1
|
São-Mateus WMB, Fernandes MF, Queiroz LPD, Meireles JE, Jardim JG, Delgado-Salinas A, Dorado Ó, Lima HCD, Rodríguez RR, González Gutiérrez PA, Lewis GP, Wojciechowski MF, Cardoso D. Molecular phylogeny and divergence time of Harpalyce (Leguminosae, Papilionoideae), a lineage with amphitropical diversification in seasonally dry forests and savannas. Mol Phylogenet Evol 2024; 194:108031. [PMID: 38360081 DOI: 10.1016/j.ympev.2024.108031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 01/31/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
Our knowledge of the systematics of the papilionoid legume tribe Brongniartieae has greatly benefitted from recent advances in molecular phylogenetics. The tribe was initially described to include species marked by a strongly bilabiate calyx and an embryo with a straight radicle, but recent research has placed taxa from the distantly related core Sophoreae and Millettieae within it. Despite these advances, the most species-rich genera within the Brongniartieae are still not well studied, and their morphological and biogeographical evolution remains poorly understood. Comprising 35 species, Harpalyce is one of these poorly studied genera. In this study, we present a comprehensive, multi-locus molecular phylogeny of the Brongniartieae, with an increased sampling of Harpalyce, to investigate morphological and biogeographical evolution within the group. Our results confirm the monophyly of Harpalyce and indicate that peltate glandular trichomes and a strongly bilabiate calyx with a carinal lip and three fused lobes are synapomorphies for the genus, which is internally divided into three distinct ecologically and geographically divergent lineages, corresponding to the previously recognized sections. Our biogeographical reconstructions demonstrate that Brongniartieae originated in South America during the Eocene, with subsequent pulses of diversification in South America, Mesoamerica, and Australia. Harpalyce also originated in South America during the Miocene at around 20 Ma, with almost synchronous later diversification in South America and Mexico/Mesoamerica beginning 10 Ma, but mostly during the Pliocene. Migration of Harpalyce from South to North America was accompanied by a biome and ecological shift from savanna to seasonally dry forest.
Collapse
Affiliation(s)
- Wallace M B São-Mateus
- Programa de Pós-Graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário Lagoa Nova, 59072-970, Natal, Rio Grande do Norte, Brazil.
| | - Moabe Ferreira Fernandes
- Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s.n., Ondina, 40170-115 Salvador, Bahia, Brazil; Department of Geography, University of Exeter, Exeter, UK; Royal Botanic Gardens, Kew, Richmond TW93AE, UK
| | - Luciano Paganucci de Queiroz
- Universidade Estadual de Feira de Santana (HUEFS), Av. Transnordestina, s/n, Novo Horizonte, 44036-900 Feira de Santana, Bahia, Brazil
| | - José Eduardo Meireles
- School of Biology and Ecology, University of Maine, 5735 Hitchner Hall, 04469 Orono, ME, USA
| | - Jomar Gomes Jardim
- Universidade Federal do Sul da Bahia, Centro de Formação em Ciências Agroflorestais, Campus Jorge Amado, 45613-204 Itabuna, Bahia, Brazil; Herbário Centro de Pesquisas do Cacau - CEPEC, Km 29, Rod. Ilhéus-Itabuna, 45603-811 Itabuna, Bahia, Brazil
| | - Alfonso Delgado-Salinas
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-233, 04510 Coyoacán, Cd. México, Mexico
| | - Óscar Dorado
- Centro de Educación Ambiental e Investigación Sierra de Huautla, Universidad Autónoma del Estado de Morelos, Mexico
| | - Haroldo Cavalcante de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão, 915 22460-030 Rio de Janeiro, Brazil
| | - Rosa Rankin Rodríguez
- Jardín Botánico Nacional, Universidad de la Habana, Carretera "El Rocío", km 3.5, Calabazar C.P. 19230, Boyeros, La Habana, Cuba
| | - Pedro Alejandro González Gutiérrez
- Centro de Investigaciones y Servicios Ambientales de Holguín (CISAT), CITMA, Calle 18 sn, entre 1ª y Maceo, Reparto "El Llano", Holguín 80 100, Cuba
| | | | | | - Domingos Cardoso
- Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s.n., Ondina, 40170-115 Salvador, Bahia, Brazil; Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão, 915 22460-030 Rio de Janeiro, Brazil.
| |
Collapse
|
2
|
Pezzini FF, Ferrari G, Forrest LL, Hart ML, Nishii K, Kidner CA. Target capture and genome skimming for plant diversity studies. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11537. [PMID: 37601316 PMCID: PMC10439825 DOI: 10.1002/aps3.11537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 06/16/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023]
Abstract
Recent technological advances in long-read high-throughput sequencing and assembly methods have facilitated the generation of annotated chromosome-scale whole-genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obtaining high-molecular-weight DNA is typically impossible for samples in historical herbarium collections, which often have degraded DNA. The need to fast-freeze newly collected living samples to conserve high-quality DNA can be complicated when plants are only found in remote areas. Therefore, short-read reduced-genome representations, such as target capture and genome skimming, remain important for evolutionary studies. Here, we review the pros and cons of each technique for non-model plant taxa. We provide guidance related to logistics, budget, the genomic resources previously available for the target clade, and the nature of the study. Furthermore, we assess the available bioinformatic analyses, detailing best practices and pitfalls, and suggest pathways to combine newly generated data with legacy data. Finally, we explore the possible downstream analyses allowed by the type of data generated using each technique. We provide a practical guide to help researchers make the best-informed choice regarding reduced genome representation for evolutionary studies of non-model plants in cases where whole-genome sequencing remains impractical.
Collapse
Affiliation(s)
| | - Giada Ferrari
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
| | | | | | - Kanae Nishii
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
| | - Catherine A Kidner
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
- School of Biological Sciences University of Edinburgh Edinburgh United Kingdom
| |
Collapse
|
3
|
Rickenback J, Pennington RT, Lehmann CER. Diversity in habit expands the environmental niche of
Ziziphus
(Rhamnaceae). Biotropica 2022. [DOI: 10.1111/btp.13152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jess Rickenback
- School of Geosciences University of Edinburgh Edinburgh UK
- Tropical Diversity Royal Botanic Garden Edinburgh Edinburgh UK
| | - R. Toby Pennington
- Tropical Diversity Royal Botanic Garden Edinburgh Edinburgh UK
- College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Caroline E. R. Lehmann
- School of Geosciences University of Edinburgh Edinburgh UK
- Tropical Diversity Royal Botanic Garden Edinburgh Edinburgh UK
| |
Collapse
|
4
|
Gómez-Maqueo X, Gamboa-deBuen A. The Biology of the Genus Ceiba, a Potential Source for Sustainable Production of Natural Fiber. PLANTS (BASEL, SWITZERLAND) 2022; 11:521. [PMID: 35214854 PMCID: PMC8876852 DOI: 10.3390/plants11040521] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 06/14/2023]
Abstract
The species of the genus Ceiba produces fruits with fibers with a high content of cellulose. The fiber is used for textiles, cushion filling and for industrial purposes and its characteristics have been studied in some species including Ceiba pentandra (kapok), C. speciosa and C. aesculifolia. The use of the trunk and seeds of Ceiba has also been described for different species. This article presents a review on the biological diversity of the genus Ceiba (Malvaceae). The genus Ceiba has 18 recognized species that are distributed naturally in America and Africa. However, some Ceiba trees have been introduced to various countries, especially in Asia, due to their ornamental interest and potential uses for their fiber. Ecophysiological studies of different Ceiba species have shown that resistance to adverse environmental conditions varies from species to species. Therefore, Ceiba species are considered potentially useful in restoring ecosystems impacted by human activity. The information related to the classification, morphological characteristics, phenology, ecophysiology and distribution of the different species will be extremely relevant for the sustainable production of kapok fiber. Finally, the recent genomic and transcriptomic studies also provide a valuable resource for further genetic improvement and effective use of Ceiba trees.
Collapse
|
5
|
Neves DM, Kerkhoff AJ, Echeverría-Londoño S, Merow C, Morueta-Holme N, Peet RK, Sandel B, Svenning JC, Wiser SK, Enquist BJ. The adaptive challenge of extreme conditions shapes evolutionary diversity of plant assemblages at continental scales. Proc Natl Acad Sci U S A 2021; 118:e2021132118. [PMID: 34504011 PMCID: PMC8449343 DOI: 10.1073/pnas.2021132118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 11/26/2022] Open
Abstract
The tropical conservatism hypothesis (TCH) posits that the latitudinal gradient in biological diversity arises because most extant clades of animals and plants originated when tropical environments were more widespread and because the colonization of colder and more seasonal temperate environments is limited by the phylogenetically conserved environmental tolerances of these tropical clades. Recent studies have claimed support of the TCH, indicating that temperate plant diversity stems from a few more recently derived lineages that are nested within tropical clades, with the colonization of the temperate zone being associated with key adaptations to survive colder temperatures and regular freezing. Drought, however, is an additional physiological stress that could shape diversity gradients. Here, we evaluate patterns of evolutionary diversity in plant assemblages spanning the full extent of climatic gradients in North and South America. We find that in both hemispheres, extratropical dry biomes house the lowest evolutionary diversity, while tropical moist forests and many temperate mixed forests harbor the highest. Together, our results support a more nuanced view of the TCH, with environments that are radically different from the ancestral niche of angiosperms having limited, phylogenetically clustered diversity relative to environments that show lower levels of deviation from this niche. Thus, we argue that ongoing expansion of arid environments is likely to entail higher loss of evolutionary diversity not just in the wet tropics but in many extratropical moist regions as well.
Collapse
Affiliation(s)
- Danilo M Neves
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil;
| | | | - Susy Echeverría-Londoño
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, W2 1PG, United Kingdom
| | - Cory Merow
- Eversource Energy Center, Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06268
| | - Naia Morueta-Holme
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen 2100, Denmark
| | - Robert K Peet
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Brody Sandel
- Department of Biology, Santa Clara University, Santa Clara, CA 95053
| | - Jens-Christian Svenning
- Center for Biodiversity Dynamics in a Changing World, Department of Biology, Aarhus University, Aarhus 8000, Denmark
| | - Susan K Wiser
- Ecosystems and Conservation Group, Manaaki Whenua - Landcare Research, Lincoln 7640, New Zealand
| | - Brian J Enquist
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721
- The Santa Fe Institute, Santa Fe, NM 87501
| |
Collapse
|