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Sun, Miao [1], Germain-Aubrey, Charlotte [2], Gitzendanner, Matthew [3], Smith, Stephen [4], Soltis, Pamela  S. [5], Chen, Zhiduan [6], Soltis, Douglas [7].

Wrestling with the Rosids I: progress and challenges for phylogenetics of a large, hyper-diverse angiosperm clade.

Perhaps no major clade of angiosperms holds more potential for detailed evolutionary study than the rosids, an enormous clade of ~87,500 species, representing approximately 25% of all angiosperms and exhibiting tremendous overall diversity in morphology, habit, reproductive strategy, and life history. However, our knowledge of this clade is remarkably limited along any metric. We have found that only 29,677 species (34%) have DNA sequences in GenBank that are usable for phylogenetic analysis. Using the PHLAWD pipeline, we evaluated the quality of five genes (atpB, rbcL, matK, matR, and ITS) in GenBank. We found that the number of sequences and the corresponding representation of species greatly declined with each step of data mining and cleaning approaches. With further bioinformatics, we assembled a large 5-gene 20,258-taxon matrix from GenBank, representing 3,071 genera, 138 families, and 14 orders, and reconstructed the largest phylogeny to date of rosids. Our results generally agree with previous estimates of rosid phylogeny and provide greater resolution and support in several areas of the topology. The topologies inferred from single-gene and combined-gene data sets are generally consistent, but with a few significant differences. Using the resulting best tree, we produced a Lineage Through Time plot to estimate the timing of the rosid radiation. The radiations detected in rosids also represent the rapid rise of angiosperm-dominated forests and associated co-diversification events that profoundly shaped much of current terrestrial biodiversity. In summary, despite a large volume of data for rosids deposited in GenBank, these data are biased toward specific subclades. Additionally, the lack of a standardized and universally accepted taxonomic name system is problematic and hinders the utility of further comparative study of biodiversity data.

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1 - University of Florida, Dickinson Hall, 1659 Museum Rd, PO. Box 117800, Gainesville, FL, 32611-7800, USA
2 - University Of Florida, Florida Museum Of Natural History, Dickinson HAll, Museum Road, Gainesville, FL, 32611, USA
3 - University Of Florida, Florida Museum Of Natural History, PO BOX 117800, GAINSVILLE, FL, 32611-7800, USA
4 - University of Michigan, Ecology and Evolutionary Biology, 2071A Kraus Natural Science Building, Ann Arbor, MI, 48109, United States
5 - University Of Florida, Florida Museum Of Natural History, PO BOX 117800, Gainesville, FL, 32611-7800, USA, 352/273-1964
6 - Institute of Botany, the Chinese Academy of Sciences, No. 20 Nanxincun, Beijing, Beijing, BJ, 100093, CN
7 - University of Florida, Dept. of Biology, 1659 Museum Road, Gainesville, Florida, 32611, United States

DNA data

Presentation Type: Oral Paper
Session: 41, Basal Rosids & Rosids I
Location: 101/Savannah International Trade and Convention Center
Date: Wednesday, August 3rd, 2016
Time: 9:15 AM
Number: 41006
Abstract ID:404
Candidate for Awards:None

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