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Data from: Skyline fossilized birth-death model is robust to violations of sampling assumptions in total-evidence dating
<p>Several total-evidence dating studies under the fossilized birth-death (FBD) model have produced very old age estimates, which are not supported by the fossil record. This phenomenon has been termed "deep root attraction (DRA)". For two specific datasets, involving divergence time estimation for the early radiations of ants, bees and wasps (Hymenoptera) and of placental mammals (Eutheria), it has been shown that the DRA effect can be greatly reduced by accommodating the fact that extant species in these trees have been sampled to maximize diversity, so called diversified sampling. Unfortunately, current methods to accommodate diversified sampling only consider the extreme case where it is possible to identify a cut-off time such that all splits occurring before this time are represented in the sampled tree but none of the younger splits. In reality, the sampling bias is rarely this extreme, and may be difficult to model properly. Similar modeling challenges apply to the sampling of the fossil record. This raises the question of whether it is possible to find dating methods that are more robust to sampling biases. Here, we show that the skyline FBD (SFBD) process, where the diversification and fossil-sampling rates can vary over time in a piecewise fashion, provides age estimates that are more robust to inadequacies in the modeling of the sampling process and less sensitive to DRA effects. In the SFBD model we consider, rates in different time intervals are either considered to be independent and identically distributed, or assumed to be autocorrelated following an Ornstein-Uhlenbeck (OU) process. Through simulations and reanalyses of the Hymenoptera and Eutheria data, we show that both variants of the SFBD model unify age estimates under random and diversified sampling assumptions. The SFBD model can resolve DRA by absorbing the deviations from the sampling assumptions into the inferred dynamics of the diversification process over time. Although this means that the inferred diversification dynamics must be interpreted with caution, taking sampling biases into account, we conclude that the SFBD model represents the most robust approach available currently for addressing DRA in total-evidence dating.</p>
FIGURE 16 in Total-evidence Phylogeny of the New World Polistes Lepeletier, 1836, Paper Wasps (Vespidae, Polistinae, Polistini)
FIGURE 16. Peduncle: A, lateral peduncle in Polistes instabilis; B, central peduncle in Polistes carolina.
FIGURE 10 in Total-evidence Phylogeny of the New World Polistes Lepeletier, 1836, Paper Wasps (Vespidae, Polistinae, Polistini)
FIGURE 10. Propodeum and propodeal orifice: A, propodeal striae absent, and propodeal orifice rounded in Polistes torresae; B, propodeal striae weak all over and propodeal orifice rounded in Polistes apachus; and C, propodeal striae strong all over and propodeal orifice elongate in Polistes versicolor.
FIGURE 15 in Total-evidence Phylogeny of the New World Polistes Lepeletier, 1836, Paper Wasps (Vespidae, Polistinae, Polistini)
FIGURE 15. Comb shape: A, circular in Polistes fuscatus; B, subcircular in Polistes instabilis; C, leaf shaped in Polistes versicolor; D, narrow in Polistes crinitus; and E, long and vertical in Polistes goeldii.
FIGURE 9 in Total-evidence Phylogeny of the New World Polistes Lepeletier, 1836, Paper Wasps (Vespidae, Polistinae, Polistini)
FIGURE 9. Mesepisternum: dorsal groove complete and epicnemial carina absent in A, Polistes cavapytiformis; and B, dorsal groove incomplete and epicnemial carina complete in Polistes thoracicus.
FIGURE 2 in Total-evidence Phylogeny of the New World Polistes Lepeletier, 1836, Paper Wasps (Vespidae, Polistinae, Polistini)
FIGURE 2. Single most parsimonious tree obtained in the analysis of morphological, behavioral and molecular data for 101 species of Polistes (opposite page and continued above). Node numbers represent support values from symmetrical resampling, reported as absolute frequencies.
FIGURE 6 in Total-evidence Phylogeny of the New World Polistes Lepeletier, 1836, Paper Wasps (Vespidae, Polistinae, Polistini)
FIGURE 6. Gena width at midlength, lateral view: A, equal to or slightly wider than eye in Polistes pacificus; and B, distinctly wider than eye in Polistes rufiventris.
FIGURE 14. Mesosoma, terga I and II in Total-evidence Phylogeny of the New World Polistes Lepeletier, 1836, Paper Wasps (Vespidae, Polistinae, Polistini)
FIGURE 14. Mesosoma, terga I and II shape and dimensions: A, Vespula squamosa (outgroup); B, Polistes apachus; C, Polistes bicolor; D, Polistes fuscatus; E, Polistes terresae; and F, Polistes versicolor.
FIGURE 8 in Total-evidence Phylogeny of the New World Polistes Lepeletier, 1836, Paper Wasps (Vespidae, Polistinae, Polistini)
FIGURE 8. Occipital carina and pronotal carina of A, Polistes cavapytiformes and B, Polistes penai. Extension of occipital carina and shape and extension of pronotal carina.
FIGURE 13. Tergum I in Total-evidence Phylogeny of the New World Polistes Lepeletier, 1836, Paper Wasps (Vespidae, Polistinae, Polistini)
FIGURE 13. Tergum I shape, lateral view: A, abruptly widened in Polistes huristicornis, and B, gradually widened in Polistes occipitalis.
FIGURE 7 in Total-evidence Phylogeny of the New World Polistes Lepeletier, 1836, Paper Wasps (Vespidae, Polistinae, Polistini)
FIGURE 7. Head and pronotum, in dorsal view: A, occiput strongly convex, anterior region of pronotum rounded and humeri outline not projecting in Polistes cavapytiformis; B, occiput almost straight or weakly convex and humeri outline slightly projecting in Polistes occipitalis; C, anterior region of pronotum with a central projection and humeri outline strongly projecting in Polistes testaceicolor.
FIGURE 12. Terga I and II in Total-evidence Phylogeny of the New World Polistes Lepeletier, 1836, Paper Wasps (Vespidae, Polistinae, Polistini)
FIGURE 12. Terga I and II, dorsal view: A, tergum I conical, as wide as long, and tergum II as wide as long in Polistes aurifer; and B, tergum I conical, longer than wide and tergum II longer than wide in Polistes exclamans.
FIGURE 11 in Total-evidence Phylogeny of the New World Polistes Lepeletier, 1836, Paper Wasps (Vespidae, Polistinae, Polistini)
FIGURE 11. Mesosoma, dimensions of scutum and scutellum: A, Vespula squamosa (outgroup); B, Polistes apachus; C, Polistes fuscatus; D, Polistes versicolor; E, Polistes bicolor; and F, Polistes terresae.
FIGURE 5 in Total-evidence Phylogeny of the New World Polistes Lepeletier, 1836, Paper Wasps (Vespidae, Polistinae, Polistini)
FIGURE 5. Face in front view: A, clypeus wider than long, clypeal apex strongly bidentate, clypeus touching for an extension greater than width of antennal socket the eye in Vespula germanica (outgroup); B, clypeus as long as wide, clypeal apex rounded, clypeus touching for an extension equal to width of antennal socket the eye Polistes cavapytiformis; C, clypeus as long as wide, clypeal apex pointed, clypeus touching for an extension shorter than width of antennal socket the eye in Polistes carnifex; and D, clypeus longer than wide, clypeal apex pointed, clypeus narrowly separated by eye in Polistes thoracicus. For all bristles length very long (A), long (B), short, becoming long toward the apex (D).
FIGURE 4 in Total-evidence Phylogeny of the New World Polistes Lepeletier, 1836, Paper Wasps (Vespidae, Polistinae, Polistini)
FIGURE 4. Summary subgenera relationships for New World Polistes obtained in our analyses compared to previous studies.
FIGURE 3 in Total-evidence Phylogeny of the New World Polistes Lepeletier, 1836, Paper Wasps (Vespidae, Polistinae, Polistini)
FIGURE 3. Single most parsimonious tree obtained in the analysis of morphological, behavioral, and molecular data, with the dataset restricted to the 53 species of Polistes for which molecular data was available. Node numbers represent support values from symmetrical resampling, reported as absolute frequencies.
Data from: Skyline fossilized birth-death model is robust to violations of sampling assumptions in total-evidence dating
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Data from: Integrating deep learning derived morphological traits and molecular data for total-evidence phylogenetics: lessons from digitized collections
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Data from: Bayesian total-evidence dating revisits sloth phylogeny and biogeography: a cautionary tale on morphological clock analyses
<p>Combining morphological and molecular characters through Bayesian total-evidence dating allows inferring the phylogenetic and timescale framework of both extant and fossil taxa, while accounting for the stochasticity and incompleteness of the fossil record. Such an integrative approach is particularly needed when dealing with clades such as sloths (Mammalia: Folivora), for which developmental and biomechanical studies have shown high levels of morphological convergence whereas molecular data can only account for a limited percentage of their total species richness. Here, we propose an alternative hypothesis of sloth evolution that emphasizes the pervasiveness of morphological convergence and the importance of considering the fossil record and an adequate taxon sampling in both phylogenetic and biogeographic inferences. Regardless of different clock models and morphological datasets, the extant sloth <em>Bradypus</em> is consistently recovered as a megatherioid, and <em>Choloepus</em> as a mylodontoid, in agreement with molecular-only analyses. The recently extinct Caribbean sloths (Megalocnoidea) are found to be a monophyletic sister-clade of Megatherioidea, in contrast to previous phylogenetic hypotheses. Our results contradict previous morphological analyses and further support the polyphyly of "Megalonychidae", whose members were found in five different clades. Regardless of taxon sampling and clock models, the Caribbean colonization of sloths is compatible with the exhumation of islands along Aves Ridge and its geological time frame. Overall, our total-evidence analysis illustrates the difficulty of positioning highly incomplete fossils, although a robust phylogenetic framework was recovered by an <em>a posteriori</em> removal of taxa with high percentages of missing characters. Elimination of these taxa improved topological resolution by reducing polytomies and increasing node support. However, it introduced a systematic and geographic bias because most of these incomplete specimens are from northern South America. This is evident in biogeographic reconstructions, which suggest Patagonia as the area of origin of many clades when taxa are underrepresented, but Amazonia and/or Central and Southern Andes when all taxa are included. More generally, our analyses demonstrate the instability of topology and divergence time estimates when using different morphological datasets and clock models, and thus caution against making macroevolutionary inferences when node support is weak or when uncertainties in the fossil record are not considered.</p>
Bayesian total-evidence inference resolves the position of the ant genus Phaulomyrma (Hymenoptera, Formicidae)
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