Limitations of molecular dating using constant birth-death rate priors in deep time reflected in Brachiopoda evolution.

Molecular clocks: Closing the gap between rocks and clocks

Timescales are of fundamental importance to evolutionary biology as they facilitate hypothesis tests of historical evolutionary processes. Through the incorporation of fossil occurrence data, the fossilized birth-death (FBD) process provides a framework for estimating divergence times using more paleontological data than traditional node calibration approaches have allowed. The inclusion of more data can refine evolutionary timescale estimates, but for many taxonomic groups it is computationally infeasible to include all available fossil occurrence data. Here, we utilize both empirical data and a simulation framework to identify approaches to subsampling fossil occurrence data that result in the most accurate estimates of divergence times. To achieve this we assess the performance of the FBD-Skyline model when implementing multiple approaches to incorporating subsampled fossil occurrence data. Our results demonstrate that it is necessary to account for all available fossil occurrence data to achieve the most accurate estimates of clade age. We show that this can be achieved if an empirical Bayes approach, accounting for fossil sampling through time, is applied to the FBD process. Random subsampling of occurrence data can lead to estimates of clade age that are incompatible with fossil evidence if no control over the affinities of fossil occurrences is enforced. Our results call into question the accuracy of previous divergence time studies incorporating the FBD process that have used only a subsample of all available fossil occurrence data.

The practice of molecular dating is an essential tool for hypothesis testing in evolutionary biology. Vagaries of fossilization and taphonomic bias commonly engender high uncertainty in molecular dating in taxonomic groups wherein few fossils can be unambiguously assigned to phylogenetic nodes. A recent and novel implementation in molecular dating, "cross-bracing", exploits gene duplications by formally linking calibrated node dates throughout the paralogous subtrees through hierarchical Bayesian models. An unexplored refinement of this method is cross-bracing nodes with unknown dates, in addition to calibrated nodes, such that all nodes representing the same cladogenetic events have linked priors. We applied such a refinement to molecular dating in chelicerates, one of the earliest groups of arthropods present in the fossil record, but whose molecular dating has been greatly inconsistent in the literature. We inferred divergence times using hemocyanin paralogs isolated from de novo assembled transcriptomic libraries, and multiple fossil calibrations. We show that extending cross-bracing to uncalibrated nodes greatly reduced variance in estimates of divergence times throughout the phylogeny, particularly for estimated diversification ages of spiders and scorpions, whereas cross-bracing calibrated nodes alone did not affect age estimation for uncalibrated, derived clades. Comparing ages inferred with extended cross-bracing to the fossil record, we observe smaller gaps between diversification and the first appearance of crown group fossils than have previously been inferred, particularly for spiders. Our dating indicates that scorpions have a Silurian origin, but diversification of extant lineages occurred near the Triassic-Jurassic boundary, falsifying previous inference of Permian diversification age based on extant distribution alone. The significant reduction of variance in divergence time estimates upon extending cross-bracing to uncalibrated nodes makes this approach greatly suited for evolutionary inference in groups with poor fossil records, with particular reference to terrestrial arthropods.

Molecular dates consistently place the divergence of major metazoan lineages in the Precambrian, leading to the suggestion that the 'Cambrian explosion' is an artefact of preservation which left earlier forms unrecorded in the fossil record. While criticisms of molecular analyses for failing to deal with variation in the rate of molecular evolution adequately have been countered by analyses which allow both site-to-site and lineage-specific rate variation, no analysis to date has allowed the rates to vary temporally. If the rates of molecular evolution were much higher early in the metazoan radiation, molecular dates could consistently overestimate the divergence times of lineages. Here, we use a new method which uses multiple calibration dates and an empirically determined range of possible substitution rates to place bounds on the basal date of divergence of lineages in order to ask whether faster rates of molecular evolution early in the metazoan radiation could possibly account for the discrepancy between molecular and palaeontological date estimates. We find that allowing basal (interphylum) lineages the fastest observed substitution rate brings the minimum possible divergence date (586 million years ago) to the Vendian period, just before the first multicellular animal fossils, but excludes divergence of the major metazoan lineages in a Cambrian explosion.

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.

Bayesian relaxed clock estimation of divergence times in foraminifera

Gene choice, base compositional heterogeneity and rate heterogeneity are known to influence phylogenetic reconstruction but are often overlooked. Here, we investigate the impact of these factors in reconstructing the phylogenetic relationships and divergence times of cypriniform fishes. We compile a multilocus data set of newly sequenced and previously published nuclear protein-coding genes from species from all major lineages of Cypriniformes. We collect data on the oldest known cypriniform fossils and gather body size information. We demonstrate that body size correlates with rates of molecular evolution and contributes to rate heterogeneity not only in Cypriniformes but also in a number of other fish lineages. We find that miniaturized cypriniforms show exceptionally high rates of molecular evolution that may lead to improper phylogenetic placement of these taxa due to issues associated with branch attraction. We identify and correct for base compositional heterogeneity and find that this has a marked impact on topology and a corresponding impact on the estimation of divergence times within Cypriniformes. Using gene sequences, fossil calibrations and two different methods, we show strong evidence that Catostomidae is sister to all other cypriniform families and the major clades of cypriniform fishes diverged long before their fossil record indicates.

AimTo infer divergence times and historical biogeography of the cosmopolitan lycophyte family Lycopodiaceae.LocationWorldwide.MethodsWe generated time‐calibrated phylogenies of the Lycopodiaceae based on six regions of chloroplast DNA using a node‐dating approach implemented in beast with eight fossil calibrations. To investigate effects of among‐lineage substitution rate heterogeneity on divergence time estimation, we compared the performance of two relaxed clock models: an uncorrelated lognormal clock model and a random local clock (RLC) model. The historical biogeography of the family was inferred using two Bayesian models implemented in BioGeoBEARS.ResultsDivergence time estimates for major groups of the Lycopodiaceae obtained using the two substitution clock models differed substantially, and the RLC model was a better fit. The Lycopodiaceae crown group age is estimated to be late Devonian, and most deep divergence events date to the Carboniferous, with most extant species diversity accumulating during the Cenozoic. The timing of divergences of major clades in the Lycopodiaceae corresponds to the breakup of the Pangaean and Gondwanan supercontinents. Long‐distance dispersal events are relatively common, but generally do not appear to be followed by subsequent radiations.Main conclusionsAccounting for among‐lineage substitution rate heterogeneity improves divergence time estimates for the Lycopodiaceae. The family has a deep evolutionary history, and continent‐scale vicariance events in the Mesozoic appear to have been associated with major cladogenesis events, with long‐distance dispersal playing a relatively minor role.

Estimation of divergence times is usually done using either the fossil record or sequence data from modern species. We provide an integrated analysis of palaeontological and molecular data to give estimates of primate divergence times that utilize both sources of information. The number of preserved primate species discovered in the fossil record, along with their geological age distribution, is combined with the number of extant primate species to provide initial estimates of the primate and anthropoid divergence times. This is done by using a stochastic forwards-modeling approach where speciation and fossil preservation and discovery are simulated forward in time. We use the posterior distribution from the fossil analysis as a prior distribution on node ages in a molecular analysis. Sequence data from two genomic regions (CFTR on human chromosome 7 and the CYP7A1 region on chromosome 8) from 15 primate species are used with the birth-death model implemented in mcmctree in PAML to infer the posterior distribution of the ages of 14 nodes in the primate tree. We find that these age estimates are older than previously reported dates for all but one of these nodes. To perform the inference, a new approximate Bayesian computation (ABC) algorithm is introduced, where the structure of the model can be exploited in an ABC-within-Gibbs algorithm to provide a more efficient analysis.

The use of molecular sequence data has increased interest in trying to date evolutionary events, with researchers wanting both an estimate of the divergence time and a confidence interval for that estimate. However, two methodological issues have recently been raised with respect to precision of the estimates: (i) the time of the ancestral event is over-estimated; and (ii) the confidence interval is asymmetrical. I argue that if the estimates of divergence time are considered to be samples from a lognormal probability distribution, then this would explain both of these problems. This implies that divergence times should be presented using geometric means rather than arithmetic means, both for estimates and for their confidence intervals. I present analyses based on both computer simulations and empirical data to show that this approach is effective for both single-gene and multiple-gene data sets. Treating divergence time as a lognormal variable thus provides a simple unifying framework for dealing with many of the problems associated with the estimation of divergence (and possibly coalescence) times. Use of this approach (based on geometric means) can, unfortunately, lead to very different biological conclusions compared to the currently used calculation methods (based on arithmetic means).

[Extract] The Mesozoic-Cenozoic transition was a period of dramatic global change during which time the Earth's continents were in the process of fragmenting from a large, relatively continuous landmass to assume a configuration similar to that seen today. The most significant tectonic activity in the southern hemisphere occurred during the Cretaceous-Paleogene interval, when the large Gondwanan sub-regions of Africa, South America, Australia, Indo- Madagascar and Antarctica became increasingly isolated from one another (Smith et al., 1994; Scotese, 2001). Continental dynamics of this scale are not only geologically significant, they also profoundly influenced the evolution of both terrestrial and marine biotas (Forster, 1999; Krause et al., 1999; Sereno, 1999; Lieberman, 2000; Upchurch et al., 2002; Humphries and Ebach, 2004). Indeed, the Cretaceous-Paleogene transition marks large-scale faunal turnover of major vertebrate and invertebrate taxa (e.g., extinction of nonavian dinosaurs, radiation of "modern" mammals and birds; Cracraft, 2001; Springer et al., 2003, 2004; Archibald and Fastovsky, 2004; Kielan-Jaworowska et al., 2004; Rose and Archibald, 2004; Clarke et al., 2005). Numerous hypotheses have been proposed to explain the origin, diversification, and extinction of many vertebrate groups living on, or dispersing through, Gondwana during the Cretaceous and Paleogene. For example, molecular studies have postulated a Cretaceous-Paleogene African origin for a number of higher-level amniote clades, including Placentalia (Murphy et al., 2001 and references therein), Afrotheria (Hedges et al., 1996; Springer et al., 1997, 2003, 2005; Madsen et al., 2001; van Dijk et al., 2001), and neornthine birds (Cracraft, 2001). In particular, an ancient ( Cretaceous/Paleocene) Gondwanan primate origin has been proposed, with a strepsirrhine-haplorhine divergence occurring shortly thereafter (e.g., Tavare et al., 2002). African origins have also been proposed for a number of Malagasy terrestrial and freshwater groups (e.g., etropline cichlids (Vences et al., 2001); lemurs (Yoder et al., 2003, Poux et al., 2005); tenrecs (Poux et al., 2005)). Yet divergence time estimates retrieved by molecular studies for various clades often vastly predate the first occurrences of those groups in the fossil record (e.g., Smith and Peterson, 2002), instigating considerable debate as to the time of origin and path of dispersal for a broad range of taxa (e.g., Martin, 2000; de Wit, 2003; Schrago and Russo, 2003; Rose and Archibald, 2004; de Queiroz, 2005; Masters et al., 2006). This is perhaps not surprising, as Martin and others have demonstrated that by any measure, the vertebrate fossil record (particularly in places like Africa) is dismayingly incomplete, such that dates derived from paleontological data alone are likely to significantly underestimate true divergence times (Martin, 1993, 2000; Paul, 1998; Tavare et al., 2002; Miller et al., 2005). Whereas questions remain regarding the reliability of molecular clocks with respect to calibration and rate heterogeneity (Smith and Peterson, 2002), it is also clear that sustained work is needed to improve sampling of the fossil record and test molecular hypotheses by providing fossil data that can be used to more rigorously calibrate and refine divergence time estimates (Seiffert et al., 2003; Yoder et al., 2003). This is particularly true of undersampled regions where new discoveries can have a profound effect on hypotheses based on presence/absence data (e.g., a Cretaceous gondwanatherian mammal from Tanzania; Krause et al., 2003b; O’Connor et al., 2006). Moreover, recent studies examining the robusticity of biogeographic reconstructions demonstrate that even a single new outgroup or ingroup fossil can powerfully influence area-of-origin interpretations (e.g., Stevens and Heesy, 2004, 2006; Heesy et al., 2006).

Uncertainty in divergence time estimation is frequently studied from many angles but rarely from the perspective of phylogenetic node age. If appropriate molecular models and fossil priors are used, a multi-locus, partitioned analysis is expected to equally minimize error in accuracy and precision across all nodes of a given phylogeny. In contrast, if available models fail to completely account for rate heterogeneity, substitution saturation and incompleteness of the fossil record, uncertainty in divergence time estimation may increase with node age. While many studies have stressed this concern with regard to deep nodes in the Tree of Life, the inference that molecular divergence time estimation of shallow nodes is less sensitive to erroneous model choice has not been tested explicitly in a Bayesian framework. Because of available divergence time estimation methods that permit fossil priors across any phylogenetic node and the present increase in efficient, cheap collection of species-level genomic data, insight is needed into the performance of divergence time estimation of shallow (<10 MY) nodes. Here, we performed multiple sensitivity analyses in a multi-locus data set of aquatic birds with six fossil constraints. Comparison across divergence time analyses that varied taxon and locus sampling, number and position of fossil constraint and shape of prior distribution showed various insights. Deviation from node ages obtained from a reference analysis was generally highest for the shallowest nodes but determined more by temporal placement than number of fossil constraints. Calibration with only the shallowest nodes significantly underestimated the aquatic bird fossil record, indicating the presence of saturation. Although joint calibration with all six priors yielded ages most consistent with the fossil record, ages of shallow nodes were overestimated. This bias was found in both mtDNA and nDNA regions. Thus, divergence time estimation of shallow nodes may suffer from bias and low precision, even when appropriate fossil priors and best available substitution models are chosen. Much care must be taken to address the possible ramifications of substitution saturation across the entire Tree of Life.

Estimation of divergence times from sequence data has become increasingly feasible in recent years. Conflicts between fossil evidence and molecular dates have sparked the development of new methods for inferring divergence times, further encouraging these efforts. In this paper, available methods for estimating divergence times are reviewed, especially those geared toward handling the widespread variation in rates of molecular evolution observed among lineages. The assumptions, strengths, and weaknesses of local clock, Bayesian, and rate smoothing methods are described. The rapidly growing literature applying these methods to key divergence times in plant evolutionary history is also reviewed. These include the crown group ages of green plants, land plants, seed plants, angiosperms, and major subclades of angiosperms. Finally, attempts to infer divergence times are described in the context of two very different temporal settings: recent adaptive radiations and much more ancient biogeographic patterns.

Phylogenomic analyses reveal incongruences between divergence times and fossil records of freshwater snails in East Asia

The Cambrian explosion has long been a basic research frontier that concerns many scientific fields. Here we discuss the cause-effect links of the Cambrian explosion on the basis of first appearances of animal phyla in the fossil record, divergence time, environmental changes, Gene Regulatory Networks, and ecological feedbacks. The first appearances of phyla in the fossil record are obviously diachronous but relatively abrupt, concentrated in the first three stages of the Cambrian period (541–514 Ma). The actual divergence time may be deep or shallow. Since the gene regulatory networks (GRNs) that control the development of metazoans were in place before the divergence, the establishment of GRNs is necessary but insufficient for the Cambrian explosion. Thus the Cambrian explosion required environmental triggers. Nutrient availability, oxygenation, and change of seawater composition were potential environmental triggers. The nutrient input, e.g., the phosphorus enrichment in the environment, would cause excess primary production, but it is not directly linked with diversity or disparity. Further increase of oxygen level and change of seawater composition during the Ediacaran-Cambrian transition were probably crucial environmental factors that caused the Cambrian explosion, but more detailed geochemical data are required. Many researchers prefer that the Cambrian explosion is an ecological phenomenon, that is, the unprecedented ecological success of metazoans during the Early Cambrian, but ecological effects need diverse and abundant animals. Therefore, the establishment of the ecological complexity among animals, and between animals and environments, is a consequence rather than a cause of the Cambrian explosion. It is no doubt that positive ecological feedbacks could facilitate the increase of biodiversity. In a word, the Cambrian explosion happened when environmental changes crossed critical thresholds, led to the initial formation of the metazoan-dominated ecosystem through a series of knock-on ecological processes, i.e., “ecological snowball” effects.