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Although several powerful methods have been developed for molecular time estimation allowing the rate change (a relaxed clock) [12] [17], the poor quality of the fossil record for early grasses has prevented us from addressing this issue.
Molecular time estimation was performed in BEAST v2.1.3 [ 29] according to Khan et al. [ 30] to estimate divergences within Noctilio.
It is worth noting that the most basal species, in which β2-m is present, belong to cartilaginous fishes; therefore, we can approximately date the appearance of the protein at about 500 Ma (455 Ma for the fossil record and 528 for molecular time, estimation based on a large scale multiple genes alignment) [ 8].
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Several papers have noticed that molecular time estimations are consistently older than paleontological ones [ 2, 3, 5- 7, 59].
Analyses of actinopterygian molecular clocks demonstrate that scrutiny of the time scale on which sequence data is informative is a fundamental, but generally overlooked, step in molecular divergence time estimation.
Phylogenetic informativeness approaches facilitate a diagnosis of when to expect a rise in homoplasious site patterns, offering an objective criterion for screening data by its utility for molecular divergence time estimation.
They performed a relaxed molecular clock Bayesian divergence time estimation using unpartitioned and partitioned data sets across these genes and found that extreme saturation obscured the underlying rate of evolution in the mitochondrial gene, resulting in overestimation of the divergence times.
For divergence time estimation, the molecular clock was evaluated using a two-cluster test in the LINTREE program [ 45].
If we accept the use of core genes for phylogeny reconstruction then they should also be of use for time estimation with molecular clocks.
Previous molecular phylogenetic analysis and divergence time estimation placed the age for the basal split within Peramelemorphia at 27 Ma (Westerman et al. 2012).
These results demonstrate that selection of sequence data appropriate for the time scale of inferences is as important as the selection of calibrations and molecular clock models for divergence time estimation.
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