Analysis of 142 genes resolves the rapid diversification of the rice genus1State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China 2Beijing Genomics Institute, Beijing, 101300, China 3Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA 4The Graduate School, Chinese Academy of Sciences, Beijing, 100039, China
Genome Biology 2008, 9:R49doi:10.1186/gb-2008-9-3-r49
Subject areas: Bioinformatics, Evolution, Plant biology Additional filesAdditional data file 1: The relative location on rice chromosomes of the 142 genes sampled in this study. Format: PDF Size: 33KB Download file This file can be viewed with: Adobe Acrobat Reader Additional data file 2: Detailed information on each of 142 loci. Format: PDF Size: 233KB Download file This file can be viewed with: Adobe Acrobat Reader Additional data file 3: GC content variation among lineages and the result of Chi-square test for the concatenated data set. Format: PDF Size: 28KB Download file This file can be viewed with: Adobe Acrobat Reader 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. Format: PDF Size: 27KB Download file This file can be viewed with: Adobe Acrobat Reader Additional data file 5: Results of testing the effect of rate bias caused by the fast-evolving genes of the F-genome. Format: PDF Size: 41KB Download file This file can be viewed with: Adobe Acrobat Reader Additional data file 6: The 14 alternative models used in BI analyses. Format: PDF Size: 67KB Download file This file can be viewed with: Adobe Acrobat Reader Additional data file 7: The effect of model components on model fit judged by Bayes factor comparisons of competing models Format: PDF Size: 81KB Download file This file can be viewed with: Adobe Acrobat Reader 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. Format: PDF Size: 25KB Download file This file can be viewed with: Adobe Acrobat Reader Additional data file 9: Results of the ILD test for pairwise comparisons of process partitions. Format: PDF Size: 12KB Download file This file can be viewed with: Adobe Acrobat Reader 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. Format: PDF Size: 82KB Download file This file can be viewed with: Adobe Acrobat Reader Additional data file 11: Topologies of bootstrap 75% majority-rule consensus trees by different methods of analyses for each gene. Format: PDF Size: 102KB Download file This file can be viewed with: Adobe Acrobat Reader Additional data file 12: Saturation analyses in the concatenated datasets of total, intron, exon, and third codon positions, respectively. Format: PDF Size: 28KB Download file This file can be viewed with: Adobe Acrobat Reader 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. Format: PDF Size: 25KB Download file This file can be viewed with: Adobe Acrobat Reader Additional data file 14: Primers for PCR amplification and the GenBank accession numbers of the sequences of 142 loci sampled. Format: PDF Size: 197KB Download file This file can be viewed with: Adobe Acrobat Reader |


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