Phylogeny, Taxonomy, and Biogeography of Pterocarya (Juglandaceae)
Abstract
:1. Introduction
2. Results
2.1. RAD-seq and Data Matrices for Phylogenetic Inference
2.2. RAD-seq Phylogenetic Reconstruction
2.3. Morphological Traits and Taxonomic Conclusions
2.4. Estimation of Divergence Times
3. Discussion
3.1. Phylogenetic Hypothesis for Pterocarya
3.2. Taxonomic Implications and Evolutionary Importance of Morphological Features
3.3. East Asian versus Southern European/West Asian Disjunctions of Relict Trees: The Importance of the Gobi Desert’s Formation and Climatic Cooling after the Middle Miocene Epoch
3.4. Late Miocene Diversification in the East Asian Refugium
4. Materials and Methods
4.1. Taxon Sampling and DNA Extraction
4.2. RAD-seq Library Preparation
4.3. Processing and Clustering RAD-seq Data
4.4. Morphological Evaluations and Data Sets
4.5. Phylogenetic Reconstruction
4.6. Fossil Constraints and Estimations of Divergence Times
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Summary Statistic | Raw Reads | Clean Reads | Total Length of Clean Reads (Gbp) | Clean Data Percentage (%) | Q30 Percentage (%) | GC Percentage (%) |
---|---|---|---|---|---|---|
Average | 11,055,000 | 9,947,083 | 1.54 | 84.30 | 91.54 | 47.10 |
Maximum | 18,580,000 | 17,290,000 | 2.36 | 90.02 | 92.39 | 58.57 |
Minimum | 4,780,000 | 3,790,000 | 0.69 | 76.16 | 88.55 | 43.03 |
SD | 3,232,889 | 3,250,324 | 0.37 | 3.64 | 0.88 | 3.91 |
Summary Statistic | RAD Tags (R1) | Total Clusters (R1) | Mean Depth of Clusters | H | E | Consensus Loci | Loci in Final Data Set |
---|---|---|---|---|---|---|---|
Average | 5,502,955 | 1,728,343 | 15.67 | 0.0413 | 0.0103 | 102,981 | 9287 |
Maximum | 8,591,043 | 3,985,579 | 17.75 | 0.0526 | 0.0136 | 204,925 | 13,650 |
Minimum | 2,495,755 | 769,873 | 13.04 | 0.0350 | 0.0075 | 38,695 | 4222 |
SD | 1,316,019 | 733,868 | 1.11 | 0.0043 | 0.0016 | 39,940 | 2668 |
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Song, Y.-G.; Li, Y.; Meng, H.-H.; Fragnière, Y.; Ge, B.-J.; Sakio, H.; Yousefzadeh, H.; Bétrisey, S.; Kozlowski, G. Phylogeny, Taxonomy, and Biogeography of Pterocarya (Juglandaceae). Plants 2020, 9, 1524. https://doi.org/10.3390/plants9111524
Song Y-G, Li Y, Meng H-H, Fragnière Y, Ge B-J, Sakio H, Yousefzadeh H, Bétrisey S, Kozlowski G. Phylogeny, Taxonomy, and Biogeography of Pterocarya (Juglandaceae). Plants. 2020; 9(11):1524. https://doi.org/10.3390/plants9111524
Chicago/Turabian StyleSong, Yi-Gang, Ying Li, Hong-Hu Meng, Yann Fragnière, Bin-Jie Ge, Hitoshi Sakio, Hamed Yousefzadeh, Sébastien Bétrisey, and Gregor Kozlowski. 2020. "Phylogeny, Taxonomy, and Biogeography of Pterocarya (Juglandaceae)" Plants 9, no. 11: 1524. https://doi.org/10.3390/plants9111524