Different ways that fossil and molecular data date lineages. Time intervals defined by the horizontal dashed lines and vertical arrows pertain to age estimates for the divergence between hypothetical lineages X and Y. Even with a complete fossil record and perfect molecular clock a discrepancy is expected between fossil (FA) and molecular (MA) age estimates. As diagnostic morphological characters generally evolve (TMorphology) after species divergence (TSpecies), the fossil record will always underestimate (by δDiagnostic character) the true speciation time. Genetic data, on the other hand, will overestimate speciation time (by δCoalescence), as polymorphisms present during species divergence will coalesce some time in the past (TGene; related to the ancestral species effective population size). The genuine difference between molecular and morphological divergence times will thus be δTrue MA-FA. With a less complete fossil record, the oldest known fossil is unlikely to temporally correspond precisely to the origination of a diagnostic character delimiting X and Y, further decreasing FA by δOldest fossil. Under the more realistic scenario of lineage-specific rate heterogeneity and limited taxon/character sampling, errors associated with molecular methods (δClock error) may result in overestimation or underestimation of the true speciation time, although underestimates are bounded by the fossil constraint (δFossil error). The observed discrepancy in age estimates, δRealized MA-FA, may be considerably larger than expectations (δTrue MA-FA).
Brown et al. BMC Biology 2008 6:6 doi:10.1186/1741-7007-6-6