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Gutiérrez-Ortega JS, Pérez-Farrera MA, Matsuo A, Sato MP, Suyama Y, Calonje M, Vovides AP, Kajita T, Watano Y. The phylogenetic reconstruction of the Neotropical cycad genus Ceratozamia (Zamiaceae) reveals disparate patterns of niche evolution. Mol Phylogenet Evol 2024; 190:107960. [PMID: 37918683 DOI: 10.1016/j.ympev.2023.107960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
The cycad genus Ceratozamia comprises 40 species from Mexico, Guatemala, Belize, and Honduras, where cycads occur throughout climatically varied montane habitats. Ceratozamia has the potential to reveal the history and processes of species diversification across diverse Neotropical habitats in this region. However, the species relationships within Ceratozamia and the ecological trends during its evolution remain unclear. Here, we aimed to clarify the phylogenetic relationships, the timing of clade and species divergences, and the niche evolution throughout the phylogenetic history of Ceratozamia. Genome-wide DNA sequences were obtained with MIG-seq, and multiple data-filtering steps were used to optimize the dataset used to construct an ultrametric species tree. Divergence times among branches and ancestral niches were estimated. The niche variation among species was evaluated, summarized into two principal components, and their ancestral states were reconstructed to test whether niche shifts among branches can be explained by random processes, under a Brownian Motion model. Ceratozamia comprises three main clades, and most species relationships within the clades were resolved. Ceratozamia has diversified since the Oligocene, with major branching events occurring during the Miocene. This timing is consistent with fossil evidence, the timing estimated for other Neotropical plant groups, and the major geological events that shaped the topographic and climatic variation in Mexico. Patterns of niche evolution in the genus do not accord with the Brownian Motion model. Rather, non-random evolution with shifts towards more seasonal environments at high latitudes, or shifts towards humid or dry environments at low latitudes explain the diversification of Ceratozamia. We present a comprehensive phylogenetic reconstruction for Ceratozamia and identify for the first time the environmental factors involved in clade and species diversification within the genus. This study alleviates the controversies regarding the species relationships in the genus and provides the first evidence that latitude-associated environmental factors may influence processes of niche evolution in cycads.
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Affiliation(s)
| | - Miguel Angel Pérez-Farrera
- Herbario Eizi Matuda, Laboratorio de Ecología Evolutiva, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez 29039, Mexico.
| | - Ayumi Matsuo
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Mitsuhiko P Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | | | - Andrew P Vovides
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C., 91070 Xalapa, Mexico
| | - Tadashi Kajita
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Uehara, Yaeyama, Okinawa 907-1541, Japan
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
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Gutiérrez-Ortega JS, Salinas-Rodríguez MM, Ito T, Pérez-Farrera MA, Vovides AP, Martínez JF, Molina-Freaner F, Hernández-López A, Kawaguchi L, Nagano AJ, Kajita T, Watano Y, Tsuchimatsu T, Takahashi Y, Murakami M. Niche conservatism promotes speciation in cycads: the case of Dioon merolae (Zamiaceae) in Mexico. New Phytol 2020; 227:1872-1884. [PMID: 32392621 DOI: 10.1111/nph.16647] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
Niche conservatism is the tendency of lineages to retain the same niche as their ancestors. It constrains biological groups and prevents ecological divergence. However, theory predicts that niche conservatism can hinder gene flow, strengthen drift and increase local adaptation: does it mean that it also can facilitate speciation? Why does this happen? We aim to answer these questions. We examined the variation of chloroplast DNA, genome-wide single nucleotide polymorphisms, morphological traits and environmental variables across the Dioon merolae cycad populations. We tested geographical structure, scenarios of demographic history, and niche conservatism between population groups. Lineage divergence is associated with the presence of a geographical barrier consisting of unsuitable habitats for cycads. There is a clear genetic and morphological distinction between the geographical groups, suggesting allopatric divergence. However, even in contrasting available environmental conditions, groups retain their ancestral niche, supporting niche conservatism. Niche conservatism is a process that can promote speciation. In D. merolae, lineage divergence occurred because unsuitable habitats represented a barrier against gene flow, incurring populations to experience isolated demographic histories and disparate environmental conditions. This study explains why cycads, despite their ancient lineage origin and biological stasis, have been able to diversify into modern ecosystems worldwide.
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Affiliation(s)
| | | | - Takuro Ito
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Miguel Angel Pérez-Farrera
- Laboratorio de Ecología Evolutiva, Herbario Eizi Matuda, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez, 29039, Mexico
| | - Andrew P Vovides
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C., Xalapa, 91070, Mexico
| | - José F Martínez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, 83250, Mexico
| | - Francisco Molina-Freaner
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, 83250, Mexico
| | - Antonio Hernández-López
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de México, León, 37684, Mexico
| | - Lina Kawaguchi
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Tadashi Kajita
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Uehara, Yaeyama, Okinawa, 907-1541, Japan
| | - Yasuyuki Watano
- Department of Biology, Faculty of Science, Chiba University, Chiba, 263-8522, Japan
| | - Takashi Tsuchimatsu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yuma Takahashi
- Department of Biology, Faculty of Science, Chiba University, Chiba, 263-8522, Japan
| | - Masashi Murakami
- Department of Biology, Faculty of Science, Chiba University, Chiba, 263-8522, Japan
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Sánchez-Chávez E, Rodríguez A, Castro-Castro A, Pérez-Farrera MA, Sosa V. Spatio-temporal evolution of climbing habit in the Dahlia-Hidalgoa group (Coreopsidae, Asteraceae). Mol Phylogenet Evol 2019; 135:166-176. [DOI: 10.1016/j.ympev.2019.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 12/23/2022]
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Gutiérrez-Ortega JS, Salinas-Rodríguez MM, Martínez JF, Molina-Freaner F, Pérez-Farrera MA, Vovides AP, Matsuki Y, Suyama Y, Ohsawa TA, Watano Y, Kajita T. The phylogeography of the cycad genus Dioon (Zamiaceae) clarifies its Cenozoic expansion and diversification in the Mexican transition zone. Ann Bot 2018; 121:535-548. [PMID: 29293877 PMCID: PMC5838841 DOI: 10.1093/aob/mcx165] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 07/10/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
Background and Aims Biogeographic transition zones are promising areas to study processes of biogeographic evolution and its influence on biological groups. The Mexican transition zone originated due to the overlap of Nearctic and Neotropical biota, which promoted great biological diversification. However, since most previous studies in this area were focused on revealing the phylogeography of Nearctic plants, how historical biogeographic configuration influenced the expansion and diversification of the Neotropical flora remains almost unknown. Using the cycad genus Dioon (Zamiaceae), this study aimed to test whether the biogeographic provinciality of the Mexican transition zone reflects the history of diversification of Neotropical plants. Methods Two chloroplast DNA (cpDNA) regions were analysed from 101 specimens of 15 Dioon species to reveal the distribution of haplogroups. In addition, genome-wide single nucleotide polymorphisms (SNPs) from 84 specimens were used to test the concordance between phylogenetic clusters and the biogeographic provinces. An ultrametric tree was constructed from the sequences containing SNPs to reconstruct the biogeographic events of vicariance and dispersal of Dioon across the Neotropical biogeographic provinces. Key Results Four Dioon lineages with strong phylogeographic structures were recognized using both cpDNA and SNP data. The lineages correspond to two clades that originated from a common ancestor in Eastern Mexico. One clade expanded and diversified in South-east Mexico and Central America. Another clade diversified into three lineages that dispersed to North-east, South and North-west Mexico. Each lineage was biogeographically delimitated. Biogeographic provinces might have provided disparate ecological conditions that facilitated speciation in Dioon since the Miocene. Conclusions The current genetic structure and species diversity of Dioon depict the history of expansion and diversification of the northernmost Neotropical provinces. Past biogeographic connectivities were favoured by elevated topographies, since mountain systems served as corridors for the migration of Dioon and as refugia of tropical communities that diversified during the formation of modern Neotropical forests.
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Affiliation(s)
| | - María Magdalena Salinas-Rodríguez
- Herbario Isidro Palacios, Instituto de Investigaciones de Zonas Desérticas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - José F Martínez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Mexico
| | - Francisco Molina-Freaner
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Mexico
- Instituto de Geología, Estación Regional del Noroeste, Universidad Nacional Autónoma de México, Hermosillo, Mexico
| | - Miguel Angel Pérez-Farrera
- Laboratorio de Ecología Evolutiva, Herbario Eizi Matuda, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez, Mexico
| | - Andrew P Vovides
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C., Xalapa, Mexico
| | - Yu Matsuki
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, Yomogida, Naruko-onsen, Osaki, Miyagi, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, Yomogida, Naruko-onsen, Osaki, Miyagi, Japan
| | - Takeshi A Ohsawa
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Tadashi Kajita
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Uehara, Yaeyama, Okinawa , Japan
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Said Gutiérrez-Ortega J, Yamamoto T, Vovides AP, Angel Pérez-Farrera M, Martínez JF, Molina-Freaner F, Watano Y, Kajita T. Aridification as a driver of biodiversity: a case study for the cycad genus Dioon (Zamiaceae). Ann Bot 2018; 121:47-60. [PMID: 29155921 PMCID: PMC5786249 DOI: 10.1093/aob/mcx123] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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: 02/15/2017] [Accepted: 09/13/2017] [Indexed: 05/19/2023]
Abstract
Background and Aims Aridification is considered a selective pressure that might have influenced plant diversification. It is suggested that plants adapted to aridity diversified during the Miocene, an epoch of global aridification (≈15 million years ago). However, evidence supporting diversification being a direct response to aridity is scarce, and multidisciplinary evidence, besides just phylogenetic estimations, is necessary to support the idea that aridification has driven diversification. The cycad genus Dioon (Zamiaceae), a tropical group including species occurring from humid forests to arid zones, was investigated as a promising study system to understand the associations among habitat shifts, diversification times, the evolution of leaf epidermal adaptations, and aridification of Mexico. Methods A phylogenetic tree was constructed from seven chloroplast DNA sequences and the ITS2 spacer to reveal the relationships among 14 Dioon species from habitats ranging from humid forests to deserts. Divergence times were estimated and the habitat shifts throughout Dioon phylogeny were detected. The epidermal anatomy among Dioon species was compared and correlation tests were performed to associate the epidermal variations with habitat parameters. Key Results Events of habitat shifts towards arid zones happened exclusively in one of the two main clades of Dioon. Such habitat shifts happened during the species diversification of Dioon, mainly during the Miocene. Comparative anatomy showed epidermal differences between species from arid and mesic habitats. The variation of epidermal structures was found to be correlated with habitat parameters. Also, most of the analysed epidermal traits showed significant phylogenetic signals. Conclusions The diversification of Dioon has been driven by the aridification of Mexico. The Miocene timing corresponds to the expansion of arid zones that embedded the ancestral Dioon populations. As response, species in arid zones evolved epidermal traits to counteract aridity stress. This case study provides a robust body of evidence supporting the idea that aridification is an important driver of biodiversity.
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Affiliation(s)
| | - Takashi Yamamoto
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Uehara, Yaeyama, Okinawa, Japan
| | - Andrew P Vovides
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C., Xalapa, Mexico
| | - Miguel Angel Pérez-Farrera
- Laboratorio de Ecología Evolutiva, Herbario Eizi Matuda, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez, Mexico
| | - José F Martínez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Mexico
| | - Francisco Molina-Freaner
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Mexico
- Instituto de Geología, Estación Regional del Noroeste, Universidad Nacional Autónoma de México, Hermosillo, Mexico
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Tadashi Kajita
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Uehara, Yaeyama, Okinawa, Japan
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Said Gutiérrez-Ortega J, Yamamoto T, Vovides AP, Angel Pérez-Farrera M, Martínez JF, Molina-Freaner F, Watano Y, Kajita T. Corrigendum: Aridification as a driver of biodiversity: a case study for the cycad genus Dioon (Zamiaceae). Ann Bot 2018; 121:193. [PMID: 29304193 PMCID: PMC5786256 DOI: 10.1093/aob/mcx201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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Ortiz-Rodriguez AE, Escobar-Castellanos MA, Pérez-Farrera MA. Phylogenetic analyses and morphological characteristics support the description of a second species of Tridimeris (Annonaceae). PhytoKeys 2016; 74:79-95. [PMID: 28127237 PMCID: PMC5234549 DOI: 10.3897/phytokeys.74.10371] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 10/31/2016] [Indexed: 05/27/2023]
Abstract
Based on phylogenetic and morphological evidence, Tridimeris chiapensis Escobar-Castellanos & Ortiz-Rodr., sp. n. (Annonaceae), a new species from the karst forest of southern Mexico, is described and illustrated. The new species differs from Tridimeris hahniana, the only described species in the genus, in that the latter has flowers with sepals densely tomentose outside, one (rarely two) carpel(s) per flower and fruits densely covered with golden-brown hairs, while Tridimeris chiapensis has flowers with glabrous sepals outside, two to five carpels per flower and glabrous fruits. Furthermore, a shallow triangular white patch at the base of the inner petals is found in Tridimeris chiapensis, a morphological character shared with the sister genus Sapranthus but absent in Tridimeris hahniana. Geographically, both species occur allopatrically. With just one known locality and seven individuals of Tridimeris chiapensis recorded in one sampling hectare, and based on application of the criteria established by the IUCN, we conclude tentatively that the species is critically endangered.
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Affiliation(s)
| | | | - Miguel Angel Pérez-Farrera
- Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutierrez, Chiapas, Mexico
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