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Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, andamphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications usingDNAsequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS),phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously wellsupported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a fewundesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata.We comment on the origins and diversification of Squamata throughout theMesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).

We report a time-calibrated stratigraphic section in Colorado that contains unusually complete fossils of mammals, reptiles, and plants and elucidates the drivers and tempo of biotic recovery during the poorly known first million years after the Cretaceous–Paleogene mass extinction (KPgE). Within ∼100 thousand years (ka) post-KPgE, mammalian taxonomic richness doubled, and maximum mammalian body mass increased to near pre-KPgE levels. A threefold increase in maximum mammalian body mass and dietary niche specialization occurred at ∼300 ka post-KPgE, concomitant with increased megafloral standing species richness. The appearance of additional large mammals occurred by ∼700 ka post-KPgE, coincident with the first appearance of Leguminosae (the bean family). These concurrent plant and mammal originations and body-mass shifts coincide with warming intervals, suggesting that climate influenced post-KPgE biotic recovery.

Dinosaurs and pterosaurs have remarkable diversity and disparity through most of the Mesozoic Era 1 – 3 . Soon after their origins, these reptiles diversified into a number of long-lived lineages, evolved unprecedented ecologies (for example, flying, large herbivorous forms) and spread across Pangaea 4 , 5 . Recent discoveries of dinosaur and pterosaur precursors 6 – 10 demonstrated that these animals were also speciose and widespread, but those precursors have few if any well-preserved skulls, hands and associated skeletons 11 , 12 . Here we present a well-preserved partial skeleton (Upper Triassic, Brazil) of the new lagerpetid Venetoraptor gassenae gen. et sp. nov. that offers a more comprehensive look into the skull and ecology of one of these precursors. Its skull has a sharp, raptorial-like beak, preceding that of dinosaurs by around 80 million years, and a large hand with long, trenchant claws that firmly establishes the loss of obligatory quadrupedalism in these precursor lineages. Combining anatomical information of the new species with other dinosaur and pterosaur precursors shows that morphological disparity of precursors resembles that of Triassic pterosaurs and exceeds that of Triassic dinosaurs. Thus, the ‘success’ of pterosaurs and dinosaurs was a result of differential survival among a broader pool of ecomorphological variation. Our results show that the morphological diversity of ornithodirans started to flourish among early-diverging lineages and not only after the origins of dinosaurs and pterosaurs. A well-preserved partial skeleton (Upper Triassic, Brazil) of the new lagerpetid Venetoraptor gassenae gen. et sp. nov. offers a more comprehensive look into the skull and ecology of dinosaur and pterosaur precursors.

To provide context for the diversification of archosaurs—the group that includes crocodilians, dinosaurs, and birds—we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.

Here, I combine previously underutilized models and priors to perform more biologically realistic phylogenetic inference from morphological data, with an example from squamate reptiles. When coding morphological characters, it is often possible to denote ordered states with explicit reference to observed or hypothetical ancestral conditions. Using this logic, we can integrate across character-state labels and estimate meaningful rates of forward and backward transitions from plesiomorphy to apomorphy. I refer to this approach as MkA, for \"asymmetric.\" The MkA model incorporates the biological reality of limited reversal for many phylogenetically informative characters, and significantly increases likelihoods in the empirical data sets. Despite this, the phylogeny of Squamata remains contentious. Total-evidence analyses using combined morphological and molecular data and the MkA approach tend toward recent consensus estimates supporting a nested Iguania. However, support for this topology is not unambiguous across data sets or analyses, and no mechanism has been proposed to explain the widespread incongruence between partitions, or the hidden support for various topologies in those partitions. Furthermore, different morphological data sets produced by different authors contain both different characters and different states for the same or similar characters, resulting in drastically different placements for many important fossil lineages. Effort is needed to standardize ontology for morphology, resolve incongruence, and estimate a robust phylogeny. The MkA approach provides a preliminary avenue for investigating morphological evolution while accounting for temporal evidence and asymmetry in character-state changes.

Protected areas (PAs) are the primary strategy for slowing terrestrial biodiversity loss. Although expansion of PA coverage is prioritized under the Convention on Biological Diversity, it remains unknown whether PAs mitigate declines across the tetrapod tree of life and to what extent land cover and climate change modify PA effectiveness 1 , 2 . Here we analysed rates of change in abundance of 2,239 terrestrial vertebrate populations across the globe. On average, vertebrate populations declined five times more slowly within PAs (−0.4% per year) than at similar sites lacking protection (−1.8% per year). The mitigating effects of PAs varied both within and across vertebrate classes, with amphibians and birds experiencing the greatest benefits. The benefits of PAs were lower for amphibians in areas with converted land cover and lower for reptiles in areas with rapid climate warming. By contrast, the mitigating impacts of PAs were consistently augmented by effective national governance. This study provides evidence for the effectiveness of PAs as a strategy for slowing tetrapod declines. However, optimizing the growing PA network requires targeted protection of sensitive clades and mitigation of threats beyond PA boundaries. Provided the conditions of targeted protection, adequate governance and well-managed landscapes are met, PAs can serve a critical role in safeguarding tetrapod biodiversity. An analysis of 2,239 terrestrial vertebrate populations shows that they decline more slowly in protected areas than outside protected areas, but the benefits vary across vertebrate classes and depend on the regional context of the protected area.

Recent analyses have reported catastrophic global declines in vertebrate populations 1 , 2 . However, the distillation of many trends into a global mean index obscures the variation that can inform conservation measures and can be sensitive to analytical decisions. For example, previous analyses have estimated a mean vertebrate decline of more than 50% since 1970 (Living Planet Index 2 ). Here we show, however, that this estimate is driven by less than 3% of vertebrate populations; if these extremely declining populations are excluded, the global trend switches to an increase. The sensitivity of global mean trends to outliers suggests that more informative indices are needed. We propose an alternative approach, which identifies clusters of extreme decline (or increase) that differ statistically from the majority of population trends. We show that, of taxonomic–geographic systems in the Living Planet Index, 16 systems contain clusters of extreme decline (comprising around 1% of populations; these extreme declines occur disproportionately in larger animals) and 7 contain extreme increases (around 0.4% of populations). The remaining 98.6% of populations across all systems showed no mean global trend. However, when analysed separately, three systems were declining strongly with high certainty (all in the Indo-Pacific region) and seven were declining strongly but with less certainty (mostly reptile and amphibian groups). Accounting for extreme clusters fundamentally alters the interpretation of global vertebrate trends and should be used to help to prioritize conservation efforts. In the geographically and taxonomically divided systems of vertebrates in the Living Planet Index, a small percentage of clusters showed extreme declines or increases, whereas most vertebrate populations across all systems showed no mean global trend.

Phylogenetic diversity measures are increasingly used in conservation planning to represent aspects of biodiversity beyond that captured by species richness. Here we develop two new metrics that combine phylogenetic diversity and the extent of human pressure across the spatial distribution of species — one metric valuing regions and another prioritising species. We evaluate these metrics for reptiles, which have been largely neglected in previous studies, and contrast these results with equivalent calculations for all terrestrial vertebrate groups. We find that regions under high human pressure coincide with the most irreplaceable areas of reptilian diversity, and more than expected by chance. The highest priority reptile species score far above the top mammal and bird species, and reptiles include a disproportionate number of species with insufficient extinction risk data. Data Deficient species are, in terms of our species-level metric, comparable to Critically Endangered species and therefore may require urgent conservation attention. In addition to species richness, evolutionary measures of biodiversity are important considerations for conservation. Here, Gumbs et al. develop new biodiversity metrics incorporating phylogenetic diversity and human pressure and highlight conservation priorities in a global analysis of reptiles.

Examining the geological past of our planet allows us to study periods of severe climatic and biological crises and recoveries, biotic and abiotic ecosystem fluctuations, and faunal and floral turnovers through time. Furthermore, the recovery dynamics of large predators provide a key for evaluation of the pattern and tempo of ecosystem recovery because predators are interpreted to react most sensitively to environmental turbulences. The end-Permian mass extinction was the most severe crisis experienced by life on Earth, and the common paradigm persists that the biotic recovery from the extinction event was unusually slow and occurred in a step-wise manner, lasting up to eight to nine million years well into the early Middle Triassic (Anisian) in the oceans, and even longer in the terrestrial realm. Here we survey the global distribution and size spectra of Early Triassic and Anisian marine predatory vertebrates (fishes, amphibians and reptiles) to elucidate the height of trophic pyramids in the aftermath of the end-Permian event. The survey of body size was done by compiling maximum standard lengths for the bony fishes and some cartilaginous fishes, and total size (estimates) for the tetrapods. The distribution and size spectra of the latter are difficult to assess because of preservation artifacts and are thus mostly discussed qualitatively. The data nevertheless demonstrate that no significant size increase of predators is observable from the Early Triassic to the Anisian, as would be expected from the prolonged and stepwise trophic recovery model. The data further indicate that marine ecosystems characterized by multiple trophic levels existed from the earliest Early Triassic onwards. However, a major change in the taxonomic composition of predatory guilds occurred less than two million years after the end-Permian extinction event, in which a transition from fish/amphibian to fish/reptile-dominated higher trophic levels within ecosystems became apparent.

The Ichthyopterygia appeared in the fossil record as fully evolved, aquatic creatures, with nothing known about their transition from land to water, but now some light is shed on this transition by a fossil from the Lower Triassic of southern China of a small, primitive and possibly amphibious ichthyosaur-like creature, close to the common ancestry of ichthyosaurs and the obscure Hupehsuchia, a group of extinct aquatic reptiles known only from southern China. An amphibious ichthyosaur forerunner? Ichthyosaurs were exclusively aquatic reptiles, with limbs that had become flippers and a body shape converged on the streamlined outline of modern dolphins. They appeared in the Triassic Period and became extinct, along with the dinosaurs, at the end of the Cretaceous. Inconveniently, their first appearance in the fossil record is as fully evolved, aquatic creatures — nothing is known about their transition from land to water. Some light might be shed on the matter by a newly discovered fossil from the Lower Triassic of southern China. It is a very small, very primitive and possibly amphibious ichthyosaur-like creature, close to the common ancestry of ichthyosaurs and the obscure Hupehsuchia, a group of extinct aquatic reptiles known only from southern China. The incompleteness of the fossil record obscures the origin of many of the more derived clades of vertebrates. One such group is the Ichthyopterygia, a clade of obligatory marine reptiles that appeared in the Early Triassic epoch, without any known intermediates 1 . Here we describe a basal ichthyosauriform from the upper Lower Triassic (about 248 million years ago) of China, whose primitive skeleton indicates possible amphibious habits. It is smaller than ichthyopterygians and had unusually large flippers that probably allowed limited terrestrial locomotion. It also retained characteristics of terrestrial diapsid reptiles, including a short snout and body trunk 2 . Unlike more-derived ichthyosauriforms 3 , it was probably a suction feeder. The new species supports the sister-group relationships between ichthyosauriforms and Hupehsuchia 4 , the two forming the Ichthyosauromorpha. Basal ichthyosauromorphs are known exclusively from south China, suggesting that the clade originated in the region, which formed a warm 5 , 6 and humid 7 tropical archipelago 8 in the Early Triassic. The oldest unequivocal record of a sauropterygian is also from the same stratigraphic unit of the region 9 .