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Andruchow-Colombo A, Rossetto-Harris G, Brodribb TJ, Gandolfo MA, Wilf P. A new fossil Acmopyle with accessory transfusion tissue and potential reproductive buds: Direct evidence for ever-wet rainforests in Eocene Patagonia. AMERICAN JOURNAL OF BOTANY 2023; 110:e16221. [PMID: 37598386 DOI: 10.1002/ajb2.16221] [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: 02/01/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 08/22/2023]
Abstract
PREMISE Acmopyle (Podocarpaceae) comprises two extant species from Oceania that are physiologically restricted to ever-wet rainforests, a confirmed fossil record based on leaf adpressions and cuticles in Australia since the Paleocene, and a few uncertain reports from New Zealand, Antarctica, and South America. We investigated fossil specimens with Acmopyle affinities from the early Eocene Laguna del Hunco site in Patagonia, Argentina. METHODS We studied 42 adpression leafy-shoot fossils and included them in a total evidence phylogenetic analysis. RESULTS Acmopyle grayae sp. nov. is based on heterophyllous leafy shoots with three distinct leaf types. Among these, bilaterally flattened leaves uniquely preserve subparallel, linear features that we interpret as accessory transfusion tissue (ATT, an extra-venous water-conducting tissue). Some apical morphologies of A. grayae shoots are compatible with the early stages of ovuliferous cone development. Our phylogenetic analysis recovers the new species in a polytomy with the two extant Acmopyle species. We report several types of insect-herbivory damage. We also transfer Acmopyle engelhardti from the middle Eocene Río Pichileufú flora to Dacrycarpus engelhardti comb. nov. CONCLUSIONS We confirm the biogeographically significant presence of the endangered West Pacific genus Acmopyle in Eocene Patagonia. Acmopyle is one of the most drought-intolerant genera in Podocarpaceae, possibly due to the high collapse risk of the ATT, and thus the new fossil species provides physiological evidence for the presence of an ever-wet rainforest environment at Laguna del Hunco during the Early Eocene Climatic Optimum.
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Affiliation(s)
- Ana Andruchow-Colombo
- Museo Paleontológico Egidio Feruglio, Av. Fontana 140, Trelew, Chubut, 9100, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina
- LH Bailey Hortorium, Plant Biology Section, School of Integrative Plant Science, Cornell University, New York, 14853, USA
| | - Gabriella Rossetto-Harris
- Department of Geosciences and Earth and Environmental Systems Institute, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Timothy J Brodribb
- School of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania, 7001, Australia
| | - María A Gandolfo
- Museo Paleontológico Egidio Feruglio, Av. Fontana 140, Trelew, Chubut, 9100, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina
- LH Bailey Hortorium, Plant Biology Section, School of Integrative Plant Science, Cornell University, New York, 14853, USA
| | - Peter Wilf
- Department of Geosciences and Earth and Environmental Systems Institute, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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Brown MJM, Jordan GJ. No cell is an island: characterising the leaf epidermis using epidermalmorph, a new R package. THE NEW PHYTOLOGIST 2023; 237:354-366. [PMID: 36205061 PMCID: PMC10098627 DOI: 10.1111/nph.18519] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
The leaf epidermis is the interface between a plant and its environment. The epidermis is highly variable in morphology, with links to both phylogeny and environment, and this diversity is relevant to several fields, including physiology, functional traits, palaeobotany, taxonomy and developmental biology. Describing and measuring leaf epidermal traits remains challenging. Current approaches are either extremely labour-intensive and not feasible for large studies or limited to measurements of individual cells. Here, we present a method to characterise individual cell size, shape (including the effect of neighbouring cells) and arrangement from light microscope images. We provide the first automated characterisation of cell arrangement (from traced images) as well as multiple new shape characteristics. We have implemented this method in an R package, epidermalmorph, and provide an example workflow using this package, which includes functions to evaluate trait reliability and optimal sampling effort for any given group of plants. We demonstrate that our new metrics of cell shape are independent of gross cell shape, unlike existing metrics. epidermalmorph provides a broadly applicable method for quantifying epidermal traits that we hope can be used to disentangle the fundamental relationships between form and function in the leaf epidermis.
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Affiliation(s)
- Matilda J. M. Brown
- Biological SciencesUniversity of TasmaniaHobart7000Tas.Australia
- Royal Botanic Gardens KewRichmondTW9 3AEUK
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Chen L, Jin WT, Liu XQ, Wang XQ. New insights into the phylogeny and evolution of Podocarpaceae inferred from transcriptomic data. Mol Phylogenet Evol 2021; 166:107341. [PMID: 34740782 DOI: 10.1016/j.ympev.2021.107341] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 12/14/2022]
Abstract
Phylogenies of an increasing number of taxa have been resolved with the development of phylogenomics. However, the intergeneric relationships of Podocarpaceae, the second largest family of conifers comprising 19 genera and approximately 187 species mainly distributed in the Southern Hemisphere, have not been well disentangled in previous studies, even when genome-scale data sets were used. Here we used 993 nuclear orthologous groups (OGs) and 54 chloroplast OGs (genes), which were generated from 47 transcriptomes of Podocarpaceae and its sister group Araucariaceae, to reconstruct the phylogeny of Podocarpaceae. Our study completely resolved the intergeneric relationships of Podocarpaceae represented by all extant genera and revealed that topological conflicts among phylogenetic trees could be attributed to synonymous substitutions. Moreover, we found that two morphological traits, fleshy seed cones and flattened leaves, might be important for Podocarpaceae to adapt to angiosperm-dominated forests and thus could have promoted its species diversification. In addition, our results indicate that Podocarpaceae originated in Gondwana in the late Triassic and both vicariance and dispersal have contributed to its current biogeographic patterns. Our study provides the first robust transcriptome-based phylogeny of Podocarpaceae, an evolutionary framework important for future studies of this family.
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Affiliation(s)
- Luo Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei-Tao Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xin-Quan Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Leslie AB, Beaulieu J, Holman G, Campbell CS, Mei W, Raubeson LR, Mathews S. An overview of extant conifer evolution from the perspective of the fossil record. AMERICAN JOURNAL OF BOTANY 2018; 105:1531-1544. [PMID: 30157290 DOI: 10.1002/ajb2.1143] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 05/29/2018] [Indexed: 05/07/2023]
Abstract
PREMISE OF THE STUDY Conifers are an important living seed plant lineage with an extensive fossil record spanning more than 300 million years. The group therefore provides an excellent opportunity to explore congruence and conflict between dated molecular phylogenies and the fossil record. METHODS We surveyed the current state of knowledge in conifer phylogenetics to present a new time-calibrated molecular tree that samples ~90% of extant species diversity. We compared phylogenetic relationships and estimated divergence ages in this new phylogeny with the paleobotanical record, focusing on clades that are species-rich and well known from fossils. KEY RESULTS Molecular topologies and estimated divergence ages largely agree with the fossil record in Cupressaceae, conflict with it in Araucariaceae, and are ambiguous in Pinaceae and Podocarpaceae. Molecular phylogenies provide insights into some fundamental questions in conifer evolution, such as the origin of their seed cones, but using them to reconstruct the evolutionary history of specific traits can be challenging. CONCLUSIONS Molecular phylogenies are useful for answering deep questions in conifer evolution if they depend on understanding relationships among extant lineages. Because of extinction, however, molecular datasets poorly sample diversity from periods much earlier than the Late Cretaceous. This fundamentally limits their utility for understanding deep patterns of character evolution and resolving the overall pattern of conifer phylogeny.
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Affiliation(s)
- Andrew B Leslie
- Department of Ecology and Evolutionary Biology, Brown University, Box G-W, 80 Waterman Street, Providence, Rhode Island, 02912, USA
| | - Jeremy Beaulieu
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Garth Holman
- School of Biology and Ecology, University of Maine, Orono, Maine, 04469, USA
| | | | - Wenbin Mei
- Department of Plant Sciences, University of California, Davis, 1 Shields Avenue, Davis, California, 95616, USA
| | - Linda R Raubeson
- Department of Biological Sciences, Central Washington University, 400 E. University Way, Ellensburg, Washington, 98926, USA
| | - Sarah Mathews
- CSIRO National Research Collections Australia, Australian National Herbarium, Canberra, ACT, 2601, Australia
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Wilf P, Donovan MP, Cúneo NR, Gandolfo MA. The fossil flip-leaves (Retrophyllum, Podocarpaceae) of southern South America. AMERICAN JOURNAL OF BOTANY 2017; 104:1344-1369. [PMID: 29885237 DOI: 10.3732/ajb.1700158] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/07/2017] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY The flip-leaved podocarp Retrophyllum has a disjunct extant distribution in South American and Australasian tropical rainforests and a Gondwanic fossil record since the Eocene. Evolutionary, biogeographic, and paleoecological insights from previously described fossils are limited because they preserve little foliar variation and no reproductive structures. METHODS We investigated new Retrophyllum material from the terminal Cretaceous Lefipán, the early Eocene Laguna del Hunco, and the early/middle Eocene Río Pichileufú floras of Patagonian Argentina. We also reviewed type material of historical Eocene fossils from southern Chile. KEY RESULTS Cretaceous Retrophyllum superstes sp. nov. is described from a leafy twig, while Eocene R. spiralifolium sp. nov. includes several foliage forms and a peduncle with 13 pollen cones. Both species preserve extensive damage from sap-feeding insects associated with foliar transfusion tissue. The Eocene species exhibits a suite of characters linking it to both Neotropical and West Pacific Retrophyllum, along with several novel features. Retrophyllum araucoensis (Berry) comb. nov. stabilizes the nomenclature for the Chilean fossils. CONCLUSIONS Retrophyllum is considerably older than previously thought and is a survivor of the end-Cretaceous extinction. Much of the characteristic foliar variation and pollen-cone morphology of the genus evolved by the early Eocene. The mixed biogeographic signal of R. spiralifolium supports vicariance and represents a rare Neotropical connection for terminal-Gondwanan Patagonia, which is predominantly linked to extant Australasian floras due to South American extinctions. The leaf morphology of the fossils suggests significant drought vulnerability as in living Retrophyllum, indicating humid paleoenvironments.
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Affiliation(s)
- Peter Wilf
- Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Michael P Donovan
- Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20013, USA
| | - N Rubén Cúneo
- Museo Paleontológico Egidio Feruglio, Consejo Nacional de Investigaciones Científicas y Técnicas, Trelew 9100, Chubut, Argentina
| | - María A Gandolfo
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
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Elliott-Kingston C, Haworth M, Yearsley JM, Batke SP, Lawson T, McElwain JC. Does Size Matter? Atmospheric CO2 May Be a Stronger Driver of Stomatal Closing Rate Than Stomatal Size in Taxa That Diversified under Low CO2. FRONTIERS IN PLANT SCIENCE 2016; 7:1253. [PMID: 27605929 PMCID: PMC4996050 DOI: 10.3389/fpls.2016.01253] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/08/2016] [Indexed: 05/02/2023]
Abstract
One strategy for plants to optimize stomatal function is to open and close their stomata quickly in response to environmental signals. It is generally assumed that small stomata can alter aperture faster than large stomata. We tested the hypothesis that species with small stomata close faster than species with larger stomata in response to darkness by comparing rate of stomatal closure across an evolutionary range of species including ferns, cycads, conifers, and angiosperms under controlled ambient conditions (380 ppm CO2; 20.9% O2). The two species with fastest half-closure time and the two species with slowest half-closure time had large stomata while the remaining three species had small stomata, implying that closing rate was not correlated with stomatal size in these species. Neither was response time correlated with stomatal density, phylogeny, functional group, or life strategy. Our results suggest that past atmospheric CO2 concentration during time of taxa diversification may influence stomatal response time. We show that species which last diversified under low or declining atmospheric CO2 concentration close stomata faster than species that last diversified in a high CO2 world. Low atmospheric [CO2] during taxa diversification may have placed a selection pressure on plants to accelerate stomatal closing to maintain adequate internal CO2 and optimize water use efficiency.
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Affiliation(s)
| | - Matthew Haworth
- Italian National Research Council, Institute of Tree and Timber IVALSARome, Italy
| | - Jon M. Yearsley
- Earth Institute, Science Centre East, School of Biology and Environmental Science, University College DublinDublin, Ireland
| | - Sven P. Batke
- Earth Institute, Science Centre East, School of Biology and Environmental Science, University College DublinDublin, Ireland
| | - Tracy Lawson
- School of Biological Science, University of EssexColchester, UK
| | - Jennifer C. McElwain
- Earth Institute, Science Centre East, School of Biology and Environmental Science, University College DublinDublin, Ireland
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Reichgelt T, Jones WA, Jones DT, Conran JG, Bannister JM, Kennedy EM, Mildenhall DC, Lee DE. The flora of Double Hill (Dunedin Volcanic Complex, Middle–Late Miocene) Otago, New Zealand. J R Soc N Z 2014. [DOI: 10.1080/03036758.2014.923476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Evolution and biogeography of gymnosperms. Mol Phylogenet Evol 2014; 75:24-40. [DOI: 10.1016/j.ympev.2014.02.005] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 02/06/2014] [Accepted: 02/10/2014] [Indexed: 11/20/2022]
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Vieira LDN, Faoro H, Rogalski M, Fraga HPDF, Cardoso RLA, de Souza EM, de Oliveira Pedrosa F, Nodari RO, Guerra MP. The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection. PLoS One 2014; 9:e90618. [PMID: 24594889 PMCID: PMC3942463 DOI: 10.1371/journal.pone.0090618] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 02/01/2014] [Indexed: 11/18/2022] Open
Abstract
Background Podocarpus lambertii (Podocarpaceae) is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp) genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of P. lambertii. Methodology/Principal Findings The P. lambertii cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR). It contains 118 unique genes and one duplicated tRNA (trnN-GUU), which occurs as an inverted repeat sequence. The rps16 gene was not found, which was previously reported for the plastid genome of another Podocarpaceae (Nageia nagi) and Araucariaceae (Agathis dammara). Structurally, P. lambertii shows 4 inversions of a large DNA fragment ∼20,000 bp compared to the Podocarpus totara cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The P. lambertii cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency. Conclusion The complete cp genome sequence of P. lambertii revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the P. lambertii cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of this genus.
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Affiliation(s)
- Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Helisson Faoro
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Marcelo Rogalski
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Hugo Pacheco de Freitas Fraga
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Rodrigo Luis Alves Cardoso
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Rubens Onofre Nodari
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Miguel Pedro Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
- * E-mail:
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