A new Palaeocene crocodylian from southern Argentina sheds light on the early history of caimanines

Ontogenetic and interelemental study of appendicular bones of Caiman latirostris Daudin, 1802 sheds light on osteohistological variability in crocodylians

The osteohistology of vertebrates provides a reliable source to deduce biological information, particularly regarding growth and development. Although osteohistological studies in Neosuchia (Crocodyliformes, Mesoeucrocodylia) are relatively numerous, the number of species studied within the group is still small. Extant crocodilians are known to exhibit intraspecific variability linked to environmental conditions, habitat, feeding, and other intrapopulation factors. Here, we analyzed the osteohistology of the living South American Caiman latirostris throughout posthatching ontogeny. The histology of several appendicular bones of 13 different-sized captive and wild individuals were examined. Although some thin sections revealed the classic lamellar, parallel-fibered, or woven bone matrices, others showed a variation and a mix between the organization of the bone tissue. These histological differences are likely related to variability in the growth dynamics of caimans. In some bones of the juveniles studied, remnants of embryonic bone were observed. Osteohistological variation related to prevailing environmental conditions is documented. Furthermore, our results show ontogenetic variation in the type of bone tissues deposited throughout the development of C. latirostris. This study offers a broad framework for life history interpretations for C. latirostris and provides insight into the evolutionary history and ontogenetic growth of extinct crocodylian lineages.

The biogeographic history of neosuchian crocodiles and the impact of saltwater tolerance variability

Extant neosuchian crocodiles are represented by only 24 taxa that are confined to the tropics and subtropics. However, at other intervals during their 200 Myr evolutionary history the clade reached considerably higher levels of species-richness, matched by more widespread distributions. Neosuchians have occupied numerous habitats and niches, ranging from dwarf riverine forms to large marine predators. Despite numerous previous studies, several unsolved questions remain with respect to their biogeographic history, including the geographical origins of major groups, e.g. Eusuchia and Neosuchia itself. We carried out the most comprehensive biogeographic analysis of Neosuchia to date, based on a multivariate K-means clustering approach followed by the application of two ancestral area estimation methods (BioGeoBEARS and Bayesian ancestral location estimation) applied to two recently published phylogenies. Our results place the origin of Neosuchia in northwestern Pangaea, with subsequent radiations into Gondwana. Eusuchia probably emerged in the European archipelago during the Late Jurassic/Early Cretaceous, followed by dispersals to the North American and Asian landmasses. We show that putative transoceanic dispersal events are statistically significantly less likely to happen in alligatoroids. This finding is consistent with the saltwater intolerant physiology of extant alligatoroids, bolstering inferences of such intolerance in their ancestral lineages.

The impact of molecular data on the phylogenetic position of the putative oldest crown crocodilian and the age of the clade

The use of molecular data for living groups is vital for interpreting fossils, especially when morphology-only analyses retrieve problematic phylogenies for living forms. These topological discrepancies impact on the inferred phylogenetic position of many fossil taxa. In Crocodylia, morphology-based phylogenetic inferences differ fundamentally in placing Gavialis basal to all other living forms, whereas molecular data consistently unite it with crocodylids. The Cenomanian Portugalosuchus azenhae was recently described as the oldest crown crocodilian, with affinities to Gavialis, based on morphology-only analyses, thus representing a potentially important new molecular clock calibration. Here, we performed analyses incorporating DNA data into these morphological datasets, using scaffold and supermatrix (total evidence) approaches, in order to evaluate the position of basal crocodylians, including Portugalosuchus. Our analyses incorporating DNA data robustly recovered Portugalosuchus outside Crocodylia (as well as thoracosaurs, planocraniids and Borealosuchus spp.), questioning the status of Portugalosuchus as crown crocodilian and any future use as a node calibration in molecular clock studies. Finally, we discuss the impact of ambiguous fossil calibration and how, with the increasing size of phylogenomic datasets, the molecular scaffold might be an efficient (though imperfect) approximation of more rigorous but demanding supermatrix analyses.

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.

The Making of Calibration Sausage Exemplified by Recalibrating the Transcriptomic Timetree of Jawed Vertebrates

Molecular divergence dating has the potential to overcome the incompleteness of the fossil record in inferring when cladogenetic events (splits, divergences) happened, but needs to be calibrated by the fossil record. Ideally but unrealistically, this would require practitioners to be specialists in molecular evolution, in the phylogeny and the fossil record of all sampled taxa, and in the chronostratigraphy of the sites the fossils were found in. Paleontologists have therefore tried to help by publishing compendia of recommended calibrations, and molecular biologists unfamiliar with the fossil record have made heavy use of such works (in addition to using scattered primary sources and copying from each other). Using a recent example of a large node-dated timetree inferred from molecular data, I reevaluate all 30 calibrations in detail, present the current state of knowledge on them with its various uncertainties, rerun the dating analysis, and conclude that calibration dates cannot be taken from published compendia or other secondary or tertiary sources without risking strong distortions to the results, because all such sources become outdated faster than they are published: 50 of the (primary) sources I cite to constrain calibrations were published in 2019, half of the total of 280 after mid-2016, and 90% after mid-2005. It follows that the present work cannot serve as such a compendium either; in the slightly longer term, it can only highlight known and overlooked problems. Future authors will need to solve each of these problems anew through a thorough search of the primary paleobiological and chronostratigraphic literature on each calibration date every time they infer a new timetree, and that literature is not optimized for that task, but largely has other objectives.

A new caimanine alligatorid from the Middle Eocene of Southwest Texas and implications for spatial and temporal shifts in Paleogene crocodyliform diversity

Dramatic early Cenozoic climatic shifts resulted in faunal reorganization on a global scale. Among vertebrates, multiple groups of mammals (e.g., adapiform and omomyiform primates, mesonychids, taeniodonts, dichobunid artiodactyls) are well known from the Western Interior of North America in the warm, greenhouse conditions of the early Eocene, but a dramatic drop in the diversity of these groups, along with the introduction of more dry-tolerant taxa, occurred near the Eocene–Oligocene boundary. Crocodyliforms underwent a striking loss of diversity at this time as well. Pre-Uintan crocodyliform assemblages in the central Western Interior are characterized by multiple taxa, whereas Chadronian assemblages are depauperate with only Alligator prenasalis previously known. Crocodyliform diversity through the intervening Uintan and Duchesnean is not well understood. The middle Eocene Devil’s Graveyard Formation (DGF) of southwest Texas provides new data from southern latitudes during that crucial period. A new specimen from the middle member of the DGF (late Uintan–Duchesnean) is the most complete cranial material of an alligatorid known from Paleogene deposits outside the Western Interior. We identify this specimen as a caimanine based on notched descending laminae of the pterygoids posterior to the choanae and long descending processes of the exoccipitals that are in contact with the basioccipital tubera. Unlike Eocaiman cavernensis, the anterior palatine process is rounded rather than quadrangular. The relationships and age of this new taxon support the hypothesis that the modern distribution of caimanines represents a contraction of a more expansive early Cenozoic distribution. We hypothesize that the range of caimanines tracked shifting warm, humid climatic conditions that contracted latitudinally toward the hothouse-icehouse transition later in the Eocene.

A new species of Bottosaurus (Alligatoroidea: Caimaninae) from the Black Peaks Formation (Palaeocene) of Texas indicates an early radiation of North American caimanines

Morphological and molecular data suggest a close relationship for alligators and caimans. The first fossil appearances combined with phylogenetic hypotheses suggest a divergence of the groups near the Cretaceous–Palaeogene boundary, but the early fossil record of Caimaninae is incomplete, and large gaps exist between the earliest representatives of the group. A new caimanine from lower Palaeocene (Tiffanian) deposits in the Black Peaks Formation of Brewster County, Texas is established upon two specimens of different size that bear similarities to Bottosaurus harlani from the uppermost Cretaceous and lowermost Palaeogene of New Jersey. The larger individual consists of a partial skull and lower jaw in addition to postcranial material. The smaller individual preserves a snout and posterior portions of the skull. Both specimens suggest an animal with a comparatively short, flat, broad snout. Species of Bottosaurus share diagnostic morphological character states but are differentiated in meaningful ways. Phylogenetic analysis shows that the new species is sister to B. harlani, indicates an early radiation of North American caimanines and elucidates a more complicated biogeographical history than previously hypothesized. A growing body of evidence suggests that Caimaninae may be diagnosed by ancestral characters, potentially drawing basal alligatoroids crownwards in phylogenetic trees.

The evolution of dermal shield vascularization in Testudinata and Pseudosuchia: phylogenetic constraints versus ecophysiological adaptations

Studies on living turtles have demonstrated that shells are involved in the resistance to hypoxia during apnea via bone acidosis buffering; a process which is complemented with cutaneous respiration, transpharyngeal and cloacal gas exchanges in the soft-shell turtles. Bone acidosis buffering during apnea has also been identified in crocodylian osteoderms, which are also known to employ heat transfer when basking. Although diverse, many of these functions rely on one common trait: the vascularization of the dermal shield. Here, we test whether the above ecophysiological functions played an adaptive role in the evolutionary transitions between land and aquatic environments in both Pseudosuchia and Testudinata. To do so, we measured the bone porosity as a proxy for vascular density in a set of dermal plates before performing phylogenetic comparative analyses. For both lineages, the dermal plate porosity obviously varies depending on the animal lifestyle, but these variations prove to be highly driven by phylogenetic relationships. We argue that the complexity of multi-functional roles of the post-cranial dermal skeleton in both Pseudosuchia and Testudinata probably is the reason for a lack of obvious physiological signal, and we discuss the role of the dermal shield vascularization in the evolution of these groups. This article is part of the theme issue 'Vertebrate palaeophysiology'.

Giant extinct caiman breaks constraint on the axial skeleton of extant crocodylians

The number of precaudal vertebrae in all extant crocodylians is remarkably conservative, with nine cervicals, 15 dorsals and two sacrals, a pattern present also in their closest extinct relatives. The consistent vertebral count indicates a tight control of axial patterning by Hox genes during development. Here we report on a deviation from this pattern based on an associated skeleton of the giant caimanine Purussaurus, a member of crown Crocodylia, and several other specimens from the Neogene of the northern neotropics. P. mirandai is the first crown-crocodylian to have three sacrals, two true sacral vertebrae and one non-pathological and functional dorsosacral, to articulate with the ilium (pelvis). The giant body size of this caiman relates to locomotory and postural changes. The iliosacral configuration, a more vertically oriented pectoral girdle, and low torsion of the femoral head relative to the condyles are hypothesized specializations for more upright limb orientation or weight support.

Taxonomic and phylogenetic review of Necrosuchus ionensis (Alligatoroidea: Caimaninae) and the early evolution and radiation of caimanines

Alligatoroidea is the most species-rich crocodylomorph clade of the Cenozoic of South America, with nearly all species belonging to the Caimaninae clade. However, the earliest records of Caimaninae in South America, which are from the Palaeocene, are based mostly on incomplete specimens, which increases the importance of detailed taxonomic and phylogenetic studies on these taxa. This paper offers a taxonomic and phylogenetic review of Necrosuchus ionensis, a caimanine species from the Salamanca Formation of the Palaeocene of Argentina. Necrosuchus ionensis is considered a valid species, albeit with a different diagnosis from that proposed by previous authors. The phylogenetic analysis shows, for the first time, that N. ionensis belongs to the derived Caimaninae clade Jacarea. However, a better understanding of the Jacarea clade is needed, and alternative placements for N. ionensis might be considered. Nevertheless, the placement of N. ionensis as a derived caimanine raises interesting perspectives on the early evolution and radiation of caimanines, which are thoroughly discussed in this paper together with other results obtained in this study, such as the recovery of the North American caimanines Bottosaurus and Tsoabichi as a clade.

Spatiotemporal palaeodiversity patterns of modern crocodiles (Crocodyliformes: Eusuchia)

Eusuchia is a crocodyliform clade with a rich and diverse fossil record dating back to the Mesozoic. There are several recent studies that analyse crocodyliform palaeodiversity over time, but none of them focuses exclusively on eusuchians. Thus, we estimated subsampled eusuchian palaeodiversity species dynamics over time not only at a global scale, but also by continents and main crocodylian lineages (Alligatoroidea, Crocodyloidea and Gavialoidea). These estimates reveal complex spatiotemporal palaeodiversity patterns, in which two maxima can be detected: the first during the Palaeocene and the second, which is also the biggest, in the middle-late Miocene. The Palaeocene shift is related to a North American alligatoroid diversification, whereas the middle–late Miocene maximum is related to a diversification of the three main Crocodylia lineages in Gondwanan land masses, but especially in South America. Additionally, a model-based study using generalized least squares was carried out to analyse the relationships between different abiotic and sampling proxies and eusuchian palaeodiversity. The results show that palaeotemperature is the most important factor amongst the analysed proxies, in accordance with previous studies. However, the results suggest that, along with palaeotemperature, other abiotic and/or biotic factors might also be driving eusuchian palaeodiversity dynamics.

Reappraisal of the morphology and phylogenetic relationships of the alligatoroid crocodylian Diplocynodon hantoniensis from the late Eocene of the United Kingdom

Diplocynodon is a genus of basal alligatoroid comprising nine species, which spanned the late Palaeocene to middle Miocene of Europe. Despite recent revisions of most Diplocynodon species, one of the earliest named and most complete, Diplocynodon hantoniensis, has not been re-described for over 150 years. This species is known from the remains of numerous individuals from the Priabonian (late Eocene) Headon Hill Formation, which crops out at Hordle (Hordwell) Cliff in Hampshire, United Kingdom. Here we re-describe and diagnose Diplocynodon hantoniensis, providing the first detailed description of postcranial anatomy in Diplocynodon, and indeed any basal alligatoroid. Diplocynodon hantoniensis is diagnosed by four autapomorphies, including retention of the ectopterygoid–pterygoid flexure through ontogeny and a unique anterior process of the ectopterygoid adjacent to the posteriormost maxillary alveoli. A critical review of previously referred remains from elsewhere in Europe and the USA restricts Diplocynodon hantoniensis to the late Eocene of the UK. Through comparisons with extant crocodylians, the well-preserved postcranial skeleton enables the interpretation of numerous muscle attachments in the forelimbs and hindlimbs, providing a potentially rich source of character data for future phylogenetic analyses. Based on a comparison of humeral morphology between a large sample of crocodylian species, we outline two new morphological characters in the humerus. We include D. hantoniensis in a phylogenetic analysis, including all putative Diplocynodon species (103 taxa scored for 187 characters). We use four different character-weighting schemes: equal weighting, implied weighting (k value = 8) and extended implied weighting with k-values of 4 and 8. In general, these weighted analyses produce congruent results with the equal-weights analysis, and increase the resolution within Diplocynodon. We recover a monophyletic Diplocynodon in three of the four analyses. However, the fourth analysis, with the strongest downweighting of homoplastic characters and missing data (extended implied weighting with k = 4), recovers the Palaeocene Diplocynodon remensis outside Diplocynodon. Our comprehensive revision of one of the most completely known Diplocynodon species facilitates comparisons in the genus, as well as between other basal alligatoroids, and forms the basis for comparing postcranial anatomy in other fossil crocodylians.

Evidence of cryptic lineages within a small South American crocodilian: the Schneider's dwarf caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae)

Schneider’s dwarf caiman Paleosuchus trigonatus is one of the smallest living crocodilians. Due to its broad distribution, cryptic behavior, and small home range, the species is well suited for the study of phylogeographic patterns on a continental scale. Additionally, this species is under threat due to habitat loss, trade and harvest, but is considered at low conservation risk by the IUCN. In the present study we test the hypothesis that P. trigonatus is comprised of geographically structured lineages. Phylogenetic reconstructions of the mitochondrial cytochrome b gene and single locus species discovery methods revealed the existence of two well-supported lineages within P. trigonatus—an Amazonian and Guianan lineage. Fossil calibrated divergence of these lineages was estimated to have occurred in the Late Miocene (7.5 Ma). The hypothesis that the Atlantic coast drainages might have been colonized from the southeast or central Amazon is supported by demographic metrics and relatively low genetic diversity of the Coastal and upper Branco populations when compared to the Amazon basin populations. The Amazon basin lineage is structured along an east-west gradient, with a sharp transition in haplotype frequencies to the east and west of the Negro and Madeira rivers. These lineages are already under anthropogenic threat and, therefore, are conservation dependent. Recognition of these lineages will foster discussion of conservation future of P. trigonatus and these lineages.

Development of the chondrocranium of two caiman species, Caiman latirostris and Caiman yacare

Little is known about the embryonic development and variation of the chondrocranium in Crocodylia and there are no works on any Caiman species. Due to the importance of cranial features in the systematics of this clade, investigating the development of the skull in embryonic stages is essential. In this study, we present for the first time the development of the cartilaginous skull of two extant Caiman species. Anatomical descriptions of the embryonic chondrocranium of Caiman latirostris and Caiman yacare were made, paying special attention to their inter- and intraspecific variation. For this purpose, pre-hatching ontogenetic cranial series of these two caiman species were prepared with a double staining and diaphanization technique. The main differences with other crocodylian species were observed in the palatoquadrate, and interspecific variation within the genus was recorded in the hyobranchial apparatus and larynx. Some characters may be distinctive of Caiman (posterior and ventral surface of the otic process of the palatoquadrate articulated with the dorsal process of the columella auris, and otic process articulated with the lateral wall of the auditory capsule), Alligatoridae (presence of an epiphanial foramen) or C. latirostris and C. yacare (Corpus hyoidei with different number and position of foramina and different shapes of its anterior contour and anterior and posterior notch, different degrees of broadening of the distal end of the Cornu branchiale I, and presence/absence of a notch in the posteroventral surface of the cricoid). Homologies of the elements belonging to the hyobranchial apparatus could not be confirmed. As in other tetrapods the trachea consists of incomplete cartilaginous rings. Morphological changes and dissimilarities found in this study are useful as a context to start studying phylogenetic constraints. Moreover, in a heterochronic context, variations may be involved.

A new Palaeocene crocodylian from southern Argentina sheds light on the early history of caimanines

Caimanines are crocodylians currently restricted to South and Central America and the oldest members are from lower Palaeocene localities of the Salamanca Formation (Chubut Province, Argentina). We report here a new caimanine from this same unit represented by a skull roof and partial braincase. Its phylogenetic relationships were explored in a cladistic analysis using standard characters and a morphogeometric two-dimensional configuration of the skull roof. The phylogenetic results were used for an event-based supermodel quantitative palaeobiogeographic analysis. The new species is recovered as the most basal member of the South American caimanines, and the Cretaceous North American lineage 'Brachychampsa and related forms' as the most basal Caimaninae. The biogeographic results estimated north-central North America as the ancestral area of Caimaninae, showing that the Cretaceous and Palaeocene species of the group were more widespread than thought and became regionally extinct in North America around the Cretaceous-Palaeocene boundary. A dispersal event from north-central North America during the middle Late Cretaceous explains the arrival of the group to South America. The Palaeogene assemblage of Patagonian crocodylians is composed of three lineages of caimanines as a consequence of independent dispersal events that occurred between North and South America and within South America around the Cretaceous-Palaeogene boundary.