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Trilobites are often considered exemplary for understanding the Cambrian explosion of animal life, due to their unsurpassed diversity and abundance. These biomineralized arthropods appear abruptly in the fossil record with an established diversity, phylogenetic disparity, and provincialism at the beginning of Cambrian Series 2 (∼521 Ma), suggesting a protracted but cryptic earlier history that possibly extends into the Precambrian. However, recent analyses indicate elevated rates of phenotypic and genomic evolution for arthropods during the early Cambrian, thereby shortening the phylogenetic fuse. Furthermore, comparatively little research has been devoted to understanding the duration of the Cambrian explosion, after which normal Phanerozoic evolutionary rates were established. We test these hypotheses by applying Bayesian tip-dating methods to a comprehensive dataset of Cambrian trilobites. We show that trilobites have a Cambrian origin, as supported by the trace fossil record and molecular clocks. Surprisingly, they exhibit constant evolutionary rates across the entire Cambrian, for all aspects of the preserved phenotype: discrete, meristic, and continuous morphological traits. Our data therefore provide robust, quantitative evidence that by the time the typical Cambrian fossil record begins (∼521 Ma), the Cambrian explosion had already largely concluded. This suggests that a modern-style marine biosphere had rapidly emerged during the latest Ediacaran and earliest Cambrian (∼20 million years), followed by broad-scale evolutionary stasis throughout the remainder of the Cambrian.

Recent discoveries have highlighted the dramatic evolutionary transformation of massive, ground-dwelling theropod dinosaurs into light, volant birds. Here, we apply Bayesian approaches (originally developed for inferring geographic spread and rates of molecular evolution in viruses) in a different context: to infer size changes and rates of anatomical innovation (across up to 1549 skeletal characters) in fossils. These approaches identify two drivers underlying the dinosaur-bird transition. The theropod lineage directly ancestral to birds undergoes sustained miniaturization across 50 million years and at least 12 consecutive branches (internodes) and evolves skeletal adaptations four times faster than other dinosaurs. The distinct, prolonged phase of miniaturization along the bird stem would have facilitated the evolution of many novelties associated with small body size, such as reorientation of body mass, increased aerial ability, and paedomorphic skulls with reduced snouts but enlarged eyes and brains.

The living coelacanth Latimeria (Sarcopterygii: Actinistia) is an iconic, so-called ‘living fossil’ within one of the most apparently morphologically conservative vertebrate groups. We describe a new, 3-D preserved coelacanth from the Late Devonian Gogo Formation in Western Australia. We assemble a comprehensive analysis of the group to assess the phylogeny, evolutionary rates, and morphological disparity of all coelacanths. We reveal a major shift in morphological disparity between Devonian and post-Devonian coelacanths. The newly described fossil fish fills a critical transitional stage in coelacanth disparity and evolution. Since the mid-Cretaceous, discrete character changes (representing major morphological innovations) have essentially ceased, while meristic and continuous characters have continued to evolve within coelacanths. Considering a range of putative environmental drivers, tectonic activity best explains variation in the rates of coelacanth evolution. Coelacanths are known for their conservative morphology. Here, the authors describe a 380 million year-old coelacanth fossil from the Gogo Formation (Western Australia) with morphology representative of a key transition where coelacanth morphology disparity shifts.

The giant flightless bird Sylviornis neocaledoniae (Aves: Sylviornithidae) existed on La Grande Terre and Ile des Pins, New Caledonia, until the late Holocene when it went extinct shortly after human arrival on these islands. The species was generally considered to be a megapode (Megapodiidae) until the family Sylviornithidae was erected for it in 2005 to reflect multiple cranial autapomorphies. However, despite thousands of bones having been reported for this unique and enigmatic taxon, the postcranial anatomy has remained largely unknown. We rectify this deficiency and describe the postcranial skeleton of S. neocaledoniae based on ~600 fossils and use data from this and its cranial anatomy to make a comprehensive assessment of its phylogenetic affinities. Sylviornis neocaledoniae is found to be a stem galliform, distant from megapodiids, and the sister taxon to the extinct flightless Megavitiornis altirostris from Fiji, which we transfer to the family Sylviornithidae. These two species form the sister group to extant crown-group galliforms. Several other fossil galloanseres also included in the phylogenetic analysis reveal novel hypotheses of their relationships as follows: Dromornis planei (Dromornithidae) is recovered as a stem galliform rather than a stem anseriform; Presbyornis pervetus (Presbyornithidae) is the sister group to Anseranatidae, not to Anatidae; Vegavis iaai is a crown anseriform but remains unresolved relative to Presbyornis pervetus, Anseranatidae and Anatidae. Sylviornis neocaledoniae was reconstructed herein to be 0.8 m tall in a resting stance and weigh 27-34 kg. The postcranial anatomy of S. neocaledoniae shows no indication of the specialised adaptation to digging seen in megapodiids, with for example, its ungual morphology differing little from that of chicken Gallus gallus. These observations and its phylogenetic placement as stem galliforms makes it improbable that this species employed ectothermic incubation or was a mound-builder. Sylviornis neocaledoniae can therefore be excluded as the constructor of tumuli in New Caledonia.

Molecular evolutionary rate estimates have been shown to depend on the time period over which they are estimated. Factors such as demographic processes, calibration errors, purifying selection, and the heterogeneity of substitution rates among sites (RHAS) are known to affect the accuracy with which rates of evolution are estimated. We use mathematical modeling and Bayesian analyses of simulated sequence alignments to explore how mutational hotspots can lead to time-dependent rate estimates. Mathematical modeling shows that underestimation of molecular rates over increasing time scales is inevitable when RHAS is ignored. Although a gamma distribution is commonly used to model RHAS, we show that when the actual RHAS deviates from a gamma-like distribution, rates can either be under- or overestimated in a time-dependent manner. Simulations performed under different scenarios of RHAS confirm the mathematical modeling and demonstrate the impacts of time-dependent rates on estimates of divergence times. Most notably, erroneous rate estimates can have narrow credibility intervals, leading to false confidence in biased estimates of rates, and node ages. Surprisingly, large errors in estimates of overall molecular rate do not necessarily generate large errors in divergence time estimates. Finally, we illustrate the correlation between time-dependent rate patterns and differential saturation between quickly and slowly evolving sites. Our results suggest that data partitioning or simple nonparametric mixture models of RHAS significantly improve the accuracy with which node ages and substitution rates can be estimated.

New fossils from Australia reveal that the Cambrian apex predator Anomalocaris possessed compound eyes more powerful than those of most living arthropods. A sharp-eyed Cambrian predator The metre-long swimming invertebrate Anomalocaris was the top predator in the Cambrian ocean more than 500 million years ago. Recent discoveries of fly-like compound eyes attributable to this creature confirm suggestions that it is related to the arthropods — jointed-limbed creatures such as insects, crustaceans and trilobites — and show that compound eyes evolved before hardened exoskeletons. The superbly preserved fossils from South Australia show that Anomalocaris had exceptional vision. Its compound eyes are among the largest and most acute to have ever existed; each eye is up to 3 centimetres long and contains more than 16,000 lenses. The existence of highly visual hunters during the Cambrian would have accelerated the pace of the predator–prey 'arms race' then under way. Until recently 1 , intricate details of the optical design of non-biomineralized arthropod eyes remained elusive in Cambrian Burgess-Shale-type deposits, despite exceptional preservation of soft-part anatomy in such Konservat-Lagerstätten 2 , 3 . The structure and development of ommatidia in arthropod compound eyes support a single origin some time before the latest common ancestor of crown-group arthropods 4 , but the appearance of compound eyes in the arthropod stem group has been poorly constrained in the absence of adequate fossils. Here we report 2–3-cm paired eyes from the early Cambrian (approximately 515 million years old) Emu Bay Shale of South Australia, assigned to the Cambrian apex predator Anomalocaris . Their preserved visual surfaces are composed of at least 16,000 hexagonally packed ommatidial lenses (in a single eye), rivalling the most acute compound eyes in modern arthropods. The specimens show two distinct taphonomic modes, preserved as iron oxide (after pyrite) and calcium phosphate, demonstrating that disparate styles of early diagenetic mineralization can replicate the same type of extracellular tissue (that is, cuticle) within a single Burgess-Shale-type deposit. These fossils also provide compelling evidence for the arthropod affinities of anomalocaridids, push the origin of compound eyes deeper down the arthropod stem lineage, and indicate that the compound eye evolved before such features as a hardened exoskeleton. The inferred acuity of the anomalocaridid eye is consistent with other evidence that these animals were highly mobile visual predators in the water column 5 , 6 . The existence of large, macrophagous nektonic predators possessing sharp vision—such as Anomalocaris —within the early Cambrian ecosystem probably helped to accelerate the escalatory ‘arms race’ that began over half a billion years ago 7 , 8 .

Like other soft-bodied organisms, ctenophores (comb jellies) produce fossils only under exceptional taphonomic conditions. Here, we present the first record of a Late Devonian ctenophore from the Escuminac Formation from Miguasha in eastern Canada. Based on the 18-fold symmetry of this disc-shaped fossil, we assign it to the total-group Ctenophora. Our phylogenetic analyses suggest that the new taxon Daihuoides jakobvintheri gen. et sp. nov. falls near Cambrian stem ctenophores such as ‘dinomischids’ and 'scleroctenophorans'. Accordingly, Daihuoides is a Lazarus-taxon, which post-dates its older relatives by over 140 million years, and overlaps temporally with modern ctenophores, whose oldest representatives are known from the Early Devonian. Our analyses also indicate that the fossil record of ctenophores does not provide strong evidence for or against the phylogenomic hypothesis that ctenophores are sister to all other metazoans.

Background The relative influence of diet and phylogeny on snake venom activity is a poorly understood aspect of snake venom evolution. We measured the activity of two enzyme toxin groups – phospholipase A 2 (PLA 2 ), and L-amino acid oxidase (LAAO) – in the venom of 39 species of Australian elapids (40% of terrestrial species diversity) and used linear parsimony and BayesTraits to investigate any correlation between enzyme activity and phylogeny or diet. Results PLA 2 activity ranged from 0 to 481 nmol/min/mg of venom, and LAAO activity ranged from 0 to 351 nmol/min/mg. Phylogenetic comparative methods, implemented in BayesTraits showed that enzyme activity was strongly correlated with phylogeny, more so for LAAO activity. For example, LAAO activity was absent in both the Vermicella and Pseudonaja/Oxyuranus clade, supporting previously proposed relationships among these disparate taxa. There was no association between broad dietary categories and either enzyme activity. There was strong evidence for faster initial rates of change over evolutionary time for LAAO (delta parameter mean 0.2), but no such pattern in PLA 2 (delta parameter mean 0.64). There were some exceptions to the phylogenetic patterns of enzyme activity: different PLA 2 activity in the ecologically similar sister-species Denisonia devisi and D. maculata ; large inter-specific differences in PLA 2 activity in Hoplocephalus and Austrelaps . Conclusions We have shown that phylogeny is a stronger influence on venom enzyme activity than diet for two of the four major enzyme families present in snake venoms. PLA 2 and LAAO activities had contrasting evolutionary dynamics with the higher delta value for PLA 2 Some species/individuals lacked activity in one protein family suggesting that the loss of single protein family may not incur a significant fitness cost.

Simultaneously analysing morphological, molecular and stratigraphic data suggests a potential resolution to a major remaining inconsistency in crocodylian evolution. The ancient, long-snouted thoracosaurs have always been placed near the Indian gharial Gavialis , but their antiquity ( ca 72 Ma) is highly incongruous with genomic evidence for the young age of the Gavialis lineage ( ca 40 Ma). We reconcile this contradiction with an updated morphological dataset and novel analysis, and demonstrate that thoracosaurs are an ancient iteration of long-snouted stem crocodylians unrelated to modern gharials. The extensive similarities between thoracosaurs and Gavialis are shown to be an almost ‘perfect storm’ of homoplasy, combining convergent adaptions to fish-eating, as well resemblances between genuinely primitive traits (thoracosaurs) and atavisms ( Gavialis ). Phylogenetic methods that ignore stratigraphy (parsimony and undated Bayesian methods) are unable to tease apart these similarities and invariably unite thoracosaurs and Gavialis. However, tip-dated Bayesian approaches additionally consider the large temporal gap separating ancient (thoracosaurs) and modern ( Gavialis ) iterations of similar long-snouted crocodyliforms. These analyses robustly favour a phylogeny which places thoracosaurs basal to crocodylians, far removed from modern gharials, which accordingly are a very young radiation. This phylogenetic uncoupling of ancient and modern gharial-like crocs is more consistent with molecular clock divergence estimates, and also the bulk of the crocodylian fossil record (e.g. all unequivocal gharial fossils are very young). Provided that the priors and models attribute appropriate relative weights to the morphological and stratigraphic signals—an issue that requires investigation—tip-dating approaches are potentially better able to detect homoplasy and improve inferences about phylogenetic relationships, character evolution and divergence dates.

Background Palaeognathae is a basal clade within Aves and include the large and flightless ratites and the smaller, volant tinamous. Although much research has been conducted on various aspects of palaeognath morphology, ecology, and evolutionary history, there are still areas which require investigation. This study aimed to fill gaps in our knowledge of the Southern Cassowary, Casuarius casuarius , for which information on the skeletal systems of the syrinx, hyoid and larynx is lacking - despite these structures having been recognised as performing key functional roles associated with vocalisation, respiration and feeding. Previous research into the syrinx and hyoid have also indicated these structures to be valuable for determining evolutionary relationships among neognath taxa, and thus suggest they would also be informative for palaeognath phylogenetic analyses, which still exhibits strong conflict between morphological and molecular trees. Results The morphology of the syrinx, hyoid and larynx of C. casuarius is described from CT scans. The syrinx is of the simple tracheo-bronchial syrinx type, lacking specialised elements such as the pessulus; the hyoid is relatively short with longer ceratobranchials compared to epibranchials; and the larynx is comprised of entirely cartilaginous, standard avian anatomical elements including a concave, basin-like cricoid and fused cricoid wings. As in the larynx, both the syrinx and hyoid lack ossification and all three structures were most similar to Dromaius. We documented substantial variation across palaeognaths in the skeletal character states of the syrinx, hyoid, and larynx, using both the literature and novel observations (e.g. of C. casuarius ). Notably, new synapomorphies linking Dinornithiformes and Tinamidae are identified, consistent with the molecular evidence for this clade. These shared morphological character traits include the ossification of the cricoid and arytenoid cartilages, and an additional cranial character, the articulation between the maxillary process of the nasal and the maxilla. Conclusion Syrinx, hyoid and larynx characters of palaeognaths display greater concordance with molecular trees than do other morphological traits. These structures might therefore be less prone to homoplasy related to flightlessness and gigantism, compared to typical morphological traits emphasised in previous phylogenetic studies.