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D'Agostino A, Di Marco G, Rolfo MF, Alessandri L, Marvelli S, Braglia R, Congestri R, Berrilli F, Fuciarelli MF, Ferracci A, Canini A, Gismondi A. Microparticles from dental calculus disclose paleoenvironmental and palaeoecological records. Ecol Evol 2024; 14:e11053. [PMID: 38405407 PMCID: PMC10891416 DOI: 10.1002/ece3.11053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/27/2024] Open
Abstract
Plants have always represented a key element in landscape delineation. Indeed, plant diversity, whose distribution is influenced by geographic/climatic variability, has affected both environmental and human ecology. The present contribution represents a multi-proxy study focused on the detection of starch, pollen and non-pollen palynomorphs in ancient dental calculus collected from pre-historical individuals buried at La Sassa and Pila archaeological sites (Central Italy). The collected record suggested the potential use of plant taxa by the people living in Central Italy during the Copper-Middle Bronze Age and expanded the body of evidence reported by previous palynological and palaeoecological studies. The application of a microscopic approach provided information about domesticated crops and/or gathered wild plants and inferred considerations on ancient environments, water sources, and past health and diseases. Moreover, the research supplied data to define the natural resources (e.g., C4-plant intake) and the social use of the space during that period. Another important aspect was the finding of plant clues referable to woody habitats, characterised by broad-leaved deciduous taxa and generally indicative of a warm-temperate climate and grassy vegetation. Other unusual records (e.g., diatoms, brachysclereids) participated in defining the prehistoric ecological framework. Thus, this work provides an overview on the potential of the human dental calculus analysis to delineate some features of the ancient plant ecology and biodiversity.
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Affiliation(s)
- Alessia D'Agostino
- Laboratory of Botany, Department of Biology University of Rome Tor Vergata Rome Italy
- Present address: PhD Program in Evolutionary Biology and Ecology, Department of Biology University of Rome Tor Vergata Rome Italy
| | - Gabriele Di Marco
- Laboratory of Botany, Department of Biology University of Rome Tor Vergata Rome Italy
| | - Mario Federico Rolfo
- Department of History, Culture and Society University of Rome Tor Vergata Rome Italy
| | - Luca Alessandri
- Groningen Institute of Archaeology University of Groningen Groningen The Netherlands
| | - Silvia Marvelli
- Laboratory of Palynology and Archaeobotany-C.A.A. Giorgio Nicoli Bologna Italy
| | - Roberto Braglia
- Laboratory of Botany, Department of Biology University of Rome Tor Vergata Rome Italy
| | - Roberta Congestri
- Laboratory of Biology of the Algae, Department of Biology University of Rome Tor Vergata Rome Italy
| | - Federica Berrilli
- Department of Clinical Sciences and Translational Medicine University of Rome Tor Vergata Rome Italy
| | | | - Angelica Ferracci
- Department of History, Culture and Society University of Rome Tor Vergata Rome Italy
| | - Antonella Canini
- Laboratory of Botany, Department of Biology University of Rome Tor Vergata Rome Italy
| | - Angelo Gismondi
- Laboratory of Botany, Department of Biology University of Rome Tor Vergata Rome Italy
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Chen X, Li B, Zhang X. Comparison of chloroplast genomes and phylogenetic analysis of four species in Quercus section Cyclobalanopsis. Sci Rep 2023; 13:18731. [PMID: 37907468 PMCID: PMC10618267 DOI: 10.1038/s41598-023-45421-8] [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: 06/01/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023] Open
Abstract
The identification in Quercus L. species was considered to be difficult all the time. The fundamental phylogenies of Quercus have already been discussed by morphological and molecular means. However, the morphological characteristics of some Quercus groups may not be consistent with the molecular results (such as the group Helferiana), which may lead to blurring of species relationships and prevent further evolutionary researches. To understand the interspecific relationships and phylogenetic positions, we sequenced and assembled the CPGs (160,715 bp-160842 bp) of four Quercus section Cyclobalanopsis species by Illumina pair-end sequencing. The genomic structure, GC content, and IR/SC boundaries exhibited significant conservatism. Six highly variable hotspots were detected in comparison analysis, among which rpoC1, clpP and ycf1 could be used as molecular markers. Besides, two genes (petA, ycf2) were detected to be under positive selection pressure. The phylogenetic analysis showed: Trigonobalanus genus and Fagus genus located at the base of the phylogeny tree; The Quercus genus species were distincted to two clades, including five sections. All Compound Trichome Base species clustered into a single branch, which was in accordance with the results of the morphological studies. But neither of group Gilva nor group Helferiana had formed a monophyly. Six Compound Trichome Base species gathered together in pairs to form three branch respectively (Quercus kerrii and Quercus chungii; Quercus austrocochinchinensis with Quercus gilva; Quercus helferiana and Quercus rex). Due to a low support rate (0.338) in the phylogeny tree, the interspecies relationship between the two branches differentiated by this node remained unclear. We believe that Q. helferiana and Q. kerrii can exist as independent species due to their distance in the phylogeny tree. Our study provided genetic information in Quercus genus, which could be applied to further studies in taxonomy and phylogenetics.
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Affiliation(s)
- Xiaoli Chen
- College of Life Sciences, China West Normal University, Nanchong, 637009, China
| | - Buyu Li
- College of Life Sciences, China West Normal University, Nanchong, 637009, China
| | - Xuemei Zhang
- College of Life Sciences, China West Normal University, Nanchong, 637009, China.
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Denk T, Grimm GW, Hipp AL, Bouchal JM, Schulze ED, Simeone MC. Niche evolution in a northern temperate tree lineage: biogeographical legacies in cork oaks (Quercus section Cerris). ANNALS OF BOTANY 2023; 131:769-787. [PMID: 36805162 PMCID: PMC10184457 DOI: 10.1093/aob/mcad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/15/2023] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS Cork oaks (Quercus section Cerris) comprise 15 extant species in Eurasia. Despite being a small clade, they display a range of leaf morphologies comparable to the largest sections (>100 spp.) in Quercus. Their fossil record extends back to the Eocene. Here, we explore how cork oaks achieved their modern ranges and how legacy effects might explain niche evolution in modern species of section Cerris and its sister section Ilex, the holly oaks. METHODS We inferred a dated phylogeny for cork and holly oaks using a reduced-representation next-generation sequencing method, restriction site-associated DNA sequencing (RAD-seq), and used D-statistics to investigate gene flow hypotheses. We estimated divergence times using a fossilized birth-death model calibrated with 47 fossils. We used Köppen profiles, selected bioclimatic parameters and forest biomes occupied by modern species to infer ancestral climatic and biotic niches. KEY RESULTS East Asian and Western Eurasian cork oaks diverged initially in the Eocene. Subsequently, four Western Eurasian lineages (subsections) differentiated during the Oligocene and Miocene. Evolution of leaf size, form and texture was correlated, in part, with multiple transitions from ancestral humid temperate climates to mediterranean, arid and continental climates. Distantly related but ecologically similar species converged on similar leaf traits in the process. CONCLUSIONS Originating in temperate (frost-free) biomes, Eocene to Oligocene ranges of the primarily deciduous cork oaks were restricted to higher latitudes (Siberia to north of Paratethys). Members of the evergreen holly oaks (section Ilex) also originated in temperate biomes but migrated southwards and south-westwards into then-(sub)tropical southern China and south-eastern Tibet during the Eocene, then westwards along existing pre-Himalayan mountain ranges. Divergent biogeographical histories and deep-time phylogenetic legacies (in cold and drought tolerance, nutrient storage and fire resistance) thus account for the modern species mosaic of Western Eurasian oak communities, which are composed of oaks belonging to four sections.
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Affiliation(s)
- Thomas Denk
- Department of Palaeobiology, Swedish Museum of Natural History, 10405 Stockholm, Sweden
| | | | | | - Johannes M Bouchal
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
| | | | - Marco C Simeone
- Department of Agricultural and Forestry Sciences, University of Tuscia, 01100 Viterbo, Italy
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D'Agostino A, Di Marco G, Marvelli S, Marchesini M, Rizzoli E, Rolfo MF, Canini A, Gismondi A. Neolithic dental calculi provide evidence for environmental proxies and consumption of wild edible fruits and herbs in central Apennines. Commun Biol 2022; 5:1384. [PMID: 36536113 PMCID: PMC9763411 DOI: 10.1038/s42003-022-04354-0] [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: 08/16/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Looking for a biological fingerprint relative to new aspects of the relationship between humans and natural environment during prehistoric times is challenging. Although many issues still need to be addressed in terms of authentication and identification, microparticles hidden in ancient dental calculus can provide interesting information for bridging this gap of knowledge. Here, we show evidence about the role of edible plants for the early Neolithic individuals in the central Apennines of the Italian peninsula and relative cultural landscape. Dental calculi from human and animal specimens exhumed at Grotta Mora Cavorso (Lazio), one of the largest prehistoric burial deposits, have returned an archaeobotanical record made up of several types of palaeoecological proxies. The organic fraction of this matrix was investigated by a multidisciplinary approach, whose novelty consisted in the application of next generation sequencing to ancient plant DNA fragments, specifically codifying for maturase K barcode gene. Panicoideae and Triticeae starches, together with genetic indicators of Rosaceae fruits, figs, and Lamiaceae herbs, suggested subsistence practices most likely still based on wild plant resources. On the other hand, pollen, and non-pollen palynomorphs allowed us to outline a general vegetational framework dominated by woodland patches alternated with meadows, where semi-permanent settlements could have been established.
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Affiliation(s)
- Alessia D'Agostino
- PhD Program in Evolutionary Biology and Ecology, Department of Biology, University of Rome Tor Vergata, Rome, Italy
- Laboratory of Botany, Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Gabriele Di Marco
- Laboratory of Botany, Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Silvia Marvelli
- Laboratorio di Palinologia e Archeobotanica-C.A.A. Giorgio Nicoli, San Giovanni in Persiceto, Bologna, Italy
| | - Marco Marchesini
- Laboratorio di Palinologia e Archeobotanica-C.A.A. Giorgio Nicoli, San Giovanni in Persiceto, Bologna, Italy
| | - Elisabetta Rizzoli
- Laboratorio di Palinologia e Archeobotanica-C.A.A. Giorgio Nicoli, San Giovanni in Persiceto, Bologna, Italy
| | - Mario Federico Rolfo
- Department of History, Culture and Society, University of Rome "Tor Vergata", Rome, Italy
| | - Antonella Canini
- Laboratory of Botany, Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Angelo Gismondi
- Laboratory of Botany, Department of Biology, University of Rome "Tor Vergata", Rome, Italy.
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Chao CT, Kuo CC, Chang JT, Chai MW, Liao PC. Evolution of floral characters and biogeography of Heloniadeae (Melanthiaceae): an example of breeding system shifts with inflorescence change. Sci Rep 2021; 11:21494. [PMID: 34728750 PMCID: PMC8563777 DOI: 10.1038/s41598-021-01049-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/08/2021] [Indexed: 11/09/2022] Open
Abstract
Heloniadeae (Melanthiaceae) presents an East Asia–North America disjunct distribution. Different molecular and morphological data nevertheless support the tribe as a monophyletic group. However, their phylogenetic relationships and biogeographic history, together with the character evolution, are not clear. Therefore, we constructed a Bayesian phylogenetic tree for Heloniadeae using cpDNA and inferred the historical biogeography and floral character evolution. The results revealed that Heloniadeae was distributed in high-latitudes of East Asia and North America, originating since 22.2 mya. The East Asia clade migrated into southwest China, and subsequently colonized the Korean Peninsula, Taiwan, the Ryukyus, and spread northward to Japan and southern Sakhalin. The evolution of the inflorescence and number of flowers were phylogenetically conserved, associated with the historical biogeography of Heloniadeae. The inflorescences transferred from raceme to sub-umbel, and the number of flowers decreased during the dispersal process, which may be accompanied by changes in the breeding system. Besides, the anthesis period was more affected by the habitat environment than phylogenetic constraints. The flowering temperature of Heloniadeae was below 20 °C in most species, except H. kawanoi. Such a low temperature might not be conductive to pollinator activities, but it could be compensated by sustaining seed production with long-lasting flowers.
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Affiliation(s)
- Chien-Ti Chao
- School of Life Science, National Taiwan Normal University, No. 88, Tingchou Rd. Section 4, Wenshan District, Taipei City, 116, Taiwan.
| | - Chu-Chia Kuo
- Department of Biological Resources, National Chiayi University, No. 300, Hsuehfu Rd., Chiayi City, Chiayi County, 600, Taiwan
| | - Jui-Tse Chang
- School of Life Science, National Taiwan Normal University, No. 88, Tingchou Rd. Section 4, Wenshan District, Taipei City, 116, Taiwan
| | - Min-Wei Chai
- School of Life Science, National Taiwan Normal University, No. 88, Tingchou Rd. Section 4, Wenshan District, Taipei City, 116, Taiwan
| | - Pei-Chun Liao
- School of Life Science, National Taiwan Normal University, No. 88, Tingchou Rd. Section 4, Wenshan District, Taipei City, 116, Taiwan.
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Maslova NP, Karasev EV, Xu SL, Spicer RA, Liu XY, Kodrul TM, Spicer TEV, Jin JH. Variations in morphological and epidermal features of shade and sun leaves of two species: Quercus bambusifolia and Q. myrsinifolia. AMERICAN JOURNAL OF BOTANY 2021; 108:1441-1463. [PMID: 34431508 DOI: 10.1002/ajb2.1706] [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: 07/26/2020] [Accepted: 02/09/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Microclimatic differences between the periphery and the interior of tree crowns result in a variety of adaptive leaf macromorphological and anatomical features. Our research was designed to reveal criteria for sun/shade leaf identification in two species of evergreen oaks, applicable to both modern and fossil leaves. We compared our results with those in other species similarly studied. METHODS For both Quercus bambusifolia and Q. myrsinifolia (section Cyclobalanopsis), leaves from single mature trees with well-developed crowns were collected in the South China Botanical Garden, Guangzhou, China. We focus on leaf characters often preserved in fossil material. SVGm software was used for macromorphological measurement. Quantitative analyses were performed and box plots generated using R software with IDE Rstudio. Leaf cuticles were prepared using traditional botanical techniques. RESULTS Principal characters for distinguishing shade and sun leaves in the studied oaks were identified as leaf lamina length to width ratio (L/W), and the degree of development of venation networks. For Q. myrsinifolia, shade and sun leaves differ in tooth morphology and the ratio of toothed lamina length to overall lamina length. The main epidermal characters are ordinary cell size and anticlinal wall outlines. For both species, plasticity within shade leaves exceeds that of sun leaves. CONCLUSIONS Morphological responses to sun and shade in the examined oaks are similar to those in other plant genera, pointing to useful generalizations for recognizing common foliar polymorphisms that must be taken into account when determining the taxonomic position of both modern and fossil plants.
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Affiliation(s)
- Natalia P Maslova
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Borissiak Paleontological Institute, Russian Academy of Sciences, Moscow, 117647, Russia
| | - Eugeny V Karasev
- Borissiak Paleontological Institute, Russian Academy of Sciences, Moscow, 117647, Russia
- Kazan Federal University, Kazan, Respublika Tatarstan, 420000, Russia
| | - Sheng-Lan Xu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Robert A Spicer
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
- School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, MK7 6AA, UK
| | - Xiao-Yan Liu
- School of Geography, South China Normal University, Guangzhou, 510631, China
| | - Tatiana M Kodrul
- Geological Institute, Russian Academy of Sciences, Moscow, 119017, Russia
| | - Teresa E V Spicer
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Jian-Hua Jin
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
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Denk T, Bouchal JM. New Fagaceous pollen taxa from the Miocene Søby flora of Denmark and their biogeographic implications. AMERICAN JOURNAL OF BOTANY 2021; 108:1500-1524. [PMID: 34458984 DOI: 10.1002/ajb2.1716] [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: 09/24/2020] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The Fagaceae comprise around 1000 tree species in the Northern Hemisphere. Despite an extensive fossil pollen record, reconstructing biogeographic patterns is hampered because it is difficult to achieve good taxonomic resolution with light microscopy alone. We investigate dispersed pollen of Fagaceae from the Miocene Søby flora, Denmark. We explore the latitudinal gradient in Fagaceae distribution during the Miocene Climatic Optimum (MCO) in Europe and the Northern Hemisphere to compare it with the Eocene Warmhouse and the present. METHODS We investigated dispersed pollen using light and scanning electron microscopy. We assessed biogeographic patterns in Fagaceae during two warm periods in Earth history (MCO, Eocene) and the present. RESULTS Eight species of Fagaceae were recognized in the Søby flora. Of these, Fagus had a continuous Mediterranean to subarctic distribution during MCO; Quercus sect. Cerris and castaneoids had northern limits in Denmark, and evergreen Quercus sect. Ilex in Central Europe. In a northern hemispheric context, Fagus and sections of Quercus had more northerly distribution limits during Eocene and MCO with maximum northward extensions during Eocene (Fagus, castaneoids) or Oligo-Miocene (Quercus sects. Cerris and Ilex). The known distribution of the extinct Tricolporopollenites theacoides during MCO included Central Europe and East China, while this taxon thrived in South China during Eocene. CONCLUSIONS More northerly distributions during MCO and Eocene probably were determined by temperature. In contrast, fossil occurrences in areas that are arid or semi-humid today were determined by maritime conditions in these areas (western North America, Central Asia) during the Cenozoic.
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Affiliation(s)
- Thomas Denk
- Department of Paleobiology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Johannes M Bouchal
- Aerobiology and Pollen Information, Medical University of Vienna, Vienna, Austria
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8
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Environmental implications and evidence of natural products from dental calculi of a Neolithic-Chalcolithic community (central Italy). Sci Rep 2021; 11:10665. [PMID: 34021220 PMCID: PMC8140145 DOI: 10.1038/s41598-021-89999-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/05/2021] [Indexed: 02/04/2023] Open
Abstract
In this contribution, we investigated the role of plants in the prehistoric community of Casale del Dolce (Anagni, FR, central Italy), through microparticles recovered from dental calculus. The finding of a great amount of pollen types, even in form of compact lumps, could indicate use of natural substances, such as honeybee products and/or conifer resins. This plant-microremain record also suggested environmental implications relative to the Neolithic and Chalcolithic period. Additionally, the stability of the tartar microenvironment had preserved starches and other microparticles, such as one epidermal trichome, a sporangium, and fragments of plant tissue, rarely detected in ancient dental calculus. The detection of secondary metabolites in the ancient matrix confirmed the familiarity of this community with plant resources. All these data supply various interesting food for thought and expand the knowledge about the potential of dental calculus in archaeological and archaeobotanical fields with a special focus on palaeoecology.
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Alonso-Forn D, Peguero-Pina JJ, Ferrio JP, Mencuccini M, Mendoza-Herrer Ó, Sancho-Knapik D, Gil-Pelegrín E. Contrasting functional strategies following severe drought in two Mediterranean oaks with different leaf habit: Quercus faginea and Quercus ilex subsp. rotundifolia. TREE PHYSIOLOGY 2021; 41:371-387. [PMID: 33079165 DOI: 10.1093/treephys/tpaa135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/04/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
Nowadays, evergreen sclerophyllous and winter-deciduous malacophyllous oaks with different paleogeographical origins coexist under Mediterranean-type climates, such as the mixed forests of the evergreen Quercus ilex subsp. rotundifolia Lam. and the winter-deciduous Quercus faginea Lam. Both Mediterranean oaks constitute two examples of contrasting leaf habit, so it could be expected that they would have different functional strategies to cope with summer drought. In this study, we analysed photosynthetic, photochemical and hydraulic traits of different organs for Q. faginea and Q. ilex subsp. rotundifolia under well-watered conditions and subjected to very severe drought. The coordinated response between photosynthetic and hydraulic traits explained the higher photosynthetic capacity of Q. faginea under well-watered conditions, which compensated its shorter leaf life span at the expense of higher water consumption. The progressive imposition of water stress evidenced that both types of Mediterranean oaks displayed different functional strategies to cope with water limitations. Specifically, the decrease in mesophyll conductance associated with edaphic drought seems to be the main factor explaining the differences found in the dynamics of net CO2 assimilation throughout the drought period. The sharp decline in photosynthetic traits of Q. faginea was coupled with a strong decrease in shoot hydraulic conductance in response to drought. This fact probably avoided extensive xylem embolism in the stems (i.e., 'vulnerability segmentation'), which enabled new leaf development after drought period in Q. faginea. By contrast, leaves of Q. ilex subsp. rotundifolia showed effective photoprotective mechanisms and high resistance to drought-induced cavitation, which would be related with the longer leaf life span of the evergreen Mediterranean oaks. The co-occurrence of both types of Mediterranean oaks could be related to edaphic conditions that ensure the maintenance of soil water potential above critical values for Q. faginea, which can be severely affected by soil degradation and climate change.
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Affiliation(s)
- David Alonso-Forn
- Unidad de Recursos Forestales, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda Montañana 930, 50059, Zaragoza, Spain
| | - José Javier Peguero-Pina
- Unidad de Recursos Forestales, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda Montañana 930, 50059, Zaragoza, Spain
- Instituto Agroalimentario de Aragón -IA2-(CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Juan Pedro Ferrio
- Unidad de Recursos Forestales, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda Montañana 930, 50059, Zaragoza, Spain
- Aragon Agency for Research and Development (ARAID), E-50018 Zaragoza, Spain
| | - Maurizio Mencuccini
- Centre de Recerca Ecològica i Aplicacions Forestals (CREAF), Campus UAB, Cerdanyola del Vallés, 08193 Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain
| | - Óscar Mendoza-Herrer
- Unidad de Recursos Forestales, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda Montañana 930, 50059, Zaragoza, Spain
| | - Domingo Sancho-Knapik
- Unidad de Recursos Forestales, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda Montañana 930, 50059, Zaragoza, Spain
- Instituto Agroalimentario de Aragón -IA2-(CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Eustaquio Gil-Pelegrín
- Unidad de Recursos Forestales, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda Montañana 930, 50059, Zaragoza, Spain
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10
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Hipp AL, Manos PS, Hahn M, Avishai M, Bodénès C, Cavender-Bares J, Crowl AA, Deng M, Denk T, Fitz-Gibbon S, Gailing O, González-Elizondo MS, González-Rodríguez A, Grimm GW, Jiang XL, Kremer A, Lesur I, McVay JD, Plomion C, Rodríguez-Correa H, Schulze ED, Simeone MC, Sork VL, Valencia-Avalos S. Genomic landscape of the global oak phylogeny. THE NEW PHYTOLOGIST 2020; 226:1198-1212. [PMID: 31609470 DOI: 10.1111/nph.16162] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/05/2019] [Indexed: 05/10/2023]
Abstract
The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny. We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing nearly 250 Quercus species to infer a time-calibrated phylogeny of the world's oaks. We use a reversible-jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20 000 RAD-seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny. Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity. The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.
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Affiliation(s)
- Andrew L Hipp
- The Morton Arboretum, Lisle, IL, 60532-1293, USA
- The Field Museum, Chicago, IL, 60605, USA
| | | | - Marlene Hahn
- The Morton Arboretum, Lisle, IL, 60532-1293, USA
| | - Michael Avishai
- Previously of, The Hebrew University of Jerusalem, Botanical Garden, Zalman Shne'ur St. 1, Jerusalem, Israel
| | | | | | | | - Min Deng
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Thomas Denk
- Swedish Museum of Natural History, Stockholm, 10405, Sweden
| | | | - Oliver Gailing
- Büsgen-Institute, Georg-August-University Göttingen, Göttingen, D-37077, Germany
| | | | - Antonio González-Rodríguez
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, 58190, México
| | | | - Xiao-Long Jiang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, 201602, China
| | | | | | | | | | - Hernando Rodríguez-Correa
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, 58190, México
| | - Ernst-Detlef Schulze
- Max Planck Institute for Biogeochemistry, Hans-Knoell-Str. 10, Jena, 07745, Germany
| | | | - Victoria L Sork
- University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Susana Valencia-Avalos
- Herbario de la Facultad de Ciencias, Departamento de Biología Comparada, Universidad Nacional Autónoma de México, Circuito Exterior, s.n., Ciudad Universitaria, Coyoacán, México City, CP 04510, México
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11
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Grímsson F, Bouchal JM, Xafis A, Zetter R. Combined LM and SEM study of the middle Miocene (Sarmatian) palynoflora from the Lavanttal Basin, Austria: Part V. Magnoliophyta 3 - Myrtales to Ericales. GRANA 2020; 59:127-193. [PMID: 32406427 DOI: 10.1080/00173134.2011.585804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/09/2019] [Indexed: 05/26/2023]
Abstract
The continued investigation of the middle Miocene palynoflora from the Lavanttal Basin reveals numerous additional angiosperm taxa. The Myrtales to Ericales pollen record documented here comprises 46 different taxa belonging to Onagraceae (Ludwigia), Ericaceae (Craigia, Reevesia, Tilia), Anacardiaceae (Pistacia), Rutaceae (Zanthoxylum), Sapindaceae (Acer), Santalaceae (Arceuthobium), Amaranthaceae, Caryophyllaceae, Polygonaceae (Persicaria, Rumex), Cornaceae (Alangium, Cornus, Nyssa), Ebenaceae (Diospyros), Ericaceae (Andromeda, Arbutus, Empetrum, Erica), Sapotaceae (Pouteria, Sideroxylon), Styracaceae (Rehderodendron) and Symplocaceae (Symplocos). Köppen signatures of potential modern analogues of the additional fossil woody elements confirm the hypothesis of a subtropical (Cfa, Cwa) climate at lower elevations and subsequent transition into a temperate climate with altitudinal succession (Cfa → Cfb/Dfa → Dfb; Cwa → Cwb → Dwb-climate). The fossil plants represent different vegetation units, from wetland lowlands to well-drained montane forests. Many of the fossil taxa have potential modern analogues that can be classified as nemoral and/or meridio-nemoral and/or semihumid-meridional vegetation elements. New is the recognition of oreotropical elements, which are direct indicators for a substantial altitudinal gradient.
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Affiliation(s)
- Friđgeir Grímsson
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Johannes M Bouchal
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Alexandros Xafis
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Reinhard Zetter
- Department of Palaeontology, University of Vienna, Vienna, Austria
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12
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Grímsson F, Bouchal JM, Xafis A, Zetter R. Combined LM and SEM study of the middle Miocene (Sarmatian) palynoflora from the Lavanttal Basin, Austria: Part V. Magnoliophyta 3 - Myrtales to Ericales. GRANA 2020; 59:127-193. [PMID: 32406427 PMCID: PMC7195176 DOI: 10.1080/00173134.2019.1696400] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/09/2019] [Indexed: 06/11/2023]
Abstract
The continued investigation of the middle Miocene palynoflora from the Lavanttal Basin reveals numerous additional angiosperm taxa. The Myrtales to Ericales pollen record documented here comprises 46 different taxa belonging to Onagraceae (Ludwigia), Ericaceae (Craigia, Reevesia, Tilia), Anacardiaceae (Pistacia), Rutaceae (Zanthoxylum), Sapindaceae (Acer), Santalaceae (Arceuthobium), Amaranthaceae, Caryophyllaceae, Polygonaceae (Persicaria, Rumex), Cornaceae (Alangium, Cornus, Nyssa), Ebenaceae (Diospyros), Ericaceae (Andromeda, Arbutus, Empetrum, Erica), Sapotaceae (Pouteria, Sideroxylon), Styracaceae (Rehderodendron) and Symplocaceae (Symplocos). Köppen signatures of potential modern analogues of the additional fossil woody elements confirm the hypothesis of a subtropical (Cfa, Cwa) climate at lower elevations and subsequent transition into a temperate climate with altitudinal succession (Cfa → Cfb/Dfa → Dfb; Cwa → Cwb → Dwb-climate). The fossil plants represent different vegetation units, from wetland lowlands to well-drained montane forests. Many of the fossil taxa have potential modern analogues that can be classified as nemoral and/or meridio-nemoral and/or semihumid-meridional vegetation elements. New is the recognition of oreotropical elements, which are direct indicators for a substantial altitudinal gradient.
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Affiliation(s)
- Friđgeir Grímsson
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Johannes M. Bouchal
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Alexandros Xafis
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Reinhard Zetter
- Department of Palaeontology, University of Vienna, Vienna, Austria
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13
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Grímsson F, Bouchal JM, Xafis A, Zetter R. Combined LM and SEM study of the middle Miocene (Sarmatian) palynoflora from the Lavanttal Basin, Austria: Part V. Magnoliophyta 3 - Myrtales to Ericales. GRANA 2020; 59:127-193. [PMID: 32406427 DOI: 10.1080/00173134.2011.641450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/09/2019] [Indexed: 05/26/2023]
Abstract
The continued investigation of the middle Miocene palynoflora from the Lavanttal Basin reveals numerous additional angiosperm taxa. The Myrtales to Ericales pollen record documented here comprises 46 different taxa belonging to Onagraceae (Ludwigia), Ericaceae (Craigia, Reevesia, Tilia), Anacardiaceae (Pistacia), Rutaceae (Zanthoxylum), Sapindaceae (Acer), Santalaceae (Arceuthobium), Amaranthaceae, Caryophyllaceae, Polygonaceae (Persicaria, Rumex), Cornaceae (Alangium, Cornus, Nyssa), Ebenaceae (Diospyros), Ericaceae (Andromeda, Arbutus, Empetrum, Erica), Sapotaceae (Pouteria, Sideroxylon), Styracaceae (Rehderodendron) and Symplocaceae (Symplocos). Köppen signatures of potential modern analogues of the additional fossil woody elements confirm the hypothesis of a subtropical (Cfa, Cwa) climate at lower elevations and subsequent transition into a temperate climate with altitudinal succession (Cfa → Cfb/Dfa → Dfb; Cwa → Cwb → Dwb-climate). The fossil plants represent different vegetation units, from wetland lowlands to well-drained montane forests. Many of the fossil taxa have potential modern analogues that can be classified as nemoral and/or meridio-nemoral and/or semihumid-meridional vegetation elements. New is the recognition of oreotropical elements, which are direct indicators for a substantial altitudinal gradient.
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Affiliation(s)
- Friđgeir Grímsson
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Johannes M Bouchal
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Alexandros Xafis
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Reinhard Zetter
- Department of Palaeontology, University of Vienna, Vienna, Austria
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14
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Sadowski EM, Hammel JU, Denk T. Synchrotron X-ray imaging of a dichasium cupule of Castanopsis from Eocene Baltic amber. AMERICAN JOURNAL OF BOTANY 2018; 105:2025-2036. [PMID: 30548995 DOI: 10.1002/ajb2.1202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/06/2018] [Indexed: 06/09/2023]
Abstract
PREMISE OF THE STUDY The Eocene Baltic amber deposit represents the largest accumulation of fossil resin worldwide, and hundreds of thousands of entrapped arthropods have been recovered. Although Baltic amber preserves delicate plant structures in high fidelity, angiosperms of the "Baltic amber forest" remain poorly studied. We describe a pistillate partial inflorescence of Castanopsis (Fagaceae), expanding the knowledge of Fagaceae diversity from Baltic amber. METHODS The amber specimen was investigated using light microscopy and synchrotron-radiation-based X-ray micro-computed tomography (SRμCT). KEY RESULTS The partial inflorescence is a cymule, consisting of an involucre of scales that surround all four pistillate flowers, indicating a dichasium cupule. Subtending bracts are basally covered with peltate trichomes. Flowers possess an urecolate perianth of six nearly free lobes, 12 staminodia hidden by the perianth, and a tri-locular ovary that is convex-triangular in cross section. The exceptional three-dimensional preservation suggests that the fossil belongs to the extant East Asian genus Castanopsis. The amber inclusion represents the first record of Castanopsis from Baltic amber and the first pistillate inflorescence of Fagaceae from Eurasia. CONCLUSIONS The partial female inflorescence reported here provides an important addition to acorns of Castanopsis described from middle Eocene strata of Europe. Furthermore, the intercontinental distribution of Castanopsis in the Eocene is confirmed. The amber fossil also broadens the picture of the Baltic amber source area, indicating oligotrophic, sandy, bog-like habitats. Finally, this study underscores the great benefit of SRμCT as a powerful tool to investigate plant inclusions from amber in a nondestructive way.
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Affiliation(s)
- Eva-Maria Sadowski
- Department of Geobiology, University of Göttingen, Goldschmidtstraße 3, Göttingen, 37077, Germany
| | - Jörg U Hammel
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht, Max-Planck-Str. 1, 21502, Geesthacht, Germany
| | - Thomas Denk
- Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden
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15
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Yin K, Zhang Y, Li Y, Du FK. Different Natural Selection Pressures on the atpF Gene in Evergreen Sclerophyllous and Deciduous Oak Species: Evidence from Comparative Analysis of the Complete Chloroplast Genome of Quercus aquifolioides with Other Oak Species. Int J Mol Sci 2018; 19:E1042. [PMID: 29601535 PMCID: PMC5979438 DOI: 10.3390/ijms19041042] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 11/23/2022] Open
Abstract
Quercus is an economically important and phylogenetically complex genus in the family Fagaceae. Due to extensive hybridization and introgression, it is considered to be one of the most challenging plant taxa, both taxonomically and phylogenetically. Quercus aquifolioides is an evergreen sclerophyllous oak species that is endemic to, but widely distributed across, the Hengduanshan Biodiversity Hotspot in the Eastern Himalayas. Here, we compared the fully assembled chloroplast (cp) genome of Q. aquifolioides with those of three closely related species. The analysis revealed a cp genome ranging in size from 160,415 to 161,304 bp and with a typical quadripartite structure, composed of two inverted repeats (IRs) separated by a small single copy (SSC) and a large single copy (LSC) region. The genome organization, gene number, gene order, and GC content of these four Quercus cp genomes are similar to those of many angiosperm cp genomes. We also analyzed the Q. aquifolioides repeats and microsatellites. Investigating the effects of selection events on shared protein-coding genes using the Ka/Ks ratio showed that significant positive selection had acted on the atpF gene of Q. aquifolioides compared to two deciduous oak species, and that there had been significant purifying selection on the atpF gene in the chloroplast of evergreen sclerophyllous oak trees. In addition, site-specific selection analysis identified positively selected sites in 12 genes. Phylogenetic analysis based on shared protein-coding genes from 14 species defined Q. aquifolioides as belonging to sect. Heterobalanus and being closely related to Q. rubra and Q. aliena. Our findings provide valuable genetic information for use in accurately identifying species, resolving taxonomy, and reconstructing the phylogeny of the genus Quercus.
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Affiliation(s)
- Kangquan Yin
- College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Yue Zhang
- College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Yuejuan Li
- College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Fang K Du
- College of Forestry, Beijing Forestry University, Beijing 100083, China.
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16
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Yang Y, Zhu J, Feng L, Zhou T, Bai G, Yang J, Zhao G. Plastid Genome Comparative and Phylogenetic Analyses of the Key Genera in Fagaceae: Highlighting the Effect of Codon Composition Bias in Phylogenetic Inference. FRONTIERS IN PLANT SCIENCE 2018; 9:82. [PMID: 29449857 PMCID: PMC5800003 DOI: 10.3389/fpls.2018.00082] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/15/2018] [Indexed: 05/10/2023]
Abstract
Fagaceae is one of the largest and economically important taxa within Fagales. Considering the incongruence among inferences from plastid and nuclear genes in the previous Fagaceae phylogeny studies, we assess the performance of plastid phylogenomics in this complex family. We sequenced and assembled four complete plastid genomes (Fagus engleriana, Quercus spinosa, Quercus aquifolioides, and Quercus glauca) using reference-guided assembly approach. All of the other 12 published plastid genomes in Fagaceae were retrieved for genomic analyses (including repeats, sequence divergence and codon usage) and phylogenetic inference. The genomic analyses reveal that plastid genomes in Fagaceae are conserved. Comparing the phylogenetic relationships of the key genera in Fagaceae inferred from different codon positions and gene function datasets, we found that the first two codon sites dataset recovered nearly all relationships and received high support. Thus, the result suggested that codon composition bias had great influence on Fagaceae phylogenetic inference. Our study not only provides basic understanding of Fagaceae plastid genomes, but also illuminates the effectiveness of plastid phylogenomics in resolving relationships of this intractable family.
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Affiliation(s)
- Yanci Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China
| | - Juan Zhu
- Middle School of Xi'an Electronic Science and Technology, Xi'an, China
| | - Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Guoqing Bai
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Xi'an, China
| | - Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China
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17
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Hipp AL, Manos PS, González-Rodríguez A, Hahn M, Kaproth M, McVay JD, Avalos SV, Cavender-Bares J. Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity. THE NEW PHYTOLOGIST 2018; 217:439-452. [PMID: 28921530 DOI: 10.1111/nph.14773] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 07/29/2017] [Indexed: 05/21/2023]
Abstract
Oaks (Quercus, Fagaceae) are the dominant tree genus of North America in species number and biomass, and Mexico is a global center of oak diversity. Understanding the origins of oak diversity is key to understanding biodiversity of northern temperate forests. A phylogenetic study of biogeography, niche evolution and diversification patterns in Quercus was performed using 300 samples, 146 species. Next-generation sequencing data were generated using the restriction-site associated DNA (RAD-seq) method. A time-calibrated maximum likelihood phylogeny was inferred and analyzed with bioclimatic, soils, and leaf habit data to reconstruct the biogeographic and evolutionary history of the American oaks. Our highly resolved phylogeny demonstrates sympatric parallel diversification in climatic niche, leaf habit, and diversification rates. The two major American oak clades arose in what is now the boreal zone and radiated, in parallel, from eastern North America into Mexico and Central America. Oaks adapted rapidly to niche transitions. The Mexican oaks are particularly numerous, not because Mexico is a center of origin, but because of high rates of lineage diversification associated with high rates of evolution along moisture gradients and between the evergreen and deciduous leaf habits. Sympatric parallel diversification in the oaks has shaped the diversity of North American forests.
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Affiliation(s)
- Andrew L Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
- The Field Museum, 1400 S Lake Shore Drive, Chicago, IL, 60605, USA
| | | | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No. 8701, Col. Ex Hacienda de Sán José de la Huerta, Morelia, Michoacán, 58190, México
| | - Marlene Hahn
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
| | - Matthew Kaproth
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
- Department of Biological Sciences, Minnesota State University, Mankato, MN 56001, USA
| | | | - Susana Valencia Avalos
- Herbario de la Facultad de Ciencias, Departamento de Biología Comparada, Universidad Nacional Autónoma de México, Circuito Exterior, s.n., Ciudad Universitaria, Coyoacán, CP, 04510, México City, México
| | - Jeannine Cavender-Bares
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
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18
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Grímsson F, Grimm GW, Zetter R. Tiny pollen grains: first evidence of Saururaceae from the Late Cretaceous of western North America. PeerJ 2017; 5:e3434. [PMID: 28626610 PMCID: PMC5472062 DOI: 10.7717/peerj.3434] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/17/2017] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The Saururaceae, a very small family of Piperales comprising only six species in four genera, have a relatively scanty fossil record outside of Europe. The phylogenetic relationships of the four genera to each other are resolved, with the type genus Saururus occurring in both eastern North America and East Asia. No extant species occurs in western Eurasia. The most exceptional find so far has been an inflorescence with in-situ pollen, Saururus tuckerae S.Y.Sm. & Stockey from Eocene of North America with strong affinities to extant species of Saururus. Recent dated trees suggest, however, an Eocene or younger crown age for the family. METHODS Dispersed fossil pollen grains from the Campanian (82-81 Ma) of North America are compared to dispersed pollen grains from the Eocene strata containing S. tuckerae, the Miocene of Europe, and extant members of the family using combined LM and SEM imaging. RESULTS The unambiguous fossil record of the Saururaceae is pushed back into the Campanian (82-81 Ma). Comparison with re-investigated pollen from the Eocene of North America, the Miocene of Europe, and modern species of the family shows that pollen morphology in Saururaceae is highly conservative, and remained largely unchanged for the last 80 million years. DISCUSSION Campanian pollen of Saururaceae precludes young (Eocene or younger) estimates for the Saururaceae root and crown age, but is in-line with maximum age scenarios. Saururus-type pollen appear to represent the primitive pollen morphology of the family. Often overlooked because of its small size, dispersed Saururaceae pollen may provide a unique opportunity to map the geographic history of a small but old group of Piperales, and should be searched for in Paleogene and Cretaceous sediment samples.
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Affiliation(s)
| | - Guido W Grimm
- Department of Palaeontology, University of Vienna, Vienna, Austria
- Unaffiliated, Orléans, France
| | - Reinhard Zetter
- Department of Palaeontology, University of Vienna, Vienna, Austria
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19
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Grímsson F, Kapli P, Hofmann CC, Zetter R, Grimm GW. Eocene Loranthaceae pollen pushes back divergence ages for major splits in the family. PeerJ 2017; 5:e3373. [PMID: 28607837 PMCID: PMC5466002 DOI: 10.7717/peerj.3373] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/04/2017] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND We revisit the palaeopalynological record of Loranthaceae, using pollen ornamentation to discriminate lineages and to test molecular dating estimates for the diversification of major lineages. METHODS Fossil Loranthaceae pollen from the Eocene and Oligocene are analysed and documented using scanning-electron microscopy. These fossils were associated with molecular-defined clades and used as minimum age constraints for Bayesian node dating using different topological scenarios. RESULTS The fossil Loranthaceae pollen document the presence of at least one extant root-parasitic lineage (Nuytsieae) and two currently aerial parasitic lineages (Psittacanthinae and Loranthinae) by the end of the Eocene in the Northern Hemisphere. Phases of increased lineage diversification (late Eocene, middle Miocene) coincide with global warm phases. DISCUSSION With the generation of molecular data becoming easier and less expensive every day, neontological research should re-focus on conserved morphologies that can be traced through the fossil record. The pollen, representing the male gametophytic generation of plants and often a taxonomic indicator, can be such a tracer. Analogously, palaeontological research should put more effort into diagnosing Cenozoic fossils with the aim of including them into modern systematic frameworks.
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Affiliation(s)
| | - Paschalia Kapli
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | | | - Reinhard Zetter
- Department of Palaeontology, University of Vienna, Wien, Austria
| | - Guido W. Grimm
- Department of Palaeontology, University of Vienna, Wien, Austria
- Orléans, France
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20
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Grímsson F, Grimm GW, Zetter R. Evolution of pollen morphology in Loranthaceae. GRANA 2017; 57:16-116. [PMID: 29386990 PMCID: PMC5771552 DOI: 10.1080/00173134.2016.1261939] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 10/04/2016] [Indexed: 05/30/2023]
Abstract
Earlier studies indicate a strong correlation of pollen morphology and ultrastructure with taxonomy in Loranthaceae. Using high-resolution light microscopy and scanning electron microscopy imaging of the same pollen grains, we document pollen types of 35 genera including 15 studied for the first time. Using a molecular phylogenetic framework based on currently available sequence data with good genus-coverage, we reconstruct trends in the evolution of Loranthaceae pollen and pinpoint traits of high diagnostic value, partly confirming earlier intuitive hypotheses based on morphological observations. We find that pollen morphology in Loranthaceae is strongly linked to phylogenetic relationships. Some pollen types are diagnostic for discrete genera or evolutionary lineages, opening the avenue to recruit dispersed fossil pollen as age constraints for dated phylogenies and as independent data for testing biogeographic scenarios; so far based exclusively on modern-day data. Correspondences and discrepancies between palynological and molecular data and current taxonomic/systematic concepts are identified and suggestions made for future palynological and molecular investigations of Loranthaceae.
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Affiliation(s)
| | - Guido W. Grimm
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Reinhard Zetter
- Department of Palaeontology, University of Vienna, Vienna, Austria
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21
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Grímsson F, Zetter R, Labandeira CC, Engel MS, Wappler T. Taxonomic description of in situ bee pollen from the middle Eocene of Germany. GRANA 2017; 56:37-70. [PMID: 28057943 PMCID: PMC5161302 DOI: 10.1080/00173134.2015.1108997] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/09/2015] [Indexed: 05/31/2023]
Abstract
The middle Eocene Messel and Eckfeld localities are renowned for their excellently preserved faunas and diverse floras. Here we describe for the first time pollen from insect-pollinated plants found in situ on well-preserved ancient bees using light and scanning electron microscopy. There have been 140 pollen types reported from Messel and 162 pollen types from Eckfeld. Here we document 23 pollen types, six from Messel and 18 from Eckfeld (one is shared). The taxa reported here are all pollinated by insects and mostly not recovered in the previously studied dispersed fossil pollen records. Typically, a single or two pollen types are found on each fossil bee specimen, the maximum number of distinct pollen types on a single individual is five. Only five of the 23 pollen types obtained are angiosperms of unknown affinity, the remainder cover a broad taxonomic range of angiosperm trees and include members of several major clades: monocots (1 pollen type), fabids (7), malvids (4), asterids (5) and other core eudicots (1). Seven types each can be assigned to individual genera or infrafamilial clades. Since bees visit only flowers in the relative vicinity of their habitat, the recovered pollen provides a unique insight into the autochthonous palaeo-flora. The coexistence of taxa such as Decodon, Elaeocarpus, Mortoniodendron and other Tilioideae, Mastixoideae, Olax, Pouteria and Nyssa confirms current views that diverse, thermophilic forests thrived at the Messel and Eckfeld localities, probably under a warm subtropical, fully humid climate. Our study calls for increased attention to pollen found in situ on pollen-harvesting insects such as bees, which can provide new insights on insect-pollinated plants and complement even detailed palaeo-palynological knowledge obtained mostly from pollen of wind-pollinated plants in the dispersed pollen record of sediments. In the case of Elaeocarpus, Mortoniodendron, Olax and Pouteria the pollen collected by the middle Eocene bees represent the earliest unambiguous records of their respective genera.
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Affiliation(s)
| | - Reinhard Zetter
- University of Vienna, Department of Palaeontology, Vienna, Austria
| | - Conrad C. Labandeira
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Entomology, University of Maryland, College Park, MD, USA
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Michael S. Engel
- Division of Entomology, Natural History Museum, University of Kansas, Lawrence, Kansas66045, USA
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
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22
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Renner SS, Grimm GW, Kapli P, Denk T. Species relationships and divergence times in beeches: new insights from the inclusion of 53 young and old fossils in a birth-death clock model. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150135. [PMID: 27325832 PMCID: PMC4920336 DOI: 10.1098/rstb.2015.0135] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2016] [Indexed: 11/12/2022] Open
Abstract
The fossilized birth-death (FBD) model can make use of information contained in multiple fossils representing the same clade, and we here apply this model to infer divergence times in beeches (genus Fagus), using 53 fossils and nuclear sequences for all nine species. We also apply FBD dating to the fern clade Osmundaceae, with about 12 living species and 36 fossils. Fagus nuclear sequences cannot be aligned with those of other Fagaceae, and we therefore use Bayes factors to choose among alternative root positions. The crown group of Fagus is dated to 53 (62-43) Ma; divergence of the sole American species to 44 (51-39) Ma and divergence between Central European F. sylvatica and Eastern Mediterranean F. orientalis to 8.7 (20-1.8) Ma, unexpectedly old. The FBD model can accommodate fossils as sampled ancestors or as extinct or unobserved lineages; however, this makes its raw output, which shows all fossils on short or long branches, problematic to interpret. We use hand-drawn depictions and a bipartition network to illustrate the uncertain placements of fossils. Inferred speciation and extinction rates imply approximately 5× higher evolutionary turnover in Fagus than in Osmundaceae, fitting a hypothesized low turnover in plants adapted to low-nutrient conditions.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
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Affiliation(s)
- S S Renner
- Systematic Botany and Mycology, University of Munich, Menzinger Street 67, 80638 Munich, Germany
| | - Guido W Grimm
- Department of Palaeontology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Paschalia Kapli
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, 68159 Heidelberg, Germany
| | - Thomas Denk
- Department of Palaeobiology, Swedish Museum of Natural History, Svante Arrhenius Väg 9, 10405 Stockholm, Sweden
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Simeone MC, Grimm GW, Papini A, Vessella F, Cardoni S, Tordoni E, Piredda R, Franc A, Denk T. Plastome data reveal multiple geographic origins of Quercus Group Ilex. PeerJ 2016; 4:e1897. [PMID: 27123376 PMCID: PMC4846808 DOI: 10.7717/peerj.1897] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 03/15/2016] [Indexed: 01/27/2023] Open
Abstract
Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One major exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilex L., Q. coccifera L., Q. aucheri Jaub. & Spach., Q. alnifolia Poech.) was explored at three chloroplast markers (rbcL, trnK/matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing all Quercus subgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. High plastid divergence in members of Quercus Group Ilex, including haplotypes shared with related, but long isolated oak lineages, point towards multiple geographic origins of this group of oaks. The results suggest that incomplete lineage sorting and repeated phases of asymmetrical introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split within Quercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.
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Affiliation(s)
- Marco Cosimo Simeone
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Guido W Grimm
- Department of Palaeontology, University of Wien , Wien , Austria
| | - Alessio Papini
- Dipartimento di Biologia, Università degli studi di Firenze , Firenze , Italy
| | - Federico Vessella
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Simone Cardoni
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Enrico Tordoni
- Department of Life Science, Università degli studi di Trieste , Trieste , Italy
| | | | - Alain Franc
- INRA, UMR BIOGECO-1202, Cestas, France; UMR BIOGECO-1202, Université Bordeaux, Talence, France
| | - Thomas Denk
- Department of Palaeobiology, Swedish Museum of Natural History , Stockholm , Sweden
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Simeone MC, Grimm GW, Papini A, Vessella F, Cardoni S, Tordoni E, Piredda R, Franc A, Denk T. Plastome data reveal multiple geographic origins of Quercus Group Ilex. PeerJ 2016. [PMID: 27123376 DOI: 10.7287/peerj.preprints.1615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One major exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilex L., Q. coccifera L., Q. aucheri Jaub. & Spach., Q. alnifolia Poech.) was explored at three chloroplast markers (rbcL, trnK/matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing all Quercus subgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. High plastid divergence in members of Quercus Group Ilex, including haplotypes shared with related, but long isolated oak lineages, point towards multiple geographic origins of this group of oaks. The results suggest that incomplete lineage sorting and repeated phases of asymmetrical introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split within Quercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.
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Affiliation(s)
- Marco Cosimo Simeone
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Guido W Grimm
- Department of Palaeontology, University of Wien , Wien , Austria
| | - Alessio Papini
- Dipartimento di Biologia, Università degli studi di Firenze , Firenze , Italy
| | - Federico Vessella
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Simone Cardoni
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Enrico Tordoni
- Department of Life Science, Università degli studi di Trieste , Trieste , Italy
| | | | - Alain Franc
- INRA, UMR BIOGECO-1202, Cestas, France; UMR BIOGECO-1202, Université Bordeaux, Talence, France
| | - Thomas Denk
- Department of Palaeobiology, Swedish Museum of Natural History , Stockholm , Sweden
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Manchester SR, Grímsson F, Zetter R. Assessing the Fossil Record of Asterids in the Context of Our Current Phylogenetic Framework. ANNALS OF THE MISSOURI BOTANICAL GARDEN. MISSOURI BOTANICAL GARDEN 2015; 100:329-363. [PMID: 31031419 PMCID: PMC6485501 DOI: 10.3417/2014033] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The fossil record provides good evidence for the minimum ages of important events in the diversification and geographic spread of Asteridae, with earliest examples extending back to the Turonian stage of the Late Cretaceous (~89 Ma). Some of the fossil identifications accepted in previous considerations of asterid phylogeny do not stand up to careful scrutiny. Nevertheless, among major clades of asterids, there is good evidence for a range of useful anchor points. Here we provide a synopsis of fossil occurrences that we consider as reliable representatives of modern Asterid families and genera. In addition, we provide new examples documented by fossil dispersed pollen investigated by both light and scanning electron microscopy studies including representatives of Loranthaceae, Amaranthaceae, Cornaceae (incl. Nyssa L., Mastixia Blume, Diplopanax Hand.-Mazz.), Sapotaceae, Ebenaceae, Ericaceae, Icacinaceae, Oleaceae, Asteraceae, Araliaceae, Adoxaceae and Caprifoliaceae from Paleogene sites in Greenland, western North America, and central Europe, and of Lamiaceae and Asteraceae from the middle to late Miocene northeastern China. We emphasize that dispersed pollen, taken along with megafossil and mesofossil data, continue to fill gaps in our knowledge of the paleobotanical record.
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Affiliation(s)
| | - Friðgeir Grímsson
- University of Vienna, Department of Palaeontology, Althanstraße 14 (UZA II), A-1090, Vienna, Austria
| | - Reinhard Zetter
- University of Vienna, Department of Palaeontology, Althanstraße 14 (UZA II), A-1090, Vienna, Austria
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