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Genomic landscape of the global oak phylogeny

View ORCID ProfileAndrew L. Hipp, Paul S. Manos, Marlene Hahn, Michael Avishai, Cathérine Bodénès, Jeannine Cavender-Bares, Andrew Crowl, Min Deng, Thomas Denk, Sorel Fitz-Gibbon, Oliver Gailing, M. Socorro González-Elizondo, Antonio González-Rodríguez, View ORCID ProfileGuido W. Grimm, Xiao-Long Jiang, Antoine Kremer, Isabelle Lesur, John D. McVay, Christophe Plomion, Hernando Rodríguez-Correa, Ernst-Detlef Schulze, Marco C. Simeone, Victoria L. Sork, Susana Valencia-Avalos
doi: https://doi.org/10.1101/587253
Andrew L. Hipp
1The Morton Arboretum, Lisle IL 60532-1293, USA
2The Field Museum, Chicago IL 60605, USA
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  • ORCID record for Andrew L. Hipp
Paul S. Manos
3Duke University, Durham NC 27708, USA
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Marlene Hahn
1The Morton Arboretum, Lisle IL 60532-1293, USA
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Michael Avishai
4Previously of The Hebrew University of Jerusalem, Botanical Garden, Jerusalem, Israel
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Cathérine Bodénès
5INRA, UMR1202 BIOGECO, Cestas F-33610, France
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Jeannine Cavender-Bares
6University of Minnesota, Minneapolis MN 55455, USA
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Andrew Crowl
3Duke University, Durham NC 27708, USA
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Min Deng
7Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602, China
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Thomas Denk
8Swedish Museum of Natural History, 10405 Stockholm, Sweden
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Sorel Fitz-Gibbon
9University of California, Los Angeles, Los Angeles CA 90095, USA
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Oliver Gailing
10Büsgen-Institute, Georg-August-University Göttingen, D-37077 Göttingen, Germany
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M. Socorro González-Elizondo
11CIIDIR Unidad Durango, Instituto Politécnico Nacional, Durango, México
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Antonio González-Rodríguez
12Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México
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Guido W. Grimm
13Unaffiliated, 45100 Orléans, France
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Xiao-Long Jiang
7Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602, China
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Antoine Kremer
5INRA, UMR1202 BIOGECO, Cestas F-33610, France
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Isabelle Lesur
5INRA, UMR1202 BIOGECO, Cestas F-33610, France
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John D. McVay
3Duke University, Durham NC 27708, USA
14Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville FL 32608, USA
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Christophe Plomion
5INRA, UMR1202 BIOGECO, Cestas F-33610, France
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Hernando Rodríguez-Correa
12Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México
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Ernst-Detlef Schulze
15Max Planck Institute for Biogeochemistry, Hans-Knoell-Str. 10, 07745 Jena, Germany
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Marco C. Simeone
16Università degli Studi della Tuscia, Viterbo, Italy
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Victoria L. Sork
9University of California, Los Angeles, Los Angeles CA 90095, USA
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Susana Valencia-Avalos
17Herbario de la Facultad de Ciencias, Departamento de Biología Comparada, Universidad Nacional Autónoma de México, Circuito Exterior, s.n., Ciudad Universitaria, Coyoacán, CP 04510, México City, México
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Summary

  • The tree of life is highly reticulate, with the history of population divergence buried amongst phylogenies deriving from introgression and lineage sorting. In this study, we test the hypothesis that there are regions of the oak (Quercus, Fagaceae) genome that are broadly informative about phylogeny and investigate global patterns of oak diversity.

  • We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing ca. 250 oak species to infer a time-calibrated phylogeny of the world’s oaks. We use reversible-jump MCMC to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20,000 RAD-seq loci back to a recently published oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.

  • Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification due to climatic transitions or ecological opportunity.

  • The support we find for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted March 24, 2019.
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Genomic landscape of the global oak phylogeny
Andrew L. Hipp, Paul S. Manos, Marlene Hahn, Michael Avishai, Cathérine Bodénès, Jeannine Cavender-Bares, Andrew Crowl, Min Deng, Thomas Denk, Sorel Fitz-Gibbon, Oliver Gailing, M. Socorro González-Elizondo, Antonio González-Rodríguez, Guido W. Grimm, Xiao-Long Jiang, Antoine Kremer, Isabelle Lesur, John D. McVay, Christophe Plomion, Hernando Rodríguez-Correa, Ernst-Detlef Schulze, Marco C. Simeone, Victoria L. Sork, Susana Valencia-Avalos
bioRxiv 587253; doi: https://doi.org/10.1101/587253
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Genomic landscape of the global oak phylogeny
Andrew L. Hipp, Paul S. Manos, Marlene Hahn, Michael Avishai, Cathérine Bodénès, Jeannine Cavender-Bares, Andrew Crowl, Min Deng, Thomas Denk, Sorel Fitz-Gibbon, Oliver Gailing, M. Socorro González-Elizondo, Antonio González-Rodríguez, Guido W. Grimm, Xiao-Long Jiang, Antoine Kremer, Isabelle Lesur, John D. McVay, Christophe Plomion, Hernando Rodríguez-Correa, Ernst-Detlef Schulze, Marco C. Simeone, Victoria L. Sork, Susana Valencia-Avalos
bioRxiv 587253; doi: https://doi.org/10.1101/587253

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