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Gutiérrez-Larruscain D, Vargas P, Fernández-Mazuecos M, Pausas JG. Phylogenomic analysis reveals the evolutionary history of Paleartic needle-leaved junipers. Mol Phylogenet Evol 2024; 199:108162. [PMID: 39067655 DOI: 10.1016/j.ympev.2024.108162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/10/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
Needle-leaved junipers (Juniperus sect. Juniperus, Cupressaceae) are coniferous trees and shrubs with red or blue fleshy cones. They are distributed across Asia, Macaronesia and the Mediterranean Basin, with one species (J. communis) having a circumboreal distribution. Here we aim to resolve the phylogeny of this clade to infer its intricate evolutionary history. To do so, we built a comprehensive, time-calibrated phylogeny using genotyping-by-sequencing (GBS) and combine it with species occurrence using phylogeographic tools. Our results provide solid phylogenetic resolution to propose a new taxonomic classification and a biogeographical history of the section. Specifically, we confirm the monophyly of two groups within J. sect. Juniperus: the Asian (blue-cone) species including the circumboreal J. communis, and the Mediterranean-Macaronesian (red-cone) species. In addition, we provide strong phylogenetic evidence for three distinct species (J. badia, J. conferta, J. lutchuensis) previously considered subspecies or varieties, as well as for the differentiation between the eastern and western Mediterranean lineages of J. macrocarpa. Our findings suggest that the Mediterranean basin was the primary center of diversification for Juniperus sect. Juniperus, followed by an East Asian-Tethyan disjunction resulting from uplifts of the Qinghai-Tibetan Plateau and climatic shifts. The colonization history of Macaronesia by red-cone junipers from the western Mediterranean appears to have taken place independently in two different geological periods: the Miocene (Azores) and the Pliocene (Madeira-Canary Islands). Overall, genomic data and phylogenetic analysis are key to consider a new taxonomic proposal and reconstruct the biogeographical history of the iconic needle-leaved junipers across the Paleartic.
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Affiliation(s)
- David Gutiérrez-Larruscain
- Department of Ecology and Global Change, Desertification Research Centre (CIDE: CSIC-UV-GVA), Valencia, Spain.
| | - Pablo Vargas
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB: CSIC), Madrid, Spain
| | - Mario Fernández-Mazuecos
- Department of Biology (Botany), Faculty of Sciences, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Juli G Pausas
- Department of Ecology and Global Change, Desertification Research Centre (CIDE: CSIC-UV-GVA), Valencia, Spain
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2
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Wutke S, Blank SM, Boevé JL, Faircloth BC, Koch F, Linnen CR, Malm T, Niu G, Prous M, Schiff NM, Schmidt S, Taeger A, Vilhelmsen L, Wahlberg N, Wei M, Nyman T. Phylogenomics and biogeography of sawflies and woodwasps (Hymenoptera, Symphyta). Mol Phylogenet Evol 2024; 199:108144. [PMID: 38972494 DOI: 10.1016/j.ympev.2024.108144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/09/2024]
Abstract
Phylogenomic approaches have recently helped elucidate various insect relationships, but large-scale comprehensive analyses on relationships within sawflies and woodwasps are still lacking. Here, we infer the relationships and long-term biogeographic history of these hymenopteran groups using a large dataset of 354 UCE loci collected from 385 species that represent all major lineages. Early Hymenoptera started diversifying during the Early Triassic ∼249 Ma and spread all over the ancient supercontinent Pangaea. We recovered Xyeloidea as a monophyletic sister group to other Hymenoptera and Pamphilioidea as sister to Unicalcarida. Within the diverse family Tenthredinidae, our taxonomically and geographically expanded taxon sampling highlights the non-monophyly of several traditionally defined subfamilies. In addition, the recent removal of Athalia and related genera from the Tenthredinidae into the separate family Athaliidae is supported. The deep historical biogeography of the group is characterised by independent dispersals and re-colonisations between the northern (Laurasia) and southern (Gondwana) palaeocontinents. The breakup of these landmasses led to ancient vicariance in several Gondwanan lineages, while interchange across the Northern Hemisphere has continued until the Recent. The little-studied African sawfly fauna is likewise a diverse mixture of groups with varying routes of colonization. Our results reveal interesting parallels in the evolution and biogeography of early hymenopterans and other ancient insect groups.
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Affiliation(s)
- Saskia Wutke
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.
| | - Stephan M Blank
- Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany
| | - Jean-Luc Boevé
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Brant C Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Frank Koch
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | | | - Tobias Malm
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Gengyun Niu
- College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Marko Prous
- Museum of Natural History, University of Tartu, Estonia
| | - Nathan M Schiff
- Formerly with the USDA Forest Service, Southern Research Station, Center for Bottomland Hardwoods Research, Stoneville, MS, USA
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Andreas Taeger
- Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany
| | - Lars Vilhelmsen
- Natural History Museum of Denmark, SCIENCE, University of Copenhagen, Denmark
| | | | - Meicai Wei
- College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
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Wood AR, Aime MC. Phylogenetics of the rust fungi (Pucciniales) of South Africa, with notes on their life histories and possible origins. Mycologia 2024; 116:509-535. [PMID: 38742888 DOI: 10.1080/00275514.2024.2334189] [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: 01/19/2023] [Accepted: 03/20/2024] [Indexed: 05/16/2024]
Abstract
South Africa has an indigenous rust (Pucciniales) funga of approximately 460 species. This funga was sampled with species from as many genera as possible. The nuclear ribosomal large subunit (28S) region was amplified from samples representing 110 indigenous species, as well as the small subunit (18S) region and the cytochrome c oxidase subunit 3 (CO3) in some cases, and these were used in phylogenetic analyses. One new species is described, 12 new combinations made, six names reinstated, and two life history connections made. The life histories of this funga were summarized; it is dominated by species with contracted life histories. The majority of species are autoecious, with a small proportion being heteroecious. Of the autoecious species, many will likely be homothallic with no spermagonia. A shortened life history with homothallism allows for a single basidiospore infection to initiate a local population buildup under the prevailing unpredictable climatic conditions. Suggestions are made as to the possible origin of this funga based on the development of the modern South African flora. It is postulated that the rusts of South Africa are of relatively recent origin, consisting of three groups. Firstly, there is an African tropical element with members of the Mikronegerineae (Hemileia), the Sphaerophragmiaceae (Puccorchidium, Sphaerophragmium), and certain Uredinineae (Stomatisora). Their immediate ancestors likely occurred in the tropical forests of Africa during the Paleogene. Secondly, there is a pantropical element including the Raveneliaceae (e.g., Diorchidium, Maravalia, Ravenelia sensu lato, Uropyxis). This likely diversified during the Neogene, when the mimosoids became the dominant trees of the developing savannas. Thirdly, the Pucciniaceae invaded Africa as this continent pushed northward closing the Tethys Sea. They diversified with the development of the savannas as these become the dominant habitat in most of Africa, and are by far the largest component of the South African rust funga.
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Affiliation(s)
- Alan R Wood
- Plant Health and Protection, Agricultural Research Council, Stellenbosch 7599, South Africa
- Discipline of Plant Pathology, College of Agriculture and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg 3209, South Africa
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47901, USA
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Nguyen AT, Atkinson BA. Cretaceous and Paleocene fossils reveal an extinct higher clade within Cornales, the dogwood order. AMERICAN JOURNAL OF BOTANY 2024; 111:e16372. [PMID: 39010697 DOI: 10.1002/ajb2.16372] [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: 11/09/2023] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 07/17/2024]
Abstract
PREMISE Characterization and phylogenetic integration of fossil angiosperms with uncertain affinities is relatively limited, which may obscure the diversity of extinct higher taxa in the flowering plant tree of life. The order Cornales contains a diversity of extinct taxa with uncertain familial affinities that make it an ideal group for studying turnover in angiosperms. Here, we describe a new extinct genus of Cornales unassignable to an extant family and conduct a series of phylogenetic analyses to reconstruct relationships of fossils across the order. METHODS Two permineralized endocarps were collected from the Cedar District Formation (Campanian, 82-80 Ma) of Sucia Island, State of Washington, United States. Fossils were sectioned with the cellulose acetate peel technique and incorporated into a morphological dataset. To assess the utility of this dataset to accurately place taxa in their respective clades, we used a series of phylogenetic pseudofossilization analyses. We then conducted a total-evidence analysis and a scaffold-based approach to determine relationships of fossils. RESULTS Based on their unique combination of characters, the fossils represent a new genus, Fenestracarpa washingtonensis gen. nov. et sp. nov. Pseudofossilization analyses indicate that our morphological dataset can be used to accurately recover taxa at the major clade to family level, generally with moderate to high support. The total-evidence and scaffold-based analyses recovered Fenestracarpa and other fossil genera in an entirely extinct clade within Cornales. CONCLUSIONS Our findings increase the reported diversity of extinct Cornales and indicate that the order's initial radiation likely included the divergence of an extinct higher clade that endured the end-Cretaceous Mass extinction but perished during the Cenozoic.
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Affiliation(s)
- Austin T Nguyen
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, 66045, KS, USA
- Biodiversity Institute, University of Kansas, Lawrence, 66045, KS, USA
| | - Brian A Atkinson
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, 66045, KS, USA
- Biodiversity Institute, University of Kansas, Lawrence, 66045, KS, USA
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Tremble K, Henkel T, Bradshaw A, Domnauer C, Brown LM, Thám LX, Furci G, Aime MC, Moncalvo JM, Dentinger B. A revised phylogeny of Boletaceae using whole genome sequences. Mycologia 2024; 116:392-408. [PMID: 38551379 DOI: 10.1080/00275514.2024.2314963] [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: 11/29/2023] [Accepted: 01/30/2024] [Indexed: 05/01/2024]
Abstract
The porcini mushroom family Boletaceae is a diverse, widespread group of ectomycorrhizal (ECM) mushroom-forming fungi that so far has eluded intrafamilial phylogenetic resolution based on morphology and multilocus data sets. In this study, we present a genome-wide molecular data set of 1764 single-copy gene families from a global sampling of 418 Boletaceae specimens. The resulting phylogenetic analysis has strong statistical support for most branches of the tree, including the first statistically robust backbone. The enigmatic Phylloboletellus chloephorus from non-ECM Argentinian subtropical forests was recovered as a new subfamily sister to the core Boletaceae. Time-calibrated branch lengths estimate that the family first arose in the early to mid-Cretaceous and underwent a rapid radiation in the Eocene, possibly when the ECM nutritional mode arose with the emergence and diversification of ECM angiosperms. Biogeographic reconstructions reveal a complex history of vicariance and episodic long-distance dispersal correlated with historical geologic events, including Gondwanan origins and inferred vicariance associated with its disarticulation. Together, this study represents the most comprehensively sampled, data-rich molecular phylogeny of the Boletaceae to date, establishing a foundation for future robust inferences of biogeography in the group.
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Affiliation(s)
- Keaton Tremble
- Natural History Museum of Utah and School of Biological Sciences, University of Utah, Salt Lake City, Utah 84108, USA
| | - Terry Henkel
- Department of Biological Sciences, California State Polytechnic University, Humboldt, Arcata 95521, California
| | - Alexander Bradshaw
- Natural History Museum of Utah and School of Biological Sciences, University of Utah, Salt Lake City, Utah 84108, USA
| | - Colin Domnauer
- Natural History Museum of Utah and School of Biological Sciences, University of Utah, Salt Lake City, Utah 84108, USA
| | - Lyda M Brown
- Natural History Museum of Utah and School of Biological Sciences, University of Utah, Salt Lake City, Utah 84108, USA
| | - Lê Xuân Thám
- Laboratory for Computation and Applications in Life Sciences, Institute for Computation Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City 700000, Viet Nam
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City 700000, Viet Nam
| | | | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47906, USA
| | - Jean-Marc Moncalvo
- Department of Natural History, Royal Ontario Museum and Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 2C6, Canada
| | - Bryn Dentinger
- Natural History Museum of Utah and School of Biological Sciences, University of Utah, Salt Lake City, Utah 84108, USA
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Peris D, Condamine FL. The angiosperm radiation played a dual role in the diversification of insects and insect pollinators. Nat Commun 2024; 15:552. [PMID: 38253644 PMCID: PMC10803743 DOI: 10.1038/s41467-024-44784-4] [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: 02/23/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Interactions with angiosperms have been hypothesised to play a crucial role in driving diversification among insects, with a particular emphasis on pollinator insects. However, support for coevolutionary diversification in insect-plant interactions is weak. Macroevolutionary studies of insect and plant diversities support the hypothesis that angiosperms diversified after a peak in insect diversity in the Early Cretaceous. Here, we used the family-level fossil record of insects as a whole, and insect pollinator families in particular, to estimate diversification rates and the role of angiosperms on insect macroevolutionary history using a Bayesian process-based approach. We found that angiosperms played a dual role that changed through time, mitigating insect extinction in the Cretaceous and promoting insect origination in the Cenozoic, which is also recovered for insect pollinator families only. Although insects pollinated gymnosperms before the angiosperm radiation, a radiation of new pollinator lineages began as angiosperm lineages increased, particularly significant after 50 Ma. We also found that global temperature, increases in insect diversity, and spore plants were strongly correlated with origination and extinction rates, suggesting that multiple drivers influenced insect diversification and arguing for the investigation of different explanatory variables in further studies.
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Affiliation(s)
- David Peris
- Institut Botànic de Barcelona (CSIC-CMCNB), 08038, Barcelona, Spain.
| | - Fabien L Condamine
- CNRS, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
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7
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Gutiérrez-Ortega JS, Pérez-Farrera MA, Matsuo A, Sato MP, Suyama Y, Calonje M, Vovides AP, Kajita T, Watano Y. The phylogenetic reconstruction of the Neotropical cycad genus Ceratozamia (Zamiaceae) reveals disparate patterns of niche evolution. Mol Phylogenet Evol 2024; 190:107960. [PMID: 37918683 DOI: 10.1016/j.ympev.2023.107960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
The cycad genus Ceratozamia comprises 40 species from Mexico, Guatemala, Belize, and Honduras, where cycads occur throughout climatically varied montane habitats. Ceratozamia has the potential to reveal the history and processes of species diversification across diverse Neotropical habitats in this region. However, the species relationships within Ceratozamia and the ecological trends during its evolution remain unclear. Here, we aimed to clarify the phylogenetic relationships, the timing of clade and species divergences, and the niche evolution throughout the phylogenetic history of Ceratozamia. Genome-wide DNA sequences were obtained with MIG-seq, and multiple data-filtering steps were used to optimize the dataset used to construct an ultrametric species tree. Divergence times among branches and ancestral niches were estimated. The niche variation among species was evaluated, summarized into two principal components, and their ancestral states were reconstructed to test whether niche shifts among branches can be explained by random processes, under a Brownian Motion model. Ceratozamia comprises three main clades, and most species relationships within the clades were resolved. Ceratozamia has diversified since the Oligocene, with major branching events occurring during the Miocene. This timing is consistent with fossil evidence, the timing estimated for other Neotropical plant groups, and the major geological events that shaped the topographic and climatic variation in Mexico. Patterns of niche evolution in the genus do not accord with the Brownian Motion model. Rather, non-random evolution with shifts towards more seasonal environments at high latitudes, or shifts towards humid or dry environments at low latitudes explain the diversification of Ceratozamia. We present a comprehensive phylogenetic reconstruction for Ceratozamia and identify for the first time the environmental factors involved in clade and species diversification within the genus. This study alleviates the controversies regarding the species relationships in the genus and provides the first evidence that latitude-associated environmental factors may influence processes of niche evolution in cycads.
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Affiliation(s)
| | - Miguel Angel Pérez-Farrera
- Herbario Eizi Matuda, Laboratorio de Ecología Evolutiva, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez 29039, Mexico.
| | - Ayumi Matsuo
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Mitsuhiko P Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | | | - Andrew P Vovides
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C., 91070 Xalapa, Mexico
| | - Tadashi Kajita
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Uehara, Yaeyama, Okinawa 907-1541, Japan
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
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Yu Q, Yang FS, Chen YX, Wu H, Ickert-Bond SM, Wang XQ. Diploid species phylogeny and evolutionary reticulation indicate early radiation of Ephedra in the Tethys coast. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2619-2630. [PMID: 37837251 DOI: 10.1111/jipb.13573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 10/13/2023] [Indexed: 10/15/2023]
Abstract
Reconstructing a robust species phylogeny and disentangling the evolutionary and biogeographic history of the gymnosperm genus Ephedra, which has a large genome and rich polyploids, remain a big challenge. Here we reconstructed a transcriptome-based phylogeny of 19 diploid Ephedra species, and explored evolutionary reticulations in this genus represented by 50 diploid and polyploid species, using four low-copy nuclear and nine plastid genes. The diploid species phylogeny indicates that the Mediterranean species diverged first, and the remaining species split into three clades, including the American species (Clade A), E. rhytidosperma, and all other Asian species (Clade B). The single-gene trees placed E. rhytidosperma sister to Clade A, Clade B, or Clades A + B in similar proportions, suggesting that radiation and gene flow likely occurred in the early evolution of Ephedra. In addition, reticulate evolution occurred not only among the deep nodes, but also in the recently evolved South American species, which further caused difficulty in phylogenetic reconstruction. Moreover, we found that allopolyploid speciation was pervasive in Ephedra. Our study also suggests that Ephedra very likely originated in the Tethys coast during the late Cretaceous, and the South American Ephedra species have a single origin by dispersal from Mexico or North America.
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Affiliation(s)
- Qiong Yu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fu-Sheng Yang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ya-Xing Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Hui Wu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Stefanie M Ickert-Bond
- Department of Biology and Wildlife & UA Museum of the North, University of Alaska Fairbanks (UAF), Fairbanks, AK, 99775, USA
| | - Xiao-Quan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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Coiro M, Allio R, Mazet N, Seyfullah LJ, Condamine FL. Reconciling fossils with phylogenies reveals the origin and macroevolutionary processes explaining the global cycad biodiversity. THE NEW PHYTOLOGIST 2023; 240:1616-1635. [PMID: 37302411 PMCID: PMC10953041 DOI: 10.1111/nph.19010] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/01/2023] [Indexed: 06/13/2023]
Abstract
The determinants of biodiversity patterns can be understood using macroevolutionary analyses. The integration of fossils into phylogenies offers a deeper understanding of processes underlying biodiversity patterns in deep time. Cycadales are considered a relict of a once more diverse and globally distributed group but are restricted to low latitudes today. We still know little about their origin and geographic range evolution. Combining molecular data for extant species and leaf morphological data for extant and fossil species, we study the origin of cycad global biodiversity patterns through Bayesian total-evidence dating analyses. We assess the ancestral geographic origin and trace the historical biogeography of cycads with a time-stratified process-based model. Cycads originated in the Carboniferous on the Laurasian landmass and expanded in Gondwana in the Jurassic. Through now-vanished continental connections, Antarctica and Greenland were crucial biogeographic crossroads for cycad biogeography. Vicariance is an essential speciation mode in the deep and recent past. Their latitudinal span increased in the Jurassic and restrained toward subtropical latitudes in the Neogene in line with biogeographic inferences of high-latitude extirpations. We show the benefits of integrating fossils into phylogenies to estimate ancestral areas of origin and to study evolutionary processes explaining the global distribution of present-day relict groups.
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Affiliation(s)
- Mario Coiro
- Department of PalaeontologyUniversity of Vienna1090ViennaAustria
- Ronin Institute for Independent ScholarshipMontclairNJ07043USA
| | - Rémi Allio
- Centre de Biologie pour la Gestion des Populations, INRAE, CIRAD, IRD, Montpellier SupAgroUniversité de Montpellier34988MontpellierFrance
| | - Nathan Mazet
- CNRS, Institut des Sciences de l'Evolution de Montpellier, Université de MontpellierPlace Eugène Bataillon34095MontpellierFrance
| | | | - Fabien L. Condamine
- CNRS, Institut des Sciences de l'Evolution de Montpellier, Université de MontpellierPlace Eugène Bataillon34095MontpellierFrance
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Habib S, Gong Y, Dong S, Lindstrom A, William Stevenson D, Liu Y, Wu H, Zhang S. Phylotranscriptomics reveal the spatio-temporal distribution and morphological evolution of Macrozamia, an Australian endemic genus of Cycadales. ANNALS OF BOTANY 2022; 130:671-685. [PMID: 36111957 PMCID: PMC9670756 DOI: 10.1093/aob/mcac117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/14/2022] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Cycads are regarded as an ancient lineage of living seed plants, and hold important clues to understand the early evolutionary trends of seed plants. The molecular phylogeny and spatio-temporal diversification of one of the species-rich genera of cycads, Macrozamia, have not been well reconstructed. METHODS We analysed a transcriptome dataset of 4740 single-copy nuclear genes (SCGs) of 39 Macrozamia species and two outgroup taxa. Based on concatenated (maximum parsimony, maximum likelihood) and multispecies coalescent analyses, we first establish a well-resolved phylogenetic tree of Macrozamia. To identify cyto-nuclear incongruence, the plastid protein coding genes (PCGs) from transcriptome data are extracted using the software HybPiper. Furthermore, we explore the biogeographical history of the genus and shed light on the pattern of floristic exchange between three distinct areas of Australia. Six key diagnostic characters are traced on the phylogenetic framework using two comparative methods, and infra-generic classification is investigated. KEY RESULTS The tree topologies of concatenated and multi-species coalescent analyses of SCGs are mostly congruent with a few conflicting nodes, while those from plastid PCGs show poorly supported relationships. The genus contains three major clades that correspond to their distinct distributional areas in Australia. The crown group of Macrozamia is estimated to around 11.80 Ma, with a major expansion in the last 5-6 Myr. Six morphological characters show homoplasy, and the traditional phenetic sectional division of the genus is inconsistent with this current phylogeny. CONCLUSIONS This first detailed phylogenetic investigation of Macrozamia demonstrates promising prospects of SCGs in resolving phylogenetic relationships within cycads. Our study suggests that Macrozamia, once widely distributed in Australia, underwent major extinctions because of fluctuating climatic conditions such as cooling and mesic biome disappearance in the past. The current close placement of morphologically distinct species in the phylogenetic tree may be related to neotenic events that occurred in the genus.
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Affiliation(s)
- Sadaf Habib
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yiqing Gong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Anders Lindstrom
- Global Biodiversity Conservancy 144/124 Moo 3, Soi Bua Thong, Bangsalae, Sattahip, Chonburi 20250, Thailand
| | | | - Yang Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Hong Wu
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shouzhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
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11
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Rivera BK, Sáez PL, Cavieres LA, Capó-Bauçà S, Iñiguez C, Sanfuentes von Stowasser E, Fuentes F, Ramírez CF, Vallejos V, Galmés J. Anatomical and biochemical evolutionary ancient traits of Araucaria araucana (Molina) K. Koch and their effects on carbon assimilation. TREE PHYSIOLOGY 2022; 42:1957-1974. [PMID: 35604362 DOI: 10.1093/treephys/tpac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
The study of ancient species provides valuable information concerning the evolution of specific adaptations to past and current environmental conditions. Araucaria araucana (Molina) K. Koch belongs to one of the oldest families of conifers in the world, but despite this, there are few studies focused on its physiology and responses to changes in environmental conditions. We used an integrated approach aimed at comprehensively characterizing the ecophysiology of this poorly known species, focusing in its stomatal, mesophyll and biochemical traits, hypothesizing that these traits govern the carbon assimilation of A. araucana under past and present levels of atmospheric CO2. Results indicated that A. araucana presents the typical traits of an ancient species, such as large stomata and low stomatal density, which trigger low stomatal conductance and slow stomatal responsiveness to changing environmental conditions. Interestingly, the quantitative analysis showed that photosynthetic rates were equally limited by both diffusive and biochemical components. The Rubisco catalytic properties proved to have a low Rubisco affinity for CO2 and O2, similar to other ancient species. This affinity for CO2, together with the low carboxylation turnover rate, are responsible for the low Rubisco catalytic efficiency of carboxylation. These traits could be the result of the diverse environmental selective pressures that A. araucana was exposed during its diversification. The increase in measured temperatures induced an increase in stomatal and biochemical limitations, which together with a lower Rubisco affinity for CO2 could explain the low photosynthetic capacity of A. araucana in warmer conditions.
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Affiliation(s)
- Betsy K Rivera
- Laboratorio Cultivo de Tejidos Vegetales, Centro de Biotecnología, Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción 4030000, Chile
| | - Patricia L Sáez
- Laboratorio Cultivo de Tejidos Vegetales, Centro de Biotecnología, Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción 4030000, Chile
- Instituto de Ecología y Biodiversidad (IEB), Santiago 8320000, Chile
| | - Lohengrin A Cavieres
- Instituto de Ecología y Biodiversidad (IEB), Santiago 8320000, Chile
- ECOBIOSIS, Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción 4030000, Chile
| | - Sebastià Capó-Bauçà
- Research Group on Plant Biology under Mediterranean Conditions, INAGEA-Universitat de les Illes Balears, Balearic Islands 07122, Spain
| | - Concepción Iñiguez
- Research Group on Plant Biology under Mediterranean Conditions, INAGEA-Universitat de les Illes Balears, Balearic Islands 07122, Spain
| | - Eugenio Sanfuentes von Stowasser
- Laboratorio de Patología Forestal, Facultad Ciencias Forestales y Centro de Biotecnología, Universidad de Concepción, Concepción 4030000, Chile
| | - Francisca Fuentes
- Laboratorio Cultivo de Tejidos Vegetales, Centro de Biotecnología, Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción 4030000, Chile
| | - Constanza F Ramírez
- Laboratorio Cultivo de Tejidos Vegetales, Centro de Biotecnología, Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción 4030000, Chile
| | - Valentina Vallejos
- Laboratorio Cultivo de Tejidos Vegetales, Centro de Biotecnología, Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción 4030000, Chile
| | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, INAGEA-Universitat de les Illes Balears, Balearic Islands 07122, Spain
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12
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Liao Y, Liu Z, Gichira AW, Yang M, Mbichi RW, Meng L, Wan T. Deep evaluation of the evolutionary history of the Heat Shock Factor (HSF) gene family and its expansion pattern in seed plants. PeerJ 2022; 10:e13603. [PMID: 35966928 PMCID: PMC9373977 DOI: 10.7717/peerj.13603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/26/2022] [Indexed: 01/17/2023] Open
Abstract
Heat shock factor (HSF) genes are essential in some of the basic developmental pathways in plants. Despite extensive studies on the structure, functional diversification, and evolution of HSF genes, their divergence history and gene duplication pattern remain unknown. To further illustrate the probable divergence patterns in these subfamilies, we analyzed the evolutionary history of HSF genes using phylogenetic reconstruction and genomic syntenic analyses, taking advantage of the increased sampling of genomic data from pteridophytes, gymnosperms and basal angiosperms. We identified a novel clade that includes HSFA2, HSFA6, HSFA7, and HSFA9 with a complex relationship, which is very likely due to orthologous or paralogous genes retained after frequent gene duplication events. We hypothesized that HSFA9 derives from HSFA2 through gene duplication in eudicots at the ancestral state, and then expanded in a lineage-specific way. Our findings indicate that HSFB3 and HSFB5 emerged before the divergence of ancestral angiosperms, but were lost in the most recent common ancestors of monocots. We also presumed that HSFC2 derives from HSFC1 in ancestral monocots. This work proposes that during the radiation of flowering plants, an era during which there was a differentiation of angiosperms, the size of the HSF gene family was also being adjusted with considerable sub- or neo-functionalization. The independent evolution of HSFs in eudicots and monocots, including lineage-specific gene duplication, gave rise to a new gene in ancestral eudicots and monocots, and lineage-specific gene loss in ancestral monocots. Our analyses provide essential insights for studying the evolutionary history of this multigene family.
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Affiliation(s)
- Yiying Liao
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Zhiming Liu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Andrew W. Gichira
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Min Yang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Ruth Wambui Mbichi
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Linping Meng
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Tao Wan
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
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13
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Yang Y, Ferguson DK, Liu B, Mao KS, Gao LM, Zhang SZ, Wan T, Rushforth K, Zhang ZX. Recent advances on phylogenomics of gymnosperms and a new classification. PLANT DIVERSITY 2022; 44:340-350. [PMID: 35967253 PMCID: PMC9363647 DOI: 10.1016/j.pld.2022.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 05/30/2023]
Abstract
Living gymnosperms comprise four major groups: cycads, Ginkgo, conifers, and gnetophytes. Relationships among/within these lineages have not been fully resolved. Next generation sequencing has made available a large number of sequences, including both plastomes and single-copy nuclear genes, for reconstruction of solid phylogenetic trees. Recent advances in gymnosperm phylogenomic studies have updated our knowledge of gymnosperm systematics. Here, we review major advances of gymnosperm phylogeny over the past 10 years and propose an updated classification of extant gymnosperms. This new classification includes three classes (Cycadopsida, Ginkgoopsida, and Pinopsida), five subclasses (Cycadidae, Ginkgoidae, Cupressidae, Pinidae, and Gnetidae), eight orders (Cycadales, Ginkgoales, Araucariales, Cupressales, Pinales, Ephedrales, Gnetales, and Welwitschiales), 13 families, and 86 genera. We also described six new tribes including Acmopyleae Y. Yang, Austrocedreae Y. Yang, Chamaecyparideae Y. Yang, Microcachrydeae Y. Yang, Papuacedreae Y. Yang, and Prumnopityeae Y. Yang, and made 27 new combinations in the genus Sabina.
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Affiliation(s)
- Yong Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, 159 Longpan Road, Nanjing Forestry University, Nanjing 210037, China
| | | | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Kang-Shan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, China
| | - Shou-Zhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, FairyLake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Tao Wan
- Key Laboratory of Southern Subtropical Plant Diversity, FairyLake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | | | - Zhi-Xiang Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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14
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Qiu T, Andrus R, Aravena MC, Ascoli D, Bergeron Y, Berretti R, Berveiller D, Bogdziewicz M, Boivin T, Bonal R, Bragg DC, Caignard T, Calama R, Camarero JJ, Chang-Yang CH, Cleavitt NL, Courbaud B, Courbet F, Curt T, Das AJ, Daskalakou E, Davi H, Delpierre N, Delzon S, Dietze M, Calderon SD, Dormont L, Espelta J, Fahey TJ, Farfan-Rios W, Gehring CA, Gilbert GS, Gratzer G, Greenberg CH, Guo Q, Hacket-Pain A, Hampe A, Han Q, Hille Ris Lambers J, Hoshizaki K, Ibanez I, Johnstone JF, Journé V, Kabeya D, Kilner CL, Kitzberger T, Knops JMH, Kobe RK, Kunstler G, Lageard JGA, LaMontagne JM, Ledwon M, Lefevre F, Leininger T, Limousin JM, Lutz JA, Macias D, McIntire EJB, Moore CM, Moran E, Motta R, Myers JA, Nagel TA, Noguchi K, Ourcival JM, Parmenter R, Pearse IS, Perez-Ramos IM, Piechnik L, Poulsen J, Poulton-Kamakura R, Redmond MD, Reid CD, Rodman KC, Rodriguez-Sanchez F, Sanguinetti JD, Scher CL, Schlesinger WH, Schmidt Van Marle H, Seget B, Sharma S, Silman M, Steele MA, Stephenson NL, Straub JN, Sun IF, Sutton S, Swenson JJ, Swift M, Thomas PA, Uriarte M, Vacchiano G, Veblen TT, Whipple AV, Whitham TG, Wion AP, Wright B, Wright SJ, Zhu K, Zimmerman JK, Zlotin R, Zywiec M, Clark JS. Limits to reproduction and seed size-number trade-offs that shape forest dominance and future recovery. Nat Commun 2022; 13:2381. [PMID: 35501313 PMCID: PMC9061860 DOI: 10.1038/s41467-022-30037-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 04/13/2022] [Indexed: 11/09/2022] Open
Abstract
The relationships that control seed production in trees are fundamental to understanding the evolution of forest species and their capacity to recover from increasing losses to drought, fire, and harvest. A synthesis of fecundity data from 714 species worldwide allowed us to examine hypotheses that are central to quantifying reproduction, a foundation for assessing fitness in forest trees. Four major findings emerged. First, seed production is not constrained by a strict trade-off between seed size and numbers. Instead, seed numbers vary over ten orders of magnitude, with species that invest in large seeds producing more seeds than expected from the 1:1 trade-off. Second, gymnosperms have lower seed production than angiosperms, potentially due to their extra investments in protective woody cones. Third, nutrient-demanding species, indicated by high foliar phosphorus concentrations, have low seed production. Finally, sensitivity of individual species to soil fertility varies widely, limiting the response of community seed production to fertility gradients. In combination, these findings can inform models of forest response that need to incorporate reproductive potential.
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Affiliation(s)
- Tong Qiu
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
| | - Robert Andrus
- Department of Geography, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Marie-Claire Aravena
- Universidad de Chile, Facultad de Ciencias Forestales y de la Conservacion de la Naturaleza (FCFCN), La Pintana, 8820808, Santiago, Chile
| | - Davide Ascoli
- Department of Agriculture, Forest and Food Sciences, University of Torino, 10095, Grugliasco, TO, Italy
| | - Yves Bergeron
- Forest Research Institute, University of Quebec in Abitibi-Temiscamingue, Rouyn-Noranda, QC, J9X 5E4, Canada
| | - Roberta Berretti
- Department of Agriculture, Forest and Food Sciences, University of Torino, 10095, Grugliasco, TO, Italy
| | - Daniel Berveiller
- Universite Paris-Saclay, Centre national de la recherche scientifique, AgroParisTech, Ecologie Systematique et Evolution, 91405, Orsay, France
| | - Michal Bogdziewicz
- Department of Systematic Zoology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland
| | - Thomas Boivin
- Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Ecologie des Forets Mediterranennes, 84000, Avignon, France
| | - Raul Bonal
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, 28040, Madrid, Spain
| | - Don C Bragg
- USDA Forest Service, Southern Research Station, Monticello, AR, 71656, USA
| | - Thomas Caignard
- Universite Bordeaux, Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Biodiversity, Genes, and Communities (BIOGECO), 33615, Pessac, France
| | - Rafael Calama
- Centro de Investigacion Forestal - Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA-CIFOR), 28040, Madrid, Spain
| | - J Julio Camarero
- Instituto Pirenaico de Ecologla, Consejo Superior de Investigaciones Cientificas (IPE-CSIC), 50059, Zaragoza, Spain
| | - Chia-Hao Chang-Yang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
| | | | - Benoit Courbaud
- Universite Grenoble Alpes, Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Laboratoire EcoSystemes et Societes En Montagne (LESSEM), 38402, St. Martin-d'Heres, France
| | - Francois Courbet
- Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Ecologie des Forets Mediterranennes, 84000, Avignon, France
| | - Thomas Curt
- Aix Marseille universite, Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), 13182, Aix-en-Provence, France
| | - Adrian J Das
- USGS Western Ecological Research Center, Three Rivers, CA, 93271, USA
| | | | - Hendrik Davi
- Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Ecologie des Forets Mediterranennes, 84000, Avignon, France
| | - Nicolas Delpierre
- Universite Paris-Saclay, Centre national de la recherche scientifique, AgroParisTech, Ecologie Systematique et Evolution, 91405, Orsay, France
| | - Sylvain Delzon
- Universite Bordeaux, Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Biodiversity, Genes, and Communities (BIOGECO), 33615, Pessac, France
| | - Michael Dietze
- Earth and Environment, Boston University, Boston, MA, 02215, USA
| | - Sergio Donoso Calderon
- Universidad de Chile, Facultad de Ciencias Forestales y de la Conservacion de la Naturaleza (FCFCN), La Pintana, 8820808, Santiago, Chile
| | - Laurent Dormont
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS), 34293, Montpellier, France
| | - Josep Espelta
- Centre de Recerca Ecologica i Aplicacions Forestals (CREAF), Bellaterra, Catalunya, 08193, Spain
| | - Timothy J Fahey
- Natural Resources, Cornell University, Ithaca, NY, 14853, USA
| | - William Farfan-Rios
- Washington University in Saint Louis, Center for Conservation and Sustainable Development, Missouri Botanical Garden, St. Louis, MO, 63110, USA
| | - Catherine A Gehring
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Gregory S Gilbert
- Department of Environmental Studies, University of California, Santa Cruz, CA, 95064, USA
| | - Georg Gratzer
- Institute of Forest Ecology, Peter-Jordan-Strasse 82, 1190, Wien, Austria
| | - Cathryn H Greenberg
- Bent Creek Experimental Forest, USDA Forest Service, Asheville, NC, 28801, USA
| | - Qinfeng Guo
- Eastern Forest Environmental Threat Assessment Center, USDA Forest Service, Southern Research Station, Research Triangle Park, NC, 27709, USA
| | - Andrew Hacket-Pain
- Department of Geography and Planning, School of Environmental Sciences, University of Liverpool, Liverpool, UK
| | - Arndt Hampe
- Universite Bordeaux, Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Biodiversity, Genes, and Communities (BIOGECO), 33615, Pessac, France
| | - Qingmin Han
- Department of Plant Ecology Forestry and Forest Products Research Institute (FFPRI), Tsukuba, Ibaraki, 305-8687, Japan
| | | | - Kazuhiko Hoshizaki
- Department of Biological Environment, Akita Prefectural University, Akita, 010-0195, Japan
| | - Ines Ibanez
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jill F Johnstone
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK, 99700, USA
| | - Valentin Journé
- Universite Grenoble Alpes, Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Laboratoire EcoSystemes et Societes En Montagne (LESSEM), 38402, St. Martin-d'Heres, France
| | - Daisuke Kabeya
- Department of Plant Ecology Forestry and Forest Products Research Institute (FFPRI), Tsukuba, Ibaraki, 305-8687, Japan
| | | | - Thomas Kitzberger
- Department of Ecology, Instituto de Investigaciones en Biodiversidad y Medioambiente (Consejo Nacional de Investigaciones Cientificas y Tecnicas - Universidad Nacional del Comahue), Quintral 1250, 8400, Bariloche, Argentina
| | - Johannes M H Knops
- Health and Environmental Sciences Department, Xian Jiaotong-Liverpool University, Suzhou, 215123, China
| | - Richard K Kobe
- Department of Plant Biology, Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Georges Kunstler
- Universite Grenoble Alpes, Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Laboratoire EcoSystemes et Societes En Montagne (LESSEM), 38402, St. Martin-d'Heres, France
| | - Jonathan G A Lageard
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, M1 5GD, UK
| | - Jalene M LaMontagne
- Department of Biological Sciences, DePaul University, Chicago, IL, 60614, USA
| | - Mateusz Ledwon
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Slawkowska 17, 31-016, Krakow, Poland
| | - Francois Lefevre
- Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Ecologie des Forets Mediterranennes, 84000, Avignon, France
| | - Theodor Leininger
- USDA, Forest Service, Southern Research Station, PO Box 227, Stoneville, MS, 38776, USA
| | - Jean-Marc Limousin
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - James A Lutz
- Department of Wildland Resources, and the Ecology Center, Utah State University, Logan, UT, 84322, USA
| | - Diana Macias
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | | | | | - Emily Moran
- School of Natural Sciences, UC Merced, Merced, CA, 95343, USA
| | - Renzo Motta
- Department of Agriculture, Forest and Food Sciences, University of Torino, 10095, Grugliasco, TO, Italy
| | - Jonathan A Myers
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Thomas A Nagel
- Department of forestry and renewable forest resources, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Kyotaro Noguchi
- Tohoku Research Center, Forestry and Forest Products Research Institute, Morioka, Iwate, 020-0123, Japan
| | - Jean-Marc Ourcival
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Robert Parmenter
- Valles Caldera National Preserve, National Park Service, Jemez Springs, NM, 87025, USA
| | - Ian S Pearse
- Fort Collins Science Center, 2150 Centre Avenue Bldg C, Fort Collins, CO, 80526, USA
| | - Ignacio M Perez-Ramos
- Inst. de Recursos Naturales y Agrobiologia de Sevilla, Consejo Superior de Investigaciones Cientificas (IRNAS-CSIC), Seville, Andalucia, Spain
| | - Lukasz Piechnik
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512, Krakow, Poland
| | - John Poulsen
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
| | | | - Miranda D Redmond
- Department of Forest and Rangeland Stewardship, COlorado State University, Fort COllins, CO, USA
| | - Chantal D Reid
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
| | - Kyle C Rodman
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Javier D Sanguinetti
- Bilogo Dpto. Conservacin y Manejo Parque Nacional Lanin Elordi y Perito Moreno, 8370, San Marten de los Andes Neuqun, Argentina
| | - C Lane Scher
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
| | | | - Harald Schmidt Van Marle
- Universidad de Chile, Facultad de Ciencias Forestales y de la Conservacion de la Naturaleza (FCFCN), La Pintana, 8820808, Santiago, Chile
| | - Barbara Seget
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512, Krakow, Poland
| | - Shubhi Sharma
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
| | - Miles Silman
- Department of Biology, Wake Forest University, 1834 Wake Forest Rd, Winston-Salem, NC, 27106, USA
| | - Michael A Steele
- Department of Biology, Wilkes University, 84 West South Street, Wilkes-Barre, PA, 18766, USA
| | | | - Jacob N Straub
- Department of Environmental Science and Ecology, State University of New York-Brockport, Brockport, NY, 14420, USA
| | - I-Fang Sun
- Center for Interdisciplinary Research on Ecology and Sustainability, College of Environmental Studies, National Dong Hwa University, Hualien, Taiwan
| | - Samantha Sutton
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
| | - Jennifer J Swenson
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
| | - Margaret Swift
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
| | - Peter A Thomas
- School of Life Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - Maria Uriarte
- Department of Ecology, Evolution and Environmental Biology, Columbia University, 1113 Schermerhorn Ext., 1200 Amsterdam Ave., New York, NY, 10027, USA
| | - Giorgio Vacchiano
- Department of Agricultural and Environmental Sciences - Production, Territory, Agroenergy (DISAA), University of Milan, 20133, Milano, Italy
| | - Thomas T Veblen
- Department of Geography, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Amy V Whipple
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Thomas G Whitham
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Andreas P Wion
- Department of Forest and Rangeland Stewardship, Colorado State University, Fort Collins, CO, 80523, USA
| | - Boyd Wright
- Botany, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2350, Australia
| | - S Joseph Wright
- Smithsonian Tropical Research Institute, Apartado 0843n03092, Balboa, Republic of Panama
| | - Kai Zhu
- Department of Environmental Studies, University of California, Santa Cruz, CA, 95064, USA
| | - Jess K Zimmerman
- Department of Environmental Sciences, University of Puerto Rico, Rio Piedras, PR, 00936, USA
| | - Roman Zlotin
- Geography Department and Russian and East European Institute, Bloomington, IN, 47405, USA
| | - Magdalena Zywiec
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512, Krakow, Poland
| | - James S Clark
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA.
- Universite Grenoble Alpes, Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Laboratoire EcoSystemes et Societes En Montagne (LESSEM), 38402, St. Martin-d'Heres, France.
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15
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Dissecting the difference in tree species richness between Africa and South America. Proc Natl Acad Sci U S A 2022; 119:e2112336119. [PMID: 35349336 PMCID: PMC9168492 DOI: 10.1073/pnas.2112336119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Our full-scale comparison of Africa and South America’s lowland tropical tree floras shows that both Africa and South America’s moist and dry tree floras are organized similarly: plant families that are rich in tree species on one continent are also rich in tree species on the other continent, and these patterns hold across moist and dry environments. Moreover, we confirm that there is an important difference in tree species richness between the two continents, which is linked to a few families that are exceptionally diverse in South American moist forests, although dry formations also contribute to this difference. Plant families only present on one of the two continents do not contribute substantially to differences in tree species richness. Differences in species diversity over continental scales represent imprints of evolutionary, ecological, and biogeographic events. Here, we investigate whether the higher tree species richness in South America relative to Africa is due to higher richness in certain taxonomic clades, irrespective of vegetation type, or instead due to higher richness in specific biomes across all taxonomic clades. We used tree species inventory data to address this topic and began by clustering inventories from each continent based on species composition to derive comparable vegetation units. We found that moist forests in South America hold approximately four times more tree species than do moist forests in Africa, supporting previous studies. We also show that dry vegetation types in South America, such as tropical dry forests and savannas, hold twice as many tree species as do those in Africa, even though they cover a much larger area in Africa, at present and over geological time. Overall, we show that the marked species richness difference between South America and Africa is due primarily to a key group of families in the South American Amazon and Atlantic moist forests, which while present and speciose in Africa, are markedly less diverse there. Moreover, we demonstrate that both South American and African tree floras are organized similarly and that speciose families on one continent are likely speciose on the other. Future phylogenetic and functional trait work focusing on these key families should provide further insight into the processes leading to South America’s exceptional plant species diversity.
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The Plastome Sequences of Triticum sphaerococcum (ABD) and Triticum turgidum subsp. durum (AB) Exhibit Evolutionary Changes, Structural Characterization, Comparative Analysis, Phylogenomics and Time Divergence. Int J Mol Sci 2022; 23:ijms23052783. [PMID: 35269924 PMCID: PMC8911259 DOI: 10.3390/ijms23052783] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 12/10/2022] Open
Abstract
The mechanism and course of Triticum plastome evolution is currently unknown; thus, it remains unclear how Triticum plastomes evolved during recent polyploidization. Here, we report the complete plastomes of two polyploid wheat species, Triticum sphaerococcum (AABBDD) and Triticum turgidum subsp. durum (AABB), and compare them with 19 available and complete Triticum plastomes to create the first map of genomic structural variation. Both T. sphaerococcum and T. turgidum subsp. durum plastomes were found to have a quadripartite structure, with plastome lengths of 134,531 bp and 134,015 bp, respectively. Furthermore, diploid (AA), tetraploid (AB, AG) and hexaploid (ABD, AGAm) Triticum species plastomes displayed a conserved gene content and commonly harbored an identical set of annotated unique genes. Overall, there was a positive correlation between the number of repeats and plastome size. In all plastomes, the number of tandem repeats was higher than the number of palindromic and forward repeats. We constructed a Triticum phylogeny based on the complete plastomes and 42 shared genes from 71 plastomes. We estimated the divergence of Hordeum vulgare from wheat around 11.04-11.9 million years ago (mya) using a well-resolved plastome tree. Similarly, Sitopsis species diverged 2.8-2.9 mya before Triticum urartu (AA) and Triticum monococcum (AA). Aegilops speltoides was shown to be the maternal donor of polyploid wheat genomes and diverged ~0.2-0.9 mya. The phylogeny and divergence time estimates presented here can act as a reference framework for future studies of Triticum evolution.
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Prediction of Suitable Distribution of a Critically Endangered Plant Glyptostrobus pensilis. FORESTS 2022. [DOI: 10.3390/f13020257] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Glyptostrobus pensilis is a critically endangered living fossil plant species of the Mesozoic era, with high scientific research and economic value. The aim of this study was to assess the impact of climate change on the potential habitat area of G. pensilis in East Asia. The MaxEnt (maximum entropy) model optimized by the ENMeval data package was used to simulate the potential distribution habitats of G. pensilis since the last interglacial period (LIG, 120–140 ka). The results showed that the optimized MaxEnt model has a high prediction accuracy with the area under the receiver operating characteristic curve (AUC) of 0.9843 ± 0.005. The Current highly suitable habitats were found in the Northeast Jiangxi, Eastern Fujian and Eastern Guangdong; the main climatic factors affecting the geographic distribution of G. pensilis are temperature and precipitation, with precipitation as the temperature factor. The minimum temperature of coldest month (Bio6) may be the key factor restricting the northward distribution of G. pensilis; during the LIG, it contracted greatly in the highly suitable habitat area. Mean Diurnal Range (Bio2), Minimum Temperature of Coldest Month (Bio6), Annual Precipitation (Bio12) and Mean Temperature of Driest Quarter (Bio9) may be important climatic factors causing the changes in geographic distribution. In the next four periods, the suitable areas all migrated southward. Except for the RCP2.6-2070s, the highly suitable areas in the other three periods showed varying degrees of shrinkage. The results will provide a theoretical basis for the management and resource protection of G. pensilis.
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Abstract
One of the most fundamental questions in ecology is how many species inhabit the Earth. However, due to massive logistical and financial challenges and taxonomic difficulties connected to the species concept definition, the global numbers of species, including those of important and well-studied life forms such as trees, still remain largely unknown. Here, based on global ground-sourced data, we estimate the total tree species richness at global, continental, and biome levels. Our results indicate that there are ∼73,000 tree species globally, among which ∼9,000 tree species are yet to be discovered. Roughly 40% of undiscovered tree species are in South America. Moreover, almost one-third of all tree species to be discovered may be rare, with very low populations and limited spatial distribution (likely in remote tropical lowlands and mountains). These findings highlight the vulnerability of global forest biodiversity to anthropogenic changes in land use and climate, which disproportionately threaten rare species and thus, global tree richness.
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Roemer RB, Irene Terry L, Booth DT, Walter GH. Insights from an ancient gymnosperm lineage: ambient temperature and light and the timing of thermogenesis in cycad cones. AMERICAN JOURNAL OF BOTANY 2022; 109:151-165. [PMID: 35025111 DOI: 10.1002/ajb2.1810] [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: 08/16/2021] [Accepted: 10/08/2021] [Indexed: 06/14/2023]
Abstract
PREMISE Although maintaining the appropriate mid-day timing of the diel thermogenic events of cones of the dioecious cycads Macrozamia lucida and M. macleayi is central to the survival of both plant and pollinator in this obligate pollination mutualism, the nature of the underlying mechanism remains obscure. We investigated whether it is under circadian control. Circadian mechanisms control the timing of many ecologically important processes in angiosperms, yet only a few gymnosperms have been studied in this regard. METHODS We subjected cones to different ambient temperature and lighting regimens (constant temperature and darkness; stepwise cool/warm ambient temperatures in constant darkness; stepwise dark/light exposures at constant temperature) to determine whether the resulting timing of their thermogenic events was consistent with circadian control. RESULTS Cones exposed to constant ambient temperature and darkness generated multiple temperature peaks endogenously, with an average interpeak-temperature period of 20.7 (±0.20) h that is temperature-compensated (Q10 = 1.02). Exposure to 24-h ambient temperature cycles (12 h cool/12 h warm, constant darkness) yielded an interpeak-temperature period of 24.0 (±0.05) h, accurately and precisely replicating the ambient temperature period. Exposure to 24-h photo-cycles (12 h light/12 h dark, constant ambient temperature) yielded a shorter, more variable interpeak-temperature period of 23 (±0.23) h. CONCLUSIONS Our results indicate that cycad cone thermogenesis is under circadian clock control and differentially affected by ambient temperature and light cycles. Our data from cycads (an ancient gymnosperm lineage) adds to what little is known about circadian timing in gymnosperms, which have rarely been studied from the circadian perspective.
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Affiliation(s)
- Robert B Roemer
- Department of Mechanical Engineering, University of Utah, 1543 Rio Tinto Kennecott Mechanical Engineering Bldg., 1495 E., 100 S., Salt Lake City, UT, 84112, USA
| | - L Irene Terry
- School of Biological Sciences, University of Utah, 257 S. 1400 E., Salt Lake City, UT, 84112, USA
| | - David T Booth
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Gimme H Walter
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
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Xie D, Liu XQ, Chen YX, Jiao D, Lou JX, Qiu XF, Xu WH, Wang ZH, Ran JH, Wang XQ. Distribution and conservation of threatened gymnosperms in China. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Asaf S, Khan AL, Jan R, Khan A, Khan A, Kim KM, Lee IJ. The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence. THE PLANT GENOME 2021; 14:e20130. [PMID: 34505399 DOI: 10.1002/tpg2.20130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/08/2021] [Indexed: 05/25/2023]
Abstract
Gymnosperms are among the most endangered groups of plant species; they include ginkgo, pines (Conifers I), cupressophytes (Conifers II), cycads, and gnetophytes. The relationships among the five extant gymnosperm groups remain equivocal. We analyzed 167 available gymnosperm plastomes and investigated their diversity and phylogeny. We found that plastome size, structure, and gene order were highly variable in the five gymnosperm groups, of which Parasitaxus usta (Vieill.) de Laub. and Macrozamia mountperriensis F.M.Bailey had the smallest and largest plastomes, respectively. The inverted repeats (IRs) of the five groups were shown to have evolved through distinctive evolutionary scenarios. The IRs have been lost in all conifers but retained in cycads and gnetophytes. A positive association between simple sequence repeat (SSR) abundance and plastome size was observed, and the SSRs with the most variation were found in Pinaceae. Furthermore, the number of repeats was negatively correlated with IR length; thus, the highest number of repeats was detected in Conifers I and II, in which the IRs had been lost. We constructed a phylogeny based on 29 shared genes from 167 plastomes. With the plastome tree and 13 calibrations, we estimated the tree height between present-day angiosperms and gymnosperms to be ∼380 million years ago (mya). The placement of Gnetales in the tree agreed with the Gnetales-other gymnosperms hypothesis. The divergence between Ginkgo and cycads was estimated as ∼284 mya; the crown age of the cycads was 251 mya. Our time-calibrated plastid-based phylogenomic tree provides a framework for comparative studies of gymnosperm evolution.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Center, Univ. of Nizwa, Nizwa, 616, Oman
| | - Abdul Latif Khan
- Dep. of Biotechnology, College of Technology, Univ. of Houston, Houston, TX, 77204, USA
| | - Rahmatullah Jan
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National Univ., Daegu, 41566, Republic of Korea
| | - Arif Khan
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord Univ., Bodø, 8049, Norway
| | - Adil Khan
- Institute of Genomics for Crop Abiotic Stress Tolerance, Dep. of Plant and Soil Science, Texas Tech Univ., Lubbock, TX, 79409, USA
| | - Kyung-Min Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National Univ., Daegu, 41566, Republic of Korea
| | - In-Jung Lee
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National Univ., Daegu, 41566, Republic of Korea
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Coiro M, Barone Lumaga MR, Rudall PJ. Stomatal development in the cycad family Zamiaceae. ANNALS OF BOTANY 2021; 128:577-588. [PMID: 34265043 PMCID: PMC8422890 DOI: 10.1093/aob/mcab095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS The gymnosperm order Cycadales is pivotal to our understanding of seed-plant phylogeny because of its phylogenetic placement close to the root node of extant spermatophytes and its combination of both derived and plesiomorphic character states. Although widely considered a 'living fossil' group, extant cycads display a high degree of morphological and anatomical variation. We investigate stomatal development in Zamiaceae to evaluate variation within the order and homologies between cycads and other seed plants. METHODS Leaflets of seven species across five genera representing all major clades of Zamiaceae were examined at various stages of development using light microscopy and confocal microscopy. KEY RESULTS All genera examined have lateral subsidiary cells of perigenous origin that differ from other pavement cells in mature leaflets and could have a role in stomatal physiology. Early epidermal patterning in a 'quartet' arrangement occurs in Ceratozamia, Zamia and Stangeria. Distal encircling cells, which are sclerified at maturity, are present in all genera except Bowenia, which shows relatively rapid elongation and differentiation of the pavement cells during leaflet development. CONCLUSIONS Stomatal structure and development in Zamiaceae highlights some traits that are plesiomorphic in seed plants, including the presence of perigenous encircling subsidiary cells, and reveals a clear difference between the developmental trajectories of cycads and Bennettitales. Our study also shows an unexpected degree of variation among subclades in the family, potentially linked to differences in leaflet development and suggesting convergent evolution in cycads.
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Affiliation(s)
- Mario Coiro
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Ronin Institute for Independent Scholarship, Montclair, NJ, USA
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Cruz-Nicolás J, Villarruel-Arroyo A, Gernandt DS, Fonseca RM, Aguirre-Planter E, Eguiarte LE, Jaramillo-Correa JP. Non-adaptive evolutionary processes governed the diversification of a temperate conifer lineage after its migration into the tropics. Mol Phylogenet Evol 2021; 160:107125. [PMID: 33636326 DOI: 10.1016/j.ympev.2021.107125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 11/16/2022]
Abstract
Constructing phylogenetic relationships among closely related species is a recurrent challenge in evolutionary biology, particularly for long-lived taxa with large effective population sizes and uncomplete reproductive isolation, like conifers. Conifers further have slow evolutionary rates, which raises the question of whether adaptive or non/adaptive processes were predominantly involved when they rapidly diversified after migrating from temperate regions into the tropical mountains. Indeed, fine-scale phylogenetic relationships within several conifer genus remain under debate. Here, we studied the phylogenetic relationships of endemic firs (Abies, Pinaceae) discontinuously distributed in the montane forests from the Southwestern United States to Guatemala, and addressed several hypotheses related to adaptive and non-adaptive radiations. We derived over 80 K SNPs from genotyping by sequencing (GBS) for 45 individuals of nine Mesoamerican species to perform phylogenetic analyses. Both Maximum Likelihood and quartets-inference phylogenies resulted in a well-resolved topology, showing a single fir lineage divided in four subgroups that coincided with the main mountain ranges of Mesoamerica; thus having important taxonomic implications. Such subdivision fitted a North-South isolation by distance framework, in which non-adaptive allopatric processes seemed the rule. Interestingly, several reticulations were observed within subgroups, especially in the central-south region, which may explain past difficulties for generating infrageneric phylogenies. Further evidence for non-adaptive processes was obtained from analyses of 21 candidate-gene regions, which exhibited diminishing values of πa/πs and Ka/Ks with latitude, thus indicating reduced efficiency of purifying selection towards the Equator. Our study indicates that non-adaptive allopatric processes may be key generators of species diversity and endemism in the tropics.
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Affiliation(s)
- Jorge Cruz-Nicolás
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico
| | - Alfredo Villarruel-Arroyo
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico
| | - David S Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, AP 70-233, Mexico City CDMX 04510, Mexico
| | - Rosa María Fonseca
- Laboratorio de Plantas Vasculares, Facultad de Ciencias, Universidad Nacional Autónoma de México, AP 70-282, Mexico City CDMX 04510, Mexico
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico
| | - Juan P Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico.
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25
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Zhang TT, Hou YK, Yang T, Zhang SY, Yue M, Liu J, Li Z. Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect. PeerJ 2020; 8:e10312. [PMID: 33304650 PMCID: PMC7698693 DOI: 10.7717/peerj.10312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 10/15/2020] [Indexed: 12/27/2022] Open
Abstract
Gymnosperms such as ginkgo, conifers, cycads, and gnetophytes are vital components of land ecosystems, and they have significant economic and ecologic value, as well as important roles as forest vegetation. In this study, we investigated the structural variation and evolution of chloroplast transfer RNAs (tRNAs) in gymnosperms. Chloroplasts are important organelles in photosynthetic plants. tRNAs are key participants in translation where they act as adapter molecules between the information level of nucleic acids and functional level of proteins. The basic structures of gymnosperm chloroplast tRNAs were found to have family-specific conserved sequences. The tRNAΨ -loop was observed to contain a conforming sequence, i.e., U-U-C-N-A-N2. In gymnosperms, tRNAIle was found to encode a "CAU" anticodon, which is usually encoded by tRNAMet. Phylogenetic analysis suggested that plastid tRNAs have a common polyphyletic evolutionary pattern, i.e., rooted in abundant common ancestors. Analyses of duplication and loss events in chloroplast tRNAs showed that gymnosperm tRNAs have experienced little more gene loss than gene duplication. Transition and transversion analysis showed that the tRNAs are iso-acceptor specific and they have experienced unequal evolutionary rates. These results provide new insights into the structural variation and evolution of gymnosperm chloroplast tRNAs, which may improve our comprehensive understanding of the biological characteristics of the tRNA family.
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Affiliation(s)
- Ting-Ting Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Yi-Kun Hou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Ting Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Shu-Ya Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Jianni Liu
- Early Life Institute, State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi’an, China
| | - Zhonghu Li
- 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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Condamine FL, Silvestro D, Koppelhus EB, Antonelli A. The rise of angiosperms pushed conifers to decline during global cooling. Proc Natl Acad Sci U S A 2020; 117:28867-28875. [PMID: 33139543 PMCID: PMC7682372 DOI: 10.1073/pnas.2005571117] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Competition among species and entire clades can impact species diversification and extinction, which can shape macroevolutionary patterns. The fossil record shows successive biotic turnovers such that a dominant group is replaced by another. One striking example involves the decline of gymnosperms and the rapid diversification and ecological dominance of angiosperms in the Cretaceous. It is generally believed that angiosperms outcompeted gymnosperms, but the macroevolutionary processes and alternative drivers explaining this pattern remain elusive. Using extant time trees and vetted fossil occurrences for conifers, we tested the hypotheses that clade competition or climate change led to the decline of conifers at the expense of angiosperms. Here, we find that both fossil and molecular data show high congruence in revealing 1) low diversification rates, punctuated by speciation pulses, during warming events throughout the Phanerozoic and 2) that conifer extinction increased significantly in the Mid-Cretaceous (100 to 110 Ma) and remained high ever since. Their extinction rates are best explained by the rise of angiosperms, rejecting alternative models based on either climate change or time alone. Our results support the hypothesis of an active clade replacement, implying that direct competition with angiosperms increased the extinction of conifers by pushing their remaining species diversity and dominance out of the warm tropics. This study illustrates how entire branches on the Tree of Life may actively compete for ecological dominance under changing climates.
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Affiliation(s)
- Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier), 34095 Montpellier, France;
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Daniele Silvestro
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, SE-405 30 Gothenburg, Sweden
| | - Eva B Koppelhus
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, SE-405 30 Gothenburg, Sweden
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, United Kingdom
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Gutiérrez-Ortega JS, Salinas-Rodríguez MM, Ito T, Pérez-Farrera MA, Vovides AP, Martínez JF, Molina-Freaner F, Hernández-López A, Kawaguchi L, Nagano AJ, Kajita T, Watano Y, Tsuchimatsu T, Takahashi Y, Murakami M. Niche conservatism promotes speciation in cycads: the case of Dioon merolae (Zamiaceae) in Mexico. THE NEW PHYTOLOGIST 2020; 227:1872-1884. [PMID: 32392621 DOI: 10.1111/nph.16647] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
Niche conservatism is the tendency of lineages to retain the same niche as their ancestors. It constrains biological groups and prevents ecological divergence. However, theory predicts that niche conservatism can hinder gene flow, strengthen drift and increase local adaptation: does it mean that it also can facilitate speciation? Why does this happen? We aim to answer these questions. We examined the variation of chloroplast DNA, genome-wide single nucleotide polymorphisms, morphological traits and environmental variables across the Dioon merolae cycad populations. We tested geographical structure, scenarios of demographic history, and niche conservatism between population groups. Lineage divergence is associated with the presence of a geographical barrier consisting of unsuitable habitats for cycads. There is a clear genetic and morphological distinction between the geographical groups, suggesting allopatric divergence. However, even in contrasting available environmental conditions, groups retain their ancestral niche, supporting niche conservatism. Niche conservatism is a process that can promote speciation. In D. merolae, lineage divergence occurred because unsuitable habitats represented a barrier against gene flow, incurring populations to experience isolated demographic histories and disparate environmental conditions. This study explains why cycads, despite their ancient lineage origin and biological stasis, have been able to diversify into modern ecosystems worldwide.
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Affiliation(s)
| | | | - Takuro Ito
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Miguel Angel Pérez-Farrera
- Laboratorio de Ecología Evolutiva, Herbario Eizi Matuda, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez, 29039, Mexico
| | - Andrew P Vovides
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C., Xalapa, 91070, Mexico
| | - José F Martínez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, 83250, Mexico
| | - Francisco Molina-Freaner
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, 83250, Mexico
| | - Antonio Hernández-López
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de México, León, 37684, Mexico
| | - Lina Kawaguchi
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Tadashi Kajita
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Uehara, Yaeyama, Okinawa, 907-1541, Japan
| | - Yasuyuki Watano
- Department of Biology, Faculty of Science, Chiba University, Chiba, 263-8522, Japan
| | - Takashi Tsuchimatsu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yuma Takahashi
- Department of Biology, Faculty of Science, Chiba University, Chiba, 263-8522, Japan
| | - Masashi Murakami
- Department of Biology, Faculty of Science, Chiba University, Chiba, 263-8522, Japan
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Affiliation(s)
- Alicia Toon
- School of Biological Sciences; The University of Queensland; Brisbane Queensland 4072 Australia
| | - L. Irene Terry
- School of Biological Sciences; University of Utah; Salt Lake City Utah USA
| | | | - Gimme H. Walter
- School of Biological Sciences; The University of Queensland; Brisbane Queensland 4072 Australia
| | - Lyn G. Cook
- School of Biological Sciences; The University of Queensland; Brisbane Queensland 4072 Australia
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Rossetto-Harris G, Wilf P, Escapa IH, Andruchow-Colombo A. Eocene Araucaria Sect. Eutacta from Patagonia and floristic turnover during the initial isolation of South America. AMERICAN JOURNAL OF BOTANY 2020; 107:806-832. [PMID: 32388874 DOI: 10.1002/ajb2.1467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/12/2020] [Indexed: 06/11/2023]
Abstract
PREMISE Eocene floras of Patagonia document biotic response to the final separation of Gondwana. The conifer genus Araucaria, distributed worldwide during the Mesozoic, has a disjunct extant distribution between South America and Australasia. Fossils assigned to Australasian Araucaria Sect. Eutacta usually are represented by isolated organs, making diagnosis difficult. Araucaria pichileufensis E.W. Berry, from the middle Eocene Río Pichileufú (RP) site in Argentine Patagonia, was originally placed in Sect. Eutacta and later reported from the early Eocene Laguna del Hunco (LH) locality. However, the relationship of A. pichileufensis to Sect. Eutacta and the conspecificity of the Araucaria material among these Patagonian floras have not been tested using modern methods. METHODS We review the type material of A. pichileufensis alongside large (n = 192) new fossil collections of Araucaria from LH and RP, including multi-organ preservation of leafy branches, ovuliferous complexes, and pollen cones. We use a total evidence phylogenetic analysis to analyze relationships of the fossils to Sect. Eutacta. RESULTS We describe Araucaria huncoensis sp. nov. from LH and improve the whole-plant concept for Araucaria pichileufensis from RP. The two species respectively resolve in the crown and stem of Sect. Eutacta. CONCLUSIONS Our results confirm the presence and indicate the survival of Sect. Eutacta in South America during early Antarctic separation. The exceptionally complete fossils significantly predate several molecular age estimates for crown Eutacta. The differentiation of two Araucaria species demonstrates conifer turnover during climate change and initial South American isolation from the early to middle Eocene.
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Affiliation(s)
| | - Peter Wilf
- Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Ignacio H Escapa
- Museo Paleontológico Egidio Feruglio, Consejo Nacional de Investigaciones Científicas y Técnicas, Trelew, 9100, Chubut, Argentina
| | - Ana Andruchow-Colombo
- Museo Paleontológico Egidio Feruglio, Consejo Nacional de Investigaciones Científicas y Técnicas, Trelew, 9100, Chubut, Argentina
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Wu J. Risk and Uncertainty of Losing Suitable Habitat Areas Under Climate Change Scenarios: A Case Study for 109 Gymnosperm Species in China. ENVIRONMENTAL MANAGEMENT 2020; 65:517-533. [PMID: 32072220 DOI: 10.1007/s00267-020-01262-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 02/01/2020] [Indexed: 06/10/2023]
Abstract
Taking 109 gymnosperm species in China as a case, the uncertainty and risk of losing habitat areas of gymnosperm species under future climate conditions were investigated via representative concentration pathways climate change scenarios, fuzzy set classifications and Monte Carlo techniques. Under nonrandom climate change scenarios, the richness of 109 species increased in the partial locations of northwestern and northeastern China and declined in the partial locations of eastern and central and southeastern China; the numbers of species that losing <20%, 20-40%, 40-60%, 60-80%, and over 80% of their current habitat areas were ~33-49, 36-40, 11-24, 7-9, and 2-8, respectively; ~99-105 species occupied over 80% of their total suitable areas and ~4-9 species occupied 60-80% their total suitable areas. Under random climate change scenarios, the number of species that losing various level of the habitat areas declined with enhancing probability; with a probabilities of over 0.6, the numbers of species that losing <20%, 20-40%, 40-60%, 60-80% and over 80% of their current habitat areas were ~19-28, 3-19, 0-3, 1-2, and 9-14, respectively, and the numbers of species that occupying ~20%, 20-40%, 40-60%, 60-80%, and over 80% of their total suitable areas were ~9-14, 4-11, 2-6, 1-3, and 34-45, respectively. Approximately 41% of 109 species will face extinction risks from climate change; the losing habitat areas in future climate condition will cause the varying of coniferous forest composition and the losing of ecosystem service related to the species; the uncertainty of losing distribution areas for species should not be ignored.
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Affiliation(s)
- Jianguo Wu
- The Institute of Environmental Ecology, Chinese Research Academy of Environmental Sciences, No 8, Da Yang Fang, Beiyuan, Anwai, Chaoyang District, Beijing, 100012, China.
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Balao F, Lorenzo MT, Sánchez-Robles JM, Paun O, García-Castaño JL, Terrab A. Early diversification and permeable species boundaries in the Mediterranean firs. ANNALS OF BOTANY 2020; 125:495-507. [PMID: 31730195 PMCID: PMC7061173 DOI: 10.1093/aob/mcz186] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/14/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Inferring the evolutionary relationships of species and their boundaries is critical in order to understand patterns of diversification and their historical drivers. Despite Abies (Pinaceae) being the second most diverse group of conifers, the evolutionary history of Circum-Mediterranean firs (CMFs) remains under debate. METHODS We used restriction site-associated DNA sequencing (RAD-seq) on all proposed CMF taxa to investigate their phylogenetic relationships and taxonomic status. KEY RESULTS Based on thousands of genome-wide single nucleotide polymorphisms (SNPs), we present here the first formal test of species delimitation, and the first fully resolved, complete species tree for CMFs. We discovered that all previously recognized taxa in the Mediterranean should be treated as independent species, with the exception of Abies tazaotana and Abies marocana. An unexpectedly early pulse of speciation in the Oligocene-Miocene boundary is here documented for the group, pre-dating previous hypotheses by millions of years, revealing a complex evolutionary history encompassing both ancient and recent gene flow between distant lineages. CONCLUSIONS Our phylogenomic results contribute to shed light on conifers' diversification. Our efforts to resolve the CMF phylogenetic relationships help refine their taxonomy and our knowledge of their evolution.
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Affiliation(s)
- Francisco Balao
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
- For correspondence. E-mail
| | - María Teresa Lorenzo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
| | - José Manuel Sánchez-Robles
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Juan Luis García-Castaño
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
| | - Anass Terrab
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
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Oskolski AA, Huang L, Stepanova AV, Jin J. Araucarioid wood from the late Oligocene-early Miocene of Hainan Island: first fossil evidence for the genus Agathis in the Northern Hemisphere. JOURNAL OF PLANT RESEARCH 2020; 133:157-173. [PMID: 31915952 DOI: 10.1007/s10265-019-01165-z] [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: 07/05/2019] [Accepted: 12/26/2019] [Indexed: 06/10/2023]
Abstract
Although many fossil and molecular data suggest migrations from Malesia and Asia to Australia appear to dominate floristic exchange between Australian and Asian rainforests, evidence is emerging that demonstrate dispersal of plant groups from Australia to Asia. In this paper, a new species Agathis ledongensis sp. nov. is described on the basis of silicified wood from the late Oligocene-early Miocene of the Qiutangling Formation in Ledong, Hainan Island, South China. It is the first fossil record of Agathis in the Northern Hemisphere, and the only known fossil evidence of its dispersal outside of Gondwana. The close affinity of the fossil wood from Ledong with the genus Agathis was confirmed by comparing quantitative traits in 31 wood samples of 20 species representing all three extant genera of the Araucariaceae. The percentage of tracheids with uniseriate pitting on radial walls is shown as an additional diagnostic trait for separating Agathis and Wollemia from Araucaria. The wood of Agathis ledongensis provides evidence for the dispersal of this important plant group from Australia, or another Gondwanan terrane, to eastern Asia based on reliable fossil data. It records the occurrence of this genus in Hainan Island by the early Miocene, i.e. at the beginning of the formation of the island chains between Australia and the South-East Asia and thus the provision of a land migration route. As the land routes between these continents were restricted at that time, the migration of Agathis to Malesia and Asia was presumably facilitated by long-distance dispersal of its winged seeds by wind.
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Affiliation(s)
- Alexei A Oskolski
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa
- Komarov Botanical Institute of the Russian Academy of Sciences, Prof. Popov str. 2, St. Petersburg, 197376, Russia
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Luliang Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Anna V Stepanova
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa
- Komarov Botanical Institute of the Russian Academy of Sciences, Prof. Popov str. 2, St. Petersburg, 197376, Russia
| | - Jianhua Jin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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Mankga LT, Yessoufou K, Mugwena T, Chitakira M. The Cycad Genus Cycas May Have Diversified From Indochina and Occupied Its Current Ranges Through Vicariance and Dispersal Events. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00044] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Jensen DA, Ma K, Svenning J. Steep topography buffers threatened gymnosperm species against anthropogenic pressures in China. Ecol Evol 2020; 10:1838-1855. [PMID: 32128120 PMCID: PMC7042744 DOI: 10.1002/ece3.5983] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 11/08/2022] Open
Abstract
China is one of the most species-rich countries in the world, harboring many rare gymnosperms. Following recent human-led loss of forests, China is now experiencing increases in forest cover resulting from efforts of reforestation schemes. As anthropogenic activities have previously been found to interact with topography in shaping forest cover in China and considering the large human population and the ongoing population increase of the country, it is important to understand the role of anthropogenic pressures relative to environmental drivers for shaping species distributions here. Based on the well-established relationship between human population density and topography, we propose a hypothesis for explaining species distributions in a country dominated by human activities, predicting that species are more likely to occur in areas of steep topography under medium human population densities compared to low and high human population densities. Using species occurrence data from the Chinese Vascular Plant Distribution Database along with a common SDM method (maximum entropy modeling), we tested this hypothesis. Our results show that steep topography has the highest importance for predicting Chinese gymnosperm species occurrences in general, and threatened species specifically, in areas of medium human population densities. Consequently, these species are more often found in areas of steep terrain, supporting the proposed hypothesis. Results from this study highlight the need to include topographically heterogeneous habitats when planning new protected areas for species conservation.
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Affiliation(s)
- Ditte Arp Jensen
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE)Department of BioscienceAarhus UniversityAarhus CDenmark
- Section for Ecoinformatics and BiodiversityDepartment of BioscienceAarhus UniversityAarhus CDenmark
- Sino‐Danish Center for Education and Research (SDC)Water and Environment Programme, Eastern Yanqihu CampusUniversity of Chinese Academy of SciencesBeijingChina
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental ChangeInstitute of BotanyChinese Academy of SciencesBeijingChina
| | - Jens‐Christian Svenning
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE)Department of BioscienceAarhus UniversityAarhus CDenmark
- Section for Ecoinformatics and BiodiversityDepartment of BioscienceAarhus UniversityAarhus CDenmark
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De La Torre AR, Piot A, Liu B, Wilhite B, Weiss M, Porth I. Functional and morphological evolution in gymnosperms: A portrait of implicated gene families. Evol Appl 2020; 13:210-227. [PMID: 31892953 PMCID: PMC6935586 DOI: 10.1111/eva.12839] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/25/2019] [Accepted: 07/02/2019] [Indexed: 12/12/2022] Open
Abstract
Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water-conducting systems, secondary metabolism, stress defense mechanisms, and small RNA-mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole-genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.
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Affiliation(s)
| | - Anthony Piot
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
| | - Bobin Liu
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
- College of ForestryFujian Agricultural and Forestry UniversityFuzhouFujianChina
| | | | - Matthew Weiss
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
| | - Ilga Porth
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
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36
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Climate and evolutionary history define the phylogenetic diversity of vegetation types in the central region of South America. Oecologia 2019; 192:191-200. [PMID: 31768739 DOI: 10.1007/s00442-019-04561-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 11/19/2019] [Indexed: 10/25/2022]
Abstract
In South America the biogeographic history has produced different biomes with different vegetation types and distinct floras. As these vegetation types may diverge in evolutionary histories, we analysed how alpha and beta phylogenetic diversity vary across them and determine the main drivers of variation in phylogenetic diversity. To this end, we compiled a list of 205 sites and 1222 tree species spread over four biomes and eight vegetation types in central South America. For each site we evaluated six measures of evolutionary alpha diversity (species richness, phylogenetic diversity sensu stricto and the standardized effect size of phylogenetic diversity, mean phylogenetic distance and mean nearest taxon distance) and beta diversity (phylogenetic Sorensen's similarity). We checked the influence of spatial and environmental variables using generalized least squares models. The greatest phylogenetic differentiation was found between west and east of central South America, mainly between the Chaco communities and the other vegetation types, suggesting that species found in this biome come from different lineages, comparing with the others vegetation types. Our results also showed a clustered phylogenetic structure for the Dry Chaco woodlands, which may be associated with harsh environmental conditions. In addition to historical process, climatic conditions are the main drivers shaping phylogenetic patterns among the distinct vegetation types. Understanding patterns of phylogenetic diversity and distribution can greatly improve conservation planning and management since it allows the conservation of unique biome characteristics.
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Louca S, Pennell MW. A General and Efficient Algorithm for the Likelihood of Diversification and Discrete-Trait Evolutionary Models. Syst Biol 2019; 69:545-556. [DOI: 10.1093/sysbio/syz055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
As the size of phylogenetic trees and comparative data continue to grow and more complex models are developed to investigate the processes that gave rise to them, macroevolutionary analyses are becoming increasingly limited by computational requirements. Here, we introduce a novel algorithm, based on the “flow” of the differential equations that describe likelihoods along tree edges in backward time, to reduce redundancy in calculations and efficiently compute the likelihood of various macroevolutionary models. Our algorithm applies to several diversification models, including birth–death models and models that account for state- or time-dependent rates, as well as many commonly used models of discrete-trait evolution, and provides an alternative way to describe macroevolutionary model likelihoods. As a demonstration of our algorithm’s utility, we implemented it for a popular class of state-dependent diversification models—BiSSE, MuSSE, and their extensions to hidden-states. Our implementation is available through the R package $\texttt{castor}$. We show that, for these models, our algorithm is one or more orders of magnitude faster than existing implementations when applied to large phylogenies. Our algorithm thus enables the fitting of state-dependent diversification models to modern massive phylogenies with millions of tips and may lead to potentially similar computational improvements for many other macroevolutionary models.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, 1210 University of Oregon, Eugene, OR 97403, USA
- Institute of Ecology and Evolution, 5289 University of Oregon, Eugene, OR 97403, USA
| | - Matthew W Pennell
- Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, V6T1Z4 British Columbia, Canada
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, V6T1Z4 British Columbia, Canada
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38
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Rundel PW. A Neogene Heritage: Conifer Distributions and Endemism in Mediterranean-Climate Ecosystems. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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39
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Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil. Nat Commun 2019; 10:4201. [PMID: 31519986 PMCID: PMC6744486 DOI: 10.1038/s41467-019-12133-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 08/23/2019] [Indexed: 12/30/2022] Open
Abstract
As Charles Darwin anticipated, living fossils provide excellent opportunities to study evolutionary questions related to extinction, competition, and adaptation. Ginkgo (Ginkgo biloba L.) is one of the oldest living plants and a fascinating example of how people have saved a species from extinction and assisted its resurgence. By resequencing 545 genomes of ginkgo trees sampled from 51 populations across the world, we identify three refugia in China and detect multiple cycles of population expansion and reduction along with glacial admixture between relict populations in the southwestern and southern refugia. We demonstrate multiple anthropogenic introductions of ginkgo from eastern China into different continents. Further analyses reveal bioclimatic variables that have affected the geographic distribution of ginkgo and the role of natural selection in ginkgo’s adaptation and resilience. These investigations provide insights into the evolutionary history of ginkgo trees and valuable genomic resources for further addressing various questions involving living fossil species. Ginkgo is one of the living fossils from the plant kingdom. Here, authors conduct population genomics analyses to reveal its refugia and demographic history, and provide evidence of multiple anthropogenic introductions of ginkgo from eastern China into different continents.
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Kondratyeva A, Grandcolas P, Pavoine S. Reconciling the concepts and measures of diversity, rarity and originality in ecology and evolution. Biol Rev Camb Philos Soc 2019; 94:1317-1337. [PMID: 30861626 PMCID: PMC6850657 DOI: 10.1111/brv.12504] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 12/29/2022]
Abstract
The concept of biological diversity, or biodiversity, is at the core of evolutionary and ecological studies. Many indices of biodiversity have been developed in the last four decades, with species being one of the central units of these indices. However, evolutionary and ecological studies need a precise description of species' characteristics to best quantify inter-species diversity, as species are not equivalent and exchangeable. One of the first concepts characterizing species in biodiversity studies was abundance-based rarity. Abundance-based rarity was then complemented by trait- and phylo-based rarity, called species' trait-based and phylogenetic originalities, respectively. Originality, which is a property of an individual species, represents a species' contribution to the overall diversity of a reference set of species. Originality can also be defined as the rarity of a species' characteristics such as the state of a functional trait, which is often assumed to be represented by the position of the species on a phylogenetic tree. We review and compare various approaches for measuring originality, rarity and diversity and demonstrate that (i) even if attempts to bridge these concepts do exist, only a few ecological and evolutionary studies have tried to combine them all in the past two decades; (ii) phylo- and trait-based diversity indices can be written as a function of species rarity and originality measures in several ways; and (iii) there is a need for the joint use of these three types of indices to understand community assembly processes and species' roles in ecosystem functioning in order to protect biodiversity efficiently.
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Affiliation(s)
- Anna Kondratyeva
- Centre d'Ecologie et des Sciences de la Conservation (CESCO), Département Homme et Environnement, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, 57 Rue Cuvier, CP 135, 75005ParisFrance
- Institut Systématique Evolution Biodiversité (ISYEB), Département Origines et Evolution, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université EPHE, 57 Rue Cuvier, CP 50, 75005ParisFrance
| | - Philippe Grandcolas
- Institut Systématique Evolution Biodiversité (ISYEB), Département Origines et Evolution, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université EPHE, 57 Rue Cuvier, CP 50, 75005ParisFrance
| | - Sandrine Pavoine
- Centre d'Ecologie et des Sciences de la Conservation (CESCO), Département Homme et Environnement, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, 57 Rue Cuvier, CP 135, 75005ParisFrance
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Nyman T, Onstein RE, Silvestro D, Wutke S, Taeger A, Wahlberg N, Blank SM, Malm T. The early wasp plucks the flower: disparate extant diversity of sawfly superfamilies (Hymenoptera: ‘Symphyta’) may reflect asynchronous switching to angiosperm hosts. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz071] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe insect order Hymenoptera originated during the Permian nearly 300 Mya. Ancestrally herbivorous hymenopteran lineages today make up the paraphyletic suborder ‘Symphyta’, which encompasses c. 8200 species with very diverse host-plant associations. We use phylogeny-based statistical analyses to explore the drivers of diversity dynamics within the ‘Symphyta’, with a particular focus on the hypothesis that diversification of herbivorous insects has been driven by the explosive radiation of angiosperms during and after the Cretaceous. Our ancestral-state estimates reveal that the first symphytans fed on gymnosperms, and that shifts onto angiosperms and pteridophytes – and back – have occurred at different time intervals in different groups. Trait-dependent analyses indicate that average net diversification rates do not differ between symphytan lineages feeding on angiosperms, gymnosperms or pteridophytes, but trait-independent models show that the highest diversification rates are found in a few angiosperm-feeding lineages that may have been favoured by the radiations of their host taxa during the Cenozoic. Intriguingly, lineages-through-time plots show signs of an early Cretaceous mass extinction, with a recovery starting first in angiosperm-associated clades. Hence, the oft-invoked assumption of herbivore diversification driven by the rise of flowering plants may overlook a Cretaceous global turnover in insect herbivore communities during the rapid displacement of gymnosperm- and pteridophyte-dominated floras by angiosperms.
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Affiliation(s)
- Tommi Nyman
- Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Renske E Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle–Jena–Leipzig, Leipzig, Germany
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg and Gothenburg Global Biodiversity Centre, Sweden
| | - Saskia Wutke
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Andreas Taeger
- Senckenberg Deutsches Entomologisches Institut Müncheberg, Germany
| | | | - Stephan M Blank
- Senckenberg Deutsches Entomologisches Institut Müncheberg, Germany
| | - Tobias Malm
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
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Abstract
AbstractTraditionally the vulnerability of threatened species to extinction has been assessed by studying their environment, genetics and population dynamics. A more comprehensive understanding of the factors promoting or limiting the long-term persistence of threatened species could be achieved by conducting an analysis of their functional responses to changing environments, their ecological interactions, and their role in ecosystem functioning. These less traditional research areas can be unified in a trait-based approach, a recent methodological advance in ecology that is being used to link individual-level functions to species, community and ecosystem processes to provide mechanistic explanations of observed patterns, particularly in changing environments. We illustrate how trait-based information can be translated into well-defined conservation strategies, using the example of Dioon sonorense, an Endangered cycad endemic to north-western Mexico. Scientific information yielded by trait-based research, coupled with existing knowledge derived from well-established traditional approaches, could facilitate the development of more integrative conservation strategies to promote the long-term persistence of individual threatened species. A comprehensive database of functional traits of threatened species would be of value in assisting the implementation of the trait-based approach.
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Davies TJ. The macroecology and macroevolution of plant species at risk. THE NEW PHYTOLOGIST 2019; 222:708-713. [PMID: 30485443 DOI: 10.1111/nph.15612] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/12/2018] [Indexed: 05/19/2023]
Abstract
Contents Summary 708 I. Introduction 708 II. Fossils and phylogenies: learning from our past 708 III. Threatened species and Red Lists 710 IV. The geography of threat 710 V. The taxonomy of threat 710 VI. Predicting species at risk 711 VII. Conclusion 711 Acknowledgements 712 References 712 SUMMARY: Current rates of extinction are unprecedented in human history. The fossil record and newer molecular phylogenies illuminate historical patterns of speciation and extinction. They reveal both spectacular radiations and the characteristic features of mass extinction events in our geological past. The IUCN Red List provides insight into present-day species declines. There is emerging synthesis that species at risk are nonrandomly distributed across space and phylogeny. This pattern may be explained by geographical variation in driver intensity and species differential sensitivities. However, traits that confer resistance to one global change driver may increase susceptibility to a different driver. A complete understanding of extinction risk requires consideration of the interaction between extinction drivers, ecological traits, and species' evolutionary histories.
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Affiliation(s)
- T Jonathan Davies
- Departments of Botany, Forest & Conservation Sciences, Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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Crisp MD, Cook LG, Bowman DMJS, Cosgrove M, Isagi Y, Sakaguchi S. Turnover of southern cypresses in the post-Gondwanan world: extinction, transoceanic dispersal, adaptation and rediversification. THE NEW PHYTOLOGIST 2019; 221:2308-2319. [PMID: 30367483 PMCID: PMC6587739 DOI: 10.1111/nph.15561] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 10/15/2018] [Indexed: 05/23/2023]
Abstract
Cupressaceae subfamily Callitroideae has been an important exemplar for vicariance biogeography, but its history is more than just disjunctions resulting from continental drift. We combine fossil and molecular data to better assess its extinction and, sometimes, rediversification after past global change. Key fossils were reassessed and their phylogenetic placement for calibration was determined using trait mapping and Bayes Factors. Five vicariance hypotheses were tested by comparing molecular divergence times with the timing of tectonic rifting. The role of adaptation to fire (serotiny) in its spread across a drying Australia was tested for Callitris. Our findings suggest that three transoceanic disjunctions within the Callitroideae probably arose from long-distance dispersal. A signature of extinction, centred on the end-Eocene global climatic chilling and drying, is evident in lineages-through-time plots and in the fossil record. Callitris, the most diverse extant callitroid genus, suffered extinctions but surviving lineages adapted and re-radiated into dry, fire-prone biomes that expanded in the Neogene. Serotiny, a key adaptation to fire, likely evolved in Callitris coincident with the biome shift. Both extinction and adaptive shifts have probably played major roles in this chronicle of turnover and renewal, but better understanding of biogeographical history requires improved taxonomy of fossils.
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Affiliation(s)
- Michael D. Crisp
- Research School of BiologyThe Australian National UniversityRN Robertson Building, 46 Sullivans Creek RoadActon (Canberra)ACT2601Australia
| | - Lyn G. Cook
- School of Biological SciencesThe University of QueenslandBrisbaneQld4072Australia
| | - David M. J. S. Bowman
- School of Natural SciencesThe University of TasmaniaPrivate Bag 55HobartTas7001Australia
| | - Meredith Cosgrove
- Research School of BiologyThe Australian National UniversityRN Robertson Building, 46 Sullivans Creek RoadActon (Canberra)ACT2601Australia
| | - Yuji Isagi
- Graduate School of AgricultureKyoto UniversityKyoto606‐8502Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental StudiesKyoto UniversityKyoto606‐8501Japan
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Pinto-Ledezma JN, Larkin DJ, Cavender-Bares J. Patterns of Beta Diversity of Vascular Plants and Their Correspondence With Biome Boundaries Across North America. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00194] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Larcombe MJ, Jordan GJ, Bryant D, Higgins SI. The dimensionality of niche space allows bounded and unbounded processes to jointly influence diversification. Nat Commun 2018; 9:4258. [PMID: 30323199 PMCID: PMC6189034 DOI: 10.1038/s41467-018-06732-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/17/2018] [Indexed: 11/18/2022] Open
Abstract
There are two prominent and competing hypotheses that disagree about the effect of competition on diversification processes. The first, the bounded hypothesis, suggests that species diversity is limited (bounded) by competition between species for finite ecological niche space. The second, the unbounded hypothesis, proposes that innovations associated with evolution render competition unimportant over macroevolutionary timescales. Here we use phylogenetically structured niche modelling to show that processes consistent with both of these diversification models drive species accumulation in conifers. In agreement with the bounded hypothesis, niche competition constrained diversification, and in line with the unbounded hypothesis, niche evolution and partitioning promoted diversification. We then analyse niche traits to show that these diversification enhancing and inhibiting processes can occur simultaneously on different niche dimensions. Together these results suggest a new hypothesis for lineage diversification based on the multi-dimensional nature of ecological niches that can accommodate both bounded and unbounded evolutionary processes.
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Affiliation(s)
- Matthew J Larcombe
- Department of Botany, University of Otago, PO Box 56,, Dunedin, 9054, New Zealand.
| | - Gregory J Jordan
- Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
| | - David Bryant
- Department of Mathematics and Statistics, University of Otago, PO Box 56,, Dunedin, 9054, New Zealand
| | - Steven I Higgins
- Department of Botany, University of Otago, PO Box 56,, Dunedin, 9054, New Zealand.
- Plant Ecology, University of Bayreuth, Universitätstraße 30, 95447, Bayreuth, Germany.
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Walas Ł, Mandryk W, Thomas PA, Tyrała-Wierucka Ż, Iszkuło G. Sexual systems in gymnosperms: A review. Basic Appl Ecol 2018. [DOI: 10.1016/j.baae.2018.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Dorsey BL, Gregory TJ, Sass C, Specht CD. Pleistocene diversification in an ancient lineage: a role for glacial cycles in the evolutionary history of Dioon Lindl. (Zamiaceae). AMERICAN JOURNAL OF BOTANY 2018; 105:1512-1530. [PMID: 30229556 DOI: 10.1002/ajb2.1149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/10/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Recent estimates of crown ages for cycad genera (Late Miocene) challenge us to consider what processes have produced the extant diversity of this ancient group in such relatively little time. Pleistocene climate change has driven major shifts in species distributions in Mexico and may have led to speciation in the genus Dioon by forcing populations to migrate up in elevation, thereby becoming separated by topography. METHODS We inferred orthologs from transcriptomes of five species and sequenced these in 42 individuals representing all Dioon species. From these data and published plastid sequences, we inferred dated species trees and lineage-specific diversification rates. KEY RESULTS Analyses of 84 newly sequenced nuclear orthologs and published plastid data confirm four major clades within Dioon, all of Pleistocene age. Gene tree analysis, divergence dates, and an increase in diversification rate support very recent and rapid divergence of extant taxa. CONCLUSIONS This study confirms the Pleistocene age of Dioon species and implicates Pleistocene climate change and established topography in lineage spitting. These results add to our understanding of the cycads as evolutionarily dynamic lineages, not relicts or evolutionary dead ends. We also find that well-supported secondary calibration points can be reliable in the absence of fossils. Our hypothesis of lineage splitting mediated by habitat shifts may be applicable to other taxa that are restricted to elevation specific ecotones.
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Affiliation(s)
- Brian L Dorsey
- The Huntington Library, Art Collections, and Botanical Gardens, San Marino, CA, 91108, USA
| | - Timothy J Gregory
- University of California Botanical Garden, 200 Centennial Drive, Berkeley, CA, 94720, USA
| | - Chodon Sass
- Department of Integrative Biology and the University and Jepson Herbaria, 431 Koshland Hall, University of California, Berkeley, CA, 94720, USA
| | - Chelsea D Specht
- School of Integrative Plant Sciences, Section of Plant Biology, Cornell University, 412 Mann Library Building, Ithaca, New York, 14853, USA
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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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Abstract
Biologists would be mistaken if they relegated living fossils to paleontological inquiry or assumed that the concept is dead. It is now used to describe entities ranging from viruses to higher taxa, despite recent warnings of misleading inferences. Current work on character evolution illustrates how analyzing living fossils and stasis in terms of parts (characters) and wholes (e.g., organisms and lineages) advances our understanding of prolonged stasis at many hierarchical levels. Instead of viewing the concept's task as categorizing living fossils, we show how its primary role is to mark out what is in need of explanation, accounting for the persistence of both molecular and morphological traits. Rethinking different conceptions of living fossils as specific hypotheses reveals novel avenues for research that integrate phylogenetics, ecological and evolutionary modeling, and evo-devo to produce a more unified theoretical outlook.
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Affiliation(s)
- Scott Lidgard
- Integrative Research Center, Field Museum, Chicago, Illinois
| | - Alan C Love
- Department of Philosophy and the Minnesota Center for Philosophy of Science, University of Minnesota, Minneapolis
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