Testing the Molecular Clock: Molecular and Paleontological Estimates of Divergence Times in the Echinoidea (Echinodermata)

Abstract

The phylogenetic relationships of 46 echinoids, with representatives from 13 of the 14 ordinal-level clades and about 70% of extant families commonly recognized, have been established from 3 genes (3,226 alignable bases) and 119 morphological characters. Morphological and molecular estimates are similar enough to be considered suboptimal estimates of one another, and the combined data provide a tree that, when calibrated against the fossil record, provides paleontological estimates of divergence times and completeness of their fossil record. The order of branching on the cladogram largely agrees with the stratigraphic order of first occurrences and implies that their fossil record is more than 85% complete at family level and at a resolution of 5-Myr time intervals. Molecular estimates of divergence times derived from applying both molecular clock and relaxed molecular clock models are concordant with estimates based on the fossil record in up to 70% of cases, with most concordant results obtained using Sanderson's semiparametric penalized likelihood method and a logarithmic-penalty function. There are 3 regions of the tree where molecular and fossil estimates of divergence time consistently disagree. Comparison with results obtained when molecular divergence dates are estimated from the combined (morphology + gene) tree suggests that errors in phylogenetic reconstruction explain only one of these. In another region the error most likely lies with the paleontological estimates because taxa in this region are demonstrated to have a very poor fossil record. In the third case, morphological and paleontological evidence is much stronger, and the topology for this part of the molecular tree differs from that derived from the combined data. Here the cause of the mismatch is unclear but could be methodological, arising from marked inequality of molecular rates. Overall, the level of agreement reached between these different data and methodological approaches leads us to believe that careful application of likelihood and Bayesian methods to molecular data provides realistic divergence time estimates in the majority of cases (almost 80% in this specific example), thus providing a remarkably well-calibrated phylogeny of a character-rich clade of ubiquitous marine benthic invertebrates.

Paleogenomics of echinoids reveals an ancient origin for the double-negative specification of micromeres in sea urchins

“…Thirteen of the 15 analyses reached convergence within time available, whereas the two analyses that failed to converge were excluded from ancestral state reconstructions. Those two topologies exhibited relationships widely different from previous molecular and morphological inferences of echinoid topology (18,51), and thus their exclusion from ancestral state reconstruction likely had no effect on our inferences.…”

“…For our dataset, we used previously published mitochondrial 16s, 18s, and 28s small subunit rRNA sequence data (49)(50)(51), which comprises the most comprehensive known molecular dataset with respect to echinoid taxonomic sampling. Although such a dataset for inference of topology has limited use compared with more widely used phylogenomic datasets, we accounted for uncertainty in topology and branch length in our downstream ancestral state reconstructions.…”

Dynamic evolutionary change in post-Paleozoic echinoids and the importance of scale when interpreting changes in rates of evolution

“…S4 and S5A), we were no longer able to infer rates for echinoids before the Jurassic (no living echinoid genera are older than midJurassic) but the rates were noticeably higher in the late Jurassic and somewhat so in the Eocene than in the rest of the time series. However, scaling the tree based only on the fossil record of living taxa imparts unreasonably young ages to deep nodes, compared with both the known fossil record and to estimates inferred from molecular phylogenies of echinoids using current methods for calibrating trees and at least some information from the fossil record to define priors (18,19). If we pruned the tree after scaling (imparting more reasonable ages to ancestral nodes), the pattern remains remarkably similar (SI Appendix, Fig.…”

“…Since originating some 265 million years ago (18,19), crown group echinoids have evolved to become ecologically and morphologically diverse in today's oceans, and are an important component of both past and present marine ecosystems (e.g., refs. [20][21][22].…”

Evaluating Hydrothermal System Evolution Using Geochronological Dating and Biological Diversity Analyses

“…Although a common calibration method of molecular clock is an examination of the fossil record (e.g. Cruzan and Templeton 2000;Smith et al 2006;Weir and Schluter 2008), fossil evidence of hydrothermal vent communities is rare because of the destruction of vent fauna by hydrothermal activity itself. Other methods of calibrating the molecular clock in gene sequences of hydrothermal vent fauna might be geochronological dating techniques of hydrothermal ore minerals and geological events.…”