1
|
Wu S, Rheindt FE, Zhang J, Wang J, Zhang L, Quan C, Li Z, Wang M, Wu F, Qu Y, Edwards SV, Zhou Z, Liu L. Genomes, fossils, and the concurrent rise of modern birds and flowering plants in the Late Cretaceous. Proc Natl Acad Sci U S A 2024; 121:e2319696121. [PMID: 38346181 PMCID: PMC10895254 DOI: 10.1073/pnas.2319696121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/29/2023] [Indexed: 02/15/2024] Open
Abstract
The phylogeny and divergence timing of the Neoavian radiation remain controversial despite recent progress. We analyzed the genomes of 124 species across all Neoavian orders, using data from 25,460 loci spanning four DNA classes, including 5,756 coding sequences, 12,449 conserved nonexonic elements, 4,871 introns, and 2,384 intergenic segments. We conducted a comprehensive sensitivity analysis to account for the heterogeneity across different DNA classes, leading to an optimal tree of Neoaves with high resolution. This phylogeny features a novel Neoavian dichotomy comprising two monophyletic clades: a previously recognized Telluraves (land birds) and a newly circumscribed Aquaterraves (waterbirds and relatives). Molecular dating analyses with 20 fossil calibrations indicate that the diversification of modern birds began in the Late Cretaceous and underwent a constant and steady radiation across the KPg boundary, concurrent with the rise of angiosperms as well as other major Cenozoic animal groups including placental and multituberculate mammals. The KPg catastrophe had a limited impact on avian evolution compared to the Paleocene-Eocene Thermal Maximum, which triggered a rapid diversification of seabirds. Our findings suggest that the evolution of modern birds followed a slow process of gradualism rather than a rapid process of punctuated equilibrium, with limited interruption by the KPg catastrophe. This study places bird evolution into a new context within vertebrates, with ramifications for the evolution of the Earth's biota.
Collapse
Affiliation(s)
- Shaoyuan Wu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Jin Zhang
- School of Computer and Communication Engineering, Changsha University of Science and Technology, Changsha, Hunan 410114, China
| | - Jiajia Wang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Lei Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Cheng Quan
- School of Earth Science and Resources, Chang'an University, Xi'an, Shaanxi 710054, China
| | - Zhiheng Li
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Min Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Feixiang Wu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Zhonghe Zhou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Liang Liu
- Department of Statistics, Institute of Bioinformatics, University of Georgia, Athens, GA 30606
| |
Collapse
|
2
|
Albert JS, Carnaval AC, Flantua SGA, Lohmann LG, Ribas CC, Riff D, Carrillo JD, Fan Y, Figueiredo JJP, Guayasamin JM, Hoorn C, de Melo GH, Nascimento N, Quesada CA, Ulloa Ulloa C, Val P, Arieira J, Encalada AC, Nobre CA. Human impacts outpace natural processes in the Amazon. Science 2023; 379:eabo5003. [PMID: 36701466 DOI: 10.1126/science.abo5003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Amazonian environments are being degraded by modern industrial and agricultural activities at a pace far above anything previously known, imperiling its vast biodiversity reserves and globally important ecosystem services. The most substantial threats come from regional deforestation, because of export market demands, and global climate change. The Amazon is currently perched to transition rapidly from a largely forested to a nonforested landscape. These changes are happening much too rapidly for Amazonian species, peoples, and ecosystems to respond adaptively. Policies to prevent the worst outcomes are known and must be enacted immediately. We now need political will and leadership to act on this information. To fail the Amazon is to fail the biosphere, and we fail to act at our peril.
Collapse
Affiliation(s)
- James S Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Ana C Carnaval
- Department of Biology and Ph.D. Program in Biology, City University of New York (CUNY) and CUNY Graduate Center, New York, NY, USA
| | - Suzette G A Flantua
- Department of Biological Sciences, University of Bergen and Bjerknes Centre for Climate Research, Bergen, Norway
| | - Lúcia G Lohmann
- Universidade de São Paulo, Instituto de Biociências, Departamento de Botânica, São Paulo, SP, Brazil
| | - Camila C Ribas
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Douglas Riff
- Instituto de Biologia, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Juan D Carrillo
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Ying Fan
- Department of Earth and Planetary Sciences, Rutgers, The State University of New Jersey, NJ, USA
| | - Jorge J P Figueiredo
- Institute of Geoscience, Center of Mathematical and Earth Sciences, Universidade Federal Rio de Janeiro, RJ, Brazil
| | - Juan M Guayasamin
- Instituto Biósfera, Laboratorio de Biología Evolutiva, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Carina Hoorn
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Gustavo H de Melo
- Department of Geology, Federal University of Ouro Preto, Ouro Preto, MG, Brazil
| | | | - Carlos A Quesada
- Coordination for Environmental Dynamics, National Institute for Research in Amazonia, Manaus, AM, Brazil
| | | | - Pedro Val
- School of Earth and Environmental Sciences, Queens College, CUNY, New York, NY, USA.,Ph.D. Program in Earth and Environmental Sciences, CUNY Graduate Center, New York, NY, USA.,Department of Geology, Federal University of Ouro Preto, Ouro Preto, MG, Brazil
| | - Julia Arieira
- Science Panel for the Amazon (SPA), São José dos Campos, SP, Brazil
| | - Andrea C Encalada
- Instituto Biósfera, Universidad San Francisco de Quito, Quito, Ecuador
| | - Carlos A Nobre
- Institute of Advanced Studies, University of São Paulo, SP, Brazil
| |
Collapse
|
3
|
Spatial patterns of climate change across the Paleocene-Eocene Thermal Maximum. Proc Natl Acad Sci U S A 2022; 119:e2205326119. [PMID: 36215472 PMCID: PMC9586325 DOI: 10.1073/pnas.2205326119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Paleocene-Eocene Thermal Maximum (PETM; 56 Ma) is one of our best geological analogs for understanding climate dynamics in a "greenhouse" world. However, proxy data representing the event are only available from select marine and terrestrial sedimentary sequences that are unevenly distributed across Earth's surface, limiting our view of the spatial patterns of climate change. Here, we use paleoclimate data assimilation (DA) to combine climate model and proxy information and create a spatially complete reconstruction of the PETM and the climate state that precedes it ("PETM-DA"). Our data-constrained results support strong polar amplification, which in the absence of an extensive cryosphere, is related to temperature feedbacks and loss of seasonal snow on land. The response of the hydrological cycle to PETM warming consists of a narrowing of the Intertropical Convergence Zone, off-equatorial drying, and an intensification of seasonal monsoons and winter storm tracks. Many of these features are also seen in simulations of future climate change under increasing anthropogenic emissions. Since the PETM-DA yields a spatially complete estimate of surface air temperature, it yields a rigorous estimate of global mean temperature change (5.6 ∘C; 5.4 ∘C to 5.9 ∘C, 95% CI) that can be used to calculate equilibrium climate sensitivity (ECS). We find that PETM ECS was 6.5 ∘C (5.7 ∘C to 7.4 ∘C, 95% CI), which is much higher than the present-day range. This supports the view that climate sensitivity increases substantially when greenhouse gas concentrations are high.
Collapse
|
4
|
Serna-Duque JA, Cuesta A, Esteban MÁ. Massive gene expansion of hepcidin, a host defense peptide, in gilthead seabream (Sparus aurata). FISH & SHELLFISH IMMUNOLOGY 2022; 124:563-571. [PMID: 35489593 DOI: 10.1016/j.fsi.2022.04.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 03/09/2022] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
Host defense peptides (HDP) are among the most ancient immune molecules in animals and clearly reflect an ancestral evolutionary history involving pathogen-host interactions. Hepcidins are a very widespread family of HDPs among vertebrates and are especially diverse in teleosts. We have investigated the identification of new hepcidins in gilthead seabream (Sparus aurata), a fish farmed in the Mediterranean. Targeted gene predictions supported with expressed sequence tags (ESTs) derived from Hidden Markov Models were used to find the hamp genes in the seabream genome. The results revealed a massively clustered hamp duplication on chromosome 17. In fact, the seabream genome contains the largest number of hepcidin copies described in any vertebrate. The evolutionary history of hepcidins in seabream, and vertebrates generally, clearly indicates high adaptation in teleosts and novel subgroups within hepcidin type II. Furthermore, basal hepcidin gene expression analysis indicates specific-tissue expression profiles, while the presence and distribution of transcription factor binding sites (TFBS) in hamp promoters as well as their transcription profile upon bacterial challenge indicates different immune roles depending on the type of hepcidin and tissue. This massive duplication of HDP genes in a bony fish could point to a far more specific and adaptive innate immune system than assumed in the classic concept of immunity in mammals. Hence, a new world of knowledge regarding hepcidins in fish and vertebrates is being initiated.
Collapse
Affiliation(s)
- Jhon A Serna-Duque
- Immunobiology for Aquaculture Group, Department of Cell Biology and Histology, Faculty of Biology, Campus of International Excellence, Campus Mare Nostrum, University of Murcia, 30100, Murcia, Spain
| | - Alberto Cuesta
- Immunobiology for Aquaculture Group, Department of Cell Biology and Histology, Faculty of Biology, Campus of International Excellence, Campus Mare Nostrum, University of Murcia, 30100, Murcia, Spain
| | - M Ángeles Esteban
- Immunobiology for Aquaculture Group, Department of Cell Biology and Histology, Faculty of Biology, Campus of International Excellence, Campus Mare Nostrum, University of Murcia, 30100, Murcia, Spain.
| |
Collapse
|
5
|
Unraveling ecological signals from a global warming event of the past. Proc Natl Acad Sci U S A 2022; 119:e2201495119. [PMID: 35312374 PMCID: PMC9060492 DOI: 10.1073/pnas.2201495119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
6
|
Isotopic filtering reveals high sensitivity of planktic calcifiers to Paleocene-Eocene thermal maximum warming and acidification. Proc Natl Acad Sci U S A 2022; 119:2115561119. [PMID: 35193977 PMCID: PMC8892336 DOI: 10.1073/pnas.2115561119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2022] [Indexed: 11/18/2022] Open
Abstract
Ocean warming and acidification driven by anthropogenic carbon emissions pose an existential threat to marine calcifying communities. A similar perturbation to global carbon cycling and ocean chemistry occurred ∼56 Ma during the Paleocene-Eocene thermal maximum (PETM), but microfossil records of the marine biotic response are distorted by sediment mixing. Here, we use the carbon isotope excursion marking the PETM to distinguish planktic foraminifer shells calcified during the PETM from those calcified prior to the event and then isotopically filter anachronous specimens from the PETM microfossil assemblages. We find that nearly one-half of foraminifer shells in a deep-sea PETM record from the central Pacific (Ocean Drilling Program Site 865) are reworked contaminants. Contrary to previous interpretations, corrected assemblages reveal a transient but significant decrease in tropical planktic foraminifer diversity at this open-ocean site during the PETM. The decrease in local diversity was caused by extirpation of shallow- and deep-dwelling taxa as they underwent extratropical migrations in response to heat stress, with one prominent lineage showing signs of impaired calcification possibly due to ocean acidification. An absence of subbotinids in the corrected assemblages suggests that ocean deoxygenation may have rendered thermocline depths uninhabitable for some deeper-dwelling taxa. Latitudinal range shifts provided a rapid-response survival mechanism for tropical planktic foraminifers during the PETM, but the rapidity of ocean warming and acidification projected for the coming centuries will likely strain the adaptability of these resilient calcifiers.
Collapse
|
7
|
Peña V, Harvey BP, Agostini S, Porzio L, Milazzo M, Horta P, Le Gall L, Hall-Spencer JM. Major loss of coralline algal diversity in response to ocean acidification. GLOBAL CHANGE BIOLOGY 2021; 27:4785-4798. [PMID: 34268846 DOI: 10.1111/gcb.15757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/17/2021] [Accepted: 06/17/2021] [Indexed: 06/13/2023]
Abstract
Calcified coralline algae are ecologically important in rocky habitats in the marine photic zone worldwide and there is growing concern that ocean acidification will severely impact them. Laboratory studies of these algae in simulated ocean acidification conditions have revealed wide variability in growth, photosynthesis and calcification responses, making it difficult to assess their future biodiversity, abundance and contribution to ecosystem function. Here, we apply molecular systematic tools to assess the impact of natural gradients in seawater carbonate chemistry on the biodiversity of coralline algae in the Mediterranean and the NW Pacific, link this to their evolutionary history and evaluate their potential future biodiversity and abundance. We found a decrease in the taxonomic diversity of coralline algae with increasing acidification with more than half of the species lost in high pCO2 conditions. Sporolithales is the oldest order (Lower Cretaceous) and diversified when ocean chemistry favoured low Mg calcite deposition; it is less diverse today and was the most sensitive to ocean acidification. Corallinales were also reduced in cover and diversity but several species survived at high pCO2 ; it is the most recent order of coralline algae and originated when ocean chemistry favoured aragonite and high Mg calcite deposition. The sharp decline in cover and thickness of coralline algal carbonate deposits at high pCO2 highlighted their lower fitness in response to ocean acidification. Reductions in CO2 emissions are needed to limit the risk of losing coralline algal diversity.
Collapse
Affiliation(s)
- Viviana Peña
- BioCost Research Group, Facultad de Ciencias, Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, A Coruña, Spain
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Ben P Harvey
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
| | - Lucia Porzio
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
| | - Marco Milazzo
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, Palermo, Italy
| | - Paulo Horta
- Laboratory of Phycology, Department of Botany, Center for Biological Sciences, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Line Le Gall
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Jason M Hall-Spencer
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| |
Collapse
|
8
|
Clarkson MO, Lenton TM, Andersen MB, Bagard ML, Dickson AJ, Vance D. Upper limits on the extent of seafloor anoxia during the PETM from uranium isotopes. Nat Commun 2021; 12:399. [PMID: 33452243 PMCID: PMC7810695 DOI: 10.1038/s41467-020-20486-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/04/2020] [Indexed: 11/20/2022] Open
Abstract
The Paleocene Eocene Thermal Maximum (PETM) represents a major carbon cycle and climate perturbation that was associated with ocean de-oxygenation, in a qualitatively similar manner to the more extensive Mesozoic Oceanic Anoxic Events. Although indicators of ocean de-oxygenation are common for the PETM, and linked to biotic turnover, the global extent and temporal progression of de-oxygenation is poorly constrained. Here we present carbonate associated uranium isotope data for the PETM. A lack of resolvable perturbation to the U-cycle during the event suggests a limited expansion of seafloor anoxia on a global scale. We use this result, in conjunction with a biogeochemical model, to set an upper limit on the extent of global seafloor de-oxygenation. The model suggests that the new U isotope data, whilst also being consistent with plausible carbon emission scenarios and observations of carbon cycle recovery, permit a maximum ~10-fold expansion of anoxia, covering <2% of seafloor area. The expansion of oceanic anoxia during the Paleocene Eocene Thermal Maximum has important implications for faunal turnover patterns and global biogeochemical cycles. Here the authors use uranium isotopes and a biogeochemical model to suggest that the areal expansion of anoxia must have been limited to 10-fold.
Collapse
Affiliation(s)
| | - Timothy M Lenton
- Global Systems Institute, University of Exeter, Exeter, EX4 4QE, UK
| | - Morten B Andersen
- School of Earth and Ocean Sciences, University of Cardiff, Cardiff, CF10 3AT, UK
| | - Marie-Laure Bagard
- School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, MK7 6AA, UK.,Department of Earth Science, University of Cambridge, Cambridge, CB2 3EQ, UK
| | - Alexander J Dickson
- Department of Earth Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Derek Vance
- Department of Earth Sciences, ETHZ, 8092, Zurich, Switzerland
| |
Collapse
|