geodiskey 28apr09地理距离嵌套单倍型树分析推理关键从在1步进化枝内开.pdfVIP

Inference Key for the Nested Haplotype Tree ysis of Geographical Distances Start with haplotypes nested within a 1-step clade and work up to clades nested within the total tree. If the tree is not rooted through an outgroup or if none of the clades nested at the total tree level have the sum of the outgroup probabilities of their haplotypes greater than or equal to 0.95, regard all clades nested at the total tree level as tips. When rooting is deemed reliable, interiors should also refer to the older clades in a nesting category, and tips to their evolutionary descendants. This key is applied only if there are some significant values for D , D , or I-T within the c n nesting clade. If there are no statistically significant distances within the clade, the null hypothesis of no geographical association of haplotypes cannot be rejected (either panmixia in ual populations, extensive dispersal in non- ual populations, small sample size, or inadequate geographical sampling). In that case, move on to another clade at the same or higher level. When performing a single-locus nested clade ysis, the significance of the test results should be corrected for multiple testing with the Dunn-Sidak correction, which is now orporated into the program. When performing multi-locus nested clade ysis, the Dunn-Sidak correction is not needed, and the original probability values should be used to determine significance. In the case of multi-locus nested clade ysis, the false positive rate is corrected by cross-validation across loci. 1. Are all clades within the nesting clade found in separate areas with no overlap? • NO – Go to step 2. • YES - Go to step 19. 2. Is at least one of the following conditions satisfied? a. The D ’s for one or