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The importance of palaeontological data in divergence time estimation has increased with the introduction of Bayesian total‐evidence dating methods, which use fossil taxa directly for calibration, facilitated by the joint analysis of morphological and molecular data. Fossil taxa are invariably incompletely known as a consequence of taphonomic processes, resulting in the decidedly non‐random distribution of missing data. The impact of non‐random missing data on the accuracy and precision of clade age estimation is unknown. In an attempt to constrain the impact of taphonomy on tip‐calibrated dating analyses, we compared clade ages estimated from a very complete morphological matrix to ages estimated from the same matrix permuted to simulate the progressive loss of anatomical information resulting from taphonomic processes. We demonstrate that systematically distributed missing data negatively influence clade age estimates, but that successive stages within the taphonomic process introduce greater differences in age estimates, when compared to estimates obtained from untreated data. Despite these effects, the general influence of missing data is weak, presumably due to the compensatory effect of extensive morphological data from extant taxa. We suggest that, in the absence of models that can explicitly account for taphonomic processes, morphological datasets should be constructed to minimize the impact of taphonomy on divergence time estimation. [ABSTRACT FROM AUTHOR]

The molecular clock provides the only viable means of establishing realistic evolutionary timescales but it remains unclear how best to calibrate divergence time analyses. Calibrations can be applied to the tips and/or to the nodes of a phylogeny. Tip‐calibration is an attractive approach since it allows fossil species to be included alongside extant relatives in molecular clock analyses. However, most fossil species are known from multiple stratigraphical horizons and it remains unclear how such age ranges should be interpreted to codify tip‐calibrations. We use simulations and empirical data to explore the impact on precision and accuracy of different approaches to informing tip‐calibrations. In particular, we focus on the effect of using tip‐calibrations defined using the oldest vs youngest stratigraphic occurrences, the full stratigraphical range, as well as confidence intervals on these data points. The results of our simulations show that using different calibration approaches leads to different divergence‐time estimates and demonstrate that concentrating tip‐calibrations near the root of the dated phylogeny improves both precision and accuracy of estimated divergence times. Finally, our results indicate that the highest levels of accuracy and precision are achieved when fossil tips are calibrated based on the fossil occurrence from which the morphological data were derived. These trends were corroborated by analysis of an empirical dataset for Ursidae. Overall, we conclude that tip‐dating analyses should, in particular, employ tip calibrations close to the root of the tree and they should be calibrated based on the age of the fossil used to inform the morphological data used in Total Evidence Dating. [ABSTRACT FROM AUTHOR]

To understand patterns and processes of the diversification of life, we require an accurate understanding of taxon interrelationships. Recent studies have suggested that analyses of morphological character data using the Bayesian and maximum likelihood Mk model provide phylogenies of higher accuracy compared to parsimony methods. This has proved controversial, particularly studies simulating morphology‐data under Markov models that assume shared branch lengths for characters, as it is claimed this leads to bias favouring the Bayesian or maximum likelihood Mk model over parsimony models which do not explicitly make this assumption. We avoid these potential issues by employing a simulation protocol in which character states are randomly assigned to tips, but datasets are constrained to an empirically realistic distribution of homoplasy as measured by the consistency index. Datasets were analysed with equal weights and implied weights parsimony, and the maximum likelihood and Bayesian Mk model. We find that consistent (low homoplasy) datasets render method choice largely irrelevant, as all methods perform well with high consistency (low homoplasy) datasets, but the largest discrepancies in accuracy occur with low consistency datasets (high homoplasy). In such cases, the Bayesian Mk model is significantly more accurate than alternative models and implied weights parsimony never significantly outperforms the Bayesian Mk model. When poorly supported branches are collapsed, the Bayesian Mk model recovers trees with higher resolution compared to other methods. As it is not possible to assess homoplasy independently of a tree estimate, the Bayesian Mk model emerges as the most reliable approach for categorical morphological analyses. [ABSTRACT FROM AUTHOR]

Fossil taxa are critical to inferences of historical diversity and the origins of modern biodiversity, but realizing their evolutionary significance is contingent on restoring fossil species to their correct position within the tree of life. For most fossil species, morphology is the only source of data for phylogenetic inference; this has traditionally been analysed using parsimony, the predominance of which is currently challenged by the development of probabilistic models that achieve greater phylogenetic accuracy. Here, based on simulated and empirical datasets, we explore the relative efficacy of competing phylogenetic methods in terms of clade support. We characterize clade support using bootstrapping for parsimony and Maximum Likelihood, and intrinsic Bayesian posterior probabilities, collapsing branches that exhibit less than 50% support. Ignoring node support, Bayesian inference is the most accurate method in estimating the tree used to simulate the data. After assessing clade support, Bayesian and Maximum Likelihood exhibit comparable levels of accuracy, and parsimony remains the least accurate method. However, Maximum Likelihood is less precise than Bayesian phylogeny estimation, and Bayesian inference recaptures more correct nodes with higher support compared to all other methods, including Maximum Likelihood. We assess the effects of these findings on empirical phylogenies. Our results indicate probabilistic methods should be favoured over parsimony. [ABSTRACT FROM AUTHOR]

Although the relationship between ontogeny and phylogeny has been of long-standing interest to palaeontologists, the fossil record has provided little insight into the development of long extinct organisms. This has changed with the discovery of numerous assemblages of fossilized invertebrate embryos and larvae, but realising their evolutionary significance is hampered by a paucity of data on the relationship between ontogeny and taphonomy. We describe the results of an experimental taphonomy study of the development of the anostracan brine shrimp Artemia salina, which show that in conditions of aqueous aerobic and anaerobic autolysis and microbial decay, the developmental stages exhibit differential preservation potential. The most decay resistant developmental stage is the diapause cyst, encapulsating the gastrula, in which the gross morphology of the embryo can be maintained for 18 months or more in simple anaerobic conditions. Otherwise, the embryo shrinks within the cyst and cellular and tissue detail of breaks down as lipid droplets coalesce. Postembryonic excysted larvae decay more rapidly. The rate of decay is similar among all larval stages with the exception of the L4 larva, which resists cuticle failure for longer than later developmental stages. The larvae decay leading to liquefaction of the muscles and viscera, leaving an intact but empty and progressively shrunken and distorted cuticle that eventually loses structural integrity and collapses. Our experimental results provide an explanatory model for the phenomenal abundance of putative diapause stage embryos, in the absence of postembryonic stages, as seen in the Ediacaran Doushantuo Formation of South China and the incompleteness of fossilized developmental sequences of embryos and larvae more generally. It also cautions against the association of developmental stages in fossil deposits without additional evidence. Finally, the pattern of decay seen in larvae provides an explanation for the preservation style of Orsten-type Lagerstätten where preservation of cuticular detail can be astonishingly fine, but extends internally to muscles and viscera only rarely. [ABSTRACT FROM AUTHOR]

The hypothesis that conodonts are vertebrates rests solely on evidence of soft tissue anatomy. This has been corroborated by microstructural, topological and developmental evidence of homology between conodont and vertebrate hard tissues. However, these conclusions have been reached on the basis of evidence from highly derived euconodont taxa and the degree to which they are representative of plesiomorphic euconodonts remains an open question. Furthermore, the range of variation in tissue types comprising the euconodont basal body has been used to establish a hypothesis of developmental plasticity early in the phylogeny of the clade, and a model of diminishing potentiality in the evolution of development systems. The microstructural fabrics of the basal tissues of the earliest euconodonts (presumed to be the most plesiomorphic) are examined to test these two hypotheses. It is found that the range of microstructural variation observed hitherto was already apparent among plesiomorphic euconodonts. Thus, established histological data are representative of the most plesiomorphic euconodonts. However, although there is evidence of a range in microstructural fabrics, these are compatible with the dentine tissue system alone, and the degree of variation is compatible with that seen in clades of comparable diversity. [ABSTRACT FROM AUTHOR]