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Daru BH, Rodriguez J. Mass production of unvouchered records fails to represent global biodiversity patterns. Nat Ecol Evol 2023:10.1038/s41559-023-02047-3. [PMID: 37127769 DOI: 10.1038/s41559-023-02047-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/26/2023] [Indexed: 05/03/2023]
Abstract
The ever-increasing human footprint even in very remote places on Earth has inspired efforts to document biodiversity vigorously in case organisms go extinct. However, the data commonly gathered come from either primary voucher specimens in a natural history collection or from direct field observations that are not traceable to tangible material in a museum or herbarium. Although both datasets are crucial for assessing how anthropogenic drivers affect biodiversity, they have widespread coverage gaps and biases that may render them inefficient in representing patterns of biodiversity. Using a large global dataset of around 1.9 billion occurrence records of terrestrial plants, butterflies, amphibians, birds, reptiles and mammals, we quantify coverage and biases of expected biodiversity patterns by voucher and observation records. We show that the mass production of observation records does not lead to higher coverage of expected biodiversity patterns but is disproportionately biased toward certain regions, clades, functional traits and time periods. Such coverage patterns are driven by the ease of accessibility to air and ground transportation, level of security and extent of human modification at each sampling site. Conversely, voucher records are vastly infrequent in occurrence data but in the few places where they are sampled, showed relative congruence with expected biodiversity patterns for all dimensions. The differences in coverage and bias by voucher and observation records have important implications on the utility of these records for research in ecology, evolution and conservation research.
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Affiliation(s)
- Barnabas H Daru
- Department of Biology, Stanford University, Stanford, CA, USA.
| | - Jordan Rodriguez
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
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2
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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. AMERICAN JOURNAL OF BOTANY 2023; 110:e16126. [PMID: 36633920 DOI: 10.1002/ajb2.16126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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3
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Colón Carrión N, Troche CL, Arnold AE. Communities of endophytic fungi in a Puerto Rican rainforest vary along a gradient of disturbance due to Hurricane Maria. Ecol Evol 2022; 12:e9618. [PMID: 36532133 PMCID: PMC9750846 DOI: 10.1002/ece3.9618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/18/2022] [Accepted: 11/17/2022] [Indexed: 12/23/2022] Open
Abstract
Increases in the frequency and intensity of hurricanes influence the structure, function, and resilience of Caribbean forests. Trees in such forests harbor diverse fungal endophytes within leaves and roots. Fungal endophytes often are important for plant health and stress responses, but how their communities are impacted by hurricanes is not well known. We measured forest disturbance in Carite State Forest in Puerto Rico ca. 16 months after the passage of Hurricane Maria, a Category 4 storm. In three sites, each comprising three plots representing a local gradient of hurricane disturbance, we evaluated soil chemistry and used culture-free analyses to measure richness, phylogenetic diversity, and composition of endophyte communities in leaves and roots. We found that endophyte richness did not vary significantly among plant families or as a function of soil chemistry. Instead, leaf endophytes peaked in richness and decreased in phylogenetic diversity at intermediate levels of disturbance. Root endophytes did not show such variation, but both leaf- and root endophyte communities differed in species composition as a function of disturbance across the forest. Locations with less disturbance typically hosted distinctive assemblages of foliar endophytes, whereas more disturbed locations had more regionally homogeneous endophyte communities. Together, our results show that changes in endophyte richness and phylogenetic diversity can be detected in aboveground tissues more than a year after major storms. In turn, pervasive shifts in endophyte community composition both aboveground and belowground suggest a subtle and lasting effect of hurricanes that merits further study, potentially contributing to the promotion of spatially heterogeneous endophyte assemblages at a landscape scale in these diverse island forests.
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Affiliation(s)
| | | | - A. Elizabeth Arnold
- School of Plant SciencesUniversity of ArizonaTucsonArizonaUSA
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
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Tellez PH, Arnold AE, Leo AB, Kitajima K, Van Bael SA. Traits along the leaf economics spectrum are associated with communities of foliar endophytic symbionts. Front Microbiol 2022; 13:927780. [PMID: 35966664 PMCID: PMC9366602 DOI: 10.3389/fmicb.2022.927780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Leaf traits of plants worldwide are classified according to the Leaf Economics Spectrum (LES), which links leaf functional traits to evolutionary life history strategies. As a continuum ranging from thicker, tough leaves that are low in nitrogen (N) to thinner, softer, leaves that are high in N, the LES brings together physical, chemical, and ecological traits. Fungal endophytes are common foliar symbionts that occur in healthy, living leaves, especially in tropical forests. Their community composition often differs among co-occurring host species in ways that cannot be explained by environmental conditions or host phylogenetic relationships. Here, we tested the over-arching hypothesis that LES traits act as habitat filters that shape communities of endophytes both in terms of composition, and in terms of selecting for endophytes with particular suites of functional traits. We used culture-based and culture-free surveys to characterize foliar endophytes in mature leaves of 30 phylogenetically diverse plant species with divergent LES traits in lowland Panama, and then measured functional traits of dominant endophyte taxa in vitro. Endophytes were less abundant and less diverse in thick, tough, leaves compared to thin, softer, leaves in the same forest, even in closely related plants. Endophyte communities differed according to leaf traits, including leaf punch strength and carbon and nitrogen content. The most common endophyte taxa in leaves at different ends of the LES differ in their cellulase, protease, chitinase, and antipathogen activity. Our results extend the LES framework for the first time to diverse and ecologically important endophytes, opening new hypotheses regarding the degree to which foliar symbionts respond to, and extend, the functional traits of leaves they inhabit.
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Affiliation(s)
- Peter H Tellez
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, United States
| | - A Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Ashton B Leo
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
| | - Kaoru Kitajima
- Smithsonian Tropical Research Institute, Panama City, Panama
- Division of Forest and Biomaterial Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Sunshine A Van Bael
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, United States
- Smithsonian Tropical Research Institute, Panama City, Panama
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Goëau H, Lorieul T, Heuret P, Joly A, Bonnet P. Can Artificial Intelligence Help in the Study of Vegetative Growth Patterns from Herbarium Collections? An Evaluation of the Tropical Flora of the French Guiana Forest. PLANTS (BASEL, SWITZERLAND) 2022; 11:530. [PMID: 35214863 PMCID: PMC8875713 DOI: 10.3390/plants11040530] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
A better knowledge of tree vegetative growth phenology and its relationship to environmental variables is crucial to understanding forest growth dynamics and how climate change may affect it. Less studied than reproductive structures, vegetative growth phenology focuses primarily on the analysis of growing shoots, from buds to leaf fall. In temperate regions, low winter temperatures impose a cessation of vegetative growth shoots and lead to a well-known annual growth cycle pattern for most species. The humid tropics, on the other hand, have less seasonality and contain many more tree species, leading to a diversity of patterns that is still poorly known and understood. The work in this study aims to advance knowledge in this area, focusing specifically on herbarium scans, as herbariums offer the promise of tracking phenology over long periods of time. However, such a study requires a large number of shoots to be able to draw statistically relevant conclusions. We propose to investigate the extent to which the use of deep learning can help detect and type-classify these relatively rare vegetative structures in herbarium collections. Our results demonstrate the relevance of using herbarium data in vegetative phenology research as well as the potential of deep learning approaches for growing shoot detection.
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Affiliation(s)
- Hervé Goëau
- Botany and Modeling of Plant Architecture and Vegetation (AMAP), French Agricultural Research Centre for International Development (CIRAD), French National Centre for Scientific Research (CNRS), French National Institute for Agriculture, Food and Environment (INRAE), Research Institute for Development (IRD), University of Montpellier, 34398 Montpellier, France; (P.H.); (P.B.)
| | - Titouan Lorieul
- ZENITH Team, Laboratory of Informatics, Robotics and Microelectronics-Joint Research Unit, Institut National de Recherche en Informatique et en Automatique (INRIA) Sophia-Antipolis, CEDEX 5, 34095 Montpellier, France; (T.L.); (A.J.)
| | - Patrick Heuret
- Botany and Modeling of Plant Architecture and Vegetation (AMAP), French Agricultural Research Centre for International Development (CIRAD), French National Centre for Scientific Research (CNRS), French National Institute for Agriculture, Food and Environment (INRAE), Research Institute for Development (IRD), University of Montpellier, 34398 Montpellier, France; (P.H.); (P.B.)
| | - Alexis Joly
- ZENITH Team, Laboratory of Informatics, Robotics and Microelectronics-Joint Research Unit, Institut National de Recherche en Informatique et en Automatique (INRIA) Sophia-Antipolis, CEDEX 5, 34095 Montpellier, France; (T.L.); (A.J.)
| | - Pierre Bonnet
- Botany and Modeling of Plant Architecture and Vegetation (AMAP), French Agricultural Research Centre for International Development (CIRAD), French National Centre for Scientific Research (CNRS), French National Institute for Agriculture, Food and Environment (INRAE), Research Institute for Development (IRD), University of Montpellier, 34398 Montpellier, France; (P.H.); (P.B.)
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Weeds harbor an impressive diversity of fungi, which offers possibilities for biocontrol. Appl Environ Microbiol 2022; 88:e0217721. [PMID: 35080907 DOI: 10.1128/aem.02177-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The use of herbicides for weed control is very common, but some of them represent a threat to human health, are environmentally detrimental and stimulate herbicide resistance. Therefore, using microorganisms as natural herbicides appears as a promising alternative. The mycoflorae colonizing different species of symptomatic and asymptomatic weeds were compared to characterize the possible mycoherbicidal candidates associated with symptomatic weeds. A collection of 475 symptomatic and asymptomatic plants belonging to 23 weed species was established. A metabarcoding approach based on amplification of the internal transcribed spacer (ITS) region combined with high-throughput amplicon sequencing revealed the diversity of fungal communities hosted by these weeds: 542 fungal genera were identified. The variability of the composition of fungal communities revealed a dispersed distribution of taxa governed neither by geographical location nor by the botanical species, suggesting a common core displaying non-specific interactions with host plants. Beyond this core, specific taxa were more particularly associated with symptomatic plants. Some of these, such as Alternaria, Blumeria, Cercospora, Puccinia, are known pathogens, while others such as Sphaerellopsis, Vishniacozyma and Filobasidium are not, at least on crops, and constitute new tracks to be followed in the search for mycoherbicidal candidates. IMPORTANCE: This approach is original because the diversity of weed-colonizing fungi has rarely been studied before. Furthermore, targeting both the ITS1 and ITS2 regions to characterize the fungal communities i) highlighted the complementarity of these two regions, ii) revealed a great diversity of weed-colonizing fungi, and iii) allowed for the identification of potential mycoherbicides, among which unexpected genera.
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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] [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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8
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Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa. J Fungi (Basel) 2021; 7:jof7090703. [PMID: 34575741 PMCID: PMC8467358 DOI: 10.3390/jof7090703] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 01/08/2023] Open
Abstract
Culture techniques are vital in both traditional and modern fungal taxonomy. Establishing sexual-asexual links and synanamorphs, extracting DNA and secondary metabolites are mainly based on cultures. However, it is widely accepted that a large number of species are not sporulating in nature while others cannot be cultured. Recent ecological studies based on culture-independent methods revealed these unculturable taxa, i.e., dark taxa. Recent fungal diversity estimation studies suggested that environmental sequencing plays a vital role in discovering missing species. However, Sanger sequencing is still the main approach in determining DNA sequences in culturable species. In this paper, we summarize culture-based and culture-independent methods in the study of ascomycetous taxa. High-throughput sequencing of leaf endophytes, leaf litter fungi and fungi in aquatic environments is important to determine dark taxa. Nevertheless, currently, naming dark taxa is not recognized by the ICN, thus provisional naming of them is essential as suggested by several studies.
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Oita S, Carey J, Kline I, Ibáñez A, Yang N, Hom EFY, Carbone I, U'Ren JM, Arnold AE. Methodological Approaches Frame Insights into Endophyte Richness and Community Composition. MICROBIAL ECOLOGY 2021; 82:21-34. [PMID: 33410938 DOI: 10.1007/s00248-020-01654-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Isolating microbes is vital to study microbiomes, but insights into microbial diversity and ecology can be constrained by recalcitrant or unculturable strains. Culture-free methods (e.g., next-generation sequencing, NGS) have become popular in part because they detect greater richness than culturing alone. Both approaches are used widely to characterize microfungi within healthy leaves (foliar endophytes), but methodological differences among studies can constrain large-scale insights into endophyte ecology. We examined endophytes in a temperate plant community to quantify how certain methodological factors, such as the choice of cultivation media for culturing and storage period after leaf collection, affect inferences regarding endophyte communities; how such effects vary among plant taxa; and how complementary culturing and NGS can be when subsets of the same plant tissue are used for each. We found that endophyte richness and composition from culturing were consistent across five media types. Insights from culturing and NGS were largely robust to differences in storage period (1, 5, and 10 days). Although endophyte richness, composition, and taxonomic diversity identified via culturing vs. NGS differed markedly, both methods revealed host-structured communities. Studies differing only in cultivation media or storage period thus can be compared to estimate endophyte richness, composition, and turnover at scales larger than those of individual studies alone. Our data show that it is likely more important to sample more host species, rather than sampling fewer species more intensively, to quantify endophyte diversity in given locations, with the richest insights into endophyte ecology emerging when culturing and NGS are paired.
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Affiliation(s)
- Shuzo Oita
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Jamison Carey
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Ian Kline
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Alicia Ibáñez
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Nathaniel Yang
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Erik F Y Hom
- Department of Biology, Center for Biodiversity & Conservation Research, University of Mississippi, University, MS, 38677, USA
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jana M U'Ren
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, 85721, USA
| | - A Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.
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10
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Trivellone V, Wei W, Filippin L, Dietrich CH. Screening potential insect vectors in a museum biorepository reveals undiscovered diversity of plant pathogens in natural areas. Ecol Evol 2021; 11:6493-6503. [PMID: 34141234 PMCID: PMC8207438 DOI: 10.1002/ece3.7502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/03/2022] Open
Abstract
Phytoplasmas (Mollicutes, Acholeplasmataceae), vector-borne obligate bacterial plant parasites, infect nearly 1,000 plant species and unknown numbers of insects, mainly leafhoppers (Hemiptera, Deltocephalinae), which play a key role in transmission and epidemiology. Although the plant-phytoplasma-insect association has been evolving for >300 million years, nearly all known phytoplasmas have been discovered as a result of the damage inflicted by phytoplasma diseases on crops. Few efforts have been made to study phytoplasmas occurring in noneconomically important plants in natural habitats. In this study, a subsample of leafhopper specimens preserved in a large museum biorepository was analyzed to unveil potential new associations. PCR screening for phytoplasmas performed on 227 phloem-feeding leafhoppers collected worldwide from natural habitats revealed the presence of 6 different previously unknown phytoplasma strains. This indicates that museum collections of herbivorous insects represent a rich and largely untapped resource for discovery of new plant pathogens, that natural areas worldwide harbor a diverse but largely undiscovered diversity of phytoplasmas and potential insect vectors, and that independent epidemiological cycles occur in such habitats, posing a potential threat of disease spillover into agricultural systems. Larger-scale future investigations will contribute to a better understanding of phytoplasma genetic diversity, insect host range, and insect-borne phytoplasma transmission and provide an early warning for the emergence of new phytoplasma diseases across global agroecosystems.
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Affiliation(s)
- Valeria Trivellone
- Illinois Natural History SurveyPrairie Research InstituteUniversity of IllinoisChampaignILUSA
| | - Wei Wei
- Molecular Plant Pathology LaboratoryBeltsville Agricultural Research CenterAgricultural Research ServiceUnited States Department of AgricultureBeltsvilleMDUSA
| | - Luisa Filippin
- CREA–VECouncil for Agricultural Research and EconomicsResearch Centre for Viticulture and EnologyConegliano, TrevisoItaly
| | - Christopher H. Dietrich
- Illinois Natural History SurveyPrairie Research InstituteUniversity of IllinoisChampaignILUSA
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Albani Rocchetti G, Armstrong CG, Abeli T, Orsenigo S, Jasper C, Joly S, Bruneau A, Zytaruk M, Vamosi JC. Reversing extinction trends: new uses of (old) herbarium specimens to accelerate conservation action on threatened species. THE NEW PHYTOLOGIST 2021; 230:433-450. [PMID: 33280123 DOI: 10.1111/nph.17133] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/22/2020] [Indexed: 05/29/2023]
Abstract
Although often not collected specifically for the purposes of conservation, herbarium specimens offer sufficient information to reconstruct parameters that are needed to designate a species as 'at-risk' of extinction. While such designations should prompt quick and efficient legal action towards species recovery, such action often lags far behind and is mired in bureaucratic procedure. The increase in online digitization of natural history collections has now led to a surge in the number new studies on the uses of machine learning. These repositories of species occurrences are now equipped with advances that allow for the identification of rare species. The increase in attention devoted to estimating the scope and severity of the threats that lead to the decline of such species will increase our ability to mitigate these threats and reverse the declines, overcoming a current barrier to the recovery of many threatened plant species. Thus far, collected specimens have been used to fill gaps in systematics, range extent, and past genetic diversity. We find that they also offer material with which it is possible to foster species recovery, ecosystem restoration, and de-extinction, and these elements should be used in conjunction with machine learning and citizen science initiatives to mobilize as large a force as possible to counter current extinction trends.
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Affiliation(s)
| | | | - Thomas Abeli
- Department of Science, University Roma Tre, Viale G. Marconi 446, Roma, 00154, Italy
| | - Simone Orsenigo
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, 27100, Italy
| | - Caroline Jasper
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Simon Joly
- Montreal Botanical Garden, Montréal, QC, H1X 2B2, Canada
- Département de Sciences Biologiques and Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Anne Bruneau
- Département de Sciences Biologiques and Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Maria Zytaruk
- Department of English, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Jana C Vamosi
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
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12
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Hill R, Llewellyn T, Downes E, Oddy J, MacIntosh C, Kallow S, Panis B, Dickie JB, Gaya E. Seed Banks as Incidental Fungi Banks: Fungal Endophyte Diversity in Stored Seeds of Banana Wild Relatives. Front Microbiol 2021; 12:643731. [PMID: 33841366 PMCID: PMC8024981 DOI: 10.3389/fmicb.2021.643731] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/19/2021] [Indexed: 01/19/2023] Open
Abstract
Seed banks were first established to conserve crop genetic diversity, but seed banking has more recently been extended to wild plants, particularly crop wild relatives (CWRs) (e.g., by the Millennium Seed Bank (MSB), Royal Botanic Gardens Kew). CWRs have been recognised as potential reservoirs of beneficial traits for our domesticated crops, and with mounting evidence of the importance of the microbiome to organismal health, it follows that the microbial communities of wild relatives could also be a valuable resource for crop resilience to environmental and pathogenic threats. Endophytic fungi reside asymptomatically inside all plant tissues and have been found to confer advantages to their plant host. Preserving the natural microbial diversity of plants could therefore represent an important secondary conservation role of seed banks. At the same time, species that are reported as endophytes may also be latent pathogens. We explored the potential of the MSB as an incidental fungal endophyte bank by assessing diversity of fungi inside stored seeds. Using banana CWRs in the genus Musa as a case-study, we sequenced an extended ITS-LSU fragment in order to delimit operational taxonomic units (OTUs) and used a similarity and phylogenetics approach for classification. Fungi were successfully detected inside just under one third of the seeds, with a few genera accounting for most of the OTUs-primarily Lasiodiplodia, Fusarium, and Aspergillus-while a large variety of rare OTUs from across the Ascomycota were isolated only once. Fusarium species were notably abundant-of significance in light of Fusarium wilt, a disease threatening global banana crops-and so were targeted for additional sequencing with the marker EF1α in order to delimit species and place them in a phylogeny of the genus. Endophyte community composition, diversity and abundance was significantly different across habitats, and we explored the relationship between community differences and seed germination/viability. Our results show that there is a previously neglected invisible fungal dimension to seed banking that could well have implications for the seed collection and storage procedures, and that collections such as the MSB are indeed a novel source of potentially useful fungal strains.
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Affiliation(s)
- Rowena Hill
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Biological and Chemical Sciences, Faculty of Science and Engineering, Queen Mary University of London, London, United Kingdom
| | - Theo Llewellyn
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Elizabeth Downes
- Department for Environment, Food and Rural Affairs, London, United Kingdom
| | - Joseph Oddy
- Department of Plant Science, Rothamsted Research, Harpenden, United Kingdom
| | - Catriona MacIntosh
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Simon Kallow
- Collections Department, Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, United Kingdom
- Division of Crop Biotechnics, Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven, Leuven, Belgium
| | - Bart Panis
- Bioversity International, Montpellier, France
| | - John B. Dickie
- Collections Department, Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, United Kingdom
| | - Ester Gaya
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
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13
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Oita S, Ibáñez A, Lutzoni F, Miadlikowska J, Geml J, Lewis LA, Hom EFY, Carbone I, U'Ren JM, Arnold AE. Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale. Commun Biol 2021; 4:313. [PMID: 33750915 PMCID: PMC7943826 DOI: 10.1038/s42003-021-01826-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/09/2021] [Indexed: 01/31/2023] Open
Abstract
Understanding how species-rich communities persist is a foundational question in ecology. In tropical forests, tree diversity is structured by edaphic factors, climate, and biotic interactions, with seasonality playing an essential role at landscape scales: wetter and less seasonal forests typically harbor higher tree diversity than more seasonal forests. We posited that the abiotic factors shaping tree diversity extend to hyperdiverse symbionts in leaves-fungal endophytes-that influence plant health, function, and resilience to stress. Through surveys in forests across Panama that considered climate, seasonality, and covarying biotic factors, we demonstrate that endophyte richness varies negatively with temperature seasonality. Endophyte community structure and taxonomic composition reflect both temperature seasonality and climate (mean annual temperature and precipitation). Overall our findings highlight the vital role of climate-related factors in shaping the hyperdiversity of these important and little-known symbionts of the trees that, in turn, form the foundations of tropical forest biodiversity.
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Affiliation(s)
- Shuzo Oita
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | | | | | | | - József Geml
- MTA-EKE Lendület Environmental Microbiome Research Group, Eszterházy Károly University, Eger, Hungary
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Erik F Y Hom
- Department of Biology, Center for Biodiversity and Conservation Research, University of Mississippi, University, MS, USA
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Jana M U'Ren
- Department of Biosystems Engineering and BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - A Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
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14
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Choudhary P, Singh BN, Chakdar H, Saxena AK. DNA barcoding of phytopathogens for disease diagnostics and bio-surveillance. World J Microbiol Biotechnol 2021; 37:54. [PMID: 33604719 DOI: 10.1007/s11274-021-03019-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
DNA barcoding has proven to be a versatile tool for plant disease diagnostics in the genomics era. As the mass parallel and next generation sequencing techniques gained importance, the role of specific barcodes came under immense scrutiny. Identification and accurate classification of phytopathogens need a universal approach which has been the main application area of the concept of barcode. The present review entails a detailed description of the present status of barcode application in plant disease diagnostics. A case study on the application of Internal Transcribed Spacer (ITS) as barcode for Aspergillus and Fusarium spp. sheds light on the requirement of other potential candidates as barcodes for accurate identification. The challenges faced while barcoding novel pathogens have also been discussed with a comprehensive outline of integrating more recent technologies like meta-barcoding and genome skimming for detecting plant pathogens.
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Affiliation(s)
- Prassan Choudhary
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India
| | - Bansh Narayan Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India.
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India
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15
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Rudgers JA, Afkhami ME, Bell-Dereske L, Chung YA, Crawford KM, Kivlin SN, Mann MA, Nuñez MA. Climate Disruption of Plant-Microbe Interactions. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-090819] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Interactions between plants and microbes have important influences on evolutionary processes, population dynamics, community structure, and ecosystem function. We review the literature to document how climate change may disrupt these ecological interactions and develop a conceptual framework to integrate the pathways of plant-microbe responses to climate over different scales in space and time. We then create a blueprint to aid generalization that categorizes climate effects into changes in the context dependency of plant-microbe pairs, temporal mismatches and altered feedbacks over time, or spatial mismatches that accompany species range shifts. We pair a new graphical model of how plant-microbe interactions influence resistance to climate change with a statistical approach to predictthe consequences of increasing variability in climate. Finally, we suggest pathways through which plant-microbe interactions can affect resilience during recovery from climate disruption. Throughout, we take a forward-looking perspective, highlighting knowledge gaps and directions for future research.
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Affiliation(s)
- Jennifer A. Rudgers
- Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA;,
| | - Michelle E. Afkhami
- Department of Biology, University of Miami, Coral Gables, Florida 33157, USA
| | - Lukas Bell-Dereske
- Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan 49060, USA
| | - Y. Anny Chung
- Departments of Plant Biology and Plant Pathology, University of Georgia, Athens, Georgia 30602, USA
| | - Kerri M. Crawford
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
| | - Stephanie N. Kivlin
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Michael A. Mann
- Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA;,
| | - Martin A. Nuñez
- Grupo de Ecología de Invasiones, Instituto de Investigaciones en Biodiversidad y Medioambiente, CONICET/Universidad Nacional del Comahue, Bariloche 8400, Argentina
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16
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Harrison JG, Griffin EA. The diversity and distribution of endophytes across biomes, plant phylogeny and host tissues: how far have we come and where do we go from here? Environ Microbiol 2020. [PMID: 32115818 DOI: 10.1111/1462-2929.14968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
The interiors of plants are colonized by diverse microorganisms that are referred to as endophytes. Endophytes have received much attention over the past few decades, yet many questions remain unanswered regarding patterns in their biodiversity at local to global scales. To characterize research effort to date, we synthesized results from ~600 published studies. Our survey revealed a global research interest and highlighted several gaps in knowledge. For instance, of the 17 biomes encompassed by our survey, 7 were understudied and together composed only 7% of the studies that we considered. We found that fungal endophyte diversity has been characterized in at least one host from 30% of embryophyte families, while bacterial endophytes have been surveyed in hosts from only 10.5% of families. We complimented our survey with a vote counting procedure to determine endophyte richness patterns among plant tissue types. We found that variation in endophyte assemblages in above-ground tissues varied with host growth habit. Stems were the richest tissue in woody plants, whereas roots were the richest tissue in graminoids. For forbs, we found no consistent differences in relative tissue richness among studies. We propose future directions to fill the gaps in knowledge we uncovered and inspire further research.
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Affiliation(s)
- Joshua G Harrison
- Department of Botany, University of Wyoming, 3165, 1000 E. University Ave., Laramie, WY, 82071, USA
| | - Eric A Griffin
- Department of Biology, New Mexico Highlands University, Las Vegas, NM, 87701, USA
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17
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Harrison JG, Griffin EA. The diversity and distribution of endophytes across biomes, plant phylogeny and host tissues: how far have we come and where do we go from here? Environ Microbiol 2020; 22:2107-2123. [PMID: 32115818 DOI: 10.1111/1462-2920.14968] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/24/2020] [Accepted: 02/27/2020] [Indexed: 12/18/2022]
Abstract
The interiors of plants are colonized by diverse microorganisms that are referred to as endophytes. Endophytes have received much attention over the past few decades, yet many questions remain unanswered regarding patterns in their biodiversity at local to global scales. To characterize research effort to date, we synthesized results from ~600 published studies. Our survey revealed a global research interest and highlighted several gaps in knowledge. For instance, of the 17 biomes encompassed by our survey, 7 were understudied and together composed only 7% of the studies that we considered. We found that fungal endophyte diversity has been characterized in at least one host from 30% of embryophyte families, while bacterial endophytes have been surveyed in hosts from only 10.5% of families. We complimented our survey with a vote counting procedure to determine endophyte richness patterns among plant tissue types. We found that variation in endophyte assemblages in above-ground tissues varied with host growth habit. Stems were the richest tissue in woody plants, whereas roots were the richest tissue in graminoids. For forbs, we found no consistent differences in relative tissue richness among studies. We propose future directions to fill the gaps in knowledge we uncovered and inspire further research.
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Affiliation(s)
- Joshua G Harrison
- Department of Botany, University of Wyoming, 3165, 1000 E. University Ave., Laramie, WY, 82071, USA
| | - Eric A Griffin
- Department of Biology, New Mexico Highlands University, Las Vegas, NM, 87701, USA
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18
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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] [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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19
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T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees. Microbiol Resour Announc 2019; 8:8/29/e00328-19. [PMID: 31320426 PMCID: PMC6639605 DOI: 10.1128/mra.00328-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata. The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata.
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20
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Meineke EK, Davies TJ, Daru BH, Davis CC. Biological collections for understanding biodiversity in the Anthropocene. Philos Trans R Soc Lond B Biol Sci 2018; 374:rstb.2017.0386. [PMID: 30455204 DOI: 10.1098/rstb.2017.0386] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2018] [Indexed: 12/16/2022] Open
Abstract
Global change has become a central focus of modern biology. Yet, our knowledge of how anthropogenic drivers affect biodiversity and natural resources is limited by a lack of biological data spanning the Anthropocene. We propose that the hundreds of millions of plant, fungal and animal specimens deposited in natural history museums have the potential to transform the field of global change biology. We suggest that museum specimens are underused, particularly in ecological studies, given their capacity to reveal patterns that are not observable from other data sources. Increasingly, museum specimens are becoming mobilized online, providing unparalleled access to physiological, ecological and evolutionary data spanning decades and sometimes centuries. Here, we describe the diversity of collections data archived in museums and provide an overview of the diverse uses and applications of these data as discussed in the accompanying collection of papers within this theme issue. As these unparalleled resources are under threat owing to budget cuts and other institutional pressures, we aim to shed light on the unique discoveries that are possible in museums and, thus, the singular value of natural history collections in a period of rapid change.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
- Emily K Meineke
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - T Jonathan Davies
- Department of Ecology and Evolutionary Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4.,African Centre for DNA Barcoding, University of Johannesburg, Johannesburg 2006, South Africa
| | - Barnabas H Daru
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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