Figure 1.
Divergence times among 16 species of frogs.
Estimates from Evans et al. [54] and Bossuyt and Roelants [56].
Table 1.
Collection data for tissue samples.
Figure 2.
Mapping success of simulated reads.
Reads simulated with average expected differences between 0 and 24% from target exons on the reference sequence, mapped against the entire Xenopus tropicalis genome. A) Number of simulated reads (out of 2×107) mapped to the correct target exon in the genome. B) Number of simulated reads mapped to the incorrect target exon on the reference genome.
Table 2.
Enrichment in Xenopus tropicalis and Pipa pipa for 933 target regions of the Xenopus tropicalis genome after array-based (454 sequencing) and solution-based (SOLiD, 35-bp sequencing) protocols.
Table 3.
Enrichment success for 16 species of frogs across 933 target exons designed from the Xenopus tropicalis draft genome.
Figure 3.
Effect of divergence time on enrichment success across 16 species of frogs.
A) Enrichment (x-fold improvement in sequencing compared to random shot-gun sequencing). Paired reads (35- and 50-bp) were sequenced for all 16 species. Xenopus tropicalis and Pipa pipa were also independently sequenced for single 35-bp reads. Trend lines were computed for all data points, and after removing three data points that likely had reduced enrichment because of experimental error: P. pipa (paired run), Rana palmipes, and Gastrophryne olivacea. B) The number of targets for which any reads mapped for each species, the average uniformity for these targets (the proportion of basepairs sequenced at 15×), and the number of targets with a uniformity of at least 0.4.
Figure 4.
Maximum likelihood estimate of relationships among frog species based on 764 target exons.
At each terminal taxon and internal node, we note the number of target exons sequenced for all species within the clade (n), the estimated time of divergence at each internal node, rounded to the nearest 5 my [54], [56], and support values: bootstrap proportion based on concatenation of all exons/bootstrap proportion based on a matrix with no empty cells/Bayesian concordance factor based on 23 exons enriched in all taxa.
Table 4.
Mean percent sequence divergence between successfully enriched targets and reference sequence used to develop enrichment probes.