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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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Estimating and Monitoring Land Surface Phenology in Rangelands: A Review of Progress and Challenges. REMOTE SENSING 2021. [DOI: 10.3390/rs13112060] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Land surface phenology (LSP) has been extensively explored from global archives of satellite observations to track and monitor the seasonality of rangeland ecosystems in response to climate change. Long term monitoring of LSP provides large potential for the evaluation of interactions and feedbacks between climate and vegetation. With a special focus on the rangeland ecosystems, the paper reviews the progress, challenges and emerging opportunities in LSP while identifying possible gaps that could be explored in future. Specifically, the paper traces the evolution of satellite sensors and interrogates their properties as well as the associated indices and algorithms in estimating and monitoring LSP in productive rangelands. Findings from the literature revealed that the spectral characteristics of the early satellite sensors such as Landsat, AVHRR and MODIS played a critical role in the development of spectral vegetation indices that have been widely used in LSP applications. The normalized difference vegetation index (NDVI) pioneered LSP investigations, and most other spectral vegetation indices were primarily developed to address the weaknesses and shortcomings of the NDVI. New indices continue to be developed based on recent sensors such as Sentinel-2 that are characterized by unique spectral signatures and fine spatial resolutions, and their successful usage is catalyzed with the development of cutting-edge algorithms for modeling the LSP profiles. In this regard, the paper has documented several LSP algorithms that are designed to provide data smoothing, gap filling and LSP metrics retrieval methods in a single environment. In the future, the development of machine learning algorithms that can effectively model and characterize the phenological cycles of vegetation would help to unlock the value of LSP information in the rangeland monitoring and management process. Precisely, deep learning presents an opportunity to further develop robust software packages such as the decomposition and analysis of time series (DATimeS) with the abundance of data processing tools and techniques that can be used to better characterize the phenological cycles of vegetation in rangeland ecosystems.
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Rimlinger A, Raharimalala N, Letort V, Rakotomalala JJ, Crouzillat D, Guyot R, Hamon P, Sabatier S. Phenotypic diversity assessment within a major ex situ collection of wild endemic coffees in Madagascar. ANNALS OF BOTANY 2020; 126:849-863. [PMID: 32303759 PMCID: PMC7539352 DOI: 10.1093/aob/mcaa073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND AIMS Like other clades, the Coffea genus is highly diversified on the island of Madagascar. The 66 endemic species have colonized various environments and consequently exhibit a wide diversity of morphological, functional and phenological features and reproductive strategies. The trends of interspecific trait variation, which stems from interactions between genetically defined species and their environment, still needed to be addressed for Malagasy coffee trees. METHODS Data acquisition was done in the most comprehensive ex situ collection of Madagascan wild Coffea. The structure of endemic wild coffees maintained in an ex situ collection was explored in terms of morphological, phenological and functional traits. The environmental (natural habitat) effect was assessed on traits in species from distinct natural habitats. Phylogenetic signal (Pagel's λ, Blomberg's K) was used to quantify trait proximities among species according to their phylogenetic relatedness. KEY RESULTS Despite the lack of environmental difference in the ex situ collection, widely diverging phenotypes were observed. Phylogenetic signal was found to vary greatly across and even within trait categories. The highest values were exhibited by the ratio of internode mass to leaf mass, the length of the maturation phase and leaf dry matter content (ratio of dry leaf mass to fresh leaf mass). By contrast, traits weakly linked to phylogeny were either constrained by the original natural environment (leaf size) or under selective pressures (phenological traits). CONCLUSIONS This study gives insight into complex patterns of trait variability found in an ex situ collection, and underlines the opportunities offered by living ex situ collections for research characterizing phenotypic variation.
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Affiliation(s)
- Aurore Rimlinger
- AMAP Univ Montpellier CIRAD, CNRS, INRAE, IRD, Montpellier, France
| | | | - Véronique Letort
- Laboratoire de Mathématiques et Informatique pour la Complexité et les Systèmes, CentraleSupélec, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | | | - Romain Guyot
- DIADE, Univ Montpellier IRD CIRAD, Montpellier, France
| | - Perla Hamon
- DIADE, Univ Montpellier IRD CIRAD, Montpellier, France
| | - Sylvie Sabatier
- AMAP Univ Montpellier CIRAD, CNRS, INRAE, IRD, Montpellier, France
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Latitudinal shift in the timing of flowering of tree species across tropical Africa: insights from field observations and herbarium collections. JOURNAL OF TROPICAL ECOLOGY 2020. [DOI: 10.1017/s0266467420000103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractTemporal and spatial patterns in flowering phenology were assessed for eight tropical African tree species. Specifically, the frequency and seasonality of flowering at seven sites in central Africa were determined using field data, graphical analysis and circular statistics. Additionally, spatial variation in the timing of flowering across species range was investigated using herbarium data, analysing the relative influence of latitude, longitude and timing of the dry season with a Bayesian circular generalized linear model. Annual flowering was found for 20 out of the 25 populations studied. For 21 populations located at the north of the climatic hinge flowering was occurring during the dry season. The analysis of herbarium collections revealed a significant shift in the timing of flowering with latitude for E. suaveolens, and with the timing of the dry season for M. excelsa (and to a lesser extent L. alata), with the coexistence of two flowering peaks near the equator where the distribution of monthly rainfall is bimodal. For the other species, none of latitude, longitude or timing of the dry season had an effect on the timing of flowering. Our study highlights the need to identify the drivers of the flowering phenology of economically important African tree species.
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Pearson KD, Nelson G, Aronson MFJ, Bonnet P, Brenskelle L, Davis CC, Denny EG, Ellwood ER, Goëau H, Heberling JM, Joly A, Lorieul T, Mazer SJ, Meineke EK, Stucky BJ, Sweeney P, White AE, Soltis PS. Machine Learning Using Digitized Herbarium Specimens to Advance Phenological Research. Bioscience 2020; 70:610-620. [PMID: 32665738 PMCID: PMC7340542 DOI: 10.1093/biosci/biaa044] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Machine learning (ML) has great potential to drive scientific discovery by harvesting data from images of herbarium specimens—preserved plant material curated in natural history collections—but ML techniques have only recently been applied to this rich resource. ML has particularly strong prospects for the study of plant phenological events such as growth and reproduction. As a major indicator of climate change, driver of ecological processes, and critical determinant of plant fitness, plant phenology is an important frontier for the application of ML techniques for science and society. In the present article, we describe a generalized, modular ML workflow for extracting phenological data from images of herbarium specimens, and we discuss the advantages, limitations, and potential future improvements of this workflow. Strategic research and investment in specimen-based ML methods, along with the aggregation of herbarium specimen data, may give rise to a better understanding of life on Earth.
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Affiliation(s)
- Katelin D Pearson
- California Polytechnic State University, San Luis Obispo, California
| | - Gil Nelson
- Florida Museum of Natural History, Gainesville, Florida
| | - Myla F J Aronson
- Department of Ecology, Evolution, and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, New Jersey
| | - Pierre Bonnet
- AMAP, the University of Montpellier and with The French Agricultural Research Centre for International Development, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut de Recherche pour le Développement, Botanique et Modélisation de l'Architecture des Plantes et des végétations in Montpellier, France
| | - Laura Brenskelle
- Florida Museum of Natural History, the University of Florida, Gainesville, Florida
| | | | - Ellen G Denny
- US National Phenology Network and with the University of Arizona, Tucson, Arizona
| | - Elizabeth R Ellwood
- Natural History Museum of Los Angeles County, La Brea Tar Pits and Museum, Los Angeles, California
| | - Hervé Goëau
- AMAP, the University of Montpellier and with The French Agricultural Research Centre for International Development, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut de Recherche pour le Développement, Botanique et Modélisation de l'Architecture des Plantes et des végétations in Montpellier, France
| | | | - Alexis Joly
- Inria Sophia-Antipolis, Zenith team, Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), Montpellier, France
| | - Titouan Lorieul
- Inria Sophia-Antipolis, Zenith team, Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), Montpellier, France
| | - Susan J Mazer
- Department of Ecology, Evolution, and Marine Biology, the University of California, Santa Barbara, Santa Barbara, California
| | - Emily K Meineke
- Department of Entomology and Nematology, the University of California, Davis, Davis, California
| | - Brian J Stucky
- Florida Museum of Natural History, the University of Florida, Gainesville, Florida
| | - Patrick Sweeney
- Yale Peabody Museum of Natural History, New Haven, Connecticut
| | - Alexander E White
- Department of Botany and the Data Science Lab, the Smithsonian Institution, Washington, DC
| | - Pamela S Soltis
- Florida Museum of Natural History and with the University of Florida Biodiversity Institute, the University of Florida, Gainesville, Florida
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Varilla González JD, Ruíz Vega R. VALOR TAXONÓMICO DE NUEVOS CARACTERES ANATÓMICOS DE LA LÁMINA FOLIAR DE TRES ESPECIES DE Cecropia (URTICACEAE: CECROPIAE) EN CÓRDOBA, COLOMBIA. ACTA BIOLÓGICA COLOMBIANA 2020. [DOI: 10.15446/abc.v25n2.79291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Se describen las características anatómicas de la epidermis foliar y mesófilo de las especies Cecropia longipes, C. membranacea y C. peltata. El material vegetal fue recolectado en Córdoba- Colombia. Se realizaron disociaciones epidérmicas y cortes transversales de la lámina media mediante técnicas histológicas convencionales. Los caracteres evaluados: forma y el contorno de las células epidérmicas, indumento aracnoideo abaxial, organización de las células de la base de los tricomas, idioblastos epidérmicos, tipo y distribución de los estomas, mostraron diferencias que permiten separar a C. membranacea de las otras especies. Las especies C. longipes y C. peltata son similares en la anatomía de la lámina foliar, sin embargo, es posible distinguirlas teniendo en cuenta la epidermis pluriestratificada y proporción del parénquima clorofiliano, aunque estas características no se presentaron en todas las muestras. Los caracteres evaluados son útiles desde el punto de vista taxonómico y pueden contribuir a la identificación de las especies de la tribu Cecropieae.
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McDonough MacKenzie C, Gallinat AS, Zipf L. Low-cost observations and experiments return a high value in plant phenology research. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11338. [PMID: 32351799 PMCID: PMC7186900 DOI: 10.1002/aps3.11338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 12/03/2019] [Indexed: 05/18/2023]
Abstract
Plant ecologists in the Anthropocene are tasked with documenting, interpreting, and predicting how plants respond to environmental change. Phenology, the timing of seasonal biological events including leaf-out, flowering, fruiting, and leaf senescence, is among the most visible and oft-recorded facets of plant ecology. Climate-driven shifts in plant phenology can alter reproductive success, interspecific competition, and trophic interactions. Low-cost phenology research, including observational records and experimental manipulations, is fundamental to our understanding of both the mechanisms and effects of phenological change in plant populations, species, and communities. Traditions of local-scale botanical phenology observations and data leveraged from written records and natural history collections provide the historical context for recent observations of changing phenologies. New technology facilitates expanding the spatial, taxonomic, and human interest in this research by combining contemporary field observations by researchers and open access community science (e.g., USA National Phenology Network) and available climate data. Established experimental techniques, such as twig cutting and common garden experiments, are low-cost methods for studying the mechanisms and drivers of plant phenology, enabling researchers to observe phenological responses under novel environmental conditions. We discuss the strengths, limitations, potential hidden costs (i.e., volunteer and student labor), and promise of each of these methods for addressing emerging questions in plant phenology research. Applied thoughtfully, economically, and creatively, many low-cost approaches offer novel opportunities to fill gaps in our geographic, taxonomic, and mechanistic understanding of plant phenology worldwide.
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Affiliation(s)
| | - Amanda S. Gallinat
- Department of BiologyUtah State UniversityLoganUtah84322USA
- Ecology CenterUtah State UniversityLoganUtah84322USA
| | - Lucy Zipf
- Biology DepartmentBoston University5 Cummington MallBostonMassachusetts02215USA
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Garcés-Restrepo MF, Peery MZ, Pauli JN. The demography of a resource specialist in the tropics: Cecropia trees and the fitness of three-toed sloths. Proc Biol Sci 2020; 286:20182206. [PMID: 30963880 DOI: 10.1098/rspb.2018.2206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Resource specialists persist in a narrow range of resources. Consequently, the abundance of key resources should drive vital rates, individual fitness, and population viability. While Neotropical forests feature both high levels of biodiversity and numbers of specialist species, no studies have directly evaluated how the variation of key resources affects the fitness of a tropical specialist. Here, we quantified the effect of key tree species density and forest cover on the fitness of three-toed sloths ( Bradypus variegatus), an arboreal folivore strongly associated with Cecropia trees in Costa Rica, using a multi-year demographic, genetic, and space-use dataset. We found that the density of Cecropia trees was strongly and positively related to both adult survival and reproductive output. A matrix model parametrized with Cecropia-demography relationships suggested positive growth of sloth populations, even at low densities of Cecropia (0.7 trees ha-1). Our study shows the first direct link between the density of a key resource to demographic consequences of a tropical specialist, underscoring the sensitivity of tropical specialists to the loss of a single key resource, but also point to targeted conservation measures to increase that resource. Finally, our study reveals that previously disturbed and regenerating environments can support viable populations of tropical specialists.
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Affiliation(s)
- Mario F Garcés-Restrepo
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison , 1630 Linden Drive, Madison, WI 53706 , USA
| | - M Zachariah Peery
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison , 1630 Linden Drive, Madison, WI 53706 , USA
| | - Jonathan N Pauli
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison , 1630 Linden Drive, Madison, WI 53706 , USA
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Mapping Periodic Patterns of Global Vegetation Based on Spectral Analysis of NDVI Time Series. REMOTE SENSING 2019. [DOI: 10.3390/rs11212497] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Vegetation seasonality assessment through remote sensing data is crucial to understand ecosystem responses to climatic variations and human activities at large-scales. Whereas the study of the timing of phenological events showed significant advances, their recurrence patterns at different periodicities has not been widely study, especially at global scale. In this work, we describe vegetation oscillations by a novel quantitative approach based on the spectral analysis of Normalized Difference Vegetation Index (NDVI) time series. A new set of global periodicity indicators permitted to identify different seasonal patterns regarding the intra-annual cycles (the number, amplitude, and stability) and to evaluate the existence of pluri-annual cycles, even in those regions with noisy or low NDVI. Most of vegetated land surface (93.18%) showed one intra-annual cycle whereas double and triple cycles were found in 5.58% of the land surface, mainly in tropical and arid regions along with agricultural areas. In only 1.24% of the pixels, the seasonality was not statistically significant. The highest values of amplitude and stability were found at high latitudes in the northern hemisphere whereas lowest values corresponded to tropical and arid regions, with the latter showing more pluri-annual cycles. The indicator maps compiled in this work provide highly relevant and practical information to advance in assessing global vegetation dynamics in the context of global change.
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Pearson KD. Spring- and fall-flowering species show diverging phenological responses to climate in the Southeast USA. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2019; 63:481-492. [PMID: 30734127 DOI: 10.1007/s00484-019-01679-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/09/2019] [Accepted: 01/19/2019] [Indexed: 06/09/2023]
Abstract
Plant phenological shifts (e.g., earlier flowering dates) are known consequences of climate change that may alter ecosystem functioning, productivity, and ecological interactions across trophic levels. Temperate, subalpine, and alpine regions have largely experienced advancement of spring phenology with climate warming, but the effects of climate change in warm, humid regions and on autumn phenology are less well understood. In this study, nearly 10,000 digitized herbarium specimen records were used to examine the phenological sensitivities of fall- and spring-flowering asteraceous plants to temperature and precipitation in the US Southeastern Coastal Plain. Climate data reveal warming trends in this already warm climate, and spring- and fall-flowering species responded differently to this change. Spring-flowering species flowered earlier at a rate of 1.8-2.3 days per 1 °C increase in spring temperature, showing remarkable congruence with studies of northern temperate species. Fall-flowering species flowered slightly earlier with warmer spring temperatures, but flowering was significantly later with warmer summer temperatures at a rate of 0.8-1.2 days per 1 °C. Spring-flowering species exhibited slightly later flowering times with increased spring precipitation. Fall phenology was less clearly influenced by precipitation. These results suggest that even warm, humid regions may experience phenological shifts and thus be susceptible to potentially detrimental effects such as plant-pollinator asynchrony.
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Affiliation(s)
- Katelin D Pearson
- Department of Biological Sciences, Florida State University, 319 Stadium Dr, Tallahassee, FL, USA.
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Lorieul T, Pearson KD, Ellwood ER, Goëau H, Molino J, Sweeney PW, Yost JM, Sachs J, Mata‐Montero E, Nelson G, Soltis PS, Bonnet P, Joly A. Toward a large-scale and deep phenological stage annotation of herbarium specimens: Case studies from temperate, tropical, and equatorial floras. APPLICATIONS IN PLANT SCIENCES 2019; 7:e01233. [PMID: 30937225 PMCID: PMC6426157 DOI: 10.1002/aps3.1233] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/28/2019] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Phenological annotation models computed on large-scale herbarium data sets were developed and tested in this study. METHODS Herbarium specimens represent a significant resource with which to study plant phenology. Nevertheless, phenological annotation of herbarium specimens is time-consuming, requires substantial human investment, and is difficult to mobilize at large taxonomic scales. We created and evaluated new methods based on deep learning techniques to automate annotation of phenological stages and tested these methods on four herbarium data sets representing temperate, tropical, and equatorial American floras. RESULTS Deep learning allowed correct detection of fertile material with an accuracy of 96.3%. Accuracy was slightly decreased for finer-scale information (84.3% for flower and 80.5% for fruit detection). DISCUSSION The method described has the potential to allow fine-grained phenological annotation of herbarium specimens at large ecological scales. Deeper investigation regarding the taxonomic scalability of this approach is needed.
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Affiliation(s)
- Titouan Lorieul
- University of MontpellierMontpellierCEDEX 5France
- Institut national de recherche en informatique et en automatique (INRIA) Sophia‐Antipolis, ZENITH team, Laboratory of InformaticsRobotics and Microelectronics–Joint Research Unit, 34095MontpellierCEDEX 5France
| | - Katelin D. Pearson
- Department of Biological ScienceFlorida State University319 Stadium DriveTallahasseeFlorida32306USA
| | - Elizabeth R. Ellwood
- La Brea Tar Pits and MuseumNatural History Museum of Los Angeles County5801 Wilshire BoulevardLos AngelesCalifornia90036USA
| | - Hervé Goëau
- AMAPUniversité de MontpellierCIRAD, CNRS, INRA, IRDMontpellierFrance
- CIRAD, UMR AMAPMontpellierFrance
| | | | - Patrick W. Sweeney
- Division of BotanyPeabody Museum of Natural HistoryYale UniversityP.O. Box 208118New HavenConnecticut06520USA
| | - Jennifer M. Yost
- Department of Biological SciencesCalifornia Polytechnic State University1 Grand AvenueSan Luis ObispoCalifornia93407USA
| | - Joel Sachs
- Agriculture and Agri‐Food CanadaOttawaCanada
| | | | - Gil Nelson
- iDigBioFlorida State UniversityTallahasseeFlorida32306USA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
| | - Pierre Bonnet
- AMAPUniversité de MontpellierCIRAD, CNRS, INRA, IRDMontpellierFrance
- CIRAD, UMR AMAPMontpellierFrance
| | - Alexis Joly
- Institut national de recherche en informatique et en automatique (INRIA) Sophia‐Antipolis, ZENITH team, Laboratory of InformaticsRobotics and Microelectronics–Joint Research Unit, 34095MontpellierCEDEX 5France
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Ellwood ER, Primack RB, Willis CG, HilleRisLambers J. Phenology models using herbarium specimens are only slightly improved by using finer-scale stages of reproduction. APPLICATIONS IN PLANT SCIENCES 2019; 7:e01225. [PMID: 30937218 PMCID: PMC6426165 DOI: 10.1002/aps3.1225] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 11/02/2018] [Indexed: 05/22/2023]
Abstract
PREMISE OF THE STUDY Herbarium specimens are increasingly used to study reproductive phenology. Here, we ask whether classifying reproduction into progressively finer-scale stages improves our understanding of the relationship between climate and reproductive phenology. METHODS We evaluated Acer rubrum herbarium specimens across eastern North America, classifying them into eight reproductive phenophases and four stages of leaf development. We fit models with different reproductive phenology categorization schemes (from detailed to broad) and compared model fits and coefficients describing temperature, elevation, and year effects. We fit similar models to leaf phenology data to compare reproductive to leafing phenology. RESULTS Finer-scale reproductive phenophases improved model fits and provided more precise estimates of reproductive phenology. However, models with fewer reproductive phenophases led to similar qualitative conclusions, demonstrating that A. rubrum reproduces earlier in warmer locations, lower elevations, and in recent years, as well as that leafing phenology is less strongly influenced by temperature than is reproductive phenology. DISCUSSION Our study suggests that detailed information on reproductive phenology provides a fuller understanding of potential climate change effects on flowering, fruiting, and leaf-out. However, classification schemes with fewer reproductive phenophases provided many similar insights and may be preferable in cases where resources are limited.
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Affiliation(s)
- Elizabeth R. Ellwood
- La Brea Tar Pits and MuseumNatural History Museum of Los Angeles County5801 Wilshire BoulevardLos AngelesCalifornia90036USA
| | - Richard B. Primack
- Biology DepartmentBoston University5 Cummington MallBostonMassachusetts02215USA
| | - Charles G. Willis
- Department of Organismic and Evolutionary Biology and Harvard University HerbariaHarvard UniversityCambridgeMassachusetts02138USA
- Department of Biology Teaching and LearningUniversity of MinnesotaMinneapolisMinnesota55455USA
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Daru BH, Bowman EA, Pfister DH, Arnold AE. A novel proof of concept for capturing the diversity of endophytic fungi preserved in herbarium specimens. Philos Trans R Soc Lond B Biol Sci 2018; 374:20170395. [PMID: 30455213 PMCID: PMC6282087 DOI: 10.1098/rstb.2017.0395] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2018] [Indexed: 12/22/2022] Open
Abstract
Herbarium specimens represent important records of morphological and genetic diversity of plants that inform questions relevant to global change, including species distributions, phenology and functional traits. It is increasingly appreciated that plant microbiomes can influence these aspects of plant biology, but little is known regarding the historic distribution of microbes associated with plants collected in the pre-molecular age. If microbiomes can be observed reliably in herbarium specimens, researchers will gain a new lens with which to examine microbial ecology, evolution, species interactions. Here, we describe a method for accessing historical plant microbiomes from preserved herbarium specimens, providing a proof of concept using two plant taxa from the imperiled boreal biome (Andromeda polifolia and Ledum palustre subsp. groenlandicum, Ericaceae). We focus on fungal endophytes, which occur within symptomless plant tissues such as leaves. Through a three-part approach (i.e. culturing, cloning and next-generation amplicon sequencing via the Illumina MiSeq platform, with extensive controls), we examined endophyte communities in dried, pressed leaves that had been processed as regular herbarium specimens and stored at room temperature in a herbarium for four years. We retrieved only one endophyte in culture, but cloning and especially the MiSeq analysis revealed a rich community of foliar endophytes. The phylogenetic distribution and diversity of endophyte assemblages, especially among the Ascomycota, resemble endophyte communities from fresh plants collected in the boreal biome. We could distinguish communities of endophytes in each plant species and differentiate likely endophytes from fungi that could be surface contaminants. Taxa found by cloning were observed in the larger MiSeq dataset, but species richness was greater when subsets of the same tissues were evaluated with the MiSeq approach. Our findings provide a proof of concept for capturing endophyte DNA from herbarium specimens, supporting the importance of herbarium records as roadmaps for understanding the dynamics of plant-associated microbial biodiversity in the Anthropocene.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
- Barnabas H Daru
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA
| | | | - Donald H Pfister
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, 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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Texier N, Deblauwe V, Stévart T, Sonké B, Simo-Droissart M, Azandi L, Bose R, Djuikouo MN, Kamdem G, Kamdem N, Mayogo S, Zemagho L, Droissart V. Spatio-temporal patterns of orchids flowering in Cameroonian rainforests. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2018; 62:1931-1944. [PMID: 30215186 DOI: 10.1007/s00484-018-1594-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 06/08/2023]
Abstract
We characterized the flowering patterns of 45 epiphytic orchid species occurring in Cameroonian rainforests to explore the environmental and evolutionary forces driving their phenology. We used a dataset of 3470 flowering events recorded over a period of 11 years in the Yaoundé living collection (82% of the flowering events) and from in situ observations (18% of the flowering events) to (i) describe flowering frequency and timing and synchronization among taxa; (ii) test flowering patterns for phylogenetic relatedness at the generic level; and (iii) investigate the spatial patterns of phenology. An annual flowering pattern prevailed among the species selected for this study. The species-rich African genera Angraecum and Polystachya are characterized by subannual and annual frequency patterns, respectively. However, in terms of flowering time, no phylogenetic signal was detected for the four most diverse genera (Ancistrorhynchus, Angraecum, Bulbophyllum, and Polystachya). Results suggest also an important role of photoperiod and precipitation as climatic triggers of flowering patterns. Moreover, 16% of the taxa cultivated ex situ, mostly Polystachya, showed significant differences in flowering time between individuals originating from distinct climatic regions, pointing toward the existence of phenological ecotypes. Phenological plasticity, suggested by the lack of synchronized flowering in spatially disjunct populations of Polystachya, could explain the widespread radiation of this genus throughout tropical Africa. Our study highlights the need to take the spatial pattern of flowering time into account when interpreting phylogeographic patterns in central African rainforests.
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Affiliation(s)
- N Texier
- Faculty of Sciences, Evolutionary Biology and Ecology, Université Libre de Bruxelles, CP160/12, 50 Av. F. Roosevelt, 1050, Brussels, Belgium.
- Herbarium et Bibliothèque de Botanique africaine, Université Libre de Bruxelles, CP 265, Boulevard du Triomphe, B-1050, Brussels, Belgium.
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon.
- Africa & Madagascar Department, Missouri Botanical Garden, P.O. Box 299, St. Louis, MO, 63166-0299, USA.
| | - V Deblauwe
- Herbarium et Bibliothèque de Botanique africaine, Université Libre de Bruxelles, CP 265, Boulevard du Triomphe, B-1050, Brussels, Belgium
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- International Institute of Tropical Agriculture, Yaoundé, Cameroon
| | - T Stévart
- Herbarium et Bibliothèque de Botanique africaine, Université Libre de Bruxelles, CP 265, Boulevard du Triomphe, B-1050, Brussels, Belgium
- Africa & Madagascar Department, Missouri Botanical Garden, P.O. Box 299, St. Louis, MO, 63166-0299, USA
- Agentschap Plantentuin Meise, Domein van Bouchout, Nieuwelaan 38, BE-1860, Meise, Belgium
| | - B Sonké
- Herbarium et Bibliothèque de Botanique africaine, Université Libre de Bruxelles, CP 265, Boulevard du Triomphe, B-1050, Brussels, Belgium
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
- Africa & Madagascar Department, Missouri Botanical Garden, P.O. Box 299, St. Louis, MO, 63166-0299, USA
| | - M Simo-Droissart
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
| | - L Azandi
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
| | - R Bose
- AMAP, IRD, CIRAD, CNRS, INRA, Univ Montpellier, Montpellier, France
| | - M-N Djuikouo
- Department of Botany and Plant Physiology, University of Buea, Buea, Cameroon
| | - G Kamdem
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
| | - N Kamdem
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
| | - S Mayogo
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
| | - L Zemagho
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
| | - V Droissart
- Herbarium et Bibliothèque de Botanique africaine, Université Libre de Bruxelles, CP 265, Boulevard du Triomphe, B-1050, Brussels, Belgium
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, Yaoundé, Cameroon
- Africa & Madagascar Department, Missouri Botanical Garden, P.O. Box 299, St. Louis, MO, 63166-0299, USA
- AMAP, IRD, CIRAD, CNRS, INRA, Univ Montpellier, Montpellier, France
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Jones CA, Daehler CC. Herbarium specimens can reveal impacts of climate change on plant phenology; a review of methods and applications. PeerJ 2018; 6:e4576. [PMID: 29632745 PMCID: PMC5888139 DOI: 10.7717/peerj.4576] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/16/2018] [Indexed: 12/12/2022] Open
Abstract
Studies in plant phenology have provided some of the best evidence for large-scale responses to recent climate change. Over the last decade, more than thirty studies have used herbarium specimens to analyze changes in flowering phenology over time, although studies from tropical environments are thus far generally lacking. In this review, we summarize the approaches and applications used to date. Reproductive plant phenology has primarily been analyzed using two summary statistics, the mean flowering day of year and first-flowering day of year, but mean flowering day has proven to be a more robust statistic. Two types of regression models have been applied to test for associations between flowering, temperature and time: flowering day regressed on year and flowering day regressed on temperature. Most studies analyzed the effect of temperature by averaging temperatures from three months prior to the date of flowering. On average, published studies have used 55 herbarium specimens per species to characterize changes in phenology over time, but in many cases fewer specimens were used. Geospatial grid data are increasingly being used for determining average temperatures at herbarium specimen collection locations, allowing testing for finer scale correspondence between phenology and climate. Multiple studies have shown that inferences from herbarium specimen data are comparable to findings from systematically collected field observations. Understanding phenological responses to climate change is a crucial step towards recognizing implications for higher trophic levels and large-scale ecosystem processes. As herbaria are increasingly being digitized worldwide, more data are becoming available for future studies. As temperatures continue to rise globally, herbarium specimens are expected to become an increasingly important resource for analyzing plant responses to climate change.
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Affiliation(s)
- Casey A Jones
- Department of Botany, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Curtis C Daehler
- Department of Botany, University of Hawaii at Manoa, Honolulu, HI, United States of America
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Willis CG, Ellwood ER, Primack RB, Davis CC, Pearson KD, Gallinat AS, Yost JM, Nelson G, Mazer SJ, Rossington NL, Sparks TH, Soltis PS. Old Plants, New Tricks: Phenological Research Using Herbarium Specimens. Trends Ecol Evol 2017; 32:531-546. [DOI: 10.1016/j.tree.2017.03.015] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 03/07/2017] [Accepted: 03/31/2017] [Indexed: 11/30/2022]
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Bush ER, Abernethy KA, Jeffery K, Tutin C, White L, Dimoto E, Dikangadissi J, Jump AS, Bunnefeld N. Fourier analysis to detect phenological cycles using long‐term tropical field data and simulations. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12704] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emma R. Bush
- Biological and Environmental Sciences Faculty of Natural Sciences University of Stirling Stirling FK9 4LA UK
| | - Katharine A. Abernethy
- Biological and Environmental Sciences Faculty of Natural Sciences University of Stirling Stirling FK9 4LA UK
- Institut de Recherche en Écologie Tropicale CENAREST BP 842 Libreville Gabon
| | - Kathryn Jeffery
- Biological and Environmental Sciences Faculty of Natural Sciences University of Stirling Stirling FK9 4LA UK
- Agence Nationale des Parcs Nationaux (ANPN) B.P. 20379 Libreville Gabon
| | - Caroline Tutin
- Biological and Environmental Sciences Faculty of Natural Sciences University of Stirling Stirling FK9 4LA UK
| | - Lee White
- Biological and Environmental Sciences Faculty of Natural Sciences University of Stirling Stirling FK9 4LA UK
- Institut de Recherche en Écologie Tropicale CENAREST BP 842 Libreville Gabon
- Agence Nationale des Parcs Nationaux (ANPN) B.P. 20379 Libreville Gabon
| | - Edmond Dimoto
- Agence Nationale des Parcs Nationaux (ANPN) B.P. 20379 Libreville Gabon
| | | | - Alistair S. Jump
- Biological and Environmental Sciences Faculty of Natural Sciences University of Stirling Stirling FK9 4LA UK
| | - Nils Bunnefeld
- Biological and Environmental Sciences Faculty of Natural Sciences University of Stirling Stirling FK9 4LA UK
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Gomez C, Despinoy M, Hamon S, Hamon P, Salmon D, Akaffou DS, Legnate H, de Kochko A, Mangeas M, Poncet V. Shift in precipitation regime promotes interspecific hybridization of introduced Coffea species. Ecol Evol 2016; 6:3240-55. [PMID: 27096083 PMCID: PMC4829533 DOI: 10.1002/ece3.2055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 11/06/2022] Open
Abstract
The frequency of plant species introductions has increased in a highly connected world, modifying species distribution patterns to include areas outside their natural ranges. These introductions provide the opportunity to gain new insight into the importance of flowering phenology as a component of adaptation to a new environment. Three Coffea species, C. arabica, C. canephora (Robusta), and C. liberica, native to intertropical Africa have been introduced to New Caledonia. On this archipelago, a secondary contact zone has been characterized where these species coexist, persist, and hybridize spontaneously. We investigated the impact of environmental changes undergone by each species following its introduction in New Caledonia on flowering phenology and overcoming reproductive barriers between sister species. We developed species distribution models and compared both environmental envelopes and climatic niches between native and introduced hybrid zones. Flowering phenology was monitored in a population in the hybrid zone along with temperature and precipitation sequences recorded at a nearby weather station. The extent and nature of hybridization events were characterized using chloroplast and nuclear microsatellite markers. The three Coffea species encountered weak environmental suitability compared to their native ranges when introduced to New Caledonia, especially C. arabica and C. canephora. The niche of the New Caledonia hybrid zone was significantly different from all three species' native niches based on identity tests (I Similarity and D Schoener's Similarity Indexes). This area appeared to exhibit intermediate conditions between the native conditions of the three species for temperature-related variables and divergent conditions for precipitation-related ones. Flowering pattern in these Coffea species was shown to have a strong genetic component that determined the time between the triggering rain and anthesis (flower opening), specific to each species. However, a precipitation regime different from those in Africa was directly involved in generating partial flowering overlap between species and thus in allowing hybridization and interspecific gene flow. Interspecific hybrids accounted for 4% of the mature individuals in the sympatric population and occurred between each pair of species with various level of introgression. Adaptation to new environmental conditions following introduction of Coffea species to New Caledonia has resulted in a secondary contact between three related species, which would not have happened in their native ranges, leading to hybridization and gene flow.
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Affiliation(s)
- Céline Gomez
- IRDUMR DIADEBP 6450134394Montpellier Cedex 5France
| | - Marc Despinoy
- IRDUMR ESPACE DEV (S140)BP A598848Cedex NouméaNouvelle Calédonie
| | - Serge Hamon
- IRDUMR DIADEBP 6450134394Montpellier Cedex 5France
| | - Perla Hamon
- IRDUMR DIADEBP 6450134394Montpellier Cedex 5France
| | | | | | | | | | - Morgan Mangeas
- IRDUMR ESPACE DEV (S140)BP A598848Cedex NouméaNouvelle Calédonie
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Horsley TWB, Bicknell JE, Lim BK, Ammerman LK. Seed Dispersal by Frugivorous Bats in Central Guyana and a Description of Previously Unknown Plant-Animal Interactions. ACTA CHIROPTEROLOGICA 2015. [DOI: 10.3161/15081109acc2015.17.2.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Park IW, Schwartz MD. Long-term herbarium records reveal temperature-dependent changes in flowering phenology in the southeastern USA. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2015; 59:347-355. [PMID: 24842521 DOI: 10.1007/s00484-014-0846-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 05/04/2014] [Accepted: 05/08/2014] [Indexed: 06/03/2023]
Abstract
In recent years, a growing body of evidence has emerged indicating that the relationship between flowering phenology and climate may differ throughout various portions of the growing season. These differences have resulted in long-term changes in flowering synchrony that may alter the quantity and diversity of pollinator attention to many species, as well as altering food availability to pollenivorous and nectarivorous animal species. However, long-term multi-season records of past flowering timing have primarily focused on temperate environments. In contrast, changes in flowering phenology within humid subtropical environments such as the southeastern USA remain poorly documented. This research uses herbarium-based methods to examine changes in flowering time across 19,328 samples of spring-, summer-, and autumn-flowering plants in the southeastern USA from the years 1951 to 2009. In this study, species that flower near the onset of the growing season were found to advance under increasing mean March temperatures (-3.391 days/°C, p = 0.022). No long-term advances in early spring flowering or spring temperature were detected during this period, corroborating previous phenological assessments for the southeastern USA. However, late spring through mid-summer flowering exhibited delays in response to higher February temperatures (over 0.1.85 days/°C, p ≤ 0.041 in all cases). Thus, it appears that flowering synchrony may undergo significant restructuring in response to warming spring temperatures, even in humid subtropical environments.
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Affiliation(s)
- Isaac W Park
- Department of Geography, University of Wisconsin, Milwaukee, WI, 53201-0413, USA,
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21
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Rawal DS, Kasel S, Keatley MR, Nitschke CR. Herbarium records identify sensitivity of flowering phenology of eucalypts to climate: Implications for species response to climate change. AUSTRAL ECOL 2014. [DOI: 10.1111/aec.12183] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Deepa S. Rawal
- Department of Forest and Ecosystem Science; University of Melbourne; 500 Yarra Boulevard Melbourne Vic. 3121 Australia
| | - Sabine Kasel
- Department of Forest and Ecosystem Science; University of Melbourne; 500 Yarra Boulevard Melbourne Vic. 3121 Australia
| | - Marie R. Keatley
- Department of Forest and Ecosystem Science; University of Melbourne; Creswick Victoria Australia
| | - Craig R. Nitschke
- Department of Forest and Ecosystem Science; University of Melbourne; 500 Yarra Boulevard Melbourne Vic. 3121 Australia
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22
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Quintero I, González-Caro S, Zalamea PC, Cadena CD. Asynchrony of seasons: genetic differentiation associated with geographic variation in climatic seasonality and reproductive phenology. Am Nat 2014; 184:352-63. [PMID: 25141144 DOI: 10.1086/677261] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Many organisms exhibit distinct breeding seasons tracking food availability. If conspecific populations inhabit areas that experience different temporal cycles in food availability spurred by variation in precipitation regimes, then they should display asynchronous breeding seasons. Thus, such populations might exhibit a temporal barrier to gene flow, which may potentially promote genetic differentiation. We test a central prediction of this hypothesis, namely, that individuals living in areas with more asynchronous precipitation regimes should be more genetically differentiated than individuals living in areas with more similar precipitation regimes. Using mitochondrial DNA sequences, climatic data, and geographical/ecological distances between individuals of 57 New World bird species mostly from the tropics, we examined the effect of asynchronous precipitation (a proxy for asynchronous resource availability) on genetic differentiation. We found evidence for a positive and significant cross-species effect of precipitation asynchrony on genetic distance after accounting for geographical/ecological distances, suggesting that current climatic conditions may play a role in population differentiation. Spatial asynchrony in climate may thus drive evolutionary divergence in the absence of overt geographic barriers to gene flow; this mechanism contrasts with those invoked by most models of biotic diversification emphasizing physical or ecological changes to the landscape as drivers of divergence.
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Affiliation(s)
- Ignacio Quintero
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
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Effect of rainfall seasonality on the growth of Cecropia sciadophylla: intra-annual variation in leaf production and node length. JOURNAL OF TROPICAL ECOLOGY 2013. [DOI: 10.1017/s0266467413000394] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Abstract:Patterns of leaf production and leaf fall directly influence leaf area index and forest productivity. Here, we focused on Cecropia sciadophylla individuals inhabiting the extremes of the gradient in seasonality in rainfall at which C. sciadophylla occurs. In Colombia and French Guiana we compared the intra-annual variation in leaf production as well as the intra-annual fluctuation in internode length on a total of 69 saplings ranging in size from 1 to 2 m. The mean rate of leaf production was ~2 leaves mo−1 in both populations, and the rate of leaf production was constant throughout the year. Our results showed monthly variation in internode length and the number of live leaves per sapling in the seasonal habitat and variation only in internode length in the everwet habitat. Because the rate of leaf production is constant at both localities, the difference in number of live leaves per sapling at the seasonal site must reflect seasonal variation in leaf life span. We show that in Cecropia, internode length can serve as an indicator of precipitation seasonality. Finally an open question is whether leaf production in other pioneer species is also independent of climatic seasonal cues. This information could allow us to link growth and climate of secondary forest species and better understand how past and future climate can affect plant growth trajectories.
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Park IW. Digital herbarium archives as a spatially extensive, taxonomically discriminate phenological record; a comparison to MODIS satellite imagery. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2012; 56:1179-1182. [PMID: 22350421 DOI: 10.1007/s00484-012-0521-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 01/13/2012] [Accepted: 01/14/2012] [Indexed: 05/31/2023]
Abstract
This study demonstrates that phenological information included in digital herbarium archives can produce annual phenological estimates correlated to satellite-derived green wave phenology at a regional scale (R = 0.183, P = 0.03). Thus, such records may be utilized in a fashion similar to other annual phenological records and, due to their longer duration and ability to discriminate among the various components of the plant community, hold significant potential for use in future research to supplement the deficiencies of other data sources as well as address a wide array of important issues in ecology and bioclimatology that cannot be addressed easily using more traditional methods.
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Affiliation(s)
- Isaac W Park
- Department of Geography, University of Wisconsin, Milwaukee, WI 53201-0413, USA.
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Zalamea PC, Heuret P, Sarmiento C, Rodríguez M, Berthouly A, Guitet S, Nicolini E, Delnatte C, Barthélémy D, Stevenson PR. The genus Cecropia: a biological clock to estimate the age of recently disturbed areas in the Neotropics. PLoS One 2012; 7:e42643. [PMID: 22916144 PMCID: PMC3416824 DOI: 10.1371/journal.pone.0042643] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 07/11/2012] [Indexed: 11/23/2022] Open
Abstract
Forest successional processes following disturbance take decades to play out, even in tropical forests. Nonetheless, records of vegetation change in this ecosystem are scarce, increasing the importance of the chronosequence approach to study forest recovery. However, this approach requires accurate dating of secondary forests, which until now was a difficult and/or expensive task. Cecropia is a widespread and abundant pioneer tree genus of the Neotropics. Here we propose and validate a rapid and straightforward method to estimate the age of secondary forest patches based on morphological observations of Cecropia trees. We found that Cecropia-inferred ages were highly correlated with known ages of the forest. We also demonstrate that Cecropia can be used to accurately date disturbances and propose twenty-one species distributed all over the geographical range of the genus as potential secondary forest chronometer species. Our method is limited in applicability by the maximal longevity of Cecropia individuals. Although the oldest chronosequence used in this study was 20 years old, we argue that at least for the first four decades after disturbance, the method described in this study provides very accurate estimations of secondary forest ages. The age of pioneer trees provides not only information needed to calculate the recovery of carbon stocks that would help to improve forest management, but also provides information needed to characterize the initial floristic composition and the rates of species remigration into secondary forest. Our contribution shows how successional studies can be reliably and inexpensively extended without the need to obtain forest ages based on expensive or potentially inaccurate data across the Neotropics.
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Affiliation(s)
- Paul-Camilo Zalamea
- IRD, UMR AMAP (Botanique et bioinformatique de l'architecture des plantes), Montpellier, France.
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Santos GGA, Santos BA, Nascimento HEM, Tabarelli M. Contrasting Demographic Structure of Short- and Long-lived Pioneer Tree Species on Amazonian Forest Edges. Biotropica 2012. [DOI: 10.1111/j.1744-7429.2012.00882.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Graciliano G. A. Santos
- Centro de Estudos Integrados em Biodiversidade Amazônica; Universidade Federal do Amapá; Macapá; Amapá; 68902-280; Brazil
| | - Bráulio A. Santos
- Departamento de Botânica; Universidade Federal de Pernambuco; Recife; Pernambuco; 50670-901; Brazil
| | - Henrique E. M. Nascimento
- Coordenação de Pesquisa em Silvicultura Tropical, Instituto Nacional de Pesquisas da Amazônia; C.P. 478; Manaus; Amazonas; 69011-970; Brazil
| | - Marcelo Tabarelli
- Departamento de Botânica; Universidade Federal de Pernambuco; Recife; Pernambuco; 50670-901; Brazil
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