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Genomic landscape o...
Genomic landscape of the global oak phylogeny
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- Denk, Thomas (author)
- Naturhistoriska riksmuseet,Enheten för paleobiologi
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- Hipp, Andrew L. (author)
- The Morton Arboretum, Lisle, IL, 60532‐1293 USA & The Field Museum, Chicago
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- Manos, Paul S. (author)
- Duke University, Durham, NC, 27708 USA
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- Hahn, Marlene (author)
- The Morton Arboretum, Lisle, IL, 60532‐1293 USA
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- Avishai, Michael (author)
- The Hebrew University of Jerusalem, Botanical Garden, Zalman Shne'ur St. 1, Jerusalem, Israel
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- Bodénès, Catherine (author)
- INRA, UMR1202 BIOGECO, Cestas, F‐33610 France
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- Cavender-Bares, Jeannine (author)
- University of Minnesota
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- Crowl, Andrew A. (author)
- Duke University, Durham, NC
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- Deng, Min (author)
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences
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Fitz-Gibbon, Sorel (author)
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Gailing, Oliver (author)
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Gonzalez-Elizondo, Antonio (author)
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Grimm, Guido W. (author)
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Jiang, Xiao-Long (author)
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Kremer, Antoine (author)
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Lesur, Isabelle (author)
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McVay, John D. (author)
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Plomion, Christophe (author)
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Rodriguez-Correa, Hernando (author)
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Schulze, Ernst-Detlef (author)
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Simeone, Marco C. (author)
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Sork, Victoria L. (author)
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Valencia-Avalos, Susana (author)
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(creator_code:org_t)
- 2019-10-14
- 2019
- English.
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In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; , s. 1-15
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https://doi.org/10.1...
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Abstract
Subject headings
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- The tree of life is highly reticulate, with the history of population divergence emerging frompopulations of gene phylogenies that reflect histories of introgression, lineage sorting anddivergence. In this study, we investigate global patterns of oak diversity and test the hypothesisthat there are regions of the oak genome that are broadly informative about phylogeny. We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632individuals representing nearly 250 Quercus species to infer a time-calibrated phylogeny ofthe world’s oaks. We use a reversible-jump Markov chain Monte Carlo method to reconstructshifts in lineage diversification rates, accounting for among-clade sampling biases. We thenmap the > 20 000 RAD-seq loci back to an annotated oak genome and investigate genomicdistribution of introgression and phylogenetic support across the phylogeny. Oak lineages have diversified among geographic regions, followed by ecological divergencewithin regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to fourclades that experienced increases in net diversification, probably in response to climatic transitionsor ecological opportunity. The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogeneticsignal and introgression. Oaks are phylogenomic mosaics, and their diversity may infact depend on the gene flow that shapes the oak genome.
Subject headings
- NATURVETENSKAP -- Geovetenskap och miljövetenskap -- Annan geovetenskap och miljövetenskap (hsv//swe)
- NATURAL SCIENCES -- Earth and Related Environmental Sciences -- Other Earth and Related Environmental Sciences (hsv//eng)
- NATURVETENSKAP -- Biologi -- Botanik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Botany (hsv//eng)
- NATURVETENSKAP -- Biologi -- Evolutionsbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Evolutionary Biology (hsv//eng)
Keyword
- diversification rates
- genomic mosaicism
- introgression
- oaks
- phylogenomics
- Quercus
- restriction-site associated DNA sequencing (RAD-seq)
- tree diversity
- Ecosystems and species history
- Ekosystem och arthistoria
- Diversity of life
- The changing Earth
Publication and Content Type
- ref (subject category)
- art (subject category)
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To the university's database
- By the author/editor
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Denk, Thomas
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Hipp, Andrew L.
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Manos, Paul S.
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Hahn, Marlene
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Avishai, Michael
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Bodénès, Catheri ...
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show more...
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Cavender-Bares, ...
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Crowl, Andrew A.
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Deng, Min
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Fitz-Gibbon, Sor ...
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Gailing, Oliver
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Gonzalez-Elizond ...
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Grimm, Guido W.
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Jiang, Xiao-Long
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Kremer, Antoine
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Lesur, Isabelle
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McVay, John D.
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Plomion, Christo ...
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Rodriguez-Correa ...
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Schulze, Ernst-D ...
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Simeone, Marco C ...
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Sork, Victoria L ...
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Valencia-Avalos, ...
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show less...
- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Earth and Relate ...
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and Other Earth and ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Botany
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Evolutionary Bio ...
- Articles in the publication
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New Phytologist
- By the university
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Swedish Museum of Natural History