Molecular Clocks without Rocks: New Solutions for Old Problems.

  title={Molecular Clocks without Rocks: New Solutions for Old Problems.},
  author={George P. Tiley and Jelmer W Poelstra and Mario dos Reis and Ziheng Yang and Anne D. Yoder},
  journal={Trends in genetics : TIG},

Figures from this paper

Rocks and clocks revised: New promises and challenges in dating the primate tree of life

How dated phylogenies provide the crucial temporal scale required to understand primate evolution is discussed and how the ever‐increasing availability of genomic‐level data for more primate species can impact the ability to accurately estimate timetrees is explored.

Meaning and Purpose: Using Phylogenies to Investigate Human History and Cultural Evolution

How phylogenies are interpreted as narratives about human diversification is explored to explore how they provide important information that can be used to test ideas about human diversity, and can help to guard against errors of inference arising from statistical artifacts.

Complexity of the simplest species tree problem

This work uses mathematical analysis aided by computer simulation to examine the identifiability, consistency, and efficiency of different species tree methods in the case of three species and three sequences under the molecular clock.

Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur.

This study provides the first direct mutation-rate estimate for a strepsirrhine (i.e., the lemurs and lorises), which comprises nearly half of the primate clade, and finds both the rate and spectrum to be robust to the manipulation of a wide range of computational filtering criteria.

RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results

Data indicate that M. murinus and M. griseorufus are reproductively isolated, and it is estimated that they diverged less than a million years ago, suggesting that completion of speciation is relatively rapid in mouse lemurs.

Phasing Alleles Improves Network Inference with Allopolyploids

It is established that the pipeline (PATÉ: Phased Alleles from Target Enrichment data) is capable of recovering a high proportion of phased loci from both diploids and polyploids, and that these data improve network estimates compared to using haplotype consensus assemblies.

The challenge and promise of estimating the de novo mutation rate from whole‐genome comparisons among closely related individuals

It is predicted that rapidly developing methods for whole‐genome comparisons hold great promise for integrating empirically derived estimates of de novo mutation rates and mutation spectra across many molecular ecological applications.



Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

It is shown that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties, and these estimates are unlikely to be improved by collecting additional molecular sequence data.

Gene Tree Discordance Causes Apparent Substitution Rate Variation.

This work uses simulations to demonstrate that SPILS has a larger effect with increasing levels of ILS, and on trees with larger numbers of taxa, and uses data from multiple Drosophila species to show that SPils can be detected in nature.

Bayesian molecular clock dating of species divergences in the genomics era

The molecular clock hypothesis has become a powerful tool in evolutionary biology, making it possible to use molecular sequences to estimate the geological ages of species divergence events and to estimate a timescale for life on Earth.

Estimation of primate speciation dates using local molecular clocks.

It is concluded that the calibration derived from the primate fossil record is too recent to be reliable and a number of problems in date estimation when the molecular clock does not hold are pointed out.

Best Practices for Justifying Fossil Calibrations

  • JamesF. Benton
  • Environmental Science
    Systematic biology
  • 2012
Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining

Heterogeneous Rates of Molecular Evolution and Diversification Could Explain the Triassic Age Estimate for Angiosperms.

A series of simulations are used to explore the possibility that the older age estimates obtained using current relaxed-clock methods are a consequence of (i) major shifts in the rate of sequence evolution near the base of the angiosperms and/or the representative taxon sampling strategy employed in such studies.

StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates

To enable fuller use of available data and more accurate inference of species tree topologies, divergence times, and substitution rates, a new version of *BEAST is developed called StarBEast2, and it is shown that StarBEAST2 is a more powerful and robust estimator of rate variation than concatenation.

Genome-scale approaches to resolving incongruence in molecular phylogenies

The results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies, and have important implications for resolving branches of the tree of life.

The Estimated Pacemaker for Great Apes Supports the Hominoid Slowdown Hypothesis

It is suggested that in great apes, life history traits were the major drivers of substitution rate variation across the genome, and the hominoid slowdown hypothesis was corroborated.


It is shown that phylogeographic studies in vertebrates suggest that divergence of alleles in ancestral species can comprise from less than 10% to over 50% of the total divergence between sister species, suggesting that the problem of ancestral polymorphism in dating population divergence can be substantial.