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Rincón-Barrado M, Villaverde T, Perez MF, Sanmartín I, Riina R. The sweet tabaiba or there and back again: phylogeographical history of the Macaronesian Euphorbia balsamifera. ANNALS OF BOTANY 2024; 133:883-904. [PMID: 38197716 PMCID: PMC11082519 DOI: 10.1093/aob/mcae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/01/2024] [Indexed: 01/11/2024]
Abstract
BACKGROUND AND AIMS Biogeographical relationships between the Canary Islands and north-west Africa are often explained by oceanic dispersal and geographical proximity. Sister-group relationships between Canarian and eastern African/Arabian taxa, the 'Rand Flora' pattern, are rare among plants and have been attributed to the extinction of north-western African populations. Euphorbia balsamifera is the only representative species of this pattern that is distributed in the Canary Islands and north-west Africa; it is also one of few species present in all seven islands. Previous studies placed African populations of E. balsamifera as sister to the Canarian populations, but this relationship was based on herbarium samples with highly degraded DNA. Here, we test the extinction hypothesis by sampling new continental populations; we also expand the Canarian sampling to examine the dynamics of island colonization and diversification. METHODS Using target enrichment with genome skimming, we reconstructed phylogenetic relationships within E. balsamifera and between this species and its disjunct relatives. A single nucleotide polymorphism dataset obtained from the target sequences was used to infer population genetic diversity patterns. We used convolutional neural networks to discriminate among alternative Canary Islands colonization scenarios. KEY RESULTS The results confirmed the Rand Flora sister-group relationship between western E. balsamifera and Euphorbia adenensis in the Eritreo-Arabian region and recovered an eastern-western geographical structure among E. balsamifera Canarian populations. Convolutional neural networks supported a scenario of east-to-west island colonization, followed by population extinctions in Lanzarote and Fuerteventura and recolonization from Tenerife and Gran Canaria; a signal of admixture between the eastern island and north-west African populations was recovered. CONCLUSIONS Our findings support the Surfing Syngameon Hypothesis for the colonization of the Canary Islands by E. balsamifera, but also a recent back-colonization to the continent. Populations of E. balsamifera from northwest Africa are not the remnants of an ancestral continental stock, but originated from migration events from Lanzarote and Fuerteventura. This is further evidence that oceanic archipelagos are not a sink for biodiversity, but may be a source of new genetic variability.
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Affiliation(s)
- Mario Rincón-Barrado
- Real Jardín Botánico (RJB), CSIC, Madrid, 28014, Spain
- Centro Nacional de Biotecnología (CNB), CSIC, Madrid, 28049, Spain
| | - Tamara Villaverde
- Universidad Rey Juan Carlos (URJC), Área de Biodiversidad y Conservación, Móstoles, 28933, Spain
| | - Manolo F Perez
- Institut de Systématique, Evolution, Biodiversité (ISYEB – URM 7205 CNRS), Muséum National d’Histoire Naturelle, SU, EPHE & UA, Paris, France
| | | | - Ricarda Riina
- Real Jardín Botánico (RJB), CSIC, Madrid, 28014, Spain
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Blanco-Gavaldà C, Galbany-Casals M, Susanna A, Andrés-Sánchez S, Bayer RJ, Brochmann C, Cron GV, Bergh NG, Garcia-Jacas N, Gizaw A, Kandziora M, Kolář F, López-Alvarado J, Leliaert F, Letsara R, Moreyra LD, Razafimandimbison SG, Schmickl R, Roquet C. Repeatedly Northwards and Upwards: Southern African Grasslands Fuel the Colonization of the African Sky Islands in Helichrysum (Compositae). PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112213. [PMID: 37299192 DOI: 10.3390/plants12112213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/17/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
The Afromontane and Afroalpine areas constitute some of the main biodiversity hotspots of Africa. They are particularly rich in plant endemics, but the biogeographic origins and evolutionary processes leading to this outstanding diversity are poorly understood. We performed phylogenomic and biogeographic analyses of one of the most species-rich plant genera in these mountains, Helichrysum (Compositae-Gnaphalieae). Most previous studies have focused on Afroalpine elements of Eurasian origin, and the southern African origin of Helichrysum provides an interesting counterexample. We obtained a comprehensive nuclear dataset from 304 species (≈50% of the genus) using target-enrichment with the Compositae1061 probe set. Summary-coalescent and concatenation approaches combined with paralog recovery yielded congruent, well-resolved phylogenies. Ancestral range estimations revealed that Helichrysum originated in arid southern Africa, whereas the southern African grasslands were the source of most lineages that dispersed within and outside Africa. Colonization of the tropical Afromontane and Afroalpine areas occurred repeatedly throughout the Miocene-Pliocene. This timing coincides with mountain uplift and the onset of glacial cycles, which together may have facilitated both speciation and intermountain gene flow, contributing to the evolution of the Afroalpine flora.
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Affiliation(s)
- Carme Blanco-Gavaldà
- Systematics and Evolution of Vascular Plants-Associated Unit to CSIC by IBB, Department of Animal Biology, Plant Biology and Ecology, Faculty of Biosciences, Autonomous University of Barcelona, ES-08193 Bellaterra, Spain
| | - Mercè Galbany-Casals
- Systematics and Evolution of Vascular Plants-Associated Unit to CSIC by IBB, Department of Animal Biology, Plant Biology and Ecology, Faculty of Biosciences, Autonomous University of Barcelona, ES-08193 Bellaterra, Spain
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Pg. Migdia s/n, ES-08038 Barcelona, Spain
| | - Santiago Andrés-Sánchez
- Department of Botany and Plant Physiology and Plant DNA Biobank, DNA National Bank, University of Salamanca, Edificio I+D+i, Espejo St., ES-37007 Salamanca, Spain
| | - Randall J Bayer
- Department of Biological Sciences, Center for Biodiversity, University of Memphis, Memphis, TN 38152, USA
| | - Christian Brochmann
- Natural History Museum, University of Oslo, P.O. Box 1172, NO-0318 Oslo, Norway
| | - Glynis V Cron
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Private Bag 3, Johannesburg 2050, South Africa
| | - Nicola G Bergh
- Foundational Biodiversity Science, Kirstenbosch Research Centre, South African National Biodiversity Institute, Private Bag X7, Newlands, Cape Town 7735, South Africa
| | - Núria Garcia-Jacas
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Pg. Migdia s/n, ES-08038 Barcelona, Spain
| | - Abel Gizaw
- Natural History Museum, University of Oslo, P.O. Box 1172, NO-0318 Oslo, Norway
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa P.O. Box 3434, Ethiopia
| | - Martha Kandziora
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-12801 Prague, Czech Republic
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-12801 Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, CZ-25243 Průhonice, Czech Republic
| | - Javier López-Alvarado
- Systematics and Evolution of Vascular Plants-Associated Unit to CSIC by IBB, Department of Animal Biology, Plant Biology and Ecology, Faculty of Biosciences, Autonomous University of Barcelona, ES-08193 Bellaterra, Spain
| | | | - Rokiman Letsara
- Herbarium of the Parc Botanique et Zoologique of Tsimbazaza (PBZT), Antananarivo 3G9G+V6C, Madagascar
| | - Lucía D Moreyra
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Pg. Migdia s/n, ES-08038 Barcelona, Spain
| | | | - Roswitha Schmickl
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-12801 Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, CZ-25243 Průhonice, Czech Republic
| | - Cristina Roquet
- Systematics and Evolution of Vascular Plants-Associated Unit to CSIC by IBB, Department of Animal Biology, Plant Biology and Ecology, Faculty of Biosciences, Autonomous University of Barcelona, ES-08193 Bellaterra, Spain
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Martín-Hernanz S, Nogales M, Valente L, Fernández-Mazuecos M, Pomeda-Gutiérrez F, Cano E, Marrero P, Olesen JM, Heleno R, Vargas P. Time-calibrated phylogenies reveal mediterranean and pre-mediterranean origin of the thermophilous vegetation of the Canary Islands. ANNALS OF BOTANY 2023; 131:667-684. [PMID: 36594263 PMCID: PMC10147335 DOI: 10.1093/aob/mcac160] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/21/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS The Canary Islands have strong floristic affinities with the Mediterranean Basin. One of the most characteristic and diverse vegetation belts of the archipelago is the thermophilous woodland (between 200 and 900 m.a.s.l.). This thermophilous plant community consists of many non-endemic species shared with the Mediterranean Floristic Region together with Canarian endemic species. Consequently, phytogeographic studies have historically proposed the hypothesis of an origin of the Canarian thermophilous species following the establishment of the summer-dry mediterranean climate in the Mediterranean Basin around 2.8 million years ago. METHODS Time-calibrated phylogenies for 39 plant groups including Canarian thermophilous species were primarily analysed to infer colonization times. In particular, we used 26 previously published phylogenies together with 13 new time-calibrated phylogenies (including newly generated plastid and nuclear DNA sequence data) to assess whether the time interval between stem and crown ages of Canarian thermophilous lineages postdates 2.8 Ma. For lineages postdating this time threshold, we additionally conducted ancestral area reconstructions to infer the potential source area for colonization. KEY RESULTS A total of 43 Canarian thermophilous lineages were identified from 39 plant groups. Both mediterranean (16) and pre-mediterranean (9) plant lineages were found. However, we failed to determine the temporal origin for 18 lineages because a stem-crown time interval overlaps with the 2.8-Ma threshold. The spatial origin of thermophilous lineages was also heterogeneous, including ancestral areas from the Mediterranean Basin (nine) and other regions (six). CONCLUSIONS Our findings reveal an unexpectedly heterogeneous origin of the Canarian thermophilous species in terms of colonization times and mainland source areas. A substantial proportion of the lineages arrived in the Canaries before the summer-dry climate was established in the Mediterranean Basin. The complex temporal and geographic origin of Canarian thermophilous species challenges the view of the Canary Islands (and Madeira) as a subregion within the Mediterranean Floristic Region.
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Affiliation(s)
- Sara Martín-Hernanz
- Department of Biodiversity and Conservation, Real Jardín Botánico de Madrid (RJB-CSIC), 28014 Madrid, Spain
- Departament of Plant Biology and Ecology, Faculty of Pharmacy, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Manuel Nogales
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38206 San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
| | - Luis Valente
- Naturalis Biodiversity Center, 2333 Leiden, The Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Mario Fernández-Mazuecos
- Department of Biology (Botany), Faculty of Sciences, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Fernando Pomeda-Gutiérrez
- Department of Biodiversity and Conservation, Real Jardín Botánico de Madrid (RJB-CSIC), 28014 Madrid, Spain
| | - Emilio Cano
- Department of Biodiversity and Conservation, Real Jardín Botánico de Madrid (RJB-CSIC), 28014 Madrid, Spain
| | - Patricia Marrero
- Department of Biodiversity and Conservation, Real Jardín Botánico de Madrid (RJB-CSIC), 28014 Madrid, Spain
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38206 San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
| | - Jens M Olesen
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Ruben Heleno
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Pablo Vargas
- Department of Biodiversity and Conservation, Real Jardín Botánico de Madrid (RJB-CSIC), 28014 Madrid, Spain
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Nge FJ, Biffin E, Waycott M, Thiele KR. Phylogenomics and continental biogeographic disjunctions: insight from the Australian starflowers (Calytrix). AMERICAN JOURNAL OF BOTANY 2022; 109:291-308. [PMID: 34671970 DOI: 10.1002/ajb2.1790] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Continental-scale disjunctions and associated drivers are core research interests in biogeographic studies. Here, we selected a species-rich Australian plant genus (Calytrix; Myrtaceae) as a case study to investigate these patterns. Species of this endemic Australian starflower genus have a disjunct distribution across the mesic fringes of the continent and are largely absent from the arid center. METHODS We used high-throughput sequencing to generate unprecedented resolution and near complete species-level nuclear and plastid phylogenies for Calytrix. BioGeoBEARS and biogeographic stochastic mapping were used to infer ancestral areas, the relative contributions of vicariance and dispersal events, and directionality of dispersal. RESULTS Present-day disjunctions in Calytrix are explained by a combination of scenarios: (1) retreat of multiple lineages from the continental center to the more mesic fringes as Australia became progressively more arid, with subsequent extinction in the center as well as (2) origination of ancestral lineages in southwestern Australia (SWA) for species-rich clades. The SWA biodiversity hotspot is a major diversification center and the most common source area of dispersals, with multiple lineages originating in SWA and subsequently spreading to the adjacent arid Eremaean region. CONCLUSIONS Our results suggest that major extinction, as a result of cooling and drying of the Australian continent in the Eocene-Miocene, shaped the present-day biogeography of Calytrix. We hypothesize that this peripheral vicariance pattern, which is similar to the African Rand flora, may explain the disjunctions of many other Australian plant groups. Further studies with densely sampled phylogenies are required to test this hypothesis.
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Affiliation(s)
- Francis J Nge
- School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- State Herbarium of South Australia, G.P.O. Box 1047, Adelaide, South Australia, 5001, Australia
| | - Ed Biffin
- School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- State Herbarium of South Australia, G.P.O. Box 1047, Adelaide, South Australia, 5001, Australia
| | - Michelle Waycott
- School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- State Herbarium of South Australia, G.P.O. Box 1047, Adelaide, South Australia, 5001, Australia
| | - Kevin R Thiele
- School of Biological Sciences, University of Western Australia, 35 Stirling Hwy, Crawley (Perth), WA, 6009, Australia
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Culshaw V, Mairal M, Sanmartín I. Biogeography Meets Niche Modeling: Inferring the Role of Deep Time Climate Change When Data Is Limited. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.662092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Geographic range shifts are one major organism response to climate change, especially if the rate of climate change is higher than that of species adaptation. Ecological niche models (ENM) and biogeographic inferences are often used in estimating the effects of climatic oscillations on species range dynamics. ENMs can be used to track climatic suitable areas over time, but have often been limited to shallow timescales; biogeographic inference can reach greater evolutionary depth, but often lacks spatial resolution. Here, we present a simple approach that treats them as independent and complementary sources of evidence, which, when used in partnership, can be employed to reconstruct geographic range shifts over deep evolutionary timescales. For testing this, we chose two extreme African disjunctions: Camptoloma (Scrophulariaceae) and Canarina (Campanulaceae), each comprising of three species disjunctly distributed in Macaronesia and eastern/southern Africa. Using inferred ancestral ranges in tandem with preindustrial and paleoclimate ENM hindcastings, we show that the disjunct pattern was the result of fragmentation and extinction events linked to Neogene aridification cycles. Our results highlight the importance of considering temporal resolution when building ENMs for rare endemics with small population sizes and restricted climatic tolerances such as Camptoloma, for which models built on averaged monthly variables were more informative than those based on annual bioclimatic variables. Additionally, we show that biogeographic information can be used as truncation threshold criteria for building ENMs in the distant past. Our approach is suitable when there is sparse sampling on species occurrences and associated patterns of genetic variation, such as in the case of ancient endemics with widely disjunct distributions as a result of climate change.
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Can species distribution models and molecular tools help unravel disjunct distribution of Rhododendron arboreum? J Genet 2021. [DOI: 10.1007/s12041-021-01270-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Couvreur TL, Dauby G, Blach‐Overgaard A, Deblauwe V, Dessein S, Droissart V, Hardy OJ, Harris DJ, Janssens SB, Ley AC, Mackinder BA, Sonké B, Sosef MS, Stévart T, Svenning J, Wieringa JJ, Faye A, Missoup AD, Tolley KA, Nicolas V, Ntie S, Fluteau F, Robin C, Guillocheau F, Barboni D, Sepulchre P. Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna. Biol Rev Camb Philos Soc 2021; 96:16-51. [PMID: 32924323 PMCID: PMC7821006 DOI: 10.1111/brv.12644] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 12/30/2022]
Abstract
Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.
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Affiliation(s)
| | - Gilles Dauby
- AMAP Lab, IRD, CIRAD, CNRS, INRAUniversity of MontpellierMontpellierFrance
- Laboratoire d'évolution Biologique et Ecologie, Faculté des SciencesUniversité Libre de BruxellesCP160/12, Avenue F.D. Roosevelt 50Brussels1050Belgium
| | - Anne Blach‐Overgaard
- Section for Ecoinformatics & Biodiversity, Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
| | - Vincent Deblauwe
- Center for Tropical Research (CTR), Institute of the Environment and SustainabilityUniversity of California, Los Angeles (UCLA)Los AngelesCA90095U.S.A.
- International Institute of Tropical Agriculture (IITA)YaoundéCameroon
| | | | - Vincent Droissart
- AMAP Lab, IRD, CIRAD, CNRS, INRAUniversity of MontpellierMontpellierFrance
- Laboratoire de Botanique Systématique et d'Écologie, École Normale SupérieureUniversité de Yaoundé IPO Box 047YaoundéCameroon
- Herbarium et Bibliothèque de Botanique AfricaineUniversité Libre de BruxellesBoulevard du TriompheBrusselsB‐1050Belgium
- Africa & Madagascar DepartmentMissouri Botanical GardenSt. LouisMOU.S.A.
| | - Oliver J. Hardy
- Laboratoire d'évolution Biologique et Ecologie, Faculté des SciencesUniversité Libre de BruxellesCP160/12, Avenue F.D. Roosevelt 50Brussels1050Belgium
| | - David J. Harris
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghU.K.
| | | | - Alexandra C. Ley
- Institut für Geobotanik und Botanischer GartenUniversity Halle‐WittenbergNeuwerk 21Halle06108Germany
| | | | - Bonaventure Sonké
- Laboratoire de Botanique Systématique et d'Écologie, École Normale SupérieureUniversité de Yaoundé IPO Box 047YaoundéCameroon
| | | | - Tariq Stévart
- Herbarium et Bibliothèque de Botanique AfricaineUniversité Libre de BruxellesBoulevard du TriompheBrusselsB‐1050Belgium
- Africa & Madagascar DepartmentMissouri Botanical GardenSt. LouisMOU.S.A.
| | - Jens‐Christian Svenning
- Section for Ecoinformatics & Biodiversity, Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
| | - Jan J. Wieringa
- Naturalis Biodiversity CenterDarwinweg 2Leiden2333 CRThe Netherlands
| | - Adama Faye
- Laboratoire National de Recherches sur les Productions Végétales (LNRPV)Institut Sénégalais de Recherches Agricoles (ISRA)Route des Hydrocarbures, Bel Air BP 1386‐ CP18524DakarSenegal
| | - Alain D. Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of ScienceUniversity of DoualaPO Box 24157DoualaCameroon
| | - Krystal A. Tolley
- South African National Biodiversity InstituteKirstenbosch Research CentrePrivate Bag X7, ClaremontCape Town7735South Africa
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandPrivate Bag 3Wits2050South Africa
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHEUniversité des AntillesCP51, 57 rue CuvierParis75005France
| | - Stéphan Ntie
- Département de Biologie, Faculté des SciencesUniversité des Sciences et Techniques de MasukuFrancevilleBP 941Gabon
| | - Frédiéric Fluteau
- Institut de Physique du Globe de Paris, CNRSUniversité de ParisParisF‐75005France
| | - Cécile Robin
- CNRS, Géosciences Rennes, UMR6118University of RennesRennes35042France
| | | | - Doris Barboni
- CEREGE, Aix‐Marseille University, CNRS, IRD, Collège de France, INRA, Technopole Arbois MéditerranéeBP80Aix‐en‐Provence cedex413545France
| | - Pierre Sepulchre
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA‐CNRS‐UVSQUniversité Paris‐SaclayGif‐sur‐YvetteF‐91191France
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Jaén-Molina R, Marrero-Rodríguez Á, Caujapé-Castells J, Ojeda DI. Molecular phylogenetics of Lotus (Leguminosae) with emphasis in the tempo and patterns of colonization in the Macaronesian region. Mol Phylogenet Evol 2020; 154:106970. [PMID: 33031929 DOI: 10.1016/j.ympev.2020.106970] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/14/2020] [Accepted: 09/28/2020] [Indexed: 01/08/2023]
Abstract
With a wide distribution range including Europe and Asia, Lotus (Leguminosae) represents the largest genus within Loteae. It is particularly diverse in the Mediterreanean region and in the five archipelagos of Macaronesia (Atlantic Ocean). However, little is known about the relationships among the 14 sections currently recognized within Lotus and about the timing and patterns of its colonization in the Macaronesian region. In this investigation, we use four DNA regions (nuclear ribosomal ITS plus three plastid regions) in the most comprehensive sampling of Lotus species to date (some endemic species within the Canary Islands were poorly represented in previous phylogenetic analyses) to infer relationships within this genus and to establish patterns of colonization in Macaronesia. Divergence time estimates and habitat reconstruction analyses indicate that Lotus likely diverged about 7.86 Ma from its sister group, but all colonization events to Macaronesia occurred more recently (ranging from the last 0.23 to 2.70 Ma). The diversification of Lotus in Macaronesia involved between four and six independent colonization events from four sections currently distributed in Africa and Europe. A major aspect shaping the current distribution of taxa involved intra-island colonization of mainly new habitats and inter-island colonization of mostly similar habitats, with Gran Canaria and Tenerife as the major sources of diversification and of further colonization events. Section Pedrosia is the most diverse in terms of colonization events, number of species, and habitat heterogeneity, including a back-colonization event to the continent. Subsections within Pedrosia radiated into diverse habitat types recently (late Pleistocene, ca 0.23-0.29 Ma) and additional molecular markers and sampling would be necessary to understand the most recent dispersal events of this group within the Canary Islands and Cape Verde.
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Affiliation(s)
- Ruth Jaén-Molina
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria, Las Palmas, Gran Canaria, Spain.
| | - Águedo Marrero-Rodríguez
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria, Las Palmas, Gran Canaria, Spain
| | - Juli Caujapé-Castells
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria, Las Palmas, Gran Canaria, Spain
| | - Dario I Ojeda
- Norwegian Institute of Bioeconomy Research, Høgskoleveien 8, 1433 Ås, Norway
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Rodrigues ASB, Martins A, Garcia CA, Sérgio C, Porley R, Fontinha S, González-Mancebo J, Gabriel R, Phephu N, Van Rooy J, Dirkse G, Long D, Stech M, Patiño J, Sim-Sim M. Climate-driven vicariance and long-distance dispersal explain the Rand Flora pattern in the liverwort Exormotheca pustulosa (Marchantiophyta). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The ‘Rand flora’ is a biogeographical disjunction which refers to plant lineages occurring at the margins of the African continent and neighbouring oceanic archipelagos. Here, we tested whether the phylogeographical pattern of Exormotheca pustulosa Mitt. was the result of vicariance induced by past climatic changes or the outcome of a series of recent long-distance dispersal events. Two chloroplast markers (rps4-trnF region and psbA-trnH spacer) and one nuclear marker (ITS2) were analysed. Phylogenetic and phylogeographical relationships were inferred as well as divergence time estimates and ancestral areas. Exormotheca possibly originated in Eastern Africa during the Late Oligocene/Early Miocene while Exormotheca putulosa diversified during the Late Miocene. Three main E. pustulosa groups were found: the northern Macaronesia/Western Mediterranean, the South Africa/Saint Helena and the Cape Verde groups. The major splits among these groups occurred during the Late Miocene/Pliocene; diversification was recent, dating back to the Pleistocene. Climate-driven vicariance and subsequent long-distance dispersal events may have shaped the current disjunct distribution of E. pustulosa that corresponds to the Rand Flora pattern. Colonization of Macaronesia seems to have occurred twice by two independent lineages. The evolutionary history of E. pustulosa populations of Cape Verde warrants further study.
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Affiliation(s)
- Ana Sofia Bartolomeu Rodrigues
- cE3c – Centre for Ecology, Evolution and Environmental Changes, Natural History and Systematics (NHS) Research Group/MUHNAC – Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Rua da Escola Politécnica, Lisboa, Portugal
| | - Anabela Martins
- cE3c – Centre for Ecology, Evolution and Environmental Changes, Natural History and Systematics (NHS) Research Group/MUHNAC – Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Rua da Escola Politécnica, Lisboa, Portugal
| | - César Augusto Garcia
- cE3c – Centre for Ecology, Evolution and Environmental Changes, Natural History and Systematics (NHS) Research Group/MUHNAC – Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Rua da Escola Politécnica, Lisboa, Portugal
| | - Cecília Sérgio
- cE3c – Centre for Ecology, Evolution and Environmental Changes, Natural History and Systematics (NHS) Research Group/MUHNAC – Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Rua da Escola Politécnica, Lisboa, Portugal
| | - Ron Porley
- Cerca dos Pomares, CxP 409M, Aljezur, Portugal
| | - Susana Fontinha
- cE3c – Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Vegetal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- Banco de Germoplasma ISOPlexis, Universidade da Madeira, Funchal, Madeira, Portugal
| | | | - Rosalina Gabriel
- cE3c/ABG – Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and University of Azores, Angra do Heroísmo, Azores, Portugal
| | - Nonkululo Phephu
- Department of Nature Conservation, Tshwane University of Technology, Pretoria, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, PO WITS, South Africa
| | - Jacques Van Rooy
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, PO WITS, South Africa
- National Herbarium, South African National Biodiversity Institute (SANBI), Pretoria, South Africa
| | - Gerard Dirkse
- Naturalis Biodiversity Center, RA Leiden, The Netherlands
| | | | - Michael Stech
- Naturalis Biodiversity Center, RA Leiden, The Netherlands
- Leiden University, Leiden, The Netherlands
| | - Jairo Patiño
- Plant Conservation and Biogeography Group, Departamento de Botánica, Ecología y Fisiología Vegetal, Facultad de Ciencias, Apartado 456, CP 38200, Universidad de La Laguna, La Laguna, Tenerife, Canary Islands, Spain
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales & Agrobiología (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
| | - Manuela Sim-Sim
- cE3c – Centre for Ecology, Evolution and Environmental Changes, Natural History and Systematics (NHS) Research Group/MUHNAC – Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Rua da Escola Politécnica, Lisboa, Portugal
- cE3c – Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Vegetal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
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10
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Shee ZQ, Frodin DG, Cámara-Leret R, Pokorny L. Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics. FRONTIERS IN PLANT SCIENCE 2020; 11:258. [PMID: 32265950 PMCID: PMC7099051 DOI: 10.3389/fpls.2020.00258] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/19/2020] [Indexed: 05/19/2023]
Abstract
With its large proportion of endemic taxa, complex geological past, and location at the confluence of the highly diverse Malesian and Australian floristic regions, Papuasia - the floristic region comprising the Bismarck Archipelago, New Guinea, and the Solomon Islands - represents an ideal natural experiment in plant biogeography. However, scattered knowledge of its flora and limited representation in herbaria have hindered our understanding of the drivers of its diversity. Focusing on the woody angiosperm genus Schefflera (Araliaceae), we ask whether its morphologically defined infrageneric groupings are monophyletic, when these lineages diverged, and where (within Papuasia or elsewhere) they diversified. To address these questions, we use a high-throughput sequencing approach (Hyb-Seq) which combines target capture (with an angiosperm-wide bait kit targeting 353 single-copy nuclear loci) and genome shotgun sequencing (which allows retrieval of regions in high-copy number, e.g., organellar DNA) of historical herbarium collections. To reconstruct the evolutionary history of the genus we reconstruct molecular phylogenies with Bayesian inference, maximum likelihood, and pseudo-coalescent approaches, and co-estimate divergence times and ancestral areas in a Bayesian framework. We find strong support for most infrageneric morphological groupings, as currently circumscribed, and we show the efficacy of the Angiosperms-353 probe kit in resolving both deep and shallow phylogenetic relationships. We infer a sequence of colonization to explain the present-day distribution of Schefflera in Papuasia: from the Sunda Shelf, Schefflera arrived to the Woodlark plate (present-day eastern New Guinea) in the late Oligocene (when most of New Guinea was submerged) and, subsequently (throughout the Miocene), it migrated westwards (to the Maoke and Bird's Head Plates and thereon) and further diversified, in agreement with previous reconstructions.
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Affiliation(s)
- Zhi Qiang Shee
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Singapore Botanic Gardens, Singapore, Singapore
| | | | - Rodrigo Cámara-Leret
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Bren School of Environmental Science and Management, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Madrid, Spain
- Real Jardín Botánico (RJB-CSIC), Madrid, Spain
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11
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The Role of Climate and Topography in Shaping the Diversity of Plant Communities in Cabo Verde Islands. DIVERSITY 2020. [DOI: 10.3390/d12020080] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The flora and vegetation of the archipelago of Cabo Verde is dominated by Macaronesian, Mediterranean, and particularly by African tropical elements, resulting from its southernmost location, when compared to the other islands of the Macaronesia (i.e., Azores, Madeira, Selvagens, and Canary Islands). Very likely, such a geographical position entailed higher susceptibility to extreme climatic fluctuations, namely those associated with the West African Monsoon oscillations. These fluctuations led to a continuous aridification, which is a clear trend shown by most recent studies based on continental shelf cores. Promoting important environmental shifts, such climatic fluctuations are accepted as determinant to explain the current spatial distribution patterns of taxa, as well as the composition of the plant communities. In this paper, we present a comprehensive characterization of the main plant communities in Cabo Verde, and we discuss the role of the climatic and topoclimatic diversity in shaping the vegetation composition and distribution of this archipelago. Our study reveals a strong variation in the diversity of plant communities across elevation gradients and distinct patterns of richness among plant communities. Moreover, we present an overview of the biogeographical relationships of the Cabo Verde flora and vegetation with the other Macaronesian Islands and northwestern Africa. We discuss how the distribution of plant communities and genetic patterns found among most of the endemic lineages can be related to Africa’s ongoing aridification, exploring the impacts of a process that marks northern Africa from the Late Miocene until the present.
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12
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Mairal M. Una historia de dos bosques: el ocaso de la vegetación subtropical Afro-Macaronésica. CONSERVACIÓN VEGETAL 2019. [DOI: 10.15366/cv2019.23.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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13
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Mairal M, Šurinová M, Castro S, Münzbergová Z. Unmasking cryptic biodiversity in polyploids: origin and diversification of Aster amellus aggregate. ANNALS OF BOTANY 2018; 122:1047-1059. [PMID: 30107389 PMCID: PMC6266133 DOI: 10.1093/aob/mcy149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/18/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND AND AIMS The origin of different cytotypes by autopolyploidy may be an important mechanism in plant diversification. Although cryptic autopolyploids probably comprise the largest fraction of overlooked plant diversity, our knowledge of their origin and evolution is still rather limited. Here we study the presumed autopolyploid aggregate of Aster amellus, which encompasses diploid and hexaploid cytotypes. Although the cytotypes of A. amellus are not morphologically distinguishable, previous studies showed spatial segregation and limited gene flow between them, which could result in different evolutionary trajectories for each cytotype. METHODS We combine macroevolutionary, microevolutionary and niche modelling tools to disentangle the origin and the demographic history of the cytotypes, using chloroplast and nuclear markers in a dense population sampling in central Europe. KEY RESULTS Our results revealed a segregation between diploid and hexaploid cytotypes in the nuclear genome, where each cytotype represents a monophyletic lineage probably homogenized by concerted evolution. In contrast, the chloroplast genome showed intermixed connections between the cytotypes, which may correspond to shared ancestral relationships. Phylogeny, demographic analyses and ecological niche modelling supported an ongoing differentiation of the cytotypes, where the hexaploid cytotype is experiencing a demographic expansion and niche differentiation with respect to its diploid relative. CONCLUSIONS The two cytotypes may be considered as two different lineages at the onset of their evolutionary diversification. Polyploidization led to the occurrence of hexaploids, which expanded and changed their ecological niche.
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Affiliation(s)
- Mario Mairal
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Population Ecology, Czech Academy of Science, Průhonice, Czech Republic
- Department of Botany and Zoology, Stellenbosch University, Matieland, South Africa
- For correspondence. E-mail
| | - Mária Šurinová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Population Ecology, Czech Academy of Science, Průhonice, Czech Republic
| | - Sílvia Castro
- Centre for Functional Ecology, Department of Life Sciences of the University of Coimbra and Botanic Garden of the University of Coimbra, Coimbra, Portugal
| | - Zuzana Münzbergová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Population Ecology, Czech Academy of Science, Průhonice, Czech Republic
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14
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Mairal M, Caujapé-Castells J, Pellissier L, Jaén-Molina R, Álvarez N, Heuertz M, Sanmartín I. A tale of two forests: ongoing aridification drives population decline and genetic diversity loss at continental scale in Afro-Macaronesian evergreen-forest archipelago endemics. ANNALS OF BOTANY 2018; 122:1005-1017. [PMID: 29905771 PMCID: PMC6266103 DOI: 10.1093/aob/mcy107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 05/25/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Various studies and conservationist reports have warned about the contraction of the last subtropical Afro-Macaronesian forests. These relict vegetation zones have been restricted to a few oceanic and continental islands around the edges of Africa, due to aridification. Previous studies on relict species have generally focused on glacial effects on narrow endemics; however, little is known about the effects of aridification on the fates of previously widespread subtropical lineages. METHODS Nuclear microsatellites and ecological niche modelling were used to understand observed patterns of genetic diversity in two emblematic species, widely distributed in these ecosystems: Canarina eminii (a palaeoendemic of the eastern Afromontane forests) and Canarina canariensis (a palaeoendemic of the Canarian laurel forests). The software DIYABC was used to test alternative demographic scenarios and an ensemble method was employed to model potential distributions of the selected plants from the end of the deglaciation to the present. KEY RESULTS All the populations assessed experienced a strong and recent population decline, revealing that locally widespread endemisms may also be alarmingly threatened. CONCLUSIONS The detected extinction debt, as well as the extinction spiral to which these populations are subjected, demands urgent conservation measures for the unique, biodiversity-rich ecosystems that they inhabit.
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Affiliation(s)
- Mario Mairal
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo, Madrid, Spain
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico ‘Viera y Clavijo’ – Unidad Asociada CSIC (Cabildo de Gran Canaria), Las Palmas de Gran Canaria, Spain
| | - Juli Caujapé-Castells
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico ‘Viera y Clavijo’ – Unidad Asociada CSIC (Cabildo de Gran Canaria), Las Palmas de Gran Canaria, Spain
| | - Loïc Pellissier
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Ruth Jaén-Molina
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico ‘Viera y Clavijo’ – Unidad Asociada CSIC (Cabildo de Gran Canaria), Las Palmas de Gran Canaria, Spain
| | - Nadir Álvarez
- Department of Ecology and Evolution, Institute of Biology, University of Lausanne, Biophore Dorigny, Lausanne, Switzerland
| | | | - Isabel Sanmartín
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo, Madrid, Spain
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15
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Villaverde T, Pokorny L, Olsson S, Rincón-Barrado M, Johnson MG, Gardner EM, Wickett NJ, Molero J, Riina R, Sanmartín I. Bridging the micro- and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above. THE NEW PHYTOLOGIST 2018; 220:636-650. [PMID: 30016546 DOI: 10.1111/nph.15312] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/04/2018] [Indexed: 05/20/2023]
Abstract
Reconstructing phylogenetic relationships at the micro- and macroevoutionary levels within the same tree is problematic because of the need to use different data types and analytical frameworks. We test the power of target enrichment to provide phylogenetic resolution based on DNA sequences from above species to within populations, using a large herbarium sampling and Euphorbia balsamifera (Euphorbiaceae) as a case study. Target enrichment with custom probes was combined with genome skimming (Hyb-Seq) to sequence 431 low-copy nuclear genes and partial plastome DNA. We used supermatrix, multispecies-coalescent approaches, and Bayesian dating to estimate phylogenetic relationships and divergence times. Euphorbia balsamifera, with a disjunct Rand Flora-type distribution at opposite sides of Africa, comprises three well-supported subspecies: western Sahelian sepium is sister to eastern African-southern Arabian adenensis and Macaronesian-southwest Moroccan balsamifera. Lineage divergence times support Late Miocene to Pleistocene diversification and climate-driven vicariance to explain the Rand Flora pattern. We show that probes designed using genomic resources from taxa not directly related to the focal group are effective in providing phylogenetic resolution at deep and shallow evolutionary levels. Low capture efficiency in herbarium samples increased the proportion of missing data but did not bias estimation of phylogenetic relationships or branch lengths.
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Affiliation(s)
- Tamara Villaverde
- Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014, Madrid, Spain
| | - Lisa Pokorny
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
| | - Sanna Olsson
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Ctra. de la Coruña km. 7.5, 28040, Madrid, Spain
| | | | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, 79409-43131, USA
- Department of Plant Science and Conservation, Chicago Botanical Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
| | | | - Norman J Wickett
- Department of Plant Science and Conservation, Chicago Botanical Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
- Program in Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Julià Molero
- Laboratori de Botànica, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia, Universitat de Barcelona, 08028, Barcelona, Spain
| | - Ricarda Riina
- Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014, Madrid, Spain
| | - Isabel Sanmartín
- Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014, Madrid, Spain
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Sancho R, Cantalapiedra CP, López-Alvarez D, Gordon SP, Vogel JP, Catalán P, Contreras-Moreira B. Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes. THE NEW PHYTOLOGIST 2018; 218:1631-1644. [PMID: 29206296 DOI: 10.1111/nph.14926] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 03/03/2017] [Indexed: 05/24/2023]
Abstract
Few pan-genomic studies have been conducted in plants, and none of them have focused on the intraspecific diversity and evolution of their plastid genomes. We address this issue in Brachypodium distachyon and its close relatives B. stacei and B. hybridum, for which a large genomic data set has been compiled. We analyze inter- and intraspecific plastid comparative genomics and phylogenomic relationships within a family-wide framework. Major indel differences were detected between Brachypodium plastomes. Within B. distachyon, we detected two main lineages, a mostly Extremely Delayed Flowering (EDF+) clade and a mostly Spanish (S+) - Turkish (T+) clade, plus nine chloroplast capture and two plastid DNA (ptDNA) introgression and micro-recombination events. Early Oligocene (30.9 million yr ago (Ma)) and Late Miocene (10.1 Ma) divergence times were inferred for the respective stem and crown nodes of Brachypodium and a very recent Mid-Pleistocene (0.9 Ma) time for the B. distachyon split. Flowering time variation is a main factor driving rapid intraspecific divergence in B. distachyon, although it is counterbalanced by repeated introgression between previously isolated lineages. Swapping of plastomes between the three different genomic groups, EDF+, T+, S+, probably resulted from random backcrossing followed by stabilization through selection pressure.
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Affiliation(s)
- Rubén Sancho
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Saragossa, Spain
| | - Carlos P Cantalapiedra
- Department of Genetics and Plant Breeding, Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
| | - Diana López-Alvarez
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spain
| | - Sean P Gordon
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - John P Vogel
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Pilar Catalán
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Saragossa, Spain
| | - Bruno Contreras-Moreira
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Saragossa, Spain
- Department of Genetics and Plant Breeding, Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
- Fundación ARAID, Zaragoza, Spain
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Albert JS, Schoolmaster DR, Tagliacollo V, Duke-Sylvester SM. Barrier Displacement on a Neutral Landscape: Toward a Theory of Continental Biogeography. Syst Biol 2018; 66:167-182. [PMID: 27590192 DOI: 10.1093/sysbio/syw080] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/23/2016] [Indexed: 01/07/2023] Open
Abstract
Macroevolutionary theory posits three processes leading to lineage diversification and the formation of regional biotas: dispersal (species geographic range expansion), speciation (species lineage splitting), and extinction (species lineage termination). The Theory of Island Biogeography (TIB) predicts species richness values using just two of these processes; dispersal and extinction. Yet most species on Earth live on continents or continental shelves, and the dynamics of evolutionary diversification at regional and continental scales are qualitatively different from those that govern the formation of species richness on biogeographic islands. Certain geomorphological processes operating perennially on continental platforms displace barriers to gene flow and organismal dispersal, and affect all three terms of macroevolutionary diversification. For example, uplift of a dissected landscape and river capture both merge and separate portions of adjacent areas, allowing dispersal and larger geographic ranges, vicariant speciation and smaller geographic ranges, and extinction when range sizes are subdivided below a minimum persistence threshold. The TIB also does not predict many biogeographic and phylogenetic patterns widely observed in continentally distributed taxa, including: (i) power function-like species-area relationships; (ii) log-normal distribution of species geographic range sizes, in which most species have restricted ranges (are endemic) and few species have broad ranges (are cosmopolitan); (iii) mid-domain effects with more species toward the geographic center, and more early-branching, species-poor clades toward the geographic periphery; (iv) exponential rates of net diversification with log-linear accumulation of lineages through geological time; and (v) power function-like relationships between species-richness and clade diversity, in which most clades are species-poor and few clades are species-rich. Current theory does not provide a robust mechanistic framework to connect these seemingly disparate patterns. Here we present SEAMLESS (Spatially Explicit Area Model of Landscape Evolution by SimulationS) that generates clade diversification by moving geographic barriers on a continuous, neutral landscape. SEAMLESS is a neutral Landscape Evolution Model (LEM) that treats species and barriers as functionally equivalent with respect to model parameters. SEAMLESS differs from other model-based biogeographic methods (e.g., Lagrange, GeoSSE, BayArea, and BioGeoBEARS) by modeling properties of dispersal barriers rather than areas, and by modeling the evolution of species lineages on a continuous landscape, rather than the evolution of geographic ranges along branches of a phylogeny. SEAMLESS shows how dispersal is required to maintain species richness and avoid clade-wide extinction, demonstrates that ancestral range size does not predict species richness, and provides a unified explanation for the suite of commonly observed biogeographic and phylogenetic patterns listed above. SEAMLESS explains how a simple barrier-displacement mechanism affects lineage diversification under neutral conditions, and is advanced here toward the formulation of a general theory of continental biogeography. [Diversification, extinction, geodispersal, macroevolution, river capture, vicariance.].
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Affiliation(s)
- James S Albert
- Department of Biology, University of Louisiana at Lafayette, 104 E. University Circle, Lafayette, LA 70503, USA
| | | | - Victor Tagliacollo
- Universidade Federal do Tocantins Avenida NS 15, 109 Norte Palmas, Tocantins 77001-090, Brazil
| | - Scott M Duke-Sylvester
- Department of Biology, University of Louisiana at Lafayette, 104 E. University Circle, Lafayette, LA 70503, USA
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18
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Liang HY, Feng ZP, Pei B, Li Y, Yang XT. Demographic expansion of two Tamarix species along the Yellow River caused by geological events and climate change in the Pleistocene. Sci Rep 2018; 8:60. [PMID: 29311687 PMCID: PMC5758526 DOI: 10.1038/s41598-017-19034-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 12/20/2017] [Indexed: 11/13/2022] Open
Abstract
The geological events and climatic fluctuations during the Pleistocene played important roles in shaping patterns of species distribution. However, few studies have evaluated the patterns of species distribution that were influenced by the Yellow River. The present work analyzed the demography of two endemic tree species that are widely distributed along the Yellow River, Tamarix austromongolica and Tamarix chinensis, to understand the role of the Yellow River and Pleistocene climate in shaping their distribution patterns. The most common chlorotype, chlorotype 1, was found in all populations, and its divergence time could be dated back to 0.19 million years ago (Ma). This dating coincides well with the formation of the modern Yellow River and the timing of Marine Isotope Stages 5e-6 (MIS 5e-6). Bayesian reconstructions along with models of paleodistribution revealed that these two species experienced a demographic expansion in population size during the Quaternary period. Approximate Bayesian computation analyses supported a scenario of expansion approximately from the upper to lower reaches of the Yellow River. Our results provide support for the roles of the Yellow River and the Pleistocene climate in driving demographic expansion of the populations of T. austromongolica and T. chinensis. These findings are useful for understanding the effects of geological events and past climatic fluctuations on species distribution patterns.
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Affiliation(s)
- Hong-Yan Liang
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China.,Sanmenxia Polytechnic, Sanmenxia, 472000, China
| | - Zhi-Pei Feng
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Bing Pei
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yong Li
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xi-Tian Yang
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China.
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19
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Menezes T, Romeiras MM, de Sequeira MM, Moura M. Phylogenetic relationships and phylogeography of relevant lineages within the complex Campanulaceae family in Macaronesia. Ecol Evol 2017; 8:88-108. [PMID: 29321854 PMCID: PMC5756848 DOI: 10.1002/ece3.3640] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 09/30/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022] Open
Abstract
Macaronesia has long been recognized as a natural model for studying evolutionary processes in plant diversification. Several studies have attempted to focus on single lineages, and few have covered the diversification of a family across all the archipelagos. We used a comprehensive sample to clarify the phylogenetic relationships and the biogeographic history of the Macaronesian Campanulaceae. Hypotheses related to the colonization of these archipelagos will be used to examine the diversification patterns of different lineages. We sequenced the ITS region and six cpDNA markers (atpB, matK, petD, rbcL, trnL-F, and psbA-trnH) from 10 Campanulaceae species, including seven endemic species in Macaronesia. The phylogeny of these taxa was reconstructed using maximum parsimony, maximum likelihood, and Bayesian inference. To study the relationships within each lineage, haplotype networks were calculated using NeighborNet and TCS algorithms. Moreover, data were combined with fossil information to construct time-calibrated trees for the Macaronesian Campanulaceae species. The phylogenetic analyses are largely congruent with current taxon circumscriptions, and all the endemic genera formed monophyletic clades, namely Azorina in Azores; Musschia in Madeira; and Campanula in Cape Verde. The Azorina clade and the Cape Verde endemic Campanula may share a common ancestor in North Africa, and the divergence was dated ca. 12.3 million years ago (Mya). The divergence of the Musschia clade began in the Pliocene ca. 3.4 Mya. Moreover, several examples of intraspecific variation were revealed among the native species with a clear geographic structured patterns, suggesting that cryptic diversity might exist within the native Macaronesian Campanulaceae when compared to the close mainland taxa (e.g., Campanula erinus, Trachelium caeruleum), but additional studies are needed to support the molecular data. This study highlights the power of combining data (e.g., phylogeny and divergence times, with species distribution data) for testing diversification hypotheses within the unique Macaronesian flora, providing useful information for future conservation efforts.
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Affiliation(s)
- Tiago Menezes
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Associate Laboratory Faculdade de Ciências e Tecnologia Universidade dos Açores Ponta Delgada Azores Portugal
| | - Maria M Romeiras
- Linking Landscape, Environment, Agriculture and Food (LEAF) Instituto Superior de Agronomia Universidade de Lisboa Lisbon Portugal.,Centre for Ecology, Evolution and Environmental Changes (cE3c) Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Miguel M de Sequeira
- Madeira Botanical Group Faculdade de Ciências da Vida Universidade de Madeira Alto da PenteadaFunchal Madeira Portugal
| | - Mónica Moura
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Associate Laboratory Faculdade de Ciências e Tecnologia Universidade dos Açores Ponta Delgada Azores Portugal
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20
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Sun Y, Vargas-Mendoza CF. Population Structure, Genetic Diversity, and Evolutionary History of Kleinia neriifolia (Asteraceae) on the Canary Islands. FRONTIERS IN PLANT SCIENCE 2017; 8:1180. [PMID: 28713419 PMCID: PMC5492869 DOI: 10.3389/fpls.2017.01180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 06/20/2017] [Indexed: 06/07/2023]
Abstract
Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat). The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote) and western islands (EI Hierro, La Palma, La Gomera, Tenerife), this west-east genetic divergence may reflect a very beginning of speciation. The evolutionary scenario with highest posterior probabilities suggests Gran Canaria as oldest population with a westward colonization path to Tenerife, La Gomera, La Palma, and EI Hierro, and eastward dispersal path to Lanzarote through Fuerteventura. In the western islands, there is a slight decrease in the effective population size toward areas of recent colonization. However, in the eastern islands, the effective population size increase in Lanzarote relative to Gran Canaria and Fuerteventura. These results further our understanding of the evolution of widespread endemic plants within Canarian archipelago.
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Affiliation(s)
- Ye Sun
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural UniversityGuangzhou, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
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21
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Pinpointing cryptic borders: Fine-scale phylogeography and genetic landscape analysis of the Hormogaster elisae complex (Oligochaeta, Hormogastridae). Mol Phylogenet Evol 2017; 112:185-193. [PMID: 28487260 DOI: 10.1016/j.ympev.2017.05.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/24/2017] [Accepted: 05/05/2017] [Indexed: 11/20/2022]
Abstract
Spatial and temporal aspects of the evolution of cryptic species complexes have received less attention than species delimitation within them. The phylogeography of the cryptic complex Hormogaster elisae (Oligochaeta, Hormogastridae) lacks knowledge on several aspects, including the small-scale distribution of its lineages or the palaeogeographic context of their diversification. To shed light on these topics, a dense specimen collection was performed in the center of the Iberian Peninsula - resulting in 28 new H. elisae collecting points, some of them as close as 760m from each other- for a higher resolution of the distribution of the cryptic lineages and the relationships between the populations. Seven molecular regions were amplified: mitochondrial subunit 1 of cytochrome c oxidase (COI), 16S rRNA and tRNA Leu, Ala, and Ser (16S t-RNAs), one nuclear ribosomal gene (a fragment of 28S rRNA) and one nuclear protein-encoding gene (histone H3) in order to infer their phylogenetic relationships. Different representation methods of the pairwise divergence in the cytochrome oxidase I sequence (heatmap and genetic landscape graphs) were used to visualize the genetic structure of H. elisae. A nested approach sensu Mairal et al. (2015) (connecting the evolutionary rates of two datasets of different taxonomic coverage) was used to obtain one approximation to a time-calibrated phylogenetic tree based on external Clitellata fossils and a wide molecular dataset. Our results indicate that limited active dispersal ability and ecological or biotic barriers could explain the isolation of the different cryptic lineages, which never co-occur. Rare events of long distance dispersal through hydrochory appear as one of the possible causes of range expansion.
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22
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Tusiime FM, Gizaw A, Wondimu T, Masao CA, Abdi AA, Muwanika V, Trávníček P, Nemomissa S, Popp M, Eilu G, Brochmann C, Pimentel M. Sweet vernal grasses (Anthoxanthum) colonized African mountains along two fronts in the Late Pliocene, followed by secondary contact, polyploidization and local extinction in the Pleistocene. Mol Ecol 2017; 26:3513-3532. [PMID: 28390111 DOI: 10.1111/mec.14136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/24/2017] [Accepted: 03/29/2017] [Indexed: 11/28/2022]
Abstract
High tropical mountains harbour remarkable and fragmented biodiversity thought to a large degree to have been shaped by multiple dispersals of cold-adapted lineages from remote areas. Few dated phylogenetic/phylogeographic analyses are however available. Here, we address the hypotheses that the sub-Saharan African sweet vernal grasses have a dual colonization history and that lineages of independent origins have established secondary contact. We carried out rangewide sampling across the eastern African high mountains, inferred dated phylogenies from nuclear ribosomal and plastid DNA using Bayesian methods, and performed flow cytometry and AFLP (amplified fragment length polymorphism) analyses. We inferred a single Late Pliocene western Eurasian origin of the eastern African taxa, whose high-ploid populations in one mountain group formed a distinct phylogeographic group and carried plastids that diverged from those of the currently allopatric southern African lineage in the Mid- to Late Pleistocene. We show that Anthoxanthum has an intriguing history in sub-Saharan Africa, including Late Pliocene colonization from southeast and north, followed by secondary contact, hybridization, allopolyploidization and local extinction during one of the last glacial cycles. Our results add to a growing body of evidence showing that isolated tropical high mountain habitats have a dynamic recent history involving niche conservatism and recruitment from remote sources, repeated dispersals, diversification, hybridization and local extinction.
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Affiliation(s)
- Felly Mugizi Tusiime
- School of Forestry, Geographical and Environmental Sciences, Department of Forestry, Biodiversity and Tourism, Makerere University, Kampala, Uganda.,Natural History Museum, University of Oslo, Oslo, Norway
| | - Abel Gizaw
- Natural History Museum, University of Oslo, Oslo, Norway.,Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tigist Wondimu
- Natural History Museum, University of Oslo, Oslo, Norway.,Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Catherine Aloyce Masao
- Natural History Museum, University of Oslo, Oslo, Norway.,Department of Forest Biology, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Ahmed Abdikadir Abdi
- Natural History Museum, University of Oslo, Oslo, Norway.,National Museums of Kenya, Nairobi, Kenya
| | - Vincent Muwanika
- School of Forestry, Geographical and Environmental Sciences, Department of Forestry, Biodiversity and Tourism, Makerere University, Kampala, Uganda
| | - Pavel Trávníček
- Department of Flow Cytometry, Institute of Botany, Průhonice, Czech Republic
| | - Sileshi Nemomissa
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Magnus Popp
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Gerald Eilu
- School of Forestry, Geographical and Environmental Sciences, Department of Forestry, Biodiversity and Tourism, Makerere University, Kampala, Uganda
| | | | - Manuel Pimentel
- Natural History Museum, University of Oslo, Oslo, Norway.,CICA, Centro de Investigacións Científicas Avanzadas, Universidade da Coruña, Galicia, Spain
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23
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Mairal M, Sanmartín I, Herrero A, Pokorny L, Vargas P, Aldasoro JJ, Alarcón M. Geographic barriers and Pleistocene climate change shaped patterns of genetic variation in the Eastern Afromontane biodiversity hotspot. Sci Rep 2017; 7:45749. [PMID: 28397796 PMCID: PMC5387718 DOI: 10.1038/srep45749] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/02/2017] [Indexed: 12/02/2022] Open
Abstract
The Eastern African Afromontane forest is getting increased attention in conservation studies because of its high endemicity levels and shrinking geographic distribution. Phylogeographic studies have found evidence of high levels of genetic variation structured across the Great Rift System. Here, we use the epiphytic plant species Canarina eminii to explore causal explanations for this pattern. Phylogeographic analyses were undertaken using plastid regions and AFLP fragments. Population genetic analyses, Statistical Parsimony, and Bayesian methods were used to infer genetic diversity, genealogical relationships, structure, gene flow barriers, and the spatiotemporal evolution of populations. A strong phylogeographic structure was found, with two reciprocally monophyletic lineages on each side of the Great Rift System, high genetic exclusivity, and restricted gene flow among mountain ranges. We explain this pattern by topographic and ecological changes driven by geological rifting in Eastern Africa. Subsequent genetic structure is attributed to Pleistocene climatic changes, in which sky-islands acted as long-term refuges and cradles of genetic diversity. Our study highlights the importance of climate change and geographic barriers associated with the African Rift System in shaping population genetic patterns, as well as the need to preserve the high levels of exclusive and critically endangered biodiversity harboured by current patches of the Afromontane forest.
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Affiliation(s)
- Mario Mairal
- Real Jardín Botánico (RJB-CSIC), 28014 Madrid, Spain
| | | | | | - Lisa Pokorny
- Royal Botanic Gardens, Kew (RBGK), Richmond, Surrey, TW9 3DS, UK
| | - Pablo Vargas
- Real Jardín Botánico (RJB-CSIC), 28014 Madrid, Spain
| | - Juan J Aldasoro
- Instituto Botánico de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Spain.,Universidad Rey Juan Carlos, Móstoles, Spain
| | - Marisa Alarcón
- Instituto Botánico de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Spain
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24
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Silvestro D, Zizka A, Bacon CD, Cascales-Miñana B, Salamin N, Antonelli A. Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150225. [PMID: 26977065 PMCID: PMC4810818 DOI: 10.1098/rstb.2015.0225] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.
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Affiliation(s)
- Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 413 19, Sweden Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Alexander Zizka
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 413 19, Sweden
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 413 19, Sweden
| | | | - Nicolas Salamin
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 413 19, Sweden Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, Gothenburg 413 19, Sweden
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25
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Colonization and diversification of the Euphorbia species (sect. Aphyllis subsect. Macaronesicae) on the Canary Islands. Sci Rep 2016; 6:34454. [PMID: 27681300 PMCID: PMC5041082 DOI: 10.1038/srep34454] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 09/14/2016] [Indexed: 12/19/2022] Open
Abstract
Diversification between islands and ecological radiation within islands are postulated to have occurred in the Euphorbia species (sect. Aphyllis subsect. Macaronesicae) on the Canary Islands. In this study, the biogeographical pattern of 11 species of subsect. Macaronesicae and the genetic differentiation among five species were investigated to distinguish the potential mode and mechanism of diversification and speciation. The biogeographical patterns and genetic structure were examined using statistical dispersal-vicariance analysis, Bayesian phylogenetic analysis, reduced median-joining haplotype network analysis, and discriminant analysis of principal components. The gene flow between related species was evaluated with an isolation-with-migration model. The ancestral range of the species of subsect. Macaronesicae was inferred to be Tenerife and the Cape Verde Islands, and Tenerife-La Gomera acted as sources of diversity to other islands of the Canary Islands. Inter-island colonization of E. lamarckii among the western islands and a colonization of E. regis-jubae from Gran Canaria to northern Africa were revealed. Both diversification between islands and radiation within islands have been revealed in the Euphorbia species (sect. Aphyllis subsect. Macaronesicae) of the Canary Islands. It was clear that this group began the speciation process in Tenerife-La Gomera, and this process occurred with gene flow between some related species.
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26
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Gizaw A, Brochmann C, Nemomissa S, Wondimu T, Masao CA, Tusiime FM, Abdi AA, Oxelman B, Popp M, Dimitrov D. Colonization and diversification in the African 'sky islands': insights from fossil-calibrated molecular dating of Lychnis (Caryophyllaceae). THE NEW PHYTOLOGIST 2016; 211:719-34. [PMID: 27037925 DOI: 10.1111/nph.13937] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 02/18/2016] [Indexed: 05/10/2023]
Abstract
The flora on the isolated high African mountains or 'sky islands' is remarkable for its peculiar adaptations, local endemism and striking biogeographical connections to remote parts of the world. Ages of the plant lineages and the timing of their radiations have frequently been debated but remain contentious as there are few estimates based on explicit models and fossil-calibrated molecular clocks. We used the plastid region maturaseK (matK) and a Caryophylloflora paleogenica fossil to infer the age of the genus Lychnis, and constructed a data set of three plastid (matK; a ribosomal protein S16 (rps16); and an intergenic spacer (psbE-petL)) and two nuclear (internal transcribed spacer (ITS) and a region spanning exon 18-24 in the second largest subunit of RNA polymerase II (RPB2)) loci for joint estimation of the species tree and divergence time of the African representatives. The time of divergence of the African high-altitude Lychnis was placed in the late Miocene to early Pliocene. A single speciation event was inferred in the early Pliocene; subsequent speciation took place sporadically from the late Pliocene to the middle Pleistocene. We provide further support for a Eurasian origin of the African 'sky islands' floral elements, which seem to have been recruited via dispersals at different times: some old, as in Lychnis, and others very recent. We show that dispersal and diversification within Africa play an important role in shaping these isolated plant communities.
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Affiliation(s)
- Abel Gizaw
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
- Department of Plant Biology and Biodiversity Management, College of Natural Science, Addis Ababa University, PO Box 3434, Addis Ababa, Ethiopia
| | - Christian Brochmann
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
| | - Sileshi Nemomissa
- Department of Plant Biology and Biodiversity Management, College of Natural Science, Addis Ababa University, PO Box 3434, Addis Ababa, Ethiopia
| | - Tigist Wondimu
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
- Department of Plant Biology and Biodiversity Management, College of Natural Science, Addis Ababa University, PO Box 3434, Addis Ababa, Ethiopia
| | - Catherine Aloyce Masao
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
- Department of Forest Biology, Sokoine University of Agriculture, PO Box 3010, Morogoro, Tanzania
- Institute of Resource Assessment, University of Dar es Salaam, Box 35097, Dar es Salaam, Tanzania
| | - Felly Mugizi Tusiime
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
- Department of Forestry Biodiversity and Tourism, School of Forestry Geographical and Environmental Sciences, Makerere University, PO Box 7062, Kampala, Uganda
| | - Ahmed Abdikadir Abdi
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
- Botany Department, National Museums of Kenya, PO Box 40658, 00100, Nairobi, Kenya
| | - Bengt Oxelman
- Department of Biology and Environmental Sciences, University of Gothenburg, PO Box 461, 405 30, Gothenburg, Sweden
| | - Magnus Popp
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
| | - Dimitar Dimitrov
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
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27
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Crowl AA, Miles NW, Visger CJ, Hansen K, Ayers T, Haberle R, Cellinese N. A global perspective on Campanulaceae: Biogeographic, genomic, and floral evolution. AMERICAN JOURNAL OF BOTANY 2016; 103:233-45. [PMID: 26865121 DOI: 10.3732/ajb.1500450] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/04/2016] [Indexed: 05/12/2023]
Abstract
PREMISE OF THE STUDY The Campanulaceae are a diverse clade of flowering plants encompassing more than 2300 species in myriad habitats from tropical rainforests to arctic tundra. A robust, multigene phylogeny, including all major lineages, is presented to provide a broad, evolutionary perspective of this cosmopolitan clade. METHODS We used a phylogenetic framework, in combination with divergence dating, ancestral range estimation, chromosome modeling, and morphological character reconstruction analyses to infer phylogenetic placement and timing of major biogeographic, genomic, and morphological changes in the history of the group and provide insights into the diversification of this clade across six continents. KEY RESULTS Ancestral range estimation supports an out-of-Africa diversification following the Cretaceous-Tertiary extinction event. Chromosomal modeling, with corroboration from the distribution of synonymous substitutions among gene duplicates, provides evidence for as many as 20 genome-wide duplication events before large radiations. Morphological reconstructions support the hypothesis that switches in floral symmetry and anther dehiscence were important in the evolution of secondary pollen presentation mechanisms. CONCLUSIONS This study provides a broad, phylogenetic perspective on the evolution of the Campanulaceae clade. The remarkable habitat diversity and cosmopolitan distribution of this lineage appears to be the result of a complex history of genome duplications and numerous long-distance dispersal events. We failed to find evidence for an ancestral polyploidy event for this clade, and our analyses indicate an ancestral base number of nine for the group. This study will serve as a framework for future studies in diverse areas of research in Campanulaceae.
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Affiliation(s)
- Andrew A Crowl
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - Nicholas W Miles
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | - Clayton J Visger
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - Kimberly Hansen
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011 USA
| | - Tina Ayers
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011 USA
| | - Rosemarie Haberle
- Biology Department, Pacific Lutheran University, Tacoma, Washington 98447 USA
| | - Nico Cellinese
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
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28
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Ho SYW, Tong KJ, Foster CSP, Ritchie AM, Lo N, Crisp MD. Biogeographic calibrations for the molecular clock. Biol Lett 2015; 11:20150194. [PMID: 26333662 PMCID: PMC4614420 DOI: 10.1098/rsbl.2015.0194] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 06/22/2015] [Indexed: 11/12/2022] Open
Abstract
Molecular estimates of evolutionary timescales have an important role in a range of biological studies. Such estimates can be made using methods based on molecular clocks, including models that are able to account for rate variation across lineages. All clock models share a dependence on calibrations, which enable estimates to be given in absolute time units. There are many available methods for incorporating fossil calibrations, but geological and climatic data can also provide useful calibrations for molecular clocks. However, a number of strong assumptions need to be made when using these biogeographic calibrations, leading to wide variation in their reliability and precision. In this review, we describe the nature of biogeographic calibrations and the assumptions that they involve. We present an overview of the different geological and climatic events that can provide informative calibrations, and explain how such temporal information can be incorporated into dating analyses.
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Affiliation(s)
- Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - K Jun Tong
- School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Charles S P Foster
- School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Andrew M Ritchie
- School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Nathan Lo
- School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Michael D Crisp
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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29
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Mairal M, Sanmartín I, Aldasoro JJ, Culshaw V, Manolopoulou I, Alarcón M. Palaeo-islands as refugia and sources of genetic diversity within volcanic archipelagos: the case of the widespread endemicCanarina canariensis(Campanulaceae). Mol Ecol 2015; 24:3944-63. [DOI: 10.1111/mec.13282] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 12/13/2022]
Affiliation(s)
- M. Mairal
- Real Jardín Botánico (RJB-CSIC); 28014 Madrid Spain
| | - I. Sanmartín
- Real Jardín Botánico (RJB-CSIC); 28014 Madrid Spain
| | - J. J. Aldasoro
- Institut Botànic de Barcelona (IBB-CSIC-ICUB); 08038 Barcelona Spain
| | - V. Culshaw
- Real Jardín Botánico (RJB-CSIC); 28014 Madrid Spain
| | | | - M. Alarcón
- Institut Botànic de Barcelona (IBB-CSIC-ICUB); 08038 Barcelona Spain
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30
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Pokorny L, Riina R, Mairal M, Meseguer AS, Culshaw V, Cendoya J, Serrano M, Carbajal R, Ortiz S, Heuertz M, Sanmartín I. Living on the edge: timing of Rand Flora disjunctions congruent with ongoing aridification in Africa. Front Genet 2015; 6:154. [PMID: 25983742 PMCID: PMC4416453 DOI: 10.3389/fgene.2015.00154] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 04/05/2015] [Indexed: 01/16/2023] Open
Abstract
The Rand Flora is a well-known floristic pattern in which unrelated plant lineages show similar disjunct distributions in the continental margins of Africa and adjacent islands—Macaronesia-northwest Africa, Horn of Africa-Southern Arabia, Eastern Africa, and Southern Africa. These lineages are now separated by environmental barriers such as the arid regions of the Sahara and Kalahari Deserts or the tropical lowlands of Central Africa. Alternative explanations for the Rand Flora pattern range from vicariance and climate-driven extinction of a widespread pan-African flora to independent dispersal events and speciation in situ. To provide a temporal framework for this pattern, we used published data from nuclear and chloroplast DNA to estimate the age of disjunction of 17 lineages that span 12 families and nine orders of angiosperms. We further used these estimates to infer diversification rates for Rand Flora disjunct clades in relation to their higher-level encompassing lineages. Our results indicate that most disjunctions fall within the Miocene and Pliocene periods, coinciding with the onset of a major aridification trend, still ongoing, in Africa. Age of disjunctions seemed to be related to the climatic affinities of each Rand Flora lineage, with sub-humid taxa dated earlier (e.g., Sideroxylon) and those with more xeric affinities (e.g., Campylanthus) diverging later. We did not find support for significant decreases in diversification rates in most groups, with the exception of older subtropical lineages (e.g., Sideroxylon, Hypericum, or Canarina), but some lineages (e.g., Cicer, Campylanthus) showed a long temporal gap between stem and crown ages, suggestive of extinction. In all, the Rand Flora pattern seems to fit the definition of biogeographic pseudocongruence, with the pattern arising at different times in response to the increasing aridity of the African continent, with interspersed periods of humidity allowing range expansions.
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Affiliation(s)
| | | | | | - Andrea S Meseguer
- INRA, UMR 1062, Centre de Biologie pour la Gestion des Populations (INRA, IRD, CIRAD, Montpellier SupAgro) Montferrier-sur-Lez, France
| | | | - Jon Cendoya
- Real Jardín Botánico (RJB-CSIC) Madrid, Spain
| | - Miguel Serrano
- Department of Botany, Pharmacy School, University of Santiago de Compostela Santiago de Compostela, Spain
| | - Rodrigo Carbajal
- Department of Botany, Pharmacy School, University of Santiago de Compostela Santiago de Compostela, Spain
| | - Santiago Ortiz
- Department of Botany, Pharmacy School, University of Santiago de Compostela Santiago de Compostela, Spain
| | - Myriam Heuertz
- Forest Research Centre (INIA-CIFOR) Madrid, Spain ; INRA, BIOGECO, UMR 1202 Cestas, France ; University of Bordeaux, BIOGECO, UMR 1202 Talence, France
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