The herbarium of the future

Trends in Ecology & Evolution - Tập 38 - Trang 412-423 - 2023
Charles C. Davis1
1Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA

Tài liệu tham khảo

Meineke, 2019, Biological collections for understanding biodiversity in the Anthropocene, Philos. Trans. R. Soc. B, 374, 10.1098/rstb.2017.0386 Kress, 2022, Lords of the biosphere: plant winners and losers in the Anthropocene, Plants People Planet, 4, 350, 10.1002/ppp3.10252 Heberling, 2019, The changing uses of herbarium data in an era of global change: an overview using automated content analysis, BioScience, 69, 812, 10.1093/biosci/biz094 Meineke, 2018, The unrealized potential of herbaria for global change biology, Ecol. Monogr., 88, 505, 10.1002/ecm.1307 Bieker, 2018, Implications and future prospects for evolutionary analyses of DNA in historical herbarium collections, Bot. Lett., 165, 409, 10.1080/23818107.2018.1458651 Funk, 2018, Collections-based science in the 21st century, J. Syst. Evol., 56, 175, 10.1111/jse.12315 Carine, 2018, Examining the spectra of herbarium uses and users, Bot. Lett., 165, 328, 10.1080/23818107.2018.1482782 Bebber, 2010, Herbaria are a major frontier for species discovery, Proc. Natl. Acad. Sci. U. S. A., 107, 22169, 10.1073/pnas.1011841108 Goodwin, 2020, How long does it take to discover a species?, Syst. Biodivers., 18, 784, 10.1080/14772000.2020.1751339 Goodwin, 2015, Widespread mistaken identity in tropical plant collections, Curr. Biol., 25, R1066, 10.1016/j.cub.2015.10.002 Hedrick, 2020, Digitization and the future of natural history collections, BioScience, 70, 243, 10.1093/biosci/biz163 Cardoso, 2017, Amazon plant diversity revealed by a taxonomically verified species list, Proc. Natl. Acad. Sci. U. S. A., 114, 10695, 10.1073/pnas.1706756114 2015, Growing knowledge: an overview of seed plant diversity in Brazil, Rodriguésia, 66, 1085, 10.1590/2175-7860201566411 Jardim Botânico do Rio de Janeiro, 2020 Cámara-Leret, 2020, New Guinea has the world’s richest island flora, Nature, 584, 579, 10.1038/s41586-020-2549-5 Grace, 2021, Botanical monography in the Anthropocene, Trends Plant Sci., 26, 433, 10.1016/j.tplants.2020.12.018 Muñoz-Rodríguez, 2019, A taxonomic monograph of Ipomoea integrated across phylogenetic scales, Nat. Plants, 5, 1136, 10.1038/s41477-019-0535-4 Raven, 2020, The distribution of biodiversity richness in the tropics, Sci. Adv., 6, 10.1126/sciadv.abc6228 Folk, 2021, High-throughput methods for efficiently building massive phylogenies from natural history collections, Appl. Plant Sci., 9, 10.1002/aps3.11410 Bieker, 2022, Uncovering the genomic basis of an extraordinary plant invasion. Science, Advances, 8 Exposito-Alonso, 2018, The rate and potential relevance of new mutations in a colonizing plant lineage, PLoS Genet., 14, 10.1371/journal.pgen.1007155 Lewin, 2018, Earth BioGenome project: sequencing life for the future of life, Proc. Natl. Acad. Sci. U. S. A., 115, 4325, 10.1073/pnas.1720115115 Shee, 2020, Reconstructing the complex evolutionary history of the Papuasian Schefflera radiation through herbariomics, Front. Plant Sci., 11, 258, 10.3389/fpls.2020.00258 Kates, 2021, The effects of herbarium specimen characteristics on short-read NGS sequencing success in nearly 8000 specimens: old, degraded samples have lower DNA yields but consistent sequencing success, Front. Plant Sci., 12, 10.3389/fpls.2021.669064 Welch, 2016, The quest to resolve recent radiations: plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae), Mol. Phylog. Evol., 99, 16, 10.1016/j.ympev.2016.02.024 Kistler, 2020, Ancient plant genomics in archaeology, herbaria, and the environment, Annu. Rev. Plant Biol., 71, 605, 10.1146/annurev-arplant-081519-035837 Card, 2021, Museum genomics, Annu. Rev. Genet., 55, 633, 10.1146/annurev-genet-071719-020506 Cai, 2022, PhyloHerb: a high-throughput phylogenomic pipeline for processing genome skimming data, Appl. Plant Sci., 10, 10.1002/aps3.11475 Wäldchen, 2018, Automated plant species identification—trends and future directions, PLoS Comp. Biol., 14, 10.1371/journal.pcbi.1005993 Hernandez, 2020, How to do scientific field work when you can’t get to the right field, The Wall Street, Journal, 3 Goëau, 2022, Overview of PlantCLEF 2022: image-based plant identification at global scale, Working Notes of CLEF, 1526 Heberling, 2021, Data integration enables global biodiversity synthesis, Proc. Natl. Acad. Sci. U. S. A., 118, 10.1073/pnas.2018093118 Mishler, 2020, Spatial phylogenetics of the North American flora, J. Syst. Evol., 58, 393, 10.1111/jse.12590 Koch, 2022, Maximizing citizen scientists' contribution to automated species recognition, Sci. Rep., 12, 7648, 10.1038/s41598-022-11257-x Davis, 2020, A new method for counting reproductive structures in digitized herbarium specimens using mask R-CNN, Front. Plant Sci., 11, 1129, 10.3389/fpls.2020.01129 Pearson, 2020, Machine learning using digitized herbarium specimens to advance phenological research, BioScience, 70, 610, 10.1093/biosci/biaa044 Hussein, 2022, Applications of computer vision and machine learning techniques for digitized herbarium specimens: a systematic literature review, Ecol. Inform., 69, 10.1016/j.ecoinf.2022.101641 Davis, 2015, Herbarium records are reliable sources of phenological change driven by climate and provide novel insights into species’ phenological cueing mechanisms, Amer. J. Bot., 102, 1599, 10.3732/ajb.1500237 Davis, 2022, New directions in tropical phenology, Trends Ecol. Evol., 37, 683, 10.1016/j.tree.2022.05.001 Park, 2022, Herbarium records provide reliable phenology estimates in the understudied tropics, J. Ecol. Park, 2019, Herbarium specimens reveal substantial and unexpected variation in phenological sensitivity across the eastern United States, Philos. Trans. R. Soc. B, 374, 10.1098/rstb.2017.0394 Park, 2022, Phenological displacement is uncommon among sympatric angiosperms, New Phytol., 233, 1466, 10.1111/nph.17784 Meineke, 2021, Phenological sensitivity to temperature mediates herbivory, Glob. Chang. Biol., 27, 2315, 10.1111/gcb.15600 Meineke, 2019, Herbarium specimens reveal increasing herbivory over the past century, J. Ecol., 107, 105, 10.1111/1365-2745.13057 Weber, 2013, The phylogenetic distribution of extrafloral nectaries in plants, Ann. Bot., 111, 1251, 10.1093/aob/mcs225 Weber, 2012, Phylogeny, ecology, and the coupling of comparative and experimental approaches, Trends Ecol. Evol., 27, 394, 10.1016/j.tree.2012.04.010 Xie, 2022, The ecological implications of intra- and inter-species variation in phenological sensitivity, New Phytol., 236, 760, 10.1111/nph.18361 Meireles, 2020, Leaf reflectance spectra capture the evolutionary history of seed plants, New Phytol., 228, 485, 10.1111/nph.16771 Kothari, 2022, Reflectance spectroscopy allows rapid, accurate and non-destructive estimates of functional traits from pressed leaves, Methods Ecol. Evol. Miller, 2019, Chemical evidence for the use of multiple psychotropic plants in a 1,000-year-old ritual bundle from South America, Proc. Natl. Acad. Sci. U. S. A., 116, 11207, 10.1073/pnas.1902174116 Foutami, 2018, Hundred fifty years of herbarium collections provide a reliable resource of volatile terpenoid profiles showing strong species effect in four medicinal species of Salvia across the Mediterranean, Front. Plant Sci., 9, 1877, 10.3389/fpls.2018.01877 Allen, 2019, Biodiversity synthesis across the green branches of the tree of life, Nat. Plants, 5, 11, 10.1038/s41477-018-0322-7 Hagen, 2021, Earth history events shaped the evolution of uneven biodiversity across tropical moist forests, Proc. Natl. Acad. Sci. U. S. A., 118, 10.1073/pnas.2026347118 Ding, 2020, Ancient orogenic and monsoon-driven assembly of the world’s richest temperate alpine flora, Science, 369, 578, 10.1126/science.abb4484 Daru, 2019, Spatial overlaps between the global protected areas network and terrestrial hotspots of evolutionary diversity, Glob. Ecol. Biogeogr., 28, 757, 10.1111/geb.12888 Simkin, 2022, Biodiversity impacts and conservation implications of urban land expansion projected to 2050, Proc. Natl. Acad. Sci. U. S. A., 119, 10.1073/pnas.2117297119 Daru, 2021, Widespread homogenization of plant communities in the Anthropocene, Nat. Commun., 12, 6983, 10.1038/s41467-021-27186-8 Exposito-Alonso, 2022, Genetic diversity loss in the Anthropocene, Science, 377, 1431, 10.1126/science.abn5642 Kling, 2019, Facets of phylodiversity: evolutionary diversification, divergence and survival as conservation targets, Philos. Trans. R. Soc. B, 374, 10.1098/rstb.2017.0397 Rønsted, 2022, Extinction risk of the endemic vascular flora of Kauai, Hawaii, based on IUCN assessments, Conserv. Biol., 36, 10.1111/cobi.13896 Jaenicke-Despres, 2003, Early allelic selection in maize as revealed by ancient DNA, Science, 302, 1206, 10.1126/science.1089056 Swarts, 2017, Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America, Science, 357, 512, 10.1126/science.aam9425 White, 2021, The origins of coca: museum genomics reveals multiple independent domestications from progenitor Erythroxylum gracilipes, Syst. Biol., 70, 1, 10.1093/sysbio/syaa074 Rosche, 2022, Tracking population genetic signatures of local extinction with herbarium specimens, Ann. Bot., 129, 857, 10.1093/aob/mcac061 Castañeda-Álvarez, 2016, Global conservation priorities for crop wild relatives, Nat. Plants, 2, 16022, 10.1038/nplants.2016.22 Howes, 2020, Molecules from nature: reconciling biodiversity conservation and global healthcare imperatives for sustainable use of medicinal plants and fungi, Plants People Planet, 2, 463, 10.1002/ppp3.10138 Park, 2021, The colonial legacy of herbaria, bioRxiv Rights, C.o.H., 1993 Gardner, 2022, Engagement with indigenous people preserves local knowledge and biodiversity alike, Curr. Biol., 32, R511, 10.1016/j.cub.2022.04.062 Drew, 2017, Digitization of museum collections holds the potential to enhance researcher diversity, Nat. Ecol. Evol., 1, 1789, 10.1038/s41559-017-0401-6 Davis, 2021, Back to the future: a refined single-user photostation for massively scaling herbarium digitization, TAXON, 70, 635, 10.1002/tax.12459 McNutt, 2016, Liberating field science samples and data, Science, 351, 1024, 10.1126/science.aad7048 Schorn, 2016, The New England Vascular Plants Project: 295,000 specimens and counting, Rhodora, 118, 324, 10.3119/15-34 Ebenezer, 2022, Africa: sequence 100,000 species to safeguard biodiversity, Nature, 603, 388, 10.1038/d41586-022-00712-4 Lendemer, 2020, The extended specimen network: a strategy to enhance US biodiversity collections, promote research and education, BioScience, 70, 23, 10.1093/biosci/biz140 Daru, 2018, Widespread sampling biases in herbaria revealed from large-scale digitization, New Phytol., 217, 939, 10.1111/nph.14855 Pearse, 2017, A statistical estimator for determining the limits of contemporary and historic phenology, Nat. Ecol. Evol., 1, 1876, 10.1038/s41559-017-0350-0 Rocchetti, 2021, A pragmatic and prudent consensus on the resurrection of extinct plant species using herbarium specimens, TAXON, 71, 168, 10.1002/tax.12601 G.A. Rocchetti, et al. (2022) Selecting the best candidates for resurrecting extinct-in-the-wild plants from herbaria. Nat. Plants https://doi.org/10.1038/s41477-022-01296-7 Feeney, 2022, In Search of Thoreau’s Flowers’ examines the famous author as citizen scientist, The Boston, Globe, 29 Carland-Adams, 2022 Flannery, 2013, The herbarium as muse: plant specimens as inspiration Mannion, 2014, The latitudinal biodiversity gradient through deep time, Trends Ecol. Evol., 29, 42, 10.1016/j.tree.2013.09.012 Beery, 2021, Scaling biodiversity monitoring for the data age, XRDS, 27, 14, 10.1145/3466857 Koski, 2020, Floral pigmentation has responded rapidly to global change in ozone and temperature, Curr. Biol., 30, 4425, 10.1016/j.cub.2020.08.077 Willis, 2008, Phylogenetic patterns of species loss in Thoreau’s woods are driven by climate change, Proceedings of the National Academy of Sciences of the United States of America, 105, 17029, 10.1073/pnas.0806446105 Willis, 2010, Favorable climate change response explains non-native species’ success in Thoreau’s woods, PLoS ONE, 5, 10.1371/journal.pone.0008878