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An Z, Zhou W, Zhang Z, Zhang X, Liu Z, Sun Y, Clemens SC, Wu L, Zhao J, Shi Z, Ma X, Yan H, Li G, Cai Y, Yu J, Sun Y, Li S, Zhang Y, Stepanek C, Lohmann G, Dong G, Cheng H, Liu Y, Jin Z, Li T, Hao Y, Lei J, Cai W. Mid-Pleistocene climate transition triggered by Antarctic Ice Sheet growth. Science 2024; 385:560-565. [PMID: 39088600 DOI: 10.1126/science.abn4861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/06/2023] [Accepted: 06/28/2024] [Indexed: 08/03/2024]
Abstract
Despite extensive investigation, the nature and causes of the Mid-Pleistocene Transition remain enigmatic. In this work, we assess its linkage to asynchronous development of bipolar ice sheets by synthesizing Pleistocene mid- to high-latitude proxy records linked to hemispheric ice sheet evolution. Our results indicate substantial growth of the Antarctic Ice Sheets (AISs) at 2.0 to 1.25 million years ago, preceding the rapid expansion of Northern Hemisphere Ice Sheets after ~1.25 million years ago. Proxy-model comparisons suggest that AIS and associated Southern Ocean sea ice expansion can induce northern high-latitude cooling and enhanced moisture transport to the Northern Hemisphere, thus triggering the Mid-Pleistocene Transition. The dynamic processes involved are crucial for assessing modern global warming that is already inducing asynchronous bipolar melting of ice sheets.
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Affiliation(s)
- Zhisheng An
- State Key Laboratory of Loess Science, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an 710049, China
- Interdisciplinary Research Center of Earth Science Frontier, Beijing Normal University, Beijing 100875, China
| | - Weijian Zhou
- State Key Laboratory of Loess Science, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an 710049, China
- Interdisciplinary Research Center of Earth Science Frontier, Beijing Normal University, Beijing 100875, China
| | - Zeke Zhang
- State Key Laboratory of Loess Science, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an 710049, China
- Department of Earth and Planetary Sciences, Nanjing University, Nanjing 210023, China
| | - Xu Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- British Antarctic Survey, Cambridge CB3 0ET, UK
| | - Zhonghui Liu
- State Key Laboratory of Loess Science, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
- Department of Earth Sciences, The University of Hong Kong, Hong Kong, China
| | - Youbin Sun
- State Key Laboratory of Loess Science, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an 710049, China
| | - Steven C Clemens
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI 02912, USA
| | - Lixin Wu
- Laoshan Laboratory, Qingdao 266000, China
- Key Laboratory of Physical Oceanography/Institute for Advanced Ocean Studies, Ocean University of China, Qingdao 266100, China
| | - Jiaju Zhao
- State Key Laboratory of Loess Science, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zhengguo Shi
- State Key Laboratory of Loess Science, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xiaolin Ma
- State Key Laboratory of Loess Science, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
| | - Hong Yan
- State Key Laboratory of Loess Science, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an 710049, China
| | - Gaojun Li
- Department of Earth and Planetary Sciences, Nanjing University, Nanjing 210023, China
| | - Yanjun Cai
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an 710049, China
| | - Jimin Yu
- Laoshan Laboratory, Qingdao 266000, China
- Research School of Earth Sciences, Australian National University, Canberra, ACT 2601, Australia
| | - Yuchen Sun
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Siqi Li
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu'ao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Christian Stepanek
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Gerrit Lohmann
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Guocheng Dong
- State Key Laboratory of Loess Science, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
| | - Hai Cheng
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yu Liu
- State Key Laboratory of Loess Science, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
| | - Zhangdong Jin
- State Key Laboratory of Loess Science, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an 710049, China
| | - Tao Li
- Key Laboratory of Palaeobiology and Petroleum Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yifei Hao
- State Key Laboratory of Loess Science, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
| | - Jing Lei
- State Key Laboratory of Loess Science, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
- Xi'an Institute for Innovative Earth Environment Research, Xi'an 710061, China
| | - Wenju Cai
- State Key Laboratory of Loess Science, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
- Laoshan Laboratory, Qingdao 266000, China
- Key Laboratory of Physical Oceanography/Institute for Advanced Ocean Studies, Ocean University of China, Qingdao 266100, China
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Marivaux L, Benammi M, Baidder L, Saddiqi O, Adnet S, Charruault AL, Tabuce R, Yans J, Benammi M. A new primate community from the earliest Oligocene of the Atlantic margin of Northwest Africa: Systematic, paleobiogeographic, and paleoenvironmental implications. J Hum Evol 2024; 193:103548. [PMID: 38896896 DOI: 10.1016/j.jhevol.2024.103548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/14/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024]
Abstract
We report a new Paleogene primate community discovered in the uppermost part of the Samlat Formation outcropping on the continental shore of the Rio de Oro, east of the Dakhla peninsula (in the south of Morocco, near the northern border of Mauritania). Fossils consist of isolated teeth, which were extracted by wet screening of estuarine sediments (DAK C2) dating from the earliest Oligocene (ca. 33.5 Ma). These dental remains testify to the presence of at least eight primate species, documenting distinct families, four of which are among the Anthropoidea (Oligopithecidae [Catopithecus aff. browni], Propliopithecidae [?Propliopithecus sp.], Parapithecidae [Abuqatrania cf. basiodontos], and Afrotarsiidae [Afrotarsius sp.]) and four in the Strepsirrhini (a Djebelemuridae [cf. 'Anchomomys' milleri], a Galagidae [Wadilemur cf. elegans], a possible lorisiform [Orogalago saintexuperyi gen. et sp. nov.], and a strepsirrhine of indeterminate affinities [Orolemur mermozi gen. et sp. nov.]). This record of various primates at Dakhla represents the first Oligocene primate community from Northwest Africa, especially from the Atlantic margin of that landmass. Considering primates plus rodents (especially hystricognaths), the taxonomic proximity at the generic (even specific) level between DAK C2 (Dakhla) and the famous Egyptian fossil-bearing localities of the Jebel Qatrani Formation (Fayum Depression), either dating from the latest Eocene (L-41) or from the early Oligocene, suggests the existence of an east-west 'trans-North African' environmental continuum during the latest Eocene-earliest Oligocene time interval. The particularly diverse mammal fauna from DAK C2, recorded within the time window of global climate deterioration characterizing the Eocene/Oligocene transition, suggests that this tropical region of northwest Africa was seemingly less affected, if at all, by the cooling and associated paleoenvironmental and biotic changes documented at that time or at least that the effects were delayed. The expected densely forested paleoenvironment bordering the western margin of North Africa at the beginning of the early Oligocene probably offered better tropical refugia than higher latitudes or more inland areas during the cooling episode.
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Affiliation(s)
- Laurent Marivaux
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, Place Eugène Bataillon, F-34095 Montpellier Cedex 05, France.
| | - Mohamed Benammi
- Département de Géologie, Faculté des Sciences, Université IBN Tofaïl, BP 133, 14000 Kénitra, Morocco
| | - Lahssen Baidder
- Laboratoire Géosciences, Faculté des Sciences Aïn Chock, Université Hassan-II-Casablanca, BP 5366, Maârif, 20100 Casablanca, Morocco
| | - Omar Saddiqi
- Laboratoire Géosciences, Faculté des Sciences Aïn Chock, Université Hassan-II-Casablanca, BP 5366, Maârif, 20100 Casablanca, Morocco
| | - Sylvain Adnet
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, Place Eugène Bataillon, F-34095 Montpellier Cedex 05, France
| | - Anne-Lise Charruault
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, Place Eugène Bataillon, F-34095 Montpellier Cedex 05, France
| | - Rodolphe Tabuce
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, Place Eugène Bataillon, F-34095 Montpellier Cedex 05, France
| | - Johan Yans
- Departement of Geology, Institute of Life Earth and Environment (ILEE), Université de Namur, rue de Bruxelles 61, 5000 Namur, Belgium
| | - Mouloud Benammi
- Laboratoire Paléontologie Évolution Paléoécosystèmes Paléoprimatologie (PALEVOPRIM, UMR-CNRS 7262), Université de Poitiers UFR SFA, 6 Rue Michel Brunet, F-86022 Poitiers Cedex, France
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3
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Tian SY, Yasuhara M, Condamine FL, Huang HHM, Fernando AGS, Aguilar YM, Pandita H, Irizuki T, Iwatani H, Shin CP, Renema W, Kase T. Cenozoic history of the tropical marine biodiversity hotspot. Nature 2024; 632:343-349. [PMID: 38926582 DOI: 10.1038/s41586-024-07617-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 05/28/2024] [Indexed: 06/28/2024]
Abstract
The region with the highest marine biodiversity on our planet is known as the Coral Triangle or Indo-Australian Archipelago (IAA)1,2. Its enormous biodiversity has long attracted the interest of biologists; however, the detailed evolutionary history of the IAA biodiversity hotspot remains poorly understood3. Here we present a high-resolution reconstruction of the Cenozoic diversity history of the IAA by inferring speciation-extinction dynamics using a comprehensive fossil dataset. We found that the IAA has exhibited a unidirectional diversification trend since about 25 million years ago, following a roughly logistic increase until a diversity plateau beginning about 2.6 million years ago. The growth of diversity was primarily controlled by diversity dependency and habitat size, and also facilitated by the alleviation of thermal stress after 13.9 million years ago. Distinct net diversification peaks were recorded at about 25, 20, 16, 12 and 5 million years ago, which were probably related to major tectonic events in addition to climate transitions. Key biogeographic processes had far-reaching effects on the IAA diversity as shown by the long-term waning of the Tethyan descendants versus the waxing of cosmopolitan and IAA taxa. Finally, it seems that the absence of major extinctions and the Cenozoic cooling have been essential in making the IAA the richest marine biodiversity hotspot on Earth.
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Affiliation(s)
- Skye Yunshu Tian
- School of Biological Sciences, Area of Ecology and Biodiversity, The University of Hong Kong, Hong Kong, Hong Kong SAR.
- Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, Hong Kong SAR.
- Institute for Climate and Carbon Neutrality, The University of Hong Kong, Hong Kong, Hong Kong SAR.
- Musketeers Foundation Institute of Data Science, The University of Hong Kong, Hong Kong, Hong Kong SAR.
- Bonner Institut für Organismische Biologie, Paläontologie, Universität Bonn, Bonn, Germany.
| | - Moriaki Yasuhara
- School of Biological Sciences, Area of Ecology and Biodiversity, The University of Hong Kong, Hong Kong, Hong Kong SAR.
- Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, Hong Kong SAR.
- Institute for Climate and Carbon Neutrality, The University of Hong Kong, Hong Kong, Hong Kong SAR.
- Musketeers Foundation Institute of Data Science, The University of Hong Kong, Hong Kong, Hong Kong SAR.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, Hong Kong SAR.
| | - Fabien L Condamine
- CNRS, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Montpellier, France
| | | | - Allan Gil S Fernando
- National Institute of Geological Sciences, University of the Philippines, Diliman, Quezon City, The Philippines
| | - Yolanda M Aguilar
- Marine Geological Survey, Mines and Geosciences Bureau, Quezon City, The Philippines
| | - Hita Pandita
- Department of Geological Engineering, Faculty of Mineral Technology, Institute Teknologi Nasional Yogyakarta, Yogyakarta, Indonesia
| | - Toshiaki Irizuki
- Department of Geoscience, Interdisciplinary Graduate School of Science and Engineering, Shimane University, Matsue, Japan
| | - Hokuto Iwatani
- Division of Earth Science, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Caren P Shin
- Paleontological Research Institution, Ithaca, NY, USA
- Department of Earth and Atmospheric Sciences, Cornell University, New York, NY, USA
| | - Willem Renema
- Naturalis Biodiversity Center, Leiden, The Netherlands
- IBED, University of Amsterdam, Amsterdam, The Netherlands
| | - Tomoki Kase
- National Museum of Nature and Science, Department of Geology and Paleontology, Tsukuba, Japan
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4
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Wang G, Dong J, Han T, Liu C, Luo F, Yang H, He M, Tang G, Zhao N, Zhang Q, Xue G, Dodson J, Li Q, Yan H. Quantitative reconstruction of a single super rainstorm using daily resolved δ 18O of land snail shells. Sci Bull (Beijing) 2024; 69:2281-2288. [PMID: 38724301 DOI: 10.1016/j.scib.2024.04.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 07/22/2024]
Abstract
A "once-in-a-millennium" super rainstorm battered Zhengzhou, central China, from 07/17/2021 to 07/22/2021 (named "7.20" Zhengzhou rainstorm). It killed 398 people and caused billions of dollars in damage. A pressing question is whether rainstorms of this intensity can be effectively documented by geological archives to understand better their historical variabilities beyond the range of meteorological data. Here, four land snail shells were collected from Zhengzhou, and weekly to daily resolved snail shell δ18O records from June to September of 2021 were obtained by gas-source mass spectrometry and secondary ion mass spectrometry. The daily resolved records show a dramatic negative shift between 06/18/2021 and 09/18/2021, which has been attributed to the "7.20" Zhengzhou rainstorm. Moreover, the measured amplitude of this shift is consistent with the theoretical value estimated from the flux balance model and instrumental data for the "7.20" Zhengzhou rainstorm. Our results suggest that the ultra-high resolution δ18O of land snail shells have the potential to reconstruct local synoptic scale rainstorms quantitatively, and thus fossil snail shells in sedimentary strata can be valuable material for investigating the historical variability of local rainstorms under different climate backgrounds.
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Affiliation(s)
- Guozhen Wang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jibao Dong
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China; National Observation and Research Station of Earth Critical Zone on the Loess Plateau of Shaanxi, Xi'an 710061, China.
| | - Tao Han
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
| | - Chengcheng Liu
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China; Xi'an Institute for Innovative Earth Environment Research, Xi'an 710061, China
| | - Fan Luo
- Xi'an Institute for Innovative Earth Environment Research, Xi'an 710061, China
| | - Haotian Yang
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an 710049, China
| | - Miaohong He
- State Key Laboratory of Isotope Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Guoqiang Tang
- State Key Laboratory of Lithospheric Evolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Nanyu Zhao
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
| | - Qian Zhang
- Yunnan Key Laboratory of Earth System Science, Yunnan University, Kunming 650500, China
| | - Gang Xue
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
| | - John Dodson
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China; School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia
| | - Qiuli Li
- State Key Laboratory of Lithospheric Evolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Hong Yan
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China; Laoshan Laboratory, Qingdao 266061, China; Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an 710049, China.
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5
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Wong MK, Chen WJ. Exploring the phylogeny and depth evolution of cusk eels and their relatives (Ophidiiformes: Ophidioidei). Mol Phylogenet Evol 2024; 199:108164. [PMID: 39084413 DOI: 10.1016/j.ympev.2024.108164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 07/27/2024] [Accepted: 07/27/2024] [Indexed: 08/02/2024]
Abstract
With 289 known species in 51 genera, the ophidiiform family Ophidiidae together with their relatives from the Carapidae (36 species in eight genera) of the same suborder Ophidioidei dominate the deep sea, but some occur also in shallow water habitats. Despite their high species diversity in the deep sea and wide bathymetric distributions, their phylogenetic relationships and evolution remain unexplored due in part to sampling difficulties. Thanks to the biodiversity exploratory program entitled "Tropical Deep-Sea Benthos" and joint efforts between Taiwan and French teams for sampling from different localities across the Indo-West Pacific over the last two decades, we are able to compile comprehensive datasets for investigations. In this study, 59 samples representing 36 of 59 known ophidioid genera are selected and used to construct a multi-gene dataset to infer the phylogenetic relationships of ophidioid fishes and their relatives. Our results reveal that the Ophidiidae forms a paraphyletic group with respect to the Carapidae. The four main clades of Ophidioidei resolved are the (1) clade comprising species from the subfamily Brotulinae; (2) clade that includes species in the genera Acanthonus and Xyelacyba; (3) clade grouping Hypopleuron caninum with species from the family Carapidae; and (4) clade containing the species in the subfamily Brotulotaenilinae, Neobythitinae (in part), and Ophidiinae. Accordingly, we suggest the following new revisions based on our results and proposed morphological diagnoses. The subfamily Brotulinae should be elevated to the family level. The genera Xyelacyba and probably Tauredophidium (unsampled in this study) should be included in the newly established family Acanthonidae with Acanthonus. The families Carapidae and Ophidiidae are re-defined. Our time-calibrated phylogenetic and ancestral depth reconstructions enable us to clarify the evolutionary history of ophidiiform fishes and infer past patterns of species distributions at different depths. While Ophidiiformes is inferred to have originated in shallow waters around 96.25 million years ago (Mya), the common ancestor to the Ophidioidei is inferred to have invaded the deep sea around 90.22 Mya, the dates coinciding with the global anoxic event of the OAE2. The observed bathymetric distribution patterns in Ophidioidei most likely point to the mesopelagic zone as the center of origin and diversification. This was followed by multiple events of depth transitions or range expansions towards either shallower waters or greater depth zones, which were likely triggered by past climate changes during the Paleogene-Neogene.
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Affiliation(s)
- Man-Kwan Wong
- Institute of Oceanography, National Taiwan University, No.1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, No.1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
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6
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Hagen O, Viana DS, Wiegand T, Chase JM, Onstein RE. The macro-eco-evolutionary interplay between dispersal, competition and landscape structure in generating biodiversity. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230140. [PMID: 38913052 DOI: 10.1098/rstb.2023.0140] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/07/2024] [Indexed: 06/25/2024] Open
Abstract
Theory links dispersal and diversity, predicting the highest diversity at intermediate dispersal levels. However, the modulation of this relationship by macro-eco-evolutionary mechanisms and competition within a landscape is still elusive. We examine the interplay between dispersal, competition and landscape structure in shaping biodiversity over 5 million years in a dynamic archipelago landscape. We model allopatric speciation, temperature niche, dispersal, competition, trait evolution and trade-offs between competitive and dispersal traits. Depending on dispersal abilities and their interaction with landscape structure, our archipelago exhibits two 'connectivity regimes', that foster speciation events among the same group of islands. Peaks of diversity (i.e. alpha, gamma and phylogenetic), occurred at intermediate dispersal; while competition shifted diversity peaks towards higher dispersal values for each connectivity regime. This shift demonstrates how competition can boost allopatric speciation events through the evolution of thermal specialists, ultimately limiting geographical ranges. Even in a simple landscape, multiple intermediate dispersal diversity relationships emerged, all shaped similarly and according to dispersal and competition strength. Our findings remain valid as dispersal- and competitive-related traits evolve and trade-off; potentially leaving identifiable biodiversity signatures, particularly when trade-offs are imposed. Overall, we scrutinize the convoluted relationships between dispersal, species interactions and landscape structure on macro-eco-evolutionary processes, with lasting imprints on biodiversity.This article is part of the theme issue 'Diversity-dependence of dispersal: interspecific interactions determine spatial dynamics'.
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Affiliation(s)
- O Hagen
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Ecological Modelling, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - D S Viana
- Estación Biológica de Doñana, CSIC, Seville, Spain
| | - T Wiegand
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Ecological Modelling, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - J M Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - R E Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Naturalis Biodiversity Center, Leiden 2333 CR, Netherlands
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7
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Hauffe T, Cantalapiedra JL, Silvestro D. Trait-mediated speciation and human-driven extinctions in proboscideans revealed by unsupervised Bayesian neural networks. SCIENCE ADVANCES 2024; 10:eadl2643. [PMID: 39047110 PMCID: PMC11268411 DOI: 10.1126/sciadv.adl2643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 06/21/2024] [Indexed: 07/27/2024]
Abstract
Species life-history traits, paleoenvironment, and biotic interactions likely influence speciation and extinction rates, affecting species richness over time. Birth-death models inferring the impact of these factors typically assume monotonic relationships between single predictors and rates, limiting our ability to assess more complex effects and their relative importance and interaction. We introduce a Bayesian birth-death model using unsupervised neural networks to explore multifactorial and nonlinear effects on speciation and extinction rates using fossil data. It infers lineage- and time-specific rates and disentangles predictor effects and importance through explainable artificial intelligence techniques. Analysis of the proboscidean fossil record revealed speciation rates shaped by dietary flexibility and biogeographic events. The emergence of modern humans escalated extinction rates, causing recent diversity decline, while regional climate had a lesser impact. Our model paves the way for an improved understanding of the intricate dynamics shaping clade diversification.
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Affiliation(s)
- Torsten Hauffe
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland
| | - Juan L. Cantalapiedra
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
- GloCEE Global Change Ecology and Evolution Research Group, Departamento de Ciencias de la Vida, Universidad de Alcalá, 28801 Alcalá de Henares, Spain
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - Daniele Silvestro
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, 40530 Gothenburg, Sweden
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8
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Klages JP, Hillenbrand CD, Bohaty SM, Salzmann U, Bickert T, Lohmann G, Knahl HS, Gierz P, Niu L, Titschack J, Kuhn G, Frederichs T, Müller J, Bauersachs T, Larter RD, Hochmuth K, Ehrmann W, Nehrke G, Rodríguez-Tovar FJ, Schmiedl G, Spezzaferri S, Läufer A, Lisker F, van de Flierdt T, Eisenhauer A, Uenzelmann-Neben G, Esper O, Smith JA, Pälike H, Spiegel C, Dziadek R, Ronge TA, Freudenthal T, Gohl K. Ice sheet-free West Antarctica during peak early Oligocene glaciation. Science 2024; 385:322-327. [PMID: 38963876 DOI: 10.1126/science.adj3931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 06/10/2024] [Indexed: 07/06/2024]
Abstract
One of Earth's most fundamental climate shifts, the greenhouse-icehouse transition 34 million years ago, initiated Antarctic ice sheet buildup, influencing global climate until today. However, the extent of the ice sheet during the Early Oligocene Glacial Maximum (~33.7 to 33.2 million years ago) that immediately followed this transition-a critical knowledge gap for assessing feedbacks between permanently glaciated areas and early Cenozoic global climate reorganization-is uncertain. In this work, we present shallow-marine drilling data constraining earliest Oligocene environmental conditions on West Antarctica's Pacific margin-a key region for understanding Antarctic ice sheet evolution. These data indicate a cool-temperate environment with mild ocean and air temperatures that prevented West Antarctic Ice Sheet formation. Climate-ice sheet modeling corroborates a highly asymmetric Antarctic ice sheet, thereby revealing its differential regional response to past and future climatic change.
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Affiliation(s)
- J P Klages
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | | | - S M Bohaty
- Institute of Earth Sciences, University of Heidelberg, Heidelberg, Germany
| | - U Salzmann
- Department of Geography and Environmental Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - T Bickert
- MARUM - Center for Marine Environmental Sciences, Bremen, Germany
| | - G Lohmann
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- MARUM - Center for Marine Environmental Sciences, Bremen, Germany
- Environmental Physics, University of Bremen, Bremen, Germany
| | - H S Knahl
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - P Gierz
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - L Niu
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - J Titschack
- MARUM - Center for Marine Environmental Sciences, Bremen, Germany
- Marine Research Department, Senckenberg am Meer (SAM), Wilhelmshaven, Germany
| | - G Kuhn
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - T Frederichs
- MARUM - Center for Marine Environmental Sciences, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - J Müller
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- MARUM - Center for Marine Environmental Sciences, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - T Bauersachs
- Chair of Organic Biogeochemistry in Geo-Systems, RWTH Aachen University, Aachen, Germany
| | | | - K Hochmuth
- Australian Centre for Excellence in Antarctic Science, Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - W Ehrmann
- Institute for Geophysics and Geology, University of Leipzig, Leipzig, Germany
| | - G Nehrke
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - F J Rodríguez-Tovar
- Departamento de Estratigrafía y Paleontología, Universidad de Granada, Granada, Spain
| | - G Schmiedl
- Center for Earth System Research and Sustainability, Institute for Geology, University of Hamburg, Hamburg, Germany
| | - S Spezzaferri
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
| | - A Läufer
- Polar Geology, Bundesanstalt für Geowissenschaften und Rohstoffe, Hannover, Germany
| | - F Lisker
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - T van de Flierdt
- Department of Earth Science and Engineering, Imperial College London, London, UK
| | - A Eisenhauer
- GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany
| | - G Uenzelmann-Neben
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - O Esper
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - J A Smith
- British Antarctic Survey, Cambridge, UK
| | - H Pälike
- MARUM - Center for Marine Environmental Sciences, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - C Spiegel
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - R Dziadek
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - T A Ronge
- International Ocean Discovery Program, Texas A&M University, College Station, TX, USA
| | - T Freudenthal
- MARUM - Center for Marine Environmental Sciences, Bremen, Germany
| | - K Gohl
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
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Jiang J, Gwee J, Fang J, Leichter SM, Sanders D, Ji X, Song J, Zhong X. Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603080. [PMID: 39071332 PMCID: PMC11275764 DOI: 10.1101/2024.07.11.603080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
DNA methylation is an important epigenetic mechanism essential for transposon silencing and genome integrity. Across evolution, the substrates of DNA methylation have diversified between kingdoms to account for genome complexity. In plants, Chromomethylase3 (CMT3) and CMT2 are the major methyltransferases mediating CHG and CHH methylation, respectively. However, how these two enzymes diverge on substrate specificities during evolution remains unknown. Here, we reveal that CMT2 originates from a duplication of the evolutionarily more ancient CMT3 in flowering plants. Lacking a key arginine residue recognizing CHG in CMT2 impairs its CHG methylation activity in most flowering plants. An engineered V1200R mutation empowers CMT2 to restore both CHG and CHH methylation in Arabidopsis cmt2cmt3 mutant, testifying a loss-of-function effect for CMT2 after ∼200 million years of evolution. Interestingly, CMT2 has evolved a long and unstructured N-terminus critical for balancing protein stability, especially under heat stress. Furthermore, CMT2 N-terminus is plastic and can be tolerant to various natural mutations. Together, this study reveals the mechanism of chromomethylase divergence for context-specific DNA methylation in plants and sheds important lights on DNA methylation evolution and function.
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10
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Harzhauser M, Landau B, Mandic O, Neubauer TA. The Central Paratethys Sea-rise and demise of a Miocene European marine biodiversity hotspot. Sci Rep 2024; 14:16288. [PMID: 39009681 PMCID: PMC11250865 DOI: 10.1038/s41598-024-67370-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 07/10/2024] [Indexed: 07/17/2024] Open
Abstract
The Miocene Climate Optimum (MCO, ~ 17-14 Ma) was a time of extraordinary marine biodiversity in the Circum-Mediterranean Region. This boom is best recorded in the deposits of the vanished Central Paratethys Sea, which covered large parts of central to southeastern Europe. This sea harbored an extraordinary tropical to subtropical biotic diversity. Here, we present a georeferenced dataset of 859 gastropod species and discuss geodynamics and climate as the main drivers to explain the changes in diversity. The tectonic reorganization around the Early/Middle Miocene boundary resulted in the formation of an archipelago-like landscape and favorable conditions of the MCO allowed the establishment of coral reefs. Both factors increased habitat heterogeneity, which boosted species richness. The subsequent cooling during the Middle Miocene Climate Transition (~ 14-13 Ma) caused a drastic decline in biodiversity of about 67%. Among the most severely hit groups were corallivorous gastropods, reflecting the loss of coral reefs. Deep-water faunas experienced a loss by 57% of the species due to changing patterns in circulation. The low sea level led to a biogeographic fragmentation reflected in higher turnover rates. The largest turnover occurred with the onset of the Sarmatian when bottom water dysoxia eradicated the deep-water fauna whilst surface waters-dwelling planktotrophic species underwent a crisis.
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Affiliation(s)
- Mathias Harzhauser
- Natural History Museum Vienna, Burgring 7, 1010, Vienna, Austria.
- Institut Für Erdwissenschaften, NAWI Graz Geocenter, Universität Graz, Heinrichstraße 26, 8010, Graz, Austria.
| | - Bernard Landau
- Instituto Dom Luiz da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
- International Health Centres, Av. Infante de Henrique 7, Areias São João, P-8200, Albufeira, Portugal
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
| | - Oleg Mandic
- Natural History Museum Vienna, Burgring 7, 1010, Vienna, Austria
| | - Thomas A Neubauer
- SNSB-Bavarian State Collection for Paleontology and Geology, Richard-Wagner-Straße 10, 80333, Munich, Germany
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
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11
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Shupinski AB, Wagner PJ, Smith FA, Lyons SK. Unique functional diversity during early Cenozoic mammal radiation of North America. Proc Biol Sci 2024; 291:20240778. [PMID: 38955231 DOI: 10.1098/rspb.2024.0778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 06/06/2024] [Indexed: 07/04/2024] Open
Abstract
Mammals influence nearly all aspects of energy flow and habitat structure in modern terrestrial ecosystems. However, anthropogenic effects have probably altered mammalian community structure, raising the question of how past perturbations have done so. We used functional diversity (FD) to describe how the structure of North American mammal palaeocommunities changed over the past 66 Ma, an interval spanning the radiation following the K/Pg and several subsequent environmental disruptions including the Palaeocene-Eocene Thermal Maximum (PETM), the expansion of grassland, and the onset of Pleistocene glaciation. For 264 fossil communities, we examined three aspects of ecological function: functional evenness, functional richness and functional divergence. We found that shifts in FD were associated with major ecological and environmental transitions. All three measures of FD increased immediately following the extinction of the non-avian dinosaurs, suggesting that high degrees of ecological disturbance can lead to synchronous responses both locally and continentally. Otherwise, the components of FD were decoupled and responded differently to environmental changes over the last ~56 Myr.
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Affiliation(s)
- Alex B Shupinski
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Peter J Wagner
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Department of Earth & Atmospheric Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Felisa A Smith
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - S Kathleen Lyons
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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12
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Park T, Burin G, Lazo-Cancino D, Rees JPG, Rule JP, Slater GJ, Cooper N. Charting the course of pinniped evolution: insights from molecular phylogeny and fossil record integration. Evolution 2024; 78:1212-1226. [PMID: 38644688 DOI: 10.1093/evolut/qpae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 04/02/2024] [Accepted: 04/19/2024] [Indexed: 04/23/2024]
Abstract
Pinnipeds (seals, sea lions, walruses, and their fossil relatives) are one of the most successful mammalian clades to live in the oceans. Despite a well-resolved molecular phylogeny and a global fossil record, a complete understanding of their macroevolutionary dynamics remains hampered by a lack of formal analyses that combine these 2 rich sources of information. We used a meta-analytic approach to infer the most densely sampled pinniped phylogeny to date (36 recent and 93 fossil taxa) and used phylogenetic paleobiological methods to study their diversification dynamics and biogeographic history. Pinnipeds mostly diversified at constant rates. Walruses, however, experienced rapid turnover in which extinction rates ultimately exceeded speciation rates from 12 to 6 Ma, possibly due to changing sea levels and/or competition with otariids (eared seals). Historical biogeographic analyses, including fossil data, allowed us to confidently identify the North Pacific and the North Atlantic (plus or minus Paratethys) as the ancestral ranges of Otarioidea (eared seals + walrus) and crown phocids (earless seals), respectively. Yet, despite the novel addition of stem pan-pinniped taxa, the region of origin for Pan-Pinnipedia remained ambiguous. These results suggest further avenues of study in pinnipeds and provide a framework for investigating other groups with substantial extinct and extant diversity.
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Affiliation(s)
- Travis Park
- School of Biological Sciences, Monash University, Melbourne, Australia
- Science Group, Natural History Museum London, London, United Kingdom
- Sciences, Museums Victoria, Melbourne, Australia
| | - Gustavo Burin
- Science Group, Natural History Museum London, London, United Kingdom
| | - Daniela Lazo-Cancino
- Laboratorio de Mastozoología, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Joseph P G Rees
- Science Group, Natural History Museum London, London, United Kingdom
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - James P Rule
- School of Biological Sciences, Monash University, Melbourne, Australia
- Science Group, Natural History Museum London, London, United Kingdom
| | - Graham J Slater
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Natalie Cooper
- Science Group, Natural History Museum London, London, United Kingdom
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13
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Zhang X, Royer DL, Shi G, Ichinnorov N, Herendeen PS, Crane PR, Herrera F. Estimates of late Early Cretaceous atmospheric CO 2 from Mongolia based on stomatal and isotopic analysis of Pseudotorellia. AMERICAN JOURNAL OF BOTANY 2024; 111:e16376. [PMID: 39020509 DOI: 10.1002/ajb2.16376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 07/19/2024]
Abstract
PREMISE The Aptian-Albian (121.4-100.5 Ma) was a greenhouse period with global temperatures estimated as 10-15°C warmer than pre-industrial conditions, so it is surprising that the most reliable CO2 estimates from this time are <1400 ppm. This low CO2 during a warm period implies a very high Earth-system sensitivity in the range of 6 to 9°C per CO2 doubling between the Aptian-Albian and today. METHODS We applied a well-vetted paleo-CO2 proxy based on leaf gas-exchange principles (Franks model) to two Pseudotorellia species from three stratigraphically similar samples at the Tevshiin Govi lignite mine in central Mongolia (~119.7-100.5 Ma). RESULTS Our median estimated CO2 concentration from the three respective samples was 2132, 2405, and 2770 ppm. The primary reason for the high estimated CO2 but with relatively large uncertainties is the very low stomatal density in both species, where small variations propagate to large changes in estimated CO2. Indeed, we found that at least 15 leaves are required before the aggregate estimated CO2 approaches that of the full data set. CONCLUSIONS Our three CO2 estimates all exceeded 2000 ppm, translating to an Earth-system sensitivity (~3-5°C/CO2 doubling) that is more in keeping with the current understanding of the long-term climate system. Because of our large sample size, the directly measured inputs did not contribute much to the overall uncertainty in estimated CO2; instead, the inferred inputs were responsible for most of the overall uncertainty and thus should be scrutinized for their value choices.
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Affiliation(s)
- Xiaoqing Zhang
- Department of Earth and Environmental Sciences, Wesleyan University, Middletown, 06459, CT, USA
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Dana L Royer
- Department of Earth and Environmental Sciences, Wesleyan University, Middletown, 06459, CT, USA
| | - Gongle Shi
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Niiden Ichinnorov
- Institute of Paleontology, Mongolian Academy of Sciences, Ulaanbaatar, 15160, Mongolia
| | | | - Peter R Crane
- Oak Spring Garden Foundation, Oak Spring, Upperville, 20184, VA, USA
- Yale School of Environment, Yale University, New Haven, 06511, CT, USA
| | - Fabiany Herrera
- Earth Sciences, Negaunee Integrative Research Center, Field Museum, Chicago, 60605, IL, USA
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14
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You Y, Yu J, Nie Z, Peng D, Barrett RL, Rabarijaona RN, Lai Y, Zhao Y, Dang VC, Chen Y, Chen Z, Wen J, Lu L. Transition of survival strategies under global climate shifts in the grape family. NATURE PLANTS 2024; 10:1100-1111. [PMID: 39009829 DOI: 10.1038/s41477-024-01726-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 05/09/2024] [Indexed: 07/17/2024]
Abstract
Faced with environmental changes, plants may either move to track their ancestral niches or evolve to adapt to new niches. Vitaceae, the grape family, has evolved diverse adaptive traits facilitating a global expansion in wide-ranging habitats, making it ideal for investigating transition between move and evolve strategies and exploring the underlying mechanisms. Here we inferred the patterns of biogeographic diversification and trait evolution in Vitaceae based on a robust phylogeny with dense sampling including 495 species (~52% of Vitaceae species). Vitaceae probably originated from Asia-the diversity centre of extant genera and the major source of dispersals. Boundaries of the Eocene, Oligocene and Miocene were identified as turning points in shifting strategies. A significant decrease in move strategy was identified during the Oligocene, followed by increases in move and evolve. After the Miocene, evolve began to dominate, during which increased niche opportunities and key trait innovations played important roles.
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Affiliation(s)
- Yichen You
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinren Yu
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zelong Nie
- Hunan Provincial Key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources and Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Danxiao Peng
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Russell L Barrett
- Botanic Gardens of Sydney, National Herbarium of New South Wales, Australian Botanic Garden, Sydney, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Romer Narindra Rabarijaona
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Yangjun Lai
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Yujie Zhao
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Viet-Cuong Dang
- University of Medicine and Pharmacy, Vietnam National University, Hanoi, Vietnam
| | - Youhua Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhiduan Chen
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- China National Botanical Garden, Beijing, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
| | - Limin Lu
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- China National Botanical Garden, Beijing, China.
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15
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Zhang S, Wang H, Liu Y, Wang X, Liu H, Sun L. Lacustrine carbon sink: A hidden driver of the Late Cretaceous Cooling Event. Sci Bull (Beijing) 2024:S2095-9273(24)00449-3. [PMID: 38997942 DOI: 10.1016/j.scib.2024.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 07/14/2024]
Abstract
Lacustrine systems since the Mesozoic have sequestered large quantities of organic carbon, which may have important value for global climate cooling, but there is still a lack of geological evidence of this sequestration. Taking the Songliao Basin in China as a case study, we elucidate the important function of lacustrine basins as sinks of a large amount of organic carbon, particularly when the contemporaneous marine sediments were poor sinks of organic carbon. Volcanic activities and orbital forcing were likely key factors influencing the water transportation between the land and oceans, as well as the alternating burial of organic carbon in the oceans and land. Microorganisms related to methane metabolism may have been highly involved in the mineralization and sequestration of lacustrine organic carbon. This study provides new insights into the coupled carbon-water cycle between the land and oceans and the influence of this process on global climate evolution.
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Affiliation(s)
- Shuichang Zhang
- Research Institute of Petroleum Exploration and Development, Beijing 100083, China; Key Laboratory of Petroleum Geochemistry, China National Petroleum Corporation, Beijing 100083, China; National Key Laboratory for Multi-resources Collaborative Green Production of Continental Shale Oil, Daqing 163712, China.
| | - Huajian Wang
- Research Institute of Petroleum Exploration and Development, Beijing 100083, China; Key Laboratory of Petroleum Geochemistry, China National Petroleum Corporation, Beijing 100083, China; National Key Laboratory for Multi-resources Collaborative Green Production of Continental Shale Oil, Daqing 163712, China
| | - Yuke Liu
- Research Institute of Petroleum Exploration and Development, Beijing 100083, China; Key Laboratory of Petroleum Geochemistry, China National Petroleum Corporation, Beijing 100083, China; National Key Laboratory for Multi-resources Collaborative Green Production of Continental Shale Oil, Daqing 163712, China
| | - Xiaomei Wang
- Research Institute of Petroleum Exploration and Development, Beijing 100083, China; Key Laboratory of Petroleum Geochemistry, China National Petroleum Corporation, Beijing 100083, China; National Key Laboratory for Multi-resources Collaborative Green Production of Continental Shale Oil, Daqing 163712, China
| | - He Liu
- Research Institute of Petroleum Exploration and Development, Beijing 100083, China; National Key Laboratory for Multi-resources Collaborative Green Production of Continental Shale Oil, Daqing 163712, China
| | - Longde Sun
- National Key Laboratory for Multi-resources Collaborative Green Production of Continental Shale Oil, Daqing 163712, China; China National Petroleum Corporation, Beijing 100007, China.
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16
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Smiley TM, Bahadori A, Rasbury ET, Holt WE, Badgley C. Tectonic extension and paleoelevation influence mammalian diversity dynamics in the Basin and Range Province of western North America. SCIENCE ADVANCES 2024; 10:eadn6842. [PMID: 38896622 PMCID: PMC11186493 DOI: 10.1126/sciadv.adn6842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/13/2024] [Indexed: 06/21/2024]
Abstract
Landscape properties have a profound influence on the diversity and distribution of biota, with present-day biodiversity hot spots occurring in topographically complex regions globally. Complex topography is created by tectonic processes and further shaped by interactions between climate and land-surface processes. These processes enrich diversity at the regional scale by promoting speciation and accommodating increased species richness along strong environmental gradients. Synthesis of the mammalian fossil record and a geophysical model of topographic evolution of the Basin and Range Province in western North America enable us to directly quantify relationships between mammal diversity and landscape dynamics over the past 30 million years. We analyze the covariation between tectonic history (extensional strain rates, paleotopography, and ruggedness), global temperature, and diversity dynamics. Mammal species richness and turnover exhibit stronger responses to rates of change in landscape properties than to the specific properties themselves, with peaks in diversity coinciding with high tectonic strain rates and large changes in elevation across spatial scales.
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Affiliation(s)
- Tara M. Smiley
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Alireza Bahadori
- Department of Geosciences, Stony Brook University, Stony Brook, NY, USA
- Lamont-Doherty Earth Observatory, Columbia University in the City of New York, Palisades, NY, USA
| | - E. Troy Rasbury
- Department of Geosciences, Stony Brook University, Stony Brook, NY, USA
| | - William E. Holt
- Department of Geosciences, Stony Brook University, Stony Brook, NY, USA
| | - Catherine Badgley
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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17
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Li C, Deng T, Wang Y, Sun F, Wolff B, Jiangzuo Q, Ma J, Xing L, Fu J, Zhang J, Wang S. The trunk replaces the longer mandible as the main feeding organ in elephant evolution. eLife 2024; 12:RP90908. [PMID: 38900028 PMCID: PMC11189625 DOI: 10.7554/elife.90908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024] Open
Abstract
The long-trunked elephantids underwent a significant evolutionary stage characterized by an exceptionally elongated mandible. The initial elongation and subsequent regression of the long mandible, along with its co-evolution with the trunk, present an intriguing issue that remains incompletely understood. Through comparative functional and eco-morphological investigations, as well as feeding preference analysis, we reconstructed the feeding behavior of major groups of longirostrine elephantiforms. In the Platybelodon clade, the rapid evolutionary changes observed in the narial region, strongly correlated with mandible and tusk characteristics, suggest a crucial evolutionary transition where feeding function shifted from the mandible to the trunk, allowing proboscideans to expand their niches to more open regions. This functional shift further resulted in elephantids relying solely on their trunks for feeding. Our research provides insights into how unique environmental pressures shape the extreme evolution of organs, particularly in large mammals that developed various peculiar adaptations during the late Cenozoic global cooling trends.
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Affiliation(s)
- Chunxiao Li
- University of Chinese Academy of SciencesBeijingChina
- Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of SciencesBeijingChina
| | - Tao Deng
- University of Chinese Academy of SciencesBeijingChina
- Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of SciencesBeijingChina
| | - Yang Wang
- Department of Earth, Ocean and Atmospheric Science, Florida State UniversityTallahasseeUnited States
| | - Fajun Sun
- Environmental Science & Technology, University of MarylandCollege ParkUnited States
| | - Burt Wolff
- Department of Earth, Ocean and Atmospheric Science, Florida State UniversityTallahasseeUnited States
| | - Qigao Jiangzuo
- Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of SciencesBeijingChina
| | - Jiao Ma
- Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of SciencesBeijingChina
| | - Luda Xing
- University of Chinese Academy of SciencesBeijingChina
- Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of SciencesBeijingChina
| | - Jiao Fu
- University of Chinese Academy of SciencesBeijingChina
- Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of SciencesBeijingChina
| | - Ji Zhang
- School of Civil and Hydraulic Engineering, Huazhong University of Science and TechnologyWuhanChina
- National Center of Technology Innovation for Digital ConstructionWuhanChina
| | - Shiqi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of SciencesBeijingChina
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18
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Chai S, Chong Y, Yin D, Qiu Q, Xu S, Yang G. Genomic insights into adaptation to bipedal saltation and desert-like habitats of jerboas. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2516-9. [PMID: 38902451 DOI: 10.1007/s11427-023-2516-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/20/2023] [Indexed: 06/22/2024]
Abstract
Jerboas is a lineage of small rodents displaying atypical mouse-like morphology with elongated strong hindlimbs and short forelimbs. They have evolved obligate bipedal saltation and acute senses, and been well-adapted to vast desert-like habitats. Using a newly sequenced chromosome-scale genome of the Mongolian five-toed jerboa (Orientallactaga sibirica), our comparative genomic analyses and in vitro functional assays showed that the genetic innovations in both protein-coding and non-coding regions played an important role in jerboa morphological and physiological adaptation. Jerboa-specific amino acid substitutions, and segment insertions/deletions (indels) in conserved non-coding elements (CNEs) were found in components of proteoglycan biosynthesis pathway (XYLT1 and CHSY1), which plays an important role in limb development. Meanwhile, we found specific evolutionary changes functionally associated with energy or water metabolism (e.g., specific amino acid substitutions in ND5 and indels in CNEs physically near ROR2) and senses (e.g., expansion of vomeronasal receptors and the FAM136A gene family) in jerboas. Further dual-luciferase reporter assay verified that some of the CNEs with jerboa-specific segment indels exerted a significantly different influence on luciferase activity, suggesting changes in their regulatory function in jerboas. Our results revealed the potential molecular mechanisms underlying jerboa adaptation since the divergence from the Eocene-Oligocene transition, and provided more resources and new insights to enhance our understanding of the molecular basis underlying the phenotypic diversity and the environmental adaptation of mammals.
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Affiliation(s)
- Simin Chai
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Yujie Chong
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Daiqing Yin
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Guang Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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19
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Kirtland Turner S, Ridgwell A, Keller AL, Vahlenkamp M, Aleksinski AK, Sexton PF, Penman DE, Hull PM, Norris RD. Sensitivity of ocean circulation to warming during the Early Eocene greenhouse. Proc Natl Acad Sci U S A 2024; 121:e2311980121. [PMID: 38830092 PMCID: PMC11181020 DOI: 10.1073/pnas.2311980121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 04/19/2024] [Indexed: 06/05/2024] Open
Abstract
Multiple abrupt warming events ("hyperthermals") punctuated the Early Eocene and were associated with deep-sea temperature increases of 2 to 4 °C, seafloor carbonate dissolution, and negative carbon isotope (δ13C) excursions. Whether hyperthermals were associated with changes in the global ocean overturning circulation is important for understanding their driving mechanisms and feedbacks and for gaining insight into the circulation's sensitivity to climatic warming. Here, we present high-resolution benthic foraminiferal stable isotope records (δ13C and δ18O) throughout the Early Eocene Climate Optimum (~53.26 to 49.14 Ma) from the deep equatorial and North Atlantic. Combined with existing records from the South Atlantic and Pacific, these indicate consistently amplified δ13C excursion sizes during hyperthermals in the deep equatorial Atlantic. We compare these observations with results from an intermediate complexity Earth system model to demonstrate that this spatial pattern of δ13C excursion size is a predictable consequence of global warming-induced changes in ocean overturning circulation. In our model, transient warming drives the weakening of Southern Ocean-sourced overturning circulation, strengthens Atlantic meridional water mass aging gradients, and amplifies the magnitude of negative δ13C excursions in the equatorial to North Atlantic. Based on model-data consistency, we conclude that Eocene hyperthermals coincided with repeated weakening of the global overturning circulation. Not accounting for ocean circulation impacts on δ13C excursions will lead to incorrect estimates of the magnitude of carbon release driving hyperthermals. Our finding of weakening overturning in response to past transient climatic warming is consistent with predictions of declining Atlantic Ocean overturning strength in our warm future.
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Affiliation(s)
- Sandra Kirtland Turner
- Department of Earth and Planetary Sciences, University of California, Riverside, CA92521
| | - Andy Ridgwell
- Department of Earth and Planetary Sciences, University of California, Riverside, CA92521
| | - Allison L. Keller
- Department of Earth and Planetary Sciences, University of California, Riverside, CA92521
| | - Maximilian Vahlenkamp
- Center for Marine Environmental Sciences (MARUM), University of Bremen, Bremen28359, Germany
| | - Adam K. Aleksinski
- Department of Earth and Planetary Sciences, University of California, Riverside, CA92521
- Department of Earth, Atmospheric and Planetary Sciences, Purdue University, West Lafayette, IN47906
| | - Philip F. Sexton
- School of Environment, Earth and Ecosystem Sciences, The Open University, Milton KeynesMK7 6AA, United Kingdom
| | - Donald E. Penman
- Department of Geosciences, Utah State University, Logan, UT84322
| | - Pincelli M. Hull
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT06511
| | - Richard D. Norris
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA92093
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20
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Zhang G, Yang J, Zhang C, Jiao B, Panero JL, Cai J, Zhang ZR, Gao LM, Gao T, Ma H. Nuclear phylogenomics of Asteraceae with increased sampling provides new insights into convergent morphological and molecular evolution. PLANT COMMUNICATIONS 2024; 5:100851. [PMID: 38409784 PMCID: PMC11211554 DOI: 10.1016/j.xplc.2024.100851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 01/22/2024] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
Convergent morphological evolution is widespread in flowering plants, and understanding this phenomenon relies on well-resolved phylogenies. Nuclear phylogenetic reconstruction using transcriptome datasets has been successful in various angiosperm groups, but it is limited to taxa with available fresh materials. Asteraceae, which are one of the two largest angiosperm families and are important for both ecosystems and human livelihood, show multiple examples of convergent evolution. Nuclear Asteraceae phylogenies have resolved relationships among most subfamilies and many tribes, but many phylogenetic and evolutionary questions regarding subtribes and genera remain, owing to limited sampling. Here, we increased the sampling for Asteraceae phylogenetic reconstruction using transcriptomes and genome-skimming datasets and produced nuclear phylogenetic trees with 706 species representing two-thirds of recognized subtribes. Ancestral character reconstruction supports multiple convergent evolutionary events in Asteraceae, with gains and losses of bilateral floral symmetry correlated with diversification of some subfamilies and smaller groups, respectively. Presence of the calyx-related pappus may have been especially important for the success of some subtribes and genera. Molecular evolutionary analyses support the likely contribution of duplications of MADS-box and TCP floral regulatory genes to innovations in floral morphology, including capitulum inflorescences and bilaterally symmetric flowers, potentially promoting the diversification of Asteraceae. Subsequent divergences and reductions in CYC2 gene expression are related to the gain and loss of zygomorphic flowers. This phylogenomic work with greater taxon sampling through inclusion of genome-skimming datasets reveals the feasibility of expanded evolutionary analyses using DNA samples for understanding convergent evolution.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China; Department of Biology, the Huck Institute of the Life Sciences, the Pennsylvania State University, State College, PA 16801, USA; State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Junbo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Caifei Zhang
- Wuhan Botanical Garden and Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Bohan Jiao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - José L Panero
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Jie Cai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Lijiang National Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan 674100, China.
| | - Tiangang Gao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Hong Ma
- Department of Biology, the Huck Institute of the Life Sciences, the Pennsylvania State University, State College, PA 16801, USA.
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21
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Brownstein CD, Zapfe KL, Lott S, Harrington R, Ghezelayagh A, Dornburg A, Near TJ. Synergistic innovations enabled the radiation of anglerfishes in the deep open ocean. Curr Biol 2024; 34:2541-2550.e4. [PMID: 38788708 DOI: 10.1016/j.cub.2024.04.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/10/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024]
Abstract
Major ecological transitions are thought to fuel diversification, but whether they are contingent on the evolution of certain traits called key innovations1 is unclear. Key innovations are routinely invoked to explain how lineages rapidly exploit new ecological opportunities.1,2,3 However, investigations of key innovations often focus on single traits rather than considering trait combinations that collectively produce effects of interest.4 Here, we investigate the evolution of synergistic trait interactions in anglerfishes, which include one of the most species-rich vertebrate clades in the bathypelagic, or "midnight," zone of the deep sea: Ceratioidea.5 Ceratioids are the only vertebrates that possess sexual parasitism, wherein males temporarily attach or permanently fuse to females to mate.6,7 We show that the rapid transition of ancestrally benthic anglerfishes into pelagic habitats occurred during a period of major global warming 50-35 million years ago.8,9 This transition coincided with the origins of sexual parasitism, which is thought to increase the probability of successful reproduction once a mate is found in the midnight zone, Earth's largest habitat.5,6,7 Our reconstruction of the evolutionary history of anglerfishes and the loss of immune genes support that permanently fusing clades have convergently degenerated their adaptive immunity. We find that degenerate adaptive immune genes and sexual body size dimorphism, both variably present in anglerfishes outside the ceratioid radiation, likely promoted their transition into the bathypelagic zone. These results show how traits from separate physiological, morphological, and reproductive systems can interact synergistically to drive major transitions and subsequent diversification in novel environments.
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Affiliation(s)
- Chase D Brownstein
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA.
| | - Katerina L Zapfe
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte, 9331 Robert D. Snyder Rd., Charlotte, NC 28223, USA
| | - Spencer Lott
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA
| | - Richard Harrington
- Department of Natural Resources, Marine Resources Division, 217 Ft. Johnson Road, Charleston, SC 29412-9110, USA
| | - Ava Ghezelayagh
- Department of Geophysical Sciences, University of Chicago, 5734 S. Ellis Avenue, Chicago, IL 60637, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte, 9331 Robert D. Snyder Rd., Charlotte, NC 28223, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA; Peabody Museum, Yale University, 21 Sachem Street, New Haven, CT 06511, USA
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22
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Rana SK, Rana HK, Landis JB, Kuang T, Chen J, Wang H, Deng T, Davis CC, Sun H. Pleistocene glaciation advances the cryptic speciation of Stellera chamaejasme L. in a major biodiversity hotspot. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1192-1205. [PMID: 38639466 DOI: 10.1111/jipb.13663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/20/2024]
Abstract
The mountains of Southwest China comprise a significant large mountain range and biodiversity hotspot imperiled by global climate change. The high species diversity in this mountain system has long been attributed to a complex set of factors, and recent large-scale macroevolutionary investigations have placed a broad timeline on plant diversification that stretches from 10 million years ago (Mya) to the present. Despite our increasing understanding of the temporal mode of speciation, finer-scale population-level investigations are lacking to better refine these temporal trends and illuminate the abiotic and biotic influences of cryptic speciation. This is largely due to the dearth of organismal sampling among closely related species and populations, spanning the incredible size and topological heterogeneity of this region. Our study dives into these evolutionary dynamics of speciation using genomic and eco-morphological data of Stellera chamaejasme L. We identified four previously unrecognized cryptic species having indistinct morphological traits and large metapopulation of evolving lineages, suggesting a more recent diversification (~2.67-0.90 Mya), largely influenced by Pleistocene glaciation and biotic factors. These factors likely influenced allopatric speciation and advocated cyclical warming-cooling episodes along elevational gradients during the Pleistocene. The study refines the evolutionary timeline to be much younger than previously implicated and raises the concern that projected future warming may influence the alpine species diversity, necessitating increased conservation efforts.
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Affiliation(s)
- Santosh Kumar Rana
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, 72401, Arkansas, USA
| | - Hum Kala Rana
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, 14853, New York, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, 14853, New York, USA
| | - Tianhui Kuang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Juntong Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
| | - Tao Deng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Herbaria, Harvard University, Cambridge, 02138, Massachusetts, USA
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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23
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Zhang Q, Yang Y, Liu B, Lu L, Sauquet H, Li D, Chen Z. Meta-analysis provides insights into the origin and evolution of East Asian evergreen broad-leaved forests. THE NEW PHYTOLOGIST 2024; 242:2369-2379. [PMID: 38186378 DOI: 10.1111/nph.19524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/18/2023] [Indexed: 01/09/2024]
Abstract
Evergreen broad-leaved forests (EBLFs) are dominated by a monsoon climate and form a distinct biome in East Asia with notably high biodiversity. However, the origin and evolution of East Asian EBLFs (EAEBLFs) remain elusive despite the estimation of divergence times for various representative lineages. Using 72 selected generic-level characteristic lineages, we constructed an integrated lineage accumulation rate (LAR) curve based on their crown ages. According to the crown-based LAR, the EAEBLF origin was identified at least as the early Oligocene (c. 31.8 million years ago (Ma)). The accumulation rate of the characteristic genera peaked at 25.2 and 6.4 Ma, coinciding with the two intensification periods of the Asian monsoon at the Oligocene - Miocene and the Miocene - Pliocene boundaries, respectively. Moreover, the LAR was highly correlated with precipitation in the EAEBLF region and negatively to global temperature, as revealed through time-lag cross-correlation analyses. An early Oligocene origin is suggested for EAEBLFs, bridging the gap between paleobotanical and molecular dating studies and solving conflicts among previous estimates based on individual representative lineages. The strong correlation between the crown-based LAR and the precipitation brought about by the Asian monsoon emphasizes its irreplaceable role in the origin and development of EAEBLFs.
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Affiliation(s)
- Qian Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yuchang Yang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Limin Lu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Hervé Sauquet
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, NSW, 2000, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Dezhu Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhiduan Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
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24
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Tejada JV, Antoine PO, Münch P, Billet G, Hautier L, Delsuc F, Condamine FL. Bayesian Total-Evidence Dating Revisits Sloth Phylogeny and Biogeography: A Cautionary Tale on Morphological Clock Analyses. Syst Biol 2024; 73:125-139. [PMID: 38041854 PMCID: PMC11129595 DOI: 10.1093/sysbio/syad069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 12/04/2023] Open
Abstract
Combining morphological and molecular characters through Bayesian total-evidence dating allows inferring the phylogenetic and timescale framework of both extant and fossil taxa, while accounting for the stochasticity and incompleteness of the fossil record. Such an integrative approach is particularly needed when dealing with clades such as sloths (Mammalia: Folivora), for which developmental and biomechanical studies have shown high levels of morphological convergence whereas molecular data can only account for a limited percentage of their total species richness. Here, we propose an alternative hypothesis of sloth evolution that emphasizes the pervasiveness of morphological convergence and the importance of considering the fossil record and an adequate taxon sampling in both phylogenetic and biogeographic inferences. Regardless of different clock models and morphological datasets, the extant sloth Bradypus is consistently recovered as a megatherioid, and Choloepus as a mylodontoid, in agreement with molecular-only analyses. The recently extinct Caribbean sloths (Megalocnoidea) are found to be a monophyletic sister-clade of Megatherioidea, in contrast to previous phylogenetic hypotheses. Our results contradict previous morphological analyses and further support the polyphyly of "Megalonychidae," whose members were found in five different clades. Regardless of taxon sampling and clock models, the Caribbean colonization of sloths is compatible with the exhumation of islands along Aves Ridge and its geological time frame. Overall, our total-evidence analysis illustrates the difficulty of positioning highly incomplete fossils, although a robust phylogenetic framework was recovered by an a posteriori removal of taxa with high percentages of missing characters. Elimination of these taxa improved topological resolution by reducing polytomies and increasing node support. However, it introduced a systematic and geographic bias because most of these incomplete specimens are from northern South America. This is evident in biogeographic reconstructions, which suggest Patagonia as the area of origin of many clades when taxa are underrepresented, but Amazonia and/or Central and Southern Andes when all taxa are included. More generally, our analyses demonstrate the instability of topology and divergence time estimates when using different morphological datasets and clock models and thus caution against making macroevolutionary inferences when node support is weak or when uncertainties in the fossil record are not considered.
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Affiliation(s)
- Julia V Tejada
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Pierre-Olivier Antoine
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Philippe Münch
- Géosciences Montpellier, UMR 5243, Université de Montpellier, CNRS, Université des Antilles, Place Eugène Bataillon, 34095 Montpellier, France
| | - Guillaume Billet
- Centre de Recherche en Paléontologie—Paris, CR2P—UMR 7207, Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, 8 rue Buffon 75005, Paris
| | - Lionel Hautier
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Frédéric Delsuc
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Fabien L Condamine
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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25
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Dallai L, Sharp ZD. A tipping point in stable isotope composition of Antarctic meteoric waters during Cenozoic glaciation. Nat Commun 2024; 15:4509. [PMID: 38802358 DOI: 10.1038/s41467-024-48811-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 05/10/2024] [Indexed: 05/29/2024] Open
Abstract
Triple oxygen isotopes of Cenozoic intrusive rocks emplaced along the Ross Sea coastline in Antarctica, reveal that meteoric-hydrothermal waters imprinted their stable isotope composition on mineral phases, leaving a clear record of oxygen and hydrogen isotope variations during the establishment of the polar cap. Calculated O- and H-isotope compositions of meteoric waters vary from -9 ± 2‰ and -92 ± 5‰ at 40 ± 0.6 Ma, to -30 and -234 ± 5‰ at 34 ± 1.9 Ma, and intersect the modern Global Meteoric Water Line. These isotopic variations likely depict the combined variations in temperature, humidity, and moisture source regions, resulting from rearrangement of oceanic currents and atmospheric cooling during the onset of continental ice cap. Here, we report a paleo-climatic proxy based on triple oxygen geochemistry of crystalline rocks that reveals changes in the hydrological cycle. We discuss the magnitude of temperature changes at high latitudes during the Eocene-Oligocene climatic transition.
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Affiliation(s)
- Luigi Dallai
- Dip. Scienze della Terra, Università degli Studi di Roma "Sapienza", Roma, Italy.
- CNR - IGG, Area della Ricerca di Pisa, Pisa, Italy.
| | - Zachary D Sharp
- Department of Earth and Planetary Sciences, University of New Mexico, Albuquerque, NM, USA
- Center for Stable Isotopes, University of New Mexico, Albuquerque, NM, USA
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26
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Lyu ZT, Zeng ZC, Wan H, Li Q, Tominaga A, Nishikawa K, Matsui M, Li SZ, Jiang ZW, Liu Y, Wang YY. Contrasting nidification behaviors facilitate diversification and colonization of the Music frogs under a changing paleoclimate. Commun Biol 2024; 7:638. [PMID: 38796601 PMCID: PMC11127999 DOI: 10.1038/s42003-024-06347-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 05/17/2024] [Indexed: 05/28/2024] Open
Abstract
In order to cope with the complexity and variability of the terrestrial environment, amphibians have developed a wide range of reproductive and parental behaviors. Nest building occurs in some anuran species as parental care. Species of the Music frog genus Nidirana are known for their unique courtship behavior and mud nesting in several congeners. However, the evolution of these frogs and their nidification behavior has yet to be studied. With phylogenomic and phylogeographic analyses based on a wide sampling of the genus, we find that Nidirana originated from central-southwestern China and the nidification behavior initially evolved at ca 19.3 Ma but subsequently lost in several descendants. Further population genomic analyses suggest that the nidification species have an older diversification and colonization history, while N. adenopleura complex congeners that do not exhibit nidification behavior have experienced a recent rapid radiation. The presence and loss of the nidification behavior in the Music frogs may be associated with paleoclimatic factors such as temperature and precipitation. This study highlights the nidification behavior as a key evolutionary innovation that has contributed to the diversification of an amphibian group under past climate changes.
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Affiliation(s)
- Zhi-Tong Lyu
- State Key Laboratory of Biocontrol, School of Ecology / School of Life Sciences, Sun Yat-sen University, Shenzhen, 518107, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610040, China
| | - Zhao-Chi Zeng
- State Key Laboratory of Biocontrol, School of Ecology / School of Life Sciences, Sun Yat-sen University, Shenzhen, 518107, China
| | - Han Wan
- State Key Laboratory of Biocontrol, School of Ecology / School of Life Sciences, Sun Yat-sen University, Shenzhen, 518107, China
| | - Qin Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
| | - Atsushi Tominaga
- Faculty of Education, University of the Ryukyus, Senbaru 1 Nishihara, Okinawa, 903-0213, Japan
| | - Kanto Nishikawa
- Graduate School of Global Environmental Studies, Kyoto University, Yoshida-hon-machi, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihon-matsu, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shi-Ze Li
- Department of Food Science and Engineering, Moutai Institute, Renhuai, 564500, China
| | - Zhong-Wen Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology / School of Life Sciences, Sun Yat-sen University, Shenzhen, 518107, China.
| | - Ying-Yong Wang
- State Key Laboratory of Biocontrol, School of Ecology / School of Life Sciences, Sun Yat-sen University, Shenzhen, 518107, China.
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Xue T, Feng T, Liang Y, Yang X, Qin F, Yu J, Janssens SB, Yu S. Radiating diversification and niche conservatism jointly shape the inverse latitudinal diversity gradient of Potentilla L. (Rosaceae). BMC PLANT BIOLOGY 2024; 24:443. [PMID: 38778263 PMCID: PMC11112792 DOI: 10.1186/s12870-024-05083-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND The latitudinal diversity gradient (LDG), characterized by an increase in species richness from the poles to the equator, is one of the most pervasive biological patterns. However, inverse LDGs, in which species richness peaks in extratropical regions, are also found in some lineages and their causes remain unclear. Here, we test the roles of evolutionary time, diversification rates, and niche conservatism in explaining the inverse LDG of Potentilla (ca. 500 species). We compiled the global distributions of ~ 90% of Potentilla species, and reconstructed a robust phylogenetic framework based on whole-plastome sequences. Next, we analyzed the divergence time, ancestral area, diversification rate, and ancestral niche to investigate the macroevolutionary history of Potentilla. RESULTS The genus originated in the Qinghai-Tibet Plateau during the late Eocene and gradually spread to other regions of the Northern Hemisphere posterior to the late Miocene. Rapid cooling after the late Pliocene promoted the radiating diversification of Potentilla. The polyploidization, as well as some cold-adaptive morphological innovations, enhanced the adaptation of Potentilla species to the cold environment. Ancestral niche reconstruction suggests that Potentilla likely originated in a relatively cool environment. The species richness peaks at approximately 45 °N, a region characterized by high diversification rates, and the environmental conditions are similar to the ancestral climate niche. Evolutionary time was not significantly correlated with species richness in the latitudinal gradient. CONCLUSIONS Our results suggest that the elevated diversification rates in middle latitude regions and the conservatism in thermal niches jointly determined the inverse LDG in Potentilla. This study highlights the importance of integrating evolutionary and ecological approaches to explain the diversity pattern of biological groups on a global scale.
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Affiliation(s)
- Tiantian Xue
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Feng
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, Gelderland, the Netherlands
| | - Yunfen Liang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xudong Yang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Department of Earth System Science, Tsinghua University, Beijing, 100084, China
| | - Fei Qin
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jianghong Yu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Steven B Janssens
- Meise Botanic Garden, Nieuwelaan 38, Meise, BE-1860, Belgium.
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, Leuven, BE-3001, Belgium.
| | - Shengxiang Yu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Cooper RB, Flannery-Sutherland JT, Silvestro D. DeepDive: estimating global biodiversity patterns through time using deep learning. Nat Commun 2024; 15:4199. [PMID: 38760390 PMCID: PMC11101433 DOI: 10.1038/s41467-024-48434-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 04/30/2024] [Indexed: 05/19/2024] Open
Abstract
Understanding how biodiversity has changed through time is a central goal of evolutionary biology. However, estimates of past biodiversity are challenged by the inherent incompleteness of the fossil record, even when state-of-the-art statistical methods are applied to adjust estimates while correcting for sampling biases. Here we develop an approach based on stochastic simulations of biodiversity and a deep learning model to infer richness at global or regional scales through time while incorporating spatial, temporal and taxonomic sampling variation. Our method outperforms alternative approaches across simulated datasets, especially at large spatial scales, providing robust palaeodiversity estimates under a wide range of preservation scenarios. We apply our method on two empirical datasets of different taxonomic and temporal scope: the Permian-Triassic record of marine animals and the Cenozoic evolution of proboscideans. Our estimates provide a revised quantitative assessment of two mass extinctions in the marine record and reveal rapid diversification of proboscideans following their expansion out of Africa and a >70% diversity drop in the Pleistocene.
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Affiliation(s)
- Rebecca B Cooper
- Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland.
- Swiss Institute of Bioinformatics, 1700, Fribourg, Switzerland.
| | | | - Daniele Silvestro
- Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland.
- Swiss Institute of Bioinformatics, 1700, Fribourg, Switzerland.
- Department of Biological and Environmental Sciences, Global Gothenburg Biodiversity Centre, University of Gothenburg, Gothenburg, 413 19, Sweden.
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Zhang R, Liu Z, Jiang D, Yu Y, Zhang Z, Yang Y, Tan N, Si D, Zhang Q, Zhou X. Cenozoic Indo-Pacific warm pool controlled by both atmospheric CO 2 and paleogeography. Sci Bull (Beijing) 2024; 69:1323-1331. [PMID: 38472018 DOI: 10.1016/j.scib.2024.02.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 03/14/2024]
Abstract
The Indo-Pacific warm pool (IPWP) is crucial for regional and global climates. However, the development of the IPWP and its effect on the regional climate during the Cenozoic remain unclear. Here, using a compilation of sea surface temperature (SST) records (mainly since the middle Miocene) and multimodel paleoclimate simulations, our results indicated that the extent, intensity and warmest temperature position of the IPWP changed markedly during the Cenozoic. Specifically, its extent decreased, its intensity weakened, and its warmest temperature position shifted from the Indian to western Pacific Ocean over time. The atmospheric CO2 dominated its extent and intensity, while paleogeography, by restricting the distribution of the Indian Ocean and the width of the tropical seaways, controlled the shift in its warmest temperature position. In particular, the eastward shift to the western Pacific Ocean from the middle to late Miocene inferred from compiled SST records likely resulted from the constriction of tropical seaways. Furthermore, by changing the atmospheric thermal structure and atmospheric circulation, the reduced extent and intensity of the IPWP decreased the annual precipitation in the western Indian Ocean, eastern Asia and Australia, while the shift in the warmest temperature position from the Indian to western Pacific Ocean promoted aridification in Australia. Qualitative model-data agreements are obtained for both the IPWP SST and regional climate. From the perspective of past warm climates with high concentrations of atmospheric CO2, the expansion and strengthening of the IPWP will occur in a warmer future and favor excessive precipitation in eastern Asia and Australia.
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Affiliation(s)
- Ran Zhang
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, China; Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Zhonghui Liu
- Department of Earth Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Dabang Jiang
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, China.
| | - Yongqiang Yu
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, China
| | - Zhongshi Zhang
- Department of Atmospheric Science, School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Yibo Yang
- State Key Laboratory of Tibetan Plateau Earth System Science, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Ning Tan
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Dong Si
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, China
| | - Qiang Zhang
- State Key Laboratory of Lithospheric Evolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Xin Zhou
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
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30
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Dagallier LPMJ, Condamine FL, Couvreur TLP. Sequential diversification with Miocene extinction and Pliocene speciation linked to mountain uplift explains the diversity of the African rain forest clade Monodoreae (Annonaceae). ANNALS OF BOTANY 2024; 133:677-696. [PMID: 37659091 PMCID: PMC11082524 DOI: 10.1093/aob/mcad130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023]
Abstract
BACKGROUND AND AIMS Throughout the Cenozoic, Africa underwent several climatic and geological changes impacting the evolution of tropical rain forests (TRFs). African TRFs are thought to have extended from east to west in a 'pan-African' TRF, followed by several events of fragmentation during drier climate periods. During the Miocene, climate cooling and mountain uplift led to the aridification of tropical Africa and open habitats expanded at the expense of TRFs, which probably experienced local extinctions. However, in plants, these drivers were previously inferred using limited taxonomic and molecular data. Here, we tested the impact of climate and geological changes on diversification within the diverse clade Monodoreae (Annonaceae) composed of 90 tree species restricted to African TRFs. METHODS We reconstructed a near-complete phylogenetic tree, based on 32 nuclear genes, and dated using relaxed clocks and fossil calibrations in a Bayesian framework. We inferred the biogeographical history and the diversification dynamics of the clade using multiple birth-death models. KEY RESULTS Monodoreae originated in East African TRFs ~25 million years ago (Ma) and expanded toward Central Africa during the Miocene. We inferred range contractions during the middle Miocene and document important connections between East and West African TRFs after 15-13 Ma. Our results indicated a sudden extinction event during the late Miocene, followed by an increase in speciation rates. Birth-death models suggested that African elevation change (orogeny) is positively linked to speciation in this clade. CONCLUSION East Africa is inferred as an important source of Monodoreae species, and possibly for African plant diversity in general. Our results support a 'sequential scenario of diversification' in which increased aridification triggered extinction of TRF species in Monodoreae. This was quickly followed by fragmentation of rain forests, subsequently enhancing lagged speciation resulting from vicariance and improved climate conditions. In contrast to previous ideas, the uplift of East Africa is shown to have played a positive role in Monodoreae diversification.
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Affiliation(s)
- Léo-Paul M J Dagallier
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY 10458, USA
| | - Fabien L Condamine
- CNRS, Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier), Place Eugène Bataillon, 34095 Montpellier, France
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31
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Swain A, Woodhouse A, Fagan WF, Fraass AJ, Lowery CM. Biogeographic response of marine plankton to Cenozoic environmental changes. Nature 2024; 629:616-623. [PMID: 38632405 DOI: 10.1038/s41586-024-07337-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 03/20/2024] [Indexed: 04/19/2024]
Abstract
In palaeontological studies, groups with consistent ecological and morphological traits across a clade's history (functional groups)1 afford different perspectives on biodiversity dynamics than do species and genera2,3, which are evolutionarily ephemeral. Here we analyse Triton, a global dataset of Cenozoic macroperforate planktonic foraminiferal occurrences4, to contextualize changes in latitudinal equitability gradients1, functional diversity, palaeolatitudinal specialization and community equitability. We identify: global morphological communities becoming less specialized preceding the richness increase after the Cretaceous-Palaeogene extinction; ecological specialization during the Early Eocene Climatic Optimum, suggesting inhibitive equatorial temperatures during the peak of the Cenozoic hothouse; increased specialization due to circulation changes across the Eocene-Oligocene transition, preceding the loss of morphological diversity; changes in morphological specialization and richness about 19 million years ago, coeval with pelagic shark extinctions5; delayed onset of changing functional group richness and specialization between hemispheres during the mid-Miocene plankton diversification. The detailed nature of the Triton dataset permits a unique spatiotemporal view of Cenozoic pelagic macroevolution, in which global biogeographic responses of functional communities and richness are decoupled during Cenozoic climate events. The global response of functional groups to similar abiotic selection pressures may depend on the background climatic state (greenhouse or icehouse) to which a group is adapted.
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Affiliation(s)
- Anshuman Swain
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA.
- Department of Paleobiology, National Museum of Natural History, Washington, DC, USA.
- Department of Biology, University of Maryland, College Park, MD, USA.
| | - Adam Woodhouse
- University of Texas Institute for Geophysics, University of Texas at Austin, Austin, TX, USA
- School of Earth Sciences, University of Bristol, Bristol, UK
| | - William F Fagan
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Andrew J Fraass
- School of Earth and Ocean Sciences, University of Victoria, Victoria, British Columbia, Canada
| | - Christopher M Lowery
- University of Texas Institute for Geophysics, University of Texas at Austin, Austin, TX, USA
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Liu YY, Cao JL, Kan SL, Wang PH, Wang JL, Cao YN, Wang HW, Li JM. Phylogenomic analyses sheds new light on the phylogeny and diversification of Corydalis DC. in Himalaya-Hengduan Mountains and adjacent regions. Mol Phylogenet Evol 2024; 193:108023. [PMID: 38342159 DOI: 10.1016/j.ympev.2024.108023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 01/27/2024] [Accepted: 02/01/2024] [Indexed: 02/13/2024]
Abstract
The Himalaya-Hengduan Mountains (HHM), a renowned biodiversity hotspot of the world, harbors the most extensive habitats for alpine plants with extraordinary high levels of endemism. Although the general evolution pattern has been elucidated, the underlying processes driving spectacular radiations in many species-rich groups remain elusive. Corydalis DC. is widely distributed throughout the Northern Hemisphere containing more than 500 species, with high diversity in HHM and adjacent regions. Using 95 plastid genes, 3,258,640 nuclear single nucleotide polymorphisms (SNPs) and eight single-copy nuclear genes (SCNs) generated from genome skimming data, we reconstructed a robust time-calibrated phylogeny of Corydalis comprising more than 100 species that represented all subgenera and most sections. Molecular dating indicated that all main clades of Corydalis began to diverge in the Eocene, with the majority of extant species in HHM emerged from a diversification burst after the middle Miocene. Global pattern of mean divergence times indicated that species distributed in HHM were considerably younger than those in other regions, particularly for the two most species-rich clades (V and VI) of Corydalis. The early divergence and the recent diversification of Corydalis were most likely promoted by the continuous orogenesis and climate change associated with the uplift of the Qinghai-Tibetan Plateau (QTP). Our study demonstrates the effectivity of phylogenomic analyses with genome skimming data on the phylogeny of species-rich taxa, and sheds lights on how the uplift of QTP has triggered the evolutionary radiations of large plant genera in HHM and adjacent regions.
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Affiliation(s)
- Yan-Yan Liu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China.
| | - Jia-Liang Cao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Sheng-Long Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China; Marine College, Shandong University, Weihai 264209, China
| | - Peng-Hang Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Jun-Li Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Ya-Nan Cao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Hong-Wei Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Jia-Mei Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China.
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Ulrich S, Vieira M, Coiro M, Bouchal JM, Geier C, Jacobs BF, Currano ED, Lenz OK, Wilde V, Zetter R, Grímsson F. Origin and Early Evolution of Hydrocharitaceae and the Ancestral Role of Stratiotes. PLANTS (BASEL, SWITZERLAND) 2024; 13:1008. [PMID: 38611537 PMCID: PMC11013807 DOI: 10.3390/plants13071008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024]
Abstract
The combined morphological features of Stratiotes (Hydrocharitaceae) pollen, observed with light and electron microscopy, make it unique among all angiosperm pollen types and easy to identify. Unfortunately, the plant is (and most likely was) insect-pollinated and produces relatively few pollen grains per flower, contributing to its apparent absence in the paleopalynological record. Here, we present fossil Stratiotes pollen from the Eocene of Germany (Europe) and Kenya (Africa), representing the first reliable pre-Pleistocene pollen records of this genus worldwide and the only fossils of this family discovered so far in Africa. The fossil Stratiotes pollen grains are described and compared to pollen from a single modern species, Stratiotes aloides L. The paleophytogeographic significance and paleoecological aspects of these findings are discussed in relation to the Hydrocharitaceae fossil records and molecular phylogeny, as well as the present-day distribution patterns of its modern genera.
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Affiliation(s)
- Silvia Ulrich
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria; (S.U.); (J.M.B.); (C.G.); (R.Z.)
- Department of Historical Archaeology, Austrian Archaeological Institute (OeAI), Austrian Academy of Sciences (OeAW), 1010 Vienna, Austria
| | - Manuel Vieira
- Department of Earth Sciences, GeoBioTec, NOVA School of Science and Technology, Campus de Caparica, 2829-516 Caparica, Portugal;
| | - Mario Coiro
- Department of Palaeontology, University of Vienna, 1090 Vienna, Austria
| | - Johannes M. Bouchal
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria; (S.U.); (J.M.B.); (C.G.); (R.Z.)
| | - Christian Geier
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria; (S.U.); (J.M.B.); (C.G.); (R.Z.)
| | - Bonnie F. Jacobs
- Roy M. Huffington Department of Earth Sciences, Southern Methodist University, Dallas, TX 75275, USA;
| | - Ellen D. Currano
- Departments of Botany and Geology & Geophysics, University of Wyoming, Laramie, WY 82071, USA;
| | - Olaf K. Lenz
- Institute of Applied Geosciences, Technical University Darmstadt, 64287 Darmstadt, Germany;
| | - Volker Wilde
- Section Palaeobotany, Division Palaeontology and Historical Geology, Senckenberg Research Institute and Natural History Museum Frankfurt, 60325 Frankfurt am Main, Germany;
| | - Reinhard Zetter
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria; (S.U.); (J.M.B.); (C.G.); (R.Z.)
| | - Friðgeir Grímsson
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria; (S.U.); (J.M.B.); (C.G.); (R.Z.)
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Liu F, Du J, Huang E, Ma W, Ma X, Lourens LJ, Tian J. Accelerated marine carbon cycling forced by tectonic degassing over the Miocene Climate Optimum. Sci Bull (Beijing) 2024; 69:823-832. [PMID: 38218634 DOI: 10.1016/j.scib.2023.12.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/15/2024]
Abstract
Global warming during the Miocene Climate Optimum (MCO, ∼17-14 million years ago) is associated with massive carbon emissions sourced from the flood basalt volcanism and ocean crustal production. However, the perturbation of tectonic carbon degassing on the interaction between climate change and carbon cycle remains unclear. Here, through time-evolutive phase analysis of new and published high-resolution benthic foraminiferal oxygen (δ18O) and carbon (δ13C) isotope records from the global ocean, we find that variations in the marine carbon cycle lead the climate-cryosphere system (δ13C-lead-δ18O) on 405,000-year eccentricity timescales during the MCO. This is in contrast to the previously reported climate-lead-carbon (δ18O-lead-δ13C) scenario during most of the Oligo-Miocene (∼34-6 million years ago). Further sensitivity analysis and model simulations suggest that the elevated atmospheric CO2 concentrations and the resulting greenhouse effect strengthened the low-latitude hydrological cycle during the MCO, accelerating the response of marine carbon cycle to eccentricity forcing. Tropical climate processes played a more important role in regulating carbon-cycle variations when Earth's climate was in a warm regime, as opposed to the dominant influence of polar ice-sheet dynamics during the Plio-Pleistocene (after ∼6 million years ago).
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Affiliation(s)
- Fenghao Liu
- State Key Laboratory of Marine Geology, Tongji University, Shanghai 200092, China
| | - Jinlong Du
- State Key Laboratory of Marine Geology, Tongji University, Shanghai 200092, China
| | - Enqing Huang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai 200092, China.
| | - Wentao Ma
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Xiaolin Ma
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
| | - Lucas J Lourens
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht CB 3584, Netherlands
| | - Jun Tian
- State Key Laboratory of Marine Geology, Tongji University, Shanghai 200092, China
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Long J, He WC, Peng HW, Erst AS, Wang W, Xiang KL. Comparative plastome analysis of the sister genera Ceratocephala and Myosurus (Ranunculaceae) reveals signals of adaptive evolution to arid and aquatic environments. BMC PLANT BIOLOGY 2024; 24:202. [PMID: 38509479 PMCID: PMC10953084 DOI: 10.1186/s12870-024-04891-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND Expansion and contraction of inverted repeats can cause considerable variation of plastid genomes (plastomes) in angiosperms. However, little is known about whether structural variations of plastomes are associated with adaptation to or occupancy of new environments. Moreover, adaptive evolution of angiosperm plastid genes remains poorly understood. Here, we sequenced the complete plastomes for four species of xerophytic Ceratocephala and hydrophytic Myosurus, as well as Ficaria verna. By an integration of phylogenomic, comparative genomic, and selection pressure analyses, we investigated evolutionary patterns of plastomes in Ranunculeae and their relationships with adaptation to dry and aquatic habitats. RESULTS Owing to the significant contraction of the boundary of IRA/LSC towards the IRA, plastome sizes and IR lengths of Myosurus and Ceratocephala are smaller within Ranunculeae. Compared to other Ranunculeae, the Myosurus plastome lost clpP and rps16, one copy of rpl2 and rpl23, and one intron of rpoC1 and rpl16, and the Ceratocephala plastome added an infA gene and lost one copy of rpl2 and two introns of clpP. A total of 11 plastid genes (14%) showed positive selection, two genes common to Myosurus and Ceratocephala, seven in Ceratocephala only, and two in Myosurus only. Four genes showed strong signals of episodic positive selection. The rps7 gene of Ceratocephala and the rpl32 and ycf4 genes of Myosurus showed an increase in the rate of variation close to 3.3 Ma. CONCLUSIONS The plastomic structure variations as well as the positive selection of two plastid genes might be related to the colonization of new environments by the common ancestor of Ceratocephala and Myosurus. The seven and two genes under positive selection might be related to the adaptation to dry and aquatic habitats in Ceratocephala and Myosurus, respectively. Moreover, intensified aridity and frequent sea-level fluctuations, as well as global cooling, might have favored an increased rate of change in some genes at about 3.3 Ma, associated with adaptation to dry and aquatic environments, respectively. These findings suggest that changing environments might have influenced structural variations of plastomes and fixed new mutations arising on some plastid genes owing to adaptation to specific habitats.
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Affiliation(s)
- Jing Long
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, 100093, China
| | - Wen-Chuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Huan-Wen Peng
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, 100093, China
| | - Andrey S Erst
- Central Siberian Botanical Garden, Siberian Branch of Russian Academy of Sciences, Zolotodolinskaya Str. 101, Novosibirsk, 630090, Russia
| | - Wei Wang
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- China National Botanical Garden, Beijing, 100093, China.
| | - Kun-Li Xiang
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
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Lamy F, Winckler G, Arz HW, Farmer JR, Gottschalk J, Lembke-Jene L, Middleton JL, van der Does M, Tiedemann R, Alvarez Zarikian C, Basak C, Brombacher A, Dumm L, Esper OM, Herbert LC, Iwasaki S, Kreps G, Lawson VJ, Lo L, Malinverno E, Martinez-Garcia A, Michel E, Moretti S, Moy CM, Ravelo AC, Riesselman CR, Saavedra-Pellitero M, Sadatzki H, Seo I, Singh RK, Smith RA, Souza AL, Stoner JS, Toyos M, de Oliveira IMVP, Wan S, Wu S, Zhao X. Five million years of Antarctic Circumpolar Current strength variability. Nature 2024; 627:789-796. [PMID: 38538940 PMCID: PMC10972744 DOI: 10.1038/s41586-024-07143-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/31/2024] [Indexed: 04/01/2024]
Abstract
The Antarctic Circumpolar Current (ACC) represents the world's largest ocean-current system and affects global ocean circulation, climate and Antarctic ice-sheet stability1-3. Today, ACC dynamics are controlled by atmospheric forcing, oceanic density gradients and eddy activity4. Whereas palaeoceanographic reconstructions exhibit regional heterogeneity in ACC position and strength over Pleistocene glacial-interglacial cycles5-8, the long-term evolution of the ACC is poorly known. Here we document changes in ACC strength from sediment cores in the Pacific Southern Ocean. We find no linear long-term trend in ACC flow since 5.3 million years ago (Ma), in contrast to global cooling9 and increasing global ice volume10. Instead, we observe a reversal on a million-year timescale, from increasing ACC strength during Pliocene global cooling to a subsequent decrease with further Early Pleistocene cooling. This shift in the ACC regime coincided with a Southern Ocean reconfiguration that altered the sensitivity of the ACC to atmospheric and oceanic forcings11-13. We find ACC strength changes to be closely linked to 400,000-year eccentricity cycles, probably originating from modulation of precessional changes in the South Pacific jet stream linked to tropical Pacific temperature variability14. A persistent link between weaker ACC flow, equatorward-shifted opal deposition and reduced atmospheric CO2 during glacial periods first emerged during the Mid-Pleistocene Transition (MPT). The strongest ACC flow occurred during warmer-than-present intervals of the Plio-Pleistocene, providing evidence of potentially increasing ACC flow with future climate warming.
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Affiliation(s)
- Frank Lamy
- Alfred Wegener Institute (AWI) Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
| | - Gisela Winckler
- Lamont-Doherty Earth Observatory, Climate School, Columbia University, Palisades, NY, USA
- Department of Earth and Environmental Sciences, Columbia University, New York, NY, USA
| | - Helge W Arz
- Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Jesse R Farmer
- School for the Environment, University of Massachusetts Boston, Boston, MA, USA
| | | | - Lester Lembke-Jene
- Alfred Wegener Institute (AWI) Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Jennifer L Middleton
- Lamont-Doherty Earth Observatory, Climate School, Columbia University, Palisades, NY, USA
| | - Michèlle van der Does
- Alfred Wegener Institute (AWI) Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Ralf Tiedemann
- Alfred Wegener Institute (AWI) Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | | | - Chandranath Basak
- Department of Earth Sciences, University of Delaware, Newark, DE, USA
| | - Anieke Brombacher
- Department of Earth & Planetary Sciences, Yale University, New Haven, CT, USA
| | | | - Oliver M Esper
- Alfred Wegener Institute (AWI) Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Lisa C Herbert
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Shinya Iwasaki
- Research and Development Center for Global Change, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Gaston Kreps
- Alfred Wegener Institute (AWI) Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Vera J Lawson
- Department of Earth and Planetary Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Li Lo
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
| | - Elisa Malinverno
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | | | - Elisabeth Michel
- Laboratoire des Sciences du Climat et de l'Environnement (LSCE), Institut Pierre Simon Laplace (IPSL), CNRS-CEA-UVSQ, Gif-sur-Yvette, France
| | - Simone Moretti
- Climate Geochemistry Department, Max Planck Institute for Chemistry (MPIC), Mainz, Germany
| | | | - Ana Christina Ravelo
- Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | | | - Henrik Sadatzki
- Alfred Wegener Institute (AWI) Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Inah Seo
- Global Ocean Research Center, Korea Institute of Ocean Science and Technology (KIOST), Busan, Republic of Korea
| | - Raj K Singh
- School of Earth, Ocean and Climate Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Rebecca A Smith
- Department of Geosciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Alexandre L Souza
- Department of Geology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joseph S Stoner
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - Maria Toyos
- Alfred Wegener Institute (AWI) Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Igor M Venancio P de Oliveira
- Postgraduate Program in Geochemistry, Department of Geochemistry, Institute of Chemistry, Fluminense Federal University, Niterói, Brazil
| | - Sui Wan
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Shuzhuang Wu
- Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | - Xiangyu Zhao
- Geoscience Group, National Institute of Polar Research, Tokyo, Japan
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Clark PU, Shakun JD, Rosenthal Y, Köhler P, Bartlein PJ. Global and regional temperature change over the past 4.5 million years. Science 2024; 383:884-890. [PMID: 38386742 DOI: 10.1126/science.adi1908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 01/16/2024] [Indexed: 02/24/2024]
Abstract
Much of our understanding of Cenozoic climate is based on the record of δ18O measured in benthic foraminifera. However, this measurement reflects a combined signal of global temperature and sea level, thus preventing a clear understanding of the interactions and feedbacks of the climate system in causing global temperature change. Our new reconstruction of temperature change over the past 4.5 million years includes two phases of long-term cooling, with the second phase of accelerated cooling during the Middle Pleistocene Transition (1.5 to 0.9 million years ago) being accompanied by a transition from dominant 41,000-year low-amplitude periodicity to dominant 100,000-year high-amplitude periodicity. Changes in the rates of long-term cooling and variability are consistent with changes in the carbon cycle driven initially by geologic processes, followed by additional changes in the Southern Ocean carbon cycle.
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Affiliation(s)
- Peter U Clark
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR 97331, USA
- School of Geography and Environmental Sciences, University of Ulster, Coleraine BT52 1SA, Northern Ireland, UK
| | - Jeremy D Shakun
- Department of Earth and Environmental Sciences, Boston College, Chestnut Hill, MA 02467, USA
| | - Yair Rosenthal
- Department of Marine and Coastal Science, Rutgers The State University, New Brunswick, NJ 08901, USA
- Department of Earth and Planetary Sciences, Rutgers The State University, New Brunswick, NJ 08901, USA
| | - Peter Köhler
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, 27570 Bremerhaven, Germany
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Hullot M, Martin C, Blondel C, Rössner GE. Life in a Central European warm-temperate to subtropical open forest: Paleoecology of the rhinocerotids from Ulm-Westtangente (Aquitanian, Early Miocene, Germany). THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2024; 111:10. [PMID: 38353735 DOI: 10.1007/s00114-024-01893-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/16/2024]
Abstract
The Ulm-Westtangente locality has yielded the most abundant vertebrate fauna from the Aquitanian stage in Germany. Its dating to the Mammal Neogene Zone 2a, a turnover in Cenozoic climate, makes it a crucial source for the understanding of faunal, paleoecological and paleoenvironmental specifics of the European Aquitanian. However, while most taxa from Ulm-Westtangente have been studied, little to no research has been conducted on the large herbivores, particularly on the two rhinocerotids Mesaceratherium paulhiacense and Protaceratherium minutum. Here, we used a multi-proxy approach to investigate the paleoecology of these two species. The remains of the smaller species P. minutum (438 to 685 kg) are twice as abundant as those of the larger M. paulhiacense (1389 to 2327 kg), but both display a similar age structure (~ 10% of juveniles, 20% of subadults and 70% of adults), mortality curves, and mild prevalence of hypoplasia (~ 17%). Results from dental mesowear, microwear, and carbon isotopes indicate different feeding preferences: both were C3 feeders but M. paulhiacense had a more abrasive diet and was probably a mixed feeder. Our study on rhinocerotids also yielded new paleoenvironmental insights, such as the mean annual temperature (15.8 °C) and precipitation (317 mm/year) suggesting rather warm and dry conditions.
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Affiliation(s)
- Manon Hullot
- SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Straße 10, 80333, Munich, Germany.
| | - Céline Martin
- Géosciences Montpellier, Université de Montpellier, Campus Triolet cc060, Bât 22 - Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Cécile Blondel
- PALEVOPRIM Poitiers, Université de Poitiers Bât B35 - TSA 51106, 6 Rue Michel Brunet, 86073, Poitiers, France
| | - Gertrud E Rössner
- SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Straße 10, 80333, Munich, Germany
- Department für Geo- und Umweltwissenschaften, Paläontologie & Geobiologie, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333, Munich, Germany
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39
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Isson T, Rauzi S. Oxygen isotope ensemble reveals Earth's seawater, temperature, and carbon cycle history. Science 2024; 383:666-670. [PMID: 38330122 DOI: 10.1126/science.adg1366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/05/2024] [Indexed: 02/10/2024]
Abstract
Earth's persistent habitability since the Archean remains poorly understood. Using an oxygen isotope ensemble approach-comprising shale, iron oxide, carbonate, silica, and phosphate records-we reconcile a multibillion-year history of seawater δ18O, temperature, and marine and terrestrial clay abundance. Our results reveal a rise in seawater δ18O and a temperate Proterozoic climate distinct to interpretations of a hot early Earth, indicating a strongly buffered climate system. Precambrian sediments are enriched in marine authigenic clay, with prominent reductions occurring in concert with Paleozoic and Cenozoic cooling, the expansion of siliceous life, and the radiation of land plants. These findings support the notion that shifts in the locus and extent of clay formation contributed to seawater 18O enrichment, clement early Earth conditions, major climate transitions, and climate stability through the reverse weathering feedback.
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Affiliation(s)
- Terry Isson
- Te Aka Mātuatua, University of Waikato (Tauranga), Bay of Plenty, Tauranga, New Zealand
| | - Sofia Rauzi
- Te Aka Mātuatua, University of Waikato (Tauranga), Bay of Plenty, Tauranga, New Zealand
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40
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Fan Z, Gao C, Lin L. Phylogeographical and population genetics of Polyspora sweet in China provides insights into its phylogenetic evolution and subtropical dispersal. BMC PLANT BIOLOGY 2024; 24:89. [PMID: 38317071 PMCID: PMC10845455 DOI: 10.1186/s12870-024-04783-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/29/2024] [Indexed: 02/07/2024]
Abstract
BACKGROUND Geological movements and climatic fluctuations stand as pivotal catalysts driving speciation and phylogenetic evolution. The genus Polyspora Sweet (Theaceae), prominently found across the Malay Archipelagos and Indochina Peninsula in tropical Asia, exhibits its northernmost distribution in China. In this study, we investigated the evolutionary and biogeographical history of the genus Polyspora in China, shedding light on the mechanisms by which these species respond to ancient geological and climatic fluctuations. METHODS Phylogenetic relationships of 32 representative species of Theaceae were reconstructed based on the chloroplast genome and ribosome 18-26 S rRNA datasets. Species divergence time was estimated using molecular clock and five fossil calibration. The phylogeography and population genetics in 379 individuals from 32 populations of eight species were analyzed using chloroplast gene sequences (trnH-psbA, rpoB-trnC and petN-psbM), revealing the glacial refugia of each species, and exploring the causes of the phylogeographic patterns. RESULTS We found that Chinese Polyspora species diverged in the middle Miocene, showing a tropical-subtropical divergence order. A total of 52 haplotypes were identified by the combined chloroplast sequences. Chinese Polyspora exhibited a distinct phylogeographical structure, which could be divided into two clades and eight genealogical subdivisions. The divergence between the two clades occurred approximately 20.67 Ma. Analysis of molecular variance revealed that the genetic variation mainly occurred between species (77.91%). At the species level, Polyspora axillaris consists of three lineages, while P. speciosa had two lineages. The major lineages of Chinese Polyspora diverged between 12 and 15 Ma during the middle to late Miocene. The peak period of haplotype differentiation in each species occurred around the transition from the last interglacial to the last glacial period, approximately 6 Ma ago. CONCLUSION The primary geographical distribution pattern of Chinese Polyspora was established prior to the last glacial maximum, and the population historical dynamics were relatively stable. The geological and climatic turbulence during the Quaternary glacial period had minimal impact on the distribution pattern of the genus. The genus coped with Quaternary climate turbulence by glacial in situ survival in multiple refuges. The Sino-Vietnam border and Nanling corridor might be the genetic mixing center of Polyspora.
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Affiliation(s)
- Zhifeng Fan
- City College, Kunming University of Science and Technology, Kunming, 650093, China.
| | - Can Gao
- College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, China
| | - Lifang Lin
- Hot Spring Sub-district Office, Anning Municipal People's Government, Kunming, 650300, China.
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41
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Peris D, Condamine FL. The angiosperm radiation played a dual role in the diversification of insects and insect pollinators. Nat Commun 2024; 15:552. [PMID: 38253644 PMCID: PMC10803743 DOI: 10.1038/s41467-024-44784-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Interactions with angiosperms have been hypothesised to play a crucial role in driving diversification among insects, with a particular emphasis on pollinator insects. However, support for coevolutionary diversification in insect-plant interactions is weak. Macroevolutionary studies of insect and plant diversities support the hypothesis that angiosperms diversified after a peak in insect diversity in the Early Cretaceous. Here, we used the family-level fossil record of insects as a whole, and insect pollinator families in particular, to estimate diversification rates and the role of angiosperms on insect macroevolutionary history using a Bayesian process-based approach. We found that angiosperms played a dual role that changed through time, mitigating insect extinction in the Cretaceous and promoting insect origination in the Cenozoic, which is also recovered for insect pollinator families only. Although insects pollinated gymnosperms before the angiosperm radiation, a radiation of new pollinator lineages began as angiosperm lineages increased, particularly significant after 50 Ma. We also found that global temperature, increases in insect diversity, and spore plants were strongly correlated with origination and extinction rates, suggesting that multiple drivers influenced insect diversification and arguing for the investigation of different explanatory variables in further studies.
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Affiliation(s)
- David Peris
- Institut Botànic de Barcelona (CSIC-CMCNB), 08038, Barcelona, Spain.
| | - Fabien L Condamine
- CNRS, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
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42
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Weppe R, Condamine FL, Guinot G, Maugoust J, Orliac MJ. Drivers of the artiodactyl turnover in insular western Europe at the Eocene-Oligocene Transition. Proc Natl Acad Sci U S A 2023; 120:e2309945120. [PMID: 38109543 PMCID: PMC10756263 DOI: 10.1073/pnas.2309945120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/10/2023] [Indexed: 12/20/2023] Open
Abstract
Simultaneously investigating the effects of abiotic and biotic factors on diversity dynamics is essential to understand the evolutionary history of clades. The Grande Coupure corresponds to a major faunal turnover at the Eocene-Oligocene transition (EOT) (~34.1 to 33.55 Mya) and is defined in western Europe as an extinction of insular European mammals coupled with the arrival of crown clades from Asia. Here, we focused on the species-rich group of endemic European artiodactyls to determine the drivers of the Grande Coupure during the major environmental disruptions at the EOT. Using Bayesian birth-death models, we analyzed an original high-resolution fossil dataset (90 species, >2,100 occurrences) from southwestern France (Quercy area) and estimated the regional diversification and diversity dynamics of endemic and immigrant artiodactyls. We show that the endemic artiodactyl radiation was mainly related to the Eocene tropical conditions, combined with biotic controls on speciation and clade-related diversity dependence. We further highlight that the major environmental changes at the transition (77% of species became extinct) and the concurrent increase in seasonality in Europe during the Oligocene were likely the main drivers of their decline. Surprisingly, our results do not support the widely-held hypothesis of active competition between endemic and immigrant artiodactyls but rather suggest a passive or opportunistic replacement by immigrants, which is further supported by morphological clustering of specific ecological traits across the Eocene-Oligocene transition. Our analyses provide insights into the evolutionary and ecological processes driving the diversification and decline of mammalian clades during a major biological and climatic crisis.
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Affiliation(s)
- Romain Weppe
- Institut des Sciences de l’Evolution de Montpellier, Univ Montpellier, CNRS, IRD, Montpellier Cedex 534095, France
| | - Fabien L. Condamine
- Institut des Sciences de l’Evolution de Montpellier, Univ Montpellier, CNRS, IRD, Montpellier Cedex 534095, France
| | - Guillaume Guinot
- Institut des Sciences de l’Evolution de Montpellier, Univ Montpellier, CNRS, IRD, Montpellier Cedex 534095, France
| | - Jacob Maugoust
- Institut des Sciences de l’Evolution de Montpellier, Univ Montpellier, CNRS, IRD, Montpellier Cedex 534095, France
| | - Maëva J. Orliac
- Institut des Sciences de l’Evolution de Montpellier, Univ Montpellier, CNRS, IRD, Montpellier Cedex 534095, France
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Harzhauser M, Landau BM. The auger snails (Gastropoda, Conoidea, Terebridae) of the Miocene Paratethys Sea. Zootaxa 2023; 5385:1-70. [PMID: 38221228 DOI: 10.11646/zootaxa.5385.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Indexed: 01/16/2024]
Abstract
We present a critical review of the Miocene Terebridae of the European Central Paratethys Sea. In total, we document 23 species placed in 7 genera. We designate lectotypes for Terebra bigranulata Hoernes & Auinger, 1880 [= Fusoterebra terebrina (Bellardi & Michelotti, 1840)], Terebra (Hastula) cinereides Hoernes & Auinger, 1880 [= Hastula duboisiana (dOrbigny, 1852)], Terebra (Myurella) lapugyensis Hoernes & Auinger 1880 [= Hastula lapugyensis (Hoernes & Auinger, 1880)] and Terebra transylvanica Hoernes & Auinger, 1880. Based on conchological similarities we assume that the extant terebrine Punctoterebra Bartsch, 1923 might be a subjective junior synonym of Strioterebrum Sacco, 1890. In this case, molecular data could resolve this question, as Strioterebrum is still represented today by Strioterebrum reticulare (Sacco, 1891). Hastulopsis Oyama, 1961 and Maculauger Fedosov, Malcolm, Terryn, Gorson, Modica, Holford & Puillandre, 2020 are recorded for the first time from the European Neogene. Terebra golebiowskii nov. sp. and Oxymeris transleithana nov. sp. are introduced as new species.
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Affiliation(s)
| | - Bernard M Landau
- Naturalis Biodiversity Center; P.O. Box 9517; 2300 RA Leiden; Netherlands; Instituto Dom Luiz da Universidade de Lisboa; Campo Grande; 1749-016 Lisboa; Portugal; and International Health Centres; Av. Infante de Henrique 7; Areias So Joo; P-8200 Albufeira; Portugal.
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Luo T, Zhao X, Lan C, Li W, Deng H, Xiao N, Zhou J. Integrated phylogenetic analyses reveal the evolutionary, biogeographic, and diversification history of Asian warty treefrog genus Theloderma (Anura, Rhacophoridae). Ecol Evol 2023; 13:e10829. [PMID: 38145017 PMCID: PMC10739124 DOI: 10.1002/ece3.10829] [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: 05/15/2023] [Revised: 11/22/2023] [Accepted: 11/29/2023] [Indexed: 12/26/2023] Open
Abstract
Asian warty treefrogs, genus Theloderma, are morphologically variable arboreal frogs endemic to Southeast Asia and Southern China. However, integrated systematic studies are lacking, and knowledge of the genus in terms of diversity, origin, and historical diversification remains limited. To address these knowledge gaps, we used three mitochondrial and five nuclear gene fragments to reconstruct the Theloderma phylogeny, estimate divergence times, and examine the biogeography of the genus. Phylogenetic and species delimitation analyses suggest that the genus Theloderma comprises three major clades corresponding to two subgenera and seven species groups, and mPTP identified at least 12 putative cryptic species, suggesting that species diversity has been underestimated. Biogeographic analyses indicated that most recent common ancestor of Theloderma originated in the Indochina Peninsula during the Middle Oligocene (ca. 27.77 Ma) and the splitting of Clade A to C occurred in the Late Oligocene (ca. 23.55-25.57 Ma). Current biogeographic patterns result from two distinct processes: in situ diversification in the Indochina Peninsula and dispersal in multiple areas, namely southward dispersal to the Malay Peninsula and Borneo, northeastward dispersal to Southern China, northward dispersal to the Himalayas, and dispersal from Southern China to the Indochina Peninsula. Ancestral character reconstruction suggests that the ancestor of Theloderma may have possessed a small body size, rough dorsal skin, and absence of vomerine teeth and hand webbing, and that these four characters have undergone multiple evolutions. Principal component analysis based on eight bioclimatic variables did not clearly distinguish the three major clades of Theloderma, suggesting that species in these clades may occupy similar climatic ecological niches. Our research highlights the importance of orogeny and paleoclimatic changes, in shaping amphibian biodiversity in mountain ecosystems.
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Affiliation(s)
- Tao Luo
- School of Life ScienceGuizhou Normal UniversityGuiyangChina
- School of Karst SciencesGuizhou Normal UniversityGuiyangChina
| | - Xin‐Rui Zhao
- School of Karst SciencesGuizhou Normal UniversityGuiyangChina
| | - Chang‐Ting Lan
- School of Life ScienceGuizhou Normal UniversityGuiyangChina
| | - Wei Li
- School of Life ScienceGuizhou Normal UniversityGuiyangChina
| | - Huai‐Qing Deng
- School of Life ScienceGuizhou Normal UniversityGuiyangChina
| | - Ning Xiao
- Guiyang Healthcare Vocational UniversityGuiyangChina
| | - Jiang Zhou
- School of Karst SciencesGuizhou Normal UniversityGuiyangChina
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Qin F, Xue T, Zhang X, Yang X, Yu J, Gadagkar SR, Yu S. Past climate cooling and orogenesis of the Hengduan Mountains have influenced the evolution of Impatiens sect. Impatiens (Balsaminaceae) in the Northern Hemisphere. BMC PLANT BIOLOGY 2023; 23:600. [PMID: 38030965 PMCID: PMC10685625 DOI: 10.1186/s12870-023-04625-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Impatiens sect. Impatiens is distributed across the Northern Hemisphere and has diversified considerably, particularly within the Hengduan Mountains (HDM) in southwest China. Yet, the infra-sectional phylogenetic relationships are not well resolved, largely due to limited taxon sampling and an insufficient number of molecular markers. The evolutionary history of its diversification is also poorly understood. In this study, plastome data and the most complete sampling to date were used to reconstruct a robust phylogenetic framework for this section. The phylogeny was then used to investigate its biogeographical history and diversification patterns, specifically with the aim of understanding the role played by the HDM and past climatic changes in its diversification. RESULTS A stable phylogeny was reconstructed that strongly supported both the monophyly of the section and its division into seven major clades (Clades I-VII). Molecular dating and ancestral area reconstruction suggest that sect. Impatiens originated in the HDM and Southeast China around 11.76 Ma, after which different lineages dispersed to Northwest China, temperate Eurasia, and North America, mainly during the Pliocene and Pleistocene. An intercontinental dispersal event from East Asia to western North America may have occurred via the Bering Land Bridge or Aleutian Islands. The diversification rate was high during its early history, especially with the HDM, but gradually decreased over time both within and outside the HDM. Multiple linear regression analysis showed that the distribution pattern of species richness was strongly associated with elevation range, elevation, and mean annual temperature. Finally, ancestral niche analysis indicated that sect. Impatiens originated in a relatively cool, middle-elevation area. CONCLUSIONS We inferred the evolutionary history of sect. Impatiens based on a solid phylogenetic framework. The HDM was the primary source or pump of its diversity in the Northern Hemisphere. Orogeny and climate change may have also shaped its diversification rates, as a steady decrease in the diversification rate coincided with the uplift of the HDM and climate cooling. These findings provide insights into the distribution pattern of sect. Impatiens and other plants in the Northern Hemisphere.
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Affiliation(s)
- Fei Qin
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, 100093, China
| | - Tiantian Xue
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, 100093, China
| | - Xiaoxia Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, 100093, China
| | - Xudong Yang
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Department of Earth System Science, Tsinghua University, Beijing, 100084, China
| | - Jianghong Yu
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Sudhindra R Gadagkar
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, Glendale, AZ, 85308, USA.
- College of Veterinary Medicine, Midwestern University, Glendale, AZ, 85308, USA.
- Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, 85308, USA.
| | - Shengxiang Yu
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- China National Botanical Garden, Beijing, 100093, China.
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Rull V. An Updated Review of Fossil Pollen Evidence for the Study of the Origin, Evolution and Diversification of Caribbean Mangroves. PLANTS (BASEL, SWITZERLAND) 2023; 12:3852. [PMID: 38005749 PMCID: PMC10674848 DOI: 10.3390/plants12223852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023]
Abstract
Recently, the evolutionary history of the Caribbean mangroves has been reconsidered using partial palynological databases organized by the time intervals of interest, namely Late Cretaceous to Eocene for the origin, the Eocene-Oligocene transition for major turnover and Neogene to Quaternary for diversification. These discussions have been published in a set of sequential papers, but the raw information remains unknown. This paper reviews all the information available and provides the first comprehensive and updated compilation of the abovementioned partial databases. This compilation is called CARMA-F (CARibbean MAngroves-Fossil) and includes nearly 90 localities from the present and past Caribbean coasts, ranging from the Late Cretaceous to the Pliocene. Details on the Quaternary localities (CARMA-Q) will be published later. CARMA-F lists and illustrates the fossil pollen from past mangrove taxa and their extant representatives, and includes a map of the studied localities and a conventional spreadsheet with the raw data. The compilation is the most complete available for the study of the origin, evolution and diversification of Caribbean mangroves, and is open to modifications for adapting it to the particular interests of each researcher.
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Affiliation(s)
- Valentí Rull
- Botanic Institute of Barcelona, Spanish National Research Council (CSIC), Pg. del Migdia s/n, 08028 Barcelona, Spain;
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, C. de les Columnes s/n, 08193 Cerdanyola del Vallès, Spain
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Hou S, Stap LB, Paul R, Nelissen M, Hoem FS, Ziegler M, Sluijs A, Sangiorgi F, Bijl PK. Reconciling Southern Ocean fronts equatorward migration with minor Antarctic ice volume change during Miocene cooling. Nat Commun 2023; 14:7230. [PMID: 37945579 PMCID: PMC10636158 DOI: 10.1038/s41467-023-43106-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Gradual climate cooling and CO2 decline in the Miocene were recently shown not to be associated with major ice volume expansion, challenging a fundamental paradigm in the functioning of the Antarctic cryosphere. Here, we explore Miocene ice-ocean-climate interactions by presenting a multi-proxy reconstruction of subtropical front migration, bottom water temperature and global ice volume change, using dinoflagellate cyst biogeography, benthic foraminiferal clumped isotopes from offshore Tasmania. We report an equatorward frontal migration and strengthening, concurrent with surface and deep ocean cooling but absence of ice volume change in the mid-late-Miocene. To reconcile these counterintuitive findings, we argue based on new ice sheet modelling that the Antarctic ice sheet progressively lowered in height while expanding seawards, to maintain a stable volume. This can be achieved with rigorous intervention in model precipitation regimes on Antarctica and ice-induced ocean cooling and requires rethinking the interactions between ice, ocean and climate.
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Affiliation(s)
- Suning Hou
- Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands.
| | - Lennert B Stap
- Institute for Marine and Atmospheric research Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Ryan Paul
- Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Mei Nelissen
- NIOZ Royal Netherlands Institute of Sea Research, Texel, The Netherlands
| | - Frida S Hoem
- Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Martin Ziegler
- Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Appy Sluijs
- Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | | | - Peter K Bijl
- Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
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Srivastava P, J Murton B, Sant'Anna LG, Florindo F, Hassan MB, Taciro Mandacaru Guerra J, de Assis Janasi V, Jovane L. Red clays indicate sub-aerial exposure of the Rio Grande Rise during the Eocene volcanic episode. Sci Rep 2023; 13:19092. [PMID: 37925541 PMCID: PMC10625572 DOI: 10.1038/s41598-023-46273-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023] Open
Abstract
Autonomous underwater vehicle (AUV) mapping of the western Rio Grande Rise (RGR), South Atlantic, and subsequent exploration and photography of horizontal lava flows exposed in near vertical, faulted escarpments, showed occurrences of red clays/weathered volcanic tops trapped between successive alkaline lava flows. These red clays indicate a hiatus in successive volcanic eruptions. Here, we report detailed mineralogical, geochemical, and rock magnetic characteristics of one such distinct red clay dredged from ~ 650 m water depth in the western RGR. The mineral constituents of the red clay are kaolinite, magnetite, oxidized magnetite (/maghemite), hematite, and goethite, with biogenic calcite and halite occupying voids or precipitated on the surface of the red clay. The chemical index of alteration (CIA) has a value of 93, showing that red clay is a product of extreme chemical weathering of the lava flows. The alkaline volcanic rocks recovered from nearby show an age of ~ 44 Ma, indicating an Eocene age for the volcanism. We show that the red clays are a product of sub-aerial chemical weathering of these Eocene volcanic rocks, in a warm-wet climate, before the thermal subsidence of the RGR to its modern-day bathymetric depth.
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Affiliation(s)
- Priyeshu Srivastava
- Instituto Oceanográfico, Universidade de São Paulo, Praça do Oceanográfico, 191, São Paulo, 05508-120, Brazil.
- Indian Institute of Geomagnetism, Navi Mumbai, 410218, India.
- Istituto Nazionale di Geofisica e Vulcanologia, Via di Vigna Murata 605, 00143, Rome, Italy.
| | - Bramley J Murton
- National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Lucy Gomes Sant'Anna
- Instituto de Energia e Ambiente, Universidade de São Paulo, Av. Prof. Luciano Gualberto, 1289, São Paulo, 05508-010, Brazil
| | - Fabio Florindo
- Istituto Nazionale di Geofisica e Vulcanologia, Via di Vigna Murata 605, 00143, Rome, Italy
| | - Muhammad Bin Hassan
- Instituto Oceanográfico, Universidade de São Paulo, Praça do Oceanográfico, 191, São Paulo, 05508-120, Brazil
| | | | - Valdecir de Assis Janasi
- Instituto de Geociências, Universidade de São Paulo, Rua do Lago, 562, São Paulo, 05508-080, Brazil
| | - Luigi Jovane
- Instituto Oceanográfico, Universidade de São Paulo, Praça do Oceanográfico, 191, São Paulo, 05508-120, Brazil
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Desvignes T, Bista I, Herrera K, Landes A, Postlethwait JH. Cold-Driven Hemoglobin Evolution in Antarctic Notothenioid Fishes Prior to Hemoglobin Gene Loss in White-Blooded Icefishes. Mol Biol Evol 2023; 40:msad236. [PMID: 37879119 PMCID: PMC10651078 DOI: 10.1093/molbev/msad236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/08/2023] [Accepted: 10/18/2023] [Indexed: 10/27/2023] Open
Abstract
Expression of multiple hemoglobin isoforms with differing physiochemical properties likely helps species adapt to different environmental and physiological conditions. Antarctic notothenioid fishes inhabit the icy Southern Ocean and display fewer hemoglobin isoforms, each with less affinity for oxygen than temperate relatives. Reduced hemoglobin multiplicity was proposed to result from relaxed selective pressure in the cold, thermally stable, and highly oxygenated Antarctic waters. These conditions also permitted the survival and diversification of white-blooded icefishes, the only vertebrates living without hemoglobin. To understand hemoglobin evolution during adaptation to freezing water, we analyzed hemoglobin genes from 36 notothenioid genome assemblies. Results showed that adaptation to frigid conditions shaped hemoglobin gene evolution by episodic diversifying selection concomitant with cold adaptation and by pervasive evolution in Antarctic notothenioids compared to temperate relatives, likely a continuing adaptation to Antarctic conditions. Analysis of hemoglobin gene expression in adult hematopoietic organs in various temperate and Antarctic species further revealed a switch in hemoglobin gene expression underlying hemoglobin multiplicity reduction in Antarctic fish, leading to a single hemoglobin isoform in adult plunderfishes and dragonfishes, the sister groups to icefishes. The predicted high hemoglobin multiplicity in Antarctic fish embryos based on transcriptomic data, however, raises questions about the molecular bases and physiological implications of diverse hemoglobin isoforms in embryos compared to adults. This analysis supports the hypothesis that the last common icefish ancestor was vulnerable to detrimental mutations affecting the single ancestral expressed alpha- and beta-globin gene pair, potentially predisposing their subsequent loss.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Iliana Bista
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt 60325, Germany
- Senckenberg Research Institute, Frankfurt 60325, Germany
| | - Karina Herrera
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Audrey Landes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
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Coiro M, Allio R, Mazet N, Seyfullah LJ, Condamine FL. Reconciling fossils with phylogenies reveals the origin and macroevolutionary processes explaining the global cycad biodiversity. THE NEW PHYTOLOGIST 2023; 240:1616-1635. [PMID: 37302411 PMCID: PMC10953041 DOI: 10.1111/nph.19010] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/01/2023] [Indexed: 06/13/2023]
Abstract
The determinants of biodiversity patterns can be understood using macroevolutionary analyses. The integration of fossils into phylogenies offers a deeper understanding of processes underlying biodiversity patterns in deep time. Cycadales are considered a relict of a once more diverse and globally distributed group but are restricted to low latitudes today. We still know little about their origin and geographic range evolution. Combining molecular data for extant species and leaf morphological data for extant and fossil species, we study the origin of cycad global biodiversity patterns through Bayesian total-evidence dating analyses. We assess the ancestral geographic origin and trace the historical biogeography of cycads with a time-stratified process-based model. Cycads originated in the Carboniferous on the Laurasian landmass and expanded in Gondwana in the Jurassic. Through now-vanished continental connections, Antarctica and Greenland were crucial biogeographic crossroads for cycad biogeography. Vicariance is an essential speciation mode in the deep and recent past. Their latitudinal span increased in the Jurassic and restrained toward subtropical latitudes in the Neogene in line with biogeographic inferences of high-latitude extirpations. We show the benefits of integrating fossils into phylogenies to estimate ancestral areas of origin and to study evolutionary processes explaining the global distribution of present-day relict groups.
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Affiliation(s)
- Mario Coiro
- Department of PalaeontologyUniversity of Vienna1090ViennaAustria
- Ronin Institute for Independent ScholarshipMontclairNJ07043USA
| | - Rémi Allio
- Centre de Biologie pour la Gestion des Populations, INRAE, CIRAD, IRD, Montpellier SupAgroUniversité de Montpellier34988MontpellierFrance
| | - Nathan Mazet
- CNRS, Institut des Sciences de l'Evolution de Montpellier, Université de MontpellierPlace Eugène Bataillon34095MontpellierFrance
| | | | - Fabien L. Condamine
- CNRS, Institut des Sciences de l'Evolution de Montpellier, Université de MontpellierPlace Eugène Bataillon34095MontpellierFrance
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