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Liu Z, Su T, Li Q, Li Z. Spatial distribution pattern of mustelids in the eastern edge of the Qinghai-Tibet Plateau. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240294. [PMID: 39113774 PMCID: PMC11303035 DOI: 10.1098/rsos.240294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/12/2024] [Accepted: 06/24/2024] [Indexed: 08/10/2024]
Abstract
Evolutionary theory predicts that the species of an evolutionarily successful taxon would not overlap in spatial distribution. To test the prediction, we document our research on the spatial associations of mustelids, an evolutionarily successful group of order Carnivore, using infrared camera trap data on species distribution collected from the national nature reserves (NNRs) of Liancheng, Wolong, Tangjiahe and Heizhugou in China in 2017-2021. Data showed seven mustelid species occurring in the study area, including Arctonyx collaris, Meles leucurus, Martes foina, Martes flavigula, Mustela altaica, Mustela nivalis and Mustela sibirica. Following Ricklef's definition of biological community, we identified five networks of species associations. The mustelids occurred in the networks. Species from the same genus, such as M. foina and M. flavigula, stayed in different networks to avoid competition owing to similar feeding habits or habitat preferences. Species with different feeding habits or habitat preferences either occurred in different networks, such as M. altaica and M. flavigula, or coexisted in the same networks but avoided direct spatial associations, such as M. foina and A. collaris. Asymmetrical associations were found between different genera, such as M. foina and M. altaica, or between different subfamilies, such as M. flavigula and A. collaris. These associations may be attributed to interspecific killing or seed dispersal. However, these associations accounted for only a small proportion and would not impact the species diversity of Mustelidae. It is thus concluded that the prediction is supported by our research findings and that spatial avoidance may be the biogeographic strategy of maintaining the species diversity of the family. We also found that the well protection of the mustelids may benefit the overall biodiversity conservation in Heizhugou, an NNR that has experienced severe deforestation.
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Affiliation(s)
- Zhuotao Liu
- Central South University of Forestry and Technology, College of Forestry, Changsha, Hunan410004, People’s Republic of China
- Southwest Forest University, College of Soil and Water Conservation, Kunming, Yunnan650224, People’s Republic of China
| | - Tengwei Su
- Yunnan Forestry Technological College, School of Ecological and Environmental Engineering, Kunming, Yunnan650224, People’s Republic of China
| | - Qian Li
- Dali University, Institute of Eastern-Himalaya Biodiversity Research, Dali, Yunnan671000, People’s Republic of China
| | - Zhaoyuan Li
- Southwest Forest University, College of Soil and Water Conservation, Kunming, Yunnan650224, People’s Republic of China
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2
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Gusmão RAF, Tessarolo G, Dobrovolski R, Gonçalves‐Souza T. Body size and trophic structure explain global asymmetric response of tetrapod diversity to climate effects. Ecol Evol 2024; 14:e11047. [PMID: 38380066 PMCID: PMC10877556 DOI: 10.1002/ece3.11047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/22/2024] Open
Abstract
Although climate-based hypotheses are widely used to explain large-scale diversity patterns, they fall short of explaining the spatial variation among taxonomic groups. Integrating food web and metabolic theories into macroecology is a promising step forward, as they allow including explicit taxon-specific traits that can potentially mediate the relationship between climate and diversity. Our investigation focuses on the role of body size and trophic structure in mediating the influence of contemporary climate and historical climate change on global tetrapods species richness. We used piecewise structural equation modeling to assess the direct effects of contemporary climate and climate instability of species richness and the indirect effects of climate on tetrapod richness mediated by community-wide species traits. We found that birds and mammals are less sensitive to the direct effect of contemporary climate than amphibians and squamates. Contemporary climate and climate instability favored the species richness of mammals and amphibians. However, for birds and squamates, this link is only associated with contemporary climate. Moreover, we showed that community-wide traits are correlated with species richness gradients. However, we highlight that this relationship is dependent upon the specific traits and taxonomic groups. Specifically, bird communities with smaller bodies and bottom-heavy structures support higher species richness. Squamates also tend to be more diverse in communities with prevalence of smaller bodies, while mammals are correlated with top-heavy structures. Moreover, we showed that higher contemporary climate and climate instability reduce the species richness of birds and mammals through community-wide traits and indirectly increase squamate species richness. We also showed that body size and trophic structure are driving a global asymmetric response of tetrapod diversity to climate effects, which highlights the limitation to use the "typical" climate-based hypotheses. Furthermore, by combining multiple theories, our research contributes to a more realistic and mechanistic understanding of diversity patterns across taxonomic groups.
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Affiliation(s)
- Reginaldo A. F. Gusmão
- Graduate Program in Ethnobiology and Nature Conservation, Department of BiologyFederal Rural University of PernambucoRecifeBrazil
| | - Geiziane Tessarolo
- Laboratory of Biogeography and Aquatic EcologyState University of GoiásAnápolisBrazil
| | | | - Thiago Gonçalves‐Souza
- Graduate Program in Ethnobiology and Nature Conservation, Department of BiologyFederal Rural University of PernambucoRecifeBrazil
- Institute for Global Change Biology, School for Environment and SustainabilityUniversity of MichiganAnn ArborMichiganUSA
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichiganUSA
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3
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García-Andrade AB, Tedesco PA, Carvajal-Quintero JD, Arango A, Villalobos F. Same process, different patterns: pervasive effect of evolutionary time on species richness in freshwater fishes. Proc Biol Sci 2023; 290:20231066. [PMID: 37700646 PMCID: PMC10498035 DOI: 10.1098/rspb.2023.1066] [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: 05/12/2023] [Accepted: 08/18/2023] [Indexed: 09/14/2023] Open
Abstract
Tropical lands harbour the highest number of species, resulting in the ubiquitous latitudinal diversity gradient (LDG). However, exceptions to this pattern have been observed in some taxa, explained by the interaction between the evolutionary histories and environmental factors that constrain species' physiological and ecological requirements. Here, we applied a deconstruction approach to map the detailed species richness patterns of Actinopterygian freshwater fishes at the class and order levels and to disentangle their drivers using geographical ranges and a phylogeny, comprising 77% (12 557) of all described species. We jointly evaluated seven evolutionary and ecological hypotheses posited to explain the LDG: diversification rate, time for speciation, species-area relationship, environmental heterogeneity, energy, temperature seasonality and past temperature stability. We found distinct diversity gradients across orders, including expected, bimodal and inverse LDGs. Despite these differences, the positive effect of evolutionary time explained patterns for all orders, where species-rich regions are inhabited by older species compared to species-poor regions. Overall, the LDG of each order has been shaped by a unique combination of factors, highlighting the importance of performing a joint evaluation of evolutionary, historical and ecological factors at different taxonomic levels to reach a comprehensive understanding on the causes driving global species richness patterns.
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Affiliation(s)
- Ana Berenice García-Andrade
- Laboratorio de Macroecología Evolutiva, Red de Biología Evolutiva, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, El Haya, 91070 Xalapa, Veracruz, México
| | - Pablo A. Tedesco
- UMR 5174 EDB—Evolution & Diversité Biologique, Institut de Recherche pour le Développement, Université Paul Sabatier - Bat. 4R1, 118 route de Narbonne, 31062 Toulouse cedex 4, France
| | - Juan D. Carvajal-Quintero
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, D-04103 Leipzig, Germany
| | - Axel Arango
- Laboratorio de Macroecología Evolutiva, Red de Biología Evolutiva, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, El Haya, 91070 Xalapa, Veracruz, México
| | - Fabricio Villalobos
- Laboratorio de Macroecología Evolutiva, Red de Biología Evolutiva, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, El Haya, 91070 Xalapa, Veracruz, México
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4
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Imfeld TS, Barker FK. Songbirds of the Americas show uniform morphological evolution despite heterogeneous diversification. J Evol Biol 2022; 35:1335-1351. [PMID: 36057939 DOI: 10.1111/jeb.14084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 06/17/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022]
Abstract
Studying the relationship between diversification and functional trait evolution among broadly co-occurring clades can shed light on interactions between ecology and evolutionary history. However, evidence from many studies is compromised because of their focus on overly broad geographic or narrow phylogenetic scales. We addressed these limitations by studying 46 independent, biogeographically delimited clades of songbirds that dispersed from the Eastern Hemisphere into the Americas and assessed (1) whether diversification has varied through time and/or among clades within this assemblage, (2) the extent of heterogeneity in clade-specific morphological trait disparity and (3) whether morphological disparity among these clades is consistent with a uniform diversification model. We found equivalent support for constant rates birth-death and density-dependent speciation processes, with notable outliers having significantly fewer or more species than expected given their age. We also found substantial variation in morphological disparity among these clades, but that variation was broadly consistent with uniform evolutionary rates, despite the existence of diversification outliers. These findings indicate relatively continuous, ongoing morphological diversification, arguing against conceptual models of adaptive radiation in these continental clades. Additionally, they suggest surprisingly consistent diversification among the majority of these clades, despite tremendous variance in colonization history, habitat valences and trophic specializations that exist among continental clades of birds.
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Affiliation(s)
- Tyler S Imfeld
- Department of Biology, Regis University, Denver, Colorado, USA
| | - F Keith Barker
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA.,Bell Museum, University of Minnesota, St. Paul, Minnesota, USA
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5
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Ritchie AM, Hua X, Bromham L. Diversification Rate is Associated with Rate of Molecular Evolution in Ray-Finned Fish (Actinopterygii). J Mol Evol 2022; 90:200-214. [PMID: 35262772 PMCID: PMC8975766 DOI: 10.1007/s00239-022-10052-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 02/24/2022] [Indexed: 10/27/2022]
Abstract
Understanding the factors that drive diversification of taxa across the tree of life is a key focus of macroevolutionary research. While the effects of life history, ecology, climate and geography on diversity have been studied for many taxa, the relationship between molecular evolution and diversification has received less attention. However, correlations between rates of molecular evolution and diversification rate have been detected in a range of taxa, including reptiles, plants and birds. A correlation between rates of molecular evolution and diversification rate is a prediction of several evolutionary theories, including the evolutionary speed hypothesis which links variation in mutation rates to differences in speciation rates. If it is widespread, such correlations could also have significant practical impacts, if they are not adequately accounted for in phylogenetic inference of evolutionary rates and timescales. Ray-finned fish (Actinopterygii) offer a prime target to test for this relationship due to their extreme variation in clade size suggesting a wide range of diversification rates. We employ both a sister-pairs approach and a whole-tree approach to test for correlations between substitution rate and net diversification. We also collect life history and ecological trait data and account for potential confounding factors including body size, latitude, max depth and reef association. We find evidence to support a relationship between diversification and synonymous rates of nuclear evolution across two published backbone phylogenies, as well as weak evidence for a relationship between mitochondrial nonsynonymous rates and diversification at the genus level.
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Affiliation(s)
- Andrew M Ritchie
- Research School of Biological Sciences, Australian National University, Canberra, ACT 2600, Australia. .,Research School of Biological Sciences, Australian National University, Robertson Building, 134 Linnaeus Way, Canberra, ACT 2600, Australia.
| | - Xia Hua
- Research School of Biological Sciences, Australian National University, Canberra, ACT 2600, Australia.,Mathematical Sciences Institute, Australian National University, Canberra, ACT 2600, Australia
| | - Lindell Bromham
- Research School of Biological Sciences, Australian National University, Canberra, ACT 2600, Australia
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6
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Benton MJ, Wilf P, Sauquet H. The Angiosperm Terrestrial Revolution and the origins of modern biodiversity. THE NEW PHYTOLOGIST 2022; 233:2017-2035. [PMID: 34699613 DOI: 10.1111/nph.17822] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Biodiversity today has the unusual property that 85% of plant and animal species live on land rather than in the sea, and half of these live in tropical rainforests. An explosive boost to terrestrial diversity occurred from c. 100-50 million years ago, the Late Cretaceous and early Palaeogene. During this interval, the Earth-life system on land was reset, and the biosphere expanded to a new level of productivity, enhancing the capacity and species diversity of terrestrial environments. This boost in terrestrial biodiversity coincided with innovations in flowering plant biology and evolutionary ecology, including their flowers and efficiencies in reproduction; coevolution with animals, especially pollinators and herbivores; photosynthetic capacities; adaptability; and ability to modify habitats. The rise of angiosperms triggered a macroecological revolution on land and drove modern biodiversity in a secular, prolonged shift to new, high levels, a series of processes we name here the Angiosperm Terrestrial Revolution.
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Affiliation(s)
- Michael J Benton
- School of Earth Sciences, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Peter Wilf
- Department of Geosciences and Earth and Environmental Systems Institute, Pennsylvania State University, University Park, PA, 16802, USA
| | - Hervé Sauquet
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, NSW, 2000, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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7
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Qian H, Leprieur F, Jin Y, Wang X, Deng T. Influence of phylogenetic scale on the relationships of taxonomic and phylogenetic turnovers with environment for angiosperms in China. Ecol Evol 2022; 12:e8544. [PMID: 35154648 PMCID: PMC8821769 DOI: 10.1002/ece3.8544] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/16/2021] [Accepted: 12/26/2021] [Indexed: 11/06/2022] Open
Abstract
We aim to assess the influence of phylogenetic scale on the relationships of taxonomic and phylogenetic turnovers with environment for angiosperms in China. Specifically, we quantify the effects of contemporary climate on β-diversity at different phylogenetic scales representing different evolutionary depths of angiosperms. We sampled a latitudinal gradient and a longitudinal gradient of angiosperm assemblages across China (each ≥3400 km). Species composition in each assemblage was documented. Three metrics of β-diversity (βsim.tax measuring taxonomic β-diversity; βsim.phy and Dpw measuring tip- and basal-weighted phylogenetic β-diversity, respectively) were quantified among assemblages at sequential depths in the evolutionary history of angiosperms from the tips to deeper branches. This was done by slicing the angiosperm phylogenetic tree at six evolutionary depths (0, 15, 30, 45, 60, and 75 million years ago). β-diversity at each evolutionary depth was related to geographic and climatic distances between assemblages. In general, the relationship between β-diversity and climatic distance decreased from shallow to deep evolutionary time slice for all the three metrics. The slopes of the decreasing trends for βsim.tax and βsim.phy were much steeper for the latitudinal gradient than for the longitudinal gradient. The decreasing trend of the strength of the relationship was monotonic in all cases except for Dpw across the longitudinal gradient. Geographic distance between assemblages explained little variation in β-diversity that was not explained by climatic distance. Our study shows that the strength of the relationship between β-diversity and climatic distance decreases conspicuously from shallow to deep evolutionary depth for the latitudinal gradient, but this decreasing trend is less steep for the longitudinal gradient than for the latitudinal gradient, which likely reflects the influence of historical processes (e.g., the collision of the Indian plate with the Eurasian plate) on β-diversity.
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Affiliation(s)
- Hong Qian
- Research and Collections CenterIllinois State MuseumSpringfieldIllinoisUSA
| | - Fabien Leprieur
- MARBECUniversité de MontpellierCNRSIfremerIRDMontpellierFrance
- Institut Universitaire de France (IUF)ParisFrance
| | - Yi Jin
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern ChinaGuizhou Normal UniversityGuiyangChina
| | - Xianli Wang
- Natural Resources CanadaCanadian Forest ServiceNorthern Forestry CentreEdmontonABCanada
| | - Tao Deng
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
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8
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Barreto E, Rangel TF, Coelho MTP, Cassemiro FAS, Zimmermann NE, Graham CH. Spatial variation in direct and indirect effects of climate and productivity on species richness of terrestrial tetrapods. GLOBAL ECOLOGY AND BIOGEOGRAPHY : A JOURNAL OF MACROECOLOGY 2021; 30:1899-1908. [PMID: 34588924 PMCID: PMC8457120 DOI: 10.1111/geb.13357] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 06/04/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
AIM We aimed to dissect the spatial variation of the direct and indirect effects of climate and productivity on global species richness of terrestrial tetrapods. LOCATION Global. TIME PERIOD Present. MAJOR TAXA STUDIED Terrestrial tetrapods. METHODS We used a geographically weighted path analysis to estimate and map the direct and indirect effects of temperature, precipitation and primary productivity on species richness of terrestrial tetrapods across the globe. RESULTS We found that all relationships shift in magnitude, and even in direction, among taxonomic groups, geographical regions and connecting paths. Direct effects of temperature and precipitation are generally stronger than both indirect effects mediated by productivity and direct effects of productivity. MAIN CONCLUSIONS Richness gradients seem to be driven primarily by effects of climate on organismal physiological limits and metabolic rates rather than by the amount of productive energy. Reptiles have the most distinct relationships across tetrapods, with a clear latitudinal pattern in the importance of temperature versus water.
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Affiliation(s)
- Elisa Barreto
- Programa de pós‐graduação em Ecologia e EvoluçãoUniversidade Federal de GoiásGoiâniaBrazil
- Swiss Federal Institute for Forest, Snow and LandscapeBirmensdorfSwitzerland
| | - Thiago F. Rangel
- Swiss Federal Institute for Forest, Snow and LandscapeBirmensdorfSwitzerland
- Departamento de EcologiaUniversidade Federal de GoiásGoiâniaBrazil
| | - Marco Túlio P. Coelho
- Programa de pós‐graduação em Ecologia e EvoluçãoUniversidade Federal de GoiásGoiâniaBrazil
| | - Fernanda A. S. Cassemiro
- Swiss Federal Institute for Forest, Snow and LandscapeBirmensdorfSwitzerland
- Departamento de EcologiaUniversidade Federal de GoiásGoiâniaBrazil
| | | | - Catherine H. Graham
- Swiss Federal Institute for Forest, Snow and LandscapeBirmensdorfSwitzerland
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Machac A. The Dynamics of Bird Diversity in the New World. Syst Biol 2021; 69:1180-1199. [PMID: 32333771 PMCID: PMC7584135 DOI: 10.1093/sysbio/syaa028] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 03/12/2020] [Accepted: 03/30/2020] [Indexed: 12/14/2022] Open
Abstract
Three prominent explanations have been proposed to explain the dramatic differences in species richness across regions and elevations, (i) time for speciation, (ii) diversification rates, and (iii) ecological limits. But the relative importance of these explanations and, especially, their interplay and possible synthesis remain largely elusive. Integrating diversification analyses, null models, and geographic information systems, I study avian richness across regions and elevations of the New World. My results reveal that even though the three explanations are differentially important (with ecological limits playing the dominant role), each contributes uniquely to the formation of richness gradients. Further, my results reveal the likely interplay between the explanations. They indicate that ecological limits hinder the diversification process, such that the accumulation of species within a region gradually slows down over time. Yet, it does not seem to converge toward a hard ceiling on regional richness. Instead, species-rich regions show suppressed, but continued, diversification, coupled with signatures of possible competition (esp. Neotropical lowlands). Conversely, species-poor, newly-colonized regions show fast diversification and weak to no signs of competition (esp. Nearctic highlands). These results held across five families of birds, across grid cells, biomes, and elevations. Together, my findings begin to illuminate the rich, yet highly consistent, interplay of the mechanisms that together shape richness gradients in the New World, including the most species-rich biodiversity hotspots on the planet, the Andes and the Amazon. [Biogeography; community; competition; macroevolution; phylogenetics; richness gradient.]
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Affiliation(s)
- Antonin Machac
- Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver V6T 1Z4, Canada.,Center for Theoretical Study, Charles University, Jilska 1, 110 00 Praha 1, Czech Republic.,Department of Ecology, Charles University, Vinicna 7, 12844 Praha 2, Czech Republic.,Center for Macroecology, Evolution and Climate, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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10
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Abstract
Closed-canopy rainforests are important for climate and ecology, yet identifying this ecosystem in the fossil record is challenging. An existing paradigm for identification of closed-canopy rainforests using fossil mammal carbon isotope data is the presence of highly negative δ13Cdiet values (<−31‰) in the herbivore community, as observed in modern equatorial African rainforest ecosystems. Our data from western Amazonian mammals, however, show that the absence of these values is not evidence for absence of closed-canopy rainforests. Our results also document that the proposed relationship between carbon isotope spacing variables and traditional dietary ecological classifications is not straightforward, and that better characterizations of the mixture of nutrients in animal diets are necessary to fully understand diet-tissue isotopic fractionation patterns. Closed-canopy rainforests are important for climate (influencing atmospheric circulation, albedo, carbon storage, etc.) and ecology (harboring the highest biodiversity of continental regions). Of all rainforests, Amazonia is the world’s most diverse, including the highest mammalian species richness. However, little is known about niche structure, ecological roles, and food resource partitioning of Amazonian mammalian communities over time. Through analyses of δ13Cbioapatite, δ13Chair, and δ15Nhair, we isotopically characterized aspects of feeding ecology in a modern western Amazonian mammalian community in Peru, serving as a baseline for understanding the evolution of Neotropical rainforest ecosystems. By comparing these results with data from equatorial Africa, we evaluated the potential influences of distinct phylogenetic and biogeographic histories on the isotopic niches occupied by mammals in analogous tropical ecosystems. Our results indicate that, despite their geographical and taxonomic differences, median δ13Cdiet values from closed-canopy rainforests in Amazonia (−27.4‰) and equatorial Africa (−26.9‰) are not significantly different, and that the median δ13Cdiet expected for mammalian herbivores in any closed-canopy rainforest is −27.2‰. Amazonian mammals seem to exploit a narrower spectrum of dietary resources than equatorial African mammals, however, as depicted by the absence of highly negative δ13Cdiet values previously proposed as indicative of rainforests (<−31‰). Finally, results of keratin and bioapatite δ13C indicate that the predictive power of trophic relationships, and traditional dietary ecological classifications in bioapatite-protein isotopic offset expectations, must be reconsidered.
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Huang XC, German DA, Koch MA. Temporal patterns of diversification in Brassicaceae demonstrate decoupling of rate shifts and mesopolyploidization events. ANNALS OF BOTANY 2020; 125:29-47. [PMID: 31314080 PMCID: PMC6948214 DOI: 10.1093/aob/mcz123] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/16/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Whole-genome duplication (WGD) events are considered important driving forces of diversification. At least 11 out of 52 Brassicaceae tribes had independent mesopolyploid WGDs followed by diploidization processes. However, the association between mesopolyploidy and subsequent diversification is equivocal. Herein we show the results from a family-wide diversification analysis on Brassicaceae, and elaborate on the hypothesis that polyploidization per se is a fundamental driver in Brassicaceae evolution. METHODS We established a time-calibrated chronogram based on whole plastid genomes comprising representative Brassicaceae taxa and published data spanning the entire Rosidae clade. This allowed us to set multiple calibration points and anchored various Brassicaceae taxa for subsequent downstream analyses. All major splits among Brassicaceae lineages were used in BEAST analyses of 48 individually analysed tribes comprising 2101 taxa in total using the internal transcribed spacers of nuclear ribosomal DNA. Diversification patterns were investigated on these tribe-wide chronograms using BAMM and were compared with family-wide data on genome size variation and species richness. KEY RESULTS Brassicaceae diverged 29.9 million years ago (Mya) during the Oligocene, and the majority of tribes started diversification in the Miocene with an average crown group age of about 12.5 Mya. This matches the cooling phase right after the Mid Miocene climatic optimum. Significant rate shifts were detected in 12 out of 52 tribes during the Mio- and Pliocene, decoupled from preceding mesopolyploid WGDs. Among the various factors analysed, the combined effect of tribal crown group age and net diversification rate (speciation minus extinction) is likely to explain sufficiently species richness across Brassicaceae tribes. CONCLUSIONS The onset of the evolutionary splits among tribes took place under cooler and drier conditions. Pleistocene glacial cycles may have contributed to the maintenance of high diversification rates. Rate shifts are not consistently associated with mesopolyploid WGD. We propose, therefore, that WGDs in general serve as a constant 'pump' for continuous and high species diversification.
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Affiliation(s)
- Xiao-Chen Huang
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
| | - Dmitry A German
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
- For correspondence. E-mail
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12
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Upham NS, Esselstyn JA, Jetz W. Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLoS Biol 2019; 17:e3000494. [PMID: 31800571 PMCID: PMC6892540 DOI: 10.1371/journal.pbio.3000494] [Citation(s) in RCA: 496] [Impact Index Per Article: 99.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/24/2019] [Indexed: 12/18/2022] Open
Abstract
Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our "backbone-and-patch" approach to tree building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (1) backbone relationships and ages among major lineages, using fossil node or tip dating, and (2) species-level "patch" phylogenies with nonoverlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ("DNA-only" trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ("completed" trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (1) node ages are broadly concordant among studies, and (2) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous "supertree" approaches, in which unresolved nodes led to branch-length artifacts. Credible sets of mammalian phylogenetic history are now available for download at http://vertlife.org/phylosubsets, enabling investigations of long-standing questions in comparative biology.
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Affiliation(s)
- Nathan S. Upham
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity & Global Change, Yale University, New Haven, Connecticut, United States of America
| | - Jacob A. Esselstyn
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Walter Jetz
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity & Global Change, Yale University, New Haven, Connecticut, United States of America
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13
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Garcia-Porta J, Irisarri I, Kirchner M, Rodríguez A, Kirchhof S, Brown JL, MacLeod A, Turner AP, Ahmadzadeh F, Albaladejo G, Crnobrnja-Isailovic J, De la Riva I, Fawzi A, Galán P, Göçmen B, Harris DJ, Jiménez-Robles O, Joger U, Jovanović Glavaš O, Karış M, Koziel G, Künzel S, Lyra M, Miles D, Nogales M, Oğuz MA, Pafilis P, Rancilhac L, Rodríguez N, Rodríguez Concepción B, Sanchez E, Salvi D, Slimani T, S'khifa A, Qashqaei AT, Žagar A, Lemmon A, Moriarty Lemmon E, Carretero MA, Carranza S, Philippe H, Sinervo B, Müller J, Vences M, Wollenberg Valero KC. Environmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards. Nat Commun 2019; 10:4077. [PMID: 31501432 PMCID: PMC6733905 DOI: 10.1038/s41467-019-11943-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 08/13/2019] [Indexed: 11/09/2022] Open
Abstract
Climatic conditions changing over time and space shape the evolution of organisms at multiple levels, including temperate lizards in the family Lacertidae. Here we reconstruct a dated phylogenetic tree of 262 lacertid species based on a supermatrix relying on novel phylogenomic datasets and fossil calibrations. Diversification of lacertids was accompanied by an increasing disparity among occupied bioclimatic niches, especially in the last 10 Ma, during a period of progressive global cooling. Temperate species also underwent a genome-wide slowdown in molecular substitution rates compared to tropical and desert-adapted lacertids. Evaporative water loss and preferred temperature are correlated with bioclimatic parameters, indicating physiological adaptations to climate. Tropical, but also some populations of cool-adapted species experience maximum temperatures close to their preferred temperatures. We hypothesize these species-specific physiological preferences may constitute a handicap to prevail under rapid global warming, and contribute to explaining local lizard extinctions in cool and humid climates.
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Affiliation(s)
- Joan Garcia-Porta
- CREAF, 08193, Cerdanyola del Vallès, Spain
- Department of Biology, Washington University in Saint Louis, St. Louis, MO, 63130, USA
| | - Iker Irisarri
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Martin Kirchner
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Ariel Rodríguez
- Institute of Zoology, Tierärztliche Hochschule Hannover, Bünteweg 17, 30559, Hannover, Germany
| | - Sebastian Kirchhof
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Jason L Brown
- Department of Zoology, Southern Illinois University, Carbondale, IL, USA
| | - Amy MacLeod
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Alexander P Turner
- School of Engineering and Computer Science, University of Hull, Cottingham Road, HU6 7RX, Kingston-Upon-Hull, UK
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C, Tehran, Iran
| | - Gonzalo Albaladejo
- Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas (CSIC), c/Astrofísico Francisco Sánchez, 38206, Tenerife, Canary Islands, Spain
| | - Jelka Crnobrnja-Isailovic
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000 Niš, Institute for Biological Research "S. Stanković" University of Belgrade, Despota Stefana 142, Belgrade, 11000, Serbia
| | - Ignacio De la Riva
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, C/José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Adnane Fawzi
- Faculty of Sciences, Biodiversity and Ecosystem Dynamics Laboratory, Cadi Ayyad University, Marrakech, Morocco
| | - Pedro Galán
- Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, Grupo de Investigación en Biología Evolutiva (GIBE), 15071, A Coruña, Spain
| | - Bayram Göçmen
- Zoology Section, Biology Department, Faculty of Science, Ege University, 35100, Bornova, Izmir, Turkey
| | - D James Harris
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Octavio Jiménez-Robles
- Department of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Ulrich Joger
- Staatliches Naturhistorisches Museum, Braunschweig, Germany
| | | | - Mert Karış
- Department of Chemistry and Chemical Process Technologies, Acıgöl Vocational High School of Technical Sciences, Nevşehir Hacı Bektaş Veli University, 50300, Nevşehir, Turkey
| | - Giannina Koziel
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106, Braunschweig, Germany
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Mariana Lyra
- Departamento de Zoologia, Instituto de Biociências, UNESP - Universidade Estadual Paulista, Rio Claro, Brazil
| | - Donald Miles
- Department of Biological Sciences, Ohio University, Athens, OH, 45701, USA
| | - Manuel Nogales
- Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas (CSIC), c/Astrofísico Francisco Sánchez, 38206, Tenerife, Canary Islands, Spain
| | - Mehmet Anıl Oğuz
- Zoology Section, Biology Department, Faculty of Science, Ege University, 35100, Bornova, Izmir, Turkey
| | - Panayiotis Pafilis
- Section of Zoology and Marine Biology, Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Ilissia, Athens, 157-84, Greece
| | - Loïs Rancilhac
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106, Braunschweig, Germany
| | - Noemí Rodríguez
- Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas (CSIC), c/Astrofísico Francisco Sánchez, 38206, Tenerife, Canary Islands, Spain
| | - Benza Rodríguez Concepción
- Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas (CSIC), c/Astrofísico Francisco Sánchez, 38206, Tenerife, Canary Islands, Spain
| | - Eugenia Sanchez
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106, Braunschweig, Germany
| | - Daniele Salvi
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Department of Health, Life and Environmental Sciences, University of L'Aquila, 67100, Coppito, L'Aquila, Italy
| | - Tahar Slimani
- Faculty of Sciences, Biodiversity and Ecosystem Dynamics Laboratory, Cadi Ayyad University, Marrakech, Morocco
| | - Abderrahim S'khifa
- Faculty of Sciences, Biodiversity and Ecosystem Dynamics Laboratory, Cadi Ayyad University, Marrakech, Morocco
| | - Ali Turk Qashqaei
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C, Tehran, Iran
| | - Anamarija Žagar
- National Institute of Biology NIB, Department of Organisms and Ecosystems Research, Vecna pot 111, 1000, Ljubljana, Slovenia
| | - Alan Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, USA
| | | | - Miguel Angel Carretero
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat, Pompeu Fabra), Passeig Marítim de la Barceloneta 37-,49, 08003, Barcelona, Spain
| | - Hervé Philippe
- Centre for Biodiversity Theory and Modelling, UMR CNRS 5321, Station of Theoretical and Experimental Ecology, 09200, Moulis, France
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, and Institute for the Study of the Ecological and Evolutionary Climate Impacts, University of California, 130 McAllister Way, Coastal Biology Building, Santa Cruz, CA, 95064, USA
| | - Johannes Müller
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Miguel Vences
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106, Braunschweig, Germany.
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14
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Pontarp M, Bunnefeld L, Cabral JS, Etienne RS, Fritz SA, Gillespie R, Graham CH, Hagen O, Hartig F, Huang S, Jansson R, Maliet O, Münkemüller T, Pellissier L, Rangel TF, Storch D, Wiegand T, Hurlbert AH. The Latitudinal Diversity Gradient: Novel Understanding through Mechanistic Eco-evolutionary Models. Trends Ecol Evol 2018; 34:211-223. [PMID: 30591209 DOI: 10.1016/j.tree.2018.11.009] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/13/2018] [Accepted: 11/22/2018] [Indexed: 11/19/2022]
Abstract
The latitudinal diversity gradient (LDG) is one of the most widely studied patterns in ecology, yet no consensus has been reached about its underlying causes. We argue that the reasons for this are the verbal nature of existing hypotheses, the failure to mechanistically link interacting ecological and evolutionary processes to the LDG, and the fact that empirical patterns are often consistent with multiple explanations. To address this issue, we synthesize current LDG hypotheses, uncovering their eco-evolutionary mechanisms, hidden assumptions, and commonalities. Furthermore, we propose mechanistic eco-evolutionary modeling and an inferential approach that makes use of geographic, phylogenetic, and trait-based patterns to assess the relative importance of different processes for generating the LDG.
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Affiliation(s)
- Mikael Pontarp
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Lynsey Bunnefeld
- Biological & Environmental Sciences, University of Stirling, Stirling FK9 4LA, Scotland
| | - Juliano Sarmento Cabral
- Ecosystem Modeling, Center for Computational and Theoretical Biology (CCTB), University of Würzburg, Emil-Fischer-Str. 32, 97074 Würzburg, Germany
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, The Netherlands
| | - Susanne A Fritz
- Senckenberg Biodiversity and Climate Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, D-60325 Frankfurt, Germany; Institute of Ecology, Evolution and Diversity, Goethe-University, D-60438 Frankfurt, Germany
| | - Rosemary Gillespie
- Environmental Science, 130 Mulford Hall, University of California, Berkeley, CA 94720, USA
| | | | - Oskar Hagen
- Swiss Federal Research Institute WSL, CH-8903 Birmensdorf, Switzerland; Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, CH-8092 Zürich, Switzerland
| | - Florian Hartig
- Theoretical Ecology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Shan Huang
- Senckenberg Biodiversity Research Centre, Senckenberganlage 25, 60327, Frankfurt am Main, Germany
| | - Roland Jansson
- Department of Ecology and Environmental Science, Umeå University, 901 87 Umeå, Sweden
| | - Odile Maliet
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Tamara Münkemüller
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, CNRS, LECA, Laboratoire d'ÉcologieAlpine, F-38000 Grenoble, France
| | - Loïc Pellissier
- Swiss Federal Research Institute WSL, CH-8903 Birmensdorf, Switzerland; Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, CH-8092 Zürich, Switzerland
| | - Thiago F Rangel
- Department of Ecology, Federal University of Goiás, Campus Samambaia, Goiânia GO, 74690-900, Brazil
| | - David Storch
- Center for Theoretical Study, Charles University and Czech Academy of Sciences, Jilská 1, 110 00 Praha 1, Czech Republic; Department of Ecology, Faculty of Science, Charles University, Viničná 7, 128 44 Praha 2, Czech Republic
| | - Thorsten Wiegand
- Department of Ecological Modeling, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Allen H Hurlbert
- Department of Biology and Curriculum in Environment and Ecology, University of North Carolina, Chapel Hill, NC 27599, USA
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