Sequences, stratigraphy and scenarios: what can we say about the fossil record of the earliest tetrapods?

Locomotion and the early Mesozoic success of Archosauromorpha

The Triassic was a time of ecological upheaval as life recovered from the Permian-Triassic mass extinction. Archosauromorphs were a key component of the recovery, diversifying substantially during the Triassic and encompassing the origins of dinosaurs, pterosaurs and crocodylomorphs. Here, we explore the evolution of locomotion in Archosauromorpha to test whether dinosaurs show any distinctive locomotory features that might explain their success. We implement geometric morphometrics on limb bone shapes and use limb ratios to calculate bipedality and cursoriality metrics. We find that the Avemetatarsalia (dinosaurs, pterosaurs and relatives) exhibit more variable limb form and limb ratios than any other group, indicating a wider range of locomotory modes. The earliest avemetatarsalians were bipedal and cursorial, and their range of form increased through the Triassic with notable diversification shifts following extinction events. This is especially true of dinosaurs, even though these changes cannot be discriminated from a stochastic process. By contrast, the Pseudosuchia (crocodilians and relatives) were more restricted in limb form and locomotor mode with disparity decreasing through time, suggesting more limited locomotor adaptation and vulnerability to extinction. Perhaps the greater locomotor plasticity of dinosaurs gave them a competitive advantage in the changing climates of the Late Triassic.

Using the Fossil Record to Evaluate Timetree Timescales

The fossil and geologic records provide the primary data used to established absolute timescales for timetrees. For the paleontological evaluation of proposed timetree timescales, and for node-based methods for constructing timetrees, the fossil record is used to bracket divergence times. Minimum brackets (minimum ages) can be established robustly using well-dated fossils that can be reliably assigned to lineages based on positive morphological evidence. Maximum brackets are much harder to establish, largely because it is difficult to establish definitive evidence that the absence of a taxon in the fossil record is real and not just due to the incompleteness of the fossil and rock records. Five primary methods have been developed to estimate maximum age brackets, each of which is discussed. The fact that the fossilization potential of a group typically decreases the closer one approaches its time of origin increases the challenge of estimating maximum age brackets. Additional complications arise: 1) because fossil data actually bracket the time of origin of the first relevant fossilizable morphology (apomorphy), not the divergence time itself; 2) due to the phylogenetic uncertainty in the placement of fossils; 3) because of idiosyncratic temporal and geographic gaps in the rock and fossil records; and 4) if the preservation potential of a group changed significantly during its history. In contrast, uncertainties in the absolute ages of fossils are typically relatively unimportant, even though the vast majority of fossil cannot be dated directly. These issues and relevant quantitative methods are reviewed, and their relative magnitudes assessed, which typically correlate with the age of the group, its geographic range, and species richness.

Non-marine palaeoenvironment associated to the earliest tetrapod tracks

Opinions differ on whether the evolution of tetrapods (limbed vertebrates) from lobe-finned fishes was directly linked to terrestrialization. The earliest known tetrapod fossils, from the Middle Devonian (approximately 390 million years old) of Zachełmie Quarry in Poland, are trackways made by limbs with digits; they document a direct environmental association and thus have the potential to help answer this question. However, the tetrapod identity of the tracks has recently been challenged, despite their well-preserved morphology, on account of their great age and supposedly shallow marine (intertidal or lagoonal) depositional environment. Here we present a new palaeoenvironmental interpretation of the track-bearing interval from Zachełmie, showing that it represents a succession of ephemeral lakes with a restricted and non-marine biota, rather than a marginal marine environment as originally thought. This context suggests that the trackmaker was capable of terrestrial locomotion, consistent with the appendage morphology recorded by the footprints, and thus provides additional support for a tetrapod identification.

Evolution of the muscular system in tetrapod limbs

While skeletal evolution has been extensively studied, the evolution of limb muscles and brachial plexus has received less attention. In this review, we focus on the tempo and mode of evolution of forelimb muscles in the vertebrate history, and on the developmental mechanisms that have affected the evolution of their morphology. Tetrapod limb muscles develop from diffuse migrating cells derived from dermomyotomes, and the limb-innervating nerves lose their segmental patterns to form the brachial plexus distally. Despite such seemingly disorganized developmental processes, limb muscle homology has been highly conserved in tetrapod evolution, with the apparent exception of the mammalian diaphragm. The limb mesenchyme of lateral plate mesoderm likely plays a pivotal role in the subdivision of the myogenic cell population into individual muscles through the formation of interstitial muscle connective tissues. Interactions with tendons and motoneuron axons are involved in the early and late phases of limb muscle morphogenesis, respectively. The mechanism underlying the recurrent generation of limb muscle homology likely resides in these developmental processes, which should be studied from an evolutionary perspective in the future.

Tropospheric ozonesonde profiles at long-term U.S. monitoring sites: 1. A climatology based on self-organizing maps

Sonde-based climatologies of tropospheric ozone (O₃) are vital for developing satellite retrieval algorithms and evaluating chemical transport model output. Typical O₃ climatologies average measurements by latitude or region, and season. Recent analysis using self-organizing maps (SOM) to cluster ozonesondes from two tropical sites found clusters of O₃ mixing ratio profiles are an excellent way to capture O₃ variability and link meteorological influences to O₃ profiles. Clusters correspond to distinct meteorological conditions, e.g. convection, subsidence, cloud cover, and transported pollution. Here, the SOM technique is extended to four long-term U.S. sites (Boulder, CO; Huntsville, AL; Trinidad Head, CA; Wallops Island, VA) with 4530 total profiles. Sensitivity tests on k-means algorithm and SOM justify use of 3×3 SOM (nine clusters). At each site, SOM clusters together O₃ profiles with similar tropopause height, 500 hPa height/temperature, and amount of tropospheric and total column O₃. Cluster means are compared to monthly O₃ climatologies. For all four sites, near-tropopause O₃ is double (over +100 parts per billion by volume; ppbv) the monthly climatological O₃ mixing ratio in three clusters that contain 13 - 16% of profiles, mostly in winter and spring. Large mid-tropospheric deviations from monthly means (-6 ppbv, +7 - 10 ppbv O₃ at 6 km) are found in two of the most populated clusters (combined 36 - 39% of profiles). These two clusters contain distinctly polluted (summer) and clean O₃ (fall-winter, high tropopause) profiles, respectively. As for tropical profiles previously analyzed with SOM, O₃ averages are often poor representations of U.S. O₃ profile statistics.

Taxonomy and Phylogeny Can Yield Comparable Results in Comparative Paleontological Analyses

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.

A simple method for estimating informative node age priors for the fossil calibration of molecular divergence time analyses

Molecular divergence time analyses often rely on the age of fossil lineages to calibrate node age estimates. Most divergence time analyses are now performed in a Bayesian framework, where fossil calibrations are incorporated as parametric prior probabilities on node ages. It is widely accepted that an ideal parameterization of such node age prior probabilities should be based on a comprehensive analysis of the fossil record of the clade of interest, but there is currently no generally applicable approach for calculating such informative priors. We provide here a simple and easily implemented method that employs fossil data to estimate the likely amount of missing history prior to the oldest fossil occurrence of a clade, which can be used to fit an informative parametric prior probability distribution on a node age. Specifically, our method uses the extant diversity and the stratigraphic distribution of fossil lineages confidently assigned to a clade to fit a branching model of lineage diversification. Conditioning this on a simple model of fossil preservation, we estimate the likely amount of missing history prior to the oldest fossil occurrence of a clade. The likelihood surface of missing history can then be translated into a parametric prior probability distribution on the age of the clade of interest. We show that the method performs well with simulated fossil distribution data, but that the likelihood surface of missing history can at times be too complex for the distribution-fitting algorithm employed by our software tool. An empirical example of the application of our method is performed to estimate echinoid node ages. A simulation-based sensitivity analysis using the echinoid data set shows that node age prior distributions estimated under poor preservation rates are significantly less informative than those estimated under high preservation rates.

Late to the table: diversification of tetrapod mandibular biomechanics lagged behind the evolution of terrestriality

The origin of digit-bearing tetrapods in the Middle to Late Devonian (ca. 393-360 Mya) and their subsequent invasion of land represent a classic case of a major evolutionary radiation driven by new ecological opportunities. In this and other examples, exploration of new eco-space is hypothesized to correlate with functional innovation and adaptive divergence of phenotypes. Simultaneous changes in all morphofunctional systems are rare in major evolutionary transitions and may be non-existent. Here, we focus on the mandibles of early tetrapods and their kin as a model system to test whether shifts in functional innovation were coeval with some major events in tetrapod history. To this end, we quantified mechanical variation in the mandibles of tetrapodomorphs ranging in age from Early Devonian to earliest Permian. Biomechanical disparity is stable from the Devonian to the Early Pennsylvanian, even though the origin of weight-bearing, digited limbs, and the initial phases of the colonization of land occurred during this interval. An appreciable increase in functional variation is detected in the latest Pennsylvanian and earliest Permian, when stem and crown amniotes began to explore new regions of mechanical morphospace, a pattern partly attributable to the origin of herbivory. We find no difference in the rate of functional change between tetrapodomorph "fish" and early digited tetrapods, although two independent shifts are detected among Devonian stem tetrapods more crownward than Acanthostega. Instead, the most profound shifts in evolutionary rate are nested well within the tetrapod crown and are associated with amniotes (particularly diadectomorphs and some synapsids). The substantial temporal gap between the origin of postcranial features associated with terrestriality, such as limbs with functional elbow/knee and wrist/ankle joints capable of weight-bearing, and the onset of divergence in jaw biomechanics provides a compelling example of "functional modularity" during a major adaptive radiation.

A marine stem-tetrapod from the Devonian of western North America

The origin of terrestrial vertebrates represents one of the major evolutionary and ecological transformations in the history of life, and the established timing and environment of this transition has recently come under scrutiny. The discovery and description of a well-preserved fossil sarcopterygian (fleshy-limbed vertebrate) from the Middle Devonian of Nevada helps to refine and question aspects of the temporal and anatomical framework that underpins the tetrapod condition. This new taxon, Tinirau clackae, demonstrates that substantial parallelism pervaded the early history of stem-tetrapods, raises additional questions about when digited sarcopterygians first evolved, and further documents that incipient stages of the terrestrial appendicular condition began when sarcopterygians still retained their median fins and occupied aquatic habitats.