Genomic landscape of the global oak phylogeny
Por:
Hipp, Andrew L., Manos, Paul S., Hahn, Marlene, Avishai, Michael, Bodenes, Catherine, Cavender-Bares, Jeannine, Crowl, Andrew A., Deng, Min, Denk, Thomas, Fitz-Gibbon, Sorel, Gailing, Oliver, Gonzalez-Elizondo, M. Socorro, Gonzalez-Rodriguez, Antonio, Grimm, Guido W., Jiang, Xiao-Long, Kremer, Antoine, Lesur, Isabelle, McVay, John D., Plomion, Christophe, Rodriguez-Correa, Hernando, Schulze, Ernst-Detlef, Simeone, Marco C., Sork, Victoria L., Valencia-Avalos, Susana
Publicada:
1 may 2020
Resumen:
The tree of life is highly reticulate, with the history of population
divergence emerging from populations of gene phylogenies that reflect
histories of introgression, lineage sorting and divergence. In this
study, we investigate global patterns of oak diversity and test the
hypothesis that 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 632 individuals representing nearly 250 Quercus species to
infer a time-calibrated phylogeny of the world's oaks. We use a
reversible-jump Markov chain Monte Carlo method to reconstruct shifts in
lineage diversification rates, accounting for among-clade sampling
biases. We then map the > 20 000 RAD-seq loci back to an annotated 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, probably in response to
climatic transitions or ecological opportunity.
The strong support 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.
Filiaciones:
Hipp, Andrew L.:
Morton Arboretum, Lisle, IL 60532 USA
Field Museum, Chicago, IL 60605 USA
Manos, Paul S.:
Duke Univ, Durham, NC 27708 USA
Hahn, Marlene:
Morton Arboretum, Lisle, IL 60532 USA
Avishai, Michael:
Hebrew Univ Jerusalem, Zalman Shneur St 1, Jerusalem, Israel
Bodenes, Catherine:
INRA, BIOGECO, UMR1202, F-33610 Cestas, France
Cavender-Bares, Jeannine:
Univ Minnesota, Minneapolis, MN 55455 USA
Crowl, Andrew A.:
Duke Univ, Durham, NC 27708 USA
Deng, Min:
Chinese Acad Sci, Shanghai Chenshan Plant Sci Res Ctr, Shanghai 201602, Peoples R China
Denk, Thomas:
Swedish Museum Nat Hist, S-10405 Stockholm, Sweden
Fitz-Gibbon, Sorel:
Univ Calif Los Angeles, Los Angeles, CA 90095 USA
Gailing, Oliver:
Georg August Univ Gottingen, Busgen Inst, D-37077 Gottingen, Germany
Gonzalez-Elizondo, M. Socorro:
Inst Politecn Nacl, CIIDIR Unidad Durango, Durango 34220, Mexico
Gonzalez-Rodriguez, Antonio:
Univ Nacl Autonoma Mexico, Escuela Nacl Estudios Super, Unidad Morelia, Morelia 58190, Michoacan, Mexico
Jiang, Xiao-Long:
Chinese Acad Sci, Shanghai Chenshan Plant Sci Res Ctr, Shanghai 201602, Peoples R China
Kremer, Antoine:
INRA, BIOGECO, UMR1202, F-33610 Cestas, France
Lesur, Isabelle:
INRA, BIOGECO, UMR1202, F-33610 Cestas, France
McVay, John D.:
Duke Univ, Durham, NC 27708 USA
Plomion, Christophe:
INRA, BIOGECO, UMR1202, F-33610 Cestas, France
Rodriguez-Correa, Hernando:
Univ Nacl Autonoma Mexico, Escuela Nacl Estudios Super, Unidad Morelia, Morelia 58190, Michoacan, Mexico
Schulze, Ernst-Detlef:
Max Planck Inst Biogeochem, Hans Knoell Str 10, D-07745 Jena, Germany
Simeone, Marco C.:
Univ Tuscia, I-01100 Viterbo, Italy
Sork, Victoria L.:
Univ Calif Los Angeles, Los Angeles, CA 90095 USA
Valencia-Avalos, Susana:
Univ Nacl Autonoma Mexico, Dept Biol Comparada, Herbario Fac Ciencias, Circuito Exterior S-N,Ciudad Univ, Mexico City 04510, DF, Mexico
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