Sasirat, Lachezar A Nikolov, Sarah Mathews, Timothy B Sackton, and Charles C Davis. 3/8/2021. “Deeply Altered genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae).” Current Biology. Publisher's Version PDF
C.J. Thorogood, L. Teixeira-Costa, G. Ceccantini, C. C. Davis, and S. J. Hiscock. 2021. “Endoparasitic plants and fungi show evolutionary convergence across phylogentic divisions.” The New Phytologist, 10, 1111. PDF
2020
Charles C. Davis, Lucas C. Marinho, and André M. Amorim. 11/2020. “Andersoniodoxa, a replacement name for Andersoniella (Malpighiaceae).” Phytotaxa, 470, 1, Pp. 121-122. PDF
Daniel S. Park, Ian K. Breckheimer, Aaron M. Ellison, Goia M. Lyra, and Charles C. Davis. 8/5/2020. “Phenological displacement is uncommon among sympatric angiosperms.” bioRxiv. Publisher's Version PDF
Charles C. Davis, Julien Champ, Daniel S. Park, Ian Breckheimer, Goia M. Lyra, Junxi Xie, Alexis Joly, Dharmesh Tarapore, Aaron M. Ellison, and Pierre Bonnet. 7/31/2020. “A New Method for Counting Reproductive Structures in Digitized Herbarium Specimens Using Mask R-CNN.” Frontiers in Plant Science, 11, 1129. PDF
Haiwen Li, Bing Liu, Charles C. Davis, and Yong Yang. 6/30/2020. “Plastome phylogenomics, systematics, and divergence time estimation of the Beilschmiedia group (Lauraceae).” Molecular Phylogenetics and Evolution, 151, 106901. PDF
Camille M. M. DeSisto, Daniel S. Park, Charles C. Davis, Veronarindra Ramananjato, Jadelys L. Tonos, and Onja H. Razafindratsima. 6/18/2020. “An invasive species spread by threatened diurnal lemurs impacts rainforest structure in Madagascar.” Biological Invasions, Pp. 1-14. PDF
Charles C. Davis, Lucas C. Marinho, and André M. Amorim. 6/2020. “Andersoniella: A new genus of neotropical malpighiaceae.” Harvard Papers in Botany, 25, 1, Pp. 51-56. PDF
Katelin D Pearson, Gil Nelson, Myla FJ Aronson, Pierre Bonnet, Laura Brenskelle, Charles C Davis, Ellen G Denny, Elizabeth R Ellwood, Hervé Goëau, Mason J Herberling, Alexis Joly, Titouan Lorieul, Susan J Mazer, Emily K Meineke, Brian J Stucky, Patrick Sweeney, Alexander E White, and Pamela S Soltis. 5/13/2020. “Machine Learning Using Digitized Herbarium Specimens to Advance Phenological Research.” BioScience.Abstract
Machine learning (ML) has great potential to drive scientific discovery by harvesting data from images of herbarium specimens—preserved plant material curated in natural history collections—but ML techniques have only recently been applied to this rich resource. ML has particularly strong prospects for the study of plant phenological events such as growth and reproduction. As a major indicator of climate change, driver of ecological processes, and critical determinant of plant fitness, plant phenology is an important frontier for the application of ML techniques for science and society. In the present article, we describe a generalized, modular ML workflow for extracting phenological data from images of herbarium specimens, and we discuss the advantages, limitations, and potential future improvements of this workflow. Strategic research and investment in specimen-based ML methods, along with the aggregation of herbarium specimen data, may give rise to a better understanding of life on Earth.
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