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Hu H, Scheben A, Verpaalen B, Tirnaz S, Bayer PE, Hodel RGJ, Batley J, Soltis DE, Soltis PS, Edwards D. Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation. New Phytol 2022; 233:1548-1555. [PMID: 34328223 PMCID: PMC9292397 DOI: 10.1111/nph.17658] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/26/2021] [Indexed: 05/03/2023]
Affiliation(s)
- Haifei Hu
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
| | - Armin Scheben
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
- Simons Center for Quantitative BiologyCold Spring Harbor LaboratoryCold Spring Harbor,NY11724USA
| | - Brent Verpaalen
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
| | - Soodeh Tirnaz
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
| | - Philipp E. Bayer
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
| | - Richard G. J. Hodel
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDC20013‐7012USA
| | - Jacqueline Batley
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
| | - Douglas E. Soltis
- Department of BiologyUniversity of FloridaGainesvilleFL32611USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFL32611USA
- The Genetics InstituteUniversity of FloridaGainesvilleFL32610USA
- The Biodiversity InstituteUniversity of FloridaGainesvilleFL32611USA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFL32611USA
- The Genetics InstituteUniversity of FloridaGainesvilleFL32610USA
- The Biodiversity InstituteUniversity of FloridaGainesvilleFL32611USA
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
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Liu HL, Harris AJ, Wang ZF, Chen HF, Li ZA, Wei X. The genome of the Paleogene relic tree Bretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs. DNA Res 2022; 29:6523039. [PMID: 35137004 PMCID: PMC8825261 DOI: 10.1093/dnares/dsac003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Indexed: 11/13/2022] Open
Abstract
Among relic species, genomic information may provide the key to inferring their long-term survival. Therefore, in this study, we investigated the genome of the Paleogene relic tree species, Bretschneidera sinensis, which is a rare endemic species within southeastern Asia. Specifically, we assembled a high-quality genome for B. sinensis using PacBio high-fidelity and high-throughput chromosome conformation capture reads and annotated it with long and short RNA sequencing reads. Using the genome, we then detected a trade-off between active and passive disease defences among the gene families. Gene families involved in salicylic acid and MAPK signalling pathways expanded as active defence mechanisms against disease, but families involved in terpene synthase activity as passive defences contracted. When inferring the long evolutionary history of B. sinensis, we detected population declines corresponding to historical climate change around the Eocene–Oligocene transition and to climatic fluctuations in the Quaternary. Additionally, based on this genome, we identified 388 single nucleotide polymorphisms (SNPs) that were likely under selection, and showed diverse functions in growth and stress responses. Among them, we further found 41 climate-associated SNPs. The genome of B. sinensis and the SNP dataset will be important resources for understanding extinction/diversification processes using comparative genomics in different lineages.
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Affiliation(s)
- Hai-Lin Liu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.,Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Guangzhou, 510640, China
| | - A J Harris
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zheng-Feng Wang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.,Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hong-Feng Chen
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhi-An Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.,Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xiao Wei
- Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin, 541006, China
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Pillon Y, Jaffré T, Birnbaum P, Bruy D, Cluzel D, Ducousso M, Fogliani B, Ibanez T, Jourdan H, Lagarde L, Léopold A, Munzinger J, Pouteau R, Read J, Isnard S. Infertile landscapes on an old oceanic island: the biodiversity hotspot of New Caledonia. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa146] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Abstract
The OCBIL theory comprises a set of hypotheses to comprehend the biota of old, climatically buffered, infertile landscapes (OCBILs). Here, we review evidence from the literature to evaluate the extent to which this theory could apply to the biodiversity hotspot of New Caledonia. We present geological, pedological and climatic evidence suggesting how the island might qualify as an OCBIL. The predictions of OCBIL theory are then reviewed in the context of New Caledonia. There is evidence for a high rate of micro-endemism, accumulation of relict lineages, a high incidence of dioecy, myrmecochory and nutritional specializations in plants. New Caledonian vegetation also exhibits several types of monodominant formations that reveal the importance of disturbances on the island. Fires and tropical storms are likely to be important factors that contribute to the dynamic of New Caledonian ecosystems. Although naturally infertile, there is archaeological evidence that humans developed specific horticultural practices in the ultramafic landscapes of New Caledonia. Further comparisons between New Caledonia and other areas of the world, such as South Africa and Southwest Australia, are desirable, to develop the OCBIL theory into a more robust and generalized, testable framework and to determine the most efficient strategies to preserve their outstanding biodiversity.
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Affiliation(s)
- Yohan Pillon
- LSTM, IRD, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Tanguy Jaffré
- AMAP, Univ Montpellier, IRD, CIRAD, CNRS, INRAE, Montpellier, France
- AMAP, IRD, CIRAD, Herbier de la Nouvelle-Calédonie, Nouméa, New Caledonia
| | - Philippe Birnbaum
- AMAP, Univ Montpellier, IRD, CIRAD, CNRS, INRAE, Montpellier, France
- AMAP, IRD, CIRAD, Herbier de la Nouvelle-Calédonie, Nouméa, New Caledonia
- Institut Agronomique Néo-Calédonien (IAC), équipe SolVeg, Nouméa, New Caledonia
| | - David Bruy
- AMAP, Univ Montpellier, IRD, CIRAD, CNRS, INRAE, Montpellier, France
- AMAP, IRD, CIRAD, Herbier de la Nouvelle-Calédonie, Nouméa, New Caledonia
| | - Dominique Cluzel
- ISEA, Université de la Nouvelle-Calédonie, Nouméa, New Caledonia
| | - Marc Ducousso
- LSTM, IRD, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Bruno Fogliani
- ISEA, Université de la Nouvelle-Calédonie, Nouméa, New Caledonia
| | - Thomas Ibanez
- Department of Biology, University of Hawai′i at Hilo, Hilo, HI, USA
| | - Hervé Jourdan
- IMBE, Aix Marseille Université, CNRS, IRD, Avignon Université, Nouméa, New Caledonia
| | - Louis Lagarde
- TROCA, Université de la Nouvelle-Calédonie, Nouméa, New Caledonia
| | - Audrey Léopold
- Institut Agronomique Néo-Calédonien (IAC), équipe SolVeg, Nouméa, New Caledonia
| | - Jérôme Munzinger
- AMAP, Univ Montpellier, IRD, CIRAD, CNRS, INRAE, Montpellier, France
| | - Robin Pouteau
- AMAP, Univ Montpellier, IRD, CIRAD, CNRS, INRAE, Montpellier, France
| | - Jennifer Read
- School of Biological Sciences, Monash University, Victoria, Australia
| | - Sandrine Isnard
- AMAP, Univ Montpellier, IRD, CIRAD, CNRS, INRAE, Montpellier, France
- AMAP, IRD, CIRAD, Herbier de la Nouvelle-Calédonie, Nouméa, New Caledonia
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Zhang X, Wei H, Zhang X, Liu J, Zhang Q, Gu W. Non-Pessimistic Predictions of the Distributions and Suitability of Metasequoia glyptostroboides under Climate Change Using a Random Forest Model. Forests 2020; 11:62. [DOI: 10.3390/f11010062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Metasequoia glyptostroboides Hu & W. C. Cheng, which is a remarkable rare relict plant, has gradually been reduced to its current narrow range due to climate change. Understanding the comprehensive distribution of M. glyptostroboides under climate change on a large spatio-temporal scale is of great significance for determining its forest adaptation. In this study, based on 394 occurrence data and 10 bioclimatic variables, the global potential distribution of M. glyptostroboides under eight different climate scenarios (i.e., the past three, the current one, and the next four) from the Quaternary glacial to the future was simulated by a random forest model built with the biomod2 package. The key bioclimatic variables affecting the distribution of M. glyptostroboides are BIO2 (mean diurnal range), BIO1 (annual mean temperature), BIO9 (mean temperature of driest quarter), BIO6 (min temperature of coldest month), and BIO18 (precipitation of warmest quarter). The result indicates that the temperature affects the potential distribution of M. glyptostroboides more than the precipitation. A visualization of the results revealed that the current relatively suitable habitats of M. glyptostroboides are mainly distributed in East Asia and Western Europe, with a total area of approximately 6.857 × 106 km2. With the intensification of global warming in the future, the potential distribution and the suitability of M. glyptostroboides have a relatively non-pessimistic trend. Whether under the mild (RCP4.5) and higher (RCP8.5) emission scenarios, the total area of suitable habitats will be wider than it is now by the 2070s, and the habitat suitability will increase to varying degrees within a wide spatial range. After speculating on the potential distribution of M. glyptostroboides in the past, the glacial refugia of M. glyptostroboides were inferred, and projections regarding the future conditions of these places are expected to be optimistic. In order to better protect the species, the locations of its priority protected areas and key protected areas, mainly in Western Europe and East Asia, were further identified. Our results will provide theoretical reference for the long-term management of M. glyptostroboides, and can be used as background information for the restoration of other endangered species in the future.
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5
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Heads M. Recent advances in New Caledonian biogeography. Biol Rev Camb Philos Soc 2018; 94:957-980. [PMID: 30523662 DOI: 10.1111/brv.12485] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/04/2018] [Accepted: 11/07/2018] [Indexed: 01/08/2023]
Abstract
The biota of New Caledonia is one of the most unusual in the world. It displays high diversity and endemism, many peculiar absences, and far-flung biogeographic affinities. For example, New Caledonia is the only place on Earth with both main clades of flowering plants - the endemic Amborella and 'all the rest', and it also has the highest concentration of diversity in conifers. The discovery of Amborella's phylogenetic position led to a surge of interest in New Caledonian biogeography, and new studies are appearing at a rapid rate. This paper reviews work on the topic (mainly molecular studies) published since 2013. One current debate is focused on whether any biota survived the marine transgressions of the Paleocene and Eocene. Total submersion would imply that the entire fauna was derived by long-distance dispersal from continental areas since the Eocene, but only if no other islands (now submerged) were emergent. A review of the literature suggests there is little actual evidence in geology for complete submersion. An alternative explanation for New Caledonia's diversity is that the archipelago acted as a refugium, and that the biota avoided the extinctions that occurred in Australia. However, this is contradicted by the many groups that are anomalously absent or depauperate in New Caledonia, although represented there by a sister group. The anomalous absences, together with the unusual levels of endemism, can both be explained by vicariance at breaks in and around New Caledonia. New Caledonia has always been situated at or near a plate boundary, and its complex geological history includes the addition of new terranes (by accretion), orogeny, and rifting. New Caledonia comprises 'basement' terranes that were part of Gondwana, as well as island arc and forearc terranes that accreted to the basement after it separated from Gondwana. The regional tectonic history helps explain the regional biogeography, as well as distribution patterns within New Caledonia. These include endemics on the basement terranes (for example, the basal angiosperm, Amborella), disjunctions at the West Caledonian fault zone, and great biotic differences between Grande Terre and the Loyalty Islands.
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Affiliation(s)
- Michael Heads
- Buffalo Museum of Science, Buffalo, NY 14211-1293, U.S.A
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6
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Bruy D, Hattermann T, Barrabé L, Mouly A, Barthélémy D, Isnard S. Evolution of Plant Architecture, Functional Diversification and Divergent Evolution in the Genus Atractocarpus (Rubiaceae) for New Caledonia. Front Plant Sci 2018; 9:1775. [PMID: 30564258 PMCID: PMC6288547 DOI: 10.3389/fpls.2018.01775] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/15/2018] [Indexed: 05/29/2023]
Abstract
The diversification of ecological roles and related adaptations in closely related species within a lineage is one of the most important processes linking plant evolution and ecology. Plant architecture offers a robust framework to study these processes as it can highlight how plant structure influences plant diversification and ecological strategies. We investigated a case of gradual evolution of branching architecture in Atractocarpus spp. (Rubiaceae), forming a monophyletic group in New Caledonia that has diversified rapidly, predominantly in rainforest understory habitats. We used a transdisciplinary approach to depict architectural variations and revealed multiple evolutionary transitions from a branched (Stone's architectural model) to a monocaulous habit (Corner's architectural model), which involved the functional reduction of branches into inflorescences. We propose an integrative functional index that assesses branching incidence on functional traits influencing both assimilation and exploration functions. We showed that architectural transitions correlate with ecologically important functional traits. Variation in ecologically important traits among closely relatives, as supported by the architectural analysis, is suggestive of intense competition that favored divergence among locally coexisting species. We propose that Pleistocene climatic fluctuations causing expansion and contraction of rainforest could also have offered ecological opportunities for colonizers in addition to the process of divergent evolution.
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Affiliation(s)
- David Bruy
- AMAP, IRD, CIRAD, CNRS, INRA, Université de Montpellier, Montpellier, France
- AMAP, IRD, Herbier de Nouméa, Nouméa, New Caledonia
| | - Tom Hattermann
- AMAP, IRD, CIRAD, CNRS, INRA, Université de Montpellier, Montpellier, France
- AMAP, IRD, Herbier de Nouméa, Nouméa, New Caledonia
| | - Laure Barrabé
- Endemia, Plant Red List Authority, Nouméa, New Caledonia
| | - Arnaud Mouly
- Laboratoire Chrono-Environnement UMR 6249 CNRS, Université Bourgogne Franche-Comté, Besançon, France
- Jardin Botanique de la Ville de Besançon et de l'Université de Franche-Comté, Besançon, France
| | - Daniel Barthélémy
- AMAP, IRD, CIRAD, CNRS, INRA, Université de Montpellier, Montpellier, France
- CIRAD, UMR AMAP, Montpellier, France
| | - Sandrine Isnard
- AMAP, IRD, CIRAD, CNRS, INRA, Université de Montpellier, Montpellier, France
- AMAP, IRD, Herbier de Nouméa, Nouméa, New Caledonia
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7
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Hodel RG, Chandler LM, Fahrenkrog AM, Kirst M, Gitzendanner MA, Soltis DE, Soltis PS. Linking genome signatures of selection and adaptation in non-model plants: exploring potential and limitations in the angiosperm Amborella. Curr Opin Plant Biol 2018; 42:81-89. [PMID: 29694936 DOI: 10.1016/j.pbi.2018.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/24/2018] [Accepted: 04/02/2018] [Indexed: 06/08/2023]
Abstract
Selective sweeps may be caused by environmental conditions that select for a gene function or trait at one locus, causing reduced variation at neighboring sites due to linkage, with specific non-selected variants being swept along with the selected variant. For many species, genomic and environmental data are available to test hypotheses that environmental conditions are correlated with selected regions. Most genomic studies relating selection to environment use model organisms or crop species; typically, these studies have genomic data from large numbers of individuals and extensive environmental data. Here, we review studies associating selective sweeps with environment and consider the impediments to successful application of these methods to non-model species. We present an initial investigation into linking genomic regions of selection to environmental conditions in the narrowly distributed, non-model plant Amborella trichopoda (Amborellaceae), the sister species to all other living flowering plants and one of over 2500 plant species endemic to New Caledonia.
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Affiliation(s)
- Richard Gj Hodel
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Luke M Chandler
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; The Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Annette M Fahrenkrog
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, USA
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, USA; The Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | | | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; The Genetics Institute, University of Florida, Gainesville, FL 32610, USA; The Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; The Genetics Institute, University of Florida, Gainesville, FL 32610, USA; The Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA.
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8
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Ibanez T, Blanchard E, Hequet V, Keppel G, Laidlaw M, Pouteau R, Vandrot H, Birnbaum P. High endemism and stem density distinguish New Caledonian from other high-diversity rainforests in the Southwest Pacific. Ann Bot 2018; 121:25-35. [PMID: 29077788 PMCID: PMC5786226 DOI: 10.1093/aob/mcx107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 08/04/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND AND AIMS The biodiversity hotspot of New Caledonia is globally renowned for the diversity and endemism of its flora. New Caledonia's tropical rainforests have been reported to have higher stem densities, higher concentrations of relictual lineages and higher endemism than other rainforests. This study investigates whether these aspects differ in New Caledonian rainforests compared to other high-diversity rainforests in the Southwest Pacific. METHODS Plants (with a diameter at breast height ≥10 cm) were surveyed in nine 1-ha rainforest plots across the main island of New Caledonia and compared with 14 1-ha plots in high-diversity rainforests of the Southwest Pacific (in Australia, Fiji, Papua New Guinea and the Solomon Islands). This facilitated a comparison of stem densities, taxonomic composition and diversity, and species turnover among plots and countries. KEY RESULTS The study inventoried 11 280 stems belonging to 335 species (93 species ha-1 on average) in New Caledonia. In comparison with other rainforests in the Southwest Pacific, New Caledonian rainforests exhibited higher stem density (1253 stems ha-1 on average) including abundant palms and tree ferns, with the high abundance of the latter being unparalleled outside New Caledonia. In all plots, the density of relictual species was ≥10 % for both stems and species, with no discernible differences among countries. Species endemism, reaching 89 % on average, was significantly higher in New Caledonia. Overall, species turnover increased with geographical distance, but not among New Caledonian plots. CONCLUSIONS High stem density, high endemism and a high abundance of tree ferns with stem diameters ≥10 cm are therefore unique characteristics of New Caledonian rainforests. High endemism and high spatial species turnover imply that the current system consisting of a few protected areas is inadequate, and that the spatial distribution of plant species needs to be considered to adequately protect the exceptional flora of New Caledonian rainforests.
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Affiliation(s)
- Thomas Ibanez
- Institut Agronomique néo-Calédonien (IAC), Diversité biologique et fonctionnelle des écosystèmes terrestres, Nouméa, New Caledonia
- For correspondence. Email
| | - E Blanchard
- Institut Agronomique néo-Calédonien (IAC), Diversité biologique et fonctionnelle des écosystèmes terrestres, Nouméa, New Caledonia
| | - V Hequet
- Institut de Recherche pour le Développement (IRD), UMR AMAP, Nouméa, New Caledonia
| | - G Keppel
- School of Natural and Built Environments, University of South Australia, GPO, Adelaide, South Australia, Australia
| | - M Laidlaw
- Queensland Herbarium, Department of Science, Information Technology and Innovation, Toowong, Queensland, Australia
| | - R Pouteau
- Institut Agronomique néo-Calédonien (IAC), Diversité biologique et fonctionnelle des écosystèmes terrestres, Nouméa, New Caledonia
| | - H Vandrot
- Institut Agronomique néo-Calédonien (IAC), Diversité biologique et fonctionnelle des écosystèmes terrestres, Nouméa, New Caledonia
| | - P Birnbaum
- Institut Agronomique néo-Calédonien (IAC), Diversité biologique et fonctionnelle des écosystèmes terrestres, Nouméa, New Caledonia
- Cirad, UMR AMAP, Montpellier, France
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Abstract
The biogeographical paradigm of New Caledonia has recently changed. Although this island is now considered by many as oceanic, its study is still often impeded by some old misconceptions concerning either regional geology or phylogenetic analysis of evolution and biogeography. I discuss ten points that I feel are especially detrimental, to help focus on the real debate and the real questions: (1) its geological history cannot be understood from the basement only; (2) the island submergence was not due simply to sea-level variation; (3) Zealandia/Tasmantis is not a lost continent; (4) short-distance dispersal is not equivalent to permanence on land; (5) long-distance dispersal is not the sole event opposing vicariance, but short-distance dispersal as well; (6) the occurrence of relicts does not prove biota permanence; (7) a major fault system was not observed in New Caledonia; (8) terranes are not rafts; (9) forest climatic refuges do not necessarily equate to centres of endemism or centres of diversity; and (10) New Caledonia is not only a sink but also a source. Study of New Caledonia will need to focus on old and non-relict clades and there is a need to improve the local fossil record.
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Affiliation(s)
- Philippe Grandcolas
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 CNRS MNHN UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, CP 50, 45 rue Buffon, 75005, Paris, France
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10
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Tournebize R, Manel S, Vigouroux Y, Munoz F, de Kochko A, Poncet V. Two disjunct Pleistocene populations and anisotropic postglacial expansion shaped the current genetic structure of the relict plant Amborella trichopoda. PLoS One 2017; 12:e0183412. [PMID: 28820899 PMCID: PMC5562301 DOI: 10.1371/journal.pone.0183412] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 08/03/2017] [Indexed: 12/04/2022] Open
Abstract
Past climate fluctuations shaped the population dynamics of organisms in space and time, and have impacted their present intra-specific genetic structure. Demo-genetic modelling allows inferring the way past demographic and migration dynamics have determined this structure. Amborella trichopoda is an emblematic relict plant endemic to New Caledonia, widely distributed in the understory of non-ultramafic rainforests. We assessed the influence of the last glacial climates on the demographic history and the paleo-distribution of 12 Amborella populations covering the whole current distribution. We performed coalescent genetic modelling of these dynamics, based on both whole-genome resequencing and microsatellite genotyping data. We found that the two main genetic groups of Amborella were shaped by the divergence of two ancestral populations during the last glacial maximum. From 12,800 years BP, the South ancestral population has expanded 6.3-fold while the size of the North population has remained stable. Recent asymmetric gene flow between the groups further contributed to the phylogeographical pattern. Spatially explicit coalescent modelling allowed us to estimate the location of ancestral populations with good accuracy (< 22 km) and provided indications regarding the mid-elevation pathways that facilitated post-glacial expansion.
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Affiliation(s)
- Rémi Tournebize
- UMR DIADE, Institut de Recherche pour le développement, University of Montpellier, Montpellier, France
| | - Stéphanie Manel
- UMR CEFE, Ecole Pratique des Hautes Etudes, PSL Research University, CNRS, University of Montpellier, Montpellier SupAgro, IRD, INRA, Montpellier, France
| | - Yves Vigouroux
- UMR DIADE, Institut de Recherche pour le développement, University of Montpellier, Montpellier, France
| | - François Munoz
- UMR AMAP, University of Montpellier, Montpellier, France
- French Institute of Pondicherry, Pondicherry, India
| | - Alexandre de Kochko
- UMR DIADE, Institut de Recherche pour le développement, University of Montpellier, Montpellier, France
| | - Valérie Poncet
- UMR DIADE, Institut de Recherche pour le développement, University of Montpellier, Montpellier, France
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11
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Nattier R, Pellens R, Robillard T, Jourdan H, Legendre F, Caesar M, Nel A, Grandcolas P. Updating the Phylogenetic Dating of New Caledonian Biodiversity with a Meta-analysis of the Available Evidence. Sci Rep 2017; 7:3705. [PMID: 28623347 PMCID: PMC5473893 DOI: 10.1038/s41598-017-02964-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/20/2017] [Indexed: 02/06/2023] Open
Abstract
For a long time, New Caledonia was considered a continental island, a fragment of Gondwana harbouring old clades that originated by vicariance and so were thought to be locally ancient. Recent molecular phylogenetic studies dating diversification and geological data indicating important events of submergence during the Paleocene and Eocene (until 37 Ma) brought evidence to dismiss this old hypothesis. In spite of this, some authors still insist on the idea of a local permanence of a Gondwanan biota, justifying this assumption through a complex scenario of survival by hopping to and from nearby and now-vanished islands. Based on a comprehensive review of the literature, we found 40 studies dating regional clades of diverse organisms and we used them to test the hypothesis that New Caledonian and inclusive Pacific island clades are older than 37 Ma. The results of this meta-analysis provide strong evidence for refuting the hypothesis of a Gondwanan refuge with a biota that originated by vicariance. Only a few inclusive Pacific clades (6 out of 40) were older than the oldest existing island. We suggest that these clades could have extinct members either on vanished islands or nearby continents, emphasizing the role of dispersal and extinction in shaping the present-day biota.
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Affiliation(s)
- Romain Nattier
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 CNRS MNHN UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, CP 50, 57 rue Cuvier, 75005, Paris, France.
| | - Roseli Pellens
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 CNRS MNHN UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, CP 50, 57 rue Cuvier, 75005, Paris, France
| | - Tony Robillard
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 CNRS MNHN UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, CP 50, 57 rue Cuvier, 75005, Paris, France
| | - Hervé Jourdan
- Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE), Aix Marseille Univ., Univ. Avignon, CNRS, IRD, Centre IRD Nouméa, BP A5, 98848, Nouméa Cedex, New Caledonia
| | - Frédéric Legendre
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 CNRS MNHN UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, CP 50, 57 rue Cuvier, 75005, Paris, France
| | - Maram Caesar
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 CNRS MNHN UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, CP 50, 57 rue Cuvier, 75005, Paris, France
| | - André Nel
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 CNRS MNHN UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, CP 50, 57 rue Cuvier, 75005, Paris, France
| | - Philippe Grandcolas
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 CNRS MNHN UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, CP 50, 57 rue Cuvier, 75005, Paris, France
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12
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Fogliani B, Gâteblé G, Villegente M, Fabre I, Klein N, Anger N, Baskin CC, Scutt CP. The morphophysiological dormancy in Amborella trichopoda seeds is a pleisiomorphic trait in angiosperms. Ann Bot 2017; 119:581-590. [PMID: 28087660 PMCID: PMC5379585 DOI: 10.1093/aob/mcw244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/05/2016] [Accepted: 10/05/2016] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS Recent parsimony-based reconstructions suggest that seeds of early angiosperms had either morphophysiological or physiological dormancy, with the former considered as more probable. The aim of this study was to determine the class of seed dormancy present in Amborella trichopoda , the sole living representative of the most basal angiosperm lineage Amborellales, with a view to resolving fully the class of dormancy present at the base of the angiosperm clade. METHODS Drupes of A. trichopoda without fleshy parts were germinated and dissected to observe their structure and embryo growth. Pre-treatments including acid scarification, gibberellin treatment and seed excision were tested to determine their influence on dormancy breakage and germination. Character-state mapping by maximum parsimony, incorporating data from the present work and published sources, was then used to determine the likely class of dormancy present in early angiosperms. KEY RESULTS Germination in A. trichopoda requires a warm stratification period of at least approx. 90 d, which is followed by endosperm swelling, causing the water-permeable pericarp-mesocarp envelope to split open. The embryo then grows rapidly within the seed, to radicle emergence some 17 d later and cotyledon emergence after an additional 24 d. Gibberellin treatment, acid scarification and excision of seeds from the surrounding drupe tissues all promoted germination by shortening the initial phase of dormancy, prior to embryo growth. CONCLUSIONS Seeds of A. trichopoda have non-deep simple morphophysiological dormancy, in which mechanical resistance of the pericarp-mesocarp envelope plays a key role in the initial physiological phase. Maximum parsimony analyses, including data obtained in the present work, indicate that morphophysiological dormancy is likely to be a pleisiomorphic trait in flowering plants. The significance of this conclusion for studies of early angiosperm evolution is discussed.
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Affiliation(s)
- Bruno Fogliani
- Institut Agronomique néo-Calédonien (IAC), BP 73 Port Laguerre, 98890 Païta, New Caledonia
- Laboratoire Insulaire du Vivant et de l’Environnement (LIVE)–EA 4243, University of New Caledonia (UNC), BP R4, 98851 Noumea, New Caledonia
| | - Gildas Gâteblé
- Institut Agronomique néo-Calédonien (IAC), BP 73 Port Laguerre, 98890 Païta, New Caledonia
| | - Matthieu Villegente
- Laboratoire Insulaire du Vivant et de l’Environnement (LIVE)–EA 4243, University of New Caledonia (UNC), BP R4, 98851 Noumea, New Caledonia
| | - Isabelle Fabre
- Institut Agronomique néo-Calédonien (IAC), BP 73 Port Laguerre, 98890 Païta, New Caledonia
| | - Nicolas Klein
- Institut Agronomique néo-Calédonien (IAC), BP 73 Port Laguerre, 98890 Païta, New Caledonia
- Laboratoire Insulaire du Vivant et de l’Environnement (LIVE)–EA 4243, University of New Caledonia (UNC), BP R4, 98851 Noumea, New Caledonia
| | - Nicolas Anger
- Institut Agronomique néo-Calédonien (IAC), BP 73 Port Laguerre, 98890 Païta, New Caledonia
| | - Carol C Baskin
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| | - Charlie P Scutt
- Reproduction et Développement des Plantes (RDP; UMR5667, CNRS-INRA-Université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d’Italie, 69364 Lyon Cedex 07, France
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13
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Trueba S, Isnard S, Barthélémy D, Olson ME. Trait coordination, mechanical behaviour and growth form plasticity of Amborella trichopoda under variation in canopy openness. AoB Plants 2016; 8:plw068. [PMID: 27672131 PMCID: PMC5142121 DOI: 10.1093/aobpla/plw068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 09/12/2016] [Indexed: 05/09/2023]
Abstract
Understanding the distribution of traits across the angiosperm phylogeny helps map the nested hierarchy of features that characterize key nodes. Finding that Amborella is sister to the rest of the angiosperms has raised the question of whether it shares certain key functional trait characteristics, and plastic responses apparently widespread within the angiosperms at large. With this in mind, we test the hypothesis that local canopy openness induces plastic responses. We used this variation in morphological and functional traits to estimate the pervasiveness of trait scaling and leaf and stem economics. We studied the architecture of Amborella and how it varies under different degrees of canopy openness. We analyzed the coordination of 12 leaf and stem structural and functional traits, and the association of this covariation with differing morphologies. The Amborella habit is made up of a series of sympodial modules that vary in size and branching pattern under different canopy openness. Amborella stems vary from self-supporting to semi-scandent. Changes in stem elongation and leaf size in Amborella produce distinct morphologies under different light environments. Correlations were found between most leaf and stem functional traits. Stem tissue rigidity decreased with increasing canopy openness. Despite substantial modulation of leaf size and leaf mass per area by light availability, branches in different light environments had similar leaf area-stem size scaling. The sympodial growth observed in Amborella could point to an angiosperm synapomorphy. Our study provides evidence of intraspecific coordination between leaf and stem economic spectra. Trait variation along these spectra is likely adaptive under different light environments and is consistent with these plastic responses having been present in the angiosperm common ancestor.
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Affiliation(s)
- Santiago Trueba
- IRD, UMR AMAP, Laboratoire de Botanique et d'Écologie Végétale Appliquées, Noumea, BPA5, 98800, New Caledonia
| | - Sandrine Isnard
- IRD, UMR AMAP, Laboratoire de Botanique et d'Écologie Végétale Appliquées, Noumea, BPA5, 98800, New Caledonia
| | - Daniel Barthélémy
- CIRAD, BIOS Direction, and INRA, UMR AMAP, F-34398 Montpellier, France
| | - Mark E Olson
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n de Ciudad Universitaria México, México DF 04510, México
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Ruhsam M, Clark A, Finger A, Wulff AS, Mill RR, Thomas PI, Gardner MF, Gaudeul M, Ennos RA, Hollingsworth PM. Hidden in plain view: Cryptic diversity in the emblematic Araucaria of New Caledonia. Am J Bot 2016; 103:888-898. [PMID: 27208357 DOI: 10.3732/ajb.1500487] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/30/2016] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Cryptic species represent a conservation challenge, because distributions and threats cannot be accurately assessed until species are recognized and defined. Cryptic species are common in diminutive and morphologically simple organisms, but are rare in charismatic and/or highly visible groups such as conifers. New Caledonia, a small island in the southern Pacific is a hotspot of diversity for the emblematic conifer genus Araucaria (Araucariaceae, Monkey Puzzle trees) where 13 of the 19 recognized species are endemic. METHODS We sampled across the entire geographical distribution of two closely related species (Araucaria rulei and A. muelleri) and screened them for genetic variation at 12 nuclear and 14 plastid microsatellites and one plastid minisatellite; a subset of the samples was also examined using leaf morphometrics. KEY RESULTS The genetic data show that populations of the endangered A. muelleri fall into two clearly distinct genetic groups: one corresponding to montane populations, the other corresponding to trees from lower elevation populations from around the Goro plateau. These Goro plateau populations are more closely related to A. rulei, but are sufficiently genetically and morphological distinct to warrant recognition as a new species. CONCLUSIONS Our study shows the presence of a previously unrecognized species in this flagship group, and that A. muelleri has 30% fewer individuals than previously thought. Combined, this clarification of species diversity and distributions provides important information to aid conservation planning for New Caledonian Araucaria.
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Affiliation(s)
- Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Alexandra Clark
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Aline Finger
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Adrien S Wulff
- SoREco-NC, 57 Route de l'Anse Vata 98800 Nouméa, New Caledonia Institut Agronomique néo-Calédonien (IAC), Axe II "Diversités biologique et fonctionnelle des écosystèmes, BP 73 98890 Païta, New Caledonia
| | - Robert R Mill
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Philip I Thomas
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Martin F Gardner
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Myriam Gaudeul
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 CNRS MNHN UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, CP39, F-75005 Paris, France
| | - Richard A Ennos
- University of Edinburgh, Institute of Evolutionary Biology, West Mains Road, Edinburgh, EH3 9JT, UK
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15
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Anso J, Barrabé L, Desutter-Grandcolas L, Jourdan H, Grandcolas P, Dong J, Robillard T. Old Lineage on an Old Island: Pixibinthus, a New Cricket Genus Endemic to New Caledonia Shed Light on Gryllid Diversification in a Hotspot of Biodiversity. PLoS One 2016; 11:e0150920. [PMID: 27027632 PMCID: PMC4814057 DOI: 10.1371/journal.pone.0150920] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 02/22/2016] [Indexed: 12/28/2022] Open
Abstract
Few studies have focused on the early colonization of New Caledonia by insects, after the re-emergence of the main island, 37 Myr ago. Here we investigate the mode and tempo of evolution of a new endemic cricket genus, Pixibinthus, recently discovered in southern New Caledonia. First we formally describe this new monotypic genus found exclusively in the open shrubby vegetation on metalliferous soils, named 'maquis minier', unique to New Caledonia. We then reconstruct a dated molecular phylogeny based on five mitochondrial and four nuclear loci in order to establish relationships of Pixibinthus within Eneopterinae crickets. Pixibinthus is recovered as the sister clade of the endemic genus Agnotecous, mostly rainforest-dwellers. Dating results show that the island colonization by their common ancestor occurred around 34.7 Myr, shortly after New Caledonia re-emergence. Pixibinthus and Agnotecous are then one of the oldest insect lineages documented so far for New Caledonia. This discovery highlights for the first time two clear-cut ecological specializations between sister clades, as Agnotecous is mainly found in rainforests with 19 species, whereas Pixibinthus is found in open habitats with a single documented species. The preference of Pixibinthus for open habitats and of Agnotecous for forest habitats nicely fits an acoustic specialization, either explained by differences in body size or in acoustic properties of their respective habitats. We hypothesize that landscape dynamics, linked to major past climatic events and recent change in fire regimes are possible causes for both present-day low diversity and rarity in genus Pixibinthus. The unique evolutionary history of this old New Caledonian lineage stresses the importance to increase our knowledge on the faunal biodiversity of 'maquis minier', in order to better understand the origin and past dynamics of New Caledonian biota.
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Affiliation(s)
- Jérémy Anso
- Muséum national d'Histoire naturelle, Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 – CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France
- Institut Méditerranéen de Biodiversité et d’Écologie marine et continentale (IMBE), Aix Marseille Université, CNRS, IRD, Avignon Université UMR IRD 237 IMBE, Centre IRD Nouméa, Nouvelle-Calédonie
| | - Laure Barrabé
- Laboratoire de Botanique et d’Ecologie Végétales Appliquées, Herbarium NOU, UMR 123: botAnique et Modélisation de l’Architecture des Plantes et des vegetations (AMAP), Centre IRD Nouméa, Nouvelle-Calédonie
| | - Laure Desutter-Grandcolas
- Muséum national d'Histoire naturelle, Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 – CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France
| | - Hervé Jourdan
- Institut Méditerranéen de Biodiversité et d’Écologie marine et continentale (IMBE), Aix Marseille Université, CNRS, IRD, Avignon Université UMR IRD 237 IMBE, Centre IRD Nouméa, Nouvelle-Calédonie
| | - Philippe Grandcolas
- Muséum national d'Histoire naturelle, Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 – CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France
| | - Jiajia Dong
- Muséum national d'Histoire naturelle, Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 – CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France
| | - Tony Robillard
- Muséum national d'Histoire naturelle, Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 – CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France
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16
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Fourcade F, Pouteau R, Jaffré T, Marmey P. In situ observations of the basal angiosperm Amborella trichopoda reveal a long fruiting cycle overlapping two annual flowering periods. J Plant Res 2015; 128:821-828. [PMID: 26178522 DOI: 10.1007/s10265-015-0744-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 06/08/2015] [Indexed: 06/04/2023]
Abstract
Amborella trichopoda is the sole living angiosperm species belonging to the sister lineage of all other extant flowering plants. In the last decade, the species has been the focus of many phylogenetic, genomic and reproductive biology studies, bringing new highlights regarding the evolution of flowering plants. However, little attention has been paid to in situ A. trichopoda populations, particularly to their fruiting cycle. In this study, an A. trichopoda population was observed during three annual flowering cycles. Individuals and branches were labeled in order to monitor the fruiting cycle precisely, from the flowering stage until the abscission of the fruit. Fruit exocarp was green during the first 9 months following flowering, turned red when the next flowering started a year later then remained on the branch during another year, between fruit ripping and abscission. Presence of fruits with two stages of maturity on shrubs was always noticed. Germination tests showed that seeds acquired their germination capacity 1 year after flowering, when fruits changed color. A. trichopoda's fruiting cycle is a long process overlapping two annual flowering periods. These results introduce a new model for flowering and fruiting cycles. The availability of mature seeds on shrubs for more than 1 year is likely to maximize opportunities to be dispersed, thus promoting the survival of this basal angiosperm.
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Affiliation(s)
- Fanny Fourcade
- Institut de Recherche pour le Développement (IRD), UMR DIADE, 101 Promenade Roger Laroque Anse Vata, BPA5, 98848, Nouméa, New Caledonia
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17
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Poncet V, Scutt C, Tournebize R, Villegente M, Cueff G, Rajjou L, Balliau T, Zivy M, Fogliani B, Job C, de Kochko A, Sarramegna-Burtet V, Job D. The Amborella vacuolar processing enzyme family. Front Plant Sci 2015; 6:618. [PMID: 26347753 PMCID: PMC4544213 DOI: 10.3389/fpls.2015.00618] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/27/2015] [Indexed: 05/30/2023]
Abstract
Most vacuolar proteins are synthesized on rough endoplasmic reticulum as proprotein precursors and then transported to the vacuoles, where they are converted into their respective mature forms by vacuolar processing enzymes (VPEs). In the case of the seed storage proteins, this process is of major importance, as it conditions the establishment of vigorous seedlings. Toward the goal of identifying proteome signatures that could be associated with the origin and early diversification of angiosperms, we previously characterized the 11S-legumin-type seed storage proteins from Amborella trichopoda, a rainforest shrub endemic to New Caledonia that is also the probable sister to all other angiosperms (Amborella Genome Project, 2013). In the present study, proteomic and genomic approaches were used to characterize the VPE family in this species. Three genes were found to encode VPEs in the Amborella's genome. Phylogenetic analyses showed that the Amborella sequences grouped within two major clades of angiosperm VPEs, indicating that the duplication that generated the ancestors of these clades occurred before the most recent common ancestor of living angiosperms. A further important duplication within the VPE family appears to have occurred in common ancestor of the core eudicots, while many more recent duplications have also occurred in specific taxa, including both Arabidopsis thaliana and Amborella. An analysis of natural genetic variation for each of the three Amborella VPE genes revealed the absence of selective forces acting on intronic and exonic single-nucleotide polymorphisms among several natural Amborella populations in New Caledonia.
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Affiliation(s)
- Valérie Poncet
- Institut de Recherche pour le Développement, UMR Diversité, Adaptation et Développement des PlantesMontpellier, France
| | - Charlie Scutt
- Laboratoire Reproduction et Développement des Plantes, UMR 5667, Ecole Normale Supérieure de LyonLyon, France
| | - Rémi Tournebize
- Institut de Recherche pour le Développement, UMR Diversité, Adaptation et Développement des PlantesMontpellier, France
| | - Matthieu Villegente
- Laboratoire Insulaire du Vivant et de l'Environnement, Université de la Nouvelle-CalédonieNouméa, New Caledonia
| | - Gwendal Cueff
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, UMR 1318 Institut National de la Recherche Agronomique/AgroParisTech, ERL Centre National de la Recherche Scientifique 3559, Laboratoire d'Excellence “Saclay Plant Sciences” (LabEx SPS), RD10Versailles, France
- AgroParisTech, Chaire de Physiologie VégétaleParis, France
| | - Loïc Rajjou
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, UMR 1318 Institut National de la Recherche Agronomique/AgroParisTech, ERL Centre National de la Recherche Scientifique 3559, Laboratoire d'Excellence “Saclay Plant Sciences” (LabEx SPS), RD10Versailles, France
- AgroParisTech, Chaire de Physiologie VégétaleParis, France
| | - Thierry Balliau
- Institut National de la Recherche Agronomique, Plateforme d'Analyse Protéomique de Paris Sud-Ouest, Institut National de la Recherche Agronomique/Université Paris-Sud/Centre National de la Recherche Scientifique/AgroParisTech, UMR 0320/UMR 8120 Génétique Quantitative et Evolution – Le MoulonGif-sur-Yvette, France
| | - Michel Zivy
- Institut National de la Recherche Agronomique, Plateforme d'Analyse Protéomique de Paris Sud-Ouest, Institut National de la Recherche Agronomique/Université Paris-Sud/Centre National de la Recherche Scientifique/AgroParisTech, UMR 0320/UMR 8120 Génétique Quantitative et Evolution – Le MoulonGif-sur-Yvette, France
| | - Bruno Fogliani
- Laboratoire Insulaire du Vivant et de l'Environnement, Université de la Nouvelle-CalédonieNouméa, New Caledonia
- Institut Agronomique Néo-Calédonien, Diversités Biologique et Fonctionnelle des Ecosystèmes TerrestresPaïta, New Caledonia
| | - Claudette Job
- UMR 5240 Laboratoire Mixte Centre National de la Recherche Scientifique/Institut National des Sciences Appliquées/Université Claude Bernard Lyon 1/Bayer CropScienceLyon, France
| | - Alexandre de Kochko
- Institut de Recherche pour le Développement, UMR Diversité, Adaptation et Développement des PlantesMontpellier, France
| | - Valérie Sarramegna-Burtet
- Laboratoire Insulaire du Vivant et de l'Environnement, Université de la Nouvelle-CalédonieNouméa, New Caledonia
| | - Dominique Job
- AgroParisTech, Chaire de Physiologie VégétaleParis, France
- UMR 5240 Laboratoire Mixte Centre National de la Recherche Scientifique/Institut National des Sciences Appliquées/Université Claude Bernard Lyon 1/Bayer CropScienceLyon, France
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Birnbaum P, Ibanez T, Pouteau R, Vandrot H, Hequet V, Blanchard E, Jaffré T. Environmental correlates for tree occurrences, species distribution and richness on a high-elevation tropical island. AoB Plants 2015; 7:plv075. [PMID: 26162898 PMCID: PMC4561634 DOI: 10.1093/aobpla/plv075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 06/27/2015] [Indexed: 05/24/2023]
Abstract
High-elevation tropical islands are ideally suited for examining the factors that determine species distribution, given the complex topographies and climatic gradients that create a wide variety of habitats within relatively small areas. New Caledonia, a megadiverse Pacific archipelago, has long focussed the attention of botanists working on the spatial and environmental ranges of specific groups, but few studies have embraced the entire tree flora of the archipelago. In this study we analyse the distribution of 702 native species of rainforest trees of New Caledonia, belonging to 195 genera and 80 families, along elevation and rainfall gradients on ultramafic (UM) and non-ultramafic (non-UM) substrates. We compiled four complementary data sources: (i) herbarium specimens, (ii) plots, (iii) photographs and (iv) observations, totalling 38 936 unique occurrences distributed across the main island. Compiled into a regular 1-min grid (1.852 × 1.852 km), this dataset covered ∼22 % of the island. The studied rainforest species exhibited high environmental tolerance; 56 % of them were not affiliated to a substrate type and they exhibited wide elevation (average 891 ± 332 m) and rainfall (average 2.2 ± 0.8 m year(-1)) ranges. Conversely their spatial distribution was highly aggregated, which suggests dispersal limitation. The observed species richness was driven mainly by the density of occurrences. However, at the highest elevations or rainfalls, and particularly on UM, the observed richness tends to be lower, independently of the sampling effort. The study highlights the imbalance of the dataset in favour of higher values of rainfall and of elevation. Projected onto a map, under-represented areas are a guide as to where future sampling efforts are most required to complete our understanding of rainforest tree species distribution.
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Affiliation(s)
- Philippe Birnbaum
- CIRAD, UMR 51 AMAP, 34398 Montpellier, France Laboratory of Applied Botany and Plant Ecology, Institut Agronomique néo-Calédonien (IAC), Diversité biologique et fonctionnelle des écosystèmes terrestes, 98848 Noumea, New Caledonia
| | - Thomas Ibanez
- Laboratory of Applied Botany and Plant Ecology, Institut Agronomique néo-Calédonien (IAC), Diversité biologique et fonctionnelle des écosystèmes terrestes, 98848 Noumea, New Caledonia
| | - Robin Pouteau
- Laboratory of Applied Botany and Plant Ecology, Institut Agronomique néo-Calédonien (IAC), Diversité biologique et fonctionnelle des écosystèmes terrestes, 98848 Noumea, New Caledonia Laboratory of Applied Botany and Plant Ecology, Institut de Recherche pour le Développement (IRD), UMR 123 AMAP, 98848 Noumea, New Caledonia
| | - Hervé Vandrot
- Laboratory of Applied Botany and Plant Ecology, Institut Agronomique néo-Calédonien (IAC), Diversité biologique et fonctionnelle des écosystèmes terrestes, 98848 Noumea, New Caledonia
| | - Vanessa Hequet
- Laboratory of Applied Botany and Plant Ecology, Institut de Recherche pour le Développement (IRD), UMR 123 AMAP, 98848 Noumea, New Caledonia
| | - Elodie Blanchard
- Laboratory of Applied Botany and Plant Ecology, Institut Agronomique néo-Calédonien (IAC), Diversité biologique et fonctionnelle des écosystèmes terrestes, 98848 Noumea, New Caledonia
| | - Tanguy Jaffré
- Laboratory of Applied Botany and Plant Ecology, Institut de Recherche pour le Développement (IRD), UMR 123 AMAP, 98848 Noumea, New Caledonia
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Gaudeul M, Gardner MF, Thomas P, Ennos RA, Hollingsworth PM. Evolutionary dynamics of emblematic Araucaria species (Araucariaceae) in New Caledonia: nuclear and chloroplast markers suggest recent diversification, introgression, and a tight link between genetics and geography within species. BMC Evol Biol 2014; 14:171. [PMID: 25189104 PMCID: PMC4182765 DOI: 10.1186/s12862-014-0171-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 07/23/2014] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND New Caledonia harbours a highly diverse and endemic flora, and 13 (out of the 19 worldwide) species of Araucaria are endemic to this territory. Their phylogenetic relationships remain largely unresolved. Using nuclear microsatellites and chloroplast DNA sequencing, we focused on five closely related Araucaria species to investigate among-species relationships and the distribution of within-species genetic diversity across New Caledonia. RESULTS The species could be clearly distinguished here, except A. montana and A. laubenfelsii that were not differentiated and, at most, form a genetic cline. Given their apparent morphological and ecological similarity, we suggested that these two species may be considered as a single evolutionary unit. We observed cases of nuclear admixture and incongruence between nuclear and chloroplast data, probably explained by introgression and shared ancestral polymorphism. Ancient hybridization was evidenced between A. biramulata and A. laubenfelsii in Mt Do, and is strongly suspected between A. biramulata and A. rulei in Mt Tonta. In both cases, extensive asymmetrical backcrossing eliminated the influence of one parent in the nuclear DNA composition. Shared ancestral polymorphism was also observed for cpDNA, suggesting that species diverged recently, have large effective sizes and/or that cpDNA experienced slow rates of molecular evolution. Within-species genetic structure was pronounced, probably because of low gene flow and significant inbreeding, and appeared clearly influenced by geography. This may be due to survival in distinct refugia during Quaternary climatic oscillations. CONCLUSIONS The study species probably diverged recently and/or are characterized by a slow rate of cpDNA sequence evolution, and introgression is strongly suspected. Within-species genetic structure is tightly linked with geography. We underline the conservation implications of our results, and highlight several perspectives.
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Rice DW, Alverson AJ, Richardson AO, Young GJ, Sanchez-Puerta MV, Munzinger J, Barry K, Boore JL, Zhang Y, dePamphilis CW, Knox EB, Palmer JD. Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella. Science 2014; 342:1468-73. [PMID: 24357311 DOI: 10.1126/science.1246275] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We report the complete mitochondrial genome sequence of the flowering plant Amborella trichopoda. This enormous, 3.9-megabase genome contains six genome equivalents of foreign mitochondrial DNA, acquired from green algae, mosses, and other angiosperms. Many of these horizontal transfers were large, including acquisition of entire mitochondrial genomes from three green algae and one moss. We propose a fusion-compatibility model to explain these findings, with Amborella capturing whole mitochondria from diverse eukaryotes, followed by mitochondrial fusion (limited mechanistically to green plant mitochondria) and then genome recombination. Amborella's epiphyte load, propensity to produce suckers from wounds, and low rate of mitochondrial DNA loss probably all contribute to the high level of foreign DNA in its mitochondrial genome.
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Affiliation(s)
- Danny W Rice
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Abstract
Amborella trichopoda is strongly supported as the single living species of the sister lineage to all other extant flowering plants, providing a unique reference for inferring the genome content and structure of the most recent common ancestor (MRCA) of living angiosperms. Sequencing the Amborella genome, we identified an ancient genome duplication predating angiosperm diversification, without evidence of subsequent, lineage-specific genome duplications. Comparisons between Amborella and other angiosperms facilitated reconstruction of the ancestral angiosperm gene content and gene order in the MRCA of core eudicots. We identify new gene families, gene duplications, and floral protein-protein interactions that first appeared in the ancestral angiosperm. Transposable elements in Amborella are ancient and highly divergent, with no recent transposon radiations. Population genomic analysis across Amborella's native range in New Caledonia reveals a recent genetic bottleneck and geographic structure with conservation implications.
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Turner B, Paun O, Munzinger J, Duangjai S, Chase MW, Samuel R. Analyses of amplified fragment length polymorphisms (AFLP) indicate rapid radiation of Diospyros species (Ebenaceae) endemic to New Caledonia. BMC Evol Biol 2013; 13:269. [PMID: 24330478 PMCID: PMC3881503 DOI: 10.1186/1471-2148-13-269] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 12/09/2013] [Indexed: 11/24/2022] Open
Abstract
Background Radiation in some plant groups has occurred on islands and due to the characteristic rapid pace of phenotypic evolution, standard molecular markers often provide insufficient variation for phylogenetic reconstruction. To resolve relationships within a clade of 21 closely related New Caledonian Diospyros species and evaluate species boundaries we analysed genome-wide DNA variation via amplified fragment length polymorphisms (AFLP). Results A neighbour-joining (NJ) dendrogram based on Dice distances shows all species except D. minimifolia, D. parviflora and D. vieillardii to form unique clusters of genetically similar accessions. However, there was little variation between these species clusters, resulting in unresolved species relationships and a star-like general NJ topology. Correspondingly, analyses of molecular variance showed more variation within species than between them. A Bayesian analysis with BEAST produced a similar result. Another Bayesian method, this time a clustering method, Structure, demonstrated the presence of two groups, highly congruent with those observed in a principal coordinate analysis (PCO). Molecular divergence between the two groups is low and does not correspond to any hypothesised taxonomic, ecological or geographical patterns. Conclusions We hypothesise that such a pattern could have been produced by rapid and complex evolution involving a widespread progenitor for which an initial split into two groups was followed by subsequent fragmentation into many diverging populations, which was followed by range expansion of then divergent entities. Overall, this process resulted in an opportunistic pattern of phenotypic diversification. The time since divergence was probably insufficient for some species to become genetically well-differentiated, resulting in progenitor/derivative relationships being exhibited in a few cases. In other cases, our analyses may have revealed evidence for the existence of cryptic species, for which more study of morphology and ecology are now required.
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Affiliation(s)
- Barbara Turner
- Department of Systematic and Evolutionary Botany, Faculty of Life Sciences, University Vienna, Rennweg 14, 1030 Wien, Austria.
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