SUMMARYCollectively, these data demonstrate an even higher degree of morphological plasticity and convergence in the evolution of plesiosaurs than previously thought, and suggest the existence of an optimal ecomorphology for short-necked piscivorous plesiosaurs through time and across phylogeny.

Extinction risk in the modern world and extinction in the geological past are often linked to aspects of life history or other facets of biology that are phylogenetically conserved within clades. These links can result in phylogenetic clustering of extinction, a measurement comparable across different clades and time periods that can be made in the absence of detailed trait data. This phylogenetic approach is particularly suitable for vertebrate taxa, which often have fragmentary fossil records, but robust, cladistically-inferred trees. Here we use simulations to investigate the adequacy of measures of phylogenetic clustering of extinction when applied to phylogenies of fossil taxa while assuming a Brownian motion model of trait evolution. We characterize expected biases under a variety of evolutionary and analytical scenarios. Recovery of accurate estimates of extinction clustering depends heavily on the sampling rate, and results can be highly variable across topologies. Clustering is often underestimated at low sampling rates, whereas at high sampling rates it is always overestimated. Sampling rate dictates which cladogram timescaling method will produce the most accurate results, as well as how much of a bias ancestor-descendant pairs introduce. We illustrate this approach by applying two phylogenetic metrics of extinction clustering (Fritz and Purvis's D and Moran's I) to three tetrapod clades across an interval including the Permo-Triassic mass extinction event. These groups consistently show phylogenetic clustering of extinction, unrelated to change in other quantitative metrics such as taxonomic diversity or extinction intensity.

Large mammals are at high risk of extinction globally. To understand the consequences of their demise for community assembly, we tracked community structure through the end-Pleistocene megafaunal extinction in North America. We decomposed the effects of biotic and abiotic factors by analyzing co-occurrence within the mutual ranges of species pairs. Although shifting climate drove an increase in niche overlap, co-occurrence decreased, signaling shifts in biotic interactions. Furthermore, the effect of abiotic factors on co-occurrence remained constant over time while the effect of biotic factors decreased. Biotic factors apparently played a key role in continental-scale community assembly before the extinctions. Specifically, large mammals likely promoted co-occurrence in the Pleistocene, and their loss contributed to the modern assembly pattern in which co-occurrence frequently falls below random expectations.

Understanding how developmental processes change on macroevolutionary timescales to generate body plan disparity is fundamental to the study of vertebrate evolution. Adult morphology of the vertebral column directly reflects the mechanisms that generate vertebral counts (somitogenesis) and their regionalisation (homeotic effects) during embryonic development. Sauropterygians were a group of Mesozoic marine reptiles that exhibited an extremely high disparity of presacral vertebral/somite counts. Using phylogenetic comparative methods, we demonstrate that somitogenesis and homeotic effects evolved in a co‐ordinated way among sauropterygians, contrasting with the wider pattern in tetrapods, in which somitogenetic and homeotic shifts are uncorrelated. Changes in sauropterygian body proportions were primarily enabled by homeotic shifts, with a lesser, but important, contribution from differences in postpatterning growth among somites. High body plan plasticity was present in Triassic sauropterygians and was maintained among their Jurassic and Cretaceous descendants. The extreme disparity in the body plan of plesiosaurian sauropterygians did not result from accelerated rates of evolutionary change in neck length, but instead reflect this ancestral versatility of sauropterygian axial development. Our results highlight variation in modes of axial development among tetrapods, and show that heterogeneous statistical models can uncover novel macroevolutionary patterns for animal body plans and the developmental mechanisms that control them.

Many extinct taxa with extensive fossil records and mature taxonomic classifications have not yet been the subject of formal phylogenetic analysis. Here, we test whether the taxonomies available for such groups represent useful (i.e., non-misleading) substitutes for trees derived from matrix-based phylogenetic analyses. We collected data for 52 animal clades that included fossil representatives, and for which a recent cladogram and pre-cladistic taxonomy were available. We quantified the difference between the time-scaled phylogenies implied by taxonomies and cladograms using the matching cluster distance metric. We simulated phenotypic trait values and used them to estimate a series of commonly used, phylogenetically explicit measures (phylogenetic signal [Blomberg's [Formula: see text]], phylogenetic generalized least squares [PGLS], mode of evolution [Brownian vs. Ornstein-Uhlenbeck], and phylogenetic clustering of extinction [Fritz and Purvis' [Formula: see text]]) in order to determine the degree to which they co-varied on taxonomic and cladistic trees. With respect to topology taxonomies are good approximations of the underlying evolutionary relationships as recorded in inferred cladograms. Detection of phylogenetic clustering of extinction could not be properly assessed. For all other evolutionary analyses, results from taxonomy-based phylogenies (TBPs) co-varied with those from cladogram-based phylogenies (CBPs), but individual comparisons could be misleading. The relative length of terminal branches (influenced by stratigraphy and sampling rate) is a key control on the shared information between, and therefore the relative performance of, TBP and CBP. Collectively these results suggest that under particular circumstances and after careful consideration some taxonomies, or composite trees that incorporate taxonomic information, could be used in place of a formal analytical solution, but workers must be cautious. This opens certain parts of a previously inaccessible section of the fossil record to interrogation within an explicit comparative framework, which will help to test many classical macroevolutionary hypotheses formulated for groups that currently lack formal phylogenetic estimates.

Throughout their evolution, tetrapods have repeatedly colonised a series of ecological niches in marine ecosystems, producing textbook examples of convergent evolution. However, this evolutionary phenomenon has typically been assessed qualitatively and in broad-brush frameworks that imply simplistic macroevolutionary landscapes. We establish a protocol to visualize the density of trait space occupancy and thoroughly test for the existence of macroevolutionary landscapes. We apply this protocol to a new phenotypic dataset describing the morphology of short-necked plesiosaurians, a major component of the Mesozoic marine food webs (ca. 201 to 66 Mya). Plesiosaurians evolved this body plan multiple times during their 135-million-year history, making them an ideal test case for the existence of macroevolutionary landscapes. We find ample evidence for a bimodal craniodental macroevolutionary landscape separating latirostrines from longirostrine taxa, providing the first phylogenetically-explicit quantitative assessment of trophic diversity in extinct marine reptiles. This bimodal pattern was established as early as the Middle Jurassic and was maintained in evolutionary patterns of short-necked plesiosaurians until a Late Cretaceous (Turonian) collapse to a unimodal landscape comprising longirostrine forms with novel morphologies. This study highlights the potential of severe environmental perturbations to profoundly alter the macroevolutionary dynamics of animals occupying the top of food chains.

Recent renewed interest in using fossil data to understand how biotic interactions have shaped the evolution of life is challenging the widely held assumption that long-term climate changes are the primary drivers of biodiversity change. New approaches go beyond traditional richness and co-occurrence studies to explicitly model biotic interactions using data on fossil and modern biodiversity. Important developments in three primary areas of research include analysis of (i) macroevolutionary rates, (ii) the impacts of and recovery from extinction events, and (iii) how humans (Homo sapiens) affected interactions among non-human species. We present multiple lines of evidence for an important and measurable role of biotic interactions in shaping the evolution of communities and lineages on long timescales. Biotic Interactions in the Fossil RecordBiotic interactions occur when organisms living in the same community directly or indirectly influence one another. Biotic interactions can occur within or among species, be positive or negative, and cover a wide range of interactions including predation, commensalism, mutualism, resource competition, and parasitism [1]. Biotic interactions play an important role in structuring modern communities (e.g., [2]). Understanding their importance in the past therefore has the potential to shed light on their role in shaping ancient and recent diversity patterns. Historically, however, the study of biotic interactions in the fossil record has largely focused on direct physical evidence of interactions such as bore holes in shells, plant damage by insects, patterns of bryozoan encrustation, rare occurrences of gut contents, and carnivore damage on bones (e.g., [3,4]). Analysis of unusually well-preserved fossil assemblages allows reconstruction of trophic relationships among diverse organisms (e.g., [5]) and earlier work documented long-term trends in ecospace (see Glossary) occupation [6]. However, temporally continuous evidence for biotic interactions (traditionally thought to structure biodiversity on only very limited spatiotemporal scales [7]) with appropriate temporal resolution (i.e., high-resolution stratigraphic sequences) is only rarely preserved. Consequently, paleontologists have focused primarily on the more accessible long-term trends in climate as important regulators of biodiversity and the differential success of species (e.g., [8]); only short-term ecological phenomena or long-term patterns that cannot be explained by climate have typically been attributed to the outcome of biotic interactions (e.g., [9], but see [6]). However, as the only source of sufficiently long-term data, and in light of several recent methodological advances, the fossil record is now uniquely positioned to answer many of the questions at the core of the evolutionary and ecological sciences. Herein, we address important recent advances in understanding the role of biotic interactions in shaping macroevolutionary and macroecological phenomena in the fossil record (Figure 1) and highlight areas o...

Recent advances in statistical approaches called Phylogenetic Comparative Methods (PCMs) have provided paleontologists with a powerful set of analytical tools for investigating evolutionary tempo and mode in fossil lineages. However, attempts to integrate PCMs with fossil data often present workers with practical challenges or unfamiliar literature. In this paper, we present guides to the theory behind, and application of, PCMs with fossil taxa. Based on an empirical dataset of Paleozoic crinoids, we present example analyses to illustrate common applications of PCMs to fossil data, including investigating patterns of correlated trait evolution, and macroevolutionary models of morphological change. We emphasize the importance of accounting for sources of uncertainty, and discuss how to evaluate model fit and adequacy. Finally, we discuss several promising methods for modelling heterogenous evolutionary dynamics with fossil phylogenies. Integrating phylogeny-based approaches with the fossil record provides a rigorous, quantitative perspective to understanding key patterns in the history of life. Bapst 2014b). The dataset we use here is for fossil crinoids (Eucladida, Echinodermata), a morphologically diverse clade of marine invertebrates with a well-sampled fossil record. Our use of this dataset is primarily intended to demonstrate the different tree-based analytical tools that can be applied, rather than to glean specific inferences about crinoid macroevolution and we caution readers our results should be viewed in this light. Key packages in R that contain implementations of PCMs that are commonly applied to fossil data, are ape (standard format and processing for phylogenies in R, [Paradis et al. 2004]), nlme (fitting Gaussian models e.g. least squares regression, [Pinheiro et al. 2019]), geiger (versatile package that performs and plots many PCMs, [Harmon et al. 2008;Pennell et al. 2014]), phytools (additional plotting and simulation functions, [Revell 2012]) and OUwie (heterogeneous macroevolutionary model fitting e.g. Brownian Motion or Early Burst, [Beaulieu and O'Meara 2016]). There are many others, so it is valuable to spend time exploring the different tools that might be best suited to answering a particular question. Once a user has gained familiarity with the above key packages, a very extensive list of all the packages that can be used for phylogenetic approaches in R can be found at this website: https://cran.rproject.org/web/views/Phylogenetics.html.