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Couvreur TLP, Helmstetter AJ, Koenen EJM, Bethune K, Brandão RD, Little SA, Sauquet H, Erkens RHJ. Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes. Front Plant Sci 2019; 9:1941. [PMID: 30687347 PMCID: PMC6334231 DOI: 10.3389/fpls.2018.01941] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/13/2018] [Indexed: 05/19/2023]
Abstract
Targeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. Annonaceae is a major pantropical plant family with 110 genera and ca. 2,450 species, occurring across all major and minor tropical forests of the world. Baits were designed by sequencing the transcriptomes of five species from two of the largest Annonaceae subfamilies. Orthologous loci were identified. The resulting baiting kit was used to reconstruct phylogenetic relationships at two different levels using concatenated and gene tree approaches: a family wide Annonaceae analysis sampling 65 genera and a species level analysis of tribe Piptostigmateae sampling 29 species with multiple individuals per species. DNA extraction was undertaken mainly on silicagel dried leaves, with two samples from herbarium dried leaves. Our kit targets 469 exons (364,653 bp of sequence data), successfully capturing sequences from across Annonaceae. Silicagel dried and herbarium DNA worked equally well. We present for the first time a nuclear gene-based phylogenetic tree at the generic level based on 317 supercontigs. Results mainly confirm previous chloroplast based studies. However, several new relationships are found and discussed. We show significant differences in branch lengths between the two large subfamilies Annonoideae and Malmeoideae. A new tribe, Annickieae, is erected containing a single African genus Annickia. We also reconstructed a well-resolved species-level phylogenetic tree of the Piptostigmteae tribe. Our baiting kit is useful for reconstructing well-supported phylogenetic relationships within Annonaceae at different taxonomic levels. The nuclear genome is mainly concordant with plastome information with a few exceptions. Moreover, we find that substitution rate heterogeneity between the two subfamilies is also found within the nuclear compartment, and not just plastomes and ribosomal DNA as previously shown. Our results have implications for understanding the biogeography, molecular dating and evolution of Annonaceae.
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Affiliation(s)
| | | | - Erik J. M. Koenen
- Institute of Systematic Botany, University of Zurich, Zurich, Switzerland
| | - Kevin Bethune
- IRD, UMR DIADE, Univ. Montpellier, Montpellier, France
| | - Rita D. Brandão
- Maastricht Science Programme, Maastricht University, Maastricht, Netherlands
| | - Stefan A. Little
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université-Paris Saclay, Orsay, France
| | - Hervé Sauquet
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université-Paris Saclay, Orsay, France
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Roy H. J. Erkens
- Maastricht Science Programme, Maastricht University, Maastricht, Netherlands
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Pirie MD, Chatrou LW, Maas PJM. A taxonomic revision of the Neotropical genus Cremastosperma (Annonaceae), including five new species. PhytoKeys 2018; 112:1-141. [PMID: 30524186 PMCID: PMC6277488 DOI: 10.3897/phytokeys.112.24897] [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] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 10/12/2018] [Indexed: 06/09/2023]
Abstract
We present a taxonomic revision of Cremastosperma, a genus of Neotropical Annonaceae occurring in lowland to premontane wet forest, mostly in areas surrounding the Andean mountain chain. We recognise 34 species, describing five as new here: from east of the Andes, C.brachypodum Pirie & Chatrou, sp. nov. and C.dolichopodum Pirie & Maas, sp. nov., endemic to Peru; C.confusum Pirie, sp. nov., from southern Peru and adjacent Bolivia and Brazil; and C.alticola Pirie & Chatrou, sp. nov., at higher elevations in northern Peru and Ecuador; and from west of the Andes, C.osicola Pirie & Chatrou, sp. nov. endemic to Costa Rica, the most northerly distributed species of the genus. We provide an identification key, document diagnostic characters and distributions and provide illustrations and extensive lists of specimens, also presenting the latter in the form of mapping data with embedded links to images available online. Of the 34 species, 22 are regional endemics. On the basis of the extent of occurrence and area of occupancy of species estimated from the distribution data, we designate IUCN threat categries for all species. Fourteen species proved to be endangered (EN) and a further one critically endangered (CR), reflecting their rarity and narrow known distributions.
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Affiliation(s)
- Michael D. Pirie
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099 Mainz, GermanyJohannes Gutenberg-UniversitätMainzGermany
| | - Lars W. Chatrou
- Wageningen University and Research, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB Wageningen, The NetherlandsWageningen UniversityWageningenNetherlands
- Ghent University, Systematic and Evolutionary Botany lab, K.L. Ledeganckstraat 35, 9000 Ghent, BelgiumGhent UniversityGhentBelgium
| | - Paul J. M. Maas
- Naturalis Biodiversity Center, section Botany, P.O. Box 9517, 2300 RA Leiden, The NetherlandsNaturalis Biodiversity CenterWageningenNetherlands
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Chatrou LW, Turner IM, Klitgaard BB, Maas PJM, Utteridge TMA. A linear sequence to facilitate curation of herbarium specimens of Annonaceae. Kew Bull 2018; 73:39. [PMID: 30956369 PMCID: PMC6413810 DOI: 10.1007/s12225-018-9764-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/19/2018] [Indexed: 06/09/2023]
Abstract
This paper provides a linear sequence of four subfamilies, 15 tribes and 106 genera of the magnoliid family Annonaceae, based on state-of-the-art and stable phylogenetic relationships. The linear sequence facilitates the organisation of Annonaceae herbarium specimens.
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Affiliation(s)
- Lars W. Chatrou
- Wageningen University and Research, Biosystematics group, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ian M. Turner
- Singapore Botanical Liaison Officer, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
- Herbarium, Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, Singapore, 259569 Singapore
| | | | - Paul J. M. Maas
- Naturalis Biodiversity Center, Section Botany, P.O. Box 9517, 2300 RA Leiden, The Netherlands
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Hoekstra PH, Wieringa JJ, Smets E, Chatrou LW. Floral evolution by simplification in Monanthotaxis (Annonaceae) and hypotheses for pollination system shifts. Sci Rep 2018; 8:12066. [PMID: 30104579 PMCID: PMC6089970 DOI: 10.1038/s41598-018-30607-2] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/16/2018] [Indexed: 12/25/2022] Open
Abstract
Simplification by reduction has occurred many times independently in the floral evolution of angiosperms. These reductions have often been attributed to changes in reproductive biology. In the angiosperm plant family Annonaceae, most species have flowers with six petals, and many stamens and carpels. In the genus Monanthotaxis several deviations from this pattern have been observed, including flowers that contain three petals and three stamens only. New DNA sequences were generated for 42 specimens of Monanthotaxis. Five chloroplast markers and two nuclear markers for 72 out of 94 species of Monanthotaxis were used to reconstruct a phylogeny of the genus, which revealed several well-supported, morphologically distinct clades. The evolution of four quantitative and two qualitative floral characters was mapped onto this phylogeny, demonstrating a reduction in flower size and number of flower parts in Monanthotaxis. A large variation in stamen forms and numbers, strong correlations between petal size, stamen and carpel number, combined with a non-gradual mode of evolution and the sympatric co-occurrence of Monanthotaxis species from different clades suggest that the high diversity in the African rainforest of this genus is caused by switches in pollination systems.
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Affiliation(s)
- Paul H Hoekstra
- Naturalis Biodiversity Center, National Herbarium of the Netherlands, Darwinweg 2, 2300 RA, Leiden, The Netherlands. .,Wageningen University & Research, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Jan J Wieringa
- Naturalis Biodiversity Center, National Herbarium of the Netherlands, Darwinweg 2, 2300 RA, Leiden, The Netherlands.,Wageningen University & Research, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Erik Smets
- Naturalis Biodiversity Center, National Herbarium of the Netherlands, Darwinweg 2, 2300 RA, Leiden, The Netherlands.,Ecology, Evolution and Biodiversity Conservation Section, KU Leuven, Kasteelpark Arenberg 31, box 2435, 3001, Leuven, Belgium
| | - Lars W Chatrou
- Wageningen University & Research, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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Ortiz-Rodriguez AE, Ornelas JF, Ruiz-Sanchez E. A jungle tale: Molecular phylogeny and divergence time estimates of the Desmopsis-Stenanona clade (Annonaceae) in Mesoamerica. Mol Phylogenet Evol 2018; 122:80-94. [PMID: 29407482 DOI: 10.1016/j.ympev.2018.01.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 01/27/2018] [Accepted: 01/27/2018] [Indexed: 01/20/2023]
Abstract
The predominantly Asian tribe Miliuseae (Annonaceae) includes over 37 Neotropical species that are mainly distributed across Mesoamerica, from southern Mexico to northern Colombia. The tremendous ecological and morphological diversity of this clade, including ramiflory, cauliflory, flagelliflory, and clonality, suggests adaptive radiation. Despite the spectacular phenotypic divergence of this clade, little is known about its phylogenetic and evolutionary history. In this study we used a nuclear DNA marker and seven chloroplast markers, and maximum parsimony, maximum likelihood and Bayesian inference methods to reconstruct a comprehensive time-calibrated phylogeny of tribe Miliuseae, especially focusing on the Desmopsis-Stenanona clade. We also perform ancestral area reconstructions to infer the biogeographic history of this group. Finally, we use ecological niche modeling, lineage distribution models, and niche overlap tests to assess whether geographic isolation and ecological specialization influenced the diversification of lineages within this clade. We reconstructed a monophyletic Miliuseae that is divided into two strongly supported clades: (i) a Sapranthus-Tridimeris clade and (ii) a Desmopsis-Stenanona clade. The colonization of the Neotropics and subsequent diversification of Neotropical Miliuseae seems to have been associated with the expansion of the boreotropical forests during the late Eocene and their subsequent fragmentation and southern displacement. Further speciation within Neotropical Miliuseae out of the Maya block seems to have occurred during the last 15 million years. Lastly, the geographic structuring of major lineages of the Desmopsis-Stenanona clade seems to have followed a climatic gradient, supporting the hypothesis that morphological differentiation between closely related species resulted from both long-term isolation between geographic ranges and adaptation to environmental conditions.
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Lopes JC, Chatrou LW, Mello-Silva R, Rudall PJ, Sajo MG. Phylogenomics and evolution of floral traits in the Neotropical tribe Malmeeae (Annonaceae). Mol Phylogenet Evol 2017; 118:379-391. [PMID: 29111476 DOI: 10.1016/j.ympev.2017.10.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/20/2017] [Accepted: 10/26/2017] [Indexed: 11/18/2022]
Abstract
Androdioecy is the rarest sexual system among plants. The majority of androdioecious species are herbaceous plants that have evolved from dioecious ancestors. Nevertheless, some woody and androdioecious plants have hermaphrodite ancestors, as in the Annonaceae, where androdioecious genera have arisen several times in different lineages. The majority of androdioecious species of Annonaceae belong to the Neotropical tribe Malmeeae. In addition to these species, Pseudoxandra spiritus-sancti was recently confirmed to be androdioecious. Here, we describe the morphology of male and bisexual flowers of Pseudoxandra spiritus-sancti, and investigate the evolution of androdioecy in Malmeeae. The phylogeny of tribe Malmeeae was reconstructed using Bayesian inference, maximum parsimony and maximum likelihood of 32 taxa, using DNA sequences of 66 molecular markers of the chloroplast genome, sequenced by next generation sequencing. The reconstruction of ancestral states was performed for characters associated with sexual systems and floral morphology. The phylogenetic analyses reconstructed three main groups in Malmeeae, (Malmea (Cremastosperma, Pseudoxandra)) sister to the rest of the tribe, and (Unonopsis (Bocageopsis, Onychopetalum)) sister to (Mosannona, Ephedranthus, Klarobelia, Oxandra, Pseudephedranthus fragrans, Pseudomalmea, Ruizodendron ovale). Hermaphroditism is plesiomorphic in the tribe, with four independent evolutions of androdieocy, which represents a synapomorphy of two groups, one that includes three genera and 14 species, the other with a single genus of seven species. Male flowers are unisexual from inception and bisexual flowers possess staminodes and functional stamens. Pseudoxandra spiritus-sancti is structurally androdioecious.
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Affiliation(s)
- J C Lopes
- Universidade de São Paulo, Instituto de Biociências, Departamento de Botânica, Rua do Matão, 277, 05508-090 São Paulo, SP, Brazil.
| | - L W Chatrou
- Wageningen University and Research, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - R Mello-Silva
- Universidade de São Paulo, Instituto de Biociências, Departamento de Botânica, Rua do Matão, 277, 05508-090 São Paulo, SP, Brazil
| | - P J Rudall
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - M G Sajo
- Universidade Estadual Paulista, Instituto de Biociências, Departamento de Botânica, Avenida 24A, 13506-900 Rio Claro, SP, Brazil
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