A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

Abstract

Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4--20 complete) and 68 extant taxa. In both cases we use molecular data from seven markers (∼5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, ∼309 Ma (95% interval: 291--347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic. [Bayesian inference; fossil dating; morphological evolution; relaxed clock; statistical phylogenetics.]

Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals

“…Similarly high variance under the IGR model was retrieved in analyses of a hymenopteran insect dataset [29]. Plots of rate against time revealed no clear evidence of elevated rates being concentrated in branches near the KPg boundary ( figure 2a,b); indeed, under both the IGR and TK models, rates are highest on branches closer to the root ( figure 2a,b), which accordingly are compressed in time-a similar result was found by Ronquist et al [28] in their analysis of hymenopterans. Perhaps unsurprisingly, molecular rates in these analyses (all under the IGR model; see above) show much less heterogeneity; median rates across different branches spanned a range of approximately 51Â both when only the age of the root was constrained and when the ages of selected internal divergences within Placentalia were also constrained (figure 2a,b; electronic supplementary material, §7).…”

“…Other studies that have used TE dating have also found that many nodes were estimated to be considerably older than indicated by the fossil record (e.g. [28,31]). Such deep inferred divergences should be treated with caution, given the evidence presented here that the IGR and TK clock models can give implausibly ancient node age estimates when using temporal information provided by fossils.…”

“…These methods simultaneously consider both character and temporal information in terminal taxa to co-estimate phylogeny, divergence dates and evolutionary rates. To date, such 'morphological clock' models have been used mainly in the context of total evidence (TE) analyses that combine morphological and molecular data [27][28][29][30][31]. However, they can also be applied to purely morphological datasets [32,33].…”

“…Here, we apply two very different relaxed clock modelsthe independent gamma rates (IGR) model [28,37] and the Thorne -Kishino (TK) model [38]-to a large morphological character matrix (102 taxa, 421 discrete characters) that includes at least one representative of every extant placental order plus a diverse range of other Mesozoic and Coenozoic eutherians. All analyses used MRBAYES v. 3.2 [39].…”

Bayesian estimation of fossil phylogenies and the evolution of early to middle Paleozoic crinoids (Echinodermata)

“…Indeed, there has been an increasing number of studies employing probabilistic approaches to estimate phylogenies with morphologic data, especially in paleontology (e.g., Wagner, 1998Wagner, , 1999Snively et al, 2004;Pollitt et al, 2005;Clarke and Middleton, 2008;Pyron, 2011;Ronquist et al, 2012;Slater, 2013Slater, , 2015Wright and Stigall, 2013;Lee et al, 2014;Close et al, 2015;Bapst et al, 2016;Gorscak and O'Connor, 2016).…”