The rise and diversification of the dinosaurs in the Late Triassic, from 230 to 200 million years ago, is a classic example of an evolutionary radiation with supposed competitive replacement. A comparison of evolutionary rates and morphological disparity of basal dinosaurs and their chief "competitors," the crurotarsan archosaurs, shows that dinosaurs exhibited lower disparity and an indistinguishable rate of character evolution. The radiation of Triassic archosaurs as a whole is characterized by declining evolutionary rates and increasing disparity, suggesting a decoupling of character evolution from body plan variety. The results strongly suggest that historical contingency, rather than prolonged competition or general "superiority," was the primary factor in the rise of dinosaurs.

The evolution of birds from theropod dinosaurs was one of the great evolutionary transitions in the history of life. The macroevolutionary tempo and mode of this transition is poorly studied, which is surprising because it may offer key insight into major questions in evolutionary biology, particularly whether the origins of evolutionary novelties or new ecological opportunities are associated with unusually elevated "bursts" of evolution. We present a comprehensive phylogeny placing birds within the context of theropod evolution and quantify rates of morphological evolution and changes in overall morphological disparity across the dinosaur-bird transition. Birds evolved significantly faster than other theropods, but they are indistinguishable from their closest relatives in morphospace. Our results demonstrate that the rise of birds was a complex process: birds are a continuum of millions of years of theropod evolution, and there was no great jump between nonbirds and birds in morphospace, but once the avian body plan was gradually assembled, birds experienced an early burst of rapid anatomical evolution. This suggests that high rates of morphological evolution after the development of a novel body plan may be a common feature of macroevolution, as first hypothesized by G.G. Simpson more than 60 years ago.

Discrete character-taxon matrices are increasingly being used in an attempt to understand the pattern and tempo of morphological evolution; however, methodological sophistication and bespoke software implementations have lagged behind. In the present study, an attempt is made to provide a state-of-the-art description of methodologies and introduce a new R package (Claddis) for performing foundational disparity (morphologic diversity) and rate calculations. Simulations using its core functions show that: (1) of the two most commonly used distance metrics (Generalized Euclidean Distance and Gower's Coefficient), the latter tends to carry forward more of the true signal; (2) a novel distance metric may improve signal retention further; (3) this signal retention may come at the cost of pruning incomplete taxa from the data set; and (4) the utility of bivariate plots of ordination spaces are undermined by their frequently extremely low variances. By contrast, challenges to estimating morphologic tempo are presented qualitatively, such as how trees are time-scaled and changes are counted. Both disparity and rates deserve better time series approaches that could unlock new macroevolutionary analyses. However, these challenges need not be fatal, and several potential future solutions and directions are suggested.

The observed diversity of dinosaurs reached its highest peak during the mid-and Late Cretaceous, the 50 Myr that preceded their extinction, and yet this explosion of dinosaur diversity may be explained largely by sampling bias. It has long been debated whether dinosaurs were part of the Cretaceous Terrestrial Revolution (KTR), from 125-80 Myr ago, when flowering plants, herbivorous and social insects, squamates, birds and mammals all underwent a rapid expansion. Although an apparent explosion of dinosaur diversity occurred in the mid-Cretaceous, coinciding with the emergence of new groups (e.g. neoceratopsians, ankylosaurid ankylosaurs, hadrosaurids and pachycephalosaurs), results from the first quantitative study of diversification applied to a new supertree of dinosaurs show that this apparent burst in dinosaurian diversity in the last 18 Myr of the Cretaceous is a sampling artefact. Indeed, major diversification shifts occurred largely in the first one-third of the group's history. Despite the appearance of new clades of medium to large herbivores and carnivores later in dinosaur history, these new originations do not correspond to significant diversification shifts. Instead, the overall geometry of the Cretaceous part of the dinosaur tree does not depart from the null hypothesis of an equal rates model of lineage branching. Furthermore, we conclude that dinosaurs did not experience a progressive decline at the end of the Cretaceous, nor was their evolution driven directly by the KTR.

strap (Stratigraphic Tree Analysis for Palaeontology) is a new package for the freely available statistical programming language R designed to perform three main tasks: (1) to time-scale phylogenies of fossil taxa; (2) to plot those time-scaled trees against stratigraphy; and (3) to assess congruence between phylogenies and stratigraphy. Time-scaling is performed with the DatePhylo function, with three approaches offered. Plotting trees against a choice of five different geological time scales is possible using the geoscalePhylo function. Finally, the function StratPhyloCongruence calculates stratigraphic congruence measures for one or more input phylogenies, with no taxon limit. All three major congruence measures are offered: Stratigraphic Consistency Index (SCI), Manhattan Stratigraphic Measure (MSM*) and the gap excess ratio (GER; including GERt and GER*), as well as the pseudocongruence measure, the Relative Completeness Index (RCI). Each measure has an accompanying significance test that works by comparing the input trees against a userdefined number of randomly generated topologies with the same taxon set and age ranges. Additional options for generating these random topologies allow the user to fix the outgroup or retain the input tree shape to make fairer comparisons. A tutorial that assumes no prior knowledge of R showcases all three functions using two different example data sets.

The evolutionary radiation of dinosaurs in the Late Triassic and Early Jurassic was a pivotal event in the Earth's history but is poorly understood, as previous studies have focused on vague driving mechanisms and have not untangled different macroevolutionary components (origination, diversity, abundance and disparity). We calculate the morphological disparity (morphospace occupation) of dinosaurs throughout the Late Triassic and Early Jurassic and present new measures of taxonomic diversity. Crurotarsan archosaurs, the primary dinosaur 'competitors', were significantly more disparate than dinosaurs throughout the Triassic, but underwent a devastating extinction at the Triassic-Jurassic boundary. However, dinosaur disparity showed only a slight non-significant increase after this event, arguing against the hypothesis of ecological release-driven morphospace expansion in the Early Jurassic. Instead, the main jump in dinosaur disparity occurred between the Carnian and Norian stages of the Triassic. Conversely, dinosaur diversity shows a steady increase over this time, and measures of diversification and faunal abundance indicate that the Early Jurassic was a key episode in dinosaur evolution. Thus, different aspects of the dinosaur radiation (diversity, disparity and abundance) were decoupled, and the overall macroevolutionary pattern of the first 50 Myr of dinosaur evolution is more complex than often considered.

Assessing the quality of the fossil record is notoriously hard, and many recent attempts have used sampling proxies that can be questioned. For example, counts of geological formations and estimated outcrop areas might not be defensible as reliable sampling proxies: geological formations are units of enormously variable dimensions that depend on rock heterogeneity and fossil content (and so are not independent of the fossil record), and outcrop areas are not always proportional to rock exposure, probably a closer indicator of rock availability. It is shown that in many cases formation counts will always correlate with fossil counts, whatever the degree of sampling. It is not clear, in any case, that these proxies provide a good estimate of what is missing in the gap between the known fossil record and reality; rather they largely explore the gap between known and potential fossil records. Further, using simple, single numerical metrics to correct global-scale raw data, or to model sampling-driven patterns may be premature. There are perhaps four approaches to exploring the incompleteness of the fossil record, (1) regional-scale studies of geological completeness; (2) regional- or clade-scale studies of sampling completeness using comprehensive measures of sampling, such as numbers of localities or specimens or fossil quality; (3) phylogenetic and gap-counting methods; and (4) model-based approaches that compare sampling as one of several explanatory variables with measures of environmental change, singly and in combination. We suggest that palaeontologists, like other scientists, should accept that their data are patchy and incomplete, and use appropriate methods to deal with this issue in each analysis. All that matters is whether the data are adequate for a designated study or not. A single answer to the question of whether the fossil record is driven by macroevolution or megabias is unlikely ever to emerge because of temporal, geographical, and taxonomic variance in the data.

Quantifying rates of morphological evolution is important in many macroevolutionary studies, and critical when assessing possible adaptive radiations and episodes of punctuated equilibrium in the fossil record. However, studies of morphological rates of change have lagged behind those on taxonomic diversification, and most authors have focused on continuous characters and quantifying patterns of morphological rates over time. Here, we provide a phylogenetic approach, using discrete characters and three statistical tests to determine points on a cladogram (branches or entire clades) that are characterized by significantly high or low rates of change. These methods include a randomization approach that identifies branches with significantly high rates and likelihood ratio tests that pinpoint either branches or clades that have significantly higher or lower rates than the pooled rate of the remainder of the tree. As a test case for these methods, we analyze a discrete character dataset of lungfish, which have long been regarded as "living fossils" due to an apparent slowdown in rates since the Devonian. We find that morphological rates are highly heterogeneous across the phylogeny and recover a general pattern of decreasing rates along the phylogenetic backbone toward living taxa, from the Devonian until the present. Compared with previous work, we are able to report a more nuanced picture of lungfish evolution using these new methods. K E Y W O R D S :Adaptive radiation, evolutionary rates, lungfish, morphological evolution, paleontology, punctuated equilibrium.