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Michaud TJ, Cline LC, Hobbie EA, Gutknecht JLM, Kennedy PG. Herbarium specimens reveal that mycorrhizal type does not mediate declining temperate tree nitrogen status over a century of environmental change. New Phytol 2024; 242:1717-1724. [PMID: 38073143 DOI: 10.1111/nph.19452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 10/27/2023] [Indexed: 04/26/2024]
Abstract
Rising atmospheric carbon dioxide concentrations (CO2) and atmospheric nitrogen (N) deposition have contrasting effects on ectomycorrhizal (EM) and arbuscular mycorrhizal (AM) symbioses, potentially mediating forest responses to environmental change. In this study, we evaluated the cumulative effects of historical environmental change on N concentrations and δ15N values in AM plants, EM plants, EM fungi, and saprotrophic fungi using herbarium specimens collected in Minnesota, USA from 1871 to 2016. To better understand mycorrhizal mediation of foliar δ15N, we also analyzed a subset of previously published foliar δ15N values from across the United States to parse the effects of N deposition and CO2 rise. Over the last century in Minnesota, N concentrations declined among all groups except saprotrophic fungi. δ15N also declined among all groups of plants and fungi; however, foliar δ15N declined less in EM plants than in AM plants. In the analysis of previously published foliar δ15N values, this slope difference between EM and AM plants was better explained by nitrogen deposition than by CO2 rise. Mycorrhizal type did not explain trajectories of plant N concentrations. Instead, plants and EM fungi exhibited similar declines in N concentrations, consistent with declining forest N status despite moderate levels of N deposition.
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Affiliation(s)
- Talia J Michaud
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | | | - Erik A Hobbie
- Earth Systems Research Center, University of New Hampshire, Durham, NH, 03824, USA
| | - Jessica L M Gutknecht
- Department of Soil, Water, and Climate, University of Minnesota, St Paul, MN, 55108, USA
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
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Musarella CM, Laface VLA, Angiolini C, Bacchetta G, Bajona E, Banfi E, Barone G, Biscotti N, Bonsanto D, Calvia G, Cambria S, Capuano A, Caruso G, Crisafulli A, Del Guacchio E, Di Gristina E, Domina G, Fanfarillo E, Fascetti S, Fiaschi T, Galasso G, Mascia F, Mazzacuva G, Mei G, Minissale P, Motti R, Perrino EV, Picone RM, Pinzani L, Podda L, Potenza G, Rosati L, Stinca A, Tavilla G, Villano C, Wagensommer RP, Spampinato G. New Alien Plant Taxa for Italy and Europe: An Update. Plants (Basel) 2024; 13:620. [PMID: 38475466 DOI: 10.3390/plants13050620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
Despite the wide amount of scientific contributions published on alien plant species, their diffusion dynamics, and their interactions with native taxa, it is increasingly difficult to slow down their spreading and their negative impact on habitats. Last recent years, in fact, a sharp rise in the number of new alien plant taxa introduced in Italy and Europe has been recorded. The aim of this work is to investigate most of the Italian territory in order to verify whether this alarming trend is still underway. Specimen collections and/or observations of alien plants have been performed in as many as 12 Italian regions. All the collected specimens are stored in public or private herbaria. Taxa have been identified according to the literature from the countries of origin of the investigated taxa, while the nomenclature followed the current international references. Updates on 106 taxa are reported. In particular, among 117 new records, 89 are first records, 27 are changes to status and there is 1 extinction. Seven new taxa for Italian alien flora are reported, two of which are new to Europe. The administrative regions with the highest number of records are Calabria (48), Sardegna (17) and Sicilia (15). Five of the surveyed taxa, for the first time, have been considered invasive aliens to Italian territory. The unfrequent amount of original results provided by this work, over the simple importance of data itself, proves how floristic investigation, still today, represents one of the most effective tools in broadening the current knowledge about alien taxa and their dynamics.
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Affiliation(s)
- Carmelo Maria Musarella
- AGRARIA Department, Mediterranean University of Reggio Calabria, Loc. Feo di Vito snc, 89122 Reggio Calabria, Italy
| | | | - Claudia Angiolini
- Department of Life Sciences, University of Siena, Via P.A. Mattioli 4, 53100 Siena, Italy
- National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy
| | - Gianluigi Bacchetta
- Centre for Conservation of Biodiversity (CCB), Department of Life and Environmental Sciences, University of Cagliari, Viale Sant'Ignazio da Laconi 13, 09123 Cagliari, Italy
| | - Enrico Bajona
- PLANTA/Center for Research, Documentation and Training, Via Serraglio Vecchio 28, 90123 Palermo, Italy
| | - Enrico Banfi
- Section of Botany, Natural History Museum of Milan, Corso Venezia 55, 20121 Milano, Italy
| | - Giulio Barone
- National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy
- Department of Agriculture, Food and Forest Science, University of Palermo, Viale delle Scienze Bldg. 4, 90128 Palermo, Italy
| | - Nello Biscotti
- Department of Agricultural, Food and Environmental Sciences (D3A), Marche Polytechnic University, 60131 Ancona, Italy
| | - Daniele Bonsanto
- Department of Agricultural, Food and Environmental Sciences (D3A), Marche Polytechnic University, 60131 Ancona, Italy
| | - Giacomo Calvia
- Centre for Conservation of Biodiversity (CCB), Department of Life and Environmental Sciences, University of Cagliari, Viale Sant'Ignazio da Laconi 13, 09123 Cagliari, Italy
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bolzano, Piazza Università 5, 39100 Bolzano, Italy
| | - Salvatore Cambria
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via A. Longo 19, 95125 Catania, Italy
| | - Alberto Capuano
- AGRARIA Department, Mediterranean University of Reggio Calabria, Loc. Feo di Vito snc, 89122 Reggio Calabria, Italy
| | - Giuseppe Caruso
- AGRARIA Department, Mediterranean University of Reggio Calabria, Loc. Feo di Vito snc, 89122 Reggio Calabria, Italy
- Istituto Tecnico Agrario "V. Emanuele II", Via Cortese 1, 88100 Catanzaro, Italy
| | | | - Emanuele Del Guacchio
- Department of Biology, University of Naples Federico II, Botanical Garden, Via Foria 223, 80139 Naples, Italy
| | - Emilio Di Gristina
- Department of Agriculture, Food and Forest Science, University of Palermo, Viale delle Scienze Bldg. 4, 90128 Palermo, Italy
| | - Gianniantonio Domina
- Department of Agriculture, Food and Forest Science, University of Palermo, Viale delle Scienze Bldg. 4, 90128 Palermo, Italy
| | - Emanuele Fanfarillo
- Department of Life Sciences, University of Siena, Via P.A. Mattioli 4, 53100 Siena, Italy
- National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy
| | - Simonetta Fascetti
- School of Agriculture, Forestry, Food and Environment, University of Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy
| | - Tiberio Fiaschi
- Department of Life Sciences, University of Siena, Via P.A. Mattioli 4, 53100 Siena, Italy
| | - Gabriele Galasso
- Section of Botany, Natural History Museum of Milan, Corso Venezia 55, 20121 Milano, Italy
| | - Francesco Mascia
- Department of Life Sciences, University of Siena, Via P.A. Mattioli 4, 53100 Siena, Italy
- Centre for Conservation of Biodiversity (CCB), Department of Life and Environmental Sciences, University of Cagliari, Viale Sant'Ignazio da Laconi 13, 09123 Cagliari, Italy
| | - Giuliana Mazzacuva
- AGRARIA Department, Mediterranean University of Reggio Calabria, Loc. Feo di Vito snc, 89122 Reggio Calabria, Italy
| | - Giacomo Mei
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bolzano, Piazza Università 5, 39100 Bolzano, Italy
- Department of Pure and Applied Sciences (DiSPeA), University of Urbino "Carlo Bo", Via Aurelio Saffi, 2, 61029 Urbino PU, Italy
| | - Pietro Minissale
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via A. Longo 19, 95125 Catania, Italy
| | - Riccardo Motti
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Naples, Italy
| | - Enrico Vito Perrino
- CIHEAM, Mediterranean Agronomic Institute of Bari, Via Ceglie 9, 70010 Valenzano, Italy
| | - Rosa Maria Picone
- Department of ChiBioFarAm, University of Messina, 98166 Messina, Italy
| | - Lorenzo Pinzani
- National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy
- Department of Science, University of Roma Tre, Viale G. Marconi, 446, 00146 Rome, Italy
| | - Lina Podda
- Centre for Conservation of Biodiversity (CCB), Department of Life and Environmental Sciences, University of Cagliari, Viale Sant'Ignazio da Laconi 13, 09123 Cagliari, Italy
| | - Giovanna Potenza
- School of Agriculture, Forestry, Food and Environment, University of Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy
| | - Leonardo Rosati
- School of Agriculture, Forestry, Food and Environment, University of Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy
| | - Adriano Stinca
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy
| | - Gianmarco Tavilla
- National Research Council of Italy, Institute of Atmospheric Pollution Research (CNR-IIA), c/o Interateneo Physics Department, 70125 Bari, Italy
| | - Clizia Villano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Naples, Italy
| | - Robert Philipp Wagensommer
- Faculty of Education, Free University of Bozen-Bolzano, Viale Ratisbona 16, 39042 Brixen-Bressanone, Italy
| | - Giovanni Spampinato
- AGRARIA Department, Mediterranean University of Reggio Calabria, Loc. Feo di Vito snc, 89122 Reggio Calabria, Italy
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Drobnik J, Stebel A, Graniszewska M. The Oldest Bryophyte Herbarium Specimens from Central Europe, Collected by M. E. Boretius in 1717: Taxonomy, Nomenclature, Datation and Ethnopharmacology. Plants (Basel) 2024; 13:349. [PMID: 38337882 PMCID: PMC10857619 DOI: 10.3390/plants13030349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
The WA Herbarium at the University of Warsaw houses a collection of plants created in 1717 by Matthew Ernest Boretius. They were gathered in former East Prussia, near Angerburg, now Węgorzewo (Poland). It is the oldest plant collection from this part of Europe. Boretius compiled the herbarium as a collection of all the surrounding plants, but their folk names (Polish and German) recorded in the herbarium confirm the ethnobiological or ethnopharmaceutical importance of some species. We identified bryophyte species and checked the accuracy of their original identifications recorded in the herbarium. We provided their Latin (scientific, pre-Linnaean) nomenclature together with German and Polish vernacular names. We contextualised this information within the history of the medicinal use of bryophytes around 1717, when the plant collection was created. We also investigated whether the specimens could have come from Northeastern Poland. Mosses and liverworts from the herbarium were identified nomenclaturally (by means of their original scientific polynomial names written on herbarium sheets) and taxonomically. The herbarium holds two species and one subspecies of liverwort and 27 species and one variety of moss. The accuracy of the original identifications was assessed, with a particular focus on the species considered medicinal at the time. We found that bryophytes were poorly known in the time of Boretius, which was the last period in bryology before the introduction of magnifying devices into this science (this crucial step was made by Dillenius in 1741). The vernacular names used in the herbarium were recorded for Marchantia polymorpha and Polytrichum commune-the only two species with confirmed medicinal use by the year 1717.
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Affiliation(s)
- Jacek Drobnik
- Department of Pharmaceutical Botany, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, ul. Ostrogórska 30, 41-200 Sosnowiec, Poland;
| | - Adam Stebel
- Department of Pharmaceutical Botany, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, ul. Ostrogórska 30, 41-200 Sosnowiec, Poland;
| | - Maja Graniszewska
- The WA Herbarium, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland;
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James N, Adkinson A, Mast A. Rapid imaging in the field followed by photogrammetry digitally captures the otherwise lost dimensions of plant specimens. Appl Plant Sci 2023; 11:e11547. [PMID: 37915433 PMCID: PMC10617317 DOI: 10.1002/aps3.11547] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/31/2023] [Accepted: 04/16/2023] [Indexed: 11/03/2023]
Abstract
Premise We recognized the need for a customized imaging protocol for plant specimens at the time of collection for the purpose of three-dimensional (3D) modeling, as well as the lack of a broadly applicable photogrammetry protocol that encompasses the heterogeneity of plant specimen geometries and the challenges introduced by processes such as wilting. Methods and Results We developed an equipment list and set of detailed protocols describing how to capture images of plant specimens in the field prior to their deformation (e.g., with pressing) and how to produce a 3D model from the image sets in Agisoft Metashape Professional. Conclusions The equipment list and protocols represent a foundation on which additional improvements can be made for specimen geometries outside of the range of the six types considered, and an easy entry into photogrammetry for those who have not previously used it.
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Affiliation(s)
- Nicole James
- Department of ArtFlorida State University540 West Call StreetTallahassee32301FloridaUSA
- Institute for Digital Information and Scientific Communication (iDigInfo)Florida State University142 Collegiate LoopTallahassee32306FloridaUSA
| | - Alex Adkinson
- Department of ArtFlorida State University540 West Call StreetTallahassee32301FloridaUSA
- Institute for Digital Information and Scientific Communication (iDigInfo)Florida State University142 Collegiate LoopTallahassee32306FloridaUSA
| | - Austin Mast
- Institute for Digital Information and Scientific Communication (iDigInfo)Florida State University142 Collegiate LoopTallahassee32306FloridaUSA
- Department of Biological ScienceFlorida State University319 Stadium DriveTallahassee32306FloridaUSA
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5
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Zhu K, Song Y. Harnessing herbaria to advance plant phenology research under global change. New Phytol 2023; 239:2057-2059. [PMID: 37376722 DOI: 10.1111/nph.19088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
This article is a Commentary on Park et al. (2023), 239: 2153–2165.
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Affiliation(s)
- Kai Zhu
- Institute for Global Change Biology and School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yiluan Song
- Institute for Global Change Biology and School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Environmental Studies, University of California, Santa Cruz, CA, 95064, USA
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Weaver WN, Smith SA. From leaves to labels: Building modular machine learning networks for rapid herbarium specimen analysis with LeafMachine2. Appl Plant Sci 2023; 11:e11548. [PMID: 37915430 PMCID: PMC10617304 DOI: 10.1002/aps3.11548] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/28/2023] [Accepted: 07/17/2023] [Indexed: 11/03/2023]
Abstract
Premise Quantitative plant traits play a crucial role in biological research. However, traditional methods for measuring plant morphology are time consuming and have limited scalability. We present LeafMachine2, a suite of modular machine learning and computer vision tools that can automatically extract a base set of leaf traits from digital plant data sets. Methods LeafMachine2 was trained on 494,766 manually prepared annotations from 5648 herbarium images obtained from 288 institutions and representing 2663 species; it employs a set of plant component detection and segmentation algorithms to isolate individual leaves, petioles, fruits, flowers, wood samples, buds, and roots. Our landmarking network automatically identifies and measures nine pseudo-landmarks that occur on most broadleaf taxa. Text labels and barcodes are automatically identified by an archival component detector and are prepared for optical character recognition methods or natural language processing algorithms. Results LeafMachine2 can extract trait data from at least 245 angiosperm families and calculate pixel-to-metric conversion factors for 26 commonly used ruler types. Discussion LeafMachine2 is a highly efficient tool for generating large quantities of plant trait data, even from occluded or overlapping leaves, field images, and non-archival data sets. Our project, along with similar initiatives, has made significant progress in removing the bottleneck in plant trait data acquisition from herbarium specimens and shifted the focus toward the crucial task of data revision and quality control.
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Affiliation(s)
- William N. Weaver
- Department of Ecology and Evolutionary BiologyUniversity of Michigan1105 N. University Ave.Ann Arbor48109MichiganUSA
| | - Stephen A. Smith
- Department of Ecology and Evolutionary BiologyUniversity of Michigan1105 N. University Ave.Ann Arbor48109MichiganUSA
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Bachir F, El Oualidi J, Benkhnigue O, Fekhaoui M. Analysis of Morphological Traits in Herbarium of Historical Cannabis Specimens from Maghreb: Morphological Characteristics of Landrace Kif. Cannabis Cannabinoid Res 2023. [PMID: 37639688 DOI: 10.1089/can.2023.0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023] Open
Abstract
Background: Exploring the morphological traits of historical Cannabis populations from the Maghreb can provide invaluable information about the characteristics of the Maghreb Landrace Kif and contribute to the preservation of this vulnerable Cannabis resource. Aim: The purpose of the present study was to analyze the morphological characteristics of Cannabis specimens collected before worldwide introgressive hybridization and summarize the morphological traits of the Maghreb Landrace Kif. Discussion: Despite the limited number of specimens collected in the Maghreb, this study identified distinct types of Cannabis in the herbaria, including the Maghreb Landrace Kif, European hemp, and potentially East Asian hemp. By examining the morphological traits of kif specimens and reviewing the relevant literature, the study identifies the morphological traits that tend to characterize Maghreb Landrace Kif. Morphologically, Kif is different from drug-type Cannabis indica ("Sativa" and "Indica"). It resembles European hemp Cannabis sativa, but has female inflorescence characteristics that allow it to be distinguished from the latter, even when the growing conditions are optimal. These are the density of pistillate inflorescences (perigonal bract-to-leaf index), and the capitate stalked glandular trichomes cover density on the perigonal bracts. Conclusion: The characteristics of pistillate inflorescences identified in this study can be used to distinguish and select plants before phytochemical and genetic analysis, thus facilitating the identification of the Maghreb Landrace Kif.
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Affiliation(s)
- Fatima Bachir
- Geo-Biodiversity and Natural Patrimony Laboratory, Department of Zoology and Animal Ecology, Scientific Institute, Mohammed V University in Rabat, Morocco
| | - Jalal El Oualidi
- Department of Botany and Plant Ecology, Scientific Institute, Mohammed V University in Rabat, Morocco
| | - Ouafae Benkhnigue
- Department of Botany and Plant Ecology, Scientific Institute, Mohammed V University in Rabat, Morocco
| | - Mohammed Fekhaoui
- Geo-Biodiversity and Natural Patrimony Laboratory, Department of Zoology and Animal Ecology, Scientific Institute, Mohammed V University in Rabat, Morocco
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Faidiga AS, Oliver MG, Budke JM, Kalisz S. Shifts in flowering phenology in response to spring temperatures in eastern Tennessee. Am J Bot 2023; 110:e16203. [PMID: 37327370 DOI: 10.1002/ajb2.16203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 06/18/2023]
Abstract
PREMISE Plant phenological shifts are among the clearest indicators of the effects of climate change. In North America, numerous studies in the northeastern United States have demonstrated earlier spring flowering compared to historical records. However, few studies have examined phenological shifts in the southeastern United States, a highly biodiverse region of North America characterized by dramatic variations in abiotic conditions over small geographic areas. METHODS We examined 1000+ digitized herbarium records along with location-specific temperature data to analyze phenological shifts of 14 spring-flowering species in two adjacent ecoregions in eastern Tennessee. RESULTS Spring-flowering plant communities in the Blue Ridge and the Ridge and Valley ecoregions differed in their sensitivity to temperature; plants in the Ridge and Valley flower 0.73 days earlier/°C on average compared to 1.09 days/°C for plants in the Blue Ridge. Additionally, for the majority of species in both ecoregions, flowering is sensitive to spring temperature; i.e., in warmer years, most species flowered earlier. Despite this sensitivity, we did not find support for community-level shifts in flowering within eastern Tennessee in recent decades, likely because increases in annual temperature in the southeast are driven primarily by warming summer (rather than spring) temperatures. CONCLUSIONS These results highlight the importance of including ecoregion as a predictor in phenological models for capturing variation in sensitivity among populations and suggest that even small shifts in temperature can have dramatic effects on phenology in response to climate in the southeastern United States.
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Affiliation(s)
- Alexandra S Faidiga
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Margaret G Oliver
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
- University of Tennessee Herbarium (TENN), University of Tennessee, Knoxville, TN, 37996, USA
| | - Jessica M Budke
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
- University of Tennessee Herbarium (TENN), University of Tennessee, Knoxville, TN, 37996, USA
| | - Susan Kalisz
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
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McAssey EV, Downs C, Yorkston M, Morden C, Heyduk K. A comparison of freezer-stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming. Appl Plant Sci 2023; 11:e11527. [PMID: 37342160 PMCID: PMC10278930 DOI: 10.1002/aps3.11527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/30/2023] [Accepted: 05/04/2023] [Indexed: 06/22/2023]
Abstract
Premise The use of DNA from herbarium specimens is an increasingly important source for evolutionary studies in plant biology, particularly in cases where species are rare or difficult to obtain. Here we compare the utility of DNA from herbarium tissues to their freezer-stored DNA counterparts via the Hawaiian Plant DNA Library. Methods Plants collected for the Hawaiian Plant DNA Library were simultaneously accessioned as herbarium specimens at the time of collection, from 1994-2019. Paired samples were sequenced using short-read sequencing and assessed for chloroplast assembly and nuclear gene recovery. Results Herbarium specimen-derived DNA was statistically more fragmented than freezer-stored DNA derived from fresh tissue, leading to poorer chloroplast assembly and overall lower coverage. The number of nuclear targets recovered varied mostly by total sequencing reads per library and age of specimen, but not by storage method (herbarium or long-term freezer). Although there was evidence of DNA damage in the samples, there was no evidence that it was related to the length of time in storage, whether frozen or as herbarium specimens. Discussion DNA extracted from herbarium tissues will continue to be invaluable, despite being highly fragmented and degraded. Rare floras would benefit from both traditional herbarium storage methods and extracted DNA freezer banks.
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Affiliation(s)
- Edward V. McAssey
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - Cassidy Downs
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
| | - Mitsuko Yorkston
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
| | - Clifford Morden
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
| | - Karolina Heyduk
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
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Johnson G, Canty SWJ, Lichter‐Marck IH, Wagner W, Wen J. Ethanol preservation and pretreatments facilitate quality DNA extractions in recalcitrant plant species. Appl Plant Sci 2023; 11:e11519. [PMID: 37342166 PMCID: PMC10278939 DOI: 10.1002/aps3.11519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 06/22/2023]
Abstract
PREMISE The preservation of plant tissues in ethanol is conventionally viewed as problematic. Here, we show that leaf preservation in ethanol combined with proteinase digestion can provide high-quality DNA extracts. Additionally, as a pretreatment, ethanol can facilitate DNA extraction for recalcitrant samples. METHODS DNA was isolated from leaves preserved with 96% ethanol or from silica-desiccated leaf samples and herbarium fragments that were pretreated with ethanol. DNA was extracted from herbarium tissues using a special ethanol pretreatment protocol, and these extracts were compared with those obtained using the standard cetyltrimethylammonium bromide (CTAB) method. RESULTS DNA extracted from tissue preserved in, or pretreated with, ethanol was less fragmented than DNA from tissues without pretreatment. Adding proteinase digestion to the lysis step increased the amount of DNA obtained from the ethanol-pretreated tissues. The combination of the ethanol pretreatment with liquid nitrogen freezing and a sorbitol wash prior to cell lysis greatly improved the quality and yield of DNA from the herbarium tissue samples. DISCUSSION This study critically reevaluates the consequences of ethanol for plant tissue preservation and expands the utility of pretreatment methods for molecular and phylogenomic studies.
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Affiliation(s)
- Gabriel Johnson
- Department of Botany/MRC 166National Museum of Natural History, Smithsonian InstitutionWashingtonD.C.20560USA
| | - Steven W. J. Canty
- Smithsonian Marine StationFort PierceFlorida34949USA
- Working Land and Seascapes, Smithsonian InstitutionWashingtonD.C.20013USA
| | - Isaac H. Lichter‐Marck
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos Angeles, 612 Charles E. Young Dr. SouthLos AngelesCalifornia90095USA
- Department of Integrative Biology and Jepson herbariumUniversity of California, Berkeley1001 Valley Life Sciences Bldg.BerkeleyCalifornia94720USA
| | - Warren Wagner
- Department of Botany/MRC 166National Museum of Natural History, Smithsonian InstitutionWashingtonD.C.20560USA
| | - Jun Wen
- Department of Botany/MRC 166National Museum of Natural History, Smithsonian InstitutionWashingtonD.C.20560USA
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Yamamoto S, Seki M, Okusa T, Murakami H, Suzuki M, Ito Y, Nakada T. Airborne contact dermatitis to epoxy resin for creating herbarium. Contact Dermatitis 2023; 88:240-241. [PMID: 36461679 DOI: 10.1111/cod.14262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/17/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Affiliation(s)
- Sayaka Yamamoto
- Department of Dermatology, Showa University School of Medicine, Tokyo, Japan
| | - Marina Seki
- Department of Dermatology, Showa University Fujigaoka Hospital, Yokohama, Kanagawa, Japan
| | - Takehiro Okusa
- Department of Dermatology, Showa University Fujigaoka Hospital, Yokohama, Kanagawa, Japan
| | - Haruko Murakami
- Department of Dermatology, Showa University Fujigaoka Hospital, Yokohama, Kanagawa, Japan
| | - Marie Suzuki
- Department of Dermatology, Showa University Fujigaoka Hospital, Yokohama, Kanagawa, Japan
| | - Yuta Ito
- Department of Dermatology, Showa University Fujigaoka Hospital, Yokohama, Kanagawa, Japan
| | - Tokio Nakada
- Department of Dermatology, Showa University Fujigaoka Hospital, Yokohama, Kanagawa, Japan
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Barnes M, Sulé-Suso J, Millett J, Roach P. Fourier transform infrared spectroscopy as a non-destructive method for analysing herbarium specimens. Biol Lett 2023; 19:20220546. [PMID: 36946131 PMCID: PMC10031417 DOI: 10.1098/rsbl.2022.0546] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Dried plant specimens stored in herbaria are an untapped treasure chest of information on environmental conditions, plant evolution and change over many hundreds of years. Owing to their delicate nature and irreplaceability, there is limited access for analysis to these sensitive samples, particularly where chemical data are obtained using destructive techniques. Fourier transform infrared (FTIR) spectroscopy is a chemical analysis technique which can be applied non-destructively to understand chemical bonding information and, therefore, functional groups within the sample. This provides the potential for understanding geographical, spatial and species-specific variation in plant biochemistry. Here, we demonstrate the use of mid-FTIR microspectroscopy for the chemical analysis of Drosera rotundifolia herbarium specimens, which were collected 100 years apart from different locations. Principal component and hierarchical clustering analysis enabled differentiation between three main regions on the plant (lamina, tentacle stalk and tentacle head), and between the different specimens. Lipids and protein spectral regions were particularly sensitive differentiators of plant tissues. Differences between the different sets of specimens were smaller. This study demonstrates that relevant information can be extracted from herbarium specimens using FTIR, with little impact on the specimens. FTIR, therefore, has the potential to be a powerful tool to unlock historic information within herbaria.
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Affiliation(s)
- M Barnes
- Department of Chemistry, Loughborough University, Loughborough, UK
| | - J Sulé-Suso
- School of Pharmacy and Bioengineering, Guy Hilton Research Centre, Keele University, Keele, UK
- Cancer Centre, University Hospitals of North Midlands, Stoke-on-Trent, UK
| | - J Millett
- Department of Geography and Environment, Loughborough University, Loughborough, UK
| | - P Roach
- Department of Chemistry, Loughborough University, Loughborough, UK
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Jenny LA, Shapiro LR, Davis CC, Jonathan Davies T, Pierce NE, Meineke E. Herbarium specimens reveal herbivory patterns across the genus Cucurbita. Am J Bot 2023; 110:e16126. [PMID: 36633920 DOI: 10.1002/ajb2.16126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
PREMISE Quantifying how closely related plant species differ in susceptibility to insect herbivory is important for understanding the variation in evolutionary pressures on plant functional traits. However, empirically measuring in situ variation in herbivory spanning the geographic range of a plant-insect complex is logistically difficult. Recently, new methods have been developed using herbarium specimens to investigate patterns in plant-insect symbioses across large geographic scales. Such investigations provide insights into how accelerated anthropogenic changes may impact plant-insect interactions that are of ecological or agricultural importance. METHODS Here, we analyze 274 pressed herbarium samples to investigate variation in herbivory damage in 13 different species of the economically important plant genus Cucurbita (Cucurbitaceae). This collection is composed of specimens of wild, undomesticated Cucurbita that were collected from across their native range, and Cucurbita cultivars collected from both within their native range and from locations where they have been introduced for agriculture in temperate North America. RESULTS Herbivory is common on individuals of all Cucurbita species collected throughout their geographic ranges. However, estimates of herbivory varied considerably among individuals, with mesophytic species accruing more insect damage than xerophytic species, and wild specimens having more herbivory than specimens collected from human-managed habitats. CONCLUSIONS Our study suggests that long-term evolutionary changes in habitat from xeric to mesic climates and wild to human-managed habitats may mediate the levels of herbivory pressure from coevolved herbivores. Future investigations into the potential factors that contribute to herbivory may inform the management of domesticated crop plants and their insect herbivores.
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Affiliation(s)
- Laura A Jenny
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
| | - Lori R Shapiro
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, 27695, United States
| | - Charles C Davis
- Harvard University Herbaria, Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
| | - T Jonathan Davies
- Departments of Botany, and Forest & Conservation Sciences, University of British Columbia, Vancouver, British Columbia, BC V6T 1Z4, Canada
- African Centre for DNA Barcoding, University of Johannesburg, Johannesburg, Gauteng, 2028, South Africa
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
| | - Emily Meineke
- Department of Entomology and Nematology, University of California, Davis, Davis, California, 95616, United States
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14
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Lohonya K, Livermore L, Wajer J, Crowther R, Devenish E. Digitisation of the Natural History Museum's collection of Dalbergia, Pterocarpus and the subtribe Phaseolinae (Fabaceae, Faboideae). Biodivers Data J 2022; 10:e94939. [PMID: 36761652 PMCID: PMC9836434 DOI: 10.3897/bdj.10.e94939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Background In 2018, the Natural History Museum (NHMUK, herbarium code: BM) undertook a pilot digitisation project together with the Royal Botanic Gardens Kew (project Lead) and the Royal Botanic Garden Edinburgh to collectively digitise non-type herbarium material of the subtribe Phaseolinae and the genera Dalbergia L.f. and Pterocarpus Jacq. (rosewoods and padauk), all from the economically important family of legumes (Leguminosae or Fabaceae).These taxonomic groups were chosen to provide specimen data for two potential use cases: 1) to support the development of dry beans as a sustainable and resilient crop; 2) to aid conservation and sustainable use of rosewoods and padauk. Collectively, these use case studies support the aims of the UK's Department for Environment Food & Rural Affairs (DEFRA)-allocated, Official Development Assistance (ODA) funding. New information We present the images and metadata for 11,222 NHMUK specimens. The metadata includes label transcription and georeferencing, along with summary data on geographic, taxonomic, collector and temporal coverage. We also provide timings and the methodology for our transcription and georeferencing protocols. Approximately 35% of specimens digitised were collected in ODA-listed countries, in tropical Africa, but also in South East Asia and South America.
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Affiliation(s)
- Krisztina Lohonya
- The Natural History Museum, London, United KingdomThe Natural History MuseumLondonUnited Kingdom
| | - Laurence Livermore
- The Natural History Museum, London, United KingdomThe Natural History MuseumLondonUnited Kingdom
| | - Jacek Wajer
- The Natural History Museum, London, United KingdomThe Natural History MuseumLondonUnited Kingdom
| | - Robyn Crowther
- The Natural History Museum, London, United KingdomThe Natural History MuseumLondonUnited Kingdom
| | - Elizabeth Devenish
- The Natural History Museum, London, United KingdomThe Natural History MuseumLondonUnited Kingdom
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Speed JDM, Evankow AM, Petersen TK, Ranke PS, Nilsen NH, Turner G, Aagaard K, Bakken T, Davidsen JG, Dunshea G, Finstad AG, Hassel K, Husby M, Hårsaker K, Koksvik JI, Prestø T, Vange V. A regionally coherent ecological fingerprint of climate change, evidenced from natural history collections. Ecol Evol 2022; 12:e9471. [PMID: 36340816 PMCID: PMC9627063 DOI: 10.1002/ece3.9471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/02/2022] [Accepted: 10/16/2022] [Indexed: 11/06/2022] Open
Abstract
Climate change has dramatic impacts on ecological systems, affecting a range of ecological factors including phenology, species abundance, diversity, and distribution. The breadth of climate change impacts on ecological systems leads to the occurrence of fingerprints of climate change. However, climate fingerprints are usually identified across broad geographical scales and are potentially influenced by publication biases. In this study, we used natural history collections spanning over 250 years, to quantify a range of ecological responses to climate change, including phenology, abundance, diversity, and distributions, across a range of taxa, including vertebrates, invertebrates, plants, and fungi, within a single region, Central Norway. We tested the hypotheses that ecological responses to climate change are apparent and coherent at a regional scale, that longer time series show stronger trends over time and in relation to temperature, and that ecological responses change in trajectory at the same time as shifts in temperature. We identified a clear regional coherence in climate signal, with decreasing abundances of limnic zooplankton (on average by 7691 individuals m-3 °C-1) and boreal forest breeding birds (on average by 1.94 territories km-2 °C-1), and earlier plant flowering phenology (on average 2 days °C-1) for every degree of temperature increase. In contrast, regional-scale species distributions and species diversity were largely stable. Surprisingly, the effect size of ecological response did not increase with study duration, and shifts in responses did not occur at the same time as shifts in temperature. This may be as the long-term studies include both periods of warming and temperature stability, and that ecological responses lag behind warming. Our findings demonstrate a regional climate fingerprint across a long timescale. We contend that natural history collections provide a unique window on a broad spectrum of ecological responses at timescales beyond most ecological monitoring programs. Natural history collections are thus an essential source for long-term ecological research.
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Affiliation(s)
- James D. M. Speed
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Ann M. Evankow
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
- Natural History MuseumUniversity of OsloOsloNorway
| | - Tanja K. Petersen
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Peter S. Ranke
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Nellie H. Nilsen
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Grace Turner
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Kaare Aagaard
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Torkild Bakken
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Jan G. Davidsen
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Glenn Dunshea
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Anders G. Finstad
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Kristian Hassel
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Magne Husby
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
- Section of ScienceNord UniversityLevangerNorway
| | - Karstein Hårsaker
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Jan Ivar Koksvik
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Tommy Prestø
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Vibekke Vange
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
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16
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Tack W, Engledow H, Veríssimo Pereira N, Amani C, Bachman SP, Barberá P, Beentje HJ, Bouka GUD, Cheek M, Cosiaux A, Dauby G, De Block P, Ewango CEN, Fischer E, Gereau RE, Hargreaves S, Harvey-Brown Y, Ikabanga DU, Ilunga wa Ilunga E, Kalema J, Kamau P, Lachenaud O, Luke Q, Mwanga Mwanga I, Ndolo Ebika ST, Nkengurutse J, Nsanzurwimo A, Ntore S, Richards SL, Shutsha Ehata R, Simo-Droissart M, Stévart T, Sosef MSM. The ECAT dataset: expert-validated distribution data of endemic and sub-endemic trees of Central Africa (Dem. Rep. Congo, Rwanda, Burundi). PhytoKeys 2022; 206:137-151. [PMID: 36761267 PMCID: PMC9849015 DOI: 10.3897/phytokeys.206.77379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 08/15/2022] [Indexed: 06/18/2023]
Abstract
In this data paper, we present a specimen-based occurrence dataset compiled in the framework of the Conservation of Endemic Central African Trees (ECAT) project with the aim of producing global conservation assessments for the IUCN Red List. The project targets all tree species endemic or sub-endemic to the Central African region comprising the Democratic Republic of the Congo (DR Congo), Rwanda, and Burundi. The dataset contains 6361 plant collection records with occurrences of 8910 specimens from 337 taxa belonging to 153 genera in 52 families. Many of these tree taxa have restricted geographic ranges and are only known from a small number of herbarium specimens. As assessments for such taxa can be compromised by inadequate data, we transcribed and geo-referenced specimen label information to obtain a more accurate and complete locality dataset. All specimen data were manually cleaned and verified by botanical experts, resulting in improved data quality and consistency.
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Affiliation(s)
- Wesley Tack
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
| | - Henry Engledow
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
| | - Nuno Veríssimo Pereira
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
| | - Christian Amani
- Université Officielle de Bukavu, Bukavu, Democratic Republic of the CongoIUCN SSC Eastern African Plant Red List Authority (EAPRLA)GlandSwitzerland
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
| | - Steven P. Bachman
- Royal Botanic Gardens, Kew, Richmond, Surrey, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Patricia Barberá
- Missouri Botanical Garden, Africa & Madagascar Department, St. Louis, MO 63110, USAMissouri Botanical Garden, Africa & Madagascar DepartmentSt. LouisUnited States of America
| | - Henk J. Beentje
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- Royal Botanic Gardens, Kew, Richmond, Surrey, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Gaël U. D. Bouka
- Laboratoire de Biodiversité, de Gestion des Ecosystèmes et de l’Environnement, Faculté des Sciences et Techniques, Université Marien Ngouabi, BP 69, Brazzaville, Democratic Republic of the CongoUniversité Marien NgouabiBrazzavilleDemocratic Republic of the Congo
| | - Martin Cheek
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- Royal Botanic Gardens, Kew, Richmond, Surrey, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Ariane Cosiaux
- Plant Systematics and Ecology Laboratory, University of Yaoundé I, P.O. Box 047, Yaoundé, CameroonUniversity of Yaoundé IYaoundéCameroon
- Institut de Recherche pour le Développement, Université de Montpellier, Montpellier, FranceUniversité de MontpellierMontpellierFrance
| | - Gilles Dauby
- Institut de Recherche pour le Développement, Université de Montpellier, Montpellier, FranceUniversité de MontpellierMontpellierFrance
| | - Petra De Block
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
| | - Corneille E. N. Ewango
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, FranceUniversité de KisanganiKisanganiDemocratic Republic of the Congo
| | - Eberhard Fischer
- Centre de Surveillance de la Biodiversité, Université de Kisangani, Kisangani, Democratic Republic of the CongoUniversity of Koblenz and LandauKoblenzGermany
- University of Koblenz-Landau, Universitätsstraße 1, Koblenz, 56070, GermanyIUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwitzerland
| | - Roy E. Gereau
- Missouri Botanical Garden, Africa & Madagascar Department, St. Louis, MO 63110, USAMissouri Botanical Garden, Africa & Madagascar DepartmentSt. LouisUnited States of America
- University of Koblenz-Landau, Universitätsstraße 1, Koblenz, 56070, GermanyIUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwitzerland
| | - Serene Hargreaves
- Royal Botanic Gardens, Kew, Richmond, Surrey, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Yvette Harvey-Brown
- IUCN SSC Central Africa Plant Red List Authority (CARLA), Gland, SwitzerlandBotanic Gardens Conservation InternationalRichmondUnited Kingdom
| | - Davy U. Ikabanga
- Botanic Gardens Conservation International, Richmond, Surrey, UKUniversity of Sciences and Techniques of MasukuFrancevilleGabon
| | - Edouard Ilunga wa Ilunga
- Department of Biology, Faculty of Sciences, University of Sciences and Techniques of Masuku, BP: 941, Franceville, GabonUniversité de LubumbashiLubumbashiDemocratic Republic of the Congo
| | - James Kalema
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- Herbarium de Lubumbashi, Université de Lubumbashi, 1825, Route Kasapa, Lubumbashi, Democratic Republic of the CongoMakerere University Herbarium, Department of Plant Sciences Microbiology and BiotechnologyKampalaUganda
| | - Peris Kamau
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- Makerere University Herbarium, Department of Plant Sciences Microbiology and Biotechnology, P.O. Box 7062, Kampala, UgandaEast African Herbarium, National Museums of KenyaNairobiKenya
| | - Olivier Lachenaud
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
- East African Herbarium, National Museums of Kenya, P.O. Box 45166-00100, Nairobi, KenyaUniversité Libre de BruxellesBrusselsBelgium
| | - Quentin Luke
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- Makerere University Herbarium, Department of Plant Sciences Microbiology and Biotechnology, P.O. Box 7062, Kampala, UgandaEast African Herbarium, National Museums of KenyaNairobiKenya
| | - Ithe Mwanga Mwanga
- Herbarium et Bibliothèque de Botanique africaine, C.P. 265, Université Libre de Bruxelles, Campus de la Plaine, Boulevard du Triomphe 1050, Brussels, BelgiumCentre de Recherche en Sciences Naturelles CRSN/Lwiro, Laboratoire de Systématiquement et Taxonomie végétaleBukavuDemocratic Republic of the Congo
| | - Sydney T. Ndolo Ebika
- Laboratoire de Biodiversité, de Gestion des Ecosystèmes et de l’Environnement, Faculté des Sciences et Techniques, Université Marien Ngouabi, BP 69, Brazzaville, Democratic Republic of the CongoUniversité Marien NgouabiBrazzavilleDemocratic Republic of the Congo
| | - Jacques Nkengurutse
- Centre de Recherche en Sciences Naturelles CRSN/Lwiro, Laboratoire de Systématiquement et Taxonomie végétale, D.S. Bukavu, Democratic Republic of the CongoUniversity of BurundiBujumburaBurundi
| | - Aimable Nsanzurwimo
- Department of Biology, Faculty of Science, University of Burundi, P.O. Box 2700, Bujumbura, BurundiDepartment of Biotechnologies, Faculty of Applied Sciences, INES-RuhengeriRuhengeriRwanda
| | - Salvator Ntore
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- University of Koblenz-Landau, Universitätsstraße 1, Koblenz, 56070, GermanyIUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwitzerland
| | - Sophie L. Richards
- Royal Botanic Gardens, Kew, Richmond, Surrey, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Reddy Shutsha Ehata
- AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, FranceUniversité de KisanganiKisanganiDemocratic Republic of the Congo
| | - Murielle Simo-Droissart
- Plant Systematics and Ecology Laboratory, University of Yaoundé I, P.O. Box 047, Yaoundé, CameroonUniversity of Yaoundé IYaoundéCameroon
- Department of Biotechnologies, Faculty of Applied Sciences, INES-Ruhengeri, B.P.155 Ruhengeri, RwandaUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwaziland
| | - Tariq Stévart
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
- Missouri Botanical Garden, Africa & Madagascar Department, St. Louis, MO 63110, USAMissouri Botanical Garden, Africa & Madagascar DepartmentSt. LouisUnited States of America
- University of Koblenz-Landau, Universitätsstraße 1, Koblenz, 56070, GermanyIUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwitzerland
- East African Herbarium, National Museums of Kenya, P.O. Box 45166-00100, Nairobi, KenyaUniversité Libre de BruxellesBrusselsBelgium
| | - Marc S. M. Sosef
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
- University of Koblenz-Landau, Universitätsstraße 1, Koblenz, 56070, GermanyIUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwitzerland
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Meineke EK, Daru BH. Bias assessments to expand research harnessing biological collections. Trends Ecol Evol 2021; 36:1071-1082. [PMID: 34489117 DOI: 10.1016/j.tree.2021.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/22/2022]
Abstract
Biological collections are arguably the most important resources for investigations into the impacts of human activities on biodiversity. However, the apparent opportunities presented by museum-derived datasets have not resulted in consistent or widespread use of specimens in ecology outside phenological research and species distribution modeling. We attribute this gap between opportunity and application to biases introduced by collectors, curators, and preservation practices and an imperfect understanding of these biases and how to mitigate them. To facilitate broader use of specimen-based data, we characterize collection biases across key axes and explore interactions among them. We then present a framework for determining the bias assessments needed when extracting data from biological collections. We show that bias assessments required by particular ecological studies will depend on the response variables being measured and the predictor axes of interest. We argue that quantification of biases in specimen-derived datasets is needed to facilitate the widespread application of these data.
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Affiliation(s)
- Emily K Meineke
- Department of Entomology and Nematology, University of California, Davis 95616, CA, USA.
| | - Barnabas H Daru
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA.
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Slimp M, Williams LD, Hale H, Johnson MG. On the potential of Angiosperms353 for population genomic studies. Appl Plant Sci 2021; 9:APS311419. [PMID: 34336401 PMCID: PMC8312745 DOI: 10.1002/aps3.11419] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/15/2021] [Indexed: 05/11/2023]
Abstract
PREMISE The successful application of universal targeted sequencing markers, such as those developed for the Angiosperms353 probe set, within populations could reduce or eliminate the need for specific marker development, while retaining the benefits of full-gene sequences in population-level analyses. However, whether the Angiosperms353 markers provide sufficient variation within species to calculate demographic parameters is untested. METHODS Using herbarium specimens from a 50-year-old floristic survey in Texas, we sequenced 95 samples from 24 species using the Angiosperms353 probe set. Our data workflow calls variants within species and prepares data for population genetic analysis using standard metrics. In our case study, gene recovery was affected by genomic library concentration only at low concentrations and displayed limited phylogenetic bias. RESULTS We identified over 1000 segregating variants with zero missing data for 92% of species and demonstrate that Angiosperms353 markers contain sufficient variation to estimate pairwise nucleotide diversity (π)-typically between 0.002 and 0.010, with most variation found in flanking non-coding regions. In a subset of variants that were filtered to reduce linkage, we uncovered high heterozygosity in many species, suggesting that denser sampling within species should permit estimation of gene flow and population dynamics. DISCUSSION Angiosperms353 should benefit conservation genetic studies by providing universal repeatable markers, low missing data, and haplotype information, while permitting inclusion of decades-old herbarium specimens.
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Affiliation(s)
- Madeline Slimp
- Department of Biological SciencesTexas Tech University2901 Main StreetLubbockTexas79409USA
| | - Lindsay D. Williams
- Department of Biological SciencesTexas Tech University2901 Main StreetLubbockTexas79409USA
| | - Haley Hale
- Department of Biological SciencesTexas Tech University2901 Main StreetLubbockTexas79409USA
| | - Matthew G. Johnson
- Department of Biological SciencesTexas Tech University2901 Main StreetLubbockTexas79409USA
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Danneels B, Viruel J, Mcgrath K, Janssens SB, Wales N, Wilkin P, Carlier A. Patterns of transmission and horizontal gene transfer in the Dioscorea sansibarensis leaf symbiosis revealed by whole-genome sequencing. Curr Biol 2021; 31:2666-2673.e4. [PMID: 33852872 DOI: 10.1016/j.cub.2021.03.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/07/2020] [Accepted: 03/15/2021] [Indexed: 11/26/2022]
Abstract
Leaves of the wild yam species Dioscorea sansibarensis display prominent forerunner or "drip" tips filled with extracellular bacteria of the species Orrella dioscoreae.1 This species of yam is native to Madagascar and tropical Africa and reproduces mainly asexually through aerial bulbils and underground tubers, which also contain a small population of O. dioscoreae.2,3 Despite apparent vertical transmission, the genome of O. dioscoreae does not show any of the hallmarks of genome erosion often found in hereditary symbionts (e.g., small genome size and accumulation of pseudogenes).4-6 We investigated here the range and distribution of leaf symbiosis between D. sansibarensis and O. dioscoreae using preserved leaf samples from herbarium collections that were originally collected from various locations in Africa. We recovered DNA from the extracellular symbiont in all samples, showing that the symbiosis is widespread throughout continental Africa and Madagascar. Despite the degraded nature of this DNA, we constructed 17 symbiont genomes using de novo methods without relying on a reference. Phylogenetic and genomic analyses revealed that horizontal transmission of symbionts and horizontal gene transfer have shaped the evolution of the symbiont. These mechanisms could help explain lack of signs of reductive genome evolution despite an obligate host-associated lifestyle. Furthermore, phylogenetic analysis of D. sansibarensis based on plastid genomes revealed a strong geographical clustering of samples and provided evidence that the symbiosis originated at least 13 mya, earlier than previously estimated.3.
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Affiliation(s)
- Bram Danneels
- Laboratory of Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Juan Viruel
- Royal Botanical Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Krista Mcgrath
- Department of Prehistory and Institute of Environmental Science and Technology (ICTA), Autonomous University of Barcelona, 08193 Bellaterra, Spain; Department of Archaeology, University of York, Heslington, York YO10 5DD, UK
| | - Steven B Janssens
- Meise Botanic Garden, 1860 Meise, Belgium; Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Nathan Wales
- Department of Archaeology, University of York, Heslington, York YO10 5DD, UK
| | - Paul Wilkin
- Royal Botanical Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Aurélien Carlier
- Laboratory of Microbiology, Ghent University, 9000 Ghent, Belgium; LIPME, Université de Toulouse, INRAE, CNRS, 31320 Castanet-Tolosan, France.
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Powell C, Shaw J. Performant barcode decoding for herbarium specimen images using vector-assisted region proposals (VARP). Appl Plant Sci 2021; 9:APS311436. [PMID: 34141497 PMCID: PMC8202828 DOI: 10.1002/aps3.11436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
PREMISE The scale and associated costs of herbarium digitization make process automation appealing. One such process for many workflows is the association of specimen image files with barcode values stored with the specimen. Here, an innovation is presented that improves the speed and accuracy of decoding barcodes from specimen images. METHODS AND RESULTS Geometric features common in barcodes are used to identify the regions of specimen images that are likely to contain a barcode. The proposed regions are then combined into a significantly reduced composite image that is decoded using traditional barcode reading libraries. Tested against existing solutions, this method demonstrated the highest success rate (96.5%) and the second fastest processing time (617 ms). CONCLUSIONS This method was developed to support a larger effort to automate specimen image post-processing in real-time, highlighting the importance of execution time. Although initially designed for herbarium digitization, this method may be useful for other high-resolution applications.
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Affiliation(s)
- Caleb Powell
- Department of Biology, Geology and Environmental ScienceUniversity of Tennessee at Chattanooga615 McCallie AvenueChattanoogaTennessee37403USA
| | - Joey Shaw
- Department of Biology, Geology and Environmental ScienceUniversity of Tennessee at Chattanooga615 McCallie AvenueChattanoogaTennessee37403USA
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Vanden Abeele S, Beeckman H, De Mil T, De Troyer C, Deklerck V, Engledow H, Hubau W, Stoffelen P, Janssens SB. When xylarium and herbarium meet: linking Tervuren xylarium wood samples with their herbarium specimens at Meise Botanic Garden. Biodivers Data J 2021; 9:e62329. [PMID: 33841020 PMCID: PMC8026533 DOI: 10.3897/bdj.9.e62329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/19/2021] [Indexed: 11/12/2022] Open
Abstract
Background The current data paper aims to interlink the African plant collections of the Meise Botanic Garden Herbarium (BR) and the Royal Museum for Central Africa Xylarium (Tw). Complementing both collections strengthens the reference value of each institutional collection, as more complete metadata are made available and it enables increased quality control for the identification of wood specimens. Furthermore, the renewed connection enables the linking of available wood trait data with data on phenology, leaf morphology or even molecular information for many tree species, allowing assessments of performance of individual trees. In addition to studies at the interspecific level, comparisons at the intraspecific level become possible, which could lead to important new insights into resilience to and impact of global change, as well as biodiversity conservation or forest management of Central African forest ecosystems. New information By interlinking the Tervuren Xylarium Wood database with the recently digitised herbarium of Meise Botanic Garden, we were able to establish a link between 6,621 xylarium and 9,641 herbarium records for 6,953 plant specimens. Both institutional databases were complemented with reliable specimen metadata. The Tervuren xylarium now profits from taxonomic revisions made by botanists at Meise Botanic Garden and a list of phenotypical features for woody African species can be extended with wood anatomical descriptors. New metadata from the Tw xylarium records were used to add the country of collection to 50 linked BR herbarium specimens for which this information was missing. Furthermore, metadata available from the labels on digitised BR herbarium specimens was used to update Tw xylarium records with the date of collection (817 records), collection locality (698 records), coordinates (482 records) and altitude (817 records). In conclusion, we created a reference database with reliable botanic identities which can be used in a range of studies, such as modelling analyses, community assessments or trait analyses, all framed in a spatiotemporal context. Furthermore, the linked collections hold historical reference data and specimens that can be studied in the context of global changes.
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Affiliation(s)
- Samuel Vanden Abeele
- Meise Botanic Garden, Meise, Belgium Meise Botanic Garden Meise Belgium.,School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, United States of America School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University Ithaca United States of America
| | - Hans Beeckman
- Service of Wood Biology, Royal Museum for Central Africa, Tervuren, Belgium Service of Wood Biology, Royal Museum for Central Africa Tervuren Belgium
| | - Tom De Mil
- UGent-Woodlab, Gent, Belgium UGent-Woodlab Gent Belgium
| | - Cecile De Troyer
- Service of Wood Biology, Royal Museum for Central Africa, Tervuren, Belgium Service of Wood Biology, Royal Museum for Central Africa Tervuren Belgium
| | - Victor Deklerck
- Service of Wood Biology, Royal Museum for Central Africa, Tervuren, Belgium Service of Wood Biology, Royal Museum for Central Africa Tervuren Belgium.,Department of Chemistry, SUNY Albany, Albany, United States of America Department of Chemistry, SUNY Albany Albany United States of America
| | - Henry Engledow
- Meise Botanic Garden, Meise, Belgium Meise Botanic Garden Meise Belgium
| | - Wannes Hubau
- Service of Wood Biology, Royal Museum for Central Africa, Tervuren, Belgium Service of Wood Biology, Royal Museum for Central Africa Tervuren Belgium
| | - Piet Stoffelen
- Meise Botanic Garden, Meise, Belgium Meise Botanic Garden Meise Belgium
| | - Steven B Janssens
- Meise Botanic Garden, Meise, Belgium Meise Botanic Garden Meise Belgium
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Abstract
Pigmentation affords resistance to abiotic stressors, and thus can respond adaptively or plastically to drought and extreme temperatures associated with global change. Plants frequently display variability in flower coloration that is underlain by anthocyanin pigmentation. While anthocyanin polymorphisms impact plant-animal interactions, they also impact reproductive performance under abiotic stress. We used descriptions of flower colour from over 1900 herbarium records representing 12 North American species spanning 124 years to test whether anthocyanin-based flower colour has responded to global change. Based on demonstrated abiotic associations with performance of anthocyanin colour morphs, we predicted pigmentation would increase in species experiencing increased aridity, but decline in those experiencing larger increases in temperature. We found that the frequency of reports of pigmented morphs increased temporally in some taxa but displayed subtle declines in others. Pigmentation was negatively associated with temperature and positively associated with vapour pressure deficit (a metric of aridity) across taxa. Species experiencing larger temperature increases over time displayed reductions in pigmentation, while those experiencing increases in aridity displayed increases in pigmentation. Change in anthocyanin-based floral colour was thus linked with climatic change. Altered flower coloration has the strong potential to impact plant-animal interactions and overall plant reproductive performance.
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Affiliation(s)
- Cierra N Sullivan
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Matthew H Koski
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
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Abstract
BACKGROUND TUL Herbarium presents collections from Tula Oblast stored at the Tula State Lev Tolstoy Pedagogical University, Russia, which is an educational and scientific institution that supports various types of scientific activities, including research on biodiversity and nature conservation. The university is a holder of some biological collections, such as herbarium of vascular plants, mosses and fungi collected mainly throughout Tula Oblast and from adjacent regions. NEW INFORMATION The collections of vascular plants (9,000 specimens) were imaged in December 2019 and January 2020. Databasing and georeferencing of the specimens from the TUL Herbarium was performed by the staff members of the Tula State Lev Tolstoy Pedagogical University and Tula Local History Museum. Digital collections of the TUL Herbarium are fully available in the Moscow Digital Herbarium (https://plant.depo.msu.ru/) and GBIF (https://doi.org/10.15468/ca08cm).
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Affiliation(s)
- Tatyana Yu. Svetasheva
- Tula State Lev Tolstoy Pedagogical University, Tula, RussiaTula State Lev Tolstoy Pedagogical UniversityTulaRussia
| | - Alexey P. Seregin
- Lomonosov Moscow State University, Moscow, RussiaLomonosov Moscow State UniversityMoscowRussia
- M.V. Lomonosov Moscow State University, Moscow, RussiaM.V. Lomonosov Moscow State UniversityMoscowRussia
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Dupin J, Raimondeau P, Hong-Wa C, Manzi S, Gaudeul M, Besnard G. Resolving the Phylogeny of the Olive Family (Oleaceae): Confronting Information from Organellar and Nuclear Genomes. Genes (Basel) 2020; 11:E1508. [PMID: 33339232 DOI: 10.3390/genes11121508] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/12/2020] [Accepted: 12/11/2020] [Indexed: 12/18/2022] Open
Abstract
The olive family, Oleaceae, is a group of woody plants comprising 28 genera and ca. 700 species, distributed on all continents (except Antarctica) in both temperate and tropical environments. It includes several genera of major economic and ecological importance such as olives, ash trees, jasmines, forsythias, osmanthuses, privets and lilacs. The natural history of the group is not completely understood yet, but its diversification seems to be associated with polyploidisation events and the evolution of various reproductive and dispersal strategies. In addition, some taxonomical issues still need to be resolved, particularly in the paleopolyploid tribe Oleeae. Reconstructing a robust phylogenetic hypothesis is thus an important step toward a better comprehension of Oleaceae's diversity. Here, we reconstructed phylogenies of the olive family using 80 plastid coding sequences, 37 mitochondrial genes, the complete nuclear ribosomal cluster and a small multigene family encoding phytochromes (phyB and phyE) of 61 representative species. Tribes and subtribes were strongly supported by all phylogenetic reconstructions, while a few Oleeae genera are still polyphyletic (Chionanthus, Olea, Osmanthus, Nestegis) or paraphyletic (Schrebera, Syringa). Some phylogenetic relationships among tribes remain poorly resolved with conflicts between topologies reconstructed from different genomic regions. The use of nuclear data remains an important challenge especially in a group with ploidy changes (both paleo- and neo-polyploids). This work provides new genomic datasets that will assist the study of the biogeography and taxonomy of the whole Oleaceae.
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25
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Marsico TD, Krimmel ER, Carter JR, Gillespie EL, Lowe PD, McCauley R, Morris AB, Nelson G, Smith M, Soteropoulos DL, Monfils AK. Small herbaria contribute unique biogeographic records to county, locality, and temporal scales. Am J Bot 2020; 107:1577-1587. [PMID: 33217783 PMCID: PMC7756855 DOI: 10.1002/ajb2.1563] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/08/2020] [Indexed: 05/25/2023]
Abstract
PREMISE With digitization and data sharing initiatives underway over the last 15 years, an important need has been prioritizing specimens to digitize. Because duplicate specimens are shared among herbaria in exchange and gift programs, we investigated the extent to which unique biogeographic data are held in small herbaria vs. these data being redundant with those held by larger institutions. We evaluated the unique specimen contributions that small herbaria make to biogeographic understanding at county, locality, and temporal scales. METHODS We sampled herbarium specimens of 40 plant taxa from each of eight states of the United States of America in four broad status categories: extremely rare, very rare, common native, and introduced. We gathered geographic information from specimens held by large (≥100,000 specimens) and small (<100,000 specimens) herbaria. We built generalized linear mixed models to assess which features of the collections may best predict unique contributions of herbaria and used an Akaike information criterion-based information-theoretic approach for our model selection to choose the best model for each scale. RESULTS Small herbaria contributed unique specimens at all scales in proportion with their contribution of specimens to our data set. The best models for all scales were the full models that included the factors of species status and herbarium size when accounting for state as a random variable. CONCLUSIONS We demonstrated that small herbaria contribute unique information for research. It is clear that unique contributions cannot be predicted based on herbarium size alone. We must prioritize digitization and data sharing from herbaria of all sizes.
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Affiliation(s)
- Travis D. Marsico
- Department of Biological SciencesArkansas State UniversityState UniversityPO Box 599AR72467USA
| | - Erica R. Krimmel
- Sagehen Creek Field StationUniversity of California Berkeley11616 Sagehen RoadTruckeeCA96160USA
- Present address:
iDigBioFlorida State University142 Collegiate LoopTallahasseeFL32306USA
| | - J. Richard Carter
- Department of BiologyValdosta State University1500 North Patterson StreetValdostaGA31698USA
| | - Emily L. Gillespie
- Department of Biological SciencesMarshall UniversityOne John Marshall DriveHuntingtonWV25755USA
- Present address:
Department of Biological SciencesButler University4600 Sunset AvenueIndianapolisIN46208USA
| | - Phillip D. Lowe
- Department of BiologyValdosta State University1500 North Patterson StreetValdostaGA31698USA
| | - Ross McCauley
- Department of BiologyFort Lewis College1000 Rim DriveDurangoCO81301USA
| | - Ashley B. Morris
- Department of BiologyMiddle Tennessee State UniversityBox 60MurfreesboroTN37132USA
- Present address:
Department of BiologyFurman University3300 Poinsett HighwayGreenvilleSC29613USA
| | - Gil Nelson
- Department of Biological ScienceFlorida State University142 Collegiate LoopTallahasseeFL32306USA
- Present address:
iDigBioFlorida Museum of Natural HistoryUniversity of Florida1659 Museum RoadGainesvilleFL32611USA
| | - Michelle Smith
- Department of Biological ScienceFlorida State University142 Collegiate LoopTallahasseeFL32306USA
- Present address:
The Institute for Regional Conservation100 E. Linton Blvd, Suite 302BDelray BeachFL33483USA
| | - Diana L. Soteropoulos
- Department of Biological SciencesArkansas State UniversityState UniversityPO Box 599AR72467USA
- Arkansas Natural Heritage Commission1100 North StreetLittle RockAR72201USA
| | - Anna K. Monfils
- Department of BiologyCentral Michigan University2401 BiosciencesMount PleasantMI48859USA
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Abstract
BACKGROUND World herbaria with 387.5M specimens (Thiers 2019) are being rapidly digitised. At least 79.9M plant specimens (20.6%) are already databased throughout the globe in the standard form of GBIF-mediated data. The contribution of smaller herbaria has been steadily growing over the last few years due to cost reduction, usage of platforms and solutions developed by the leaders. A web-resource the Moscow Digital Herbarium (Seregin 2020b) was launched by the Lomonosov Moscow State University in October, 2016 for publication of specimens imaged and databased in the Moscow University Herbarium (MW). As of 31 December 2018, the web-portal included 968,031 images of 971,732 specimens digitised in MW. This dataset is available in GBIF (Seregin 2020). The global trend is largely the same in Russia, where a dozen herbaria started to scan their holdings after imaging of the nation's second largest herbarium (Kislov et al. 2017, Kovtonyuk et al. 2019, Seregin 2020a). In 2019, we started to use Moscow Digital Herbarium as a web-repository for digitised herbarium specimens from some Russian collections, starting with the Herbarium of Tsitsin Main Botanical Gaden, Russian Academy of Sciences (MHA). Due to this, a single-university system became a multi-institutional consortium in April 2019 (Seregin 2020a). The dataset of the Moscow collections and partly of the Eastern European collections of the MHA Herbarium is now available in GBIF (Seregin and Stepanova 2020). NEW INFORMATION MHA Herbarium imaged 64,008 specimens from Moscow Region and partly from other regions of Eastern Europe at 600 dpi and provided key metadata. These data are now fully available in the Moscow Digital Herbarium and GBIF. Complete georeferencing of the specimens from the City of Moscow was a key task in 2020. As of May 2020, 50,324 specimens, including 49,732 specimens from Russia, have been georeferenced (78.6%) and 39,448 specimens have fully-captured label transcriptions (61.6%). Based on these data, we give a detailed overview of the collections including spatial, temporal and taxonomic description of the dataset.
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Affiliation(s)
- Alexey P. Seregin
- Lomonosov Moscow State University, Moscow, RussiaLomonosov Moscow State UniversityMoscowRussia
- M.V. Lomonosov Moscow State University, Moscow, RussiaM.V. Lomonosov Moscow State UniversityMoscowRussia
| | - Nina Yu. Stepanova
- Tsitsin Main Botanical Garden, RAS, Moscow, RussiaTsitsin Main Botanical Garden, RASMoscowRussia
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27
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Koski MH, MacQueen D, Ashman TL. Floral Pigmentation Has Responded Rapidly to Global Change in Ozone and Temperature. Curr Biol 2020; 30:4425-4431.e3. [PMID: 32946752 DOI: 10.1016/j.cub.2020.08.077] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/03/2020] [Accepted: 08/24/2020] [Indexed: 12/22/2022]
Abstract
Across kingdoms, organisms ameliorate UV stress by increasing UV-absorbing pigmentation. Rapid ozone degradation during the 20th century resulted in elevated UV incidence, but pigmentation responses to this aspect of global change have yet to be demonstrated. In flowering plants, UV exposure favors larger areas of UV-absorbing pigmentation on petals, which protects pollen from UV-damage. Pigmentation also affects floral thermoregulation, suggesting climate warming may additionally impact pigmentation. We used 1,238 herbarium specimens collected from 1941 to 2017 to test whether change in UV floral pigmentation was associated with altered ozone and temperature in 42 species spanning three continents. We tested three predictions: first, UV-absorbing pigmentation will increase temporally and be correlated with reduced ozone (higher UV) when accounting for effects of temperature; second, taxa that experienced larger ozone declines will display larger increases in pigmentation; and third, taxa with anthers exposed to ambient UV will respond more strongly than those with anthers protected by petals. Globally, the extent of petal UV pigmentation increased significantly across taxa by ∼2% per year. However, temporal change was species specific-increasing in some taxa but declining in others. Species with exposed anthers experiencing larger declines in ozone displayed more dramatic pigmentation increases. For taxa with anthers enclosed within petals, pigmentation declined with increases in temperature, supporting a thermoregulatory role of UV pigmentation. Results document a rapid phenotypic response of floral pigmentation to anthropogenic climatic change, suggesting that global change may alter pollination through its impact on floral color, with repercussions for plant reproductive fitness.
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Affiliation(s)
- Matthew H Koski
- Clemson University, Department of Biological Sciences, Clemson, SC 29631, USA; University of Virginia, Department of Biology, Charlottesville, VA 22904, USA.
| | - Drew MacQueen
- University of Virginia Library Scholars Lab, PO Box 40010, Charlottesville, VA 22904-4129, USA
| | - Tia-Lynn Ashman
- University of Pittsburgh, Department of Biological Sciences, Pittsburgh, PA 15260, USA
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28
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Meeus S, Van den Bulcke J, wyffels F. From leaf to label: A robust automated workflow for stomata detection. Ecol Evol 2020; 10:9178-9191. [PMID: 32953053 PMCID: PMC7487252 DOI: 10.1002/ece3.6571] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 12/24/2022] Open
Abstract
Plant leaf stomata are the gatekeepers of the atmosphere-plant interface and are essential building blocks of land surface models as they control transpiration and photosynthesis. Although more stomatal trait data are needed to significantly reduce the error in these model predictions, recording these traits is time-consuming, and no standardized protocol is currently available. Some attempts were made to automate stomatal detection from photomicrographs; however, these approaches have the disadvantage of using classic image processing or targeting a narrow taxonomic entity which makes these technologies less robust and generalizable to other plant species. We propose an easy-to-use and adaptable workflow from leaf to label. A methodology for automatic stomata detection was developed using deep neural networks according to the state of the art and its applicability demonstrated across the phylogeny of the angiosperms.We used a patch-based approach for training/tuning three different deep learning architectures. For training, we used 431 micrographs taken from leaf prints made according to the nail polish method from herbarium specimens of 19 species. The best-performing architecture was tested on 595 images of 16 additional species spread across the angiosperm phylogeny.The nail polish method was successfully applied in 78% of the species sampled here. The VGG19 architecture slightly outperformed the basic shallow and deep architectures, with a confidence threshold equal to 0.7 resulting in an optimal trade-off between precision and recall. Applying this threshold, the VGG19 architecture obtained an average F-score of 0.87, 0.89, and 0.67 on the training, validation, and unseen test set, respectively. The average accuracy was very high (94%) for computed stomatal counts on unseen images of species used for training.The leaf-to-label pipeline is an easy-to-use workflow for researchers of different areas of expertise interested in detecting stomata more efficiently. The described methodology was based on multiple species and well-established methods so that it can serve as a reference for future work.
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Affiliation(s)
| | | | - Francis wyffels
- Department of Electronics and Information SystemsIDLab‐AIROGhent University‐‐imecZwijnaardeBelgium
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29
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Bauters M, Meeus S, Barthel M, Stoffelen P, De Deurwaerder HPT, Meunier F, Drake TW, Ponette Q, Ebuy J, Vermeir P, Beeckman H, Wyffels F, Bodé S, Verbeeck H, Vandelook F, Boeckx P. Century-long apparent decrease in intrinsic water-use efficiency with no evidence of progressive nutrient limitation in African tropical forests. Glob Chang Biol 2020; 26:4449-4461. [PMID: 32364642 DOI: 10.1111/gcb.15145] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
Forests exhibit leaf- and ecosystem-level responses to environmental changes. Specifically, rising carbon dioxide (CO2 ) levels over the past century are expected to have increased the intrinsic water-use efficiency (iWUE) of tropical trees while the ecosystem is gradually pushed into progressive nutrient limitation. Due to the long-term character of these changes, however, observational datasets to validate both paradigms are limited in space and time. In this study, we used a unique herbarium record to go back nearly a century and show that despite the rise in CO2 concentrations, iWUE has decreased in central African tropical trees in the Congo Basin. Although we find evidence that points to leaf-level adaptation to increasing CO2 -that is, increasing photosynthesis-related nutrients and decreasing maximum stomatal conductance, a decrease in leaf δ13 C clearly indicates a decreasing iWUE over time. Additionally, the stoichiometric carbon to nitrogen and nitrogen to phosphorus ratios in the leaves show no sign of progressive nutrient limitation as they have remained constant since 1938, which suggests that nutrients have not increasingly limited productivity in this biome. Altogether, the data suggest that other environmental factors, such as increasing temperature, might have negatively affected net photosynthesis and consequently downregulated the iWUE. Results from this study reveal that the second largest tropical forest on Earth has responded differently to recent environmental changes than expected, highlighting the need for further on-ground monitoring in the Congo Basin.
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Affiliation(s)
- Marijn Bauters
- Isotope Bioscience Laboratory - ISOFYS, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
- Computational and Applied Vegetation Ecology - CAVElab, Department of Environment, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | | | - Matti Barthel
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | | | - Hannes P T De Deurwaerder
- Computational and Applied Vegetation Ecology - CAVElab, Department of Environment, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Félicien Meunier
- Computational and Applied Vegetation Ecology - CAVElab, Department of Environment, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Travis W Drake
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Quentin Ponette
- UCL-ELI, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Jerôme Ebuy
- UCL-ELI, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
- Université de Kisangani (UNIKIS/FGRNR), Kisangani, République Démocratique du Congo
| | - Pieter Vermeir
- Laboratory for Chemical Analyses - LCA, Department of Green Chemistry and Technology, Ghent University, Ghent, Belgium
| | | | - Francis Wyffels
- AIRO, Electronics and Information Systems Department, Ghent University-Imec, Ghent, Belgium
| | - Samuel Bodé
- Isotope Bioscience Laboratory - ISOFYS, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Hans Verbeeck
- Computational and Applied Vegetation Ecology - CAVElab, Department of Environment, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | | | - Pascal Boeckx
- Isotope Bioscience Laboratory - ISOFYS, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
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30
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Meineke EK, Tomasi C, Yuan S, Pryer KM. Applying machine learning to investigate long-term insect-plant interactions preserved on digitized herbarium specimens. Appl Plant Sci 2020; 8:e11369. [PMID: 32626611 PMCID: PMC7328658 DOI: 10.1002/aps3.11369] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/04/2020] [Indexed: 05/28/2023]
Abstract
PREMISE Despite the economic significance of insect damage to plants (i.e., herbivory), long-term data documenting changes in herbivory are limited. Millions of pressed plant specimens are now available online and can be used to collect big data on plant-insect interactions during the Anthropocene. METHODS We initiated development of machine learning methods to automate extraction of herbivory data from herbarium specimens by training an insect damage detector and a damage type classifier on two distantly related plant species (Quercus bicolor and Onoclea sensibilis). We experimented with (1) classifying six types of herbivory and two control categories of undamaged leaf, and (2) detecting two of the damage categories for which several hundred annotations were available. RESULTS Damage detection results were mixed, with a mean average precision of 45% in the simultaneous detection and classification of two types of damage. However, damage classification on hand-drawn boxes identified the correct type of herbivory 81.5% of the time in eight categories. The damage classifier was accurate for categories with 100 or more test samples. DISCUSSION These tools are a promising first step for the automation of herbivory data collection. We describe ongoing efforts to increase the accuracy of these models, allowing researchers to extract similar data and apply them to biological hypotheses.
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Affiliation(s)
- Emily K. Meineke
- Department of Entomology and NematologyUniversity of CaliforniaDavisCalifornia95616USA
| | - Carlo Tomasi
- Department of Computer ScienceDuke UniversityDurhamNorth Carolina27708USA
| | - Song Yuan
- Department of Mechanical Engineering and Materials ScienceDuke UniversityDurhamNorth Carolina27708USA
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Lang PLM, Weiß CL, Kersten S, Latorre SM, Nagel S, Nickel B, Meyer M, Burbano HA. Hybridization ddRAD-sequencing for population genomics of nonmodel plants using highly degraded historical specimen DNA. Mol Ecol Resour 2020; 20:1228-1247. [PMID: 32306514 DOI: 10.1111/1755-0998.13168] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/06/2020] [Accepted: 03/30/2020] [Indexed: 12/29/2022]
Abstract
Species' responses at the genetic level are key to understanding the long-term consequences of anthropogenic global change. Herbaria document such responses, and, with contemporary sampling, provide high-resolution time-series of plant evolutionary change. Characterizing genetic diversity is straightforward for model species with small genomes and a reference sequence. For nonmodel species-with small or large genomes-diversity is traditionally assessed using restriction-enzyme-based sequencing. However, age-related DNA damage and fragmentation preclude the use of this approach for ancient herbarium DNA. Here, we combine reduced-representation sequencing and hybridization-capture to overcome this challenge and efficiently compare contemporary and historical specimens. Specifically, we describe how homemade DNA baits can be produced from reduced-representation libraries of fresh samples, and used to efficiently enrich historical libraries for the same fraction of the genome to produce compatible sets of sequence data from both types of material. Applying this approach to both Arabidopsis thaliana and the nonmodel plant Cardamine bulbifera, we discovered polymorphisms de novo in an unbiased, reference-free manner. We show that the recovered genetic variation recapitulates known genetic diversity in A. thaliana, and recovers geographical origin in both species and over time, independent of bait diversity. Hence, our method enables fast, cost-efficient, large-scale integration of contemporary and historical specimens for assessment of genome-wide genetic trends over time, independent of genome size and presence of a reference genome.
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Affiliation(s)
- Patricia L M Lang
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Clemens L Weiß
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Department of Genetics, Stanford University, Stanford, CA, USA
| | - Sonja Kersten
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sergio M Latorre
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hernán A Burbano
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, London, UK
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Maher P, Fischer W, Liang Z, Soriano-Castell D, Pinto AFM, Rebman J, Currais A. The Value of Herbarium Collections to the Discovery of Novel Treatments for Alzheimer's Disease, a Case Made With the Genus Eriodictyon. Front Pharmacol 2020; 11:208. [PMID: 32210808 PMCID: PMC7076189 DOI: 10.3389/fphar.2020.00208] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 02/14/2020] [Indexed: 11/13/2022] Open
Abstract
Plants, in particular those with a history in traditional medicine, hold enormous potential as sources of new therapies for dementias such as Alzheimer’s disease (AD). The largest collections of plants can be found in herbaria all over the world, but the value of these collections to AD drug discovery has been significantly neglected. As a proof of principle, we investigated the neuroprotective activity of herbarium specimens of Eriodictyon (yerba santa), a genus with a long history of usage by the indigenous tribes in California to treat respiratory and age-related complications. Dichloromethane extracts were prepared from leaves of 14 Eriodictyon taxa preserved in the SD Herbarium located at the San Diego Natural History Museum. The extracts were tested for neuroprotection in nerve cells against oxytosis and ferroptosis and for anti-inflammatory activity in brain microglial cells exposed to bacterial lipopolysaccharide. In parallel, the levels of the flavanones sterubin, eriodictyol and homoeriodictyol were measured by mass spectrometry. Several Eriodictyon species presented strong neuroprotective and anti-inflammatory activities. The protective properties of the extracts correlated with the amount of sterubin, but not with eriodictyol or homoeriodictyol, indicating that sterubin is the major active compound in these species. The occurrence of eriodictyol and homoeriodictyol may be predictive of the phylogenetic relationship between members in the genus Eriodictyon. The data offer insight into the traditional use of yerba santa across indigenous tribes in California, while demonstrating the value of herbarium collections for the discovery of novel therapeutic compounds for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Pamela Maher
- Cellular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Wolfgang Fischer
- Cellular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Zhibin Liang
- Cellular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - David Soriano-Castell
- Cellular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Antonio F M Pinto
- Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Jon Rebman
- Department of Botany, San Diego Natural History Museum, San Diego, CA, United States
| | - Antonio Currais
- Cellular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States
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Saarela JM, Sokoloff PC, Gillespie LJ, Bull RD, Bennett BA, Ponomarenko S. Vascular plants of Victoria Island (Northwest Territories and Nunavut, Canada): a specimen-based study of an Arctic flora. PhytoKeys 2020; 141:1-330. [PMID: 32201471 PMCID: PMC7070024 DOI: 10.3897/phytokeys.141.48810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
Victoria Island in Canada's western Arctic is the eighth largest island in the world and the second largest in Canada. Here, we report the results of a floristic study of vascular plant diversity of Victoria Island. The study is based on a specimen-based dataset comprising 7031 unique collections from the island, including some 2870 new collections gathered between 2008 and 2019 by the authors and nearly 1000 specimens variously gathered by N. Polunin (in 1947), M. Oldenburg (1940s-1950s) and S. Edlund (1980s) that, until recently, were part of the unprocessed backlog of the National Herbarium of Canada and unavailable to researchers. Results are presented in an annotated checklist, including keys and distribution maps for all taxa, citation of specimens, comments on taxonomy, distribution and the history of documentation of taxa across the island, and photographs for a subset of taxa. The vascular plant flora of Victoria Island comprises 38 families, 108 genera, 272 species, and 17 additional taxa. Of the 289 taxa known on the island, 237 are recorded from the Northwest Territories portion of the island and 277 from the Nunavut part. Thirty-nine taxa are known on the island from a single collection, seven from two collections and three from three collections. Twenty-one taxa in eight families are newly recorded for the flora of Victoria Island: Artemisia tilesii, Senecio lugens, Taraxacum scopulorum (Asteraceae); Crucihimalaya bursifolia, Draba fladnizensis, D. juvenilis, D. pilosa, D. simmonsii (Brassicaceae); Carex bigelowii subsp. bigelowii, Eriophorum russeolum subsp. albidum (Cyperaceae); Anthoxanthum monticola subsp. monticola, Bromus pumpellianus, Deschampsia cespitosa subsp. cespitosa, D. sukatschewii, Festuca rubra subsp. rubra, Lolium perenne, Poa pratensis subsp. pratensis (Poaceae); Stuckenia filiformis (Potamogetonaceae); Potentilla × prostrata (Rosaceae); Galium aparine (Rubiaceae); and Salix ovalifolia var. ovalifolia (Salicaceae). Eight of these are new to the flora of the Canadian Arctic Archipelago: Senecio lugens, Draba juvenilis, D. pilosa, Anthoxanthum monticola subsp. monticola, Bromus pumpellianus, Deschampsia cespitosa subsp. cespitosa, Poa pratensis subsp. pratensis and Salix ovalifolia var. ovalifolia. One of these, Galium aparine, is newly recorded for the flora of Nunavut. Four first records for Victoria Island are introduced plants discovered in Cambridge Bay in 2017: three grasses (Festuca rubra subsp. rubra, Lolium perenne, and Poa pratensis subsp. pratensis) and Galium aparine. One taxon, Juncus arcticus subsp. arcticus, is newly recorded from the Northwest Territories. Of the general areas on Victoria Island that have been botanically explored the most, the greatest diversity of vascular plants is recorded in Ulukhaktok (194 taxa) and the next most diverse area is Cambridge Bay (183 taxa). The floristic data presented here represent a new baseline on which continued exploration of the vascular flora of Victoria Island - particularly the numerous areas of the island that remain unexplored or poorly explored botanically - will build.
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Affiliation(s)
- Jeffery M. Saarela
- Centre for Arctic Knowledge and Exploration and Botany Section, Research & Collections, Canadian Museum of Nature, Ottawa, Ontario, CanadaCanadian Museum of NatureOttawaCanada
| | - Paul C. Sokoloff
- Centre for Arctic Knowledge and Exploration and Botany Section, Research & Collections, Canadian Museum of Nature, Ottawa, Ontario, CanadaCanadian Museum of NatureOttawaCanada
| | - Lynn J. Gillespie
- Centre for Arctic Knowledge and Exploration and Botany Section, Research & Collections, Canadian Museum of Nature, Ottawa, Ontario, CanadaCanadian Museum of NatureOttawaCanada
| | - Roger D. Bull
- Centre for Arctic Knowledge and Exploration and Botany Section, Research & Collections, Canadian Museum of Nature, Ottawa, Ontario, CanadaCanadian Museum of NatureOttawaCanada
| | | | - Serguei Ponomarenko
- Centre for Arctic Knowledge and Exploration and Botany Section, Research & Collections, Canadian Museum of Nature, Ottawa, Ontario, CanadaCanadian Museum of NatureOttawaCanada
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Ledesma DA, Powell CA, Shaw J, Qin H. Enabling automated herbarium sheet image post-processing using neural network models for color reference chart detection. Appl Plant Sci 2020; 8:e11331. [PMID: 32185122 PMCID: PMC7073326 DOI: 10.1002/aps3.11331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/20/2019] [Indexed: 06/01/2023]
Abstract
PREMISE Large-scale efforts to digitize herbaria have resulted in more than 18 million publicly available Plantae images on sites such as iDigBio. The automation of image post-processing will lead to time savings in the digitization of biological specimens, as well as improvements in data quality. Here, new and modified neural network methodologies were developed to automatically detect color reference charts (CRC), enabling the future automation of various post-processing tasks. METHODS AND RESULTS We used 1000 herbarium specimen images from 52 herbaria to test our novel neural network model, ColorNet, which was developed to identify CRCs smaller than 4 cm2, resulting in a 30% increase in accuracy over the performance of other state-of-the-art models such as Faster R-CNN. For larger CRCs, we propose modifications to Faster R-CNN to increase inference speed. CONCLUSIONS Our proposed neural networks detect a range of CRCs, which may enable the automation of post-processing tasks found in herbarium digitization workflows, such as image orientation or white balance correction.
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Affiliation(s)
- Dakila A. Ledesma
- Department of Computer Science and EngineeringUniversity of Tennessee at ChattanoogaChattanoogaTennesseeUSA
| | - Caleb A. Powell
- Department of Biology, Geology and Environmental ScienceUniversity of Tennessee at ChattanoogaChattanoogaTennesseeUSA
| | - Joey Shaw
- Department of Biology, Geology and Environmental ScienceUniversity of Tennessee at ChattanoogaChattanoogaTennesseeUSA
| | - Hong Qin
- Department of Computer Science and EngineeringUniversity of Tennessee at ChattanoogaChattanoogaTennesseeUSA
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35
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Affiliation(s)
- Allyson Kido
- Department of BiologyAmherst CollegeAmherstMassachusettsUSA
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36
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Rose ED. From the South Seas to Soho Square: Joseph Banks's Library, collection and Kingdom of natural history. Notes Rec R Soc Lond 2019; 73:499-526. [PMID: 31754287 PMCID: PMC6863077 DOI: 10.1098/rsnr.2018.0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The library and herbarium of Joseph Banks was one of the most prominent natural history collections of late eighteenth-century Britain. The examination of the working practices used in Banks's library, which was based at 32 Soho Square from 1777, reveals the activities of the numerous individuals who worked for Banks and on his collections from the early 1770s until 1820. Banks's librarians and their assistants used a range of paper technologies to classify and catalogue the vast numbers of new botanical species being discovered at this time. These practices of managing information changed as the decades progressed, reflecting the changes to systems of classification and the different research projects of Banks and his natural history staff. Banks's great wealth and powerful position as President of the Royal Society gave him the means to build and use this rigorously organized collection and library to influence a range of other private and institutional collections for almost 50 years.
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Rokni S, Wursten B, Darbyshire I. Synsepalum chimanimani (Sapotaceae), a new species from the Chimanimani Mountains of Mozambique and Zimbabwe, with notes on the botanical importance of this area. PhytoKeys 2019; 133:115-132. [PMID: 31662617 PMCID: PMC6811373 DOI: 10.3897/phytokeys.133.38694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
Synsepalum chimanimani S.Rokni & I.Darbysh., sp. nov., a small tree endemic to the forests of the southern foothills of the Chimanimani Mountains of Mozambique and Zimbabwe, is described and illustrated. The differences in morphology and distribution between the new species and the related S. kaessneri and S. muelleri, with which it has been confused, are clarified. The new species is globally Endangered due to ongoing habitat loss within its restricted range. The botanical importance and conservation of the Chimanimani foothills is also discussed, and they are highlighted as a candidate Important Plant Area.
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Affiliation(s)
- Saba Rokni
- Herbarium, Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UKHerbarium, Royal Botanic GardensRichmondUnited Kingdom
| | - Bart Wursten
- Herbarium, Nieuwelaan 38, Meise 1860, BelgiumHerbariumMeiseBelgium
| | - Iain Darbyshire
- Herbarium, Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UKHerbarium, Royal Botanic GardensRichmondUnited Kingdom
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Malakasi P, Bellot S, Dee R, Grace OM. Museomics Clarifies the Classification of Aloidendron (Asphodelaceae), the Iconic African Tree Aloes. Front Plant Sci 2019; 10:1227. [PMID: 31681358 PMCID: PMC6803536 DOI: 10.3389/fpls.2019.01227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/04/2019] [Indexed: 05/24/2023]
Abstract
Arborescent succulent plants are regarded as keystone and indicator species in desert ecosystems due to their large stature and long lifespans. Tree aloes, the genus Aloidendron, are icons of the southern African deserts yet have proved elusive subjects due to the difficulty of obtaining material of known provenance for comparative study. Consequently, evolutionary relationships among representatives of the unusual arborescent life form have remained unclear until now. We used a museomics approach to overcome this challenge. Chloroplast genomes of six Aloidendron species and 12 other members of Asphodelaceae were sequenced from modern living collections and herbarium specimens, including the type specimens of all but two Aloidendron species, the earliest of which was collected 130 years ago. Maximum-likelihood trees estimated from full chloroplast genomes and the nuclear internal transcribed spacer (ITS) region show that Aloidendron sabaeum, from the Arabian Peninsula, is nested within Aloe while the Madagascar endemic Aloestrela suzannae is most closely related to the Somalian Aloidendron eminens. We observed phylogenetic conflicts between the plastid and nuclear topologies, which may be indicative of recurrent hybridisation or incomplete lineage sorting events in Aloe and in Aloidendron. Comparing species ecology in the context provided by our phylogeny suggests that habitat preference to either xeric deserts or humid forests/thickets evolved repeatedly in Aloidendron. Our findings demonstrate the value of botanical collections for the study and classification of taxonomically challenging succulent plants.
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Wolkis D, Deans S. Picking from the Past in Preparation for a Pest: Seed Banks Outperform Herbaria as Sources of Preserved 'Ōhi'a Seed. Biopreserv Biobank 2019; 17:583-590. [PMID: 31429591 DOI: 10.1089/bio.2019.0044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Seed banks serve the purpose of maintaining germplasm for ex situ species preservation. Herbarium vouchers may be a viable source of unique and/or additional seeds for restoration as they can sometimes be from larger and more representative populations compared with seed banks. Rapid 'ōhi'a death (ROD) has emerged as a serious threat against Hawaii's most iconic and foundational forest tree (Metrosideros spp.), and seed banking has been identified as an important strategy in preserving the genetic diversity of 'ōhi'a. With respect to 'ōhi'a we ask the following: (1) what is the long-term viability of 'ōhi'a seeds stored in herbarium conditions, (2) how do herbarium curation practices affect seed viability, and (3) how long do seeds survive using conventional storage methods? We placed fresh 'ōhi'a seeds in a herbarium dryer (57°C/5% relative humidity) for 5 days, freezer (-18°C/95% RH) for 2 weeks, and dryer then freezer, and compared against fresh control seeds. Seeds were harvested from a chronosequence of herbarium specimens, withdrawn from conventional storage conditions up to 3.75 and 6.5 years before experiments began, and germination assessed. There was no difference in the proportion germinated among treatments and control testing for herbarium entry (p = 0.56). Although no seeds from herbarium specimens germinated, freshly collected dried and frozen seeds germinated at a level equivalent to the control (p = 0.76). For seeds stored using conventional storage methods at 3.75 and 6.5 years, germination was equivalent to freshly harvested seeds. This suggests that seeds can survive the extreme climate conditions necessary to enter herbaria, but lose viability after storage at ambient conditions in 4 years or less. Although 'ōhi'a seeds may be plentiful in herbaria, we recommend using seeds deposited into seed banks using conventional storage methods for orthodox seeds for postdisturbance restoration, and to combat ROD.
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Affiliation(s)
- Dustin Wolkis
- Department of Science and Conservation, National Tropical Botanical Garden, Kalāheo, Hawaii
| | - Susan Deans
- Department of Science and Conservation, National Tropical Botanical Garden, Kalāheo, Hawaii.,Department of Plant Science, Chicago Botanic Garden, Glencoe, Illinois.,Plant Biology and Conservation, Northwestern University, Evanston, Illinois
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Hoare RJ, Patrick BH, Buckley TR. A new leaf-mining moth from New Zealand, Sabulopteryxbotanica sp. nov. (Lepidoptera, Gracillariidae, Gracillariinae), feeding on the rare endemic shrub Teucriumparvifolium (Lamiaceae), with a revised checklist of New Zealand Gracillariidae. Zookeys 2019; 865:39-65. [PMID: 31379443 PMCID: PMC6663935 DOI: 10.3897/zookeys.865.34265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/03/2019] [Indexed: 11/25/2022] Open
Abstract
Sabulopteryxbotanica Hoare & Patrick, sp. nov. (Lepidoptera, Gracillariidae, Gracillariinae) is described as a new species from New Zealand. It is regarded as endemic, and represents the first record of its genus from the southern hemisphere. Though diverging in some morphological features from previously described species, it is placed in genus Sabulopteryx Triberti, based on wing venation, abdominal characters, male and female genitalia and hostplant choice; this placement is supported by phylogenetic analysis based on the COI mitochondrial gene. The life history is described: the larva is an underside leaf-miner on the endemic divaricating shrub Teucriumparvifolium (Lamiaceae), and exits the mine to pupate in a cocoon in a folded leaf of the host plant. The remarkable history of the discovery and rediscovery of this moth is discussed: for many years it was only known from a single sap-feeding larva found in a leaf-mine in a pressed herbarium specimen of the host. The adult was discovered by BHP in Christchurch Botanic Gardens in 2013. Most distribution records of the moth come from a recent search for mines and cocoons on herbarium specimens of T.parvifolium. Sabulopteryxbotanica has high conservation status, and is regarded as 'Nationally Vulnerable' according to the New Zealand Department of Conservation threat classification system, based on the rarity and declining status of its host plant. However, the presence of apparently thriving populations of S.botanica on cultivated plants of T.parvifolium, especially at the type locality, Christchurch Botanic Gardens, suggests that encouraging cultivation of the plant could greatly improve the conservation status of the moth. A revised checklist of New Zealand Gracillariidae is presented, assigning all species to the currently recognised subfamilies. The Australian Macarostolaida (Meyrick, 1880) is newly recorded from New Zealand (Auckland), where it is established on Eucalyptus.
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Affiliation(s)
- Robert J.B. Hoare
- New Zealand Arthropod Collection (NZAC), Manaaki Whenua–Landcare Research, Private Bag 92170, Auckland, New ZealandNew Zealand Arthropod CollectionAucklandNew Zealand
| | - Brian H. Patrick
- Wildlands Consultants Ltd, PO Box 9276, Tower Junction, Christchurch 8149, New ZealandWildlands Consultants LtdChristchurchNew Zealand
| | - Thomas R. Buckley
- New Zealand Arthropod Collection (NZAC), Manaaki Whenua–Landcare Research, Private Bag 92170, Auckland, New ZealandNew Zealand Arthropod CollectionAucklandNew Zealand
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, New ZealandThe University of AucklandAucklandNew Zealand
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Love NLR, Park IW, Mazer SJ. A new phenological metric for use in pheno-climatic models: A case study using herbarium specimens of Streptanthus tortuosus. Appl Plant Sci 2019; 7:e11276. [PMID: 31346508 PMCID: PMC6636619 DOI: 10.1002/aps3.11276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/17/2019] [Indexed: 05/13/2023]
Abstract
PREMISE Herbarium specimens have been used to detect climate-induced shifts in flowering time by using the day of year of collection (DOY) as a proxy for first or peak flowering date. Variation among herbarium sheets in their phenological status, however, undermines the assumption that DOY accurately represents any particular phenophase. Ignoring this variation can reduce the explanatory power of pheno-climatic models (PCMs) designed to predict the effects of climate on flowering date. METHODS Here we present a protocol for the phenological scoring of imaged herbarium specimens using an ImageJ plugin, and we introduce a quantitative metric of a specimen's phenological status, the phenological index (PI), which we use in PCMs to control for phenological variation among specimens of Streptanthus tortuosus (Brassicaceeae) when testing for the effects of climate on DOY. We demonstrate that including PI as an independent variable improves model fit. RESULTS Including PI in PCMs increased the model R 2 relative to PCMs that excluded PI; regression coefficients for climatic parameters, however, remained constant. DISCUSSION Our protocol provides a simple, quantitative phenological metric for any observed plant. Including PI in PCMs increases R 2 and enables predictions of the DOY of any phenophase under any specified climatic conditions.
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Affiliation(s)
- Natalie L. Rossington Love
- Department of Ecology, Evolution, and Marine BiologyUniversity of California, Santa BarbaraSanta BarbaraCalifornia93106USA
| | - Isaac W. Park
- Department of Ecology, Evolution, and Marine BiologyUniversity of California, Santa BarbaraSanta BarbaraCalifornia93106USA
| | - Susan J. Mazer
- Department of Ecology, Evolution, and Marine BiologyUniversity of California, Santa BarbaraSanta BarbaraCalifornia93106USA
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Nic Lughadha EM, Graziele Staggemeier V, Vasconcelos TNC, Walker BE, Canteiro C, Lucas EJ. Harnessing the potential of integrated systematics for conservation of taxonomically complex, megadiverse plant groups. Conserv Biol 2019; 33:511-522. [PMID: 30779869 PMCID: PMC6850456 DOI: 10.1111/cobi.13289] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 05/30/2023]
Abstract
The value of natural history collections for conservation science research is increasingly recognized, despite their well-documented limitations in terms of taxonomic, geographic, and temporal coverage. Specimen-based analyses are particularly important for tropical plant groups for which field observations are scarce and potentially unreliable due to high levels of diversity-amplifying identification challenges. Specimen databases curated by specialists are rich sources of authoritatively identified, georeferenced occurrence data, and such data are urgently needed for large genera. We compared entries in a monographic database for the large Neotropical genus Myrcia in 2007 and 2017. We classified and quantified differences in specimen records over this decade and determined the potential impact of these changes on conservation assessments. We distinguished misidentifications from changes due to taxonomic remodeling and considered the effects of adding specimens and georeferences. We calculated the potential impact of each change on estimates of extent of occurrence (EOO), the most frequently used metric in extinction-risk assessments of tropical plants. We examined whether particular specimen changes were associated with species for which changes in EOO over the decade were large enough to change their conservation category. Corrections to specimens previously misidentified or lacking georeferences were overrepresented in such species, whereas changes associated with taxonomic remodeling (lumping and splitting) were underrepresented. Among species present in both years, transitions to less threatened status outnumbered those to more threatened (8% vs 3%, respectively). Species previously deemed data deficient transitioned to threatened status more often than to not threatened (10% vs 7%, respectively). Conservation scientists risk reaching unreliable conclusions if they use specimen databases that are not actively curated to reflect changing knowledge.
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Affiliation(s)
| | - Vanessa Graziele Staggemeier
- Royal Botanic Gardens, KewTW9 3AERichmondSurreyU.K.
- Universidade Estadual Paulista, Instituto de Biociências, Departamento de BotânicaLaboratório de FenologiaAvenida 24A 1515, CEP 13506–900Rio ClaroSão PauloBrazil
- Departamento de Ecologia, Centro de BiociênciasUniversidade Federal do Rio Grande do NorteCEP 59072–970NatalRio Grande do NorteBrazil
| | - Thais N. C. Vasconcelos
- Royal Botanic Gardens, KewTW9 3AERichmondSurreyU.K.
- Laboratório de Sistemática VegetalDepartamento de Botânica, Universidade de São Paulo, São PauloSP 05508–090Brazil
| | | | | | - Eve J. Lucas
- Royal Botanic Gardens, KewTW9 3AERichmondSurreyU.K.
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Soto Gomez M, Pokorny L, Kantar MB, Forest F, Leitch IJ, Gravendeel B, Wilkin P, Graham SW, Viruel J. A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae). Appl Plant Sci 2019; 7:e11254. [PMID: 31236313 PMCID: PMC6580989 DOI: 10.1002/aps3.11254] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 04/01/2019] [Indexed: 05/14/2023]
Abstract
PREMISE We developed a target enrichment panel for phylogenomic studies of Dioscorea, an economically important genus with incompletely resolved relationships. METHODS Our bait panel comprises 260 low- to single-copy nuclear genes targeted to work in Dioscorea, assessed here using a preliminary taxon sampling that includes both distantly and closely related taxa, including several yam crops and potential crop wild relatives. We applied coalescent-based and maximum likelihood phylogenomic inference approaches to the pilot taxon set, incorporating new and published transcriptome data from additional species. RESULTS The custom panel retrieved ~94% of targets and >80% of full gene length from 88% and 68% of samples, respectively. It has minimal gene overlap with existing panels designed for angiosperm-wide studies and generally recovers longer and more variable targets. Pilot phylogenomic analyses consistently resolve most deep and recent relationships with strong support across analyses and point to revised relationships between the crop species D. alata and candidate crop wild relatives. DISCUSSION Our customized panel reliably retrieves targeted loci from Dioscorea, is informative for resolving relationships in denser samplings, and is suitable for refining our understanding of the independent origins of cultivated yam species; the panel likely has broader promise for phylogenomic studies across Dioscoreales.
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Affiliation(s)
- Marybel Soto Gomez
- Department of BotanyUniversity of British Columbia6270 University BoulevardVancouverBritish ColumbiaV6T 1Z4Canada
- UBC Botanical Garden and Centre for Plant ResearchUniversity of British Columbia6804 Marine Drive SWVancouverBritish ColumbiaV6T 1Z4Canada
| | - Lisa Pokorny
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
| | - Michael B. Kantar
- Department of Tropical Plant and Soil SciencesUniversity of Hawai‘i at ManoaHonoluluHawai‘i96822USA
| | - Félix Forest
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
| | - Ilia J. Leitch
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
| | - Barbara Gravendeel
- Naturalis Biodiversity CenterEndless FormsSylviusweg 72Leiden2333 BEThe Netherlands
- Institute Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEThe Netherlands
- Faculty of Science and TechnologyUniversity of Applied Sciences LeidenZernikedreef 11Leiden2333 CKThe Netherlands
| | - Paul Wilkin
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
| | - Sean W. Graham
- Department of BotanyUniversity of British Columbia6270 University BoulevardVancouverBritish ColumbiaV6T 1Z4Canada
- UBC Botanical Garden and Centre for Plant ResearchUniversity of British Columbia6804 Marine Drive SWVancouverBritish ColumbiaV6T 1Z4Canada
| | - Juan Viruel
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
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Abstract
PREMISE OF THE STUDY Human activities threaten thousands of species with extinction. However, it remains difficult to predict extinction risk for many vulnerable species. Species traits, species characteristics such as rarity or habitat use, and phylogenetic patterns are associated with responses to anthropogenic environmental change and may help predict likelihood of extinction. METHODS We used historical botanical data from Kalamazoo County, Michigan, USA, to examine whether species traits (growth form, life history, nitrogen-fixation, photosynthetic pathway), species characteristics (community association, species origin, range edge, habitat specialization, rarity), or phylogenetic relatedness explain local species loss at the county level. KEY RESULTS Across Kalamazoo County, prairie species, species at the edge of their native range, regionally rare species, and habitat specialists were most likely to become locally extinct. Prairie species experienced the highest local extinction rates of any habitat type, and among prairie species, regionally rare and specialist species were most vulnerable to loss. We found no evidence for a phylogenetic pattern in plant extinctions. CONCLUSIONS Our study illustrates the value of historical datasets for understanding and potentially predicting biodiversity loss. Not surprisingly, rare, specialist species occupying threatened habitats are most at risk of local extinction. As a result, identifying mechanisms to conserve or restore rare or declining species and preventing further habitat destruction may be the most effective strategies for reducing future extinction.
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Affiliation(s)
- Meredith A Zettlemoyer
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824-6406, USA
- Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, 49060-9505, USA
| | - Duane D McKenna
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee, 38152-3560, USA
| | - Jennifer A Lau
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824-6406, USA
- Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, 49060-9505, USA
- Department of Biology, Indiana University-Bloomington, Bloomington, Indiana, 47405-7005, USA
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Chollet-Krugler M, Nguyen TTT, Sauvager A, Thüs H, Boustie J. Mycosporine-Like Amino Acids (MAAs) in Time-Series of Lichen Specimens from Natural History Collections. Molecules 2019; 24:E1070. [PMID: 30893758 PMCID: PMC6471344 DOI: 10.3390/molecules24061070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/14/2019] [Accepted: 03/16/2019] [Indexed: 01/15/2023] Open
Abstract
Mycosporine-like amino acids (MAAs) were quantified in fresh and preserved material of the chlorolichen Dermatocarpon luridum var. luridum (Verrucariaceae/Ascomycota). The analyzed samples represented a time-series of over 150 years. An HPLC coupled with a diode array detector (HPLC-DAD) in hydrophilic interaction liquid chromatography (HILIC) mode method was developed and validated for the quantitative determination of MAAs. We found evidence for substance specific differences in the quality of preservation of two MAAs (mycosporine glutamicol, mycosporine glutaminol) in Natural History Collections. We found no change in average mycosporine glutamicol concentrations over time. Mycosporine glutaminol concentrations instead decreased rapidly with no trace of this substance detectable in collections older than nine years. Our data predict that a screening for MAAs in organism samples from Natural History Collections can deliver results that are comparable to those obtained from fresh collections only for some MAAs (e.g., mycosporine glutamicol). For other MAAs, misleading, biased, or even false negative results will occur as a result of the storage sensitivity of substances such as mycosporine glutaminol. Our study demonstrates the value of pilot studies with time-series based on model taxa with a rich representation in the Natural History Collections.
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Affiliation(s)
- Marylène Chollet-Krugler
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, Univ Rennes, F-35000 Rennes, France.
| | - Thi Thu Tram Nguyen
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, Univ Rennes, F-35000 Rennes, France.
- Department of Chemistry, Faculty of Science, Can Tho University of Medicine and Pharmacy, 179 Nguyen Van Cu Street, An Khanh, Ninh Kieu, Can Tho, 902495 Vietnam.
| | - Aurelie Sauvager
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, Univ Rennes, F-35000 Rennes, France.
| | - Holger Thüs
- State Museum of Natural History Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany.
- The Natural History Museum London, Cromwell Rd, Kensington, London SW7 5BD, UK.
| | - Joël Boustie
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, Univ Rennes, F-35000 Rennes, France.
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Boyle JH, Dalgleish HJ, Puzey JR. Monarch butterfly and milkweed declines substantially predate the use of genetically modified crops. Proc Natl Acad Sci U S A 2019; 116:3006-11. [PMID: 30723147 DOI: 10.1073/pnas.1811437116] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Monarch butterfly (Danaus plexippus) decline over the past 25 years has received considerable public and scientific attention, in large part because its decline, and that of its milkweed (Asclepias spp.) host plant, have been linked to genetically modified (GM) crops and associated herbicide use. Here, we use museum and herbaria specimens to extend our knowledge of the dynamics of both monarchs and milkweeds in the United States to more than a century, from 1900 to 2016. We show that both monarchs and milkweeds increased during the early 20th century and that recent declines are actually part of a much longer-term decline in both monarchs and milkweed beginning around 1950. Herbicide-resistant crops, therefore, are clearly not the only culprit and, likely, not even the primary culprit: Not only did monarch and milkweed declines begin decades before GM crops were introduced, but other variables, particularly a decline in the number of farms, predict common milkweed trends more strongly over the period studied here.
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Groh JS, Percy DM, Björk CR, Cronk QCB. On the origin of orphan hybrids between Aquilegia formosa and Aquilegia flavescens. AoB Plants 2019; 11:ply071. [PMID: 30687492 PMCID: PMC6341775 DOI: 10.1093/aobpla/ply071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 11/14/2018] [Indexed: 06/01/2023]
Abstract
We report the investigation of an Aquilegia flavescens × A. formosa population in British Columbia that is disjunct from its parents-the latter species is present locally but ecologically separated, while the former is entirely absent. To confirm hybridity, we used multivariate analysis of floral characters of field-sampled populations to ordinate phenotypes of putative hybrids in relation to those of the parental species. Microsatellite genotypes at 11 loci from 72 parental-type and putative hybrid individuals were analysed to assess evidence for admixture. Maternally inherited plastid sequences were analysed to infer the direction of hybridization and test hypotheses on the origin of the orphan hybrid population. Plants from the orphan hybrid population are on average intermediate between typical A. formosa and A. flavescens for most phenotypes examined and show evidence of genetic admixture. This population lies beyond the range of A. flavescens, but within the range of A. formosa. No pure A. flavescens individuals were observed in the vicinity, nor is this species known to occur within 200 km of the site. The hybrids share a plastid haplotype with local A. formosa populations. Alternative explanations for this pattern are evaluated. While we cannot rule out long-distance pollen dispersal followed by proliferation of hybrid genotypes, we consider the spread of an A. formosa plastid during genetic swamping of a historical A. flavescens population to be more parsimonious.
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Affiliation(s)
- Jeffrey S Groh
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Diana M Percy
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Curtis R Björk
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Couvreur TLP, Helmstetter AJ, Koenen EJM, Bethune K, Brandão RD, Little SA, Sauquet H, Erkens RHJ. Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes. Front Plant Sci 2019; 9:1941. [PMID: 30687347 PMCID: PMC6334231 DOI: 10.3389/fpls.2018.01941] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/13/2018] [Indexed: 05/19/2023]
Abstract
Targeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. Annonaceae is a major pantropical plant family with 110 genera and ca. 2,450 species, occurring across all major and minor tropical forests of the world. Baits were designed by sequencing the transcriptomes of five species from two of the largest Annonaceae subfamilies. Orthologous loci were identified. The resulting baiting kit was used to reconstruct phylogenetic relationships at two different levels using concatenated and gene tree approaches: a family wide Annonaceae analysis sampling 65 genera and a species level analysis of tribe Piptostigmateae sampling 29 species with multiple individuals per species. DNA extraction was undertaken mainly on silicagel dried leaves, with two samples from herbarium dried leaves. Our kit targets 469 exons (364,653 bp of sequence data), successfully capturing sequences from across Annonaceae. Silicagel dried and herbarium DNA worked equally well. We present for the first time a nuclear gene-based phylogenetic tree at the generic level based on 317 supercontigs. Results mainly confirm previous chloroplast based studies. However, several new relationships are found and discussed. We show significant differences in branch lengths between the two large subfamilies Annonoideae and Malmeoideae. A new tribe, Annickieae, is erected containing a single African genus Annickia. We also reconstructed a well-resolved species-level phylogenetic tree of the Piptostigmteae tribe. Our baiting kit is useful for reconstructing well-supported phylogenetic relationships within Annonaceae at different taxonomic levels. The nuclear genome is mainly concordant with plastome information with a few exceptions. Moreover, we find that substitution rate heterogeneity between the two subfamilies is also found within the nuclear compartment, and not just plastomes and ribosomal DNA as previously shown. Our results have implications for understanding the biogeography, molecular dating and evolution of Annonaceae.
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Affiliation(s)
| | | | - Erik J. M. Koenen
- Institute of Systematic Botany, University of Zurich, Zurich, Switzerland
| | - Kevin Bethune
- IRD, UMR DIADE, Univ. Montpellier, Montpellier, France
| | - Rita D. Brandão
- Maastricht Science Programme, Maastricht University, Maastricht, Netherlands
| | - Stefan A. Little
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université-Paris Saclay, Orsay, France
| | - Hervé Sauquet
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université-Paris Saclay, Orsay, France
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Roy H. J. Erkens
- Maastricht Science Programme, Maastricht University, Maastricht, Netherlands
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Darbyshire I, Timberlake J, Osborne J, Rokni S, Matimele H, Langa C, Datizua C, de Sousa C, Alves T, Massingue A, Hadj-Hammou J, Dhanda S, Shah T, Wursten B. The endemic plants of Mozambique: diversity and conservation status. PhytoKeys 2019; 136:45-96. [PMID: 31866738 PMCID: PMC6920223 DOI: 10.3897/phytokeys.136.39020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/22/2019] [Indexed: 05/21/2023]
Abstract
An annotated checklist of the 271 strict-endemic taxa (235 species) and 387 near-endemic taxa (337 species) of vascular plants in Mozambique is provided. Together, these taxa constitute c. 9.3% of the total currently known flora of Mozambique and include five strict-endemic genera (Baptorhachis, Emicocarpus, Gyrodoma, Icuria and Micklethwaitia) and two near-endemic genera (Triceratella and Oligophyton). The mean year of first publication of these taxa is 1959, with a marked increase in description noted following the onset of the two major regional floristic programmes, the "Flora of Tropical East Africa" and "Flora Zambesiaca", and an associated increase in botanical collecting effort. New taxa from Mozambique continue to be described at a significant rate, with 20 novelties described in 2018. Important plant families for endemic and near-endemic taxa include Fabaceae, Rubiaceae and Euphorbiaceae s.s. There is a high congruence between species-rich plant families and endemism with the notable exceptions of the Poaceae, which is the second-most species rich plant family, but outside of the top ten families in terms of endemism, and the Euphorbiaceae, which is the seventh-most species rich plant family, but third in terms of endemism. A wide range of life-forms are represented in the endemic and near-endemic flora, with 49% being herbaceous or having herbaceous forms and 55% being woody or having woody forms. Manica Province is by far the richest locality for near-endemic taxa, highlighting the importance of the cross-border Chimanimani-Nyanga (Manica) Highlands shared with Zimbabwe. A total of 69% of taxa can be assigned to one of four cross-border Centres of Endemism: the Rovuma Centre, the Maputaland Centre sensu lato, and the two mountain blocks, Chimanimani-Nyanga and Mulanje-Namuli-Ribaue. Approximately 50% of taxa have been assessed for their extinction risk and, of these, just over half are globally threatened (57% for strict-endemics), with a further 10% (17% for strict-endemics) currently considered to be Data Deficient, highlighting the urgent need for targeted conservation of Mozambique's unique flora. This dataset will be a key resource for ongoing efforts to identify "Important Plant Areas - IPAs" in Mozambique, and to promote the conservation and sustainable management of these critical sites and species, thus enabling Mozambique to meet its commitments under the Convention on Biological Diversity (CBD).
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Affiliation(s)
- Iain Darbyshire
- Royal Botanic Gardens, Kew (RBG Kew), Richmond, Surrey, TW9 3AE, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Jonathan Timberlake
- 30 Warren Lane, East Dean, East Sussex BN20 0EW, UKUnaffiliatedEast DeanUnited Kingdom
| | - Jo Osborne
- Royal Botanic Gardens, Kew (RBG Kew), Richmond, Surrey, TW9 3AE, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Saba Rokni
- Royal Botanic Gardens, Kew (RBG Kew), Richmond, Surrey, TW9 3AE, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Hermenegildo Matimele
- Instituto de Investigação Agrária de Moçambique (IIAM), P.O. Box 3658, Mavalane, Maputo, MozambiqueInstituto de Investigação Agrária de MoçambiqueMaputoMozambique
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Marlowe Building, University of Kent, Canterbury, Kent, CT2 7NR, UKUniversity of KentCanterburyUnited Kingdom
| | - Clayton Langa
- Instituto de Investigação Agrária de Moçambique (IIAM), P.O. Box 3658, Mavalane, Maputo, MozambiqueInstituto de Investigação Agrária de MoçambiqueMaputoMozambique
| | - Castigo Datizua
- Instituto de Investigação Agrária de Moçambique (IIAM), P.O. Box 3658, Mavalane, Maputo, MozambiqueInstituto de Investigação Agrária de MoçambiqueMaputoMozambique
| | - Camila de Sousa
- Instituto de Investigação Agrária de Moçambique (IIAM), P.O. Box 3658, Mavalane, Maputo, MozambiqueInstituto de Investigação Agrária de MoçambiqueMaputoMozambique
| | - Tereza Alves
- Instituto de Investigação Agrária de Moçambique (IIAM), P.O. Box 3658, Mavalane, Maputo, MozambiqueInstituto de Investigação Agrária de MoçambiqueMaputoMozambique
| | - Alice Massingue
- Department of Biological Sciences, Eduardo Mondlane University, P.O. Box 257, Maputo, MozambiqueEduardo Mondlane UniversityMaputoMozambique
| | - Jeneen Hadj-Hammou
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UKLancaster UniversityLancasterUnited Kingdom
| | - Sonia Dhanda
- Royal Botanic Gardens, Kew (RBG Kew), Richmond, Surrey, TW9 3AE, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Toral Shah
- Royal Botanic Gardens, Kew (RBG Kew), Richmond, Surrey, TW9 3AE, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Bart Wursten
- Herbarium, Nieuwelaan 38, Meise 1860, BelgiumHerbariumMeiseBelgium
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Lang PLM, Willems FM, Scheepens JF, Burbano HA, Bossdorf O. Using herbaria to study global environmental change. New Phytol 2019; 221:110-122. [PMID: 30160314 PMCID: PMC6585664 DOI: 10.1111/nph.15401] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/19/2018] [Indexed: 05/14/2023]
Abstract
During the last centuries, humans have transformed global ecosystems. With their temporal dimension, herbaria provide the otherwise scarce long-term data crucial for tracking ecological and evolutionary changes over this period of intense global change. The sheer size of herbaria, together with their increasing digitization and the possibility of sequencing DNA from the preserved plant material, makes them invaluable resources for understanding ecological and evolutionary species' responses to global environmental change. Following the chronology of global change, we highlight how herbaria can inform about long-term effects on plants of at least four of the main drivers of global change: pollution, habitat change, climate change and invasive species. We summarize how herbarium specimens so far have been used in global change research, discuss future opportunities and challenges posed by the nature of these data, and advocate for an intensified use of these 'windows into the past' for global change research and beyond.
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Affiliation(s)
- Patricia L. M. Lang
- Research Group for Ancient Genomics and EvolutionMax Planck Institute for Developmental Biology72076TübingenGermany
| | - Franziska M. Willems
- Plant Evolutionary EcologyInstitute of Evolution and EcologyUniversity of Tübingen72076TübingenGermany
| | - J. F. Scheepens
- Plant Evolutionary EcologyInstitute of Evolution and EcologyUniversity of Tübingen72076TübingenGermany
| | - Hernán A. Burbano
- Research Group for Ancient Genomics and EvolutionMax Planck Institute for Developmental Biology72076TübingenGermany
| | - Oliver Bossdorf
- Plant Evolutionary EcologyInstitute of Evolution and EcologyUniversity of Tübingen72076TübingenGermany
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