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As such, these fields should pay attention more closely to the historical sequence of range dynamics—nonetheless, at least until recently, phylogeography has not taken its "geography" base seriously enough (Peterson 2009), particularly in light of rampant blind application of molecular clock methodologies to complex geographic and historical questions (Peterson 2007).
The continued development of molecular clock methodologies over the past two decades has allowed for the estimation of divergence times under more complex models of rate variation.
Molecular clock methodologies allow for the estimation of divergence times across a variety of organisms; this can be particularly useful for groups lacking robust fossil histories, such as microbial eukaryotes with few distinguishing morphological traits.
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It has been hoped that these questions may be answered, and a timescale for animal evolutionary history established, using molecular clock methodology.
The disparity between molecular clock estimates and fossil evidence of clade age minima has diminished in association with the development of molecular clock methodology, particularly in accommodating rate variation.
We do this by updating the B. tabaci species complex phylogeny with newly available mtCOI sequence data from GenBank and then apply the best practice molecular clock methodology of [ 33] to explore when diversification within the complex most likely occurred.
Evidently, fossil ages do not directly represent clade ages and it is for this reason that in attempting to derive an evolutionary timescale, literal reading of the fossil record has given way to molecular clock methodology which uses statistical distributions to describe uncertainties in fossil calibrations.
This is in agreement with previous molecular clock analyses using mostly different data sets and methodology [ 28, 30].
We make cautious recommendations for the use of nrITS as an approximate plant molecular clock, including an outline of more appropriate phylogenetic methodology and caveats against over interpretation of results.
Most previous molecular clock dating studies, however, have suffered from limited data and biases in methodologies, and virtually all have failed to acknowledge the large uncertainties associated with the fossil record of early animals, leading to inconsistent estimates among studies.
We followed standard methodology here, generating trees under a pure birth process, and deviating these from ultrametricity (the molecular clock hypothesis).
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