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Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach.
  • M. Sanderson
  • Biology, Medicine
  • Molecular biology and evolution
  • 2002
TLDR
A semiparametric smoothing method is developed using penalized likelihood, a saturated model in which every lineage has a separate rate combined with a roughness penalty that discourages rates from varying too much across a phylogeny. Expand
R8s: Inferring Absolute Rates of Molecular Evolution, Divergence times in the Absence of a Molecular Clock
TLDR
R8s version 1.5 is a program which uses parametric, nonparametric and semiparametric methods to relax the assumption of constant rates of evolution to obtain better estimates of rates and times. Expand
A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy
A new method for estimating divergence times when evolutionary rates are variable across lineages is proposed. The method, called nonparametric rate smoothing (NPRS), relies on minimization ofExpand
ABSOLUTE DIVERSIFICATION RATES IN ANGIOSPERM CLADES
TLDR
The phylogenetic distribution of clades with an exceedingly high number of species suggests that traits that confer high rates of diversification evolved independently in different instances and do not characterize the angiosperms as a whole. Expand
A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family.
TLDR
Analysis of the matK data consistently resolves but modestly supports a clade comprising papilionoid taxa that accumulate canavanine in the seeds, which suggests a single origin for the biosynthesis of this most commonly produced of the nonprotein amino acids in legumes. Expand
Age and rate of diversification of the Hawaiian silversword alliance (Compositae).
TLDR
This work took advantage of rate-constant rDNA sequence evolution and an "external" calibration using paleoclimatic and fossil data to determine the maximum age and minimum diversification rate of the Hawaiian silversword alliance (Compositae), a textbook example of insular adaptive radiation in plants. Expand
PATTERNS OF VARIATION IN LEVELS OF HOMOPLASY
TLDR
There is no significant difference between plant and animal data sets in the amount of homoplasy when the relationship between consistency index and number of taxa is taken into account, although there are still too few molecular studies to be confident of this result. Expand
TESTING FOR DIFFERENT RATES OF CONTINUOUS TRAIT EVOLUTION USING LIKELIHOOD
TLDR
General predictions regarding changes in phenotypic diversity as a function of evolutionary history and rates are developed, and tests are derived to evaluate rate changes, showing that these tests are more powerful than existing tests using standardized contrasts. Expand
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