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Oliver EGH, Forshaw N, Oliver IM, Volk F, Schumann AWS, Dorr LJ, Hoekstra RD, Musker SD, Nürk NM, Pirie MD, Rebelo AG. Genus Erica: An identification aid version 4.00. PhytoKeys 2024; 241:143-154. [PMID: 38699680 PMCID: PMC11063621 DOI: 10.3897/phytokeys.241.117604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 02/22/2024] [Indexed: 05/05/2024]
Abstract
Species identification is fundamental to all aspects of biology and conservation. The process can be challenging, particularly in groups including many closely related or similar species. The problem is confounded by the absence of an up-to-date taxonomic revision, but even with such a resource all but professional botanists may struggle to recognise key species, presenting a substantial barrier to vital work such as surveys, threat assessments, and seed collection for ex situ conservation. Genus Erica: An Identification Aid is a tool to help both amateurs and professionals identify (using a limited number of accessible characteristics) and find information about the 851 species and many subspecific taxa of the genus Erica. We present an updated version 4.00, with new features including integrating distribution data from GBIF and iNaturalist, links to taxonomic resources through World Flora Online, and a probability function for identifications, that is freely available for PCs. It remains a work in progress: We discuss routes forward for collaboratively improving this resource.
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Affiliation(s)
- E. G. H. Oliver
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, 7602 Matieland, South Africa
| | | | | | | | | | - Laurence J. Dorr
- National Museum of Natural History, Department of Botany, MRC-166, Smithsonian Institution, P.O. Box 37012, Washington, D.C, 20013-7012, USA
| | | | - Seth D. Musker
- Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch 7701, Cape Town, South Afric
| | - Nicolai M. Nürk
- Department of Plant Systematics, Bayreuth Centre of Ecology and Environmental Research (BayCEER), University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Michael D. Pirie
- University Museum, University of Bergen, Postboks 7800, NO-5020 Bergen, Norway
| | - Anthony G. Rebelo
- Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch 7701, Cape Town, South Afric
- Threatened Species Unit, South African National Biodiversity Institute, Cape Town, South Africa
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Nelson EC, Oliver EGH, Pirie MD. Erica L. (Ericaceae): homonyms amongst published names for African species and proposed replacement names. PhytoKeys 2023; 236:157-178. [PMID: 38155765 PMCID: PMC10753580 DOI: 10.3897/phytokeys.236.110498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/05/2023] [Indexed: 12/30/2023]
Abstract
In support of ongoing taxonomic work on the large and complex flowering plant genus Erica (Ericaceae), we document nineteen pairs of homonyms representing currently used illegitimate names. We provide replacements for thirteen names and new typifications for five. We relegate five names to synonymy: Ericaaemula Guthrie & Bolus under Ericadistorta Bartl.; Ericaarmata Klotzsch ex Benth. under Ericaumbrosa H. A. Baker; Ericacapensis T.M. Salter under Ericaturbiniflora Salisb.; Ericalanata Andrews under Ericaflaccida Link; and Ericatomentosa Salisb. under Ericavelutina Bartl. Finally, we suggest conservation of Ericaaristata Andrews. The new names are: Ericaadelopetala E.C. Nelson & E.G.H. Oliv. replacing Ericainsignis E.G.H. Oliv.; Ericabombycina E.C. Nelson & Pirie replacing Ericaniveniana E.G.H. Oliv.; Ericaconcordia E.C. Nelson & E.G.H. Oliv. replacing Ericaconstantia Nois. ex Benth.; Ericadidymocarpa E.C. Nelson & E.G.H. Oliv. replacing Ericarugata E.G.H. Oliv.; Ericagalantha E.C. Nelson & E.G.H. Oliv. replacing Ericaperlata Benth.; Ericamallotocalyx E.C. Nelson & E.G.H. Oliv. replacing Ericaflocciflora Benth.; Ericanotoporina E.C. Nelson & E.G.H. Oliv. replacing E.autumnalis L.Bolus; Ericaoliveranthus E.C. Nelson & Pirie replacing Ericatenuis Salisb.; Ericaoraria E.C. Nelson & E.G.H. Oliv. replacing Ericaspectabilis Klotzsch ex Benth.; Ericaoresbia E.C. Nelson & E.G.H. Oliv. replacing Ericademissa Klotzsch ex Benth.; Ericapoculiflora E.C. Nelson & E.G.H. Oliv. replacing Ericastenantha Klotzsch ex Benth.; Ericarhodella E.C. Nelson & E.G.H. Oliv. replacing Ericarhodantha Guthrie & Bolus; Ericasupranubia E.C. Nelson & Pirie replacing Ericapraecox Klotzsch.
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Affiliation(s)
- E. Charles Nelson
- Tippitiwitchet Cottage, 255A Broadgate, Sutton St Edmund PE12 0LT, UKUnaffiliatedSpaldingUnited Kingdom
| | - E. G. H. Oliver
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Stellenbosch, 7602 Matieland, South AfricaUniversity of StellenboschStellenboschSouth Africa
| | - Michael D. Pirie
- University Museum, University of Bergen, Postboks 7800, NO-5020 Bergen, NorwayUniversity of BergenBergenNorway
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Strijk JS, Hinsinger DD, Roeder MM, Chatrou LW, Couvreur TLP, Erkens RHJ, Sauquet H, Pirie MD, Thomas DC, Cao K. Chromosome-level reference genome of the soursop (Annona muricata): A new resource for Magnoliid research and tropical pomology. Mol Ecol Resour 2021; 21:1608-1619. [PMID: 33569882 PMCID: PMC8251617 DOI: 10.1111/1755-0998.13353] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 11/27/2022]
Abstract
The flowering plant family Annonaceae includes important commercially grown tropical crops, but development of promising species is hindered by a lack of genomic resources to build breeding programs. Annonaceae are part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades remain unclear. To provide resources to breeders and evolutionary researchers, we report a chromosome-level genome assembly of the soursop (Annona muricata). We assembled the genome using 444.32 Gb of DNA sequences (676× sequencing depth) from PacBio and Illumina short-reads, in combination with 10× Genomics and Bionano data (v1). A total of 949 scaffolds were assembled to a final size of 656.77 Mb, with a scaffold N50 of 3.43 Mb (v1), and then further improved to seven pseudo-chromosomes using Hi-C sequencing data (v2; scaffold N50: 93.2 Mb, total size in chromosomes: 639.6 Mb). Heterozygosity was very low (0.06%), while repeat sequences accounted for 54.87% of the genome, and 23,375 protein-coding genes with an average of 4.79 exons per gene were annotated using de novo, RNA-seq and homology-based approaches. Reconstruction of the historical population size showed a slow continuous contraction, probably related to Cenozoic climate changes. The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in magnoliids, providing an essential resource for delineating relationships of ancient angiosperm lineages. Both genome-assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome. As a community resource, this assembly will further strengthen the role of Annonaceae as model species for research on the ecology, evolution and domestication potential of tropical species in pomology and agroforestry.
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Affiliation(s)
- Joeri S. Strijk
- Institute for Biodiversity and Environmental ResearchUniversiti Brunei DarussalamJalan Tungku LinkBrunei Darussalam
- Alliance for Conservation Tree GenomicsPha Tad Ke Botanical GardenLuang PrabangLaos
- Guangxi Key Laboratory of Forest Ecology and ConservationBiodiversity Genomics TeamNanningGuangxiChina
| | - Damien D. Hinsinger
- Alliance for Conservation Tree GenomicsPha Tad Ke Botanical GardenLuang PrabangLaos
- Génomique Métabolique, GenoscopeInstitut de Biologie François JacobCommissariat à l′Énergie Atomique (CEA), CNRSUniversité ÉvryUniversité Paris‐SaclayÉvryFrance
| | - Mareike M. Roeder
- Community Ecology and Conservation GroupXishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglun, MenglaYunnanChina
- AueninstitutInstitute for Geography and GeoecologyKarlsruhe Institute of TechnologyRastattGermany
| | - Lars W. Chatrou
- Systematic and Evolutionary Botany LaboratoryGhent UniversityGhentBelgium
| | | | - Roy H. J. Erkens
- Maastricht Science ProgrammeMaastricht UniversityMaastrichtThe Netherlands
| | - Hervé Sauquet
- National Herbarium of New South Wales (NSW)Royal Botanic Gardens and Domain TrustSydneyNSWAustralia
| | - Michael D. Pirie
- Department of Natural HistoryUniversity MuseumUniversity of BergenBergenNorway
| | | | - Kunfang Cao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangxi UniversityNanningGuangxiChina
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Nürk NM, Linder HP, Onstein RE, Larcombe MJ, Hughes CE, Piñeiro Fernández L, Schlüter PM, Valente L, Beierkuhnlein C, Cutts V, Donoghue MJ, Edwards EJ, Field R, Flantua SGA, Higgins SI, Jentsch A, Liede‐Schumann S, Pirie MD. Diversification in evolutionary arenas-Assessment and synthesis. Ecol Evol 2020; 10:6163-6182. [PMID: 32607221 PMCID: PMC7319112 DOI: 10.1002/ece3.6313] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/30/2020] [Accepted: 04/06/2020] [Indexed: 12/23/2022] Open
Abstract
Understanding how and why rates of evolutionary diversification vary is a key issue in evolutionary biology, ecology, and biogeography. Evolutionary rates are the net result of interacting processes summarized under concepts such as adaptive radiation and evolutionary stasis. Here, we review the central concepts in the evolutionary diversification literature and synthesize these into a simple, general framework for studying rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions, and across spatial and temporal scales. Our framework describes the diversification rate (d) as a function of the abiotic environment (a), the biotic environment (b), and clade-specific phenotypes or traits (c); thus, d ~ a,b,c. We refer to the four components (a-d) and their interactions collectively as the "Evolutionary Arena." We outline analytical approaches to this framework and present a case study on conifers, for which we parameterize the general model. We also discuss three conceptual examples: the Lupinus radiation in the Andes in the context of emerging ecological opportunity and fluctuating connectivity due to climatic oscillations; oceanic island radiations in the context of island formation and erosion; and biotically driven radiations of the Mediterranean orchid genus Ophrys. The results of the conifer case study are consistent with the long-standing scenario that low competition and high rates of niche evolution promote diversification. The conceptual examples illustrate how using the synthetic Evolutionary Arena framework helps to identify and structure future directions for research on evolutionary radiations. In this way, the Evolutionary Arena framework promotes a more general understanding of variation in evolutionary rates by making quantitative results comparable between case studies, thereby allowing new syntheses of evolutionary and ecological processes to emerge.
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Affiliation(s)
- Nicolai M. Nürk
- Department of Plant SystematicsBayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
| | - H. Peter Linder
- Department of Systematic & Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Renske E. Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | | | - Colin E. Hughes
- Department of Systematic & Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Laura Piñeiro Fernández
- Department of Systematic & Evolutionary BotanyUniversity of ZurichZurichSwitzerland
- Department of BotanyUniversity of HohenheimStuttgartGermany
| | | | - Luis Valente
- Naturalis Biodiversity CenterUnderstanding Evolution GroupLeidenThe Netherlands
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Carl Beierkuhnlein
- Department of BiogeographyBayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
| | - Vanessa Cutts
- School of GeographyUniversity of NottinghamNottinghamUK
| | - Michael J. Donoghue
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
| | - Erika J. Edwards
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
| | - Richard Field
- School of GeographyUniversity of NottinghamNottinghamUK
| | | | | | - Anke Jentsch
- Department of Disturbance EcologyBayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
| | - Sigrid Liede‐Schumann
- Department of Plant SystematicsBayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
| | - Michael D. Pirie
- Johannes Gutenberg‐UniversitätMainzGermany
- University MuseumUniversity of BergenBergenNorway
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Pirie MD, Kandziora M, Nürk NM, Le Maitre NC, Mugrabi de Kuppler A, Gehrke B, Oliver EGH, Bellstedt DU. Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica. BMC Evol Biol 2019; 19:222. [PMID: 31805850 PMCID: PMC6896773 DOI: 10.1186/s12862-019-1545-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 11/21/2019] [Indexed: 12/28/2022] Open
Abstract
Background The coincidence of long distance dispersal (LDD) and biome shift is assumed to be the result of a multifaceted interplay between geographical distance and ecological suitability of source and sink areas. Here, we test the influence of these factors on the dispersal history of the flowering plant genus Erica (Ericaceae) across the Afrotemperate. We quantify similarity of Erica climate niches per biogeographic area using direct observations of species, and test various colonisation scenarios while estimating ancestral areas for the Erica clade using parametric biogeographic model testing. Results We infer that the overall dispersal history of Erica across the Afrotemperate is the result of infrequent colonisation limited by geographic proximity and niche similarity. However, the Drakensberg Mountains represent a colonisation sink, rather than acting as a “stepping stone” between more distant and ecologically dissimilar Cape and Tropical African regions. Strikingly, the most dramatic examples of species radiations in Erica were the result of single unique dispersals over longer distances between ecologically dissimilar areas, contradicting the rule of phylogenetic biome conservatism. Conclusions These results highlight the roles of geographical and ecological distance in limiting LDD, but also the importance of rare biome shifts, in which a unique dispersal event fuels evolutionary radiation.
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Affiliation(s)
- Michael D Pirie
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany. .,Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa. .,Current address: University Museum, The University of Bergen, Postboks 7800, N-5020, Bergen, Norway.
| | - Martha Kandziora
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany.,Life and Environmental Sciences, School of Natural Sciences, University of California, Merced, USA
| | - Nicolai M Nürk
- Department of Plant Systematics, Bayreuth Centre of Ecology and Environmental Research (BayCEER), University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Nicholas C Le Maitre
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.,Department of Plant Science, University of the Free State, QwaQwa, Bloemfontein, South Africa
| | - Ana Mugrabi de Kuppler
- INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-Universität Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Berit Gehrke
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany.,Current address: University Museum, The University of Bergen, Postboks 7800, N-5020, Bergen, Norway
| | - Edward G H Oliver
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Dirk U Bellstedt
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
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Le Maitre NC, Pirie MD, Bellstedt DU. An approach to determining anthocyanin synthesis enzyme gene expression in an evolutionary context: an example from Erica plukenetii. Ann Bot 2019; 124:121-130. [PMID: 31008513 PMCID: PMC6676384 DOI: 10.1093/aob/mcz046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 03/24/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Floral colour in angiosperms can be controlled by variations in the expression of the genes of the anthocyanin pathway. Floral colour shifts influence pollinator specificity. Multiple shifts in floral colour occurred in the diversification of the genus Erica (Ericaceae), from plesiomorphic pink to, for example, red or white flowers. Variation in anthocyanin gene expression and its effects on floral colour in the red-, pink- and white-flowered Erica plukenetii species complex was investigated. METHODS Next generation sequencing, reverse transcriptase PCR and real-time reverse transcriptase quantitative PCR were used to quantify anthocyanin gene expression. KEY RESULTS Non-homologous mutations causing loss of expression of single genes were found, indicating that the cause was likely to be mutations in transcription factor binding sites upstream of the 5'-untranslated region of the genes, and this was confirmed by sequencing. CONCLUSIONS Independent evolution and subsequent loss of expression of anthocyanin genes may have influenced diversification in the E. plukenetii species complex. The approach developed here should find more general application in studies on the role of floral colour shifts in diversification.
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Affiliation(s)
- N C Le Maitre
- Biochemistry Department, Stellenbosch University, Private Bag X1, Matieland, South Africa
- University of the Free State, Bloemfontein, South Africa
| | - M D Pirie
- Johannes Gutenberg-Universität, Mainz, Mainz, Germany
- University Museum, University of Bergen, Postboks, Bergen, Norway
| | - D U Bellstedt
- Biochemistry Department, Stellenbosch University, Private Bag X1, Matieland, South Africa
- For correspondence. E-mail
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Pirie MD, Chatrou LW, Maas PJM. A taxonomic revision of the Neotropical genus Cremastosperma (Annonaceae), including five new species. PhytoKeys 2018; 112:1-141. [PMID: 30524186 PMCID: PMC6277488 DOI: 10.3897/phytokeys.112.24897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 10/12/2018] [Indexed: 06/09/2023]
Abstract
We present a taxonomic revision of Cremastosperma, a genus of Neotropical Annonaceae occurring in lowland to premontane wet forest, mostly in areas surrounding the Andean mountain chain. We recognise 34 species, describing five as new here: from east of the Andes, C.brachypodum Pirie & Chatrou, sp. nov. and C.dolichopodum Pirie & Maas, sp. nov., endemic to Peru; C.confusum Pirie, sp. nov., from southern Peru and adjacent Bolivia and Brazil; and C.alticola Pirie & Chatrou, sp. nov., at higher elevations in northern Peru and Ecuador; and from west of the Andes, C.osicola Pirie & Chatrou, sp. nov. endemic to Costa Rica, the most northerly distributed species of the genus. We provide an identification key, document diagnostic characters and distributions and provide illustrations and extensive lists of specimens, also presenting the latter in the form of mapping data with embedded links to images available online. Of the 34 species, 22 are regional endemics. On the basis of the extent of occurrence and area of occupancy of species estimated from the distribution data, we designate IUCN threat categries for all species. Fourteen species proved to be endangered (EN) and a further one critically endangered (CR), reflecting their rarity and narrow known distributions.
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Affiliation(s)
- Michael D. Pirie
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099 Mainz, GermanyJohannes Gutenberg-UniversitätMainzGermany
| | - Lars W. Chatrou
- Wageningen University and Research, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB Wageningen, The NetherlandsWageningen UniversityWageningenNetherlands
- Ghent University, Systematic and Evolutionary Botany lab, K.L. Ledeganckstraat 35, 9000 Ghent, BelgiumGhent UniversityGhentBelgium
| | - Paul J. M. Maas
- Naturalis Biodiversity Center, section Botany, P.O. Box 9517, 2300 RA Leiden, The NetherlandsNaturalis Biodiversity CenterWageningenNetherlands
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Pirie MD, Maas PJM, Wilschut RA, Melchers-Sharrott H, Chatrou LW. Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of South America. R Soc Open Sci 2018; 5:171561. [PMID: 29410860 PMCID: PMC5792937 DOI: 10.1098/rsos.171561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/21/2017] [Indexed: 05/15/2023]
Abstract
Much of the immense present day biological diversity of Neotropical rainforests originated from the Miocene onwards, a period of geological and ecological upheaval in South America. We assess the impact of the Andean orogeny, drainage of Lake Pebas and closure of the Panama isthmus on two clades of tropical trees (Cremastosperma, ca 31 spp.; and Mosannona, ca 14 spp.; both Annonaceae). Phylogenetic inference revealed similar patterns of geographically restricted clades and molecular dating showed diversifications in the different areas occurred in parallel, with timing consistent with Andean vicariance and Central American geodispersal. Ecological niche modelling approaches show phylogenetically conserved niche differentiation, particularly within Cremastosperma. Niche similarity and recent common ancestry of Amazon and Guianan Mosannona species contrast with dissimilar niches and more distant ancestry of Amazon, Venezuelan and Guianan species of Cremastosperma, suggesting that this element of the similar patterns of disjunct distributions in the two genera is instead a biogeographic parallelism, with differing origins. The results provide further independent evidence for the importance of the Andean orogeny, the drainage of Lake Pebas, and the formation of links between South and Central America in the evolutionary history of Neotropical lowland rainforest trees.
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Affiliation(s)
- Michael D. Pirie
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099 Mainz, Germany
| | - Paul J. M. Maas
- Naturalis Biodiversity Center, Section Botany, PO Box 9517, 2300 RA Leiden, The Netherlands
| | - Rutger A. Wilschut
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | | | - Lars W. Chatrou
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Kadlec M, Bellstedt DU, Le Maitre NC, Pirie MD. Targeted NGS for species level phylogenomics: "made to measure" or "one size fits all"? PeerJ 2017; 5:e3569. [PMID: 28761782 PMCID: PMC5530999 DOI: 10.7717/peerj.3569] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/22/2017] [Indexed: 12/05/2022] Open
Abstract
Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools, or custom made for particular clades at considerably greater effort. We applied custom made scripts to select sets of homologous sequence markers from transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae). We compared the resulting targets to those that would be selected both using different available tools (Hyb-Seq; MarkerMiner), and when optimising for broader clades of more distantly related taxa (Ericales; eudicots). Approaches comparing more divergent genomes (including MarkerMiner, irrespective of input data) delivered fewer and shorter potential markers than those targeted for Erica. The latter may nevertheless be effective for sequence capture across the wider family Ericaceae. We tested the targets delivered by our scripts by obtaining an empirical dataset. The resulting sequence variation was lower than that of standard nuclear ribosomal markers (that in Erica fail to deliver a well resolved gene tree), confirming the importance of maximising the lengths of individual markers. We conclude that rather than searching for "one size fits all" universal markers, we should improve and make more accessible the tools necessary for developing "made to measure" ones.
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Affiliation(s)
- Malvina Kadlec
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Dirk U. Bellstedt
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, South Africa
| | | | - Michael D. Pirie
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes-Gutenberg Universität Mainz, Mainz, Germany
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Abstract
Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools, or custom made for particular clades at considerably greater effort. We applied custom made scripts to select sets of homologous sequence markers from transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae). We compared the resulting targets to those that would be selected both using different available tools (Hyb-Seq; MarkerMiner), and when optimising for broader clades of more distantly related taxa (Ericales; eudicots). Approaches comparing more divergent genomes (including MarkerMiner, irrespective of input data) delivered fewer and shorter potential markers than those targeted for Erica. The latter may nevertheless be effective for sequence capture across the wider family Ericaceae. We tested the targets delivered by our scripts by obtaining an empirical dataset. The resulting sequence variation was lower than that of standard nuclear ribosomal markers (that in Erica fail to deliver a well resolved gene tree), confirming the importance of maximising the lengths of individual markers. We conclude that rather than searching for "one size fits all" universal markers, we should improve and make more accessible the tools necessary for developing "made to measure" ones.
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Affiliation(s)
- Malvina Kadlec
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Dirk U Bellstedt
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, South Africa
| | - Nicholas C Le Maitre
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, South Africa
| | - Michael D Pirie
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes-Gutenberg Universität Mainz, Mainz, Germany
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Pirie MD, Oliver EGH, Mugrabi de Kuppler A, Gehrke B, Le Maitre NC, Kandziora M, Bellstedt DU. The biodiversity hotspot as evolutionary hot-bed: spectacular radiation of Erica in the Cape Floristic Region. BMC Evol Biol 2016; 16:190. [PMID: 27639849 PMCID: PMC5027107 DOI: 10.1186/s12862-016-0764-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 09/08/2016] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The disproportionate species richness of the world's biodiversity hotspots could be explained by low extinction (the evolutionary "museum") and/or high speciation (the "hot-bed") models. We test these models using the largest of the species rich plant groups that characterise the botanically diverse Cape Floristic Region (CFR): the genus Erica L. We generate a novel phylogenetic hypothesis informed by nuclear and plastid DNA sequences of c. 60 % of the c. 800 Erica species (of which 690 are endemic to the CFR), and use this to estimate clade ages (using RELTIME; BEAST), net diversification rates (GEIGER), and shifts in rates of diversification in different areas (BAMM; MuSSE). RESULTS The diversity of Erica species in the CFR is the result of a single radiation within the last c. 15 million years. Compared to ancestral lineages in the Palearctic, the rate of speciation accelerated across Africa and Madagascar, with a further burst of speciation within the CFR that also exceeds the net diversification rates of other Cape clades. CONCLUSIONS Erica exemplifies the "hotbed" model of assemblage through recent speciation, implying that with the advent of the modern Cape a multitude of new niches opened and were successively occupied through local species diversification.
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Affiliation(s)
- M D Pirie
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany.
| | - E G H Oliver
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - A Mugrabi de Kuppler
- INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-Universität Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - B Gehrke
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany
| | - N C Le Maitre
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - M Kandziora
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany
| | - D U Bellstedt
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
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Lauterbach M, van der Merwe PDW, Keßler L, Pirie MD, Bellstedt DU, Kadereit G. Evolution of leaf anatomy in arid environments – A case study in southern African Tetraena and Roepera (Zygophyllaceae). Mol Phylogenet Evol 2016; 97:129-144. [DOI: 10.1016/j.ympev.2016.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 01/05/2016] [Accepted: 01/06/2016] [Indexed: 12/28/2022]
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Pirie MD, Litsios G, Bellstedt DU, Salamin N, Kissling J. Back to Gondwanaland: can ancient vicariance explain (some) Indian Ocean disjunct plant distributions? Biol Lett 2016; 11:20150086. [PMID: 26063747 DOI: 10.1098/rsbl.2015.0086] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Oceans, or other wide expanses of inhospitable environment, interrupt present day distributions of many plant groups. Using molecular dating techniques, generally incorporating fossil evidence, we can estimate when such distributions originated. Numerous dating analyses have recently precipitated a paradigm shift in the general explanations for the phenomenon, away from older geological causes, such as continental drift, in favour of more recent, long-distance dispersal (LDD). For example, the 'Gondwanan vicariance' scenario has been dismissed in various studies of Indian Ocean disjunct distributions. We used the gentian tribe Exaceae to reassess this scenario using molecular dating with minimum (fossil), maximum (geological), secondary (from wider analyses) and hypothesis-driven age constraints. Our results indicate that ancient vicariance cannot be ruled out as an explanation for the early origins of Exaceae across Africa, Madagascar and the Indian subcontinent unless a strong assumption is made about the maximum age of Gentianales. However, both the Gondwanan scenario and the available evidence suggest that there were also several, more recent, intercontinental dispersals during the diversification of the group.
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Affiliation(s)
- Michael D Pirie
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099 Mainz, Germany
| | - Glenn Litsios
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015 Lausanne, Switzerland Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland
| | - Dirk U Bellstedt
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - Nicolas Salamin
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015 Lausanne, Switzerland Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland
| | - Jonathan Kissling
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015 Lausanne, Switzerland Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
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Gehrke B, Kandziora M, Pirie MD. The evolution of dwarf shrubs in alpine environments: a case study of Alchemilla in Africa. Ann Bot 2016; 117:121-31. [PMID: 26520565 PMCID: PMC4701153 DOI: 10.1093/aob/mcv159] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/27/2015] [Accepted: 09/02/2015] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS Alpine and arctic environments worldwide, including high mountains, are dominated by short-stature woody plants (dwarf shrubs). This conspicuous life form asserts considerable influence on local environmental conditions above the treeline, creating its own microhabitat. This study reconstructs the evolution of dwarf shrubs in Alchemilla in the African tropical alpine environment, where they represent one of the largest clades and are among the most common and abundant plants. METHODS Different phylogenetic inference methods were used with plastid and nuclear DNA sequence markers, molecular dating (BEAST and RelTime), analyses of diversification rate shifts (MEDUSA and BAMM) and ancestral character and area reconstructions (Mesquite). KEY RESULTS It is inferred that African Alchemilla species originated following long-distance dispersal to tropical East Africa, but that the evolution of dwarf shrubs occurred in Ethiopia and in tropical East Africa independently. Establishing a timeframe is challenging given inconsistencies in age estimates, but it seems likely that they originated in the Pleistocene, or at the earliest in the late Miocene. The adaptation to alpine-like environments in the form of dwarf shrubs has apparently not led to enhanced diversification rates. Ancestral reconstructions indicate reversals in Alchemilla from plants with a woody base to entirely herbaceous forms, a transition that is rarely reported in angiosperms. CONCLUSIONS Alchemilla is a clear example of in situ tropical alpine speciation. The dwarf shrub life form typical of African Alchemilla has evolved twice independently, further indicating its selective advantage in these harsh environments. However, it has not influenced diversification, which, although recent, was not rapid.
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Affiliation(s)
- Berit Gehrke
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg Universität, Mainz, Germany and
| | - Martha Kandziora
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg Universität, Mainz, Germany and
| | - Michael D Pirie
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg Universität, Mainz, Germany and Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
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Maree HJ, Pirie MD, Oosthuizen K, Bester R, Rees DJG, Burger JT. Phylogenomic analysis reveals deep divergence and recombination in an economically important grapevine virus. PLoS One 2015; 10:e0126819. [PMID: 25992606 PMCID: PMC4436351 DOI: 10.1371/journal.pone.0126819] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/08/2015] [Indexed: 11/28/2022] Open
Abstract
The evolutionary history of the exclusively grapevine (Vitis spp.) infecting, grapevine leafroll-associated virus 3 (GLRaV-3) has not been studied extensively, partly due to limited available sequence data. In this study we trace the evolutionary history of GLRaV-3, focussing on isolate GH24, a newly discovered variant. GH24 was discovered through the use of next-generation sequencing (NGS) and the whole genome sequence determined and validated with Sanger sequencing. We assembled an alignment of all 13 available whole genomes of GLRaV-3 isolates and all other publicly available GLRaV-3 sequence data. Using multiple recombination detection methods we identified a clear signal for recombination in one whole genome sequence and further evidence for recombination in two more, including GH24. We inferred phylogenetic trees and networks and estimated the ages of common ancestors of GLRaV-3 clades by means of relaxed clock models calibrated with asynchronous sampling dates. Our results generally confirm previously identified variant groups as well as two new groups (VII and VIII). Higher order groups were defined as supergroups designated A to D. Supergroup A includes variant groups I-V and supergroup B group VI and its related unclassified isolates. Supergroups C and D are less well known, including the newly identified groups VII (including isolate GH24) and VIII respectively. The inferred node ages suggest that the origins of the major groups of GLRaV-3, including isolate GH24, may have occurred prior to worldwide cultivation of grapevines, whilst the current diversity represents closely related isolates that diverged from common ancestors within the last century.
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Affiliation(s)
- Hans J. Maree
- Agricultural Research Council, Infruitec-Nietvoorbij (The Fruit, Vine and Wine Institute), Private Bag X5026, Stellenbosch, 7599, South Africa
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
- * E-mail:
| | - Michael D. Pirie
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-University, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany
- Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Kristin Oosthuizen
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Rachelle Bester
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - D. Jasper G. Rees
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, 0110, South Africa
| | - Johan T. Burger
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
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Mugrabi de Kuppler AL, Fagúndez J, Bellstedt DU, Oliver EGH, Léon J, Pirie MD. Testing reticulate versus coalescent origins of Erica lusitanica using a species phylogeny of the northern heathers (Ericeae, Ericaceae). Mol Phylogenet Evol 2015; 88:121-31. [PMID: 25888972 DOI: 10.1016/j.ympev.2015.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 04/02/2015] [Accepted: 04/06/2015] [Indexed: 10/23/2022]
Abstract
Whilst most of the immense species richness of heathers (Calluna, Daboecia and Erica: Ericeae; Ericaceae) is endemic to Africa, particularly the Cape Floristic Region, the oldest lineages are found in the Northern Hemisphere. We present phylogenetic hypotheses for the major clades of Ericeae represented by multiple accessions of all northern Erica species and placeholder taxa for the large nested African/Madagascan clade. We identified consistent, strongly supported conflict between gene trees inferred from ITS and chloroplast DNA sequences with regard to the position of Erica lusitanica. We used coalescent simulations to test whether this conflict could be explained by coalescent stochasticity, as opposed to reticulation (e.g. hybridisation), given estimates of clade ages, generation time and effective population sizes (Ne). A standard approach, comparing overall differences between real and simulated trees, could not clearly reject coalescence. However, additional simulations showed that at the (higher) Ne necessary to explain conflict in E. lusitanica, further topological conflict would also be expected. Ancient hybridisation between ancestors of northern species is therefore a plausible scenario to explain the origin of E. lusitanica, and its morphological similarities to E. arborea. Assuming either process influences the results of species tree and further evolutionary inference. The coalescence scenario is equivocal with regard the standing hypothesis of stepping stone dispersal of Erica from Europe into Africa; whereas reticulate evolution in E. lusitanica would imply that the colonisation of Tropical East Africa by E. arborea instead occurred independently of dispersals within the rest of the African/Madagascan clade.
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Affiliation(s)
- A L Mugrabi de Kuppler
- INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-Universität Bonn, Katzenburgweg 5, 53115 Bonn, Germany
| | - J Fagúndez
- Department of Plant and Animal Biology and Ecology, University of A Coruña, Faculty of Science, 15001 A Coruña, Spain
| | - D U Bellstedt
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - E G H Oliver
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - J Léon
- INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-Universität Bonn, Katzenburgweg 5, 53115 Bonn, Germany
| | - M D Pirie
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa; Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099 Mainz, Germany.
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Kadereit G, Lauterbach M, Pirie MD, Arafeh R, Freitag H. When do different C4 leaf anatomies indicate independent C4 origins? Parallel evolution of C4 leaf types in Camphorosmeae (Chenopodiaceae). J Exp Bot 2014; 65:3499-511. [PMID: 24811953 DOI: 10.1093/jxb/eru169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Broad-scale phylogenetic studies give first insights in numbers, relationships, and ages of C4 lineages. They are, however, generally limited to a model that treats the evolution of the complex C4 syndrome in different lineages as a directly comparable process. Here, we use a resolved and well-sampled phylogenetic tree of Camphorosmeae, based on three chloroplast and one nuclear marker and on leaf anatomical traits to infer a more detailed picture of C4 leaf-type evolution in this lineage. Our ancestral character state reconstructions allowed two scenarios: (i) Sedobassia is a derived C3/C4 intermediate, implying two independent gains of C4 in Bassia and Camphorosma; or (ii) Sedobassia is a plesiomorphic C3/C4 intermediate, representing a syndrome ancestral to the Bassia/Camphorosma/Sedobassia lineage. In Bassia, a kochioid leaf type (Bassia muricata and/or Bassia prostrata type) is ancestral. At least three independent losses of water-storage tissue occurred, resulting in parallel shifts towards an atriplicoid leaf type. These changes in leaf anatomy are adaptations to different survival strategies in steppic or semi-desert habitats with seasonal rainfall. In contrast, Camphorosma shows a fixed C4 anatomy differing from Bassia types in its continuous Kranz layer, which indeed points to an independent origin of the full C4 syndrome in Camphorosma, either from an independent C3 or from a common C3/C4 intermediate ancestor, perhaps similar to its C3/C4 intermediate sister genus Sedobassia. The enlarged bundle sheath cells of Sedobassia might represent an important early step in C4 evolution in Camphorosmeae.
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Affiliation(s)
- Gudrun Kadereit
- Institut für Allgemeine und Spezielle Botanik und Botanischer Garten der Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
| | - Maximilian Lauterbach
- Institut für Allgemeine und Spezielle Botanik und Botanischer Garten der Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
| | - Michael D Pirie
- Institut für Allgemeine und Spezielle Botanik und Botanischer Garten der Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany Department of Biochemistry, University of Stellenbosch, Matieland 7600, South Africa
| | - Rami Arafeh
- Biotechnology Research Center, Palestine Polytechnic University, PO Box 198, Hebron, Palestine
| | - Helmut Freitag
- Institut für Biologie, Arbeitsgruppe Systematik und Morphologie der Pflanzen, Universität Kassel, D-34109 Kassel, Germany
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Van der Niet T, Pirie MD, Shuttleworth A, Johnson SD, Midgley JJ. Do pollinator distributions underlie the evolution of pollination ecotypes in the Cape shrub Erica plukenetii? Ann Bot 2014; 113:301-15. [PMID: 24071499 PMCID: PMC3890384 DOI: 10.1093/aob/mct193] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS According to the Grant-Stebbins model of pollinator-driven divergence, plants that disperse beyond the range of their specialized pollinator may adapt to a new pollination system. Although this model provides a compelling explanation for pollination ecotype formation, few studies have directly tested its validity in nature. Here we investigate the distribution and pollination biology of several subspecies of the shrub Erica plukenetii from the Cape Floristic Region in South Africa. We analyse these data in a phylogenetic context and combine these results with information on pollinator ranges to test whether the evolution of pollination ecotypes is consistent with the Grant-Stebbins model. METHODS AND KEY RESULTS Pollinator observations showed that the most common form of E. plukenetii with intermediate corolla length is pollinated by short-billed Orange-breasted sunbirds. Populations at the northern fringe of the distribution are characterized by long corollas, and are mainly pollinated by long-billed Malachite sunbirds. A population with short corollas in the centre of the range was mainly pollinated by insects, particularly short-tongued noctuid moths. Bird exclusion in this population did not have an effect on fruit set, while insect exclusion reduced fruit set. An analysis of floral scent across the range, using coupled gas chromatography-mass spectrometry, showed that the scent bouquets of flowers from moth-pollinated populations are characterized by a larger number of scent compounds and higher emission rates than those in bird-pollinated populations. This was also reflected in clear separation of moth- and bird-pollinated populations in a two-dimensional phenotype space based on non-metric multidimensional scaling analysis of scent data. Phylogenetic analyses of chloroplast and nuclear DNA sequences strongly supported monophyly of E. plukenetii, but not of all the subspecies. Reconstruction of ancestral character states suggests two shifts from traits associated with short-billed Orange-breasted sunbird pollination: one towards traits associated with moth pollination, and one towards traits associated with pollination by long-billed Malachite sunbirds. The latter shift coincided with the colonization of Namaqualand in which Orange-breasted sunbirds are absent. CONCLUSIONS Erica plukenetii is characterized by three pollination ecotypes, but only the evolutionary transition from short- to long-billed sunbird pollination can be clearly explained by the Grant-Stebbins model. Corolla length is a key character for both ecotype transitions, while floral scent emission was important for the transition from bird to moth pollination.
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Affiliation(s)
- Timotheüs Van der Niet
- Naturalis Biodiversity Center, PO Box 9514, 2300 RA, Leiden, The Netherlands
- Leiden University, PO Box 9514, 2300 RA, Leiden, The Netherlands
- Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch 7701, South Africa
- For correspondence. E-mail
| | - Michael D. Pirie
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, D-55099 Mainz, Germany
| | - Adam Shuttleworth
- School of Life Sciences, University of KwaZulu Natal, P/Bag X01, Scottsville 3209, Pietermaritzburg, South Africa
| | - Steven D. Johnson
- School of Life Sciences, University of KwaZulu Natal, P/Bag X01, Scottsville 3209, Pietermaritzburg, South Africa
| | - Jeremy J. Midgley
- Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch 7701, South Africa
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de Villiers MJ, Pirie MD, Hughes M, Möller M, Edwards TJ, Bellstedt DU. An approach to identify putative hybrids in the 'coalescent stochasticity zone', as exemplified in the African plant genus Streptocarpus (Gesneriaceae). New Phytol 2013; 198:284-300. [PMID: 23373903 DOI: 10.1111/nph.12133] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 11/29/2012] [Indexed: 06/01/2023]
Abstract
The inference of phylogenetic relationships is often complicated by differing evolutionary histories of independently-inherited markers. The causes of the resulting gene tree incongruence can be challenging to identify, often relying on coalescent simulations dependent on unverifiable assumptions. We investigated alternative techniques using the South African rosulate species of Streptocarpus as a study group. Two independent gene trees - from the nuclear ITS region and from three concatenated plastid regions (trnL-F, rpl20-rps12 and trnC-D) - displayed widespread, strongly supported incongruence. We investigated the causes by detecting genetic exchange across morphological borders using morphological optimizations and genetic exchange across species boundaries using the genealogical sorting index. Incongruence between gene trees was associated with ancestral shifts in growth form (in four species) but not in pollination syndrome, suggesting introgression limited by reproductive barriers. Genealogical sorting index calculations showed polyphyly of two additional species, while individuals of all others were significantly associated. In one case the association was stronger according to the internal transcribed spacer data than according to the plastid data, which, given the smaller effective population size of the plastid, may also indicate introgression. These approaches offer alternative ways to identify potential hybridization events where incomplete lineage sorting cannot be rejected using simulations.
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Affiliation(s)
- Margaret J de Villiers
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Michael D Pirie
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Mark Hughes
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Michael Möller
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Trevor J Edwards
- Botany Department, La Trobe University, Melbourne, Vic., Australia
| | - Dirk U Bellstedt
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
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Kadereit G, Ackerly D, Pirie MD. A broader model for C₄ photosynthesis evolution in plants inferred from the goosefoot family (Chenopodiaceae s.s.). Proc Biol Sci 2012; 279:3304-11. [PMID: 22628474 PMCID: PMC3385724 DOI: 10.1098/rspb.2012.0440] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 05/01/2012] [Indexed: 11/12/2022] Open
Abstract
C(4) photosynthesis is a fascinating example of parallel evolution of a complex trait involving multiple genetic, biochemical and anatomical changes. It is seen as an adaptation to deleteriously high levels of photorespiration. The current scenario for C(4) evolution inferred from grasses is that it originated subsequent to the Oligocene decline in CO(2) levels, is promoted in open habitats, acts as a pre-adaptation to drought resistance, and, once gained, is not subsequently lost. We test the generality of these hypotheses using a dated phylogeny of Amaranthaceae s.l. (including Chenopodiaceae), which includes the largest number of C(4) lineages in eudicots. The oldest chenopod C(4) lineage dates back to the Eocene/Oligocene boundary, representing one of the first origins of C(4) in plants, but still corresponding with the Oligocene decline of atmospheric CO(2). In contrast to grasses, the rate of transitions from C(3) to C(4) is highest in ancestrally drought resistant (salt-tolerant and succulent) lineages, implying that adaptation to dry or saline habitats promoted the evolution of C(4); and possible reversions from C(4) to C(3) are apparent. We conclude that the paradigm established in grasses must be regarded as just one aspect of a more complex system of C(4) evolution in plants in general.
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Affiliation(s)
- Gudrun Kadereit
- Institut für Allgemeine Botanik, Johannes Gutenberg Universität Mainz, 55099 Mainz, Germany.
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Pirie MD, Oliver EGH, Bellstedt DU. A densely sampled ITS phylogeny of the Cape flagship genus Erica L. suggests numerous shifts in floral macro-morphology. Mol Phylogenet Evol 2011; 61:593-601. [PMID: 21722743 DOI: 10.1016/j.ympev.2011.06.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 06/07/2011] [Accepted: 06/08/2011] [Indexed: 11/26/2022]
Abstract
Erica L. is the largest of the 'Cape' clades that together comprise around half of the disproportionately high species richness of the Cape Floristic Region (CFR) of South Africa. Around 840 species of Erica are currently recognised, C.680 of which are found in the CFR, the rest distributed across the rest of Southern Africa, the highlands of Tropical Africa and Madagascar, and Europe. Erica is taxonomically well documented, but very little is known about species-level relationships. We present the first densely sampled phylogenetic analysis of Erica, using nuclear ribosomal DNA sequences (internal transcribed spacers; ITS) of c. 45% of the species from across the full geographic range of the genus, both Calluna and Daboecia (Ericeae; monotypic genera and putative sister groups of Erica), and further Ericoideae outgroups. Our results show both morphological and geographic coherence of some clades, but numerous shifts in floral macro-morphology as represented by variation in individual morphological characters and pollination syndromes. European Ericeae is a paraphyletic grade subtending a monophyletic African/Malagasy Erica. Given the limited resolution of this single gene tree, more data are needed for further conclusions. Clades are identified that will serve as an effective guide for targeted sampling from multiple linkage groups.
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Affiliation(s)
- Michael D Pirie
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa.
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Bellstedt DU, Pirie MD, Visser JC, de Villiers MJ, Gehrke B. A rapid and inexpensive method for the direct PCR amplification of DNA from plants. Am J Bot 2010; 97:e65-8. [PMID: 21616856 DOI: 10.3732/ajb.1000181] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
PREMISE OF THE STUDY We present a rapid and inexpensive alternative to DNA isolation for polymerase chain reaction (PCR) amplification from plants. • METHODS AND RESULTS The method involves direct PCR amplification from material macerated in one buffer, followed by dilution and incubation in a second buffer. We describe the procedure and demonstrate its application for nuclear and plastid DNA amplification across a broad range of vascular plants. • CONCLUSIONS The method is fast, easy to perform, cost-effective, and consequently ideal for large sample numbers. It represents a considerable simplification of present approaches requiring DNA isolation prior to PCR amplification and will be useful in plant systematics and biotechnology, including applications such as DNA barcoding.
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Affiliation(s)
- Dirk U Bellstedt
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, South Africa
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Pirie MD, Humphreys AM, Galley C, Barker NP, Verboom GA, Orlovich D, Draffin SJ, Lloyd K, Baeza CM, Negritto M, Ruiz E, Sanchez JHC, Reimer E, Linder HP. A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses. Mol Phylogenet Evol 2008; 48:1106-19. [PMID: 18599319 DOI: 10.1016/j.ympev.2008.05.030] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Revised: 05/15/2008] [Accepted: 05/22/2008] [Indexed: 11/28/2022]
Abstract
Phylogeny reconstruction is challenging when branch lengths vary and when different genetic loci show conflicting signals. The number of DNA sequence characters required to obtain robust support for all the nodes in a phylogeny becomes greater with denser taxon sampling. We test the usefulness of an approach mixing densely sampled, variable non-coding sequences (trnL-F; rpl16; atpB-rbcL; ITS) with sparsely sampled, more conservative protein coding and ribosomal sequences (matK; ndhF; rbcL; 26S), for the grass subfamily Danthonioideae. Previous phylogenetic studies of Danthonioideae revealed extensive generic paraphyly, but were often impeded by insufficient character and taxon sampling and apparent inter-gene conflict. Our variably-sampled supermatrix approach allowed us to represent 79% of the species with up to c. 9900 base pairs for taxa representing the major clades. A 'taxon duplication' approach for taxa with conflicting phylogenetic signals allowed us to combine the data whilst representing the differences between chloroplast and nuclear encoded gene trees. This approach efficiently improves resolution and support whilst maximising representation of taxa and their sometimes composite evolutionary histories, resulting in a phylogeny of the Danthonioideae that will be useful both for a wide range of evolutionary studies and to inform forthcoming realignment of generic delimitations in the subfamily.
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Affiliation(s)
- Michael D Pirie
- Institute for Systematic Botany, University of Zurich, Switzerland.
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Pirie MD, Vargas MPB, Botermans M, Bakker FT, Chatrou LW. Ancient paralogy in the cpDNA trnL-F region in Annonaceae: implications for plant molecular systematics. Am J Bot 2007; 94:1003-1016. [PMID: 21636470 DOI: 10.3732/ajb.94.6.1003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The plastid trnL-F region has proved useful in molecular phylogenetic studies addressing diverse evolutionary questions from biogeographic history to character evolution in a broad range of plant groups. An important assumption for phylogenetic reconstruction is that data used in combined analyses contain the same phylogenetic signal. The trnL-F region is often used in combined analyses of multiple chloroplast markers. These markers are assumed to contain congruent phylogenetic signal due to lack of recombination. Here we show that trnL-F sequences display a phylogenetic signal conflicting with that of other chloroplast markers in Annonaceae, and we demonstrate that this conflict results from ancient paralogy. TrnL-F copy 2 diverged from trnL-F copy 1 (as used in family-wide phylogenetic analyses) in a direct ancestor of the Annonaceae. Although this divergence dates back 88 million years or more, the exons of both copies appear to be intact. In this case, assuming that (putative) chloroplast markers contain the same phylogenetic signal results in an incorrect topology and an incorrect estimate of ages. Our study demonstrates that researchers should be cautious when interpreting gene phylogenies, irrespective of the genome from which they are presumed to have been sampled.
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Affiliation(s)
- Michael D Pirie
- Nationaal Herbarium Nederland, Universiteit Utrecht branch, Heidelberglaan 2, 3584 CS Utrecht, Netherlands; and Nationaal Herbarium Nederland, Wageningen Universiteit branch, Generaal Foulkesweg 37, 6703 BL Wageningen, Netherlands
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Richardson JE, Chatrou LW, Mols JB, Erkens RHJ, Pirie MD. Historical biogeography of two cosmopolitan families of flowering plants: Annonaceae and Rhamnaceae. Philos Trans R Soc Lond B Biol Sci 2004; 359:1495-508. [PMID: 15519968 PMCID: PMC1693429 DOI: 10.1098/rstb.2004.1537] [Citation(s) in RCA: 196] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Annonaceae are a pantropically distributed family found predominantly in rainforests, so they are megathermal taxa, whereas Rhamnaceae are a cosmopolitan family that tend to be found in xeric regions and may be classified as mesothermal. Phylogenetic analyses of these families are presented based on rbcL and trnL-F plastid DNA sequences. Likelihood ratio tests revealed rate heterogeneity in both phylogenetic trees and they were therefore made ultrametric using non-parametric rate smoothing and penalized likelihood. Divergence times were then estimated using fossil calibration points. The historical biogeography of these families that are species rich in different biomes is discussed and compared with other published reconstructions. Rhamnaceae and most lineages within Annonaceae are too young to have had their distribution patterns influenced by break-up of previously connected Gondwanan landmasses. Contrasts in the degree of geographical structure between these two families may be explained by differences in age and dispersal capability. In both groups, long-distance dispersal appears to have played a more significant role in establishing modern patterns than had previously been assumed. Both families also contain examples of recent diversification of species-rich lineages. An understanding of the processes responsible for shaping the distribution patterns of these families has contributed to our understanding of the historical assembly of the biomes that they occupy.
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Affiliation(s)
- J E Richardson
- Nationaal Herbarium Nederland, Wageningen Universiteit Branch, Generaal Foulkesweg 37, 6703 BL Wageningen, The Netherlands.
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Mols JB, Gravendeel B, Chatrou LW, Pirie MD, Bygrave PC, Chase MW, Keßler PJA. Identifying clades in Asian Annonaceae: monophyletic genera in the polyphyletic Miliuseae. Am J Bot 2004; 91:590-600. [PMID: 21653415 DOI: 10.3732/ajb.91.4.590] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The tribe Miliuseae (Annonaceae) comprises six genera distributed in Asia: Alphonsea, Mezzettia, Miliusa, Orophea, Platymitra, and Phoenicanthus. A phylogenetic study to investigate the putative monophyly of the tribe and the intergeneric relationships is presented here. Nucleotide sequences of the plastid gene rbcL, trnL intron, and trnL-trnF intergenic spacer were analyzed from 114 Annonaceae taxa, including 24 Miliuseae species and two outgroups using maximum parsimony and Bayesian inference. The two data sets (rbcL and the trnL-trnF regions) were analyzed separately and in combination. Miliuseae were found to be polyphyletic due to the position of Mezzettia and are part of a large, predominantly Asian and Central-American clade (miliusoid clade). Although intergeneric relationships were poorly resolved, all genera, except Polyalthia, were monophyletic, supporting previous generic delimitation based on morphology. A group of three Polyalthia species seems the most likely sister group of Miliusa. Several infrageneric groups of Miliusa, Orophea, and Polyalthia are supported by both molecular and morphological data. No morphological synapomorphies have yet been found for the miliusoid clade. Molecular clades within the miliusoid clade, however, can be characterized by size and the shape of the outer petals, number of ovules per carpel, and the size of the fruits.
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Affiliation(s)
- Johan B Mols
- Nationaal Herbarium Nederland, Universiteit Leiden branch, P.O. Box 9514, 2300 RA Leiden, The Netherlands
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