Abstract
Bayesian estimates of divergence times based on the molecular clock yield uncertainty of parameter estimates measured by the width of posterior distributions of node ages. For the relaxed molecular clock, previous works have reported that some of the uncertainty inherent to the variation of rates among lineages may be reduced by partitioning data. Here we test this effect for the purely morphological clock, using placental mammals as a case study. We applied the uncorrelated lognormal relaxed clock to morphological data of 40 extant mammalian taxa and 4,533 characters, taken from the largest published matrix of discrete phenotypic characters. The morphologically derived timescale was compared to divergence times inferred from molecular and combined data. We show that partitioning data into anatomical units significantly reduced the uncertainty of divergence time estimates for morphological data. For the first time, we demonstrate that ascertainment bias has an impact on the precision of morphological clock estimates. While analyses including molecular data suggested most divergences between placental orders occurred near the K‐Pg boundary, the partitioned morphological clock recovered older interordinal splits and some younger intraordinal ones, including significantly later dates for the radiation of bats and rodents, which accord to the short‐fuse hypothesis.
Highlights
The radiation of placental mammals culminated in a variety of body forms and life histories (Feldhamer, Drickamer, Vessey, Merritt, & Krajewski, 2007)
We have shown that partitioning of morphological data reduced the uncertainty of posterior divergence time estimates using the relaxed morphological clock, a behavior that has been previously reported with the molecular clock (Zhu et al, 2015)
Zhu et al (2015) listed three major factors contributing to the uncertainty of divergence time estimates from molecular data: sam‐ pling error due to short sequences, evolutionary rate variation due to the relaxed clock, and inherent uncertainty of fossil calibrations
Summary
The radiation of placental mammals culminated in a variety of body forms and life histories (Feldhamer, Drickamer, Vessey, Merritt, & Krajewski, 2007). For the relaxed molecular clock, the larger the variation in rates across lineages, the larger is the uncertainty of inferred divergence times This outcome may be circumvented by increasing the number of partitions the data is di‐ vided in, as each partition is treated as an independent loci (dos Reis et al, 2012; Rannala & Yang, 2007; Zhu, Reis, & Yang, 2015) In this case, the rate of decrease of the variance of age estimates is roughly the reciprocal of the number of partitions (Zhu et al, 2015). We verify here whether data parti‐ tioning affects uncertainty of age estimates in the case of the pure morphological clock This was carried out employing an experimen‐ tal design that allowed for comparisons among discrete phenotypic, molecular, or both sources of data. We do so in the context of pla‐ cental mammals, in the hope of uncovering novel information about their much‐disputed radiation
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