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Exploring the phylogeny of rosids with a five-locus supermatrix from GenBank

View ORCID ProfileMiao Sun, Ryan A. Folk, Matthew A. Gitzendanner, Stephen A. Smith, Charlotte Germain-Aubrey, Robert P. Guralnick, Pamela S. Soltis, Douglas E. Soltis, Zhiduan Chen
doi: https://doi.org/10.1101/694950
Miao Sun
Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USADepartment of Biology, University of Florida, Gainesville, FL 32611, USAState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
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  • For correspondence: cactusresponsible@gmail.com zhiduan@ibcas.ac.cn
Ryan A. Folk
Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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Matthew A. Gitzendanner
Department of Biology, University of Florida, Gainesville, FL 32611, USABiodiversity Institute, University of Florida, Gainesville, FL 32611, USA
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Stephen A. Smith
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Charlotte Germain-Aubrey
Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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Robert P. Guralnick
Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USABiodiversity Institute, University of Florida, Gainesville, FL 32611, USA
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Pamela S. Soltis
Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USAGenetics Institute, University of Florida, Gainesville, FL 32608, USABiodiversity Institute, University of Florida, Gainesville, FL 32611, USA
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Douglas E. Soltis
Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USADepartment of Biology, University of Florida, Gainesville, FL 32611, USAGenetics Institute, University of Florida, Gainesville, FL 32608, USABiodiversity Institute, University of Florida, Gainesville, FL 32611, USA
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Zhiduan Chen
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
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  • For correspondence: cactusresponsible@gmail.com zhiduan@ibcas.ac.cn
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Abstract

Current advances in sequencing technology have greatly increased the availability of sequence data from public genetic databases. With data from GenBank, we assemble and phylogenetically investigate a 19,740-taxon, five-locus supermatrix (i.e., atpB, rbcL, matK, matR, and ITS) for rosids, a large clade containing over 90,000 species, or approximately a quarter of all angiosperms (assuming an estimate of 400,000 angiosperm species). The topology and divergence times of the five-locus tree generally agree with previous estimates of rosid phylogeny, and we recover greater resolution and support in several areas along the rosid backbone, but with a few significant differences (e.g., the placement of the COM clade, as well as Myrtales, Vitales, and Zygophyllales). Our five-locus phylogeny is the most comprehensive DNA data set yet compiled for the rosid clade. Yet, even with 19,740 species, current sampling represents only 16-22% of all rosids, and we also find evidence of strong phylogenetic bias in the accumulation of GenBank data, highlighting continued challenges for species coverage. These limitations also exist in other major angiosperm clades (e.g., asterids, monocots) as well as other large, understudied branches of the Tree of Life, highlighting the need for broader molecular sampling. Nevertheless, the phylogeny presented here improves upon sampling by more than two-fold and will be an important resource for macroevolutionary studies of this pivotal clade.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 08, 2019.
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Exploring the phylogeny of rosids with a five-locus supermatrix from GenBank
Miao Sun, Ryan A. Folk, Matthew A. Gitzendanner, Stephen A. Smith, Charlotte Germain-Aubrey, Robert P. Guralnick, Pamela S. Soltis, Douglas E. Soltis, Zhiduan Chen
bioRxiv 694950; doi: https://doi.org/10.1101/694950
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Exploring the phylogeny of rosids with a five-locus supermatrix from GenBank
Miao Sun, Ryan A. Folk, Matthew A. Gitzendanner, Stephen A. Smith, Charlotte Germain-Aubrey, Robert P. Guralnick, Pamela S. Soltis, Douglas E. Soltis, Zhiduan Chen
bioRxiv 694950; doi: https://doi.org/10.1101/694950

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