Ecological opportunity and the rise and fall of crocodylomorph evolutionary innovation

Morphological innovation did not drive diversification in Mesozoic-Cenozoic brachiopods

Over long spans of geological time, various groups of organisms may wax and wane, experiencing times of apparent success and contraction. These rises and falls are often said to reflect either opportunities created by climate change or the relative success of innovative characteristics. Phylum Brachiopoda was one of the most successful marine clades before the Permian/Triassic mass extinction (PTME), but after this event, they became marginal components of marine communities through to the present day. How brachiopod morphological innovations reacted to swiftly declining diversity has long remained poorly understood. Here we analyse morphological evolution over the 300 Myr (Permian-Quaternary) history of the four major Mesozoic-Cenozoic brachiopod orders (Terebratulida, Rhynchonellida, Spiriferinida, Athyridida). Unexpectedly, their disparities reached or exceeded pre-PTME levels, but were decoupled from generic richness, which was generally low. Distribution of taxa in morphospace and shifts in centroid indicate that all four orders exploited new morphospaces when adapting to post-Permian environments. A comparison of morphospace occupation and diversity evolution suggests that the high extinction rate of brachiopods and the limited diversification of new forms may have accounted for the depauperate nature of modern-day brachiopods.

The rise of dietary diversity in coral reef fishes

Diet has been identified as a major driver of reef fish lineage diversification, producing one of the most speciose vertebrate assemblages today. Yet, there is minimal understanding of how, when and why diet itself has evolved. To address this, we used a comprehensive gut content dataset, alongside a recently developed phylogenetic comparative method to assess multivariate prey use across a diverse animal assemblage, coral reef fishes. Specifically, we investigated the diversification, transitions and phylogenetic conservatism of fish diets through evolutionary time. We found two major pulses of diet diversification: one at the end-Cretaceous and one during the Eocene, suggesting that the Cretaceous-Palaeogene mass extinction probably provided the initial ecological landscape for fish diets to diversify. The birth of modern families during the Eocene then provided the foundation for a second wave of dietary expansion. Together, our findings showcase the role of extinction rebound events in shaping the dietary diversity of fishes on present-day coral reefs.

Widespread convergence towards functional optimization in the lower jaws of crocodile-line archosaurs

Extant crocodilian jaws are subject to functional demands induced by feeding and hydrodynamics. However, the morphological and ecological diversity of extinct crocodile-line archosaurs is far greater than that of living crocodilians, featuring repeated convergence towards disparate ecologies including armoured herbivores, terrestrial macropredators and fully marine forms. Crocodile-line archosaurs, therefore, present a fascinating case study for morphological and functional divergence and convergence within a clade across a wide range of ecological scenarios. Here, we build performance landscapes of two-dimensional theoretical jaw shapes to investigate the influence of strength, speed and hydrodynamics in the morphological evolution of crocodile-line archosaur jaws, and test whether ecologically convergent lineages evolved similarly optimal jaw function. Most of the 243 sampled jaw morphologies occupy optimized regions of theoretical morphospace for either rotational efficiency, resistance to Von Mises stress, hydrodynamic efficiency or a trade-off between multiple functions, though some seemingly viable shapes remain unrealized. Jaw speed is optimized only in a narrow region of morphospace whereas many shapes possess optimal jaw strength, which may act as a minimum boundary rather than a strong driver for most taxa. This study highlights the usefulness of theoretical morphology in assessing functional optimality, and for investigating form-function relationships in diverse clades.

The pseudosuchian record in paleohistology: A small review

Archosauria originated around the Earth's largest biotic crisis that severely affected all ecosystems globally, the Permotriassic Mass extinction event, and comprises two crown-group lineages: the bird-lineage and the crocodylian lineage. The bird lineage includes the iconic pterosaurs, as well as dinosaurs and birds, whereas the crocodylian lineage includes clades such as aetosaurs, poposaurs, "rauisuchians," as well as Crocodylomorpha; the latter being represented today only by less than 30 extant species of Crocodylia. Despite playing important roles during Mesozoic and Cenozoic ecosystems, both on land and in water, Pseudosuchia received far less attention compared to the bird-lineage, which is also reflected in number and scope of histological studies so far. Lately, the field has seen a shift of focus toward pseudosuchians, however, and the symposium on "Paleohistological Inferences of Paleobiological Traits in Pseudosuchia" held during the International Congress of Vertebrate Morphology 2023 in Cairns, Queensland, Australia, is the latest proof of that. To put these novel aspects of paleohistological and paleobiological research into context, an overview of the non-extant pseudosuchian taxa whose postcranial bones were studied so far is provided here (c. 80 species out of a total of more than 700 extinct species described) and recent trends in pseudosuchian osteohistology are highlighted. In addition, histological studies on cranial and dental material and other potential hard tissues, such as eggshells and otoliths, are briefly reviewed as well.

Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia)

BACKGROUND

Crocodilians are one of the oldest extant vertebrate lineages, exhibiting a combination of evolutionary success and morphological resilience that has persisted throughout the history of life on Earth. This ability to endure over such a long geological time span is of great evolutionary importance. Here, we have utilized the combination of genomic and chromosomal data to identify and compare the full catalogs of satellite DNA families (satDNAs, i.e., the satellitomes) of 5 out of the 8 extant Alligatoridae species. As crocodilian genomes reveal ancestral patterns of evolution, by employing this multispecies data collection, we can investigate and assess how satDNA families evolve over time.

RESULTS

Alligators and caimans displayed a small number of satDNA families, ranging from 3 to 13 satDNAs in A. sinensis and C. latirostris, respectively. Together with little variation both within and between species it highlighted long-term conservation of satDNA elements throughout evolution. Furthermore, we traced the origin of the ancestral forms of all satDNAs belonging to the common ancestor of Caimaninae and Alligatorinae. Fluorescence in situ experiments showed distinct hybridization patterns for identical orthologous satDNAs, indicating their dynamic genomic placement.

CONCLUSIONS

Alligators and caimans possess one of the smallest satDNA libraries ever reported, comprising only four sets of satDNAs that are shared by all species. Besides, our findings indicated limited intraspecific variation in satellite DNA, suggesting that the majority of new satellite sequences likely evolved from pre-existing ones.

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.

Decoupling speciation and extinction reveals both abiotic and biotic drivers shaped 250 million years of diversity in crocodile-line archosaurs

Whereas living representatives of Pseudosuchia, crocodylians, number fewer than 30 species, more than 700 pseudosuchian species are known from their 250-million-year fossil record, displaying far greater ecomorphological diversity than their extant counterparts. With a new time-calibrated tree of >500 species, we use a phylogenetic framework to reveal that pseudosuchian evolutionary history and diversification dynamics were directly shaped by the interplay of abiotic and biotic processes over hundreds of millions of years, supported by information theory analyses. Speciation, but not extinction, is correlated with higher temperatures in terrestrial and marine lineages, with high sea level associated with heightened extinction in non-marine taxa. Low lineage diversity and increased speciation in non-marine species is consistent with opportunities for niche-filling, whereas increased competition may have led to elevated extinction rates. In marine lineages, competition via increased lineage diversity appears to have driven both speciation and extinction. Decoupling speciation and extinction, in combination with ecological partitioning, reveals a more complex picture of pseudosuchian evolution than previously understood. As the number of species threatened with extinction by anthropogenic climate change continues to rise, the fossil record provides a unique window into the drivers that led to clade success and those that may ultimately lead to extinction.

A new species of Comahuesuchus Bonaparte, 1991 (Crocodyliformes: Notosuchia) from the Upper Cretaceous of Neuquén, Lake Barreales, Patagonia, Argentina

Notosuchian crocodyliforms were major components of the South American Cretaceous biota and, for over 125 years, paleontological fieldwork in this continent recovered several well-preserved fossils of these animals. They are largely recognized for terrestrial life and specialized feeding habits, frequently presenting bizarre taxa such as Comahuesuchus. A new species, Comahuesuchus bonapartei n. sp. (MUCPv 597; cast MN), is described from geological strata of Sierra Barrosa Formation (Upper Turonian) and Portezuelo Formation (Lower Coniacian) of Lake Barreales, Patagonia, Argentina. The new fossil comprises a right dentary bone that shares important and unique anatomical features with specimens of Comahuesuchus brachybuccalis, such as the presence of a well-marked shelf on the lateral surface of the bone; a flat, low, and wide mandibular symphysis; an enlarged, labiolingually compressed caniniform tooth at caudal position in the dentary; the presence of serrated mesial and distal carinae in the caniniform with a faceted labial surface, and the absence or extremely reduction in number of the postcaniniform dentition. C. bonapartei differs from C. brachybuccalis in having individual dentary alveoli, rather a dentition set in groove. Phylogenetic analyses support a sister-relationship between both species, which are well nested within notosuchians.

Shark mandible evolution reveals patterns of trophic and habitat-mediated diversification

Environmental controls of species diversity represent a central research focus in evolutionary biology. In the marine realm, sharks are widely distributed, occupying mainly higher trophic levels and varied dietary preferences, mirrored by several morphological traits and behaviours. Recent comparative phylogenetic studies revealed that sharks present a fairly uneven diversification across habitats, from reefs to deep-water. We show preliminary evidence that morphological diversification (disparity) in the feeding system (mandibles) follows these patterns, and we tested hypotheses linking these patterns to morphological specialisation. We conducted a 3D geometric morphometric analysis and phylogenetic comparative methods on 145 specimens representing 90 extant shark species using computed tomography models. We explored how rates of morphological evolution in the jaw correlate with habitat, size, diet, trophic level, and taxonomic order. Our findings show a relationship between disparity and environment, with higher rates of morphological evolution in reef and deep-water habitats. Deep-water species display highly divergent morphologies compared to other sharks. Strikingly, evolutionary rates of jaw disparity are associated with diversification in deep water, but not in reefs. The environmental heterogeneity of the offshore water column exposes the importance of this parameter as a driver of diversification at least in the early part of clade history.

Shifts in food webs and niche stability shaped survivorship and extinction at the end-Cretaceous

It has long been debated why groups such as non-avian dinosaurs became extinct whereas mammals and other lineages survived the Cretaceous/Paleogene mass extinction 66 million years ago. We used Markov networks, ecological niche partitioning, and Earth System models to reconstruct North American food webs and simulate ecospace occupancy before and after the extinction event. We find a shift in latest Cretaceous dinosaur faunas, as medium-sized species counterbalanced a loss of megaherbivores, but dinosaur niches were otherwise stable and static, potentially contributing to their demise. Smaller vertebrates, including mammals, followed a consistent trajectory of increasing trophic impact and relaxation of niche limits beginning in the latest Cretaceous and continuing after the mass extinction. Mammals did not simply proliferate after the extinction event; rather, their earlier ecological diversification might have helped them survive.

The ecological diversification and evolution of Teleosauroidea (Crocodylomorpha, Thalattosuchia), with insights into their mandibular biomechanics

Throughout the Jurassic, a plethora of marine reptiles dominated ocean waters, including ichthyosaurs, plesiosaurs and thalattosuchian crocodylomorphs. These Jurassic ecosystems were characterized by high niche partitioning and spatial variation in dietary ecology. However, while the ecological diversity of many marine reptile lineages is well known, the overall ecological diversification of Teleosauroidea (one of the two major groups within thalattosuchian crocodylomorphs) has never been explored. Teleosauroids were previously deemed to have a morphologically conservative body plan; however, they were in actuality morphofunctionally more diverse than previously thought. Here we investigate the ecology and feeding specializations of teleosauroids, using morphological and functional cranio-dental characteristics. We assembled the most comprehensive dataset to date of teleosauroid taxa (approximately 20 species) and ran a series of principal component analyses (PC) to categorize them into various feeding ecomorphotypes based on 17 dental characteristics (38 specimens) and 16 functionally significant mandibular characters (18 specimens). The results were examined in conjunction with a comprehensive thalattosuchian phylogeny (153 taxa and 502 characters) to evaluate macroevolutionary patterns and significant ecological shifts. Machimosaurids display a well-developed ecological shift from: (1) slender, pointed tooth apices and an elongate gracile mandible; to (2) more robust, pointed teeth with a slightly deeper mandible; and finally, (3) rounded teeth and a deep-set, shortened mandible with enlarged musculature. Overall, there is limited mandibular functional variability in teleosaurids and machimosaurids, despite differing cranial morphologies and habitat preferences in certain taxa. This suggests a narrow feeding ecological divide between teleosaurids and machimosaurids. Resource partitioning was primarily related to snout and skull length as well as habitat; only twice did teleosauroids manage to make a major evolutionary leap to feed distinctly differently, with only the derived machimosaurines successfully radiating into new feeding ecologies.

Anatomy informs geology: Hydrodynamic dispersal of alligator bones, with implications for taphonomic interpretations of fossil deposits of crocodylians, dinosaurs, and other morphologically novel taxa

Distinctive anatomical features of bones can influence not only how these structures perform in living animals but also the tendency of elements to be transported by flowing water after death. Such transport can be critical in the concentration of fossils from animals that live near freshwater habitats, providing important context for interpreting the composition of paleocommunities. Measurements of the tendency of flowing water to disperse skeletal elements have been collected for diverse taxa, including mammals, turtles, and birds. However, these extant models may not be entirely appropriate for many morphologically distinct extinct lineages, such as non-avian dinosaurs. To expand the range of models available for evaluating the influence of hydrodynamic transport on the assembly of fossil deposits, we used a flow tank to measure the water speeds that disperse bones from a subadult American alligator (Alligator mississippiensis), with the skull and mandible tested in multiple starting orientations. Alligator bones are sorted into three main dispersal groups: early (vertebrae, most girdle elements), intermediate (ribs, most limb bones), and late (pubis, femur), with the skull and mandible varying between intermediate and late depending on orientation. Late dispersing elements tended to be heavy or very flat. These results can refine interpretations of the taphonomic context for deposits of fossil crocodylians and morphologically similar taxa (e.g., choristoderes, phytosaurs) and provide an additional comparative model for deposits of non-avian dinosaurs. Moreover, variation in hydrodynamic sorting across lineages highlights how distinctive anatomical features can influence the concentration of fossils, shaping understanding of assemblage composition and paleofaunal evolution.

The effects of skull flattening on suchian jaw muscle evolution

Jaw muscles are key features of the vertebrate feeding apparatus. The jaw musculature is housed in the skull whose morphology reflects a compromise between multiple functions, including feeding, housing sensory structures, and defense, and the skull constrains jaw muscle geometry. Thus, jaw muscle anatomy may be suboptimally oriented for the production of bite force. Crocodylians are a group of vertebrates that generate the highest bite forces ever measured with a flat skull suited to their aquatic ambush predatory style. However, basal members of the crocodylian line (e.g., Prestosuchus) were terrestrial predators with plesiomorphically tall skulls, and thus the origin of modern crocodylians involved a substantial reorganization of the feeding apparatus and its jaw muscles. Here, we reconstruct jaw muscles across a phylogenetic range of crocodylians and fossil suchians to investigate the impact of skull flattening on muscle anatomy. We used imaging data to create 3D models of extant and fossil suchians that demonstrate the evolution of the crocodylian skull, using osteological correlates to reconstruct muscle attachment sites. We found that jaw muscle anatomy in early fossil suchians reflected the ancestral archosaur condition but experienced progressive shifts in the lineage leading to Metasuchia. In early fossil suchians, musculus adductor mandibulae posterior and musculus pterygoideus (mPT) were of comparable size, but by Metasuchia, the jaw musculature is dominated by mPT. As predicted, we found that taxa with flatter skulls have less efficient muscle orientations for the production of high bite force. This study highlights the diversity and evolution of jaw muscles in one of the great transformations in vertebrate evolution.

Global ecomorphological restructuring of dominant marine reptiles prior to the Cretaceous-Palaeogene mass extinction

Mosasaurid squamates were the dominant amniote predators in marine ecosystems during most of the Late Cretaceous. Here, we use a suite of biomechanically rooted, functionally descriptive ratios in a framework adapted from population ecology to investigate how the morphofunctional disparity of mosasaurids evolved prior to the Cretaceous-Palaeogene (K/Pg) mass extinction. Our results suggest that taxonomic turnover in mosasaurid community composition from Campanian to Maastrichtian is reflected by a notable global increase in morphofunctional disparity, especially driving the North American record. Ecomorphospace occupation becomes polarized during the Late Maastrichtian, with morphofunctional disparity plateauing in the Southern Hemisphere and decreasing in the Northern Hemisphere. We show that these changes are not strongly associated with mosasaurid size, but rather with the functional capacities of their skulls. Our novel approach indicates that mosasaurid morphofunctional disparity was in decline in multiple provincial communities before the K/Pg mass extinction, highlighting region-specific patterns of disparity evolution and the importance of assessing vertebrate extinctions both globally and locally. Ecomorphological differentiation in mosasaurid communities, coupled with declines in other formerly abundant marine reptile groups, indicates widespread restructuring of higher trophic levels in marine food webs was well underway when the K/Pg mass extinction took place.

Miocene fossils from the southeastern Pacific shed light on the last radiation of marine crocodylians

The evolution of crocodylians as sea dwellers remains obscure because living representatives are basically freshwater inhabitants and fossil evidence lacks crucial aspects about crocodylian occupation of marine ecosystems. New fossils from marine deposits of Peru reveal that crocodylians were habitual coastal residents of the southeastern Pacific (SEP) for approximately 14 million years within the Miocene (ca 19 to 5 Ma), an epoch including the highest global peak of marine crocodylian diversity. The assemblage of the SEP comprised two long and slender-snouted (longirostrine) taxa of the Gavialidae: the giant Piscogavialis and a new early diverging species, Sacacosuchus cordovai. Although living gavialids (Gavialis and Tomistoma) are freshwater forms, this remarkable fossil record and a suite of evolutionary morphological analyses reveal that the whole evolution of marine crocodylians pertained to the gavialids and their stem relatives (Gavialoidea). This adaptive radiation produced two longirostrine ecomorphs with dissimilar trophic roles in seawaters and involved multiple transmarine dispersals to South America and most landmasses. Marine gavialoids were shallow sea dwellers, and their Cenozoic diversification was influenced by the availability of coastal habitats. Soon after the richness peak of the Miocene, gavialoid crocodylians disappeared from the sea, probably as part of the marine megafauna extinction of the Pliocene.

Large size in aquatic tetrapods compensates for high drag caused by extreme body proportions

Various Mesozoic marine reptile lineages evolved streamlined bodies and efficient lift-based swimming, as seen in modern aquatic mammals. Ichthyosaurs had low-drag bodies, akin to modern dolphins, but plesiosaurs were strikingly different, with long hydrofoil-like limbs and greatly variable neck and trunk proportions. Using computational fluid dynamics, we explore the effect of this extreme morphological variation. We find that, independently of their body fineness ratio, plesiosaurs produced more drag than ichthyosaurs and modern cetaceans of equal mass due to their large limbs, but these differences were not significant when body size was accounted for. Additionally, necks longer than twice the trunk length can substantially increase the cost of forward swimming, but this effect was cancelled out by the evolution of big trunks. Moreover, fast rates in the evolution of neck proportions in the long-necked elasmosaurs suggest that large trunks might have released the hydrodynamic constraints on necks thus allowing their extreme enlargement.

An intermediate crocodylian linking two extant gharials from the Bronze Age of China and its human-induced extinction

A solid phylogenetic framework is the basis of biological studies, yet higher level relationships are still unresolved in some major vertebrate lineages. One such group is Crocodylia, where the branching pattern of three major families (Alligatoridae, Crocodylidae and Gavialidae) has been disputed over decades due to the uncertain relationship of two slender-snouted lineages, gavialines and tomistomines. Here, we report a bizarre crocodylian from the Bronze Age of China, which shows a mosaic of gavialine and tomistomine features across the skeleton, rendering support to their sister taxon relationship as molecular works have consistently postulated. Gavialine characters of the new Chinese crocodylian include a novel configuration of the pterygoid bulla, a vocal structure known in mature male Indian gharials. Extinct gavialines have repeatedly evolved potentially male-only acoustic apparatus of various shapes, illuminating the deep history of sexual selection on acoustic signalling in a slender-snouted group of crocodylians. Lastly, a cutmark analysis combined with accelerator mass spectrometry (AMS) radiocarbon dating of bone remains demonstrated that two individuals from Shang and Zhou dynasties in Guangdong, China, suffered head injuries and decapitation. Archaeological evidence together with historical accounts suggests the human-induced extinction of this unique crocodylian only a few hundred years ago.

A second peirosaurid crocodyliform from the Mid-Cretaceous Kem Kem Group of Morocco and the diversity of Gondwanan notosuchians outside South America

Notosuchians are an extinct clade of terrestrial crocodyliforms with a particularly rich record in the late Early to Late Cretaceous (approx. 130-66 Ma) of Gondwana. Although much of this diversity comes from South America, Africa and Indo-Madagascar have also yielded numerous notosuchian remains. Three notosuchian species are currently recognized from the early Late Cretaceous (approx. 100 Ma) Kem Kem Group of Morocco, including the peirosaurid Hamadasuchus rebouli. Here, we describe two new specimens that demonstrate the presence of at least a fourth notosuchian species in this fauna. Antaeusuchus taouzensis n. gen. n. sp. is incorporated into one of the largest notosuchian-focused character-taxon matrices yet to be compiled, comprising 443 characters scored for 63 notosuchian species, with an increased sampling of African and peirosaurid species. Parsimony analyses run under equal and extended implied weighting consistently recover Antaeusuchus as a peirosaurid notosuchian, supported by the presence of two distinct waves on the dorsal dentary surface, a surangular which laterally overlaps the dentary above the mandibular fenestra, and a relatively broad mandibular symphysis. Within Peirosauridae, Antaeusuchus is recovered as the sister taxon of Hamadasuchus. However, it differs from Hamadasuchus with respect to several features, including the ornamentation of the lateral surface of the mandible, the angle of divergence of the mandibular rami, the texture of tooth enamel and the shape of the teeth, supporting their generic distinction. We present a critical reappraisal of the non-South American Gondwanan notosuchian record, which spans the Middle Jurassic-late Eocene. This review, as well as our phylogenetic analyses, indicate the existence of at least three approximately contemporaneous peirosaurid lineages within the Kem Kem Group, alongside other notosuchians, and support the peirosaurid affinities of the 'trematochampsid' Miadanasuchus oblita from the Maastrichtian of Madagascar. Furthermore, the Cretaceous record demonstrates the presence of multiple lineages of approximately contemporaneous notosuchians in several African and Madagascan faunas, and supports previous suggestions regarding an undocumented pre-Aptian radiation of Notosuchia. By contrast, the post-Cretaceous record is depauperate, comprising rare occurrences of sebecosuchians in north Africa prior to their extirpation.

Phylogenetic analysis of a new morphological dataset elucidates the evolutionary history of Crocodylia and resolves the long-standing gharial problem

First appearing in the latest Cretaceous, Crocodylia is a clade of semi-aquatic, predatory reptiles, defined by the last common ancestor of extant alligators, caimans, crocodiles, and gharials. Despite large strides in resolving crocodylian interrelationships over the last three decades, several outstanding problems persist in crocodylian systematics. Most notably, there has been persistent discordance between morphological and molecular datasets surrounding the affinities of the extant gharials, Gavialis gangeticus and Tomistoma schlegelii. Whereas molecular data consistently support a sister taxon relationship, in which they are more closely related to crocodylids than to alligatorids, morphological data indicate that Gavialis is the sister taxon to all other extant crocodylians. Here we present a new morphological dataset for Crocodylia based on a critical reappraisal of published crocodylian character data matrices and extensive firsthand observations of a global sample of crocodylians. This comprises the most taxonomically comprehensive crocodylian dataset to date (144 OTUs scored for 330 characters) and includes a new, illustrated character list with modifications to the construction and scoring of characters, and 46 novel characters. Under a maximum parsimony framework, our analyses robustly recover Gavialis as more closely related to Tomistoma than to other extant crocodylians for the first time based on morphology alone. This result is recovered regardless of the weighting strategy and treatment of quantitative characters. However, analyses using continuous characters and extended implied weighting (with high k-values) produced the most resolved, well-supported, and stratigraphically congruent topologies overall. Resolution of the gharial problem reveals that: (1) several gavialoids lack plesiomorphic features that formerly drew them towards the stem of Crocodylia; and (2) more widespread similarities occur between species traditionally divided into tomistomines and gavialoids, with these interpreted here as homology rather than homoplasy. There remains significant temporal incongruence regarding the inferred divergence timing of the extant gharials, indicating that several putative gavialids ('thoracosaurs') are incorrectly placed and require future re-appraisal. New alligatoroid interrelationships include: (1) support for a North American origin of Caimaninae in the latest Cretaceous; (2) the recovery of the early Paleogene South American taxon Eocaiman as a 'basal' alligatoroid; and (3) the paraphyly of the Cenozoic European taxon Diplocynodon. Among crocodyloids, notable results include modifications to the taxonomic content of Mekosuchinae, including biogeographic affinities of this clade with latest Cretaceous-early Paleogene Asian crocodyloids. In light of our new results, we provide a comprehensive review of the evolutionary and biogeographic history of Crocodylia, which included multiple instances of transoceanic and continental dispersal.

Complex macroevolutionary dynamics underly the evolution of the crocodyliform skull

All modern crocodyliforms (alligators, crocodiles and the gharial) are semi-aquatic generalist carnivores that are relatively similar in cranial form and function. However, this homogeneity represents just a fraction of the variation that once existed in the clade, which includes extinct herbivorous and marine forms with divergent skull structure and function. Here, we use high-dimensional three-dimensional geometric morphometrics to quantify whole-skull morphology across modern and fossil crocodyliforms to untangle the factors that shaped the macroevolutionary history and relatively low phenotypic variation of this clade through time. Evolutionary modelling demonstrates that the pace of crocodyliform cranial evolution is initially high, particularly in the extinct Notosuchia, but slows near the base of Neosuchia, with a late burst of rapid evolution in crown-group crocodiles. Surprisingly, modern crocodiles, especially Australian, southeast Asian, Indo-Pacific species, have high rates of evolution, despite exhibiting low variation. Thus, extant lineages are not in evolutionary stasis but rather have rapidly fluctuated within a limited region of morphospace, resulting in significant convergence. The structures related to jaw closing and bite force production (e.g. pterygoid flange and quadrate) are highly variable, reinforcing the importance of function in driving phenotypic variation. Together, these findings illustrate that the apparent conservativeness of crocodyliform skulls betrays unappreciated complexity in their macroevolutionary dynamics.

Revisiting the Karyotypes of Alligators and Caimans (Crocodylia, Alligatoridae) after a Half-Century Delay: Bridging the Gap in the Chromosomal Evolution of Reptiles

Although crocodilians have attracted enormous attention in other research fields, from the cytogenetic point of view, this group remains understudied. Here, we analyzed the karyotypes of eight species formally described from the Alligatoridae family using differential staining, fluorescence in situ hybridization with rDNA and repetitive motifs as a probe, whole chromosome painting (WCP), and comparative genome hybridization. All Caimaninae species have a diploid chromosome number (2n) 42 and karyotypes dominated by acrocentric chromosomes, in contrast to both species of Alligatorinae, which have 2n = 32 and karyotypes that are predominantly metacentric, suggesting fusion/fission rearrangements. Our WCP results supported this scenario by revealing the homeology of the largest metacentric pair present in both Alligator spp. with two smaller pairs of acrocentrics in Caimaninae species. The clusters of 18S rDNA were found on one chromosome pair in all species, except for Paleosuchus spp., which possessed three chromosome pairs bearing these sites. Similarly, comparative genomic hybridization demonstrated an advanced stage of sequence divergence among the caiman genomes, with Paleosuchus standing out as the most divergent. Thus, although Alligatoridae exhibited rather low species diversity and some level of karyotype stasis, their genomic content indicates that they are not as conserved as previously thought. These new data deepen the discussion of cytotaxonomy in this family.

Ecological opportunity and the rise and fall of crocodylomorph evolutionary innovation

Understanding the origin, expansion and loss of biodiversity is fundamental to evolutionary biology. The approximately 26 living species of crocodylomorphs (crocodiles, caimans, alligators and gharials) represent just a snapshot of the group's rich 230-million-year history, whereas the fossil record reveals a hidden past of great diversity and innovation, including ocean and land-dwelling forms, herbivores, omnivores and apex predators. In this macroevolutionary study of skull and jaw shape disparity, we show that crocodylomorph ecomorphological variation peaked in the Cretaceous, before declining in the Cenozoic, and the rise and fall of disparity was associated with great heterogeneity in evolutionary rates. Taxonomically diverse and ecologically divergent Mesozoic crocodylomorphs, like marine thalattosuchians and terrestrial notosuchians, rapidly evolved novel skull and jaw morphologies to fill specialized adaptive zones. Disparity in semi-aquatic predatory crocodylians, the only living crocodylomorph representatives, accumulated steadily, and they evolved more slowly for most of the last 80 million years, but despite their conservatism there is no evidence for long-term evolutionary stagnation. These complex evolutionary dynamics reflect ecological opportunities, that were readily exploited by some Mesozoic crocodylomorphs but more limited in Cenozoic crocodylians.