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Hofmann S, Podsiadlowski L, Andermann T, Matschiner M, Baniya CB, Litvinchuk SN, Martin S, Masroor R, Yang J, Zheng Y, Jablonski D, Schmidt J. The last of their kind: Is the genus Scutiger (Anura: Megophryidae) a relict element of the paleo-Transhimalaya biota? Mol Phylogenet Evol 2024; 201:108166. [PMID: 39127262 DOI: 10.1016/j.ympev.2024.108166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 07/08/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024]
Abstract
The orographic evolution of the Himalaya-Tibet Mountain system continues to be a subject of controversy, leading to considerable uncertainty regarding the environment and surface elevation of the Tibetan Plateau during the Cenozoic era. As many geoscientific (but not paleontological) studies suggest, elevations close to modern heights exist in vast areas of Tibet since at least the late Paleogene, implicating the presence of large-scale alpine environments for more than 30 million years. To explore a recently proposed alternative model that assumes a warm temperate environment across paleo-Tibet, we carried out a phylogeographic survey using genomic analyses of samples covering the range of endemic lazy toads (Scutiger) across the Himalaya-Tibet orogen. We identified two main clades, with several, geographically distinct subclades. The long temporal gap between the stem and crown age of Scutiger may suggest high extinction rates. Diversification within the crown group, depending on the calibration, occurred either from the Mid-Miocene or Late-Miocene and continued until the Holocene. The present-day Himalayan Scutiger fauna could have evolved from lineages that existed on the southern edges of the paleo-Tibetan area (the Transhimalaya = Gangdese Shan), while extant species living on the eastern edge of the Plateau originated probably from the eastern edges of northern parts of the ancestral Tibetan area (Hoh Xil, Tanggula Shan). Based on the Mid-Miocene divergence time estimation and ancestral area reconstruction, we propose that uplift-associated aridification of a warm temperate Miocene-Tibet, coupled with high extirpation rates of ancestral populations, and species range shifts along drainage systems and epigenetic transverse valleys of the rising mountains, is a plausible scenario explaining the phylogenetic structure of Scutiger. This hypothesis aligns with the fossil record but conflicts with geoscientific concepts of high elevated Tibetan Plateau since the late Paleogene. Considering a Late-Miocene/Pliocene divergence time, an alternative scenario of dispersal from SE Asia into the East, Central, and West Himalaya cannot be excluded, although essential evolutionary and biogeographic aspects remain unresolved within this model.
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Affiliation(s)
- Sylvia Hofmann
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, 53113 Bonn, Germany.
| | - Lars Podsiadlowski
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, 53113 Bonn, Germany.
| | - Tobias Andermann
- Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden.
| | | | - Chitra B Baniya
- Central Department of Botany, Tribhuvan University, Kirtipur 44618, Kathmandu, Nepal
| | - Spartak N Litvinchuk
- Institute of Cytology of the Russian Academy of Sciences, St. Peterburg 194064, Russia
| | - Sebastian Martin
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, 53113 Bonn, Germany.
| | - Rafaqat Masroor
- Pakistan Museum of Natural History, Islamabad 44000, Pakistan
| | - Jianhuan Yang
- Kadoorie Conservation China, Kadoorie Farm and Botanic Garden, Hongkong, China.
| | - Yuchi Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, 842 15 Bratislava, Slovakia.
| | - Joachim Schmidt
- General and Systematic Zoology, Institute of Biosciences, University of Rostock, 18055 Rostock, Germany
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Fernández-Palacios JM, Otto R, Capelo J, Caujapé-Castells J, de Nascimento L, Duarte MC, Elias RB, García-Verdugo C, Menezes de Sequeira M, Médail F, Naranjo-Cigala A, Patiño J, Price J, Romeiras MM, Sánchez-Pinto L, Whittaker RJ. In defence of the entity of Macaronesia as a biogeographical region. Biol Rev Camb Philos Soc 2024. [PMID: 38888215 DOI: 10.1111/brv.13112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 05/29/2024] [Accepted: 06/04/2024] [Indexed: 06/20/2024]
Abstract
Since its coinage ca. 1850 AD by Philip Barker Webb, the biogeographical region of Macaronesia, consisting of the North Atlantic volcanic archipelagos of the Azores, Madeira with the tiny Selvagens, the Canaries and Cabo Verde, and for some authors different continental coastal strips, has been under dispute. Herein, after a brief introduction on the terminology and purpose of regionalism, we recover the origins of the Macaronesia name, concept and geographical adscription, as well as its biogeographical implications and how different authors have positioned themselves, using distinct terrestrial or marine floristic and/or faunistic taxa distributions and relationships for accepting or rejecting the existence of this biogeographical region. Four main issues related to Macaronesia are thoroughly discussed: (i) its independence from the Mediterranean phytogeographical region; (ii) discrepancies according to different taxa analysed; (iii) its geographical limits and the role of the continental enclave(s), and, (iv) the validity of the phytogeographical region level. We conclude that Macaronesia has its own identity and a sound phytogeographical foundation, and that this is mainly based on three different floristic components that are shared by the Macaronesian core (Madeira and the Canaries) and the outermost archipelagos (Azores and Cabo Verde). These floristic components are: (i) the Palaeotropical-Tethyan Geoflora, formerly much more widely distributed in Europe and North Africa and currently restricted to the three northern archipelagos (the Azores, Madeira and the Canaries); (ii) the African Rand Flora, still extant in the coastal margins of Africa and Arabia, and present in the southern archipelagos (Madeira, the Canaries and Cabo Verde), and (iii) the Macaronesian neoendemic floristic component, represented in all the archipelagos, a result of allopatric diversification promoted by isolation of Mediterranean ancestors that manage to colonize Central Macaronesia and, from there, the outer archipelagos. Finally, a differentiating floristic component recently colonized the different archipelagos from the nearest continental coast, providing them with different biogeographic flavours.
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Affiliation(s)
- José María Fernández-Palacios
- Grupo de Ecología y Biogeografía Insular, Departamento de Botánica, Ecología y Fisiología Vegetal e Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Avenida Astrofísico Francisco Sánchez, s/n. Campus de Anchieta, Apartado 456, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Código postal 38200, Spain
| | - Rüdiger Otto
- Grupo de Ecología y Biogeografía Insular, Departamento de Botánica, Ecología y Fisiología Vegetal e Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Avenida Astrofísico Francisco Sánchez, s/n. Campus de Anchieta, Apartado 456, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Código postal 38200, Spain
| | - Jorge Capelo
- Herbarium, National Institute of Agrarian and Veterinarian Research, Avenida da República, Quinta do Marquês, Oeiras, 2780-157, Portugal
- LEAF Research Centre - Linking Landscape, Environment, Agriculture and Food, University of Lisbon, Tapada de Ajuda, Lisbon, 1349-017, Portugal
| | - Juli Caujapé-Castells
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico Canario 'Viera y Clavijo' - Unidad Asociada de I+D+i al CSIC, Cabildo de Gran Canaria, Carretera del Dragonal Km 7 (GC-310), Las Palmas de Gran Canaria, 35017, Spain
| | - Lea de Nascimento
- Grupo de Ecología y Biogeografía Insular, Departamento de Botánica, Ecología y Fisiología Vegetal e Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Avenida Astrofísico Francisco Sánchez, s/n. Campus de Anchieta, Apartado 456, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Código postal 38200, Spain
| | - Maria Cristina Duarte
- cE3c - Center for Ecology, Evolution and Environmental Change & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisbon, 1749-016, Portugal
| | - Rui B Elias
- Azorean Biodiversity Group, Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculty of Agriculture and Environmental Sciences, Universidade dos Açores, Angra do Heroismo, 9700-042, Portugal
| | - Carlos García-Verdugo
- Departamento de Botánica, Universidad de Granada, Facultad de Ciencias, Avenida de Fuente Nueva, s/n, Beiro, Granada, 18071, Spain
| | - Miguel Menezes de Sequeira
- Madeira Botanical Group (GBM), Universidade da Madeira, Campus Universitário da Penteada, Funchal, 9020-105, Portugal
| | - Frédéric Médail
- Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Aix Marseille Univ, Avignon Univ, CNRS, IRD. Campus Aix, Technopôle de l'Environnement Arbois-Méditerranée, Aix-en-Provence cedex 4, 13545, France
| | - Agustín Naranjo-Cigala
- Departamento de Geografía, Universidad de Las Palmas de Gran Canaria, c/ Pérez del Toro, 1, Las Palmas de Gran Canaria, 35004, Spain
| | - Jairo Patiño
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez, 3, San Cristóbal de La Laguna, Santa Cruz de Tenerife, 38206, Spain
- Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez, s/n. Facultad de Farmacia. Apartado 456, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Código postal 38206, Spain
| | - Jonathan Price
- Department of Geography and Environmental Studies, University of Hawaii at Hilo, 200 W. Kāwili St, Hilo, HI, 96720-4091, USA
| | - Maria M Romeiras
- LEAF Research Centre - Linking Landscape, Environment, Agriculture and Food, University of Lisbon, Tapada de Ajuda, Lisbon, 1349-017, Portugal
- cE3c - Center for Ecology, Evolution and Environmental Change & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisbon, 1749-016, Portugal
| | - Lázaro Sánchez-Pinto
- Museo de Ciencias Naturales, c/ Fuente Morales, 1, Santa Cruz de Tenerife, 38003, Spain
| | - Robert J Whittaker
- School of Geography and the Environment, University of Oxford, South Parks Road, Oxford, OX1 3QY, UK
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Universitetsparken 15, Building 3, 2nd FL, Copenhagen, DK-2100, Denmark
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Dagallier LPMJ, Condamine FL, Couvreur TLP. Sequential diversification with Miocene extinction and Pliocene speciation linked to mountain uplift explains the diversity of the African rain forest clade Monodoreae (Annonaceae). ANNALS OF BOTANY 2024; 133:677-696. [PMID: 37659091 PMCID: PMC11082524 DOI: 10.1093/aob/mcad130] [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: 04/28/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023]
Abstract
BACKGROUND AND AIMS Throughout the Cenozoic, Africa underwent several climatic and geological changes impacting the evolution of tropical rain forests (TRFs). African TRFs are thought to have extended from east to west in a 'pan-African' TRF, followed by several events of fragmentation during drier climate periods. During the Miocene, climate cooling and mountain uplift led to the aridification of tropical Africa and open habitats expanded at the expense of TRFs, which probably experienced local extinctions. However, in plants, these drivers were previously inferred using limited taxonomic and molecular data. Here, we tested the impact of climate and geological changes on diversification within the diverse clade Monodoreae (Annonaceae) composed of 90 tree species restricted to African TRFs. METHODS We reconstructed a near-complete phylogenetic tree, based on 32 nuclear genes, and dated using relaxed clocks and fossil calibrations in a Bayesian framework. We inferred the biogeographical history and the diversification dynamics of the clade using multiple birth-death models. KEY RESULTS Monodoreae originated in East African TRFs ~25 million years ago (Ma) and expanded toward Central Africa during the Miocene. We inferred range contractions during the middle Miocene and document important connections between East and West African TRFs after 15-13 Ma. Our results indicated a sudden extinction event during the late Miocene, followed by an increase in speciation rates. Birth-death models suggested that African elevation change (orogeny) is positively linked to speciation in this clade. CONCLUSION East Africa is inferred as an important source of Monodoreae species, and possibly for African plant diversity in general. Our results support a 'sequential scenario of diversification' in which increased aridification triggered extinction of TRF species in Monodoreae. This was quickly followed by fragmentation of rain forests, subsequently enhancing lagged speciation resulting from vicariance and improved climate conditions. In contrast to previous ideas, the uplift of East Africa is shown to have played a positive role in Monodoreae diversification.
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Affiliation(s)
- Léo-Paul M J Dagallier
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY 10458, USA
| | - Fabien L Condamine
- CNRS, Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier), Place Eugène Bataillon, 34095 Montpellier, France
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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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Coello AJ, Vargas P, Cano E, Riina R, Fernández-Mazuecos M. Phylogenetics and phylogeography of Euphorbia canariensis reveal an extreme Canarian-Asian disjunction but limited inter-island colonization. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:398-414. [PMID: 38444147 DOI: 10.1111/plb.13635] [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: 07/27/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024]
Abstract
Euphorbia canariensis is an iconic endemic species representative of the lowland xerophytic communities of the Canary Islands. It is widely distributed in the archipelago despite having diasporas unspecialized for long-distance dispersal. Here, we reconstructed the evolutionary history of E. canariensis at two levels: a time-calibrated phylogenetic analysis aimed at clarifying interspecific relationships and large-scale biogeographic patterns; and a phylogeographic study focused on the history of colonization across the Canary Islands. For the phylogenetic study, we sequenced the ITS region for E. canariensis and related species of Euphorbia sect. Euphorbia. For the phylogeographic study, we sequenced two cpDNA regions for 28 populations representing the distribution range of E. canariensis. The number of inter-island colonization events was explored using PAICE, a recently developed method that includes a sample size correction. Additionally, we used species distribution modelling (SDM) to evaluate environmental suitability for E. canariensis through time. Phylogenetic results supported a close relationship between E. canariensis and certain Southeast Asian species (E. epiphylloides, E. lacei, E. sessiliflora). In the Canaries, E. canariensis displayed a west-to-east colonization pattern, not conforming to the "progression rule", i.e. the concordance between phylogeographic patterns and island emergence times. We estimated between 20 and 50 inter-island colonization events, all of them in the Quaternary, and SDM suggested a late Quaternary increase in environmental suitability for E. canariensis. The extreme biogeographic disjunction between Macaronesia and Southeast Asia (ca. 11,000 km) parallels that found in a few other genera (Pinus, Dracaena). We hypothesize that these disjunctions are better explained by extinction across north Africa and southwest Asia rather than long-distance dispersal. The relatively low number of inter-island colonization events across the Canaries is congruent with the low dispersal capabilities of E. canariensis.
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Affiliation(s)
- A J Coello
- Departamento de Biología (Botánica), Universidad Autónoma de Madrid, Madrid, Spain
- Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| | - P Vargas
- Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| | - E Cano
- Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| | - R Riina
- Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| | - M Fernández-Mazuecos
- Departamento de Biología (Botánica), Universidad Autónoma de Madrid, Madrid, Spain
- Real Jardín Botánico (RJB), CSIC, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
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Seeholzer GF, Brumfield RT. Speciation-by-Extinction. Syst Biol 2023; 72:1433-1442. [PMID: 37542735 DOI: 10.1093/sysbio/syad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/07/2023] Open
Abstract
Extinction is a dominant force shaping patterns of biodiversity through time; however its role as a catalyst of speciation through its interaction with intraspecific variation has been overlooked. Here, we synthesize ideas alluded to by Darwin and others into the model of "speciation-by-extinction" in which speciation results from the extinction of intermediate populations within a single geographically variable species. We explore the properties and distinguishing features of speciation-by-extinction with respect to other established speciation models. We demonstrate its plausibility by showing that the experimental extinction of populations within variable species can result in speciation. The prerequisites for speciation-by-extinction, geographically structured intraspecific variation and local extinction, are ubiquitous in nature. We propose that speciation-by-extinction may be a prevalent, but underappreciated, speciation mechanism.
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Affiliation(s)
- Glenn F Seeholzer
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
- Macaulay Library, Cornell Lab of Ornithology, Ithaca, NY, 14850, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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Villaverde T, Larridon I, Shah T, Fowler RM, Chau JH, Olmstead RG, Sanmartín I. Phylogenomics sheds new light on the drivers behind a long-lasting systematic riddle: the figwort family Scrophulariaceae. THE NEW PHYTOLOGIST 2023; 240:1601-1615. [PMID: 36869601 DOI: 10.1111/nph.18845] [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: 10/13/2022] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
The figwort family, Scrophulariaceae, comprises c. 2000 species whose evolutionary relationships at the tribal level have proven difficult to resolve, hindering our ability to understand their origin and diversification. We designed a specific probe kit for Scrophulariaceae, targeting 849 nuclear loci and obtaining plastid regions as by-products. We sampled c. 87% of the genera described in the family and use the nuclear dataset to estimate evolutionary relationships, timing of diversification, and biogeographic patterns. Ten tribes, including two new tribes, Androyeae and Camptolomeae, are supported, and the phylogenetic positions of Androya, Camptoloma, and Phygelius are unveiled. Our study reveals a major diversification at c. 60 million yr ago in some Gondwanan landmasses, where two different lineages diversified, one of which gave rise to nearly 81% of extant species. A Southern African origin is estimated for most modern-day tribes, with two exceptions, the American Leucophylleae, and the mainly Australian Myoporeae. The rapid mid-Eocene diversification is aligned with geographic expansion within southern Africa in most tribes, followed by range expansion to tropical Africa and multiple dispersals out of Africa. Our robust phylogeny provides a framework for future studies aimed at understanding the role of macroevolutionary patterns and processes that generated Scrophulariaceae diversity.
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Affiliation(s)
- Tamara Villaverde
- Real Jardín Botánico (CSIC), Plaza de Murillo, 2, Madrid, 28014, Spain
| | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Toral Shah
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| | - Rachael M Fowler
- School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - John H Chau
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Richard G Olmstead
- Department of Biology and Burke Museum, University of Washington, Seattle, WA, 98155, USA
| | - Isabel Sanmartín
- Real Jardín Botánico (CSIC), Plaza de Murillo, 2, Madrid, 28014, 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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Messerschmid TFE, Abrahamczyk S, Bañares-Baudet Á, Brilhante MA, Eggli U, Hühn P, Kadereit JW, dos Santos P, de Vos JM, Kadereit G. Inter- and intra-island speciation and their morphological and ecological correlates in Aeonium (Crassulaceae), a species-rich Macaronesian radiation. ANNALS OF BOTANY 2023; 131:697-721. [PMID: 36821492 PMCID: PMC10147336 DOI: 10.1093/aob/mcad033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 02/22/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS The most species-rich and ecologically diverse plant radiation on the Canary Islands is the Aeonium alliance (Crassulaceae). In island radiations like this, speciation can take place either within islands or following dispersal between islands. Aiming at quantifying intra- and inter-island speciation events in the evolution of Aeonium, and exploring their consequences, we hypothesized that (1) intra-island diversification resulted in stronger ecological divergence of sister lineages, and that (2) taxa on islands with a longer history of habitation by Aeonium show stronger ecological differentiation and produce fewer natural hybrids. METHODS We studied the biogeographical and ecological setting of diversification processes in Aeonium with a fully sampled and dated phylogeny inferred using a ddRADseq approach. Ancestral areas and biogeographical events were reconstructed in BioGeoBEARS. Eleven morphological characters and three habitat characteristics were taken into account to quantify the morphological and ecological divergence between sister lineages. A co-occurrence matrix of all Aeonium taxa is presented to assess the spatial separation of taxa on each island. KEY RESULTS We found intra- and inter-island diversification events in almost equal numbers. In lineages that diversified within single islands, morphological and ecological divergence was more pronounced than in lineages derived from inter-island diversification, but only the difference in morphological divergence was significant. Those islands with the longest history of habitation by Aeonium had the lowest percentages of co-occurring and hybridizing taxon pairs compared with islands where Aeonium arrived later. CONCLUSIONS Our findings illustrate the importance of both inter- and intra-island speciation, the latter of which is potentially sympatric speciation. Speciation on the same island entailed significantly higher levels of morphological divergence compared with inter-island speciation, but ecological divergence was not significantly different. Longer periods of shared island habitation resulted in the evolution of a higher degree of spatial separation and stronger reproductive barriers.
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Affiliation(s)
- Thibaud F E Messerschmid
- Botanischer Garten München-Nymphenburg, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80638 München, Germany
- Prinzessin Therese von Bayern-Lehrstuhl für Systematik, Biodiversität & Evolution der Pflanzen, Ludwig-Maximilians-Universität München, 80638 München, Germany
| | - Stefan Abrahamczyk
- Nees-Institut für Biodiversität der Pflanzen, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
- Abteilung Botanik, Staatliches Museum für Naturkunde Stuttgart, 70191 Stuttgart, Germany
| | - Ángel Bañares-Baudet
- Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de La Laguna, E-38200 La Laguna, Tenerife, Spain
| | - Miguel A Brilhante
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1340-017 Lisboa, Portugal
| | - Urs Eggli
- Sukkulenten-Sammlung Zürich/Grün Stadt Zürich, 8002 Zürich, Switzerland
| | - Philipp Hühn
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Joachim W Kadereit
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Patrícia dos Santos
- Centre for Ecology, Evolution and Environmental Changes (cE3c) and Global Change and Sustainability Institute (CHANGE), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Department of Environmental Sciences – Botany, University of Basel, 4056 Basel, Switzerland
| | - Jurriaan M de Vos
- Department of Environmental Sciences – Botany, University of Basel, 4056 Basel, Switzerland
| | - Gudrun Kadereit
- Botanischer Garten München-Nymphenburg, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80638 München, Germany
- Prinzessin Therese von Bayern-Lehrstuhl für Systematik, Biodiversität & Evolution der Pflanzen, Ludwig-Maximilians-Universität München, 80638 München, Germany
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10
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Bozkurt M, Calleja Alarcón JA, Uysal T, Garcia-Jacas N, Ertuğrul K, Susanna A. Biogeography of Rhaponticoides, an Irano-Turanian element in the Mediterranean flora. Sci Rep 2022; 12:22019. [PMID: 36539442 PMCID: PMC9768164 DOI: 10.1038/s41598-022-24947-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Floristic relationships between the Irano-Turanian and Mediterranean regions have been known from old. However, only a few biogeographical analyses based on molecular data have evaluated the history of steppe plants within the Mediterranean basin. Our study aims to contribute to a better understanding of the migratory and diversification processes by reconstructing the biogeography of Rhaponticoides (Cardueae), distributed in the Mediterranean and Irano-Turanian regions. We generated nuclear and plastid sequences that were analyzed by Bayesian inference. We used the resulting phylogeny for dating the diversification of the genus and examining the dispersal pathways. Two clades were recovered, an Irano-Turanian clade and a Mediterranean clade. The origin of the genus was placed in the Anatolian plateau in the Middle Miocene. The genus experienced several diversifications and expansions correlated to the Messinian salinity crisis and the environmental changes in the Pliocene and the Quaternary. Rhaponticoides migrated following two routes reflecting the two souls of the genus: Irano-Turanian taxa colonized the steppes of Eurasia whilst Mediterranean species migrated via eastern and central Mediterranean and North Africa, leaving a trail of species; both pathways ended in the Iberian Peninsula. Our study also confirms that more work is needed to unravel phylogenetic relationships in Rhaponticoides.
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Affiliation(s)
- Meryem Bozkurt
- Department of Biology, Faculty of Science, Selçuk University, 42130, Konya, Turkey
| | - Juan Antonio Calleja Alarcón
- Departament of Biology (Botany), Faculty of Sciences, Research Centre on Biodiversity and Global Change (CIBC-UAM), 28049, Madrid, Spain.
| | - Tuna Uysal
- Department of Biology, Faculty of Science, Selçuk University, 42130, Konya, Turkey
| | - Nuria Garcia-Jacas
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, S.N., 08038, Barcelona, Spain
| | - Kuddisi Ertuğrul
- Department of Biology, Faculty of Science, Selçuk University, 42130, Konya, Turkey
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, S.N., 08038, Barcelona, Spain
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Liu X, Wang Z, Wang W, Huang Q, Zeng Y, Jin Y, Li H, Du S, Zhang J. Origin and evolutionary history of Populus (Salicaceae): Further insights based on time divergence and biogeographic analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:1031087. [PMID: 36618663 PMCID: PMC9815717 DOI: 10.3389/fpls.2022.1031087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Populus (Salicaceae) species harbour rich biodiversity and are widely distributed throughout the Northern Hemisphere. However, the origin and biogeography of Populus remain poorly understood. METHODS We infer the divergence times and the historical biogeography of the genus Populus through phylogenetic analysis of 34 chloroplast fragments based on a large sample. RESULTS AND DISCUSSION Eurasia is the likely location of the early divergences of Salicaceae after the Cretaceous-Paleogene (K-Pg) mass extinction, followed by recurrent spread to the remainder of the Old World and the New World beginning in the Eocene; the extant Populus species began to diversity during the early Oligocene (approximately 27.24 Ma), climate changes during the Oligocene may have facilitated the diversification of modern poplar species; three separate lineages of Populus from Eurasia colonized North America in the Cenozoic via the Bering Land Bridges (BLB); We hypothesize that the present day disjunction in Populus can be explained by two scenarios: (i) Populus likely originated in Eurasia and subsequently colonized other regions, including North America; and (ii) the fact that the ancestor of the genus Populus that was once widely distributed in the Northern Hemisphere and eventually wiped out due to the higher extinction rates in North America, similar to the African Rand flora. We hypothesize that disparities in extinction across the evolutionary history of Populus in different regions shape the modern biogeography of Populus. Further studies with dense sampling and more evidence are required to test these hypotheses. Our research underscores the significance of combining phylogenetic analyses with biogeographic interpretations to enhance our knowledge of the origin, divergence, and distribution of biodiversity in temperate plant floras.
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Affiliation(s)
- Xia Liu
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Zhaoshan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Qinqin Huang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Yanfei Zeng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yu Jin
- Henan Academy of Forestry/Quality Testing Center for Forestry Products of National and Grassland Administration, Zhengzhou, China
| | - Honglei Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
| | - Shuhui Du
- Forestry College, Shanxi Agricultural University, Shanxi, China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Haran J, Procheş Ş, Benoit L, Kergoat GJ. From monocots to dicots: host shifts in Afrotropical derelomine weevils shed light on the evolution of non-obligatory brood pollination mutualism. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Weevils from the tribe Derelomini (Curculionidae: Curculioninae) are specialized brood pollinators engaged in mutualistic relationships with several angiosperm lineages. In brood pollination systems, reproductive plant tissues are used for the development of insect larval stages, whereas adult insects pollinate their plant hosts as a reward. The evolutionary history of derelomines in relationship to their hosts is poorly understood and potentially contrasts with other brood pollination systems, wherein a pollinator lineage is usually associated with a single host plant family. In the case of Afrotropical Derelomini, host records indicate a diverse host repertoire consisting of several families of monocot and dicot plants. In this study, we investigate their phylogenetic relationships, timing of diversification and evolution of host use. Our results suggest that derelomine lineages started their diversification ~40 Mya. Reconstructions of host use evolution support an ancestral association with the monocotyledonous palm family (Arecaceae), followed by several shifts towards other plant families in Afrotropical lineages, especially to dicotyledonous plants from the family Ebenaceae (on the genus Euclea L.). Some level of phylogenetic conservatism of host use is recovered for the lineages associated with either palms or Euclea. Multiple instances of sympatric weevil assemblages on the same plant are also unravelled, corresponding to either single or independent colonization events. Overall, the diversity of hosts colonized and the frequency of sympatric assemblages highlighted in non-obligatory plant–derelomine brood pollination systems contrast with what is generally expected from plant–insect brood pollination systems.
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Affiliation(s)
- Julien Haran
- CBGP, CIRAD, INRAE, IRD, Institut Agro, Univ. Montpellier , Montpellier , France
| | - Şerban Procheş
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal , Durban , South Africa
| | - Laure Benoit
- CBGP, CIRAD, INRAE, IRD, Institut Agro, Univ. Montpellier , Montpellier , France
| | - Gael J Kergoat
- CBGP, INRAE, CIRAD, IRD, Montpellier Institut Agro, Univ. Montpellier , Montpellier , France
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13
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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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14
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Coyotee Howard C, Crowl AA, Harvey TS, Cellinese N. Peeling Back the Layers: First Phylogenomic Insights into the Ledebouriinae (Scilloideae, Asparagaceae). Mol Phylogenet Evol 2022; 169:107430. [DOI: 10.1016/j.ympev.2022.107430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 01/11/2022] [Accepted: 01/25/2022] [Indexed: 11/26/2022]
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15
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Bonatelli IAS, Gehara M, Carstens BC, Colli GR, Moraes EM. Comparative and predictive phylogeography in the South American diagonal of open formations: Unravelling the biological and environmental influences on multitaxon demography. Mol Ecol 2021; 31:331-342. [PMID: 34614269 DOI: 10.1111/mec.16210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/28/2022]
Abstract
Phylogeography investigates historical drivers of the geographical distribution of intraspecific lineages. Particular attention has been given to ecological, climatic and geological processes in the diversification of the Neotropical biota. Several species sampled across the South American diagonal of open formations (DOF), comprising the Caatinga, Cerrado and Chaco biomes, experienced range shifts coincident with Quaternary climatic changes. However, comparative studies across different spatial, temporal and biological scales on DOF species are still meagre. Here, we combine phylogeographical model selection and machine learning predictive frameworks to investigate the influence of Pleistocene climatic changes on several plant and animal species from the DOF. We assembled mitochondrial/chloroplastic DNA sequences in public repositories and inferred the demographic responses of 44 species, comprising 70 intraspecific lineages of plants, lizards, frogs, spiders and insects. We then built a random forest model using biotic and abiotic information to identify the best predictors of demographic responses in the Pleistocene. Finally, we assessed the temporal synchrony of species demographic responses with hierarchical approximate Bayesian computation. Biotic variables related to population connectivity, gene flow and habitat preferences largely predicted how species responded to Pleistocene climatic changes, and demographic changes were synchronous primarily during the Middle Pleistocene. Although 22 (~31%) lineages underwent demographic expansion, presumably associated with the spread of aridity during the glacial Pleistocene periods, our findings suggest that nine lineages (~13%) exhibited the opposite response due to taxon-specific attributes.
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Affiliation(s)
- Isabel A S Bonatelli
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, Brazil.,Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Diadema, Brazil
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University-Newark, Newark, New Jersey, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, Brazil
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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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17
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Culshaw V, Villaverde T, Mairal M, Olsson S, Sanmartín I. Rare and widespread: integrating Bayesian MCMC approaches, Sanger sequencing and Hyb-Seq phylogenomics to reconstruct the origin of the enigmatic Rand Flora genus Camptoloma. AMERICAN JOURNAL OF BOTANY 2021; 108:1673-1691. [PMID: 34550605 DOI: 10.1002/ajb2.1727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Genera that are widespread, with geographically discontinuous distributions and represented by few species, are intriguing. Is their achieved disjunct distribution recent or ancient in origin? Why are they species-poor? The Rand Flora is a continental-scale pattern in which closely related species appear codistributed in isolated regions over the continental margins of Africa. Genus Camptoloma (Scrophulariaceae) is the most notable example, comprising three species isolated from each other on the northwest, eastern, and southwest Africa. METHODS We employed Sanger sequencing of nuclear and plastid markers, together with genomic target sequencing of 2190 low-copy nuclear genes, to infer interspecies relationships and the position of Camptoloma within Scrophulariaceae by using supermatrix and multispecies-coalescent approaches. Lineage divergence times and ancestral ranges were inferred with Bayesian Markov chain Monte Carlo (MCMC) approaches. The population history was estimated with phylogeographic coalescent methods. RESULTS Camptoloma rotundifolium, restricted to Southern Africa, was shown to be a sister species to the disjunct clade formed by C. canariense, endemic to the Canary Islands, and C. lyperiiflorum, distributed in the Horn of Africa-Southern Arabia. Camptoloma was inferred to be sister to the mostly South African tribes Teedieae and Buddlejeae. Stem divergence was dated in the Late Miocene, while the origin of the extant disjunction was inferred as Early Pliocene. CONCLUSIONS The current disjunct distribution of Camptoloma across Africa was likely the result of fragmentation and extinction and/or population bottlenecking events associated with historical aridification cycles during the Neogene; the pattern of species divergence, from south to north, is consistent with the "climatic refugia" Rand Flora hypothesis.
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Affiliation(s)
- Victoria Culshaw
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo, 2, Madrid, 28014, Spain
| | - Tamara Villaverde
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo, 2, Madrid, 28014, Spain
- Department of Botany, Universidad de Almeria, Carretera Sacramento, La Cañada de San Urbano, Almeria, 04120, Spain
| | - Mario Mairal
- Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, Madrid, Spain
| | - Sanna Olsson
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Carretera de la Coruña km 7.5, Madrid, 28040, Spain
| | - Isabel Sanmartín
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo, 2, Madrid, 28014, Spain
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Moiloa NA, Mesbah M, Nylinder S, Manning J, Forest F, de Boer HJ, Bacon CD, Oxelman B. Biogeographic origins of southern African Silene (Caryophyllaceae). Mol Phylogenet Evol 2021; 162:107199. [PMID: 33984468 DOI: 10.1016/j.ympev.2021.107199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 11/25/2022]
Abstract
Silene (Caryophyllaceae) is distributed predominantly in the northern Hemisphere, where it is most diverse around the Mediterranean Basin. The genus is also well represented in North Africa, extending into tropical, sub-Saharan and southern Africa. Eight native species are recognized in southern Africa, taxonomically placed in two sections: Elisanthe and Silene s.l. Although the taxonomy of the southern African taxa has recently been revised, their phylogenetic relationships and biogeographic history remain unclear. This study aims to infer the phylogenetic position and geographic origins of the southern African taxa. We generated DNA sequences of nuclear and plastid loci from several individuals belonging to all eight species of Silene recognized from southern Africa, and combined our DNA sequences with existing data representing species from major clades (i.e. sections) based on the recently revised Silene infrageneric taxonomy. We used a Bayesian coalescent species tree continuous diffusion approach to co-estimate the species tree and the ancestral areas of representative members of the genus. Our results show that the perennial southern African members of section Elisanthe form a strongly-supported clade with the Eurasian annual S. noctiflora and the Central Asian perennial S. turkestanica. The rest of the perennial species form a strongly-supported clade together with the annual S. aethiopica, which is nested in a larger Mediterranean clade comprising mostly annual species classified in section Silene s.l. Estimates of ancestral areas indicate a late Pleistocene dispersal to southern Africa from central and East Africa for the sub-Saharan members of section Silene s.l. The Elisanthe clade is inferred to have colonized southern Africa through long-distance dispersal from Eurasia during the late Pleistocene. Our findings support the hypothesis of a relatively recent colonization into southern Africa resulting from two independent dispersal events during the Pleistocene.
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Affiliation(s)
- Ntwai A Moiloa
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs Gata 22 B, 413 19 Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden.
| | - Melilia Mesbah
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden; Laboratory of Ecology and Environment, Faculty of Natural and Life Sciences, University of Bejaia, 06000 Bejaia, Algeria
| | - Stephan Nylinder
- Swedish National Data Service, University of Gothenburg, Box 463, 405 30 Gothenburg, Sweden
| | - John Manning
- South African National Biodiversity Institute, Private Bag X7, Claremont, Cape Town 7735, South Africa; Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, Private Bag X01, Scottsville 3209, South Africa
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom
| | - Hugo J de Boer
- Natural History Museum, University of Oslo, Postboks 1172, Blindern, 0318 Oslo, Norway
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs Gata 22 B, 413 19 Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs Gata 22 B, 413 19 Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden
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Toker C, Berger J, Eker T, Sari D, Sari H, Gokturk RS, Kahraman A, Aydin B, von Wettberg EJ. Cicer turcicum: A New Cicer Species and Its Potential to Improve Chickpea. FRONTIERS IN PLANT SCIENCE 2021; 12:662891. [PMID: 33936152 PMCID: PMC8082243 DOI: 10.3389/fpls.2021.662891] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
Genetic resources of the genus Cicer L. are not only limited when compared to other important food legumes and major cereal crops but also, they include several endemic species with endangered status based on the criteria of the International Union for Conservation of Nature. The chief threats to endemic and endangered Cicer species are over-grazing and habitat change in their natural environments driven by climate changes. During a collection mission in east and south-east Anatolia (Turkey), a new Cicer species was discovered, proposed here as C. turcicum Toker, Berger & Gokturk. Here, we describe the morphological characteristics, images, and ecology of the species, and present preliminary evidence of its potential utility for chickpea improvement. C. turcicum is an annual species, endemic to southeast Anatolia and to date has only been located in a single population distant from any other known annual Cicer species. It belongs to section Cicer M. Pop. of the subgenus Pseudononis M. Pop. of the genus Cicer L. (Fabaceae) and on the basis of internal transcribed spacer (ITS) sequence similarity appears to be a sister species of C. reticulatum Ladiz. and C. echinospermum P.H. Davis, both of which are inter-fertile with domestic chickpea (C. arietinum L.). With the addition of C. turcicum, the genus Cicer now comprises 10 annual and 36 perennial species. As a preliminary evaluation of its potential for chickpea improvement two accessions of C. turcicum were field screened for reproductive heat tolerance and seeds were tested for bruchid resistance alongside a representative group of wild and domestic annual Cicer species. C. turcicum expressed the highest heat tolerance and similar bruchid resistance as C. judaicum Boiss. and C. pinnatifidum Juab. & Spach, neither of which are in the primary genepool of domestic chickpea. Given that C. arietinum and C. reticulatum returned the lowest and the second lowest tolerance and resistance scores, C. turcicum may hold much potential for chickpea improvement if its close relatedness supports interspecific hybridization with the cultigen. Crossing experiments are currently underway to explore this question.
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Affiliation(s)
- Cengiz Toker
- Department of Field Crops, Akdeniz University, Antalya, Turkey
| | - Jens Berger
- CSIRO Agriculture and Food, Wembley, WA, Australia
| | - Tuba Eker
- Department of Field Crops, Akdeniz University, Antalya, Turkey
| | - Duygu Sari
- Department of Field Crops, Akdeniz University, Antalya, Turkey
| | - Hatice Sari
- Department of Field Crops, Akdeniz University, Antalya, Turkey
| | | | | | - Bilal Aydin
- Department of Field Crops, Harran University, Şanlıurfa, Turkey
| | - Eric J. von Wettberg
- Department of Plant and Soil Science and Gund Institute for Environment, University of Vermont, Burlington, VT, United States
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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: 64] [Impact Index Per Article: 21.3] [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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Goldenberg J, D'Alba L, Bisschop K, Vanthournout B, Shawkey MD. Substrate thermal properties influence ventral brightness evolution in ectotherms. Commun Biol 2021; 4:26. [PMID: 33398079 PMCID: PMC7782800 DOI: 10.1038/s42003-020-01524-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 11/25/2020] [Indexed: 01/29/2023] Open
Abstract
The thermal environment can affect the evolution of morpho-behavioral adaptations of ectotherms. Heat is transferred from substrates to organisms by conduction and reflected radiation. Because brightness influences the degree of heat absorption, substrates could affect the evolution of integumentary optical properties. Here, we show that vipers (Squamata:Viperidae) inhabiting hot, highly radiative and superficially conductive substrates have evolved bright ventra for efficient heat transfer. We analyzed the brightness of 4161 publicly available images from 126 species, and we found that substrate type, alongside latitude and body mass, strongly influences ventral brightness. Substrate type also significantly affects dorsal brightness, but this is associated with different selective forces: activity-pattern and altitude. Ancestral estimation analysis suggests that the ancestral ventral condition was likely moderately bright and, following divergence events, some species convergently increased their brightness. Vipers diversified during the Miocene and the enhancement of ventral brightness may have facilitated the exploitation of arid grounds. We provide evidence that integument brightness can impact the behavioral ecology of ectotherms.
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Affiliation(s)
- Jonathan Goldenberg
- Evolution and Optics of Nanostructures group, Department of Biology, Ghent University, 9000, Ghent, Belgium.
| | - Liliana D'Alba
- Evolution and Optics of Nanostructures group, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Karen Bisschop
- Terrestrial Ecology Unit, Department of Biology, Ghent University, 9000, Ghent, Belgium
- Theoretical Research in Evolutionary Life Sciences, Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9700 CC, Groningen, The Netherlands
| | - Bram Vanthournout
- Evolution and Optics of Nanostructures group, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Matthew D Shawkey
- Evolution and Optics of Nanostructures group, Department of Biology, Ghent University, 9000, Ghent, Belgium
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A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature 2021; 599:622-627. [PMID: 34759320 PMCID: PMC8612933 DOI: 10.1038/s41586-021-04066-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 09/28/2021] [Indexed: 11/17/2022]
Abstract
Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.
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Zhao Z, Heideman N, Bester P, Jordaan A, Hofmeyr MD. Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa. BMC Evol Biol 2020; 20:153. [PMID: 33187474 PMCID: PMC7666511 DOI: 10.1186/s12862-020-01717-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/02/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world's tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa. RESULTS We investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63-5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensification of the cold Benguela current, which caused western aridification and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fluctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by different climatic parameters, and that the niches differed substantially among the clades of the northern group but were similar among clades of the southern group. CONCLUSION Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B-Ptr, Ptt-A and Pv-A.
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Affiliation(s)
- Zhongning Zhao
- Department of Zoology and Entomology, University of the Free State, Biology Building B19, 205 Nelson Mandela Dr, Park West, Bloemfontein, South Africa.
| | - Neil Heideman
- Department of Zoology and Entomology, University of the Free State, Biology Building B19, 205 Nelson Mandela Dr, Park West, Bloemfontein, South Africa
| | - Phillip Bester
- Department of Virology, University of the Free State and National Health Laboratory Service (NHLS), Bloemfontein, South Africa
| | - Adriaan Jordaan
- Department of Zoology and Entomology, University of the Free State, Biology Building B19, 205 Nelson Mandela Dr, Park West, Bloemfontein, South Africa
| | - Margaretha D Hofmeyr
- Department of Biodiversity and Conservation Biology, Chelonian Biodiversity and Conservation, University of the Western Cape, Bellville, South Africa
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Combination of Sanger and target-enrichment markers supports revised generic delimitation in the problematic 'Urera clade' of the nettle family (Urticaceae). Mol Phylogenet Evol 2020; 158:107008. [PMID: 33160040 DOI: 10.1016/j.ympev.2020.107008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 10/20/2020] [Accepted: 10/29/2020] [Indexed: 11/20/2022]
Abstract
Urera Gaudich, s.l. is a pantropical genus comprising c. 35 species of trees, shrubs, and vines. It has a long history of taxonomic uncertainty, and is repeatedly recovered as polyphyletic within a poorly resolved complex of genera in the Urticeae tribe of the nettle family (Urticaceae). To provide generic delimitations concordant with evolutionary history, we use increased taxonomic and genomic sampling to investigate phylogenetic relationships among Urera and associated genera. A cost-effective two-tier genome-sampling approach provides good phylogenetic resolution by using (i) a taxon-dense sample of Sanger sequence data from two barcoding regions to recover clades of putative generic rank, and (ii) a genome-dense sample of target-enrichment data for a subset of representative species from each well-supported clade to resolve relationships among them. The results confirm the polyphyly of Urera s.l. with respect to the morphologically distinct genera Obetia, Poikilospermum and Touchardia. Afrotropic members of Urera s.l. are recovered in a clade sister to the xerophytic African shrubs Obetia; and Hawaiian ones with Touchardia, also from Hawaii. Combined with distinctive morphological differences between Neotropical and African members of Urera s.l., these results lead us to resurrect the previously synonymised name Scepocarpus Wedd. for the latter. The new species epiphet Touchardia oahuensis T.Wells & A.K. Monro is offered as a replacement name for Touchardia glabra non H.St.John, and subgenera are created within Urera s.s. to account for the two morphologically distinct Neotropical clades. This new classification minimises taxonomic and nomenclatural disruption, while more accurately reflecting evolutionary relationships within the group.
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Biogeography, phylogenetic relationships and morphological analyses of the South American genus Mutisia L.f. (Asteraceae) shows early connections of two disjunct biodiversity hotspots. ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-020-00454-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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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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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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Choo LM, Forest F, Wieringa JJ, Bruneau A, de la Estrella M. Phylogeny and biogeography of the Daniellia clade (Leguminosae: Detarioideae), a tropical tree lineage largely threatened in Africa and Madagascar. Mol Phylogenet Evol 2020; 146:106752. [PMID: 32028029 DOI: 10.1016/j.ympev.2020.106752] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 11/28/2022]
Abstract
The legume subfamily Detarioideae is exceptionally diverse in tropical Africa and Madagascar, compared to South America or Asia, a trend contrary to that shown by most other pantropical plant groups. We aim to elucidate the process of diversification giving rise to these high diversity levels by focussing our investigations on the Daniellia clade, which is present in both Africa and Madagascar. The Daniellia clade is an early-diverging lineage of subfamily Detarioideae (Leguminosae; pea family) and consists of three genera: Daniellia, Brandzeia and Neoapaloxylon. The species belonging to this group exhibit a wide range of habitat types. The Madagascar endemics Brandzeia (1 species) and Neoapaloxylon (3 species) occupy dry woodlands and arid succulent habitats respectively. Daniellia alsteeniana and D. oliveri are found in savannahs while the remaining eight species within Daniellia all occupy rainforest habitats. Phylogenetic analyses were generated from a dense, multi-individual species level sampling of the clade. Divergence time estimates were carried out using a molecular clock method to investigate biogeographical patterns and shifts in habitat types within the Daniellia clade, and conservation assessments were conducted to determine the levels of extinction risks these species are facing. We estimate that the Daniellia clade first emerged during the Early Eocene from an ancestor present in the rainforests of North Africa at that time, reflecting an ancestral habitat preference. There was a first major split over the course of the Eocene, giving rise to both African rainforest and Madagascan savannah lineages. With the emergence of a drier climate and vegetation type in Africa during the Eocene, it is likely that a dry-climate adapted lineage from the Daniellia clade ancestor could have dispersed through suitable savannah or woodland regions to reach Madagascar, subsequently giving rise to the savannah-adapted ancestor of Brandzeia and Neoapaloxylon in the Early Miocene. The African rainforest lineage gave rise to the genus Daniellia, which is postulated to have first diversified in the Middle Miocene, while savannah species of Daniellia emerged independently during the Pliocene, coinciding with the global rise of C4-dominated grasslands. More than half of the species in the Daniellia clade are near threatened or threatened, which highlights the need to understand the threats of anthropogenic pressures and climate change these species are facing to prioritise their conservation.
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Affiliation(s)
- Le Min Choo
- Herbarium, Research & Conservation Branch, Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569 Singapore; Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK.
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - Jan J Wieringa
- Naturalis Biodiversity Centre, National Herbarium of the Netherlands, Darwinweg 2, 2333 CR Leiden, the Netherlands
| | - Anne Bruneau
- Institut de recherche en biologie végétale and Département de Sciences biologiques, Université de Montréal, 4101 Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Manuel de la Estrella
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de Córdoba, Campus de Rabanales, 14071 Córdoba, Spain
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Clade-Specific Biogeographic History and Climatic Niche Shifts of the Southern Andean-Southern Brazilian Disjunction in Plants. NEOTROPICAL DIVERSIFICATION: PATTERNS AND PROCESSES 2020. [DOI: 10.1007/978-3-030-31167-4_24] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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30
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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] [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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Vitales D, García-Fernández A, Garnatje T, Vallès J, Font J, Robert Y, Vigo J. <em>Pellaea calomelanos</em> (Pteridaceae) en Cataluña: es realmente una disyunción ancestral? COLLECTANEA BOTANICA 2019. [DOI: 10.3989/collectbot.2019.v38.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Pellaea calomelanos es una especie que fue descubierta en África y cuya área de distribución se ha ido ampliando más recientemente a Asia y a una única localidad europea, que comprende tres poblaciones, en Cataluña. El hecho de pertenecer a los helechos y de presentar esta distribución disyunta alimentaron la idea de una especie relicta resultante de distribución amplia en tiempos remotos. Los valores 2C van desde 16,45 pg para el individuo de la Isla de la Reunión hasta 17,40 pg para la población de Boadella (Cataluña). Aunque existe una cierta variabilidad, no se han encontrado diferencias estadísticamente significativas entre ellos. El análisis filogenético revela un clado bien soportado que agrupa a todos los individuos de las diferentes poblaciones de P. calomelanos pero sin ningún tipo de resolución interna. Los resultados del presente trabajo, basado en medidas de cantidad de ADN nuclear y en secuencias de dos regiones del ADN cloroplástico, junto con las características de su hábitat, permiten a los autores hipotetizar sobre una colonización reciente del continente europeo por esta especie.
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Malakasi P, Bellot S, Dee R, Grace OM. Museomics Clarifies the Classification of Aloidendron (Asphodelaceae), the Iconic African Tree Aloes. FRONTIERS IN PLANT SCIENCE 2019; 10:1227. [PMID: 31681358 PMCID: PMC6803536 DOI: 10.3389/fpls.2019.01227] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/04/2019] [Indexed: 05/24/2023]
Abstract
Arborescent succulent plants are regarded as keystone and indicator species in desert ecosystems due to their large stature and long lifespans. Tree aloes, the genus Aloidendron, are icons of the southern African deserts yet have proved elusive subjects due to the difficulty of obtaining material of known provenance for comparative study. Consequently, evolutionary relationships among representatives of the unusual arborescent life form have remained unclear until now. We used a museomics approach to overcome this challenge. Chloroplast genomes of six Aloidendron species and 12 other members of Asphodelaceae were sequenced from modern living collections and herbarium specimens, including the type specimens of all but two Aloidendron species, the earliest of which was collected 130 years ago. Maximum-likelihood trees estimated from full chloroplast genomes and the nuclear internal transcribed spacer (ITS) region show that Aloidendron sabaeum, from the Arabian Peninsula, is nested within Aloe while the Madagascar endemic Aloestrela suzannae is most closely related to the Somalian Aloidendron eminens. We observed phylogenetic conflicts between the plastid and nuclear topologies, which may be indicative of recurrent hybridisation or incomplete lineage sorting events in Aloe and in Aloidendron. Comparing species ecology in the context provided by our phylogeny suggests that habitat preference to either xeric deserts or humid forests/thickets evolved repeatedly in Aloidendron. Our findings demonstrate the value of botanical collections for the study and classification of taxonomically challenging succulent plants.
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Acuña Castillo R, Luebert F, Henning T, Weigend M. Major lineages of Loasaceae subfam. Loasoideae diversified during the Andean uplift. Mol Phylogenet Evol 2019; 141:106616. [PMID: 31520779 DOI: 10.1016/j.ympev.2019.106616] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/14/2022]
Abstract
The Loasoideae is the largest clade in the Loasaceae. This subfamily is widespread throughout the Neotropics and centered in the Andes, presenting an excellent opportunity to study diversification across much of temperate and mid to high-elevation areas of South America. Despite that, no studies have addressed the historical biogeography of the Loasoideae to date, leaving an important knowledge gap in this plant group. Here, we used four plastid markers (i.e., trnL-trnF, matK, trnS-trnG, and rps16) and sequenced 170 accessions (134 ingroup taxa) to infer the phylogeny of Loasoideae. We then used this phylogeny as basis to estimate divergence times using an uncorrelated relaxed molecular clock approach and seven fossils as primary calibration points. We employed the Dispersal-Extinction-Cladogenesis (DEC) approach to reconstruct the ancestral ranges of the subfamily. Our results indicate that stem Loasoideae diverged from its sister group in the Late Cretaceous to Early Paleocene (ca. 83-62 Ma). The crown node of the whole clade goes back to the Middle Paleocene to Middle Eocene (ca. 60-45 Ma), corresponding to the earliest diversification events of the extant groups, prior to most of the Andean orogeny and roughly coinciding with the Paleocene-Eocene Thermal Maximum. On the other hand, the crown nodes of most genera appear to have originated in the Oligocene and Miocene (median ages: 28-10 Ma). The diversification of some extant lineages appears to have happened in parallel to Andean uplift pulses that seem to have had an effect on the orogeny and concomitant establishment of new habitats and latitudinal corridors. The most likely ancestral areas retrieved for crown Loasoideae, are the tropical Andes and Pacific arid coast. Most of the extant clades have remained restricted to their ancestral areas. Transoceanic Long Distance Dispersal appears to have been involved in the arrival of Loasoid ancestors to South America, and in the distribution of the small clades Kissenia in Africa and Plakothira on the Marquesas Archipelago. The results presented here suggest that the historical biogeography of the continental scale radiation of Loasoideae, follows the sequence and timing of the development of temperate and mid to high-elevation habitats across South America during the Tertiary.
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Affiliation(s)
- Rafael Acuña Castillo
- Universität Bonn, Nees-Institut für Biodiversität der Pflanzen, Meckenheimer Allee 170, 53115 Bonn, Germany; Universidad de Costa Rica, Escuela de Biología, Apdo. Postal: 11501-2060 San Pedro de Montes de Oca, Costa Rica.
| | - Federico Luebert
- Universität Bonn, Nees-Institut für Biodiversität der Pflanzen, Meckenheimer Allee 170, 53115 Bonn, Germany; Universidad de Chile, Departamento de Silvicultura y Conservación de la Naturaleza, Santiago, Chile
| | - Tilo Henning
- Freie Universität Berlin, Botanischer Garten Botanisches Museum, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
| | - Maximilian Weigend
- Universität Bonn, Nees-Institut für Biodiversität der Pflanzen, Meckenheimer Allee 170, 53115 Bonn, Germany
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The evolutionary history of the Cape hare (Lepus capensis sensu lato): insights for systematics and biogeography. Heredity (Edinb) 2019; 123:634-646. [PMID: 31073237 DOI: 10.1038/s41437-019-0229-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/11/2019] [Accepted: 04/19/2019] [Indexed: 12/27/2022] Open
Abstract
Inferring the phylogeography of species with large distributions helps deciphering major diversification patterns that may occur in parallel across taxa. Here, we infer the evolutionary history of the Cape hare, Lepus capensis sensu lato, a species distributed from southern Africa to Asia, by analyzing variation at 18 microsatellites and 9 DNA (1 mitochondrial and 8 nuclear) sequenced loci, from field and museum-collected samples. Using a combination of assignment and coalescent-based methods, we show that the Cape hare is composed of five evolutionary lineages, distributed in distinct biogeographic regions-north-western Africa, eastern Africa, southern Africa, the Near East and the Arabian Peninsula. A deep phylogenetic break possibly dating to the Early Pleistocene was inferred between the African and Asian L. capensis groups, and the latter appear more closely related to other Eurasian hare species than to African Cape hares. The inferred phylogeographic structure is shared by numerous taxa distributed across the studied range, suggesting that environmental changes, such as the progressive aridification of the Saharo-Arabian desert and the fluctuations of savannah habitats in Sub-Saharan Africa, had comparable impacts across species. Fine-scale analyses of the western Sahara-Sahel populations showed rich fragmentation patterns for mitochondrial DNA but not for microsatellites, compatible with the environmental heterogeneity of the region and female philopatry. The complex evolutionary history of L. capensis sensu lato, which possibly includes interspecific gene flow, is not reflected by taxonomy. Integrating evolutionary inference contributes to an improved characterization of biodiversity, which is fundamental to foster the conservation of relevant evolutionary units.
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Gamisch A, Comes HP. Clade-age-dependent diversification under high species turnover shapes species richness disparities among tropical rainforest lineages of Bulbophyllum (Orchidaceae). BMC Evol Biol 2019; 19:93. [PMID: 31014234 PMCID: PMC6480529 DOI: 10.1186/s12862-019-1416-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 03/31/2019] [Indexed: 01/05/2023] Open
Abstract
Background Tropical rainforests (TRFs) harbour almost half of the world’s vascular plant species diversity while covering only about 6–7% of land. However, why species richness varies amongst the Earth’s major TRF regions remains poorly understood. Here we investigate the evolutionary processes shaping continental species richness disparities of the pantropical, epiphytic and mostly TRF-dwelling orchid mega-genus Bulbophyllum (c. 1948 spp. in total) using diversification analyses based on a time-calibrated molecular phylogeny (including c. 45–50% spp. each from Madagascar, Africa, Neotropics, and 8.4% from the Asia-Pacific region), coupled with ecological niche modelling (ENM) of geographic distributions under present and past (Last Glacial Maximum; LGM) conditions. Results Our results suggest an early-to-late Miocene scenario of ‘out-of-Asia-Pacific’ origin and progressive, dispersal-mediated diversification in Madagascar, Africa and the Neotropics, respectively. Species richness disparities amongst these four TRF lineages are best explained by a time-for-speciation (i.e. clade age) effect rather than differences in net diversification or diversity-dependent diversification due to present or past spatial-bioclimatic limits. For each well-sampled lineage (Madagascar, Africa, Neotropics), we inferred high rates of speciation and extinction over time (i.e. high species turnover), yet with the origin of most extant species falling into the Quaternary. In contrast to predictions of classical ‘glacial refuge’ theories, all four lineages experienced dramatic range expansions during the LGM. Conclusions As the Madagascan, African and Neotropical lineages display constant-rate evolution since their origin (early-to-mid-Miocene), Quaternary environmental change might be a less important cause of their high species turnover than intrinsic features generally conferring rapid population turnover in tropical orchids (e.g., epiphytism, specialization on pollinators and mycorrhizal fungi, wind dispersal). Nonetheless, climate-induced range fluctuations during the Quaternary could still have played an influential role in the origination and extinction of Bulbophyllum species in those three, if not in all four TRF regions. Electronic supplementary material The online version of this article (10.1186/s12862-019-1416-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander Gamisch
- Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria.
| | - Hans Peter Comes
- Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
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Kriebel R, Drew BT, Drummond CP, González‐Gallegos JG, Celep F, Mahdjoub MM, Rose JP, Xiang C, Hu G, Walker JB, Lemmon EM, Lemmon AR, Sytsma KJ. Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data. AMERICAN JOURNAL OF BOTANY 2019; 106:573-597. [PMID: 30986330 PMCID: PMC6850103 DOI: 10.1002/ajb2.1268] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/31/2019] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species-rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega-genus Salvia. METHODS A chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of the nearly 1000 Salvia species. Ancestral areas and biomes were reconstructed using BioGeoBEARS. Pollinator guilds were scored, ancestral pollinators determined, shifts in pollinator guilds identified, and rates of pollinator switches compared. KEY RESULTS A well-resolved phylogenetic backbone of Salvia and updated subgeneric designations are presented. Salvia originated in Southwest Asia in the Oligocene and subsequently dispersed worldwide. Biome shifts are frequent from a likely ancestral lineage utilizing broadleaf and/or coniferous forests and/or arid shrublands. None of the four species diversification shifts are correlated to shifts in biomes. Shifts in pollination system are not correlated to species diversification shifts, except for one hummingbird shift that precedes a major shift in diversification near the crown of New World subgen. Calosphace. Multiple reversals back to bee pollination occurred within this hummingbird clade. CONCLUSIONS Salvia diversified extensively in different continents, biomes, and with both bee and bird pollinators. The lack of tight correlation of area, biome, and most pollinator shifts to the four documented species diversification shifts points to other important drivers of speciation in Salvia.
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Affiliation(s)
- Ricardo Kriebel
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Bryan T. Drew
- Department of BiologyUniversity of Nebraska at KearneyKearneyNE68849USA
| | - Chloe P. Drummond
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | | | - Ferhat Celep
- Mehmet Akif Ersoy mah. 269. cad. Urankent Prestij KonutlarıC16 Blok, No. 53DemetevlerAnkaraTurkey
| | - Mohamed M. Mahdjoub
- Research Laboratory of Ecology and EnvironmentDepartment of Environment Biological SciencesFaculty of Nature and Life SciencesUniversité de BejaiaTarga Ouzemmour06000BejaiaAlgeria
| | - Jeffrey P. Rose
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Chun‐Lei Xiang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingYunnan650201China
| | - Guo‐Xiong Hu
- College of Life SciencesGuizhou UniversityGuiyang550025GuizhouChina
| | | | - Emily M. Lemmon
- Department of Biological ScienceFlorida State UniversityTallahasseeFL32306USA
| | - Alan R. Lemmon
- Department of Scientific ComputingFlorida State UniversityTallahasseeFL32306USA
| | - Kenneth J. Sytsma
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
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Kriebel R, Drew BT, Drummond CP, González-Gallegos JG, Celep F, Mahdjoub MM, Rose JP, Xiang CL, Hu GX, Walker JB, Lemmon EM, Lemmon AR, Sytsma KJ. Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data. AMERICAN JOURNAL OF BOTANY 2019. [PMID: 30986330 DOI: 10.5061/dryad.8m40rb0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
PREMISE OF THE STUDY A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species-rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega-genus Salvia. METHODS A chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of the nearly 1000 Salvia species. Ancestral areas and biomes were reconstructed using BioGeoBEARS. Pollinator guilds were scored, ancestral pollinators determined, shifts in pollinator guilds identified, and rates of pollinator switches compared. KEY RESULTS A well-resolved phylogenetic backbone of Salvia and updated subgeneric designations are presented. Salvia originated in Southwest Asia in the Oligocene and subsequently dispersed worldwide. Biome shifts are frequent from a likely ancestral lineage utilizing broadleaf and/or coniferous forests and/or arid shrublands. None of the four species diversification shifts are correlated to shifts in biomes. Shifts in pollination system are not correlated to species diversification shifts, except for one hummingbird shift that precedes a major shift in diversification near the crown of New World subgen. Calosphace. Multiple reversals back to bee pollination occurred within this hummingbird clade. CONCLUSIONS Salvia diversified extensively in different continents, biomes, and with both bee and bird pollinators. The lack of tight correlation of area, biome, and most pollinator shifts to the four documented species diversification shifts points to other important drivers of speciation in Salvia.
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Affiliation(s)
- Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Bryan T Drew
- Department of Biology, University of Nebraska at Kearney, Kearney, NE, 68849, USA
| | - Chloe P Drummond
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Ferhat Celep
- Mehmet Akif Ersoy mah. 269. cad. Urankent Prestij Konutları, C16 Blok, No. 53, Demetevler, Ankara, Turkey
| | - Mohamed M Mahdjoub
- Research Laboratory of Ecology and Environment, Department of Environment Biological Sciences, Faculty of Nature and Life Sciences, Université de Bejaia, Targa Ouzemmour, 06000, Bejaia, Algeria
| | - Jeffrey P Rose
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Chun-Lei Xiang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Guo-Xiong Hu
- College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Jay B Walker
- Union High School, 6636 S. Mingo Road, Tulsa, OK, 74133, USA
| | - Emily M Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, 32306, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
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García-Verdugo C, Caujapé-Castells J, Mairal M, Monroy P. How repeatable is microevolution on islands? Patterns of dispersal and colonization-related plant traits in a phylogeographical context. ANNALS OF BOTANY 2019; 123:557-568. [PMID: 30380011 PMCID: PMC6377097 DOI: 10.1093/aob/mcy191] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 10/04/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND AND AIMS Archipelagos provide a valuable framework for investigating phenotypic evolution under different levels of geographical isolation. Here, we analysed two co-distributed, widespread plant lineages to examine if incipient island differentiation follows parallel patterns of variation in traits related to dispersal and colonization. METHODS Twenty-one populations of two anemochorous Canarian endemics, Kleinia neriifolia and Periploca laevigata, were sampled to represent mainland congeners and two contrasting exposures across all the main islands. Leaf size, seed size and dispersability (estimated as diaspore terminal velocity) were characterized in each population. For comparison, dispersability was also measured in four additional anemochorous island species. Plastid DNA data were used to infer genetic structure and to reconstruct the phylogeographical pattern of our focal species. KEY RESULTS In both lineages, mainland-island phenotypic divergence probably started within a similar time frame (i.e. Plio-Pleistocene). Island colonization implied parallel increases in leaf size and dispersability, but seed size showed opposite patterns of variation between Kleinia and Periploca species pairs. Furthermore, dispersability in our focal species was low when compared with other island plants, mostly due to large diaspore sizes. At the archipelago scale, island exposure explained a significant variation in leaf size across islands, but not in dispersability or seed size. Combined analyses of genetic and phenotypic data revealed two consistent patterns: (1) extensive within-island but very limited among-island dispersal, and (2) recurrent phenotypic differentiation between older (central) and younger (peripheral) island populations. CONCLUSIONS Leaf size follows a more predictable pattern than dispersability, which is affected by stochastic shifts in seed size. Increased dispersability is associated with high population connectivity at the island scale, but does not preclude allopatric divergence among islands. In sum, phenotypic convergent patterns between species suggest a major role of selection, but deviating traits also indicate the potential contribution of random processes, particularly on peripheral islands.
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Affiliation(s)
- Carlos García-Verdugo
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico Canario ‘Viera y Clavijo’ – Unidad Asociada CSIC, Cabildo de Gran Canaria, Camino del Palmeral 15 de Tafira Alta, Las Palmas de Gran Canaria, Spain
- Institut Mediterrani d’Estudis Avançats (CSIC-UIB), C/Miquel Marqués, Esporles, Balearic Islands, Spain
| | - Juli Caujapé-Castells
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico Canario ‘Viera y Clavijo’ – Unidad Asociada CSIC, Cabildo de Gran Canaria, Camino del Palmeral 15 de Tafira Alta, Las Palmas de Gran Canaria, Spain
| | - Mario Mairal
- Department of Botany, Charles University Faculty of Science, Albertov, Praha, Czech Republic
| | - Pedro Monroy
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico Canario ‘Viera y Clavijo’ – Unidad Asociada CSIC, Cabildo de Gran Canaria, Camino del Palmeral 15 de Tafira Alta, Las Palmas de Gran Canaria, Spain
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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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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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Condamine FL, Rolland J, Höhna S, Sperling FAH, Sanmartín I. Testing the Role of the Red Queen and Court Jester as Drivers of the Macroevolution of Apollo Butterflies. Syst Biol 2018; 67:940-964. [DOI: 10.1093/sysbio/syy009] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 02/06/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l’Evolution (Université de Montpellier
- CNRS IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
- Department of Biodiversity and Conservation, Real Jardín Botánico, CSIC, Plaza de Murillo, 2, 28014 Madrid, Spain
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, Alberta, Canada
| | - Jonathan Rolland
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Sebastian Höhna
- Division of Evolutionary Biology, Ludwig-Maximilian-Universität München, Grosshaderner Strasse 2, Planegg-Martinsried 82152, Germany
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, Alberta, Canada
| | - Isabel Sanmartín
- Department of Biodiversity and Conservation, Real Jardín Botánico, CSIC, Plaza de Murillo, 2, 28014 Madrid, Spain
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Pérez-Escobar OA, Chomicki G, Condamine FL, de Vos JM, Martins AC, Smidt EC, Klitgård B, Gerlach G, Heinrichs J. Multiple Geographical Origins of Environmental Sex Determination enhanced the diversification of Darwin's Favourite Orchids. Sci Rep 2017; 7:12878. [PMID: 29018291 PMCID: PMC5635016 DOI: 10.1038/s41598-017-12300-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/06/2017] [Indexed: 11/17/2022] Open
Abstract
Environmental sex determination (ESD) - a change in sexual function during an individual life span driven by environmental cues - is an exceedingly rare sexual system among angiosperms. Because ESD can directly affect reproduction success, it could influence diversification rate as compared with lineages that have alternative reproductive systems. Here we test this hypothesis using a solid phylogenetic framework of Neotropical Catasetinae, the angiosperm lineage richest in taxa with ESD. We assess whether gains of ESD are associated with higher diversification rates compared to lineages with alternative systems while considering additional traits known to positively affect diversification rates in orchids. We found that ESD has evolved asynchronously three times during the last ~5 Myr. Lineages with ESD have consistently higher diversification rates than related lineages with other sexual systems. Habitat fragmentation due to mega-wetlands extinction, and climate instability are suggested as the driving forces for ESD evolution.
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Affiliation(s)
| | - Guillaume Chomicki
- Department of Plant Sciences, University of Oxford, South Park Road, OX1 3RB, Oxford, United Kingdom
| | - Fabien L Condamine
- CNRS, UMR 5554 Institut de Sciences de l'Evolution (Université de Montpellier), Place Eugène Bataillon, 34095, Montpellier, France
| | - Jurriaan M de Vos
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens Kew, Richmond, TW9 3AB, United Kingdom.
- Department of Environmental Sciences - Botany, University of Basel, Totengässlein 3, 4051, Basel, Switzerland.
| | - Aline C Martins
- Department of Botany, Federal University of Paraná, PB 19031, Curitiba, PR, 81531-980, Brazil
| | - Eric C Smidt
- Department of Botany, Federal University of Paraná, PB 19031, Curitiba, PR, 81531-980, Brazil
| | - Bente Klitgård
- Department of Identification and Naming, Royal Botanic Gardens Kew, Richmond, TW9 3AB, UK
| | - Günter Gerlach
- Botanischer Garten München, Menzinger Straße 67, D-80638, München, Germany
| | - Jochen Heinrichs
- Department für Biologie I, Systematische Botanik und Mykologie, Ludwig-Maximilians-Universität, Menzinger Straße 67, D-80638, München, Germany
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García-Aloy S, Sanmartín I, Kadereit G, Vitales D, Millanes AM, Roquet C, Vargas P, Alarcón M, Aldasoro JJ. Opposite trends in the genus Monsonia (Geraniaceae): specialization in the African deserts and range expansions throughout eastern Africa. Sci Rep 2017; 7:9872. [PMID: 28852053 PMCID: PMC5575343 DOI: 10.1038/s41598-017-09834-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 07/31/2017] [Indexed: 11/09/2022] Open
Abstract
The African Austro-temperate Flora stands out by its important species richness. A distinctive element of this flora is Monsonia (Geraniaceae), mostly found in the Namib-Karoo but also in the Natal-Drakensberg, the Somalian Zambezian and the Saharo-Arabian regions. Here, we reconstruct the evolution and biogeographic history of Monsonia based on nuclear and plastid markers, and examine the role of morphological and niche evolution in its diversification using species distribution modeling and macroevolutionary models. Our results indicate that Monsonia first diversified in the Early Miocene c.21 Ma, coinciding with the start of desertification in southwestern Africa. An important diversification occurred c. 4-6 Ma, after a general cooling trend in western South Africa and the rising of the Eastern African Mountains. The resulting two main lineages of Monsonia are constituted by: (1) Namib-Karoo succulents, and (2) herbs of the Natal-Drakensberg plus three species that further colonised steppes in north and eastern Africa. The highest diversity of Monsonia is found in the Namib-Karoo coastal belt, within a mosaic-like habitat structure. Diversification was likely driven by biome shifts and key innovations such as water-storing succulent stems and anemochorous fruits. In contrast, and unlike other arid-adapted taxa, all species of Monsonia share a C3 metabolism.
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Affiliation(s)
- Sara García-Aloy
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Passeig del Migdia s/n, Parc de Montjuïc, E-08038, Barcelona, Spain.
| | - Isabel Sanmartín
- Real Jardín Botánico, (RJB-CSIC), Plaza de Murillo 2, E-28014, Madrid, Spain
| | - Gudrun Kadereit
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, D-55099, Mainz, Germany
| | - Daniel Vitales
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Passeig del Migdia s/n, Parc de Montjuïc, E-08038, Barcelona, Spain
| | - Ana María Millanes
- Universidad Rey Juan Carlos (URJC), C/ Tulipán s.n., E-, 28933, Móstoles, Spain
| | - Cristina Roquet
- Laboratoire d'Écologie Alpine, CNRS UMR 5553, Université Grenoble Alpes, BP 53, F-38041, Grenoble Cedex 9, France
| | - Pablo Vargas
- Real Jardín Botánico, (RJB-CSIC), Plaza de Murillo 2, E-28014, Madrid, Spain
| | - Marisa Alarcón
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Passeig del Migdia s/n, Parc de Montjuïc, E-08038, Barcelona, Spain
| | - Juan José Aldasoro
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Passeig del Migdia s/n, Parc de Montjuïc, E-08038, Barcelona, Spain.,Universidad Rey Juan Carlos (URJC), C/ Tulipán s.n., E-, 28933, Móstoles, Spain
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de la Estrella M, Forest F, Wieringa JJ, Fougère-Danezan M, Bruneau A. Insights on the evolutionary origin of Detarioideae, a clade of ecologically dominant tropical African trees. THE NEW PHYTOLOGIST 2017; 214:1722-1735. [PMID: 28323330 DOI: 10.1111/nph.14523] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/13/2017] [Indexed: 06/06/2023]
Abstract
African tropical forests are generally considered less diverse than their Neotropical and Asian counterparts. By contrast, the Detarioideae is much more diverse in Africa than in South America and Asia. To better understand the evolution of this contrasting diversity pattern, we investigated the biogeographical and ecological origin of this subfamily, testing whether they originated in dry biomes surrounding the Tethys Seaway as currently hypothesized for many groups of Leguminosae. We constructed the largest time-calibrated phylogeny for the subfamily to date, reconstructed ancestral states for geography and biome/habitat, estimated diversification and extinction rates, and evaluated biome/habitat and geographic shifts in Detarioideae. The ancestral habitat of Detarioideae is postulated to be a primary forest (terra firme) originated in Africa-South America, in the early Palaeocene, after which several biome/habitat and geographic shifts occurred. The origin of Detarioideae is older than previous estimates, which postulated a dry (succulent) biome origin according to the Tethys Seaway hypothesis, and instead we reveal a post Gondwana and terra firme origin for this early branching clade of legumes. Detarioideae include some of the most dominant trees in evergreen forests and have likely played a pivotal role in shaping continental African forest diversity.
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Affiliation(s)
- Manuel de la Estrella
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
- Institut de recherche en biologie végétale and Département de Sciences biologiques, Université de Montréal, 4101 Sherbrooke est, Montréal, QC, H1X 2B2, Canada
| | - Félix Forest
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
| | - Jan J Wieringa
- Naturalis Biodiversity Centre, National Herbarium of the Netherlands, Darwinweg 2, 2333, CR Leiden, the Netherlands
| | - Marie Fougère-Danezan
- Institut de recherche en biologie végétale and Département de Sciences biologiques, Université de Montréal, 4101 Sherbrooke est, Montréal, QC, H1X 2B2, Canada
- Université de Toulouse, EDB (Laboratoire Evolution et Diversité Biologique), UMR5174, F-31062, Toulouse, France
- CNRS, UPS, EDB (Laboratoire Evolution et Diversité Biologique), UMR5174, 118 route de Narbonne, F-31062, Toulouse, France
| | - Anne Bruneau
- Institut de recherche en biologie végétale and Département de Sciences biologiques, Université de Montréal, 4101 Sherbrooke est, Montréal, QC, H1X 2B2, Canada
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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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Sanmartín I, Meseguer AS. Extinction in Phylogenetics and Biogeography: From Timetrees to Patterns of Biotic Assemblage. Front Genet 2016; 7:35. [PMID: 27047538 PMCID: PMC4802293 DOI: 10.3389/fgene.2016.00035] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 02/29/2016] [Indexed: 01/03/2023] Open
Abstract
Global climate change and its impact on biodiversity levels have made extinction a relevant topic in biological research. Yet, until recently, extinction has received less attention in macroevolutionary studies than speciation; the reason is the difficulty to infer an event that actually eliminates rather than creates new taxa. For example, in biogeography, extinction has often been seen as noise, introducing homoplasy in biogeographic relationships, rather than a pattern-generating process. The molecular revolution and the possibility to integrate time into phylogenetic reconstructions have allowed studying extinction under different perspectives. Here, we review phylogenetic (temporal) and biogeographic (spatial) approaches to the inference of extinction and the challenges this process poses for reconstructing evolutionary history. Specifically, we focus on the problem of discriminating between alternative high extinction scenarios using time trees with only extant taxa, and on the confounding effect introduced by asymmetric spatial extinction – different rates of extinction across areas – in biogeographic inference. Finally, we identify the most promising avenues of research in both fields, which include the integration of additional sources of evidence such as the fossil record or environmental information in birth–death models and biogeographic reconstructions, the development of new models that tie extinction rates to phenotypic or environmental variation, or the implementation within a Bayesian framework of parametric non-stationary biogeographic models.
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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
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