Abstract
AbstractA universal method of molecular dating that can be applied to all families and genera regardless of their fossil records, or lack thereof, is highly desirable. A possible method for eudicots is to use a large phylogeny calibrated using deep fossils including tricolpate pollen as a fixed (124 mya) calibration point. This method was used to calculate node ages within three species‐poor disjunct basal eudicot genera, Caulophyllum, Podophyllum and Pachysandra, and sensitivity of these ages to effects such as taxon sampling were then quantified. By deleting from one to three accessions related to each genus in 112 different combinations, a confidence range describing variation due only to taxon sampling was generated. Ranges for Caulophyllum, Podophyllum and Pachysandra were 8.4–10.6, 7.6–20.0, and 17.6–25.0 mya, respectively. However, the confidence ranges calculated using bootstrapping were much wider, at 3–19, 0–32 and 11–32 mya, respectively. Furthermore, deleting 10 adjacent taxa had a large effect in Pachysandra only, indicating that undersampling effects are significant among Buxales. Changes to sampling density in neighboring clades, or to the position of the fixed fossil calibration point had small to negligible effects. Non‐parametric rate smoothing was more sensitive to taxon sampling effects than was penalized likelihood. The wide range for Podophyllum, compared to the other two genera, was probably due to a high degree of rate heterogeneity within this genus. Confidence ranges calculated by this method could be narrowed by sampling more individuals within the genus of interest, and by sequencing multiple DNA regions from all species in the phylogeny.
Highlights
A universal method of molecular dating that can be applied to all families and genera regardless of their fossil records, or lack thereof, is highly desirable
These were Cocculus trilobus D85696, Podophyllum emodi AF203487, and Platanus occidentalis L01943
Bootstrapping was used in all analyses except B and J. 1.7.2 Analysis B: 112 variant trees generated by taxon sampling variation This analysis was designed to test the extent to which target node ages might be altered by the removal of up to three taxon samples from the dataset
Summary
A universal method of molecular dating that can be applied to all families and genera regardless of their fossil records, or lack thereof, is highly desirable. A possible method for eudicots is to use a large phylogeny calibrated using deep fossils including tricolpate pollen as a fixed (124 mya) calibration point This method was used to calculate node ages within three species-poor disjunct basal eudicot genera, Caulophyllum, Podophyllum and Pachysandra, and sensitivity of these ages to effects such as taxon sampling were quantified. /or where fossils are relatively abundant, allows assertions that nodes are probably not much older than the calculated dates (Feng et al, 2005; Renner, 2005; Xiang et al, 2005), and permits upper age limits to be calculated directly from the fossil record (Tavareet al., 2002; Marshall, 2008) This solves the problem only in groups with a better than average fossil record. Perhaps the most reliable fixed age fossil calibration point for angiosperms is the appearance of tricolpate pollen 124 mya marking the origin of eudicots
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