Research
Analysis of 142 genes resolves the rapid diversification of the rice genus
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* Corresponding author: Song Ge gesong@ibcas.ac.cn
- † Equal contributors
1 State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
2 Beijing Genomics Institute, Beijing, 101300, China
3 Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
4 The Graduate School, Chinese Academy of Sciences, Beijing, 100039, China
Genome Biology 2008, 9:R49 doi:10.1186/gb-2008-9-3-r49
Published: 3 March 2008Additional files
Additional data file 1:
The relative location on rice chromosomes of the 142 genes sampled in this study.
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Additional data file 2:
Detailed information on each of 142 loci.
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Additional data file 3:
GC content variation among lineages and the result of Chi-square test for the concatenated data set.
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Additional data file 4:
Summary of the Tajima's relative rate test for concatenated sequences using Leersia as outgroup, with estimates of the ratio of substitution rate between lineages.
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Additional data file 5:
Results of testing the effect of rate bias caused by the fast-evolving genes of the F-genome.
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Additional data file 6:
The 14 alternative models used in BI analyses.
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Additional data file 7:
The effect of model components on model fit judged by Bayes factor comparisons of competing models
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Additional data file 8:
Consensus networks of a collection of 106 optimal ML trees from the 106 genes with the complete set of seven species, applying thresholds of 0.05, 0.1, 0.15, 0.2, 0.25 and 0.3, respectively.
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Additional data file 9:
Results of the ILD test for pairwise comparisons of process partitions.
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Additional data file 10:
The number of genes that failed the ILD test with the target gene at P < 0.01 for total, intron, exon and the third codon sites, respectively, and the P value of the ILD test between the target gene and all the rest of genes.
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Additional data file 11:
Topologies of bootstrap 75% majority-rule consensus trees by different methods of analyses for each gene.
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Additional data file 12:
Saturation analyses in the concatenated datasets of total, intron, exon, and third codon positions, respectively.
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Additional data file 13:
Proportions of topology (or clades) identical to those shown in Figure 1 inferred from randomly sampled genes or sites in 500 replicates.
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Additional data file 14:
Primers for PCR amplification and the GenBank accession numbers of the sequences of 142 loci sampled.
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