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Caviglia B, Di Bari D, Timr S, Guiral M, Giudici-Orticoni MT, Petrillo C, Peters J, Sterpone F, Paciaroni A. Decoding the Role of the Global Proteome Dynamics for Cellular Thermal Stability. J Phys Chem Lett 2024; 15:1435-1441. [PMID: 38291814 DOI: 10.1021/acs.jpclett.3c03351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Molecular mechanisms underlying the thermal response of cells remain elusive. On the basis of the recent result that the short-time diffusive dynamics of the Escherichia coli proteome is an excellent indicator of temperature-dependent bacterial metabolism and death, we used neutron scattering (NS) spectroscopy and molecular dynamics (MD) simulations to investigate the sub-nanosecond proteome mobility in psychro-, meso-, and hyperthermophilic bacteria over a wide temperature range. The magnitude of thermal fluctuations, measured by atomic mean square displacements, is similar among all studied bacteria at their respective thermal cell death. Global roto-translational motions turn out to be the main factor distinguishing the bacterial dynamical properties. We ascribe this behavior to the difference in the average proteome net charge, which becomes less negative for increasing bacterial thermal stability. We propose that the chemical-physical properties of the cytoplasm and the global dynamics of the resulting proteome are fine-tuned by evolution to uphold optimal thermal stability conditions.
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Affiliation(s)
- Beatrice Caviglia
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Laboratoire de Biochimie Théorique (UPR 9080), Centre National de la Recherche Scientifique (CNRS), Université de Paris Cité, 75005 Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Daniele Di Bari
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Stepan Timr
- Laboratoire de Biochimie Théorique (UPR 9080), Centre National de la Recherche Scientifique (CNRS), Université de Paris Cité, 75005 Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, 182 23 Prague, Czech Republic
| | - Marianne Guiral
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, 13400 Marseille, France
| | - Marie-Thérèse Giudici-Orticoni
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, 13400 Marseille, France
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Judith Peters
- Laboratoire Interdisciplinaire de Physique, Centre National de la Recherche Scientifique (CNRS), Univ. Grenoble Alpes, 140 Rue de la Physique, 38402 Saint-Martin-d'Hères, France
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble, France
- Institut Universitaire de France, 75231 Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique (UPR 9080), Centre National de la Recherche Scientifique (CNRS), Université de Paris Cité, 75005 Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
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2
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Algeo TJ, Shen J. Theory and classification of mass extinction causation. Natl Sci Rev 2024; 11:nwad237. [PMID: 38116094 PMCID: PMC10727847 DOI: 10.1093/nsr/nwad237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 12/21/2023] Open
Abstract
Theory regarding the causation of mass extinctions is in need of systematization, which is the focus of this contribution. Every mass extinction has both an ultimate cause, i.e. the trigger that leads to various climato-environmental changes, and one or more proximate cause(s), i.e. the specific climato-environmental changes that result in elevated biotic mortality. With regard to ultimate causes, strong cases can be made that bolide (i.e. meteor) impacts, large igneous province (LIP) eruptions and bioevolutionary events have each triggered one or more of the Phanerozoic Big Five mass extinctions, and that tectono-oceanic changes have triggered some second-order extinction events. Apart from bolide impacts, other astronomical triggers (e.g. solar flares, gamma bursts and supernova explosions) remain entirely in the realm of speculation. With regard to proximate mechanisms, most extinctions are related to either carbon-release or carbon-burial processes, the former being associated with climatic warming, ocean acidification, reduced marine productivity and lower carbonate δ13C values, and the latter with climatic cooling, increased marine productivity and higher carbonate δ13C values. Environmental parameters such as marine redox conditions and terrestrial weathering intensity do not show consistent relationships with carbon-cycle changes. In this context, mass extinction causation can be usefully classified using a matrix of ultimate and proximate factors. Among the Big Five mass extinctions, the end-Cretaceous biocrisis is an example of a bolide-triggered carbon-release event, the end-Permian and end-Triassic biocrises are examples of LIP-triggered carbon-release events, and the Late Ordovician and Late Devonian biocrises are examples of bioevolution-triggered carbon-burial events. Whereas the bolide-impact and LIP-eruption mechanisms appear to invariably cause carbon release, bioevolutionary triggers can result in variable carbon-cycle changes, e.g. carbon burial during the Late Ordovician and Late Devonian events, carbon release associated with modern anthropogenic climate warming, and little to no carbon-cycle impact due to certain types of ecosystem change (e.g. the advent of the first predators around the end-Ediacaran; the appearance of Paleolithic human hunters in Australasia and the Americas). Broadly speaking, studies of mass extinction causation have suffered from insufficiently critical thinking-an impartial survey of the extant evidence shows that (i) hypotheses of a common ultimate cause (e.g. bolide impacts or LIP eruptions) for all Big Five mass extinctions are suspect given manifest differences in patterns of environmental and biotic change among them; (ii) the Late Ordovician and Late Devonian events were associated with carbon burial and long-term climatic cooling, i.e. changes that are inconsistent with a bolide-impact or LIP-eruption mechanism; and (iii) claims of periodicity in Phanerozoic mass extinctions depended critically on the now-disproven idea that they shared a common extrinsic trigger (i.e. bolide impacts).
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Affiliation(s)
- Thomas J Algeo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences—Wuhan, Wuhan430074, China
- State Key Laboratory of Geological Processes and Mineral Resources, China University of Geosciences—Wuhan, Wuhan430074, China
- Department of Geosciences, University of Cincinnati, Cincinnati, OH45221, USA
| | - Jun Shen
- State Key Laboratory of Geological Processes and Mineral Resources, China University of Geosciences—Wuhan, Wuhan430074, China
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3
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Rousseau DD, Bagniewski W, Lucarini V. A punctuated equilibrium analysis of the climate evolution of cenozoic exhibits a hierarchy of abrupt transitions. Sci Rep 2023; 13:11290. [PMID: 37438407 DOI: 10.1038/s41598-023-38454-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 07/08/2023] [Indexed: 07/14/2023] Open
Abstract
The Earth's climate has experienced numerous critical transitions during its history, which have often been accompanied by massive and rapid changes in the biosphere. Such transitions are evidenced in various proxy records covering different timescales. The goal is then to identify, date, characterize, and rank past critical transitions in terms of importance, thus possibly yielding a more thorough perspective on climatic history. To illustrate such an approach, which is inspired by the punctuated equilibrium perspective on the theory of evolution, we have analyzed 2 key high-resolution datasets: the CENOGRID marine compilation (past 66 Myr), and North Atlantic U1308 record (past 3.3 Myr). By combining recurrence analysis of the individual time series with a multivariate representation of the system based on the theory of the quasi-potential, we identify the key abrupt transitions associated with major regime changes that separate various clusters of climate variability. This allows interpreting the time-evolution of the system as a trajectory taking place in a dynamical landscape, whose multiscale features describe a hierarchy of metastable states and associated tipping points.
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Affiliation(s)
- Denis-Didier Rousseau
- Géosciences Montpellier, Université Montpellier, Montpellier, France.
- Institute of Physics-CSE, Division of Geochronology and Environmental Isotopes, Silesian University of Technology, Gliwice, Poland.
- Lamont Doherty Earth Observatory, Columbia University, Palisades, NY, USA.
| | - Witold Bagniewski
- Ecole Normale Supérieure-Paris Sciences et Lettres, Laboratoire de Météorologie Dynamique, Paris, France
| | - Valerio Lucarini
- Department of Mathematics and Statistics, University of Reading, Reading, UK
- Centre for the Mathematics of Planet Earth, University of Reading, Reading, UK
- School of Systems Science, Beijing Normal University, Beijing, People's Republic of China
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4
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Li F, Wu N, Dong Y, Yang Y, Zhang Y, Zhang D, Hao Q, Lu H. Seasonal climatic instability in the western Chinese Loess Plateau during Marine Isotope Stages 12-10. Sci Rep 2023; 13:5725. [PMID: 37029154 PMCID: PMC10082009 DOI: 10.1038/s41598-023-32923-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 04/04/2023] [Indexed: 04/09/2023] Open
Abstract
Because of similar astronomical background, Marine Isotope Stage (MIS) 11 is viewed as an analogue of the Holocene, but the evolution of seasonal climatic instability during MIS 11 has not been well investigated. Here we present a time series of land-snail eggs-a recently-developed proxy of seasonal cooling events-from the Chinese Loess Plateau (CLP) to investigate seasonal climatic instability during MIS 11 and adjacent glacials. Due to the impact of low temperatures on egg hatching, egg-abundance peaks document seasonal cooling events. A total of five egg-abundance peaks were recorded in the CLP during MIS 12, MIS 11 and MIS 10. Three peaks are strong and occur close to glacial inception or interglacial-to-glacial transition; two weaker peaks occur during MIS11. These peaks imply seasonal climatic instability intensifies mainly during glacial initiation or transition. All these events correspond to ice-sheet growth and the loss of ice-rafted debris at high northern latitudes. Moreover, they occurred at the minima of local spring insolation during the MIS 12 and MIS 10 glacials, but at the maxima during the MIS 11 interglacial. This may contribute to the difference in the intensity of seasonal cooling events between low-eccentricity glacials and interglacials. Our results provide new evidence for understanding low-eccentricity interglacial-glacial evolution.
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Affiliation(s)
- Fengjiang Li
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.
- Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China.
| | - Naiqin Wu
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China
| | - Yajie Dong
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China
| | - Yiquan Yang
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- Gansu Civil Air Defence, Lanzhou, 730010, China
| | - Yueting Zhang
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- College of Earth Sciences, Hebei GEO University, Shijiazhuang, 050031, China
| | - Dan Zhang
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- School of History, Renmin University of China, Beijing, 100872, China
| | - Qingzhen Hao
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Houyuan Lu
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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5
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Feng C, Wang K, Xu W, Yang L, Wanghe K, Sun N, Wu B, Wu F, Yang L, Qiu Q, Gan X, Chen Y, He S. Monsoon boosted radiation of the endemic East Asian carps. SCIENCE CHINA. LIFE SCIENCES 2023; 66:563-578. [PMID: 36166180 DOI: 10.1007/s11427-022-2141-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/21/2022] [Indexed: 10/14/2022]
Abstract
Major historical events often trigger the rapid flourishing of a few lineages, which in turn shape established biodiversity patterns. How did this process occur and develop? This study provides a window into this issue. The endemic East Asian carps (EEAC) dominated the ichthyofauna of East Asia and exhibited a high degree of adaptation to monsoonal river-lake ecosystems. A series of evidence, including ecogeography, phylogenetics, and macroevolution, suggests that the EEAC is a lineage that arose with the East Asian monsoon and thrived intimately with subsequent monsoon activities. We further deduce the evolution of the EEAC and find that a range of historical events in the monsoon setting (e.g., marine transgression and regression and glacial-interglacial cycle) have further reshaped the distribution patterns of EEAC's members. Comparative genomics analyses reveal that introgressions during the initial period of EEAC radiation and innovations in the regulation of the brain and nervous system may have aided their adaptation to river-lake ecosystems in a monsoon setting, which boosted radiation. Overall, this study strengthens knowledge of the evolutionary patterns of freshwater fishes in East Asia and provides a model case for understanding the impact of major historical events on the evolution of biota.
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Affiliation(s)
- Chenguang Feng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Kunyuan Wanghe
- Key Laboratory of Adaptation and Evolution of Plateau Biota of Chinese Academy of Sciences, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Baosheng Wu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Feixiang Wu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Lei Yang
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xiaoni Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yiyu Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- National Natural Science Foundation of China, Beijing, 100085, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
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6
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Procheş Ş, Watkeys MK, Ramsay LF, Cowling RM. Why we should be looking for longitudinal patterns in biodiversity. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1032827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Our understanding of global diversity patterns relies overwhelmingly on ecological and evolutionary correlates of latitude, and largely ignores longitude. However, the two major explanations of biodiversity patterns – energy and stability – are confounded across latitudes, and longitude offers potential solutions. Recent literature shows that the global biogeography of the Cenozoic world is structured by longitudinal barriers. In a few well-studied regions, such as South Africa’s Cape, the Himalayas and the Amazon-Andes continuum, there are strong longitudinal gradients in biodiversity. Often, such gradients occur where high and low past climatic velocities are juxtaposed, and there is clear evidence of higher biodiversity at the climatically-stable end. Understanding longitudinal biodiversity variations more widely can offer new insights towards biodiversity conservation in the face of anthropogenic climatic change.
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7
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Di Bari D, Timr S, Guiral M, Giudici-Orticoni MT, Seydel T, Beck C, Petrillo C, Derreumaux P, Melchionna S, Sterpone F, Peters J, Paciaroni A. Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death. ACS CENTRAL SCIENCE 2023; 9:93-102. [PMID: 36712493 PMCID: PMC9881203 DOI: 10.1021/acscentsci.2c01078] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Indexed: 05/30/2023]
Abstract
Temperature variations have a big impact on bacterial metabolism and death, yet an exhaustive molecular picture of these processes is still missing. For instance, whether thermal death is determined by the deterioration of the whole or a specific part of the proteome is hotly debated. Here, by monitoring the proteome dynamics of E. coli, we clearly show that only a minor fraction of the proteome unfolds at the cell death. First, we prove that the dynamical state of the E. coli proteome is an excellent proxy for temperature-dependent bacterial metabolism and death. The proteome diffusive dynamics peaks at about the bacterial optimal growth temperature, then a dramatic dynamical slowdown is observed that starts just below the cell's death temperature. Next, we show that this slowdown is caused by the unfolding of just a small fraction of proteins that establish an entangling interprotein network, dominated by hydrophobic interactions, across the cytoplasm. Finally, the deduced progress of the proteome unfolding and its diffusive dynamics are both key to correctly reproduce the E. coli growth rate.
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Affiliation(s)
- Daniele Di Bari
- Università
degli Studi di Perugia, Dipartimento di
Fisica e Geologia, Via
A. Pascoli, 06123Perugia PG, Italy
- Université
Grenoble Alpes, CNRS, Laboratoire Interdisciplinaire de Physique, 38400Saint-Martin-d’Héres, France
- Institut
Laue-Langevin, 38000Grenoble, France
| | - Stepan Timr
- Laboratoire
de Biochimie Théorique (UPR9080), CNRS, Université de Paris Cité, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut
de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005Paris, France
- J.
Heyrovský
Institute of Physical Chemistry, Czech Academy
of Sciences, 182 23Prague 8, Czechia
| | - Marianne Guiral
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, BIP, CNRS, Aix-Marseille Université, 13400Marseille, France
| | | | - Tilo Seydel
- Institut
Laue-Langevin, 38000Grenoble, France
| | | | - Caterina Petrillo
- Università
degli Studi di Perugia, Dipartimento di
Fisica e Geologia, Via
A. Pascoli, 06123Perugia PG, Italy
| | - Philippe Derreumaux
- Laboratoire
de Biochimie Théorique (UPR9080), CNRS, Université de Paris Cité, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut
de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut Universitaire de France, 75005Paris, France
| | - Simone Melchionna
- ISC-CNR,
Dipartimento di Fisica, Università
Sapienza, 00185Rome, Italy
- Lexma
Technology1337 Massachusetts
Avenue, Arlington, Massachusetts02476, United States
| | - Fabio Sterpone
- Laboratoire
de Biochimie Théorique (UPR9080), CNRS, Université de Paris Cité, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut
de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005Paris, France
| | - Judith Peters
- Université
Grenoble Alpes, CNRS, Laboratoire Interdisciplinaire de Physique, 38400Saint-Martin-d’Héres, France
- Institut
Laue-Langevin, 38000Grenoble, France
- Institut Universitaire de France, 75005Paris, France
| | - Alessandro Paciaroni
- Università
degli Studi di Perugia, Dipartimento di
Fisica e Geologia, Via
A. Pascoli, 06123Perugia PG, Italy
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8
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Brée B, Condamine FL, Guinot G. Combining palaeontological and neontological data shows a delayed diversification burst of carcharhiniform sharks likely mediated by environmental change. Sci Rep 2022; 12:21906. [PMID: 36535995 PMCID: PMC9763247 DOI: 10.1038/s41598-022-26010-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Estimating deep-time species-level diversification processes remains challenging. Both the fossil record and molecular phylogenies allow the estimation of speciation and extinction rates, but each type of data may still provide an incomplete picture of diversification dynamics. Here, we combine species-level palaeontological (fossil occurrences) and neontological (molecular phylogenies) data to estimate deep-time diversity dynamics through process-based birth-death models for Carcharhiniformes, the most speciose shark order today. Despite their abundant fossil record dating back to the Middle Jurassic, only a small fraction of extant carcharhiniform species is recorded as fossils, which impedes relying only on the fossil record to study their recent diversification. Combining fossil and phylogenetic data, we recover a complex evolutionary history for carcharhiniforms, exemplified by several variations in diversification rates with an early low diversity period followed by a Cenozoic radiation. We further reveal a burst of diversification in the last 30 million years, which is partially recorded with fossil data only. We also find that reef expansion and temperature change can explain variations in speciation and extinction through time. These results pinpoint the primordial importance of these environmental variables in the evolution of marine clades. Our study also highlights the benefit of combining the fossil record with phylogenetic data to address macroevolutionary questions.
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Affiliation(s)
- Baptiste Brée
- grid.462058.d0000 0001 2188 7059Institut des Sciences de l’Evolution de Montpellier, CNRS, IRD, EPHE, Université de Montpellier, 34095 Montpellier, France
| | - Fabien L. Condamine
- grid.462058.d0000 0001 2188 7059Institut des Sciences de l’Evolution de Montpellier, CNRS, IRD, EPHE, Université de Montpellier, 34095 Montpellier, France
| | - Guillaume Guinot
- grid.462058.d0000 0001 2188 7059Institut des Sciences de l’Evolution de Montpellier, CNRS, IRD, EPHE, Université de Montpellier, 34095 Montpellier, France
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9
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Liu X, Wang Z, Wang W, Huang Q, Zeng Y, Jin Y, Li H, Du S, Zhang J. Origin and evolutionary history of Populus (Salicaceae): Further insights based on time divergence and biogeographic analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:1031087. [PMID: 36618663 PMCID: PMC9815717 DOI: 10.3389/fpls.2022.1031087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Populus (Salicaceae) species harbour rich biodiversity and are widely distributed throughout the Northern Hemisphere. However, the origin and biogeography of Populus remain poorly understood. METHODS We infer the divergence times and the historical biogeography of the genus Populus through phylogenetic analysis of 34 chloroplast fragments based on a large sample. RESULTS AND DISCUSSION Eurasia is the likely location of the early divergences of Salicaceae after the Cretaceous-Paleogene (K-Pg) mass extinction, followed by recurrent spread to the remainder of the Old World and the New World beginning in the Eocene; the extant Populus species began to diversity during the early Oligocene (approximately 27.24 Ma), climate changes during the Oligocene may have facilitated the diversification of modern poplar species; three separate lineages of Populus from Eurasia colonized North America in the Cenozoic via the Bering Land Bridges (BLB); We hypothesize that the present day disjunction in Populus can be explained by two scenarios: (i) Populus likely originated in Eurasia and subsequently colonized other regions, including North America; and (ii) the fact that the ancestor of the genus Populus that was once widely distributed in the Northern Hemisphere and eventually wiped out due to the higher extinction rates in North America, similar to the African Rand flora. We hypothesize that disparities in extinction across the evolutionary history of Populus in different regions shape the modern biogeography of Populus. Further studies with dense sampling and more evidence are required to test these hypotheses. Our research underscores the significance of combining phylogenetic analyses with biogeographic interpretations to enhance our knowledge of the origin, divergence, and distribution of biodiversity in temperate plant floras.
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Affiliation(s)
- Xia Liu
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Zhaoshan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Qinqin Huang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Yanfei Zeng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yu Jin
- Henan Academy of Forestry/Quality Testing Center for Forestry Products of National and Grassland Administration, Zhengzhou, China
| | - Honglei Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
| | - Shuhui Du
- Forestry College, Shanxi Agricultural University, Shanxi, China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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10
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Eocene Sedimentary–Diagenetic Environment Analysis of the Pingtai Area of the Qaidam Basin. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12146850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Based on the petrological characteristics and elemental geochemical analysis of core samples from the Pingtai area in the northern structural belt of the Qaidam Basin, this study shows that the clay mineral assemblage of Lulehe Formation sandstone is dominated by high contents of smectite, chlorite and illite, and does not contain illite–smectite mixed layers or kaolinite. The chlorite and illite in the Xiaganchaigou Formation decreased gradually and the smectite disappeared. In addition, illite–smectite mixed layers began to appear and kaolinite was not present. These results indicate that the diagenetic environment of the Pingtai area in the early Eocene was dominated by alkaline media poor in K+ and rich in Mg2+, Na+ and Ca2+. In the late Eocene, K+ content in the diagenetic medium increased significantly, and smectite began to transform into illite. From the early Eocene to the late Eocene, the overall climate and environmental characteristics showed a transition from cold and dry to a cold climate that alternated between dry and wet. The content changes of common oxides, such as CaO, MgO, K2O, Na2O, SiO2, Al2O3, Fe2O3 and TiO2, showed obvious correlation. Based on the content and ratio change tendencies of Sr, Ba, Cu, Zn, U, Th, Ce and other trace elements, combined with the variation characteristics of rare earth element contents, it is suggested that the Lulehe Formation was dominated by a dry and cold freshwater sedimentary environment, and that paleoclimatic conditions were relatively cold and arid during this sedimentary period. However, the climate in the sedimentary period of the Xiaganchaigou Formation was dominated by a cold environment alternating between dry and wet, which also reflected the finding that the global climate was mainly cold and dry in the early Eocene and gradually became warm and humid in the late Eocene.
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11
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Zhang L, Zhu X, Zhao Y, Guo J, Zhang T, Huang W, Huang J, Hu Y, Huang CH, Ma H. Phylotranscriptomics Resolves the Phylogeny of Pooideae and Uncovers Factors for Their Adaptive Evolution. Mol Biol Evol 2022; 39:6521033. [PMID: 35134207 PMCID: PMC8844509 DOI: 10.1093/molbev/msac026] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Adaptation to cool climates has occurred several times in different angiosperm groups. Among them, Pooideae, the largest grass subfamily with ∼3,900 species including wheat and barley, have successfully occupied many temperate regions and play a prominent role in temperate ecosystems. To investigate possible factors contributing to Pooideae adaptive evolution to cooling climates, we performed phylogenetic reconstruction using five gene sets (with 1,234 nuclear genes and their subsets) from 157 transcriptomes/genomes representing all 15 tribes and 24 of 26 subtribes. Our phylogeny supports the monophyly of all tribes (except Diarrheneae) and all subtribes with at least two species, with strongly supported resolution of their relationships. Molecular dating suggests that Pooideae originated in the late Cretaceous, with subsequent divergences under cooling conditions first among many tribes from the early middle to late Eocene and again among genera in the middle Miocene and later periods. We identified a cluster of gene duplications (CGD5) shared by the core Pooideae (with 80% Pooideae species) near the Eocene–Oligocene transition, coinciding with the transition from closed to open habitat and an upshift of diversification rate. Molecular evolutionary analyses homologs of CBF for cold resistance uncovered tandem duplications during the core Pooideae history, dramatically increasing their copy number and possibly promoting adaptation to cold habitats. Moreover, duplication of AP1/FUL-like genes before the Pooideae origin might have facilitated the regulation of the vernalization pathway under cold environments. These and other results provide new insights into factors that likely have contributed to the successful adaptation of Pooideae members to temperate regions.
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Affiliation(s)
- Lin Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Xinxin Zhu
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Yiyong Zhao
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Jing Guo
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Taikui Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Weichen Huang
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA, USA
| | - Jie Huang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yi Hu
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA, USA
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Hong Ma
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA, USA
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12
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Perception of Climate Change Effects over Time and the Contribution of Different Areas of Knowledge to Its Understanding and Mitigation. CLIMATE 2022. [DOI: 10.3390/cli10010007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Climate change is a current subject that is attracting more and more attention, whether from academics or the public. This public attention is mainly due to the frequently published news in the media, reporting consequences caused by extreme weather events. On the other hand, scientists are looking into the origins of the phenomenon, seeking answers that will somehow help to mitigate the effects of climate change. This article presents a review of some of the different possible approaches taken on climate change, to demonstrate the need to build a multidisciplinary perspective of the problem. It is understood that only the integration of different perspectives, presented by different areas of knowledge, such as natural sciences, social and economic sciences and human sciences, will make it possible to build modeling and predictive scenarios, which realistically may represent the development of the earth system under the influence of climate change. In this way, with the support of all areas of knowledge, the creation of forecast models where all possible changes to the different variables of the earth system may be simulated will allow for the mitigation measures presented to be analyzed in advance and, thus, prioritized. This review shows that a multi and interdisciplinary approach, based on the knowledge acquired from different knowledge and science fields, presents itself as the way to solve this global and complex problem caused by climate change.
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Bernardes SC, von Rintelen K, von Rintelen T, Pepato AR, Page TJ, de Bruyn M. Ecological changes have driven biotic exchanges across the Indian Ocean. Sci Rep 2021; 11:23357. [PMID: 34857837 PMCID: PMC8640032 DOI: 10.1038/s41598-021-02799-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/19/2021] [Indexed: 11/08/2022] Open
Abstract
The Indian Ocean has a complex geological history that has drawn the attention of naturalists for almost a century now. Due to its tectonic history, many geological elements and processes have been evoked to explain the exchange of species between landmasses. Here, we revisited previous studies on twenty-three taxa to investigate trends across time since the Gondwana breakup. We investigated these datasets by applying a time-calibrated Bayesian framework to them and reconstructing their ancestral ranges. We conclude that ecological transformations have presented opportunities for the establishment of migrants. The role of donating and receiving migrants has shifted several times according to these transformations. Time-specific trends show weak evidence for the stepping-stones commonly suggested as physical routes between landmasses. However, before its collision with Asia, India may have served as an intermediary for such exchanges.
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Affiliation(s)
- Samuel C Bernardes
- Museum Für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115, Berlin, Germany.
| | - Kristina von Rintelen
- Museum Für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115, Berlin, Germany
| | - Thomas von Rintelen
- Museum Für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115, Berlin, Germany
| | - Almir R Pepato
- Laboratório de Acarologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Timothy J Page
- Australian Rivers Institute, Griffith University, Queensland, Australia
| | - Mark de Bruyn
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
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14
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Earth history events shaped the evolution of uneven biodiversity across tropical moist forests. Proc Natl Acad Sci U S A 2021; 118:2026347118. [PMID: 34599095 PMCID: PMC8501849 DOI: 10.1073/pnas.2026347118] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2021] [Indexed: 02/07/2023] Open
Abstract
Tropical moist forests harbor much of the world’s biodiversity, but this diversity is not evenly distributed globally, with tropical moist forests in the Neotropics and Indomalaya generally exhibiting much greater diversity than in the Afrotropics. Here, we assess the ubiquity of this “pantropical diversity disparity” (PDD) using the present-day distributions of over 150,000 species of plants and animals, and we compare these distributions with a spatial model of diversification combined with reconstructions of plate tectonics, temperature, and aridity. Our study demonstrates that differences in paleoenvironmental dynamics between continents, including mountain building, aridification, and global temperature fluxes, can explain the PDD by shaping spatial and temporal patterns of species origination and extinction, providing a close match to observed distributions of plants and animals. Far from a uniform band, the biodiversity found across Earth’s tropical moist forests varies widely between the high diversity of the Neotropics and Indomalaya and the relatively lower diversity of the Afrotropics. Explanations for this variation across different regions, the “pantropical diversity disparity” (PDD), remain contentious, due to difficulty teasing apart the effects of contemporary climate and paleoenvironmental history. Here, we assess the ubiquity of the PDD in over 150,000 species of terrestrial plants and vertebrates and investigate the relationship between the present-day climate and patterns of species richness. We then investigate the consequences of paleoenvironmental dynamics on the emergence of biodiversity gradients using a spatially explicit model of diversification coupled with paleoenvironmental and plate tectonic reconstructions. Contemporary climate is insufficient in explaining the PDD; instead, a simple model of diversification and temperature niche evolution coupled with paleoaridity constraints is successful in reproducing the variation in species richness and phylogenetic diversity seen repeatedly among plant and animal taxa, suggesting a prevalent role of paleoenvironmental dynamics in combination with niche conservatism. The model indicates that high biodiversity in Neotropical and Indomalayan moist forests is driven by complex macroevolutionary dynamics associated with mountain uplift. In contrast, lower diversity in Afrotropical forests is associated with lower speciation rates and higher extinction rates driven by sustained aridification over the Cenozoic. Our analyses provide a mechanistic understanding of the emergence of uneven diversity in tropical moist forests across 110 Ma of Earth’s history, highlighting the importance of deep-time paleoenvironmental legacies in determining biodiversity patterns.
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15
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Hancock ZB, Ogawa H, Light JE, Wicksten MK. Origin and evolution of the Haustoriidae (Amphipoda): a eulogy for the Haustoriidira. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Abstract
Haustoriid amphipods have received little recent attention and their systematics and phylogenetics are largely unresolved. Some efforts have been made at classifying the family within the broader Amphipoda, but there is persistent incongruence in its placement among different authors and techniques. Furthermore, there exists no phylogenetic hypothesis of intrafamilial relationships. In this work, we evaluate the competing hypotheses on the phylogenetic position of the Haustoriidae within Amphipoda by examining new and previously published sequences of nearly 100 species across 38 families. We find strong support for the Haustoriidae as basal gammarids, and that other families placed within the parvorder ‘Haustoriidira’ are spread across Amphipoda. The radiation began during the Eocene and may have been driven in North America by the rapid filling of a coastal niche opened by the Chesapeake Bay impact crater. Unlike previous work, we find that the Pacific-endemic genus Eohaustorius is the most basal haustoriid, and that it separated from the rest of the family ~31 Mya. Finally, we provide taxonomic recommendations for relationships within Haustoriidae, including the elevation of a new genus, Cryptohaustorius gen. nov.. We conclude by recommending that the ‘Haustoriidira’ be abandoned.
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Affiliation(s)
- Zachary B Hancock
- Department of Biology, Texas A&M University, Butler Hall, 3258, 525 Lubbock St, College Station, TX, USA
- Ecology and Evolutionary Biology Interdisciplinary Program, Texas A&M University, College Station, TX, USA
| | - Hiroshi Ogawa
- Association for Protection of Marine Communities, 69 Jodoji-shimobanbacho, Sakyo, Kyoto, Japan
| | - Jessica E Light
- Ecology and Evolutionary Biology Interdisciplinary Program, Texas A&M University, College Station, TX, USA
- Department of Ecology and Conservation Biology, Texas A&M University, Building #1537–534 John Kimbrough Blvd, College Station, TX, USA
| | - Mary K Wicksten
- Department of Biology, Texas A&M University, Butler Hall, 3258, 525 Lubbock St, College Station, TX, USA
- Ecology and Evolutionary Biology Interdisciplinary Program, Texas A&M University, College Station, TX, USA
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16
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Zhang C, Huang CH, Liu M, Hu Y, Panero JL, Luebert F, Gao T, Ma H. Phylotranscriptomic insights into Asteraceae diversity, polyploidy, and morphological innovation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1273-1293. [PMID: 33559953 DOI: 10.1111/jipb.13078] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/08/2021] [Indexed: 05/29/2023]
Abstract
Biodiversity is not evenly distributed among related groups, raising questions about the factors contributing to such disparities. The sunflower family (Asteraceae, >26,000 species) is among the largest and most diverse plant families, but its species diversity is concentrated in a few subfamilies, providing an opportunity to study the factors affecting biodiversity. Phylotranscriptomic analyses here of 244 transcriptomes and genomes produced a phylogeny with strong support for the monophyly of Asteraceae and the monophyly of most subfamilies and tribes. This phylogeny provides a reference for detecting changes in diversification rates and possible factors affecting Asteraceae diversity, which include global climate shifts, whole-genome duplications (WGDs), and morphological evolution. The origin of Asteraceae was estimated at ~83 Mya, with most subfamilies having diverged before the Cretaceous-Paleocene boundary. Phylotranscriptomic analyses supported the existence of 41 WGDs in Asteraceae. Changes to herbaceousness and capitulescence with multiple flower-like capitula, often with distinct florets and scaly pappus/receptacular bracts, are associated with multiple upshifts in diversification rate. WGDs might have contributed to the survival of early Asteraceae by providing new genetic materials to support morphological transitions. The resulting competitive advantage for adapting to different niches would have increased biodiversity in Asteraceae.
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Affiliation(s)
- Caifei Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Biodiversity Sciences, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Biodiversity Sciences, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennslyvania, 16802, USA
| | - Mian Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Biodiversity Sciences, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yi Hu
- Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennslyvania, 16802, USA
| | - Jose L Panero
- Department of Integrative Biology, The University of Texas, University Station C0930, Austin, Texas, 78712, USA
| | - Federico Luebert
- Institut für Bodiversität der Pflanzen, Universität Bonn, Bonn, D - 53115, Germany
- Department of Silviculture and Nature Conservation, University of Chile, Santiago, 9206, Chile
| | - Tiangang Gao
- State Key Laboratory of Evolutionary and Systematic Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Hong Ma
- Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennslyvania, 16802, USA
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17
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Chouvenc T, Šobotník J, Engel MS, Bourguignon T. Termite evolution: mutualistic associations, key innovations, and the rise of Termitidae. Cell Mol Life Sci 2021; 78:2749-2769. [PMID: 33388854 PMCID: PMC11071720 DOI: 10.1007/s00018-020-03728-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/20/2020] [Accepted: 12/01/2020] [Indexed: 12/17/2022]
Abstract
Termites are a clade of eusocial wood-feeding roaches with > 3000 described species. Eusociality emerged ~ 150 million years ago in the ancestor of modern termites, which, since then, have acquired and sometimes lost a series of adaptive traits defining of their evolution. Termites primarily feed on wood, and digest cellulose in association with their obligatory nutritional mutualistic gut microbes. Recent advances in our understanding of termite phylogenetic relationships have served to provide a tentative timeline for the emergence of innovative traits and their consequences on the ecological success of termites. While all "lower" termites rely on cellulolytic protists to digest wood, "higher" termites (Termitidae), which comprise ~ 70% of termite species, do not rely on protists for digestion. The loss of protists in Termitidae was a critical evolutionary step that fostered the emergence of novel traits, resulting in a diversification of morphology, diets, and niches to an extent unattained by "lower" termites. However, the mechanisms that led to the initial loss of protists and the succession of events that took place in the termite gut remain speculative. In this review, we provide an overview of the key innovative traits acquired by termites during their evolution, which ultimately set the stage for the emergence of "higher" termites. We then discuss two hypotheses concerning the loss of protists in Termitidae, either through an externalization of the digestion or a dietary transition. Finally, we argue that many aspects of termite evolution remain speculative, as most termite biological diversity and evolutionary trajectories have yet to be explored.
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Affiliation(s)
- Thomas Chouvenc
- Entomology and Nematology Department, Institute of Food and Agricultural Science, Ft Lauderdale Research and Education Center, University of Florida, Davie, FL, USA.
| | - Jan Šobotník
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Michael S Engel
- Division of Entomology, Natural History Museum, and Department of Ecology and Evolutionary Biology, University of Kansas, 1501 Crestline Drive, Suite 140, Lawrence, KS, 66045, USA
| | - Thomas Bourguignon
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic.
- Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan.
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18
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Kirchhof S, Lyra ML, Rodríguez A, Ineich I, Müller J, Rödel MO, Trape JF, Vences M, Boissinot S. Mitogenome analyses elucidate the evolutionary relationships of a probable Eocene wet tropics relic in the xerophile lizard genus Acanthodactylus. Sci Rep 2021; 11:4858. [PMID: 33649347 PMCID: PMC7921649 DOI: 10.1038/s41598-021-83422-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/25/2021] [Indexed: 11/09/2022] Open
Abstract
Climate has a large impact on diversity and evolution of the world's biota. The Eocene-Oligocene transition from tropical climate to cooler, drier environments was accompanied by global species turnover. A large number of Old World lacertid lizard lineages have diversified after the Eocene-Oligocene boundary. One of the most speciose reptile genera in the arid Palearctic, Acanthodactylus, contains two sub-Saharan species with unresolved phylogenetic relationship and unknown climatic preferences. We here aim to understand how and when adaptation to arid conditions occurred in Acanthodactylus and when tropical habitats where entered. Using whole mitogenomes from fresh and archival DNA and published sequences we recovered a well-supported Acanthodactylus phylogeny and underpinned the timing of diversification with environmental niche analyses of the sub-Saharan species A. guineensis and A. boueti in comparison to all arid Acanthodactylus. We found that A. guineensis represents an old lineage that splits from a basal node in the Western clade, and A. boueti is a derived lineage and probably not its sister. Their long branches characterize them-and especially A. guineensis-as lineages that may have persisted for a long time without further diversification or have undergone multiple extinctions. Environmental niche models verified the occurrence of A. guineensis and A. boueti in hot humid environments different from the other 42 arid Acanthodactylus species. While A. guineensis probably remained in tropical habitat from periods prior to the Eocene-Oligocene boundary, A. boueti entered tropical environments independently at a later period. Our results provide an important baseline for studying adaptation and the transition from humid to arid environments in Lacertidae.
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Affiliation(s)
- Sebastian Kirchhof
- New York University Abu Dhabi, Abu Dhabi, Saadiyat Island, United Arab Emirates.
| | - Mariana L Lyra
- Instituto de Biociências, Departamento de Biodiversidade and Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista, Rio Claro, SP, CEP 13506-900, Brazil
| | - Ariel Rodríguez
- Institute of Zoology, University of Veterinary Medicine of Hannover, Bünteweg 17, 30559, Hannover, Germany
| | - Ivan Ineich
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, École Pratique des Hautes Études, Université des Antilles, CP 30, 57 rue Cuvier, 75005, Paris, France
| | - Johannes Müller
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Mark-Oliver Rödel
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Jean-François Trape
- Laboratoire de Paludologie et Zoologie médicale, IRD, UMR MIVEGEC, B. P. 1386, Dakar, Senegal
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106, Braunschweig, Germany
| | - Stéphane Boissinot
- New York University Abu Dhabi, Abu Dhabi, Saadiyat Island, United Arab Emirates
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19
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Broberg M, Dubey M, Iqbal M, Gudmundssson M, Ihrmark K, Schroers H, Funck Jensen D, Brandström Durling M, Karlsson M. Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in Clonostachys subgenus Bionectria (Fungi, Ascomycota, Hypocreales). Evol Appl 2021; 14:476-497. [PMID: 33664789 PMCID: PMC7896725 DOI: 10.1111/eva.13134] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 08/09/2020] [Accepted: 09/02/2020] [Indexed: 12/16/2022] Open
Abstract
Various strains of the mycoparasitic fungal species Clonostachys rosea are used commercially as biological control agents for the control of fungal plant diseases in agricultural crop production. Further improvements of the use and efficacy of C. rosea in biocontrol require a mechanistic understanding of the factors that determines the outcome of the interaction between C. rosea and plant pathogenic fungi. Here, we determined the genome sequences of 11 Clonostachys strains, representing five species in Clonostachys subgenus Bionectria, and performed a comparative genomic analysis with the aim to identify gene families evolving under selection for gene gains or losses. Several gene families predicted to encode proteins involved in biosynthesis of secondary metabolites, including polyketide synthases, nonribosomal peptide syntethases and cytochrome P450s, evolved under selection for gene gains (p ≤ .05) in the Bionectria subgenus lineage. This was accompanied with gene copy number increases (p ≤ .05) in ATP-binding cassette (ABC) transporters and major facilitator superfamily (MFS) transporters predicted to contribute to drug efflux. Most Clonostachys species were also characterized by high numbers of auxiliary activity (AA) family 9 lytic polysaccharide monooxygenases, AA3 glucose-methanol-choline oxidoreductases and additional carbohydrate-active enzyme gene families with putative activity (or binding) towards xylan and rhamnose/pectin substrates. Particular features of the C. rosea genome included expansions (p ≤ .05) of the ABC-B4 multidrug resistance transporters, the ABC-C5 multidrug resistance-related transporters and the 2.A.1.3 drug:H + antiporter-2 MFS drug resistance transporters. The ABC-G1 pleiotropic drug resistance transporter gene abcG6 in C. rosea was induced (p ≤ .009) by exposure to the antifungal Fusarium mycotoxin zearalenone (1121-fold) and various fungicides. Deletion of abcG6 resulted in mutants with reduced (p < .001) growth rates on media containing the fungicides boscalid, fenhexamid and iprodione. Our results emphasize the role of biosynthesis of, and protection against, secondary metabolites in Clonostachys subgenus Bionectria.
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Affiliation(s)
- Martin Broberg
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Mudassir Iqbal
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Mikael Gudmundssson
- Department of Molecular SciencesSwedish University of Agricultural SciencesUppsalaSweden
| | - Katarina Ihrmark
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | | | - Dan Funck Jensen
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
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20
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Liu Q, Xie Y, Liu B, Zhou Z, Feng Z, Chen Y. A transcriptomic variation map provides insights into the genetic basis of Pinus massoniana Lamb. evolution and the association with oleoresin yield. BMC PLANT BIOLOGY 2020; 20:375. [PMID: 32791991 PMCID: PMC7427074 DOI: 10.1186/s12870-020-02577-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/26/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND Masson pine (Pinus massoniana Lamb.), the dominant native coniferous species in southern China, is commercially important for supplying timber and oleoresin. However, knowledge of the genetic variability of masson pine germplasm is still limited. In this study, the genetic diversity and population structure of masson pine germplasm were assessed using 204 wild accessions from 10 main distribution regions using 94,194 core single-nucleotide polymorphisms (SNPs) obtained from transcriptome sequencing data. RESULTS The average expected heterozygosity was 0.2724, implying abundant genetic diversity within masson pine germplasm. Analysis of molecular variance (AMOVA) revealed that 3.29% of the variation was sourced from genetic differentiation. Structure analysis identified two geographically distinct groups. Discriminant analysis of principal components (DAPC) showed that one of those groups was further divided into two clusters. Sichuan and Chongqing provenance is the geographical origin, which diffused outward along two different lines. Oleoresin yield is reflected in the evolution of the two groups, and exhibits two different trends along the two lines of diffusion. The oleoresin yield may be associated with the genes of chitinase, CYP720B, cytochrome P450, ABC transporter, and AP2/ethylene-responsive transcription factor (ERF) based on SNPs and expression. CONCLUSIONS SNP markers from transcriptome sequencing are highly capable of evaluating genetic diversity within different species, as well as the genetic control of objective traits. The functions of these genes will be verified in future studies, and those genes strongly associated with oleoresin yield will be used to improve yields by means of early genotype selection and genetic engineering.
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Affiliation(s)
- Qinghua Liu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Tree Breeding, Hangzhou, 311400, Zhejiang, People's Republic of China
| | - Yini Xie
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Tree Breeding, Hangzhou, 311400, Zhejiang, People's Republic of China
| | - Bin Liu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Tree Breeding, Hangzhou, 311400, Zhejiang, People's Republic of China
| | - Zhichun Zhou
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, People's Republic of China.
- Zhejiang Provincial Key Laboratory of Tree Breeding, Hangzhou, 311400, Zhejiang, People's Republic of China.
| | - Zhongping Feng
- Laoshan Forest Farm of Chunan County, Chunan, 311700, Zhejiang, People's Republic of China
| | - Yadong Chen
- Biomarker Technologies Corporation, Beijing, 101300, People's Republic of China
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21
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Godfrey LR, Samonds KE, Baldwin JW, Sutherland MR, Kamilar JM, Allfisher KL. Mid-Cenozoic climate change, extinction, and faunal turnover in Madagascar, and their bearing on the evolution of lemurs. BMC Evol Biol 2020; 20:97. [PMID: 32770933 PMCID: PMC7414565 DOI: 10.1186/s12862-020-01628-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/18/2020] [Indexed: 01/16/2023] Open
Abstract
Background Was there a mid-Cenozoic vertebrate extinction and recovery event in Madagascar and, if so, what are its implications for the evolution of lemurs? The near lack of an early and mid-Cenozoic fossil record on Madagascar has inhibited direct testing of any such hypotheses. We compare the terrestrial vertebrate fauna of Madagascar in the Holocene to that of early Cenozoic continental Africa to shed light on the probability of a major mid-Cenozoic lemur extinction event, followed by an “adaptive radiation” or recovery. We also use multiple analytic approaches to test competing models of lemur diversification and the null hypothesis that no unusual mid-Cenozoic extinction of lemurs occurred. Results Comparisons of the terrestrial vertebrate faunas of the early Cenozoic on continental Africa and Holocene on Madagascar support the inference that Madagascar suffered a major mid-Cenozoic extinction event. Evolutionary modeling offers some corroboration, although the level of support varies by phylogeny and model used. Using the lemur phylogeny and divergence dates generated by Kistler and colleagues, RPANDA and TESS offer moderate support for the occurrence of unusual extinction at or near the Eocene-Oligocene (E-O) boundary (34 Ma). TreePar, operating under the condition of obligate mass extinction, found peak diversification at 31 Ma, and low probability of survival of prior lineages. Extinction at the E-O boundary received greater support than other candidate extinctions or the null hypothesis of no major extinction. Using the lemur phylogeny and divergence dates generated by Herrera & Dàvalos, evidence for large-scale extinction diminishes and its most likely timing shifts to before 40 Ma, which fails to conform to global expectations. Conclusions While support for large-scale mid-Cenozoic lemur extinction on Madagascar based on phylogenetic modeling is inconclusive, the African fossil record does provide indirect support. Furthermore, a major extinction and recovery of lemuriforms during the Eocene-Oligocene transition (EOT) would coincide with other major vertebrate extinctions in North America, Europe, and Africa. It would suggest that Madagascar’s lemurs were impacted by the climate shift from “greenhouse” to “ice-house” conditions that occurred at that time. This could, in turn, help to explain some of the peculiar characteristics of the lemuriform clade.
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Affiliation(s)
- Laurie R Godfrey
- Department of Anthropology, University of Massachusetts, 217 Machmer Hall, 240 Hicks Way, Amherst, MA, 01003, USA.
| | - Karen E Samonds
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Justin W Baldwin
- Department of Public Health, School of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA, 01003, USA.,Present Address: Department of Biology, Washington University, St. Louis, MO, 63130, USA
| | - Michael R Sutherland
- Department of Mathematics and Statistics, University of Massachusetts, Amherst, MA, 01003, USA
| | - Jason M Kamilar
- Department of Anthropology, University of Massachusetts, 217 Machmer Hall, 240 Hicks Way, Amherst, MA, 01003, USA
| | - Kristen L Allfisher
- Department of Anthropology, University of Massachusetts, 217 Machmer Hall, 240 Hicks Way, Amherst, MA, 01003, USA.,Present Address: USDA, APHIS, Riverdale, MD, 20737, USA
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22
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Yang B, Zhang G, Guo F, Wang M, Wang H, Xiao H. A Genomewide Scan for Genetic Structure and Demographic History of Two Closely Related Species, Rhododendron dauricum and R. mucronulatum ( Rhododendron, Ericaceae). FRONTIERS IN PLANT SCIENCE 2020; 11:1093. [PMID: 32765570 PMCID: PMC7380098 DOI: 10.3389/fpls.2020.01093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
Understanding the processes of divergence and speciation is an important task for evolutionary research, and climate oscillations play a pivotal role. We estimated the genetic structure and demographic history of two closely related species of Rhododendron, R. dauricum, and R. mucronulatum, distributed in northeastern China using 664,406 single nucleotide polymorphic loci of specific-locus amplified fragment sequencing (SLAF-seq) and 4 chloroplast DNA (cpDNA) fragments, sampling 376 individuals from 39 populations of these two species across their geographic distributions. The geographical distribution of cpDNA haplotypes revealed that R. dauricum and R. mucronulatum have different spatial genetic structures and haplotype diversity. Analysis of molecular variance (AMOVA) results showed that these two species have significant genetic differentiation and that the phylogeny demonstrates that these two species clustered a monophyletic group based on SLAF data, respectively, but not in cpDNA data. The evidence of significant gene flow was also detected from R. mucronulatum to R. dauricum. A deep divergence between the two species was observed and occurred during the early Oligocene. The niche models showed that the two species have different demographic histories. Thus, our results imply that geography and climate changes played important roles in the evolutionary process of R. dauricum and R. mucronulatum, and although there was an interspecific gene flow, the divergence was maintained by natural selection.
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Affiliation(s)
- Baiming Yang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
- Changchun Guoxin Modern Agricultural Technology Development Co., Ltd., Changchun, China
| | - Guoli Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
| | - Fengping Guo
- Biology Group, No. 30 Middle School of Shenyang, Shenyang, China
| | - Manqi Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
| | - Huaying Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
| | - Hongxing Xiao
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
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23
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Farahani RM, Rezaei-Lotfi S, Hunter N. Genomic competition for noise reduction shaped evolutionary landscape of mir-4673. NPJ Syst Biol Appl 2020; 6:12. [PMID: 32376854 PMCID: PMC7203229 DOI: 10.1038/s41540-020-0131-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 04/09/2020] [Indexed: 12/24/2022] Open
Abstract
The genomic platform that informs evolution of microRNA cascades remains unknown. Here we capitalised on the recent evolutionary trajectory of hominin-specific miRNA-4673, encoded in intron 4 of notch-1, to uncover the identity of one such precursor genomic element and the selective forces acting upon it. The miRNA targets genes that regulate Wnt/β-catenin signalling cascade. Primary sequence of the microRNA and its target region in Wnt modulating genes evolved from homologous signatures mapped to homotypic cis-clusters recognised by TCF3/4 and TFAP2A/B/C families. Integration of homologous TFAP2A/B/C cis-clusters (short range inhibitor of β-catenin) into the transcriptional landscape of Wnt cascade genes can reduce noise in gene expression. Probabilistic adoption of miRNA secondary structure by one such cis-signature in notch-1 reflected selection for superhelical curvature symmetry of precursor DNA to localise a nucleosome that overlapped the latter cis-cluster. By replicating the cis-cluster signature, non-random interactions of the miRNA with key Wnt modulator genes expanded the transcriptional noise buffering capacity via a coherent feed-forward loop mechanism. In consequence, an autonomous transcriptional noise dampener (the cis-cluster/nucleosome) evolved into a post-transcriptional one (the miRNA). The findings suggest a latent potential for remodelling of transcriptional landscape by miRNAs that capitalise on non-random distribution of genomic cis-signatures.
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Affiliation(s)
- Ramin M Farahani
- IDR/Westmead Institute for Medical Research and Westmead Centre for Oral Health, Sydney, NSW, Australia.
- Faculty of Medicine and Health Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Saba Rezaei-Lotfi
- Faculty of Medicine and Health Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Neil Hunter
- IDR/Westmead Institute for Medical Research and Westmead Centre for Oral Health, Sydney, NSW, Australia
- Faculty of Medicine and Health Sciences, University of Sydney, Sydney, NSW, 2006, Australia
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24
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Foster WJ, Garvie CL, Weiss AM, Muscente AD, Aberhan M, Counts JW, Martindale RC. Resilience of marine invertebrate communities during the early Cenozoic hyperthermals. Sci Rep 2020; 10:2176. [PMID: 32034228 PMCID: PMC7005832 DOI: 10.1038/s41598-020-58986-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 01/16/2020] [Indexed: 11/21/2022] Open
Abstract
The hyperthermal events of the Cenozoic, including the Paleocene-Eocene Thermal Maximum, provide an opportunity to investigate the potential effects of climate warming on marine ecosystems. Here, we examine the shallow benthic marine communities preserved in the late Cretaceous to Eocene strata on the Gulf Coastal Plain (United States). In stark contrast to the ecological shifts following the end-Cretaceous mass extinction, our data show that the early Cenozoic hyperthermals did not have a long-term impact on the generic diversity nor composition of the Gulf Coastal Plain molluscan communities. We propose that these communities were resilient to climate change because molluscs are better adapted to high temperatures than other taxa, as demonstrated by their physiology and evolutionary history. In terms of resilience, these communities differ from other shallow-water carbonate ecosystems, such as reef communities, which record significant changes during the early Cenozoic hyperthermals. These data highlight the strikingly different responses of community types, i.e., the almost imperceptible response of molluscs versus the marked turnover of foraminifera and reef faunas. The impact on molluscan communities may have been low because detrimental conditions did not devastate the entire Gulf Coastal Plain, allowing molluscs to rapidly recolonise vacated areas once harsh environmental conditions ameliorated.
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Affiliation(s)
- William J Foster
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity, Invalidenstraße 43, Berlin, 10115, Germany. .,University of Potsdam, Institute for Geosciences, Karl-Liebknecht Straße 24-25, Potsdam-Golm, 14476, Germany. .,University College Dublin, School of Earth Sciences, Belfield, Dublin, 4, Ireland.
| | - Christopher L Garvie
- Non-Vertebrate Paleontology Laboratory, Texas Natural Science Center, The University of Texas at Austin, 10100 Burnet Road, Austin, Texas, 78758, USA
| | - Anna M Weiss
- The University of Texas at Austin, Department of Geological Sciences, 2275 Speedway, Austin, Texas, 78712, USA
| | - A D Muscente
- The University of Texas at Austin, Department of Geological Sciences, 2275 Speedway, Austin, Texas, 78712, USA.,Cornell College, Department of Geology, Mount Vernon, Iowa, 600 First Street SW, 52314, USA
| | - Martin Aberhan
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity, Invalidenstraße 43, Berlin, 10115, Germany
| | - John W Counts
- University College Dublin, School of Earth Sciences, Belfield, Dublin, 4, Ireland
| | - Rowan C Martindale
- The University of Texas at Austin, Department of Geological Sciences, 2275 Speedway, Austin, Texas, 78712, USA
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25
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Lajmi A, Karanth PK. Eocene–Oligocene cooling and the diversification of Hemidactylus geckos in Peninsular India. Mol Phylogenet Evol 2020; 142:106637. [DOI: 10.1016/j.ympev.2019.106637] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 09/11/2019] [Accepted: 09/30/2019] [Indexed: 11/25/2022]
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26
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A fossil-calibrated phylogeny reveals the biogeographic history of the Cladrastis clade, an amphi-Pacific early-branching group in papilionoid legumes. Mol Phylogenet Evol 2019; 143:106673. [PMID: 31707137 DOI: 10.1016/j.ympev.2019.106673] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 11/24/2022]
Abstract
The early-branching Cladrastis clade of papilionoid legumes (Leguminosae, Papilionoideae) has an intriguing amphi-Pacific disjunct distribution in eastern Asia and temperate-tropical Americas. Here we used nuclear and three plastid regions to reconstruct the phylogenetic relationships and divergence times in the Cladrastis clade, as well as the evolution of morphological characters that might have been key in its biogeographic history. The ancestral character state estimation revealed that the most recent common ancestor of the Cladrastis clade was deciduous trees possessing compressed, winged fruits. The Cladrastis clade was inferred to have originated in the mid-latitude thermophilic forests of North America in the early Eocene, followed by the split between ancestors of wing-fruited Platyosprion and the non-wing-fruited group, and later the divergence of Cladrastis s.s. from the non-wing-fruited group in middle Eocene. Platyosprion and Cladrastis s.s. display an "out-of-North-America" biogeographic pattern and might have migrated to Asia via the Bering land bridge (BLB) or the North Atlantic land bridges (NALB) during middle to late Eocene. Our results, coupled with the relatively well documented fossil record for the clade, suggest that Platyosprion experienced an extinction event in North America caused by climatic cooling around the Eocene-Oligocene transition, which drove a major vegetation shift in western North America, in turn serving as a barrier for the vicariance of Pickeringia and Styphnolobium. The evolution of shrubby habit and sclerophyllous leaves in the former might be adaption to the chaparral vegetation in southwestern North America; the latter gained the trait of moniliform, succulent fruit. Styphnolobium further dispersed southward to tropical North America in the Oligocene, and eastward to Asia through BLB during middle Miocene. Subsequent sundering of BLB facilitated the vicariance of St. affine and St. japonicum.
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27
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Clay Minerals and Element Geochemistry of Clastic Reservoirs in the Xiaganchaigou Formation of the Lenghuqi Area, Northern Qaidam Basin, China. MINERALS 2019. [DOI: 10.3390/min9110678] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We performed mineralogical and geochemical analyses of core samples from the Lenghuqi area in the northern marginal tectonic belt of the Qaidam Basin. The clay mineralogy of the Xiaganchaigou Formation sandstone is dominated by I + I/S + C types and characterized by high illite, a higher mixed-layer illite/smectite and chlorite, lesser smectite, and an absence of kaolinite. The clay minerals reflect that the Oligocene sedimentary basin formed in an arid-semi-arid climate with weak leaching and chemical weathering, and that diagenesis occurred in a K+- and Mg2+-rich alkaline environment. Measured major oxide concentrations show clear correlations. The lower Xiaganchaigou Formation is representative of a dry and cold freshwater sedimentary environment, whereas the upper Xiaganchaigou Formation is warmer and more humid. Trace element and rare earth element variations indicate that the paleoclimate conditions of the lower Xiaganchaigou Formation sedimentary period were relatively cold and dry, while the upper Xiaganchaigou Formation formed under warmer and more humid climate conditions. These findings reflect a global climate of a cold and dry period from the late Eocene to early Oligocene, and a short warming period in the late Oligocene.
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28
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Paterson R, Samuels JX, Rybczynski N, Ryan MJ, Maddin HC. The earliest mustelid in North America. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AbstractUntil now, the pre-Miocene fossil record of mustelids in North America has been restricted to specimens attributable to oligobunine taxa and isolated remains tentatively allocated to the genus Plesictis. In the present study, we report on a nearly complete cranium and a referred dentary of a new genus and species of mustelid. The specimens were recovered from the Turtle Cove and Kimberly Members of the John Day Formation, Oregon, USA.These excellently preserved specimens more confidently confirm the presence of mustelids in the Early and Late Oligocene (Early and Late Arikareean) of North America. Like the holotype specimen of ‘Plesictis’ julieni, the new species lacks an alisphenoid canal and a postprotocrista on the M1 (synapomorphies of Mustelidae), but retains a dorsally deep suprameatal fossa (a feature occasionally suggested to be unique to Procyonidae). Phylogenetic analyses, applying parsimony and Bayesian inference to combined molecular (five genes totalling 5490 bp) and morphological data, recover this new species of mustelid as sister-species to ‘Plesictis’ julieni. The results of these analyses reveal that the new genus is a close relative of other species of Plesictis and several taxa traditionally allied with Oligobuninae, thereby rendering Oligobuninae paraphyletic. We further discuss the significance of the relatively small size of this new mustelid as it relates to predictions based on increased aridification of the palaeoclimate and the expansion of open habitats in the Oligocene.
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Affiliation(s)
- Ryan Paterson
- Department of Earth Sciences, Carleton University, Ottawa, Ontario, Canada
- Department of Paleobiology, Canadian Museum of Nature, Gatineau, Ontario, Canada
| | - Joshua X Samuels
- Department of Geosciences, East Tennessee State University, Johnson City, TN, USA
| | - Natalia Rybczynski
- Department of Earth Sciences, Carleton University, Ottawa, Ontario, Canada
- Department of Paleobiology, Canadian Museum of Nature, Gatineau, Ontario, Canada
| | - Michael J Ryan
- Department of Earth Sciences, Carleton University, Ottawa, Ontario, Canada
- Department of Vertebrate Paleontology, Cleveland Museum of Natural History, Cleveland, OH, USA
| | - Hillary C Maddin
- Department of Earth Sciences, Carleton University, Ottawa, Ontario, Canada
- Department of Paleobiology, Canadian Museum of Nature, Gatineau, Ontario, Canada
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29
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Climate cooling and clade competition likely drove the decline of lamniform sharks. Proc Natl Acad Sci U S A 2019; 116:20584-20590. [PMID: 31548392 DOI: 10.1073/pnas.1902693116] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding heterogeneity in species richness between closely related clades is a key research question in ecology and evolutionary biology. Multiple hypotheses have been proposed to interpret such diversity contrasts across the tree of life, with most studies focusing on speciation rates to explain clades' evolutionary radiations, while often neglecting extinction rates. Here we study a notorious biological model as exemplified by the sister relationships between mackerel sharks (Lamniformes, 15 extant species) and ground sharks (Carcharhiniformes, ∼290 extant species). Using a comprehensive fossil dataset, we found that the diversity dynamics of lamniforms waxed and waned following repeated cycles of radiation phases and declining phases. Radiation phases peaked up to 3 times the current diversity in the early Late Cretaceous. In the last 20 million years, the group declined to its present-day diversity. Along with a higher extinction risk for young species, we further show that this declining pattern is likely attributed to a combination of abiotic and biotic factors, with a cooling-driven extinction (negative correlation between temperature and extinction) and clade competition with some ground sharks. Competition from multiple clades successively drove the demise and replacement of mackerel sharks due to a failure to originate facing the rise of ground sharks, particularly since the Eocene. These effects came from ecologically similar carcharhiniform species inhibiting diversification of medium- and large-sized lamniforms. These results imply that the interplay between abiotic and biotic drivers had a substantial role in extinction and speciation, respectively, which determines the sequential rise and decline of marine apex predators.
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30
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Garcia-Porta J, Irisarri I, Kirchner M, Rodríguez A, Kirchhof S, Brown JL, MacLeod A, Turner AP, Ahmadzadeh F, Albaladejo G, Crnobrnja-Isailovic J, De la Riva I, Fawzi A, Galán P, Göçmen B, Harris DJ, Jiménez-Robles O, Joger U, Jovanović Glavaš O, Karış M, Koziel G, Künzel S, Lyra M, Miles D, Nogales M, Oğuz MA, Pafilis P, Rancilhac L, Rodríguez N, Rodríguez Concepción B, Sanchez E, Salvi D, Slimani T, S'khifa A, Qashqaei AT, Žagar A, Lemmon A, Moriarty Lemmon E, Carretero MA, Carranza S, Philippe H, Sinervo B, Müller J, Vences M, Wollenberg Valero KC. Environmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards. Nat Commun 2019; 10:4077. [PMID: 31501432 PMCID: PMC6733905 DOI: 10.1038/s41467-019-11943-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 08/13/2019] [Indexed: 11/09/2022] Open
Abstract
Climatic conditions changing over time and space shape the evolution of organisms at multiple levels, including temperate lizards in the family Lacertidae. Here we reconstruct a dated phylogenetic tree of 262 lacertid species based on a supermatrix relying on novel phylogenomic datasets and fossil calibrations. Diversification of lacertids was accompanied by an increasing disparity among occupied bioclimatic niches, especially in the last 10 Ma, during a period of progressive global cooling. Temperate species also underwent a genome-wide slowdown in molecular substitution rates compared to tropical and desert-adapted lacertids. Evaporative water loss and preferred temperature are correlated with bioclimatic parameters, indicating physiological adaptations to climate. Tropical, but also some populations of cool-adapted species experience maximum temperatures close to their preferred temperatures. We hypothesize these species-specific physiological preferences may constitute a handicap to prevail under rapid global warming, and contribute to explaining local lizard extinctions in cool and humid climates.
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Affiliation(s)
- Joan Garcia-Porta
- CREAF, 08193, Cerdanyola del Vallès, Spain
- Department of Biology, Washington University in Saint Louis, St. Louis, MO, 63130, USA
| | - Iker Irisarri
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Martin Kirchner
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Ariel Rodríguez
- Institute of Zoology, Tierärztliche Hochschule Hannover, Bünteweg 17, 30559, Hannover, Germany
| | - Sebastian Kirchhof
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Jason L Brown
- Department of Zoology, Southern Illinois University, Carbondale, IL, USA
| | - Amy MacLeod
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Alexander P Turner
- School of Engineering and Computer Science, University of Hull, Cottingham Road, HU6 7RX, Kingston-Upon-Hull, UK
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C, Tehran, Iran
| | - Gonzalo Albaladejo
- Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas (CSIC), c/Astrofísico Francisco Sánchez, 38206, Tenerife, Canary Islands, Spain
| | - Jelka Crnobrnja-Isailovic
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000 Niš, Institute for Biological Research "S. Stanković" University of Belgrade, Despota Stefana 142, Belgrade, 11000, Serbia
| | - Ignacio De la Riva
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, C/José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Adnane Fawzi
- Faculty of Sciences, Biodiversity and Ecosystem Dynamics Laboratory, Cadi Ayyad University, Marrakech, Morocco
| | - Pedro Galán
- Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, Grupo de Investigación en Biología Evolutiva (GIBE), 15071, A Coruña, Spain
| | - Bayram Göçmen
- Zoology Section, Biology Department, Faculty of Science, Ege University, 35100, Bornova, Izmir, Turkey
| | - D James Harris
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Octavio Jiménez-Robles
- Department of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Ulrich Joger
- Staatliches Naturhistorisches Museum, Braunschweig, Germany
| | | | - Mert Karış
- Department of Chemistry and Chemical Process Technologies, Acıgöl Vocational High School of Technical Sciences, Nevşehir Hacı Bektaş Veli University, 50300, Nevşehir, Turkey
| | - Giannina Koziel
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106, Braunschweig, Germany
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Mariana Lyra
- Departamento de Zoologia, Instituto de Biociências, UNESP - Universidade Estadual Paulista, Rio Claro, Brazil
| | - Donald Miles
- Department of Biological Sciences, Ohio University, Athens, OH, 45701, USA
| | - Manuel Nogales
- Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas (CSIC), c/Astrofísico Francisco Sánchez, 38206, Tenerife, Canary Islands, Spain
| | - Mehmet Anıl Oğuz
- Zoology Section, Biology Department, Faculty of Science, Ege University, 35100, Bornova, Izmir, Turkey
| | - Panayiotis Pafilis
- Section of Zoology and Marine Biology, Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Ilissia, Athens, 157-84, Greece
| | - Loïs Rancilhac
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106, Braunschweig, Germany
| | - Noemí Rodríguez
- Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas (CSIC), c/Astrofísico Francisco Sánchez, 38206, Tenerife, Canary Islands, Spain
| | - Benza Rodríguez Concepción
- Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas (CSIC), c/Astrofísico Francisco Sánchez, 38206, Tenerife, Canary Islands, Spain
| | - Eugenia Sanchez
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106, Braunschweig, Germany
| | - Daniele Salvi
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Department of Health, Life and Environmental Sciences, University of L'Aquila, 67100, Coppito, L'Aquila, Italy
| | - Tahar Slimani
- Faculty of Sciences, Biodiversity and Ecosystem Dynamics Laboratory, Cadi Ayyad University, Marrakech, Morocco
| | - Abderrahim S'khifa
- Faculty of Sciences, Biodiversity and Ecosystem Dynamics Laboratory, Cadi Ayyad University, Marrakech, Morocco
| | - Ali Turk Qashqaei
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C, Tehran, Iran
| | - Anamarija Žagar
- National Institute of Biology NIB, Department of Organisms and Ecosystems Research, Vecna pot 111, 1000, Ljubljana, Slovenia
| | - Alan Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, USA
| | | | - Miguel Angel Carretero
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat, Pompeu Fabra), Passeig Marítim de la Barceloneta 37-,49, 08003, Barcelona, Spain
| | - Hervé Philippe
- Centre for Biodiversity Theory and Modelling, UMR CNRS 5321, Station of Theoretical and Experimental Ecology, 09200, Moulis, France
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, and Institute for the Study of the Ecological and Evolutionary Climate Impacts, University of California, 130 McAllister Way, Coastal Biology Building, Santa Cruz, CA, 95064, USA
| | - Johannes Müller
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Miguel Vences
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106, Braunschweig, Germany.
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Starko S, Soto Gomez M, Darby H, Demes KW, Kawai H, Yotsukura N, Lindstrom SC, Keeling PJ, Graham SW, Martone PT. A comprehensive kelp phylogeny sheds light on the evolution of an ecosystem. Mol Phylogenet Evol 2019; 136:138-150. [PMID: 30980936 DOI: 10.1016/j.ympev.2019.04.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 12/24/2022]
Abstract
Reconstructing phylogenetic topologies and divergence times is essential for inferring the timing of radiations, the appearance of adaptations, and the historical biogeography of key lineages. In temperate marine ecosystems, kelps (Laminariales) drive productivity and form essential habitat but an incomplete understanding of their phylogeny has limited our ability to infer their evolutionary origins and the spatial and temporal patterns of their diversification. Here, we reconstruct the diversification of habitat-forming kelps using a global genus-level phylogeny inferred primarily from organellar genome datasets, and investigate the timing of kelp radiation. We resolve several important phylogenetic features, including relationships among the morphologically simple kelp families and the broader radiation of complex kelps, demonstrating that the initial radiation of the latter resulted from an increase in speciation rate around the Eocene-Oligocene boundary. This burst in speciation rate is consistent with a possible role of recent climatic cooling in triggering the kelp radiation and pre-dates the origin of benthic-foraging carnivores. Historical biogeographical reconstructions point to a northeast Pacific origin of complex kelps, with subsequent colonization of new habitats likely playing an important role in driving their ecological diversification. We infer that complex morphologies associated with modern kelp forests (e.g. branching, pneumatocysts) evolved several times over the past 15-20 MY, highlighting the importance of morphological convergence in establishing modern upright kelp forests. Our phylogenomic findings provide new insights into the geographical and ecological proliferation of kelps and provide a timeline along which feedbacks between kelps and their food-webs could have shaped the structure of temperate ecosystems.
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Affiliation(s)
- Samuel Starko
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada; Bamfield Marine Sciences Centre, 100 Pachena Rd., Bamfield V0R 1B0, Canada; Hakai Institute, Heriot Bay, Quadra Island, Canada.
| | - Marybel Soto Gomez
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Hayley Darby
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Kyle W Demes
- Department of Zoology, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Hiroshi Kawai
- Department of Biology, Kobe University, Rokkodaicho 657-8501, Japan
| | - Norishige Yotsukura
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo 060-0809, Japan
| | - Sandra C Lindstrom
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Patrick J Keeling
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada; Department of Zoology, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Sean W Graham
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Patrick T Martone
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada; Bamfield Marine Sciences Centre, 100 Pachena Rd., Bamfield V0R 1B0, Canada; Hakai Institute, Heriot Bay, Quadra Island, Canada
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32
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Kubicek CP, Steindorff AS, Chenthamara K, Manganiello G, Henrissat B, Zhang J, Cai F, Kopchinskiy AG, Kubicek EM, Kuo A, Baroncelli R, Sarrocco S, Noronha EF, Vannacci G, Shen Q, Grigoriev IV, Druzhinina IS. Evolution and comparative genomics of the most common Trichoderma species. BMC Genomics 2019; 20:485. [PMID: 31189469 PMCID: PMC6560777 DOI: 10.1186/s12864-019-5680-7] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 04/09/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the innate feature of Trichoderma. However, the evolution of these traits is not yet understood. RESULTS We selected 12 most commonly occurring Trichoderma species and studied the evolution of their genome sequences. Trichoderma evolved in the time of the Cretaceous-Palaeogene extinction event 66 (±15) mya, but the formation of extant sections (Longibrachiatum, Trichoderma) or clades (Harzianum/Virens) happened in Oligocene. The evolution of the Harzianum clade and section Trichoderma was accompanied by significant gene gain, but the ancestor of section Longibrachiatum experienced rapid gene loss. The highest number of genes gained encoded ankyrins, HET domain proteins and transcription factors. We also identified the Trichoderma core genome, completely curated its annotation, investigated several gene families in detail and compared the results to those of other fungi. Eighty percent of those genes for which a function could be predicted were also found in other fungi, but only 67% of those without a predictable function. CONCLUSIONS Our study presents a time scaled pattern of genome evolution in 12 Trichoderma species from three phylogenetically distant clades/sections and a comprehensive analysis of their genes. The data offer insights in the evolution of a mycoparasite towards a generalist.
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Affiliation(s)
- Christian P Kubicek
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
- , Vienna, Austria
| | - Andrei S Steindorff
- Departamento de Biologia Celular, Universidade de Brasília, Brasíla, DF, Brazil
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Komal Chenthamara
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Gelsomina Manganiello
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
- Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", Naples, Portici, Italy
| | - Bernard Henrissat
- CNRS, Aix-Marseille Université, Marseille, France
- INRA, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jian Zhang
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Feng Cai
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Alexey G Kopchinskiy
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | | | - Alan Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Riccardo Baroncelli
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Campus de Villamayor, Calle Del Duero, Villamayor, España
| | - Sabrina Sarrocco
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | | | - Giovanni Vannacci
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Campus de Villamayor, Calle Del Duero, Villamayor, España
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.
| | - Irina S Druzhinina
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria.
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.
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33
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Letsch H, Gottsberger B, Metzl C, Astrin J, Friedman ALL, McKenna DD, Fiedler K. Climate and host-plant associations shaped the evolution of ceutorhynch weevils throughout the Cenozoic. Evolution 2018; 72:1815-1828. [PMID: 30040114 PMCID: PMC6175111 DOI: 10.1111/evo.13520] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 04/26/2018] [Accepted: 05/30/2018] [Indexed: 12/19/2022]
Abstract
Using molecular phylogenetic data and methods we inferred divergence times and diversification patterns for the weevil subfamily Ceutorhynchinae in the context of host‐plant associations and global climate over evolutionary time. We detected four major diversification shifts that correlate with both host shifts and major climate events. Ceutorhynchinae experienced an increase in diversification rate at ∼53 Ma, during the Early Eocene Climate Optimum, coincident with a host shift to Lamiaceae. A second major diversification phase occurred at the end of the Eocene (∼34 Ma). This contrasts with the overall deterioration in climate equability at the Eocene‐Oligocene boundary, but tracks the diversification of important host plant clades in temperate (higher) latitudes, leading to increased diversification rates in the weevil clades infesting temperate hosts. A third major phase of diversification is correlated with the rising temperatures of the Late Oligocene Warming Event (∼26.5 Ma); diversification rates then declined shortly after the Middle Miocene Climate Transition (∼14.9 Ma). Our results indicate that biotic and abiotic factors together explain the evolution of Ceutorhynchinae better than each of these drivers viewed in isolation.
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Affiliation(s)
- Harald Letsch
- Department für Botanik und Biodiversitätsforschung, Universität Wien, Rennweg 14, 1030, Vienna, Austria
| | - Brigitte Gottsberger
- Department für Botanik und Biodiversitätsforschung, Universität Wien, Rennweg 14, 1030, Vienna, Austria
| | - Christian Metzl
- Department für Botanik und Biodiversitätsforschung, Universität Wien, Rennweg 14, 1030, Vienna, Austria
| | - Jonas Astrin
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | | | - Duane D McKenna
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee, 38152
| | - Konrad Fiedler
- Department für Botanik und Biodiversitätsforschung, Universität Wien, Rennweg 14, 1030, Vienna, Austria
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34
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Tavera J, Acero P. A, Wainwright PC. Multilocus phylogeny, divergence times, and a major role for the benthic-to-pelagic axis in the diversification of grunts (Haemulidae). Mol Phylogenet Evol 2018; 121:212-223. [DOI: 10.1016/j.ympev.2017.12.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/17/2017] [Accepted: 12/29/2017] [Indexed: 10/18/2022]
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Cleary TJ, Benson RBJ, Evans SE, Barrett PM. Lepidosaurian diversity in the Mesozoic-Palaeogene: the potential roles of sampling biases and environmental drivers. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171830. [PMID: 29657788 PMCID: PMC5882712 DOI: 10.1098/rsos.171830] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/13/2018] [Indexed: 05/27/2023]
Abstract
Lepidosauria is a speciose clade with a long evolutionary history, but there have been few attempts to explore its taxon richness through time. Here we estimate patterns of terrestrial lepidosaur genus diversity for the Triassic-Palaeogene (252-23 Ma), and compare observed and sampling-corrected richness curves generated using Shareholder Quorum Subsampling and classical rarefaction. Generalized least-squares regression (GLS) is used to investigate the relationships between richness, sampling and environmental proxies. We found low levels of richness from the Triassic until the Late Cretaceous (except in the Kimmeridgian-Tithonian of Europe). High richness is recovered for the Late Cretaceous of North America, which declined across the K-Pg boundary but remained relatively high throughout the Palaeogene. Richness decreased following the Eocene-Oligocene Grande Coupure in North America and Europe, but remained high in North America and very high in Europe compared to the Late Cretaceous; elsewhere data are lacking. GLS analyses indicate that sampling biases (particularly, the number of fossil collections per interval) are the best explanation for long-term face-value genus richness trends. The lepidosaur fossil record presents many problems when attempting to reconstruct past diversity, with geographical sampling biases being of particular concern, especially in the Southern Hemisphere.
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Affiliation(s)
- Terri J. Cleary
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Roger B. J. Benson
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Susan E. Evans
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Paul M. Barrett
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
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36
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Ferreira GS, Bronzati M, Langer MC, Sterli J. Phylogeny, biogeography and diversification patterns of side-necked turtles (Testudines: Pleurodira). ROYAL SOCIETY OPEN SCIENCE 2018; 5:171773. [PMID: 29657780 PMCID: PMC5882704 DOI: 10.1098/rsos.171773] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/26/2018] [Indexed: 05/13/2023]
Abstract
Pleurodires or side-necked turtles are today restricted to freshwater environments of South America, Africa-Madagascar and Australia, but in the past they were distributed much more broadly, being found also on Eurasia, India and North America, and marine environments. Two hypotheses were proposed to explain this distribution; in the first, vicariance would have shaped the current geographical distribution and, in the second, extinctions constrained a previously widespread distribution. Here, we aim to reconstruct pleurodiran biogeographic history and diversification patterns based on a new phylogenetic hypothesis recovered from the analysis of the largest morphological dataset yet compiled for the lineage, testing which biogeographical process prevailed during its evolutionary history. The resulting topology generally agrees with previous hypotheses of the group and shows that most diversification shifts were related to the exploration of new niches, e.g. littoral or marine radiations. In addition, as other turtles, pleurodires do not seem to have been much affected by either the Cretaceous-Palaeogene or the Eocene-Oligocene mass extinctions. The biogeographic analyses highlight the predominance of both anagenetic and cladogenetic dispersal events and support the importance of transoceanic dispersals as a more common driver of area changes than previously thought, agreeing with previous studies with other non-turtle lineages.
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Affiliation(s)
- Gabriel S. Ferreira
- Biology Department, FFCLRP, University of São Paulo, Ribeirão Preto, Brazil
- Senckenberg Center for Human Evolution and Palaeoenvironment (HEP) at Eberhard Karls Universität, Sigwartstraße 10, 72076 Tübingen, Germany
- Fachbereich Geowissenschaften der Eberhard Karls Universität Tübingen, Hölderlinstraße 12, 72074 Tübingen, Germany
| | - Mario Bronzati
- Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Strasse 10, 80333 Munich, Germany
- Department of Earth and Enviromental Sciences, Ludwig–Maximilians–Universität, Richard-Wagner-Strasse 10, 80333 Munich, Germany
| | - Max C. Langer
- Biology Department, FFCLRP, University of São Paulo, Ribeirão Preto, Brazil
| | - Juliana Sterli
- CONICET-Museo Paleontológico Egidio Feruglio, Fontana 140, 9100 Trelew, Chubut, Argentina
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37
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Phylogeny and biogeography of East Asian evergreen oaks (Quercus section Cyclobalanopsis; Fagaceae): Insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia. Mol Phylogenet Evol 2018; 119:170-181. [DOI: 10.1016/j.ympev.2017.11.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 11/14/2017] [Accepted: 11/14/2017] [Indexed: 11/17/2022]
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Cyriac VP, Kodandaramaiah U. Paleoclimate determines diversification patterns in the fossorial snake family Uropeltidae Cuvier, 1829. Mol Phylogenet Evol 2017; 116:97-107. [PMID: 28867076 DOI: 10.1016/j.ympev.2017.08.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/17/2017] [Accepted: 08/24/2017] [Indexed: 11/15/2022]
Abstract
Understanding how and why diversification rates vary across evolutionary time is central to understanding how biodiversity is generated and maintained. Recent mathematical models that allow estimation of diversification rates across time from reconstructed phylogenies have enabled us to make inferences on how biodiversity copes with environmental change. Here, we explore patterns of temporal diversification in Uropeltidae, a diverse fossorial snake family. We generate a time-calibrated phylogenetic hypothesis for Uropeltidae and show a significant correlation between diversification rate and paleotemperature during the Cenozoic. We show that the temporal diversification pattern of this group is punctuated by one rate shift event with a decrease in diversification and turnover rate between ca. 11Ma to present, but there is no strong support for mass extinction events. The analysis indicates higher turnover during periods of drastic climatic fluctuations and reduced diversification rates associated with contraction and fragmentation of forest habitats during the late Miocene. Our study highlights the influence of environmental fluctuations on diversification rates in fossorial taxa such as uropeltids, and raises conservation concerns related to present rate of climate change.
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Affiliation(s)
- Vivek Philip Cyriac
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE) and School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala P.O., Vithura, Thiruvananthapuram, Kerala 695551, India.
| | - Ullasa Kodandaramaiah
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE) and School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala P.O., Vithura, Thiruvananthapuram, Kerala 695551, India
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Conodonts and the Paleoclimatological and Paleoecological Applications of Phosphate Δ18O Measurements. ACTA ACUST UNITED AC 2017. [DOI: 10.1017/s1089332600002552] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Oxygen isotopic analysis of the phosphate in bioapatite has become a standard paleoclimatological tool with results documented in a rapidly expanding literature. Phosphate-based measurements are particularly important for samples where carbonates preservation is suspect (as is the case for many Paleozoic sites). Important analytical and observational advances that have fueled the expansion of phosphate-based studies include: 1) Oxygen isotopic ratios of biogenic apatite can be measured on small enough samples (≥ ~300 μg), quickly enough, cheaply enough, and accurately enough to permit meaningful high resolution paleoclimatic studies of trends through time, along spatial transects, and/or among taxa, 2) biogenic apatite is precipitated in approximate equilibrium with ambient waters and thus records the interplay of temperature and the isotopic composition of the water in which a sample grew, 3) tooth enamel and conodont crown material are quite resistant to diagenetic alteration and are preferred targets for both paleotemperature and paleoecological studies, 4) Paleozoic conodont δ18O records seem to provide robust paleotemperature information on time scales ranging from thousands of years to 100's of millions of years, and generation of increasingly refined paleotemperature records from this diagenetically resistant phase is likely to continue to be a useful field of study, 5) paleoenvironmental variations in δ18O values of seawater have been documented (e.g., differences between glacial and interglacial oceans), but whether and by how much the δ18O value of the hydrosphere may have increased since the Cambrian remains unresolved, and 6) differences in δ18O values among conodont taxa are increasingly well documented and, coupled with the potential to study growth series using ion microprobe techniques, are providing novel perspectives on and important tests of conodont paleoecology.
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40
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Finnegan S, Rasmussen CMØ, Harper DAT. Biogeographic and bathymetric determinants of brachiopod extinction and survival during the Late Ordovician mass extinction. Proc Biol Sci 2017; 283:rspb.2016.0007. [PMID: 27122567 DOI: 10.1098/rspb.2016.0007] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 04/04/2016] [Indexed: 11/12/2022] Open
Abstract
The Late Ordovician mass extinction (LOME) coincided with dramatic climate changes, but there are numerous ways in which these changes could have driven marine extinctions. We use a palaeobiogeographic database of rhynchonelliform brachiopods to examine the selectivity of Late Ordovician-Early Silurian genus extinctions and evaluate which extinction drivers are best supported by the data. The first (latest Katian) pulse of the LOME preferentially affected genera restricted to deeper waters or to relatively narrow (less than 35°) palaeolatitudinal ranges. This pattern is only observed in the latest Katian, suggesting that it reflects drivers unique to this interval. Extinction of exclusively deeper-water genera implies that changes in water mass properties such as dissolved oxygen content played an important role. Extinction of genera with narrow latitudinal ranges suggests that interactions between shifting climate zones and palaeobiogeography may also have been important. We test the latter hypothesis by estimating whether each genus would have been able to track habitats within its thermal tolerance range during the greenhouse-icehouse climate transition. Models including these estimates are favoured over alternative models. We argue that the LOME, long regarded as non-selective, is highly selective along biogeographic and bathymetric axes that are not closely correlated with taxonomic identity.
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Affiliation(s)
- Seth Finnegan
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Christian M Ø Rasmussen
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark Center for Macroecology, Evolution and Climate, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark Department of Geology, University of Lund, Lund, Sweden
| | - David A T Harper
- Palaeoecosystems Group, Department of Earth Sciences, Durham University, Durham DH1 3LE, UK Department of Geology, University of Lund, Lund, Sweden
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41
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Klaus KV, Schulz C, Bauer DS, Stützel T. Historical biogeography of the ancient lycophyte genusSelaginella: early adaptation to xeric habitats on Pangea. Cladistics 2016; 33:469-480. [DOI: 10.1111/cla.12184] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2016] [Indexed: 02/06/2023] Open
Affiliation(s)
- Kristina V. Klaus
- Department of Evolution and Biodiversity of Plants; Ruhr-Universität Bochum; Universitätsstraße 150 Bochum 44801 Germany
| | - Christian Schulz
- Department of Evolution and Biodiversity of Plants; Ruhr-Universität Bochum; Universitätsstraße 150 Bochum 44801 Germany
| | - Dennise S. Bauer
- Department of Evolution and Biodiversity of Plants; Ruhr-Universität Bochum; Universitätsstraße 150 Bochum 44801 Germany
| | - Thomas Stützel
- Department of Evolution and Biodiversity of Plants; Ruhr-Universität Bochum; Universitätsstraße 150 Bochum 44801 Germany
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Vuataz L, Rutschmann S, Monaghan MT, Sartori M. Molecular phylogeny and timing of diversification in Alpine Rhithrogena (Ephemeroptera: Heptageniidae). BMC Evol Biol 2016; 16:194. [PMID: 27654122 PMCID: PMC5031269 DOI: 10.1186/s12862-016-0758-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Larvae of the Holarctic mayfly genus Rhithrogena Eaton, 1881 (Ephemeroptera, Heptageniidae) are a diverse and abundant member of stream and river communities and are routinely used as bio-indicators of water quality. Rhithrogena is well diversified in the European Alps, with a number of locally endemic species, and several cryptic species have been recently detected. While several informal species groups are morphologically well defined, a lack of reliable characters for species identification considerably hampers their study. Their relationships, origin, timing of speciation and mechanisms promoting their diversification in the Alps are unknown. RESULTS Here we present a species-level phylogeny of Rhithrogena in Europe using two mitochondrial and three nuclear gene regions. To improve sampling in a genus with many cryptic species, individuals were selected for analysis according to a recent DNA-based taxonomy rather than traditional nomenclature. A coalescent-based species tree and a reconstruction based on a supermatrix approach supported five of the species groups as monophyletic. A molecular clock, mapped on the most resolved phylogeny and calibrated using published mitochondrial evolution rates for insects, suggested an origin of Alpine Rhithrogena in the Oligocene/Miocene boundary. A diversification analysis that included simulation of missing species indicated a constant speciation rate over time, rather than any pronounced periods of rapid speciation. Ancestral state reconstructions provided evidence for downstream diversification in at least two species groups. CONCLUSIONS Our species-level analyses of five gene regions provide clearer definitions of species groups within European Rhithrogena. A constant speciation rate over time suggests that the paleoclimatic fluctuations, including the Pleistocene glaciations, did not significantly influence the tempo of diversification of Alpine species. A downstream diversification trend in the hybrida and alpestris species groups supports a previously proposed headwater origin hypothesis for aquatic insects.
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Affiliation(s)
- Laurent Vuataz
- Musée cantonal de zoologie, Palais de Rumine, Place de la Riponne 6, 1014, Lausanne, Switzerland.
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Sereina Rutschmann
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, 14195, Berlin, Germany
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, 14195, Berlin, Germany
| | - Michel Sartori
- Musée cantonal de zoologie, Palais de Rumine, Place de la Riponne 6, 1014, Lausanne, Switzerland
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
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Abstract
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We review how major cell behaviors,
such as bacterial growth laws,
are derived from the physical chemistry of the cell’s proteins.
On one hand, cell actions depend on the individual biological functionalities
of their many genes and proteins. On the other hand, the common physics
among proteins can be as important as the unique biology that distinguishes
them. For example, bacterial growth rates depend strongly on temperature.
This dependence can be explained by the folding stabilities across
a cell’s proteome. Such modeling explains how thermophilic
and mesophilic organisms differ, and how oxidative damage of highly
charged proteins can lead to unfolding and aggregation in aging cells.
Cells have characteristic time scales. For example, E. coli can duplicate as fast as 2–3 times per hour. These time scales
can be explained by protein dynamics (the rates of synthesis and degradation,
folding, and diffusional transport). It rationalizes how bacterial
growth is slowed down by added salt. In the same way that the behaviors
of inanimate materials can be expressed in terms of the statistical
distributions of atoms and molecules, some cell behaviors can be expressed
in terms of distributions of protein properties, giving insights into
the microscopic basis of growth laws in simple cells.
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Affiliation(s)
- Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver , Denver, Colorado 80209, United States
| | - Adam M R de Graff
- Laufer Center for Physical and Quantitative Biology and Departments of Chemistry and Physics and Astronomy, Stony Brook University , Stony Brook, New York 11794, United States
| | - Lucas Sawle
- Department of Physics and Astronomy, University of Denver , Denver, Colorado 80209, United States
| | - Ken A Dill
- Laufer Center for Physical and Quantitative Biology and Departments of Chemistry and Physics and Astronomy, Stony Brook University , Stony Brook, New York 11794, United States
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Jia SW, Zhang ML, Raab-Straube EV, Thulin M. Evolutionary history ofGymnocarpos(Caryophyllaceae) in the arid regions from North Africa to Central Asia. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12834] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shu-Wen Jia
- Key Laboratory of Biogeography and Bioresource in Arid Land; Xinjiang Institute of Ecology and Geography; Chinese Academy of Sciences; Urumqi 830011 China
- Graduate University of the Chinese Academy of Sciences; Beijing 100049 China
| | - Ming-Li Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land; Xinjiang Institute of Ecology and Geography; Chinese Academy of Sciences; Urumqi 830011 China
- Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Eckhard V. Raab-Straube
- Botanischer Garten und Botanisches Museum Berlin-Dahlem; Freie Universität Berlin; Königin-Luise-Str. 6-8 14195 Berlin Germany
| | - Mats Thulin
- Department of Systematic Biology; EBC; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
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45
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Bellwood DR, Goatley CHR, Bellwood O. The evolution of fishes and corals on reefs: form, function and interdependence. Biol Rev Camb Philos Soc 2016; 92:878-901. [PMID: 26970292 DOI: 10.1111/brv.12259] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 02/02/2016] [Accepted: 02/04/2016] [Indexed: 11/30/2022]
Abstract
Coral reefs are renowned for their spectacular biodiversity and the close links between fishes and corals. Despite extensive fossil records and common biogeographic histories, the evolution of these two key groups has rarely been considered together. We therefore examine recent advances in molecular phylogenetics and palaeoecology, and place the evolution of fishes and corals in a functional context. In critically reviewing the available fossil and phylogenetic evidence, we reveal a marked congruence in the evolution of the two groups. Despite one group consisting of swimming vertebrates and the other colonial symbiotic invertebrates, fishes and corals have remarkably similar evolutionary histories. In the Paleocene and Eocene [66-34 million years ago (Ma)] most modern fish and coral families were present, and both were represented by a wide range of functional morphotypes. However, there is little evidence of diversification at this time. By contrast, in the Oligocene and Miocene (34-5.3 Ma), both groups exhibited rapid lineage diversification. There is also evidence of increasing reef area, occupation of new habitats, increasing coral cover, and potentially, increasing fish abundance. Functionally, the Oligocene-Miocene is marked by the appearance of new fish and coral taxa associated with high-turnover fast-growth ecosystems and the colonization of reef flats. It is in this period that the functional characteristics of modern coral reefs were established. Most species, however, only arose in the last 5.3 million years (Myr; Plio-Pleistocene), with the average age of fish species being 5.3 Myr, and corals just 1.9 Myr. While these species are genetically distinct, phenotypic differences are often limited to variation in colour or minor morphological features. This suggests that the rapid increase in biodiversity during the last 5.3 Myr was not matched by changes in ecosystem function. For reef fishes, colour appears to be central to recent diversification. However, the presence of pigment patterns in the Eocene suggests that colour may not have driven recent diversification. Furthermore, the lack of functional changes in fishes or corals over the last 5 Myr raises questions over the role and importance of biodiversity in shaping the future of coral reefs.
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Affiliation(s)
- David R Bellwood
- College of Marine and Environmental Sciences and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Christopher H R Goatley
- College of Marine and Environmental Sciences and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Orpha Bellwood
- College of Marine and Environmental Sciences and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
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46
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Gold JR, Willis SC, Renshaw MA, Buentello A, Walker HJ, Puritz JB, Hollenbeck CM, Voelker G. Phylogenetic relationships of tropical eastern Pacific snappers (Lutjanidae) inferred from mitochondrial DNA sequences. SYST BIODIVERS 2015. [DOI: 10.1080/14772000.2015.1078857] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Hogg RT, Godfrey LR, Schwartz GT, Dirks W, Bromage TG. Lemur Biorhythms and Life History Evolution. PLoS One 2015; 10:e0134210. [PMID: 26267241 PMCID: PMC4534448 DOI: 10.1371/journal.pone.0134210] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 07/07/2015] [Indexed: 11/18/2022] Open
Abstract
Skeletal histology supports the hypothesis that primate life histories are regulated by a neuroendocrine rhythm, the Havers-Halberg Oscillation (HHO). Interestingly, subfossil lemurs are outliers in HHO scaling relationships that have been discovered for haplorhine primates and other mammals. We present new data to determine whether these species represent the general lemur or strepsirrhine condition and to inform models about neuroendocrine-mediated life history evolution. We gathered the largest sample to date of HHO data from histological sections of primate teeth (including the subfossil lemurs) to assess the relationship of these chronobiological measures with life history-related variables including body mass, brain size, age at first female reproduction, and activity level. For anthropoids, these variables show strong correlations with HHO conforming to predictions, though body mass and endocranial volume are strongly correlated with HHO periodicity in this group. However, lemurs (possibly excepting Daubentonia) do not follow this pattern and show markedly less variability in HHO periodicity and lower correlation coefficients and slopes. Moreover, body mass is uncorrelated, and brain size and activity levels are more strongly correlated with HHO periodicity in these animals. We argue that lemurs evolved this pattern due to selection for risk-averse life histories driven by the unpredictability of the environment in Madagascar. These results reinforce the idea that HHO influences life history evolution differently in response to specific ecological selection regimes.
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Affiliation(s)
- Russell T. Hogg
- Department of Rehabilitation Sciences, Florida Gulf Coast University, Fort Myers, Florida, United States of America
| | - Laurie R. Godfrey
- Department of Anthropology, University of Massachusetts at Amherst, Amherst, Massachusetts, United States of America
| | - Gary T. Schwartz
- Institute of Human Origins and School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States of America
| | - Wendy Dirks
- Department of Anthropology, Durham University, Durham, United Kingdom
| | - Timothy G. Bromage
- Department of Biomaterials and Biomimetics, and Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, New York, United States of America
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48
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Guinot G, Cavin L. 'Fish' (Actinopterygii and Elasmobranchii) diversification patterns through deep time. Biol Rev Camb Philos Soc 2015; 91:950-981. [PMID: 26105527 DOI: 10.1111/brv.12203] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 05/20/2015] [Accepted: 05/27/2015] [Indexed: 11/30/2022]
Abstract
Actinopterygii (ray-finned fishes) and Elasmobranchii (sharks, skates and rays) represent more than half of today's vertebrate taxic diversity (approximately 33000 species) and form the largest component of vertebrate diversity in extant aquatic ecosystems. Yet, patterns of 'fish' evolutionary history remain insufficiently understood and previous studies generally treated each group independently mainly because of their contrasting fossil record composition and corresponding sampling strategies. Because direct reading of palaeodiversity curves is affected by several biases affecting the fossil record, analytical approaches are needed to correct for these biases. In this review, we propose a comprehensive analysis based on comparison of large data sets related to competing phylogenies (including all Recent and fossil taxa) and the fossil record for both groups during the Mesozoic-Cainozoic interval. This approach provides information on the 'fish' fossil record quality and on the corrected 'fish' deep-time phylogenetic palaeodiversity signals, with special emphasis on diversification events. Because taxonomic information is preserved after analytical treatment, identified palaeodiversity events are considered both quantitatively and qualitatively and put within corresponding palaeoenvironmental and biological settings. Results indicate a better fossil record quality for elasmobranchs due to their microfossil-like fossil distribution and their very low diversity in freshwater systems, whereas freshwater actinopterygians are diverse in this realm with lower preservation potential. Several important diversification events are identified at familial and generic levels for elasmobranchs, and marine and freshwater actinopterygians, namely in the Early-Middle Jurassic (elasmobranchs), Late Jurassic (actinopterygians), Early Cretaceous (elasmobranchs, freshwater actinopterygians), Cenomanian (all groups) and the Paleocene-Eocene interval (all groups), the latter two representing the two most exceptional radiations among vertebrates. For each of these events along with the Cretaceous-Paleogene extinction, we provide an in-depth review of the taxa involved and factors that may have influenced the diversity patterns observed. Among these, palaeotemperatures, sea-levels, ocean circulation and productivity as well as continent fragmentation and environment heterogeneity (reef environments) are parameters that largely impacted on 'fish' evolutionary history, along with other biotic constraints.
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Affiliation(s)
- Guillaume Guinot
- Department of Geology and Palaeontology, Natural History Museum of Geneva, Route de Malagnou 1, CP 6434, CH-1211, Geneva 6, Switzerland.
| | - Lionel Cavin
- Department of Geology and Palaeontology, Natural History Museum of Geneva, Route de Malagnou 1, CP 6434, CH-1211, Geneva 6, Switzerland
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49
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Comparative and population mitogenomic analyses of Madagascar's extinct, giant ‘subfossil’ lemurs. J Hum Evol 2015; 79:45-54. [DOI: 10.1016/j.jhevol.2014.06.016] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 03/25/2014] [Accepted: 06/04/2014] [Indexed: 11/21/2022]
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50
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Sun J, Ni X, Bi S, Wu W, Ye J, Meng J, Windley BF. Synchronous turnover of flora, fauna, and climate at the Eocene-Oligocene Boundary in Asia. Sci Rep 2014; 4:7463. [PMID: 25501388 PMCID: PMC4264005 DOI: 10.1038/srep07463] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 11/25/2014] [Indexed: 01/31/2023] Open
Abstract
The Eocene–Oligocene Boundary (~34 million years ago) marks one of the largest extinctions of marine invertebrates in the world oceans and of mammalian fauna in Europe and Asia in the Cenozoic era. A shift to a cooler climate across this boundary has been suggested as the cause of this extinction in the marine environment, but there is no manifold evidence for a synchronous turnover of flora, fauna and climate at the Eocene–Oligocene Boundary in a single terrestrial site in Asia to support this hypothesis. Here we report new data of magnetostratigraphy, pollen and climatic proxies in the Asian interior across the Eocene–Oligocene Boundary; our results show that climate change forced a turnover of flora and fauna, suggesting there was a change from large-size perissodactyl-dominant fauna in forests under a warm-temperate climate to small rodent/lagomorph-dominant fauna in forest-steppe in a dry-temperate climate across the Eocene–Oligocene Boundary. These data provide a new terrestrial record for this significant Cenozoic environmental event.
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Affiliation(s)
- Jimin Sun
- 1] Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China [2] CAS Center for Excellence in Tibetan Plateau Earth Sciences
| | - Xijun Ni
- Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Shundong Bi
- Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Wenyu Wu
- Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Jie Ye
- Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Jin Meng
- 1] Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China [2] American Museum of Natural History, New York, New York 10024, USA
| | - Brian F Windley
- Department of Geology, University of Leicester, Leicester LEI 7RH, UK
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