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Gan Y, Ping J, Liu X, Peng C. Repetitive Sequences, Codon Usage Bias and Phylogenetic Analysis of the Plastome of Miliusa glochidioides. Biochem Genet 2024:10.1007/s10528-024-10874-7. [PMID: 38954211 DOI: 10.1007/s10528-024-10874-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 06/18/2024] [Indexed: 07/04/2024]
Abstract
Annonaceae is the largest family in Magnoliales, exhibiting the greatest diversity among and within genera. In this study, we conducted an analysis of repetitive sequences and codon usage bias in the previously acquired plastome of Miliusa glochidioides. Using a concatenated dataset of shared genes, we constructed the phylogenetic relationships among 27 Annonaceae species. The results showed that the size of the plastomes in the Annonaceae ranged from 159 to 202 kb, with the size of the inverted repeat region ranging from 40 to 65 kb. Within the plastome of M. glochidioides, we identified 42 SSRs, 36 tandem repeats, and 9 dispersed repeats. These SSRs consist of three nucleotide types and eight motif types, with a preference for A/T bases, primarily located in the large single-copy regions and intergenic spacers. Tandem and dispersed repeat sequences were predominantly detected in the IR region. Through codon usage bias analysis, we identified 30 high-frequency codons and 11 optimal codons. The plastome of M. glochidioides demonstrated relatively weak codon usage bias, favoring codons with A/T endings, primarily influenced by natural selection. Phylogenetic analysis revealed that all four subfamilies formed monophyletic groups, with Cananga odorata (Ambavioideae) and Anaxagorea javanica (Anaxagoreoideae) successively nested outside Annonoideae + Malmeoideae. These findings improve our understanding of the plastome of M. glochidioides and provide additional insights for studying plastome evolution in Annonaceae.
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Affiliation(s)
- Yangying Gan
- Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Economics and Information, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Jingyao Ping
- College of Life Sciences, Sun Yet-sen University, Guangzhou, 510275, China
| | - Xiaojing Liu
- Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Economics and Information, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Caixia Peng
- Horticulture Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
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Ping J, Hao J, Wang T, Su Y. Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the Annonaceae. FRONTIERS IN PLANT SCIENCE 2024; 15:1351388. [PMID: 38693922 PMCID: PMC11061511 DOI: 10.3389/fpls.2024.1351388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
The Annonaceae stands as the most species rich family in the Magnoliales, a basal group of angiosperms. Widely distributed in tropical and subtropical regions, it holds significant ecological and economic value. The plastid genome (plastome) is often employed in studies related to plant phylogenetics, comparative genomics, evolutionary biology, and genetic engineering. Nonetheless, research progress on plastid genomics in the Annonaceae has been relatively slow. In this study, we analyzed the structure and repetitive sequence features of plastomes from 28 Annonaceae species. Among them, Mitrephora tomentosa and Desmos chinensis were newly sequenced, with sizes of 160,157 bp and 192,167 bp, and GC contents of 38.3% and 38.4%, respectively. The plastome size in the Annonaceae ranged from 158,837 bp to 202,703 bp, with inverted repeat (IR) region sizes ranging from 64,621 bp to 25,861 bp. Species exhibiting expansion in the IR region showed an increase in plastome size and gene number, frequent boundary changes, different expansion modes (bidirectional or unidirectional), and an increase in repetitive sequences. Specifically, a large number of dispersed repetitive sequences lead to an increase in the size of the LSC region in Goniothalamus tamirensis. Phylogenetic analysis revealed Annonoideae and Malmeoideae as monophyletic groups and sister clades, with Cananga odorata outside of them, followed by Anaxagorea javanica. This research uncovers the structural variation characteristics of plastomes in the Annonaceae, providing valuable information for understanding the phylogeny and plastome evolution of Annonaceae.
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Affiliation(s)
- Jingyao Ping
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jing Hao
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Research Institute of Sun Yat-Sen University, Shenzhen, China
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Terrones-Ramírez AK, Robles-Bello SM, Vázquez-López M, Ramírez-Barrera SM, Zamudio-Beltrán LE, López López A, Arizmendi MDC, Durán-Suárez del Real AP, Eguiarte LE, Hernández-Baños BE. Recent genetic, phenetic and ecological divergence across the Mesoamerican highlands: a study case with Diglossa baritula (Aves: Thraupidae). PeerJ 2024; 12:e16797. [PMID: 38529306 PMCID: PMC10962342 DOI: 10.7717/peerj.16797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 12/24/2023] [Indexed: 03/27/2024] Open
Abstract
The topographical, geological, climatic and biodiversity complexity of Mesoamerica has made it a primary research focus. The Mesoamerican highlands is a region with particularly high species richness and within-species variation. The Cinnamon-bellied Flowerpiercer, Diglossa baritula (Wagler, 1832), is a species endemic to the Mesoamerican highlands, with three allopatric subspecies currently recognized. To characterize divergence within this species, we integrated genomics, morphology, coloration and ecological niche modeling approaches, obtained from sampling individuals across the entire geographic distribution of the species. Our results revealed a clear genomic divergence between the populations to the east versus the west of the Isthmus of Tehuantepec. In contrast to the genomic results, morphology and coloration analyses showed intermediate levels of differentiation, indicating that population groups within D. baritula have probably been under similar selective pressures. Our morphology results indicated that the only sexually dimorphic morphological variable is the wing chord, with males having a longer wing chord than females. Finally, ecological data indicated that there are differences in ecological niche within D. baritula. Our data suggest that D. baritula could contain two or more incipient species at the intermediate phase of the speciation continuum. These results highlight the importance of the geographical barrier of the Isthmus of Tehuantepec and Pleistocene climatic events in driving isolation and population divergence in D. baritula. The present investigation illustrates the speciation potential of the D. baritula complex and the capacity of Mesoamerican highlands to create cryptic biodiversity and endemism.
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Affiliation(s)
- Alondra K. Terrones-Ramírez
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, CdMx, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, CDMX, México
| | - Sahid M. Robles-Bello
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, CdMx, Mexico
| | - Melisa Vázquez-López
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, CdMx, Mexico
| | - Sandra M. Ramírez-Barrera
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, CdMx, Mexico
| | - Luz E. Zamudio-Beltrán
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, CdMx, Mexico
| | - Anuar López López
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, CdMx, Mexico
| | - Maria del Coro Arizmendi
- Laboratorio de Ecología, UBIPRO Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Estado de México, Mexico
| | - Ana Paula Durán-Suárez del Real
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, CdMx, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, CdMx, Mexico
| | - Blanca E. Hernández-Baños
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, CdMx, Mexico
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Dagallier LPMJ, Mbago FM, Couderc M, Gaudeul M, Grall A, Loup C, Wieringa JJ, Sonké B, Couvreur TLP. Phylogenomic inference of the African tribe Monodoreae (Annonaceae) and taxonomic revision of Dennettia, Uvariodendron and Uvariopsis. PHYTOKEYS 2023; 233:1-200. [PMID: 37811332 PMCID: PMC10552675 DOI: 10.3897/phytokeys.233.103096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/16/2023] [Indexed: 10/10/2023]
Abstract
Monodoreae (Annonaceae) is a tribe composed of 11 genera and 90 species restricted to the tropical African rain forests. All the genera are taxonomically well circumscribed except the species rich genera Uvariodendron and Uvariopsis which lack a recent taxonomic revision. Here, we used a robust phylogenomic approach, including all the 90 currently accepted species, with several specimens per species, and based on more than 300 Annonaceae-specific nuclear genes, to infer the phylogenetic tree of the Monodoreae and test the limits between the genera and species. We recover all the genera as monophyletic, except the genus Uvariopsis for which the species Uvariopsistripetala falls outside this clade. We thus reinstate the monotypic genus Dennettia for its single species Dennettiatripetala. We also erect a new tribe, Ophrypetaleae trib. nov., to accommodate the genera Ophrypetalum and Sanrafaelia, as we recover them excluded from the Monodoreae tribe with good support. Below the genus level, the genera Isolona, Monodora, Uvariastrum, Uvariodendron and Uvariopsis show weakly supported nodes and phylogenetic conflicts, suggesting that population level processes of evolution might occur in these clades. Our results also support, at the molecular level, the description of several new species of Uvariodendron and Uvariopsis, as well as several new synonymies. Finally, we present a taxonomic revision of the genera Dennettia, Uvariodendron and Uvariopsis, which contain one, 18 and 17 species respectively. We provide a key to the 11 genera of the Monodoraeae and describe four new species to science: Uvariodendronkimbozaense Dagallier & Couvreur, sp. nov., Uvariodendronmossambicense Robson ex Dagallier & Couvreur, sp. nov., Uvariodendronpilosicarpum Dagallier & Couvreur, sp. nov. and Uvariopsisoligocarpa Dagallier & Couvreur, sp. nov., and provide provisional descriptions of three putatively new species. We also present lectotypifications and nomenclatural changes implying synonymies and new combinations (Uvariodendroncitriodorum (Le Thomas) Dagallier & Couvreur, comb. et stat. nov., Uvariodendronfuscumvar.magnificum (Verdc.) Dagallier & Couvreur, comb. et stat. nov., Uvariopsiscongensisvar.angustifolia Dagallier & Couvreur, var. nov., Uvariopsisguineensisvar.globiflora (Keay) Dagallier & Couvreur, comb. et stat. nov., and Uvariopsissolheidiivar.letestui (Pellegr.) Dagallier & Couvreur, comb. et stat. nov.).
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Affiliation(s)
- Léo-Paul M. J. Dagallier
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, New York 10458, USA
| | - Frank M. Mbago
- The Herbarium, Botany Department, Box 35060, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Marie Couderc
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, France
| | - Aurélie Grall
- Herbaria Basel, Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Caroline Loup
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Jan J. Wieringa
- Herbier MPU, DCSPH – CC 99010, Université de Montpellier, 163 rue A. Broussonnet, F-34090 Montpellier, France
| | - Bonaventure Sonké
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, Netherlands
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Shen CZ, Zhang CJ, Chen J, Guo YP. Clarifying Recent Adaptive Diversification of the Chrysanthemum-Group on the Basis of an Updated Multilocus Phylogeny of Subtribe Artemisiinae (Asteraceae: Anthemideae). FRONTIERS IN PLANT SCIENCE 2021; 12:648026. [PMID: 34122473 PMCID: PMC8187803 DOI: 10.3389/fpls.2021.648026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/20/2021] [Indexed: 05/12/2023]
Abstract
Understanding the roles played by geography and ecology in driving species diversification and in the maintenance of species cohesion is the central objective of evolutionary and ecological studies. The multi-phased orogenesis of Qinghai-Tibetan Plateau (QTP) and global climate changes over late-Miocene has profoundly influenced the environments and evolution of organisms in this region and the vast areas of Asia. In this study, we investigate the lineage diversification of Chrysanthemum-group in subtribe Artemisiinae (tribe Anthemideae, Asteraceae) likely under the effects of climate changes during this period. Using DNA sequences of seven low-copy nuclear loci and nrITS and the coalescent analytical methods, a time-calibrated phylogeny of subtribe Artemisiinae was reconstructed with emphasis on Chrysanthemum-group. The monophyletic Chrysanthemum-group was well resolved into two major clades corresponding to Chrysanthemum and Ajania, two genera which can be well identified by capitulum morphology but have been intermingled in previous plastid and ITS trees. Within Chrysanthemum, a later divergence between Ch. indicum-complex and Ch. zawadskii-complex can be recognized. The time frames of these sequential divergences coincide with the late Cenozoic uplift of the Northern QTP and the concomitant climatic heterogeneity between eastern and inland Asia. Reconstruction of historical biogeography suggested the origin of Chrysanthemum-group in Central Asia, followed by eastward migration of Chrysanthemum and in situ diversification of Ajania. Within Chrysanthemum, Ch. indicum-complex and Ch. zawadskii-complex exhibited contemporary distributional division, the former in more southern and the latter in more northern regions. The geographic structure of the three lineages in Chrysanthemum-group have been associated with the niche differentiation, and environmental heterogenization in Asia interior.
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Affiliation(s)
- Chu-Ze Shen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Chu-Jie Zhang
- School of Life Sciences, Peking University, Beijing, China
| | - Jie Chen
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Yan-Ping Guo
- School of Life Sciences, Peking University, Beijing, China
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Moreno-Contreras I, Sánchez-González LA, Arizmendi MDC, Prieto-Torres DA, Navarro-Sigüenza AG. Climatic Niche Evolution in the Arremon brunneinucha Complex (Aves: Passerellidae) in a Mesoamerican Landscape. Evol Biol 2020. [DOI: 10.1007/s11692-020-09498-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Xue B, Guo X, Landis JB, Sun M, Tang CC, Soltis PS, Soltis DE, Saunders RMK. Accelerated diversification correlated with functional traits shapes extant diversity of the early divergent angiosperm family Annonaceae. Mol Phylogenet Evol 2019; 142:106659. [PMID: 31639525 DOI: 10.1016/j.ympev.2019.106659] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/04/2019] [Accepted: 10/17/2019] [Indexed: 12/15/2022]
Abstract
A major goal of phylogenetic systematics is to understand both the patterns of diversification and the processes by which these patterns are formed. Few studies have focused on the ancient, species-rich Magnoliales clade and its diversification pattern. Within Magnoliales, the pantropically distributed Annonaceae are by far the most genus-rich and species-rich family-level clade, with c. 110 genera and c. 2,400 species. We investigated the diversification patterns across Annonaceae and identified traits that show varied associations with diversification rates using a time-calibrated phylogeny of 835 species (34.6% sampling) and 11,211 aligned bases from eight regions of the plastid genome (rbcL, matK, ndhF, psbA-trnH, trnL-F, atpB-rbcL, trnS-G, and ycf1). Twelve rate shifts were identified using BAMM: in Annona, Artabotrys, Asimina, Drepananthus, Duguetia, Goniothalamus, Guatteria, Uvaria, Xylopia, the tribes Miliuseae and Malmeeae, and the Desmos-Dasymaschalon-Friesodielsia-Monanthotaxis clade. TurboMEDUSA and method-of-moments estimator analyses showed largely congruent results. A positive relationship between species richness and diversification rate is revealed using PGLS. Our results show that the high species richness in Annonaceae is likely the result of recent increased diversification rather than the steady accumulation of species via the 'museum model'. We further explore the possible role of selected traits (habit, pollinator trapping, floral sex expression, pollen dispersal unit, anther septation, and seed dispersal unit) in shaping diversification patterns, based on inferences of BiSSE, MuSSE, HiSSE, and FiSSE analyses. Our results suggest that the liana habit, the presence of circadian pollinator trapping, androdioecy, and the dispersal of seeds as single-seeded monocarp fragments are closely correlated with higher diversification rates; pollen aggregation and anther septation, in contrast, are associated with lower diversification rates.
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Affiliation(s)
- B Xue
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, China; Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China; Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, Guangdong, China
| | - X Guo
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China; Current address: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - J B Landis
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - M Sun
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - C C Tang
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - P S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - D E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - R M K Saunders
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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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] [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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