1
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Wieman ST, Kapit J, Michel APM, Guo W. Development of a quantum cascade laser absorption spectrometer for simultaneous measurement of 13C- 18O and 18O- 18O clumping in CO 2. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9836. [PMID: 38887894 DOI: 10.1002/rcm.9836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/08/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024]
Abstract
RATIONALE Dual clumped isotope paleothermometry determines carbonate formation temperatures by measuring the frequency of 13C-18O (∆638) and 18O-18O (∆828) pairs in carbonates. It resolves isotopic kinetic biases and thus enables more accurate paleotemperature reconstructions. However, high-precision measurements of 18O-18O clumping using current techniques requires large sample sizes and long acquisition times. METHODS We developed a mid-infrared isotope ratio laser spectrometer (IRLS) for simultaneous measurement of the isotopologue ratios ∆638 and ∆828 in gas-phase carbon dioxide (CO2) at room temperature. Our IRLS uses a single laser scanning from 2290.7 to 2291.1 cm-1 and a 31 m pathlength optical cell, and it simultaneously measures the five isotopologues required for calculating ∆638 and ∆828: 16O12C16O, 16O13C16O, 16O12C18O, 16O13C18O, and 18O12C18O. In addition, our IRLS can measure 16O12C17O, enabling ∆17O analysis. RESULTS At ~20°C and a CO2 pressure of ~2 Torr, our IRLS system achieved precisions of 0.128‰ and 0.140‰ within 20 s for abundances of the clumped isotopologues 16O13C18O and 18O12C18O, respectively, and precisions of 0.267‰, 0.245‰, and 0.128‰ for 16O12C16O, 16O13C16O, and 16O12C18O. This yielded precisions of 0.348‰ (∆638) and 0.302‰ (∆828) within 25 s. Simulated sample-reference switching highlights the potential of our system and the need for further development. CONCLUSIONS We demonstrated simultaneous measurements of ∆638 and ∆828 in CO2 to precisions of <0.35‰ within 25 s using a room-temperature, single-laser IRLS. Future developments on better resolving 16O12C16O and 16O13C16O peaks and system temperature control could further improve the measurement precision.
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Affiliation(s)
- Scott T Wieman
- The MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Woods Hole, MA, USA
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Jason Kapit
- Department of Applied Ocean Physics and Engineering, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Anna P M Michel
- Department of Applied Ocean Physics and Engineering, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Weifu Guo
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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2
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Jiao N, Luo T, Chen Q, Zhao Z, Xiao X, Liu J, Jian Z, Xie S, Thomas H, Herndl GJ, Benner R, Gonsior M, Chen F, Cai WJ, Robinson C. The microbial carbon pump and climate change. Nat Rev Microbiol 2024; 22:408-419. [PMID: 38491185 DOI: 10.1038/s41579-024-01018-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2024] [Indexed: 03/18/2024]
Abstract
The ocean has been a regulator of climate change throughout the history of Earth. One key mechanism is the mediation of the carbon reservoir by refractory dissolved organic carbon (RDOC), which can either be stored in the water column for centuries or released back into the atmosphere as CO2 depending on the conditions. The RDOC is produced through a myriad of microbial metabolic and ecological processes known as the microbial carbon pump (MCP). Here, we review recent research advances in processes related to the MCP, including the distribution patterns and molecular composition of RDOC, links between the complexity of RDOC compounds and microbial diversity, MCP-driven carbon cycles across time and space, and responses of the MCP to a changing climate. We identify knowledge gaps and future research directions in the role of the MCP, particularly as a key component in integrated approaches combining the mechanisms of the biological and abiotic carbon pumps for ocean negative carbon emissions.
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Affiliation(s)
- Nianzhi Jiao
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China.
| | - Tingwei Luo
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
| | - Quanrui Chen
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
| | - Zhao Zhao
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
| | - Xilin Xiao
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
| | - Jihua Liu
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Zhimin Jian
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Shucheng Xie
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Helmuth Thomas
- Institute of Carbon Cycles, Helmholtz-Zentrum Hereon, Geesthacht, Germany
- Institut für Chemie und Biologie des Meeres (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Ronald Benner
- Department of Biological Sciences, School of the Earth, Ocean and Environment, University of South Carolina, Columbia, SC, USA
| | - Micheal Gonsior
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Solomons, MD, USA
| | - Feng Chen
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Wei-Jun Cai
- School of Marine Science and Policy, University of Delaware, Newark, DE, USA
| | - Carol Robinson
- UN Global ONCE joint focal points at Shandong University, University of East Anglia, University of Maryland Center for Environmental Science, and Xiamen University, Xiamen, China.
- Centre for Ocean and Atmospheric Sciences (COAS), School of Environmental Sciences, University of East Anglia, Norwich, UK.
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3
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Zhang Q, Zhang R, Hao Q, Clift PD, Roberts AP, Florindo F, Li Q, Liu J, Liu Z, Gui K, Che H, Liu S, Qiao Q, Ju L, Jin C, Liu C, Liu Q, Xiao W, Guo Z. East Asian winter monsoon intensification over the Northwest Pacific Ocean driven by late Miocene atmospheric CO 2 decline. SCIENCE ADVANCES 2024; 10:eadm8270. [PMID: 38896619 DOI: 10.1126/sciadv.adm8270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
East Asian winter monsoon (EAWM) activity has had profound effects on environmental change throughout East Asia and the western Pacific. Much attention has been paid to Quaternary EAWM evolution, while long-term EAWM fluctuation characteristics and drivers remain unclear, particularly during the late Miocene when marked global climate and Asian paleogeographic changes occurred. To clarify understanding of late Miocene EAWM evolution, we developed a high-precision 9-million-year-long stacked EAWM record from Northwest Pacific Ocean abyssal sediments based on environmental magnetism, sedimentology, and geochemistry, which reveals a strengthened late Miocene EAWM. Our paleoclimate simulations also indicate that atmospheric CO2 decline played a vital role in this EAWM intensification over the Northwest Pacific Ocean compared to other factors, including central Asian orogenic belt and northeastern Tibetan Plateau uplift and Antarctic ice-sheet expansion. Our results expand understanding of EAWM evolution from inland areas to the open ocean and indicate the importance of atmospheric CO2 fluctuations on past EAWM variability over large spatial scales.
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Affiliation(s)
- Qiang Zhang
- State Key Laboratory of Lithospheric Evolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
| | - Ran Zhang
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, China
| | - Qingzhen Hao
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
| | - Peter D Clift
- Department of Earth Sciences, University College, London, UK
| | - Andrew P Roberts
- Research School of Earth Sciences, Australian National University, Canberra, ACT, Australia
| | - Fabio Florindo
- Istituto Nazionale di Geofisica e Vulcanologia, Rome, Italy
| | - Qian Li
- Laoshan Laboratory, Qingdao, China
| | - Jianxing Liu
- Key Laboratory of Marine Geology and Metallogeny, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Ze Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Submarine Geosciences and Prospecting Techniques, MOE and College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Ke Gui
- State Key Laboratory of Severe Weather and Key Laboratory of Atmospheric Chemistry of China Meteorological Administration, Chinese Academy of Meteorological Sciences, Beijing, China
| | - Huizheng Che
- State Key Laboratory of Severe Weather and Key Laboratory of Atmospheric Chemistry of China Meteorological Administration, Chinese Academy of Meteorological Sciences, Beijing, China
| | - Shuangchi Liu
- State Key Laboratory of Lithospheric Evolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
| | - Qingqing Qiao
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Xinjiang, China
| | - Lixia Ju
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, China
| | - Chunsheng Jin
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
| | - Chuanzhou Liu
- State Key Laboratory of Lithospheric Evolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
| | - Qingsong Liu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Wenjiao Xiao
- State Key Laboratory of Lithospheric Evolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Xinjiang, China
| | - Zhengtang Guo
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
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4
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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 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 Sciences, Beijing, China
- Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Tao Deng
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Yang Wang
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, United States
| | - Fajun Sun
- Environmental Science & Technology, University of Maryland, College Park, United States
| | - Burt Wolff
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, United 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 Sciences, Beijing, China
| | - 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 Sciences, Beijing, China
| | - Luda Xing
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Jiao Fu
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Ji Zhang
- School of Civil and Hydraulic Engineering, Huazhong University of Science and Technology, Wuhan, China
- National Center of Technology Innovation for Digital Construction, Wuhan, China
| | - 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 Sciences, Beijing, China
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5
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Lu XM, Yu XF, Li GQ, Qu MH, Wang H, Liu C, Man YP, Jiang XH, Li MZ, Wang J, Chen QQ, Lei R, Zhao CC, Zhou YQ, Jiang ZW, Li ZZ, Zheng S, Dong C, Wang BL, Sun YX, Zhang HQ, Li JW, Mo QH, Zhang Y, Lou X, Peng HX, Yi YT, Wang HX, Zhang XJ, Wang YB, Wang D, Li L, Zhang Q, Wang WX, Liu Y, Gao L, Wu JH, Wang YC. Genome assembly of autotetraploid Actinidia arguta highlights adaptive evolution and enables dissection of important economic traits. PLANT COMMUNICATIONS 2024; 5:100856. [PMID: 38431772 DOI: 10.1016/j.xplc.2024.100856] [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: 05/28/2023] [Revised: 07/07/2023] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Actinidia arguta, the most widely distributed Actinidia species and the second cultivated species in the genus, can be distinguished from the currently cultivated Actinidia chinensis on the basis of its small and smooth fruit, rapid softening, and excellent cold tolerance. Adaptive evolution of tetraploid Actinidia species and the genetic basis of their important agronomic traits are still unclear. Here, we generated a chromosome-scale genome assembly of an autotetraploid male A. arguta accession. The genome assembly was 2.77 Gb in length with a contig N50 of 9.97 Mb and was anchored onto 116 pseudo-chromosomes. Resequencing and clustering of 101 geographically representative accessions showed that they could be divided into two geographic groups, Southern and Northern, which first diverged 12.9 million years ago. A. arguta underwent two prominent expansions and one demographic bottleneck from the mid-Pleistocene climate transition to the late Pleistocene. Population genomics studies using paleoclimate data enabled us to discern the evolution of the species' adaptation to different historical environments. Three genes (AaCEL1, AaPME1, and AaDOF1) related to flesh softening were identified by multi-omics analysis, and their ability to accelerate flesh softening was verified through transient expression assays. A set of genes that characteristically regulate sexual dimorphism located on the sex chromosome (Chr3) or autosomal chromosomes showed biased expression during stamen or carpel development. This chromosome-level assembly of the autotetraploid A. arguta genome and the genes related to important agronomic traits will facilitate future functional genomics research and improvement of A. arguta.
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Affiliation(s)
- Xue-Mei Lu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xiao-Fen Yu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Guo-Qiang Li
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Ming-Hao Qu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Huan Wang
- Wuhan Frasergen Bioinformatics Co., Ltd, Wuhan, Hubei, China
| | - Chuang Liu
- Institute of Soil and Fertilizer, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yu-Ping Man
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xiao-Han Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Mu-Zi Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qi-Qi Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Rui Lei
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Cheng-Cheng Zhao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yun-Qiu Zhou
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zheng-Wang Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Zuo-Zhou Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Shang Zheng
- Wuhan Frasergen Bioinformatics Co., Ltd, Wuhan, Hubei, China
| | - Chang Dong
- College of Agricultural Sciences, Xichang University, Xichang, Sichuan, China
| | - Bai-Lin Wang
- Department of Horticulture, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Yan-Xiang Sun
- College of Life Sciences, Langfang Normal University, Langfang, Hebei, China
| | - Hui-Qin Zhang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Jie-Wei Li
- Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin, Guangxi, China
| | - Quan-Hui Mo
- Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin, Guangxi, China
| | - Ying Zhang
- Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Xi'an, Shaanxi, China
| | - Xin Lou
- Institute of Modern Agricultural Research, Dalian University, Dalian, Liaoning, China
| | - Hai-Xu Peng
- Bioinformatics Center, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Ya-Ting Yi
- Bioinformatics Center, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - He-Xin Wang
- Institute of Modern Agricultural Research, Dalian University, Dalian, Liaoning, China
| | - Xiu-Jun Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yi-Bo Wang
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Dan Wang
- College of Agriculture, Eastern Liaoning University, Dandong, Liaoning, China
| | - Li Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qiong Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Wen-Xia Wang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China
| | - Yongbo Liu
- State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China.
| | - Lei Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Hubei Hongshan Laboratory, Wuhan, Hubei, China.
| | - Jin-Hu Wu
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand.
| | - Yan-Chang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.
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Liu M, Hu SY, Li M, Sun H, Yuan ML. Comparative mitogenomic analysis provides evolutionary insights into Formica (Hymenoptera: Formicidae). PLoS One 2024; 19:e0302371. [PMID: 38857223 PMCID: PMC11164359 DOI: 10.1371/journal.pone.0302371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 04/02/2024] [Indexed: 06/12/2024] Open
Abstract
Formica is a large genus in the family Formicidae with high diversity in its distribution, morphology, and physiology. To better understand evolutionary characteristics of Formica, the complete mitochondrial genomes (mitogenomes) of two Formica species were determined and a comparative mitogenomic analysis for this genus was performed. The two newly sequenced Formica mitogenomes each included 37 typical mitochondrial genes and a large non-coding region (putative control region), as observed in other Formica mitogenomes. Base composition, gene order, codon usage, and tRNA secondary structure were well conserved among Formica species, whereas diversity in sequence size and structural characteristics was observed in control regions. We also observed several conserved motifs in the intergenic spacer regions. These conserved genomic features may be related to mitochondrial function and their highly conserved physiological constraints, while the diversity of the control regions may be associated with adaptive evolution among heterogenous habitats. A negative AT-skew value on the majority chain was presented in each of Formica mitogenomes, indicating a reversal of strand asymmetry in base composition. Strong codon usage bias was observed in Formica mitogenomes, which was predominantly determined by nucleotide composition. All 13 mitochondrial protein-coding genes of Formica species exhibited molecular signatures of purifying selection, as indicated by the ratio of non-synonymous substitutions to synonymous substitutions being less than 1 for each protein-coding gene. Phylogenetic analyses based on mitogenomic data obtained fairly consistent phylogenetic relationships, except for two Formica species that had unstable phylogenetic positions, indicating mitogenomic data are useful for constructing phylogenies of ants. Beyond characterizing two additional Formica mitogenomes, this study also provided some key evolutionary insights into Formica.
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Affiliation(s)
- Min Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Shi-Yun Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Min Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Hao Sun
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ming-Long Yuan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
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7
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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 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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8
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Nzei JM, Martínez-Médez N, Mwanzia VM, Kurauka JK, Wang QF, Li ZZ, Chen JM. Climatic niche evolution and niche conservatism of Nymphaea species in Africa, South America, and Australia. BMC PLANT BIOLOGY 2024; 24:476. [PMID: 38816799 PMCID: PMC11137912 DOI: 10.1186/s12870-024-05141-1] [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: 03/23/2024] [Accepted: 05/13/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND Interest in the evolution of climatic niches, particularly in understanding the potential adaptive responses of species under climate change, has increased both theoretically and within macroecological studies. These studies have provided valuable insights into how climatic traits of species influence their niche evolution. In this study, we aim to investigate whether niche conservatism plays a role in the species diversification of Nymphaea, a group of aquatic plants with a cosmopolitan distribution that is facing severe habitat loss. We will use climatic models and phylogenetic data for 23 species to reconstruct Nymphaea's niche evolution, measure niche overlap, and assess disparity through time while testing for evolutionary models. RESULTS There was a lot of overlap in niches both within and between groups, especially for species that can be found in many places. The breadth and peaks of the niche profile varied depending on the bioclimatic variables, which suggested that the species evolved differently to cope with changes in climate. The analysis also showed that evolutionary changes happened across the phylogeny, with weak to moderate signals. The morphological disparity index (MDI) values indicated that there were disparities within subclades over time but not between or among them. Niche reconstruction and evolution analysis revealed both convergent and divergent evolution among various variables. For example, N. immutabilis, N. atrans, N. violancea, and N. nouchali evolved towards intermediate temperatures for bio2 and bio3 (isothermity) while moving towards extreme temperatures for bio8 and bio9 (wettest and driest average quarterly temperatures). CONCLUSION Our study will improve our understanding of how changes in climatic niches are potentially driving the evolution of Nymphaea. It has significant scientific implications for the limits, assemblages, evolution, and diversification of species. This information is crucial for the ongoing efforts of conservation and management, particularly considering the inevitable effects of climate change.
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Affiliation(s)
- John M Nzei
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Norberto Martínez-Médez
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Ciudad de México, México
| | - Virginia M Mwanzia
- School of Agriculture Technical Studies and Natural Sciences, Lukenya University, P.O Box 90-90128, Mtito Andei, Kenya
| | - Joseph K Kurauka
- School of Agriculture and Environmental Sciences, Kenyatta University, P.O. Box 43844-00100, Nairobi, Kenya
| | - Qing-Feng Wang
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Zhi-Zhong Li
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Jin-Ming Chen
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
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9
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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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10
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Li E, Wang Y, Liu K, Liu Y, Xu C, Dong W, Zhang Z. Historical climate change and vicariance events contributed to the intercontinental disjunct distribution pattern of ash species (Fraxinus, Oleaceae). Commun Biol 2024; 7:603. [PMID: 38769470 PMCID: PMC11106067 DOI: 10.1038/s42003-024-06296-1] [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: 01/18/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
The Northern Hemisphere temperate forests exhibit a disjunct distributional pattern in Europe, North America, and East Asia. Here, to reveal the promoter of intercontinental disjunct distribution, Fraxinus was used as a model organism to integrate abundant fossil evidence with high-resolution phylogenies in a phytogeographic analysis. We constructed a robust phylogenetic tree using genomic data, reconstructed the geographic ancestral areas, and evaluated the effect of incorporating fossil information on the reconstructed biogeographic history. The phylogenetic relationships of Fraxinus were highly resolved and divided into seven clades. Fraxinus originated in western North America during Eocene, and six intercontinental dispersal events and five intercontinental vicariance events were occured. Results suggest that climate change and vicariance contributed to the intercontinental disjunct distribution pattern of Fraxinus. Moreover, results highlight the necessity of integrating phylogenetic relationship and fossil to improve the reliability of inferred biogeographic events and our understanding of the processes underlying disjunct distributions.
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Affiliation(s)
- Enze Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yushuang Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Kangjia Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yanlei Liu
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
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11
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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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12
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Lopes JC, Fonseca LHM, Johnson DM, Luebert F, Murray N, Nge FJ, Rodrigues-Vaz C, Soulé V, Onstein RE, Lohmann LG, Couvreur TLP. Dispersal from Africa to the Neotropics was followed by multiple transitions across Neotropical biomes facilitated by frugivores. ANNALS OF BOTANY 2024; 133:659-676. [PMID: 37968940 PMCID: PMC11082516 DOI: 10.1093/aob/mcad175] [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: 09/25/2023] [Accepted: 11/10/2023] [Indexed: 11/17/2023]
Abstract
BACKGROUND AND AIM Plant disjunctions have fascinated biogeographers and ecologists for a long time. We use tribe Bocageeae (Annonaceae), a predominantly Neotropical plant group distributed across several present-day Neotropical biomes and with an African-American disjunction, to investigate long-distance dispersal mediated by frugivorous animals at both intercontinental and intracontinental scales. METHODS We reconstructed a species-level phylogeny of tribe Bocageeae with a dataset composed of 116 nuclear markers. We sampled 70 % of Bocageeae species, covering their geographical range and representing all eight genera. We estimated divergence times using BEAST, inferred ancestral range distributions and reconstructed ancestral states for fruit traits related to long-distance dispersal in a Bayesian framework. KEY RESULTS The ancestral Bocageeae date to the Early Eocene and were inferred to occur in Africa and proto-Amazonia. Their ancestral fruits were large and dehiscent. The first lineage split gave rise to an exclusively Neotropical clade during the Middle Eocene, in proto-Amazonia. Range exchange between the Amazon and the Atlantic Forest occurred at least once during the Miocene, and from Amazonia to Central America and Mexico during the Early Miocene. Transitions in different sets of fruit morphologies were inferred to be related to dispersal events across South American regions/biomes. CONCLUSIONS In Bocageeae, mammals might have been responsible for long-distance dispersal through the Boreotropics. In the Neotropics, proto-Amazonia is proposed to be the source for dispersal to other tropical American biomes. Long-distance dispersal might have happened via a wide range of dispersal guilds, depending on frugivore radiations, diversity and abundance in particular time periods and places. Hence, inter- and intracontinental dispersal might not rely on a single dispersal syndrome or guild, but more on the availability of frugivorous lineages for seed dispersal.
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Affiliation(s)
- Jenifer C Lopes
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA, USA
| | | | - David M Johnson
- Department of Biological Sciences, Ohio Wesleyan University, Delaware, OH, USA
| | - Federico Luebert
- Departamento de Ciencias Ambientales y Recursos Naturales Renovables Universidad de Chile, Santiago, Chile
- Departmento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
| | - Nancy Murray
- Department of Biological Sciences, Ohio Wesleyan University, Delaware, OH, USA
| | - Francis J Nge
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Carlos Rodrigues-Vaz
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle-CNRS-SU-EPHE-UA, Paris, France
| | - Vincent Soulé
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Renske E Onstein
- Naturalis Biodiversity Center, Leiden, The Netherlands
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Lúcia G Lohmann
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- University and Jepson Herbaria, and Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Thomas L P Couvreur
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France
- Naturalis Biodiversity Center, Leiden, The Netherlands
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13
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Almeida-Silva D, Vera Candioti F. Shape Evolution in Two Acts: Morphological Diversity of Larval and Adult Neoaustraranan Frogs. Animals (Basel) 2024; 14:1406. [PMID: 38791625 PMCID: PMC11117230 DOI: 10.3390/ani14101406] [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: 04/01/2024] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
Phenotypic traits can evolve independently at different stages of ontogeny, optimizing adaptation to distinct ecological contexts and increasing morphological diversity in species with complex life cycles. Given the relative independence resulting from the profound changes induced by metamorphosis, niche occupation and resource utilization in tadpoles may prompt evolutionary responses that do not necessarily affect the adults. Consequently, diversity patterns observed in the larval shape may not necessarily correspond to those found in the adult shape for the same species, a premise that can be tested through the Adaptive Decoupling Hypothesis (ADH). Herein, we investigate the ADH for larval and adult shape differentiation in Neoaustrarana frogs. Neoaustrarana frogs, particularly within the Cycloramphidae family, exhibit remarkable diversity in tadpole morphology, making them an ideal model for studying adaptive decoupling. By analyzing 83 representative species across four families (Alsodidae, Batrachylidae, Cycloramphidae, and Hylodidae), we generate a morphological dataset for both larval and adult forms. We found a low correlation between larval and adult shapes, species with a highly distinct larval shape having relatively similar shape when adults. Larval morphological disparity is not a good predictor for adult morphological disparity within the group, with distinct patterns observed among families. Differences between families are notable in other aspects as well, such as the role of allometric components influencing shape and morphospace occupancy. The larval shape has higher phylogenetic structure than the adult. Evolutionary convergence emerges as a mechanism of diversification for both larval and adult shapes in the early evolution of neoaustraranans, with shape disparity of tadpoles reaching stable levels since the Oligocene. The widest occupation in morphospace involves families associated with dynamically changing environments over geological time. Our findings support the ADH driving phenotypic diversity in Neoaustrarana, underscoring the importance of considering ontogenetic stages in evolutionary studies.
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Affiliation(s)
- Diego Almeida-Silva
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas–Fundación Miguel Lillo, San Miguel de Tucumán 4000, Argentina;
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo 09606-045, SP, Brazil
| | - Florencia Vera Candioti
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas–Fundación Miguel Lillo, San Miguel de Tucumán 4000, Argentina;
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14
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Silva FLD, de Medeiros BAS, Farrell BD. Once upon a fly: The biogeographical odyssey of Labrundinia (Chironomidae, Tanypodinae), an aquatic non-biting midge towards diversification. Mol Phylogenet Evol 2024; 194:108025. [PMID: 38342160 DOI: 10.1016/j.ympev.2024.108025] [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: 07/23/2023] [Revised: 01/17/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Labrundinia is a highly recognizable lineage in the Pentaneurini tribe (Diptera, Chironomidae). The distinct predatory free-swimming larvae of this genus are typically present in unpolluted aquatic environments, such as small streams, ponds, lakes, and bays. They can be found on the bottom mud, clinging to rocks and wood, and dwelling among aquatic vegetation. Labrundinia has been extensively studied in ecological research and comprises 39 species, all but one of which has been described from regions outside the Palearctic. Earlier phylogenetic studies have suggested that the initial diversification of the genus likely occurred in the Neotropical Region, with its current presence in the Nearctic Region and southern South America being the result of subsequent dispersal events. Through the integration of molecular and morphological data in a calibrated phylogeny, we reveal a complex and nuanced evolutionary history for Labrundinia, providing insights into its biogeographical and diversification patterns. In this comprehensive study, we analyze a dataset containing 46 Labrundinia species, totaling 10,662 characters, consisting of 10,616 nucleotide sites and 46 morphological characters. The molecular data was generated mainly by anchored enrichment hybrid methods. Using this comprehensive dataset, we inferred the phylogeny of the group based on a total evidence matrix. Subsequently, we employed the generated tree for time calibration and further analysis of biogeography and diversification patterns. Our findings reveal multiple dispersal events out of the Neotropics, where the group originated in the late Cretaceous approximately 72 million years ago (69-78 Ma). We further reveal that the genus experienced an early burst of diversification rates during the Paleocene, which gradually decelerated towards the present-day. We also find that the Neotropics have played a pivotal role in the evolution of Labrundinia by serving as both a cradle and a museum. By "cradle," we mean that the region has been a hotspot for the origin and diversification of new Labrundinia lineages, while "museum" refers to the region's ability to preserve ancestral lineages over extended periods. In summary, our findings indicate that the Neotropics have been a key source of genetic diversity for Labrundinia, resulting in the development of distinctive adaptations and characteristics within the genus. This evidence highlights the crucial role that these regions have played in shaping the evolutionary trajectory of Labrundinia.
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Affiliation(s)
- Fabio Laurindo da Silva
- Laboratory of Aquatic Insect Biodiversity and Ecology, Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA.
| | - Bruno A S de Medeiros
- Field Museum of Natural History, Negaunee Integrative Research Center, Chicago, USA; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA
| | - Brian D Farrell
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA
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15
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Wu H, Li DZ, Ma PF. Unprecedented variation pattern of plastid genomes and the potential role in adaptive evolution in Poales. BMC Biol 2024; 22:97. [PMID: 38679718 PMCID: PMC11057118 DOI: 10.1186/s12915-024-01890-5] [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: 07/27/2023] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND The plastid is the photosynthetic organelle in plant cell, and the plastid genomes (plastomes) are generally conserved in evolution. As one of the most economically and ecologically important order of angiosperms, Poales was previously documented to exhibit great plastomic variation as an order of photoautotrophic plants. RESULTS We acquired 93 plastomes, representing all the 16 families and 5 major clades of Poales to reveal the extent of their variation and evolutionary pattern. Extensive variation including the largest one in monocots with 225,293 bp in size, heterogeneous GC content, and a wide variety of gene duplication and loss were revealed. Moreover, rare occurrences of three inverted repeat (IR) copies in angiosperms and one IR loss were observed, accompanied by short IR (sIR) and small direct repeat (DR). Widespread structural heteroplasmy, diversified inversions, and unusual genomic rearrangements all appeared in Poales, occasionally within a single species. Extensive repeats in the plastomes were found to be positively correlated with the observed inversions and rearrangements. The variation all showed a "small-large-moderate" trend along the evolution of Poales, as well as for the sequence substitution rate. Finally, we found some positively selected genes, mainly in C4 lineages, while the closely related lineages of those experiencing gene loss tended to have undergone more relaxed purifying selection. CONCLUSIONS The variation of plastomes in Poales may be related to its successful diversification into diverse habitats and multiple photosynthetic pathway transitions. Our order-scale analyses revealed unusual evolutionary scenarios for plastomes in the photoautotrophic order of Poales and provided new insights into the plastome evolution in angiosperms as a whole.
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Affiliation(s)
- Hong Wu
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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16
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Datta D, Bajpai S. Largest known madtsoiid snake from warm Eocene period of India suggests intercontinental Gondwana dispersal. Sci Rep 2024; 14:8054. [PMID: 38637509 DOI: 10.1038/s41598-024-58377-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/28/2024] [Indexed: 04/20/2024] Open
Abstract
Here we report the discovery of fossils representing partial vertebral column of a giant madtsoiid snake from an early Middle Eocene (Lutetian, ~ 47 Ma) lignite-bearing succession in Kutch, western India. The estimated body length of ~ 11-15 m makes this new taxon (Vasuki indicus gen et sp. nov.) the largest known madtsoiid snake, which thrived during a warm geological interval with average temperatures estimated at ~ 28 °C. Phylogenetically, Vasuki forms a distinct clade with the Indian Late Cretaceous taxon Madtsoia pisdurensis and the North African Late Eocene Gigantophis garstini. Biogeographic considerations, seen in conjunction with its inter-relationship with other Indian and North African madtsoiids, suggest that Vasuki represents a relic lineage that originated in India. Subsequent India-Asia collision at ~ 50 Ma led to intercontinental dispersal of this lineage from the subcontinent into North Africa through southern Eurasia.
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Affiliation(s)
- Debajit Datta
- Department of Earth Sciences, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
| | - Sunil Bajpai
- Department of Earth Sciences, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
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17
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Zhang T, Huang W, Zhang L, Li DZ, Qi J, Ma H. Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages. Nat Commun 2024; 15:3305. [PMID: 38632270 PMCID: PMC11024178 DOI: 10.1038/s41467-024-47428-9] [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: 07/13/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Poaceae members shared a whole-genome duplication called rho. However, little is known about the evolutionary pattern of the rho-derived duplicates among Poaceae lineages and implications in adaptive evolution. Here we present phylogenomic/phylotranscriptomic analyses of 363 grasses covering all 12 subfamilies and report nine previously unknown whole-genome duplications. Furthermore, duplications from a single whole-genome duplication were mapped to multiple nodes on the species phylogeny; a whole-genome duplication was likely shared by woody bamboos with possible gene flow from herbaceous bamboos; and recent paralogues of a tetraploid Oryza are implicated in tolerance of seawater submergence. Moreover, rho duplicates showing differential retention among subfamilies include those with functions in environmental adaptations or morphogenesis, including ACOT for aquatic environments (Oryzoideae), CK2β for cold responses (Pooideae), SPIRAL1 for rapid cell elongation (Bambusoideae), and PAI1 for drought/cold responses (Panicoideae). This study presents a Poaceae whole-genome duplication profile with evidence for multiple evolutionary mechanisms that contribute to gene retention and losses.
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Affiliation(s)
- Taikui Zhang
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Weichen Huang
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Lin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Ji Qi
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Hong Ma
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA.
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18
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Esteban JM, Martín-Serra A, Pérez-Ramos A, Rybczynski N, Jones K, Figueirido B. The influence of the land-to-sea macroevolutionary transition on vertebral column disparification in Pinnipedia. Proc Biol Sci 2024; 291:20232752. [PMID: 38593849 PMCID: PMC11003777 DOI: 10.1098/rspb.2023.2752] [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: 12/06/2023] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
The repeated returns of vertebrates to the marine ecosystems since the Triassic serve as an evolutionary model to understand macroevolutionary change. Here we investigate the effects of the land-to-sea transition on disparity and constraint of the vertebral column in aquatic carnivorans (Carnivora; Pinnipedia) to assess how their functional diversity and evolutionary innovations influenced major radiations of crown pinnipeds. We use three-dimensional geometric morphometrics and multivariate analysis for high-dimensional data under a phylogenetic framework to quantify vertebral size and shape in living and extinct pinnipeds. Our analysis demonstrates an important shift in vertebral column evolution by 10-12 million years ago, from an unconstrained to a constrained evolutionary scenario, a point of time that coincides with the major radiation of crown pinnipeds. Moreover, we also demonstrate that the axial skeleton of phocids and otariids followed a different path of morphological evolution that was probably driven by their specialized locomotor strategies. Despite this, we found a significant effect of habitat preference (coastal versus pelagic) on vertebral morphology of crown taxa regardless of the family they belong. In summary, our analysis provides insights into how the land-to-sea transition influenced the complex evolutionary history of pinniped vertebral morphology.
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Affiliation(s)
- Juan Miguel Esteban
- Departamento de Ecología y Geología, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071, Málaga, Spain
| | - Alberto Martín-Serra
- Departamento de Ecología y Geología, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071, Málaga, Spain
| | - Alejandro Pérez-Ramos
- Departamento de Ecología y Geología, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071, Málaga, Spain
| | - Natalia Rybczynski
- Department of Palaeobiology, Canadian Museum of Nature, Ottawa, ON, Canada K1P 6P4
- Department of Earth Sciences & Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1S 5B6
| | - Katrina Jones
- Department of Earth and Environmental Sciences, University of Manchester, Williamson Building, Oxford Road, Manchester M13 9PL, UK
| | - Borja Figueirido
- Departamento de Ecología y Geología, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071, Málaga, Spain
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19
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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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20
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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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21
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Omollo WO, Rabarijaona RN, Ranaivoson RM, Rakotoarinivo M, Barrett RL, Zhang Q, Lai YJ, Ye JF, Le CT, Antonelli A, Chen ZD, Liu B, Lu LM. Spatial heterogeneity of neo- and paleo-endemism for plants in Madagascar. Curr Biol 2024; 34:1271-1283.e4. [PMID: 38460512 DOI: 10.1016/j.cub.2024.02.023] [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: 11/27/2023] [Revised: 01/21/2024] [Accepted: 02/13/2024] [Indexed: 03/11/2024]
Abstract
Madagascar is a biogeographically unique island with a remarkably high level of endemism. However, endemic taxa in Madagascar are massively threatened due to unprecedented pressures from anthropogenic habitat modification and climate change. A comprehensive phylogeny-based biodiversity evaluation of the island remains lacking. Here, we identify hotspots of taxonomic and phylogenetic plant diversity and neo- and paleo-endemism by generating a novel dated tree of life for the island. The tree is based on unprecedented sampling of 3,950 species (33% of the total known species) and 1,621 genera (93% of the total known genera and 69% of endemic genera) of Malagasy vascular plants. We find that island-endemic genera are concentrated in multiple lineages combining high taxonomic and phylogenetic diversity. Integrating phylogenetic and geographic distribution data, our results reveal that taxon richness and endemism are concentrated in the northern, eastern, and southeastern humid forests. Paleo-endemism centers are concentrated in humid eastern and central regions, whereas neo-endemism centers are concentrated in the dry and spiny forests in western and southern Madagascar. Our statistical analysis of endemic genera in each vegetation region supports a higher proportion of ancient endemic genera in the east but a higher proportion of recent endemic genera in the south and west. Overlaying centers of phylogenetic endemism with protected areas, we identify conservation gaps concentrated in western and southern Madagascar. These gaps should be incorporated into conservation strategies to aid the protection of multiple facets of biodiversity and their benefits to the Malagasy people.
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Affiliation(s)
- Wyckliffe Omondi Omollo
- 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
| | - Romer Narindra Rabarijaona
- 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
| | - Rindra Manasoa Ranaivoson
- 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; Department of Plant Biology and Ecology, Faculty of Sciences, University of Antananarivo, Antananarivo 101, Madagascar
| | - Mijoro Rakotoarinivo
- Department of Plant Biology and Ecology, Faculty of Sciences, University of Antananarivo, Antananarivo 101, Madagascar
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, NSW 2567, Australia; School of Biological, Earth, and Environmental Sciences, University of New South Wales, Kensington, NSW 2052, Australia
| | - Qiang 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
| | - Yang-Jun Lai
- 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
| | - Jian-Fei Ye
- 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
| | - Chi Toan Le
- Hanoi Pedagogical University 2, 32 Nguyen Van Linh, Xuanhoa, Phucyen, Vinhphuc 15000, Vietnam
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, TW9 3AE Richmond, Surrey, UK; Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, 41319 Gothenburg, Sweden; Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Zhi-Duan 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; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, 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; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Li-Min 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.
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22
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Orbán LL. Principles to guide research and policy on psychological well-being in remote island developing states in the South Pacific. Front Psychiatry 2024; 15:1325292. [PMID: 38577401 PMCID: PMC10993693 DOI: 10.3389/fpsyt.2024.1325292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 02/26/2024] [Indexed: 04/06/2024] Open
Abstract
Adverse climatic changes around the globe and predictions of catastrophic and irreversible alteration in global weather patterns, temperature rise, and coast-line habitability require a careful examination of consequences on the resilience and mental health of people who will endure these changes. This paper is concerned with the South Pacific region. This geography has benefited from a relatively stable climate that is seen in the lush and vibrant natural world with many unique species of plants and animals exclusively found here. This paper examines the psychological profile of the people in the South Pacific using an evolutionary framework, and considers their local climate risks and lifestyle patterns with the aim of exploring possible mental health trajectories.
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Affiliation(s)
- Levente L. Orbán
- School of Law and Social Sciences, The University of the South Pacific, Suva, Fiji
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23
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Kemeny PC, Torres MA, Fischer WW, Blättler CL. Balance and imbalance in biogeochemical cycles reflect the operation of closed, exchange, and open sets. Proc Natl Acad Sci U S A 2024; 121:e2316535121. [PMID: 38478696 PMCID: PMC10962936 DOI: 10.1073/pnas.2316535121] [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: 09/22/2023] [Accepted: 02/09/2024] [Indexed: 03/27/2024] Open
Abstract
Biogeochemical reactions modulate the chemical composition of the oceans and atmosphere, providing feedbacks that sustain planetary habitability over geological time. Here, we mathematically evaluate a suite of biogeochemical processes to identify combinations of reactions that stabilize atmospheric carbon dioxide by balancing fluxes of chemical species among the ocean, atmosphere, and geosphere. Unlike prior modeling efforts, this approach does not prescribe functional relationships between the rates of biogeochemical processes and environmental conditions. Our agnostic framework generates three types of stable reaction combinations: closed sets, where sources and sinks mutually cancel for all chemical reservoirs; exchange sets, where constant ocean-atmosphere conditions are maintained through the growth or destruction of crustal reservoirs; and open sets, where balance in alkalinity and carbon fluxes is accommodated by changes in other chemical components of seawater or the atmosphere. These three modes of operation have different characteristic timescales and may leave distinct evidence in the rock record. To provide a practical example of this theoretical framework, we applied the model to recast existing hypotheses for Cenozoic climate change based on feedbacks or shared forcing mechanisms. Overall, this work provides a systematic and simplified conceptual framework for understanding the function and evolution of global biogeochemical cycles.
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Affiliation(s)
| | - Mark A. Torres
- Department of Earth, Environmental, and Planetary Sciences, Rice University, Houston, TX
| | - Woodward W. Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA
| | - Clara L. Blättler
- Department of the Geophysical Sciences, The University of Chicago, Chicago, IL
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24
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Dutkiewicz A, Boulila S, Dietmar Müller R. Deep-sea hiatus record reveals orbital pacing by 2.4 Myr eccentricity grand cycles. Nat Commun 2024; 15:1998. [PMID: 38472187 PMCID: PMC10933315 DOI: 10.1038/s41467-024-46171-5] [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: 09/05/2023] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
Astronomical forcing of Earth's climate is embedded in the rhythms of stratigraphic records, most famously as short-period (104-105 year) Milankovitch cycles. Astronomical grand cycles with periods of millions of years also modulate climate variability but have been detected in relatively few proxy records. Here, we apply spectral analysis to a dataset of Cenozoic deep-sea hiatuses to reveal a ~2.4 Myr eccentricity signal, disrupted by episodes of major tectonic forcing. We propose that maxima in the hiatus cycles correspond to orbitally-forced intensification of deep-water circulation and erosive bottom current activity, linked to eccentricity maxima and peaks in insolation and seasonality. A prominent episode of cyclicity disturbance coincides with the Paleocene-Eocene Thermal Maximum (PETM) at ~56 Myr ago, and correlates with a chaotic orbital transition in the Solar System evident in several astronomical solutions. This hints at a potential intriguing coupling between the PETM and Solar System chaos.
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Affiliation(s)
- Adriana Dutkiewicz
- EarthByte Group, School of Geosciences, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Slah Boulila
- Sorbonne Université, CNRS, Institut des Sciences de la Terre Paris, ISTeP, 75005, Paris, France
- ASD/IMCCE, CNRS‑UMR8028, Observatoire de Paris, PSL University, Sorbonne Université, 75014, Paris, France
| | - R Dietmar Müller
- EarthByte Group, School of Geosciences, The University of Sydney, Sydney, NSW, 2006, Australia
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25
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Stanojković A, Skoupý S, Johannesson H, Dvořák P. The global speciation continuum of the cyanobacterium Microcoleus. Nat Commun 2024; 15:2122. [PMID: 38459017 PMCID: PMC10923798 DOI: 10.1038/s41467-024-46459-6] [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: 07/10/2023] [Accepted: 02/27/2024] [Indexed: 03/10/2024] Open
Abstract
Speciation is a continuous process driven by genetic, geographic, and ecological barriers to gene flow. It is widely investigated in multicellular eukaryotes, yet we are only beginning to comprehend the relative importance of mechanisms driving the emergence of barriers to gene flow in microbial populations. Here, we explored the diversification of the nearly ubiquitous soil cyanobacterium Microcoleus. Our dataset consisted of 291 genomes, of which 202 strains and eight herbarium specimens were sequenced for this study. We found that Microcoleus represents a global speciation continuum of at least 12 lineages, which radiated during Eocene/Oligocene aridification and exhibit varying degrees of divergence and gene flow. The lineage divergence has been driven by selection, geographical distance, and the environment. Evidence of genetic divergence and selection was widespread across the genome, but we identified regions of exceptional differentiation containing candidate genes associated with stress response and biosynthesis of secondary metabolites.
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Affiliation(s)
- Aleksandar Stanojković
- Palacký University Olomouc, Faculty of Sciences, Department of Botany, Olomouc, Czech Republic
| | - Svatopluk Skoupý
- Palacký University Olomouc, Faculty of Sciences, Department of Botany, Olomouc, Czech Republic
| | - Hanna Johannesson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Royal Swedish Academy of Sciences, Stockholm, Sweden
| | - Petr Dvořák
- Palacký University Olomouc, Faculty of Sciences, Department of Botany, Olomouc, Czech Republic.
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26
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Li W, Wang R, Liu MF, Folk RA, Xue B, Saunders RMK. Climatic and biogeographic processes underlying the diversification of the pantropical flowering plant family Annonaceae. FRONTIERS IN PLANT SCIENCE 2024; 15:1287171. [PMID: 38525154 PMCID: PMC10957689 DOI: 10.3389/fpls.2024.1287171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/20/2024] [Indexed: 03/26/2024]
Abstract
Tropical forests harbor the richest biodiversity among terrestrial ecosystems, but few studies have addressed the underlying processes of species diversification in these ecosystems. We use the pantropical flowering plant family Annonaceae as a study system to investigate how climate and biogeographic events contribute to diversification. A super-matrix phylogeny comprising 835 taxa (34% of Annonaceae species) based on eight chloroplast regions was used in this study. We show that global temperature may better explain the recent rapid diversification in Annonaceae than time and constant models. Accelerated accumulation of niche divergence (around 15 Ma) lags behind the increase of diversification rate (around 25 Ma), reflecting a heterogeneous transition to recent diversity increases. Biogeographic events are related to only two of the five diversification rate shifts detected. Shifts in niche evolution nevertheless appear to be associated with increasingly seasonal environments. Our results do not support the direct correlation of any particular climatic niche shifts or historical biogeographical event with shifts in diversification rate. Instead, we suggest that Annonaceae diversification can lead to later niche divergence as a result of increasing interspecific competition arising from species accumulation. Shifts in niche evolution appear to be associated with increasingly seasonal environments. Our results highlight the complexity of diversification in taxa with long evolutionary histories.
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Affiliation(s)
- Weixi Li
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Runxi Wang
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Ming-Fai Liu
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Ryan A. Folk
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States
| | - Bine Xue
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Richard M. K. Saunders
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
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27
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Ren Y, Zhang L, Yang X, Lin H, Sang Y, Feng L, Liu J, Kang M. Cryptic divergences and repeated hybridizations within the endangered "living fossil" dove tree ( Davidia involucrata) revealed by whole genome resequencing. PLANT DIVERSITY 2024; 46:169-180. [PMID: 38807904 PMCID: PMC11128880 DOI: 10.1016/j.pld.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/05/2024] [Accepted: 02/08/2024] [Indexed: 05/30/2024]
Abstract
The identification and understanding of cryptic intraspecific evolutionary units (lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species. However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a "living fossil" dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range. Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.
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Affiliation(s)
- Yumeng Ren
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Lushui Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xuchen Yang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Hao Lin
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yupeng Sang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Landi Feng
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jianquan Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Minghui Kang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
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28
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Zhou N, Miao K, Liu C, Jia L, Hu J, Huang Y, Ji Y. Historical biogeography and evolutionary diversification of Lilium (Liliaceae): New insights from plastome phylogenomics. PLANT DIVERSITY 2024; 46:219-228. [PMID: 38807906 PMCID: PMC11128834 DOI: 10.1016/j.pld.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/22/2023] [Accepted: 07/30/2023] [Indexed: 05/30/2024]
Abstract
Here, we infer the historical biogeography and evolutionary diversification of the genus Lilium. For this purpose, we used the complete plastomes of 64 currently accepted species in the genus Lilium (14 plastomes were newly sequenced) to recover the phylogenetic backbone of the genus and a time-calibrated phylogenetic framework to estimate biogeographical history scenarios and evolutionary diversification rates of Lilium. Our results suggest that ancient climatic changes and geological tectonic activities jointly shaped the distribution range and drove evolutionary radiation of Lilium, including the Middle Miocene Climate Optimum (MMCO), the late Miocene global cooling, as well as the successive uplift of the Qinghai-Tibet Plateau (QTP) and the strengthening of the monsoon climate in East Asia during the late Miocene and the Pliocene. This case study suggests that the unique geological and climatic events in the Neogene of East Asia, in particular the uplift of QTP and the enhancement of monsoonal climate, may have played an essential role in formation of uneven distribution of plant diversity in the Northern Hemisphere.
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Affiliation(s)
- Nian Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ke Miao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changkun Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Linbo Jia
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jinjin Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yongjiang Huang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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29
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Moretti S, Auderset A, Deutsch C, Schmitz R, Gerber L, Thomas E, Luciani V, Petrizzo MR, Schiebel R, Tripati A, Sexton P, Norris R, D'Onofrio R, Zachos J, Sigman DM, Haug GH, Martínez-García A. Oxygen rise in the tropical upper ocean during the Paleocene-Eocene Thermal Maximum. Science 2024; 383:727-731. [PMID: 38359106 DOI: 10.1126/science.adh4893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 01/14/2024] [Indexed: 02/17/2024]
Abstract
The global ocean's oxygen inventory is declining in response to global warming, but the future of the low-oxygen tropics is uncertain. We report new evidence for tropical oxygenation during the Paleocene-Eocene Thermal Maximum (PETM), a warming event that serves as a geologic analog to anthropogenic warming. Foraminifera-bound nitrogen isotopes indicate that the tropical North Pacific oxygen-deficient zone contracted during the PETM. A concomitant increase in foraminifera size implies that oxygen availability rose in the shallow subsurface throughout the tropical North Pacific. These changes are consistent with ocean model simulations of warming, in which a decline in biological productivity allows tropical subsurface oxygen to rise even as global ocean oxygen declines. The tropical oxygen increase may have helped avoid a mass extinction during the PETM.
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Affiliation(s)
- Simone Moretti
- Climate Geochemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
- Istituto di Scienze Polari, Consiglio Nazionale delle Ricerche, Bologna, Italy
| | - Alexandra Auderset
- Climate Geochemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
- School of Ocean and Earth Science, University of Southampton, Southampton, UK
| | - Curtis Deutsch
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Ronja Schmitz
- Climate Geochemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | - Lukas Gerber
- Climate Geochemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | - Ellen Thomas
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT, USA
- Department of Earth and Environmental Sciences, Wesleyan University, Middletown, CT, USA
| | - Valeria Luciani
- Dipartimento di Fisica e Scienze della Terra, Università di Ferrara, Ferrara, Italy
| | - Maria Rose Petrizzo
- Dipartimento di Scienze della Terra "Ardito Desio," Università Degli Studi di Milano, Milan, Italy
| | - Ralf Schiebel
- Climate Geochemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | - Aradhna Tripati
- Department of Earth, Planetary, and Space Sciences, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Atmospheric and Oceanic Sciences, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
| | - Philip Sexton
- School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, UK
| | - Richard Norris
- Scripps Institute of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Roberta D'Onofrio
- Dipartimento di Fisica e Scienze della Terra, Università di Ferrara, Ferrara, Italy
- Present address: CNR, Marine Science Institute (ISMAR), Arsenale Castello 2737/f, 30122 Venezia, Italy
| | - James Zachos
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Daniel M Sigman
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Gerald H Haug
- Climate Geochemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
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30
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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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31
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Carruthers T, Moerland MS, Ebersbach J, Favre A, Folk RA, Hawkins JA, Muellner-Riehl AN, Röser M, Soltis DE, Tkach N, Baker WJ, de Vos JM, Eiserhardt WL. Repeated upslope biome shifts in Saxifraga during late-Cenozoic climate cooling. Nat Commun 2024; 15:1100. [PMID: 38321017 PMCID: PMC10847498 DOI: 10.1038/s41467-024-45289-w] [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: 05/14/2023] [Accepted: 01/19/2024] [Indexed: 02/08/2024] Open
Abstract
Mountains are among the most biodiverse places on Earth, and plant lineages that inhabit them have some of the highest speciation rates ever recorded. Plant diversity within the alpine zone - the elevation above which trees cannot grow-contributes significantly to overall diversity within mountain systems, but the origins of alpine plant diversity are poorly understood. Here, we quantify the processes that generate alpine plant diversity and their changing dynamics through time in Saxifraga (Saxifragaceae), an angiosperm genus that occurs predominantly in mountain systems. We present a time-calibrated molecular phylogenetic tree for the genus that is inferred from 329 low-copy nuclear loci and incorporates 73% (407) of known species. We show that upslope biome shifts into the alpine zone are considerably more prevalent than dispersal of alpine specialists between regions, and that the rate of upslope biome shifts increased markedly in the last 5 Myr, a timeframe concordant with a cooling and fluctuating climate that is likely to have increased the extent of the alpine zone. Furthermore, alpine zone specialists have lower speciation rates than generalists that occur inside and outside the alpine zone, and major speciation rate increases within Saxifraga significantly pre-date increased rates of upslope biome shifts. Specialisation to the alpine zone is not therefore associated with speciation rate increases. Taken together, this study presents a quantified and broad scale perspective of processes underpinning alpine plant diversity.
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Affiliation(s)
- Tom Carruthers
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Michelangelo S Moerland
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- School of Biological Sciences, University of Reading, Whiteknights, Reading, Berkshire, RG6 6EX, UK
| | - Jana Ebersbach
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology, Leipzig University, D-04103, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, D-04103, Leipzig, Germany
| | - Adrien Favre
- Regional Nature Park of the Trient Valley, la Place 24, 1922, Salvan, Switzerland
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA
| | - Julie A Hawkins
- School of Biological Sciences, University of Reading, Whiteknights, Reading, Berkshire, RG6 6EX, UK
| | - Alexandra N Muellner-Riehl
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology, Leipzig University, D-04103, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, D-04103, Leipzig, Germany
| | - Martin Röser
- Martin Luther University Halle-Wittenberg, Institute of Biology, Geobotany and Botanical Garden, Dept. of Systematic Botany, Neuwerk 21, 06108, Halle, Germany
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Natalia Tkach
- Martin Luther University Halle-Wittenberg, Institute of Biology, Geobotany and Botanical Garden, Dept. of Systematic Botany, Neuwerk 21, 06108, Halle, Germany
| | - William J Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Biology, Aarhus University, 8000, Aarhus C, Denmark
| | - Jurriaan M de Vos
- Department of Environmental Sciences-Botany, University of Basel, Schönbeinstrasse 6, 4056, Basel, Switzerland
| | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK.
- Department of Biology, Aarhus University, 8000, Aarhus C, Denmark.
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32
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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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33
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Tian Q, Stull GW, Kellermann J, Medan D, Nge FJ, Liu SY, Kates HR, Soltis DE, Soltis PS, Guralnick RP, Folk RA, Onstein RE, Yi TS. Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales. THE NEW PHYTOLOGIST 2024; 241:1851-1865. [PMID: 38229185 DOI: 10.1111/nph.19504] [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: 08/27/2023] [Accepted: 11/20/2023] [Indexed: 01/18/2024]
Abstract
The macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change. We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes. Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high in situ diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than the other regions. The relatively common lineage dispersals out of temperate hotspots highlight strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae. The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid in situ diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high in situ diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales.
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Affiliation(s)
- Qin Tian
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
- Naturalis Biodiversity Center, Darwinweg 2, 2333CR, Leiden, the Netherlands
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jürgen Kellermann
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Hackney Road, Adelaide, SA, 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Diego Medan
- Cátedra de Botánica General, Facultad de Agronomía, Universidad de Buenos Aires, Ave San Martín 4453, C1417DSE, Buenos Aires, Argentina
| | - Francis J Nge
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Hackney Road, Adelaide, SA, 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
- IRD - Institut de Recherche pour le Développement, Ave Agropolis BP 64501, Montpellier, 34394, France
| | - Shui-Yin Liu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
| | - Heather R Kates
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Robert P Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi, MS, 39762, USA
| | - Renske E Onstein
- Naturalis Biodiversity Center, Darwinweg 2, 2333CR, Leiden, the Netherlands
- Evolution and Adaptation, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
- Leipzig University, Leipzig, 04013, Germany
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
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Liu M, Song Y, Zhang S, Yu L, Yuan Z, Yang H, Zhang M, Zhou Z, Seim I, Liu S, Fan G, Yang H. A chromosome-level genome of electric catfish ( Malapterurus electricus) provided new insights into order Siluriformes evolution. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:1-14. [PMID: 38433969 PMCID: PMC10901758 DOI: 10.1007/s42995-023-00197-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 09/22/2023] [Indexed: 03/05/2024]
Abstract
The electric catfish (Malapterurus electricus), belonging to the family Malapteruridae, order Siluriformes (Actinopterygii: Ostariophysi), is one of the six branches that has independently evolved electrical organs. We assembled a 796.75 Mb M. electricus genome and anchored 88.72% sequences into 28 chromosomes. Gene family analysis revealed 295 expanded gene families that were enriched on functions related to glutamate receptors. Convergent evolutionary analyses of electric organs among different lineage of electric fishes further revealed that the coding gene of rho guanine nucleotide exchange factor 4-like (arhgef4), which is associated with G-protein coupled receptor (GPCR) signaling pathway, underwent adaptive parallel evolution. Gene identification suggests visual degradation in catfishes, and an important role for taste in environmental adaptation. Our findings fill in the genomic data for a branch of electric fish and provide a relevant genetic basis for the adaptive evolution of Siluriformes. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00197-8.
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Affiliation(s)
- Meiru Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Yue Song
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Suyu Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Lili Yu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Zengbao Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Hengjia Yang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Mengqi Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Zhuocheng Zhou
- Professional Committee of Native Aquatic Organisms and Water Ecosystem of China Fisheries Association, Beijing, 100125 China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210023 China
| | - Shanshan Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083 China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
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35
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Kahanamoku-Meyer SS, Samuels-Fair M, Kamel SM, Stewart D, Wu B, Kahn LX, Titcomb M, Mei YA, Bridge RC, Li YS, Sinco C, Moreno J, Epino JT, Gonzalez-Marin G, Latt C, Fergus H, Duijnstee IAP, Finnegan S. An 800-year record of benthic foraminifer images and 2D morphometrics from the Santa Barbara Basin. Sci Data 2024; 11:144. [PMID: 38291058 PMCID: PMC10828449 DOI: 10.1038/s41597-024-02934-9] [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: 06/07/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
The Santa Barbara Basin is an extraordinary archive of environmental and ecological change, where varved sediments preserve microfossils that provide an annual to decadal record of the dynamics of surrounding ecosystems. Of the microfossils preserved in these sediments, benthic foraminifera are the most abundant seafloor-dwelling organisms. While they have been extensively utilized for geochemical and paleoceanographic work, studies of their morphology are lacking. Here we use a high-throughput imaging method (AutoMorph) designed to extract 2D data from photographic images of fossils to produce a large image and 2D shape dataset of recent benthic foraminifera from two core records sampled from the center of the Santa Barbara Basin that span an ~800-year-long interval during the Common Era (1249-2008 CE). Information on more than 36,000 objects is included, of which more than 22,000 are complete or partially-damaged benthic foraminifera. The dataset also includes other biogenic microfossils including ostracods, pteropods, diatoms, radiolarians, fish teeth, and shark dermal denticles. We describe our sample preparation, imaging, and identification techniques, and outline potential data uses.
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Affiliation(s)
- Sara S Kahanamoku-Meyer
- Department of Integrative Biology and Museum of Paleontology, University of California at Berkeley, Berkeley, CA, 94720, USA.
- School of Ocean and Earth Sciences and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.
| | - Maya Samuels-Fair
- Department of Integrative Biology and Museum of Paleontology, University of California at Berkeley, Berkeley, CA, 94720, USA
- School of Ocean and Earth Sciences and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Sarah M Kamel
- Department of Psychology, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Da'shaun Stewart
- Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Bryan Wu
- Department of Electrical Engineering and Computer Sciences, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Leah X Kahn
- Department of Integrative Biology and Museum of Paleontology, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Earth and Planetary Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- School of Ocean and Earth Sciences and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Max Titcomb
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Yingyan Alyssa Mei
- Department of Integrative Biology and Museum of Paleontology, University of California at Berkeley, Berkeley, CA, 94720, USA
- School of Ocean and Earth Sciences and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - R Cheyenne Bridge
- Department of Earth and Planetary Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- College of Chemistry, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Yuerong Sophie Li
- Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Carolina Sinco
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Julissa Moreno
- Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Josef T Epino
- Department of Sociology, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Gerson Gonzalez-Marin
- Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Earth and Planetary Science, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Chloe Latt
- Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Heather Fergus
- Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Ivo A P Duijnstee
- Department of Integrative Biology and Museum of Paleontology, University of California at Berkeley, Berkeley, CA, 94720, USA
- School of Ocean and Earth Sciences and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Seth Finnegan
- Department of Integrative Biology and Museum of Paleontology, University of California at Berkeley, Berkeley, CA, 94720, USA
- School of Ocean and Earth Sciences and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
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Zhang TT, Yan CL, Qiao JX, Yang AS, Liu ML, Kou YX, Li ZH. Demographic dynamics and molecular evolution of the rare and endangered subsect. Gerardianae of Pinus: insights from chloroplast genomes and mitochondrial DNA markers. PLANTA 2024; 259:45. [PMID: 38281265 DOI: 10.1007/s00425-023-04316-8] [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: 07/11/2023] [Accepted: 12/21/2023] [Indexed: 01/30/2024]
Abstract
MAIN CONCLUSION The divergence of subsect. Gerardianae was likely triggered by the uplift of the Qinghai-Tibetan Plateau and adjacent mountains. Pinus bungeana might have probably experienced expansion since Last Interglacial period. Historical geological and climatic oscillations have profoundly affected patterns of nucleotide variability, evolutionary history, and species divergence in numerous plants of the Northern Hemisphere. However, how long-lived conifers responded to geological and climatic fluctuations in East Asia remain poorly understood. Here, based on paternally inherited chloroplast genomes and maternally inherited mitochondrial DNA markers, we investigated the population demographic history and molecular evolution of subsect. Gerardianae (only including three species, Pinus bungeana, P. gerardiana, and P. squamata) of Pinus. A low level of nucleotide diversity was found in P. bungeana (π was 0.00016 in chloroplast DNA sequences, and 0.00304 in mitochondrial DNAs). The haplotype-based phylogenetic topology and unimodal distributions of demographic analysis suggested that P. bungeana probably originated in the southern Qinling Mountains and experienced rapid population expansion since Last Interglacial period. Phylogenetic analysis revealed that P. gerardiana and P. squamata had closer genetic relationship. The species divergence of subsect. Gerardianae occurred about 27.18 million years ago (Mya) during the middle to late Oligocene, which was significantly associated with the uplift of the Qinghai-Tibetan Plateau and adjacent mountains from the Eocene to the mid-Pliocene. The molecular evolutionary analysis showed that two chloroplast genes (psaI and ycf1) were under positive selection, the genetic lineages of P. bungeana exhibited higher transition and nonsynonymous mutations, which were involved with the strongly environmental adaptation. These findings shed light on the population evolutionary history of white pine species and provide striking insights for comprehension of their species divergence and molecular evolution.
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Affiliation(s)
- Ting-Ting Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Chun-Li Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jin-Xia Qiao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Ao-Shuang Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Mi-Li Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Yi-Xuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China.
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Kiel S, Goedert JL, Huynh TL, Krings M, Parkinson D, Romero R, Looy CV. Early Oligocene kelp holdfasts and stepwise evolution of the kelp ecosystem in the North Pacific. Proc Natl Acad Sci U S A 2024; 121:e2317054121. [PMID: 38227671 PMCID: PMC10823212 DOI: 10.1073/pnas.2317054121] [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: 10/02/2023] [Accepted: 11/27/2023] [Indexed: 01/18/2024] Open
Abstract
Kelp forests are highly productive and economically important ecosystems worldwide, especially in the North Pacific Ocean. However, current hypotheses for their evolutionary origins are reliant on a scant fossil record. Here, we report fossil hapteral kelp holdfasts from western Washington State, USA, indicating that kelp has existed in the northeastern Pacific Ocean since the earliest Oligocene. This is consistent with the proposed North Pacific origin of kelp associated with global cooling around the Eocene-Oligocene transition. These fossils also support the hypotheses that a hapteral holdfast, rather than a discoid holdfast, is the ancestral state in complex kelps and suggest that early kelps likely had a flexible rather than a stiff stipe. Early kelps were possibly grazed upon by mammals like desmostylians, but fossil evidence of the complex ecological interactions known from extant kelp forests is lacking. The fossil record further indicates that the present-day, multi-story kelp forest had developed at latest after the mid-Miocene climate optimum. In summary, the fossils signify a stepwise evolution of the kelp ecosystem in the North Pacific, likely enabled by changes in the ocean-climate system.
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Affiliation(s)
- Steffen Kiel
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm10405, Sweden
| | - James L. Goedert
- Burke Museum of Natural History and Culture, University of Washington, Seattle, WA98195
| | - Tony L. Huynh
- School of Medicine, University of California, San Francisco, CA94143
| | - Michael Krings
- Staatliche Naturwissenschaftliche Sammlungen Bayerns-Bayerische Staatssammlung für Paläontologie und Geologie, Munich80333, Germany
- Department für Geo- und Umweltwissenschaften, Paläontologie und Geobiologie, Ludwig-Maximilians-Universität, Munich80333, Germany
| | - Dula Parkinson
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Rosemary Romero
- Department of Integrative Biology, University of California, Berkeley, CA94720
| | - Cindy V. Looy
- Department of Integrative Biology, Museum of Paleontology, and Herbarium, University of California, Berkeley, CA94720
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ElShafie SJ. Body size estimation from isolated fossil bones reveals deep time evolutionary trends in North American lizards. PLoS One 2024; 19:e0296318. [PMID: 38180961 PMCID: PMC10769094 DOI: 10.1371/journal.pone.0296318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 12/11/2023] [Indexed: 01/07/2024] Open
Abstract
Lizards play vital roles in extant ecosystems. However, their roles in extinct ecosystems are poorly understood because the fossil record of lizards consists mostly of isolated bones. This makes it difficult to document changes in lizard morphology and body size over time, which is essential for studies of lizard paleoecology and evolution. It is also difficult to compare available fossil lizard data with existing sources of extant lizard data because extant studies rarely measure individual bones. Furthermore, no previous study has regressed measurements of individual bones to body length across crown lizard groups, nor tested those regressions on fossil skeletons. An extensive dataset of individual bone measurements from extant lizards across crown taxonomic groups is here employed to develop novel methods for estimating lizard body size from isolated fossil elements. These methods were applied to a comparably large dataset of fossil lizard specimens from the robust Paleogene record (66-23 Ma) of the Western Interior of North America. This study tests the hypothesis that anatomical proportions have been conserved within higher-level crown lizard groups since the Paleogene and can therefore be used to reconstruct snout-vent length (SVL) and mass for fossil specimens referred to the same groups. Individual bones demonstrated strong correlation with SVL in extant as well as fossil lizard specimens (R2 ≥ 0.69). Equations for mass estimation from individual bones were derived from the SVL regressions using published equations for calculating lizard body mass from SVL. The resulting body size estimates from regression equations for the entire fossil dataset revealed that lizards reached greatest maximum body size in the middle Paleogene, with the largest size class dominated by anguid lizards that exceeded 1 meter in SVL and 1.5 kg in body mass. Maximum body size decreased to under 400 mm and below 1.5 kg in the late Paleogene. No association was found between changes in maximum lizard body size and marine isotope proxies of global temperature through the Paleogene. This is the first study to investigate body size evolution across lizard clades over a deep time interval and for a large geographic region. The proposed methods can be used to generate body size regressions and provide estimates of body size for isolated lizard bones referred to any crown group.
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Affiliation(s)
- Sara J. ElShafie
- Department of Integrative Biology and Museum of Paleontology, University of California, Berkeley, California, United States of America
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39
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Dibán MJ, Hinojosa LF. Testing the Tropical Niche Conservatism Hypothesis: Climatic Niche Evolution of Escallonia Mutis ex L. F. (Escalloniaceae). PLANTS (BASEL, SWITZERLAND) 2024; 13:133. [PMID: 38202441 PMCID: PMC10781032 DOI: 10.3390/plants13010133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024]
Abstract
We assess the Tropical Niche Conservatism Hypothesis in the genus Escallonia in South America using phylogeny, paleoclimate estimation and current niche modelling. We tested four predictions: (1) the climatic condition where the ancestor of Escallonia grew is megathermal; (2) the temperate niche is a derived condition from tropical clades; (3) the most closely related species have a similar current climate niche (conservation of the phylogenetic niche); and (4) there is a range expansion from the northern Andes to high latitudes during warm times. Our phylogenetic hypothesis shows that Escallonia originated 52.17 ± 0.85 My, in the early Eocene, with an annual mean temperature of 13.8 °C and annual precipitation of 1081 mm, corresponding to a microthermal to mesothermal climate; the species of the northern and central tropical Andes would be the ancestral ones, and the temperate species evolved between 32 and 20 My in a microthermal climate. The predominant evolutionary models were Brownian and Ornstein-Uhlenbeck. There was phylogenetic signal in 7 of the 9 variables, indicating conservation of the climatic niche. Escallonia would have originated in the central and southern Andes and reached the other environments by dispersion.
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Affiliation(s)
- María José Dibán
- Laboratory of Paleoecology, Department of Ecological Science, Faculty of Science, University of Chile, Santiago 7800003, Chile
| | - Luis Felipe Hinojosa
- Laboratory of Paleoecology, Department of Ecological Science, Faculty of Science, University of Chile, Santiago 7800003, Chile
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40
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Gentis N, Licht A, De Franceschi D, Win Z, Aung DW, Dupont-Nivet G, Boura A. First fossil woods and palm stems from the mid-Paleocene of Myanmar and implications for biogeography and wood anatomy. AMERICAN JOURNAL OF BOTANY 2024; 111:e16259. [PMID: 38031479 DOI: 10.1002/ajb2.16259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
PREMISE The rise of angiosperm-dominated tropical rainforests has been proposed to have occurred shortly after the Cretaceous-Paleogene transition. Paleocene fossil wood assemblages are rare yet provide important data for understanding these forests and whether their wood anatomical features can be used to document the changes that occurred during this transition. METHODS We used standard techniques to section 11 fossil wood specimens of Paleocene-age, described the anatomy using standard terminology, and investigated their affinities to present-day taxa. RESULTS We report here the first middle Paleocene fossil wood specimens from Myanmar, which at the time was near the equator and anchored to India. Some fossils share affinities with Arecaceae, Sapindales (Anacardiaceae, Meliaceae) and Moraceae and possibly Fabaceae or Lauraceae. One specimen is described as a new species and genus: Compitoxylon paleocenicum gen. et sp. nov. CONCLUSIONS This assemblage reveals the long-lasting presence of these aforementioned groups in South Asia and suggests the early presence of multiple taxa of Laurasian affinity in Myanmar and India. The wood anatomical features of the dicotyledonous specimens reveal that both "modern" and "primitive" features (in a Baileyan scheme) are present with proportions similar to features in specimens from Paleocene Indian localities. Their anatomical diversity corroborates that tropical flora display "modern" features early in the history of angiosperms and that their high diversity remained steady afterward.
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Affiliation(s)
- Nicolas Gentis
- CR2P, UMR7207, MNHN, Sorbonne Université, CNRS, 57 rue Cuvier, CP 48, 75005, Paris, France
| | - Alexis Licht
- CEREGE, Aix Marseille Université, CNRS, IRD, INRAE, Collège de France, Europole Méditerranéen de l'Arbois, BP 80, 13545, Aix-en-Provence, France
| | - Dario De Franceschi
- CR2P, UMR7207, MNHN, Sorbonne Université, CNRS, 57 rue Cuvier, CP 48, 75005, Paris, France
| | - Zaw Win
- Geology Department, Shwebo University, Sagaing Region, Myanmar
| | - Day Wa Aung
- Geology Department, University of Yangon, Pyay Rd, Yangon, Myanmar
| | - Guillaume Dupont-Nivet
- Géosciences Rennes, Université de Rennes 1, 35042, Rennes, France
- Helmholtz Centre Potsdam, German Research Centre for Geosciences, 14473, Potsdam, Germany
| | - Anaïs Boura
- CR2P, UMR7207, MNHN, Sorbonne Université, CNRS, 57 rue Cuvier, CP 48, 75005, Paris, France
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41
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Payne ARD, Mannion PD, Lloyd GT, Davis KE. Decoupling speciation and extinction reveals both abiotic and biotic drivers shaped 250 million years of diversity in crocodile-line archosaurs. Nat Ecol Evol 2024; 8:121-132. [PMID: 38049481 PMCID: PMC10781641 DOI: 10.1038/s41559-023-02244-0] [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: 06/17/2022] [Accepted: 09/26/2023] [Indexed: 12/06/2023]
Abstract
Whereas living representatives of Pseudosuchia, crocodylians, number fewer than 30 species, more than 700 pseudosuchian species are known from their 250-million-year fossil record, displaying far greater ecomorphological diversity than their extant counterparts. With a new time-calibrated tree of >500 species, we use a phylogenetic framework to reveal that pseudosuchian evolutionary history and diversification dynamics were directly shaped by the interplay of abiotic and biotic processes over hundreds of millions of years, supported by information theory analyses. Speciation, but not extinction, is correlated with higher temperatures in terrestrial and marine lineages, with high sea level associated with heightened extinction in non-marine taxa. Low lineage diversity and increased speciation in non-marine species is consistent with opportunities for niche-filling, whereas increased competition may have led to elevated extinction rates. In marine lineages, competition via increased lineage diversity appears to have driven both speciation and extinction. Decoupling speciation and extinction, in combination with ecological partitioning, reveals a more complex picture of pseudosuchian evolution than previously understood. As the number of species threatened with extinction by anthropogenic climate change continues to rise, the fossil record provides a unique window into the drivers that led to clade success and those that may ultimately lead to extinction.
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Affiliation(s)
- Alexander R D Payne
- Department of Biology, University of York, York, UK
- Leverhulme Centre for Anthropocene Biodiversity, University of York, York, UK
| | - Philip D Mannion
- Department of Earth Sciences, University College London, London, UK
| | | | - Katie E Davis
- Department of Biology, University of York, York, UK.
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42
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Núñez-Flores M, Solórzano A, Avaria-Llautureo J, Gomez-Uchida D, López-González PJ. Diversification dynamics of a common deep-sea octocoral family linked to the Paleocene-Eocene thermal maximum. Mol Phylogenet Evol 2024; 190:107945. [PMID: 37863452 DOI: 10.1016/j.ympev.2023.107945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
The deep-sea has experienced dramatic changes in physical and chemical variables in the geological past. However, little is known about how deep-sea species richness responded to such changes over time and space. Here, we studied the diversification dynamics of one of the most diverse octocorallian families inhabiting deep sea benthonic environments worldwide and sustaining highly diverse ecosystems, Primnoidae. A newly dated species-level phylogeny was constructed to infer their ancestral geographic locations and dispersal rates initially. Then, we tested whether their global and regional (the Southern Ocean) diversification dynamics were mediated by dispersal rate and abiotic factors as changes in ocean geochemistry. Finally, we tested whether primnoids showed changes in speciation and extinction at discrete time points. Our results suggested primnoids likely originated in the southwestern Pacific Ocean during the Lower Cretaceous ∼112 Ma, with further dispersal after the physical separation of continental landmasses along the late Mesozoic and Cenozoic. Only the speciation rate of the Southern Ocean primnoids showed a significant correlation to ocean chemistry. Moreover, the Paleocene-Eocene thermal maximum marked a significant increase in the diversification of primnoids at global and regional scales. Our results provide new perspectives on the macroevolutionary and biogeographic patterns of an ecologically important benthic organism typically found in deep-sea environments.
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Affiliation(s)
- Mónica Núñez-Flores
- Centro de Investigación de Estudios Avanzados del Maule, Vicerrectoría de Investigación y Postgrado Universidad Católica del Maule, Talca, Chile; Laboratorio Ecología de Abejas, Departamento de Biología y Química, Facultad de Ciencias Básicas, Universidad Católica del Maule, Talca, Chile.
| | - Andrés Solórzano
- Escuela de Geología, Departamento de Biología y Química, Facultad de Ciencias Básicas, Universidad Católica del Maule, Talca, Chile
| | | | - Daniel Gomez-Uchida
- Genomics in Ecology, Evolution, and Conservation Laboratory (GEECLAB), Department of Zoology, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Pablo J López-González
- Biodiversidad y Ecología Acuática. Departamento de Zoología, Facultad de Biología, Universidad de Sevilla, Reina Mercedes 6, 41012 Sevilla, Spain
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Algeo TJ, Shen J. Theory and classification of mass extinction causation. Natl Sci Rev 2024; 11:nwad237. [PMID: 38116094 PMCID: PMC10727847 DOI: 10.1093/nsr/nwad237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 12/21/2023] Open
Abstract
Theory regarding the causation of mass extinctions is in need of systematization, which is the focus of this contribution. Every mass extinction has both an ultimate cause, i.e. the trigger that leads to various climato-environmental changes, and one or more proximate cause(s), i.e. the specific climato-environmental changes that result in elevated biotic mortality. With regard to ultimate causes, strong cases can be made that bolide (i.e. meteor) impacts, large igneous province (LIP) eruptions and bioevolutionary events have each triggered one or more of the Phanerozoic Big Five mass extinctions, and that tectono-oceanic changes have triggered some second-order extinction events. Apart from bolide impacts, other astronomical triggers (e.g. solar flares, gamma bursts and supernova explosions) remain entirely in the realm of speculation. With regard to proximate mechanisms, most extinctions are related to either carbon-release or carbon-burial processes, the former being associated with climatic warming, ocean acidification, reduced marine productivity and lower carbonate δ13C values, and the latter with climatic cooling, increased marine productivity and higher carbonate δ13C values. Environmental parameters such as marine redox conditions and terrestrial weathering intensity do not show consistent relationships with carbon-cycle changes. In this context, mass extinction causation can be usefully classified using a matrix of ultimate and proximate factors. Among the Big Five mass extinctions, the end-Cretaceous biocrisis is an example of a bolide-triggered carbon-release event, the end-Permian and end-Triassic biocrises are examples of LIP-triggered carbon-release events, and the Late Ordovician and Late Devonian biocrises are examples of bioevolution-triggered carbon-burial events. Whereas the bolide-impact and LIP-eruption mechanisms appear to invariably cause carbon release, bioevolutionary triggers can result in variable carbon-cycle changes, e.g. carbon burial during the Late Ordovician and Late Devonian events, carbon release associated with modern anthropogenic climate warming, and little to no carbon-cycle impact due to certain types of ecosystem change (e.g. the advent of the first predators around the end-Ediacaran; the appearance of Paleolithic human hunters in Australasia and the Americas). Broadly speaking, studies of mass extinction causation have suffered from insufficiently critical thinking-an impartial survey of the extant evidence shows that (i) hypotheses of a common ultimate cause (e.g. bolide impacts or LIP eruptions) for all Big Five mass extinctions are suspect given manifest differences in patterns of environmental and biotic change among them; (ii) the Late Ordovician and Late Devonian events were associated with carbon burial and long-term climatic cooling, i.e. changes that are inconsistent with a bolide-impact or LIP-eruption mechanism; and (iii) claims of periodicity in Phanerozoic mass extinctions depended critically on the now-disproven idea that they shared a common extrinsic trigger (i.e. bolide impacts).
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Affiliation(s)
- Thomas J Algeo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences—Wuhan, Wuhan430074, China
- State Key Laboratory of Geological Processes and Mineral Resources, China University of Geosciences—Wuhan, Wuhan430074, China
- Department of Geosciences, University of Cincinnati, Cincinnati, OH45221, USA
| | - Jun Shen
- State Key Laboratory of Geological Processes and Mineral Resources, China University of Geosciences—Wuhan, Wuhan430074, China
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Richerson PJ, Boyd RT, Efferson C. Agentic processes in cultural evolution: relevance to Anthropocene sustainability. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220252. [PMID: 37952614 PMCID: PMC10645076 DOI: 10.1098/rstb.2022.0252] [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: 12/23/2022] [Accepted: 07/11/2023] [Indexed: 11/14/2023] Open
Abstract
Humans have evolved culturally and perhaps genetically to be unsustainable. We exhibit a deep and consistent pattern of short-term resource exploitation behaviours and institutions. We distinguish agentic and naturally selective forces in cultural evolution. Agentic forces are quite important compared to the blind forces (random variation and natural selection) in cultural evolution and gene-culture coevolution. We need to use the agentic policy-making processes to evade the impact of blind natural selection. We argue that agentic forces became important during our Pleistocene history and into the Anthropocene present. Human creativity in the form of deliberate innovations and the deliberate selective diffusion of technical and social advances drove this process forward for a long time before planetary limits became a serious issue. We review models with multiple positive feedbacks that roughly fit this observed pattern. Policy changes in the case of large-scale existential threats like climate change are made by political and diplomatic agents grasping and moving levers of institutional power in order to avoid the operation of blind natural selection and agentic forces driven by narrow or short-term goals. This article is part of the theme issue 'Evolution and sustainability: gathering the strands for an Anthropocene synthesis'.
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Affiliation(s)
- Peter J. Richerson
- Department of Environmental Science and Policy, University of California, Davis, 95616, CA, USA
| | - Robert T. Boyd
- School of Human Evolution and Social Change, Institute of Human Origins, Arizona State University, Tempe, 85281, AZ, USA
| | - Charles Efferson
- Faculty of Business and Economics, University of Lausanne, 1015, Lausanne, Switzerland
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45
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Li QQ, Khasbagan, Zhang ZP, Wen J, Yu Y. Plastid phylogenomics of the tribe potentilleae (Rosaceae). Mol Phylogenet Evol 2024; 190:107961. [PMID: 37918684 DOI: 10.1016/j.ympev.2023.107961] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 04/08/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
The tribe Potentilleae comprises approximately 1700 species in 13 genera, making it one of the largest of the 16 tribes in Rosaceae. Our understanding of the composition and relationships among members of Potentilleae has advanced dramatically with the application of molecular markers in the last two decades. Yet there is still much work remaining toward a robust phylogenetic framework for the entire Potentilleae and a comprehensive genus-level dating framework for the tribe. The goals of the present study were to establish a phylogenetic framework for Potentilleae, infer the origin and diversification of the tribe using a temporal framework, and explore the taxonomic implications in light of the updated phylogenetic framework. We used the plastome sequences from 158 accessions representing 139 taxa covering all 13 recognized genera of the tribe to reconstruct the Potentilleae phylogeny. High phylogenetic resolution was recovered along the Potentilleae backbone. Two major clades were recovered within Potentilleae, corresponding to the two subtribes Fragariinae and Potentillinae. Within Fragariinae, two subclades were recovered. In one subclade, Sibbaldia sensu stricto is sister to a clade containing Sibbaldianthe, Comarum, Farinopsis, and Alchemilla sensu lato. In the other subclade, Fragaria is sister to a clade comprising Chamaerhodos, Chamaecallis, Drymocallis, Dasiphora, and Potaninia. Within Potentillinae, Argentina is sister to Potentilla sensu stricto. Within Potentilla sensu stricto, clade Himalaya is sister to Alba, and the Himalaya-Alba clade together is sister to a clade comprising Reptans, Potentilla ancistrifolia Bunge, Fragarioides, Ivesioid, and Argentea. Divergence time estimates indicated that tribe Potentilleae originated during the middle Eocene, and subtribes Fragariinae and Potentillinae diverged around the Eocene-Oligocene transition, and divergence times dated for Potentilleae genera ranged from the early Miocene to the late Pleistocene.
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Affiliation(s)
- Qin-Qin Li
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot 010022, Inner Mongolia, China; Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA
| | - Khasbagan
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot 010022, Inner Mongolia, China
| | - Zhi-Ping Zhang
- College of Computer Science and Technology, Inner Mongolia Normal University, Hohhot 010022, Inner Mongolia, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA.
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China.
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46
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Zhao Y, Su C, He B, Nie R, Wang Y, Ma J, Song J, Yang Q, Hao J. Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome. Nat Commun 2023; 14:8190. [PMID: 38081828 PMCID: PMC10713551 DOI: 10.1038/s41467-023-44023-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Parnassius glacialis is a typical "Out of the QTP" alpine butterfly that originated on the Qinghai-Tibet Plateau (QTP) and dispersed into relatively low-altitude mountainous. Here we assemble a chromosome-level genome of P. glacialis and resequence 9 populations in order to explore the genome evolution and local adaptation of this species. These results indicated that the rapid accumulation and slow unequal recombination of transposable elements (TEs) contributed to the formation of its large genome. Several ribosomal gene families showed extensive expansion and selective evolution through transposon-mediated processed pseudogenes. Additionally, massive structural variations (SVs) of TEs affected the genetic differentiation of low-altitude populations. These low-altitude populations might have experienced a genetic bottleneck in the past and harbor genes with selective signatures which may be responsible for the potential adaptation to low-altitude environments. These results provide a foundation for understanding genome evolution and local adaptation for "Out of the QTP" of P. glacialis.
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Affiliation(s)
- Youjie Zhao
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224, Yunnan, China
| | - Chengyong Su
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Bo He
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Ruie Nie
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Yunliang Wang
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Junye Ma
- State Key Laboratory of Palaeobiology and Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jingyu Song
- College of Animal Science, Shandong Agricultural University, Taian, 271000, China
| | - Qun Yang
- State Key Laboratory of Palaeobiology and Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, 210008, China.
- Nanjing College, University of Chinese Academy of Sciences, Nanjing, 211135, China.
| | - Jiasheng Hao
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
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Liu L, Galbrun E, Tang H, Kaakinen A, Zhang Z, Zhang Z, Žliobaitė I. The emergence of modern zoogeographic regions in Asia examined through climate-dental trait association patterns. Nat Commun 2023; 14:8194. [PMID: 38081824 PMCID: PMC10713550 DOI: 10.1038/s41467-023-43807-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
The complex and contrasted distribution of terrestrial biota in Asia has been linked to active tectonics and dramatic climatic changes during the Neogene. However, the timings of the emergence of these distributional patterns and the underlying climatic and tectonic mechanisms remain disputed. Here, we apply a computational data analysis technique, called redescription mining, to track these spatiotemporal phenomena by studying the associations between the prevailing herbivore dental traits of mammalian communities and climatic conditions during the Neogene. Our results indicate that the modern latitudinal zoogeographic division emerged after the Middle Miocene climatic transition, and that the modern monsoonal zoogeographic pattern emerged during the late Late Miocene. Furthermore, the presence of a montane forest biodiversity hotspot in the Hengduan Mountains alongside Alpine fauna on the Tibetan Plateau suggests that the modern distribution patterns may have already existed since the Pliocene.
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Affiliation(s)
- Liping Liu
- Department of Geosciences and Geography, University of Helsinki, P.O. Box 64, Helsinki, FI-00014, Finland.
- Department of Palaeobiology, The Swedish Museum of Natural History, P.O. Box 50007, Stockholm, SE-104 05, Sweden.
| | - Esther Galbrun
- School of Computing, University of Eastern Finland, Technopolis, Microkatu 1, Kuopio, FI-70210, Finland.
| | - Hui Tang
- Department of Geosciences and Geography, University of Helsinki, P.O. Box 64, Helsinki, FI-00014, Finland
- Climate System Research Unit, Finnish Meteorological Institute, P.O. Box 503, Helsinki, FI-00101, Finland
- Department of Geosciences, University of Oslo, P.O. Box 1022, Oslo, NO-0315, Norway
| | - Anu Kaakinen
- Department of Geosciences and Geography, University of Helsinki, P.O. Box 64, Helsinki, FI-00014, Finland
| | - Zhongshi Zhang
- Department of Atmospheric Science, School of Environmental Studies, China University of Geosciences, 388 Lumo Road, 430074, Wuhan, China
| | - Zijian Zhang
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, 19, Beitucheng Western Road, Chaoyang District, 100029, Beijing, China
| | - Indrė Žliobaitė
- Department of Geosciences and Geography, University of Helsinki, P.O. Box 64, Helsinki, FI-00014, Finland
- Department of Computer Science, University of Helsinki, P.O. Box 68, University of Helsinki, FI-00014, Finland
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48
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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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49
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Herrando-Moraira S, Roquet C, Calleja JA, Chen YS, Fujikawa K, Galbany-Casals M, Garcia-Jacas N, Liu JQ, López-Alvarado J, López-Pujol J, Mandel JR, Mehregan I, Sáez L, Sennikov AN, Susanna A, Vilatersana R, Xu LS. Impact of the climatic changes in the Pliocene-Pleistocene transition on Irano-Turanian species. The radiation of genus Jurinea (Compositae). Mol Phylogenet Evol 2023; 189:107928. [PMID: 37714444 DOI: 10.1016/j.ympev.2023.107928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
The Irano-Turanian region is one of the world's richest floristic regions and the centre of diversity for numerous xerophytic plant lineages. However, we still have limited knowledge on the timing of evolution and biogeographic history of its flora, and potential drivers of diversification remain underexplored. To fill this knowledge gap, we focus on the Eurasian genus Jurinea (ca. 200 species), one of the largest plant radiations that diversified in the region. We applied a macroevolutionary integrative approach to explicitly test diversification hypotheses and investigate the relative roles of geography vs. ecology and niche conservatism vs. niche lability in speciation processes. To do so, we gathered a sample comprising 77% of total genus richness and obtained data about (1) its phylogenetic history, recovering 502 nuclear loci sequences; (2) growth forms; (3) ecological niche, compiling data of 21 variables for more than 2500 occurrences; and (4) paleoclimatic conditions, to estimate climatic stability. Our results revealed that climate was a key factor in the evolutionary dynamics of Jurinea. The main diversification and biogeographic events that occurred during past climate changes, which led to colder and drier conditions, are the following: (1) the origin of the genus (10.7 Ma); (2) long-distance dispersals from the Iranian Plateau to adjacent regions (∼7-4 Ma); and (3) the diversification shift during Pliocene-Pleistocene Transition (ca. 3 Ma), when net diversification rate almost doubled. Our results supported the pre-adaptation hypothesis, i.e., the evolutionary success of Jurinea was linked to the retention of the ancestral niche adapted to aridity. Interestingly, the paleoclimatic analyses revealed that in the Iranian Plateau long-term climatic stability favoured old-lineage persistence, resulting in current high species richness of semi-arid and cold adapted clades; whereas moderate climate oscillations stimulated allopatric diversification in the lineages distributed in the Circumboreal region. In contrast, growth form lability and high niche disparity among closely related species in the Central Asian clade suggest adaptive radiation to mountain habitats. In sum, the radiation of Jurinea is the result of both adaptive and non-adaptive processes influenced by climatic, orogenic and ecological factors.
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Affiliation(s)
- Sonia Herrando-Moraira
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Cristina Roquet
- Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Juan-Antonio Calleja
- Departament of Biology (Botany), Faculty of Sciences, Research Centre on Biodiversity and Global Change (CIBC-UAM), 28049 Madrid, Spain
| | - You-Sheng Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Kazumi Fujikawa
- Kochi Prefectural Makino Botanical Garden, 4200-6, Godaisan, Kochi 781-8125, Japan
| | - Mercè Galbany-Casals
- Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Núria Garcia-Jacas
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Jian-Quan Liu
- Key Laboratory for Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Javier López-Alvarado
- Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain; Escuela de Ciencias Ambientales, Universidad Espíritu Santo (UEES), Samborondón 091650, Ecuador
| | - Jennifer R Mandel
- Department of Biological Sciences, Center for Biodiversity, University of Memphis, Memphis, TN 38152, USA
| | - Iraj Mehregan
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Llorenç Sáez
- Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Alexander N Sennikov
- Botanical Museum, Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Roser Vilatersana
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Lian-Sheng Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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50
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Zhang N, Li Y, Shang W, Song X, Liu W, Hao C. Role of excited-state hydrogen bonding in CO 2 photoreduction catalyzed by sodium magnesium chlorophyll. Phys Chem Chem Phys 2023; 25:32158-32165. [PMID: 37986583 DOI: 10.1039/d3cp03638c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
In this paper, we report a joint experimental and computational study to elaborate the mechanism for the photocatalytic CO2 reduction reaction (CO2RR). Experimental results indicate that the catalyst (sodium magnesium chlorophyll, MgChlNa2), which has a well-defined structure for calculation and understanding, can achieve the photoreduction of CO2 to CO only using water as a dispersant, without adding any photosensitizer or sacrificial agent. Subsequently, a series of structural models of the hydrogen-bonded complexes of the catalyst were constructed and outlined via utilizing density functional theory (DFT) calculations, including photophysical and photochemical processes. The results confirm that the rate-limiting step of the whole CO2RR was the intersystem crossing process. The electron and proton transfers involved in photophysical and photochemical processes are induced by hydrogen bonds in the excited states. The combination of experiments and calculations will provide an important reference for the design of high-efficiency photocatalysts in the photocatalytic CO2RR.
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Affiliation(s)
- Naitian Zhang
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, Liaoning, China.
| | - Yuehui Li
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, Liaoning, China.
| | - Wenzhe Shang
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, Liaoning, China.
| | - Xuedan Song
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, Liaoning, China.
| | - Wei Liu
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, Liaoning, China.
| | - Ce Hao
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, Liaoning, China.
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