Neuroanatomy and pneumaticity of the extinct Malagasy "horned" crocodile Voay robustus and its implications for crocodylid phylogeny and palaeoecology

Voay robustus, the extinct Malagasy "horned" crocodile, was originally considered to be the only crocodylian representative in Madagascar during most part of the Holocene. However, Malagasy crocodylian remains have had confused taxonomic attributions and recent studies have underlined that Crocodylus and Voay populations coexisted on the island for at least 7500 years. Here, we describe the inner braincase anatomy of Voay robustus using x-ray computed tomography on four specimens, to provide new anatomical information that distinguishes Voay from Crocodylus, especially features of the brain endocast and the paratympanic sinuses. Geometric morphometric analyses are performed on 3D models of the internal organs to compare statistically Voay with a subset of extant Crocodylidae. Following these comparisons, we build an endocranial morphological matrix to discuss the proposed phylogenetic affinities of Voay with Osteolaeminae from an endocranial point of view. Additionally, we discuss the use of internal characters in systematic studies and find that they can have a major impact on morphological analyses. Finally, new radiocarbon data on Voay and subfossil Crocodylus specimens are recovered between 2010 and 2750 cal BP, which confirm the cohabitation of the two species in the same area for a long period of time. We thus assess several extinction scenarios, and propose a slightly different ecology of Voay compared to Crocodylus, which could have allowed habitat partitioning on the island. Our approach complements information obtained from previous molecular and morphological phylogenies, as well as previous radiocarbon dating, together revealing past diversity and faunal turnovers in Madagascar.

Central African dwarf crocodiles found in syntopy are comparably divergent to South American dwarf caimans

Recent molecular taxonomic advancements have expanded our understanding of crocodylian diversity, revealing the existence of previously overlooked species, including the Congo dwarf crocodile (Osteolaemus osborni) in the central Congo Basin rainforests. This study explores the genomic divergence between O. osborni and its better-known relative, the true dwarf crocodile (Osteolaemus tetraspis), shedding light on their evolutionary history. Field research conducted in the northwestern Republic of the Congo uncovered a locality where both species coexist in sympatry/syntopy. Genomic analysis of sympatric individuals reveals a level of divergence comparable to that between ecologically similar South American dwarf caimans (Paleosuchus palpebrosus and Paleosuchus trigonatus), suggesting parallel speciation in the Afrotropics and Neotropics during the Middle to Late Miocene, 10-12 Ma. Comparison of the sympatric and allopatric dwarf crocodiles indicates no gene flow between the analysed sympatric individuals of O. osborni and O. tetraspis. However, a larger sample will be required to answer the question of whether or to what extent these species hybridize. This study emphasizes the need for further research on the biology and conservation status of the Congo dwarf crocodile, highlighting its significance in the unique biodiversity of the Congolian rainforests and thus its potential as a flagship species.

Cross-species chromosome painting and repetitive DNA mapping illuminate the karyotype evolution in true crocodiles (Crocodylidae)

Crocodilians have maintained very similar karyotype structures and diploid chromosome numbers for around 100 million years, with only minor variations in collinearity. Why this karyotype structure has largely stayed unaltered for so long is unclear. In this study, we analyzed the karyotypes of six species belonging to the genera Crocodylus and Osteolaemus (Crocodylidae, true crocodiles), among which the Congolian endemic O. osborni was included and investigated. We utilized various techniques (differential staining, fluorescence in situ hybridization with repetitive DNA and rDNA probes, whole chromosome painting, and comparative genomic hybridization) to better understand how crocodile chromosomes evolved. We studied representatives of three of the four main diploid chromosome numbers found in crocodiles (2n = 30/32/38). Our data provided new information about the species studied, including the identification of four major chromosomal rearrangements that occurred during the karyotype diversification process in crocodiles. These changes led to the current diploid chromosome numbers of 2n = 30 (fusion) and 2n = 38 (fissions), derived from the ancestral state of 2n = 32. The conserved cytogenetic tendency in crocodilians, where extant species keep near-ancestral state, contrasts with the more dynamic karyotype evolution seen in other major reptile groups.

Ontogenetic variability of the intertympanic sinus distinguishes lineages within Crocodylia

The phylogenetic relationships within crown Crocodylia remain contentious due to conflicts between molecular and morphological hypotheses. However, morphology-based datasets are mostly constructed on external characters, overlooking internal structures. Here, we use 3D geometric morphometrics to study the shape of the intertympanic sinus system in crown crocodylians during ontogeny, in order to assess its significance in a taxonomic context. Intertympanic sinus shape was found to be highly correlated with size and modulated by cranial shape during development. Still, adult sinus morphology distinguishes specimens at the family, genus and species level. We observe a clear distinction between Alligatoridae and Longirostres, a separation of different Crocodylus species and the subfossil Malagasy genus Voay, and a distinction between the Tomistoma and Gavialis lineages. Our approach is independent of molecular methods but concurs with the molecular topologies. Therefore, sinus characters could add significantly to morphological datasets, offering an alternative viewpoint to resolve problems in crocodylian relationships.

Revised phylogeny from complete mitochondrial genomes of phyllostomid bats resolves subfamilial classification

Classically, molecular phylogenetic trees of Phyllostomidae have been inferred using a combination of a few mitochondrial and nuclear markers. However, there is still uncertainty in the relationships, especially among deep clades within the family. In this study, we provide newly sequenced complete mitochondrial genomes from 26 bat species, including genomes of 23 species reported here for the first time. By carefully analysing these genomes using maximum likelihood and Bayesian methods and different ingroup and outgroup samples, partition schemes and data types, we investigated the robustness and sensitivity of our phylogenetic results. The optimal topologies were those inferred from the complete data matrix of nucleotides, with complex and highly parameterized substitution models and partition schemes. Our results show a statistically robust picture of the evolutionary relationships between phyllostomid subfamilies and clarify hitherto uncertain relationships of Lonchorhininae and Macrotinae.

Giant dwarf crocodiles from the Miocene of Kenya and crocodylid faunal dynamics in the late Cenozoic of East Africa

We describe two new osteolaemine crocodylids from the Early and early Middle Miocene of Kenya: Kinyang mabokoensis tax. nov. (Maboko, 15 Ma) and Kinyang tchernovi tax. nov. (Karungu and Loperot, 18 Ma). Additional material referable to Kinyang is known from Chianda and Moruorot. The skull was broad and dorsoventrally deep, and the genus can be diagnosed based on the combined presence of a partial overbite, a subdivided fossa for the lateral collateral ligament on the surangular, and a maxilla with no more than 13 alveoli. Phylogenetic analyses based on morphological and combined morphological and molecular data support a referral of Kinyang to Osteolaeminae, and morphological data alone put the new taxon at the base of Euthecodontini. Some Kinyang maxillae preserve blind pits on the medial caviconchal recess wall. Kinyang co‐occurs with the osteolaemine Brochuchus at some localities, and together, they reinforce the phylogenetic disparity between early Neogene osteolaemine‐dominated faunas and faunas dominated by crocodylines beginning in the Late Miocene in the Kenya Rift. The causes of this turnover remain unclear, though changes in prevailing vegetation resulting from tectonic and climatic drivers may provide a partial explanation.

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.

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.

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.

Genital anatomy and copulatory interactions in the broad snouted Caiman (Caiman latirostris)

The broad snouted caiman is a crocodylian native to South America that is subject to extensive conservation management in both wild and farming environments. Although reproductive behaviors like egg laying and clutch care have been examined in this species, little else is known about their copulatory system. We examined the anatomy of male and female cloacal and genital tissues ex vivo to build hypotheses of their interactions during copulation and the effects of that interaction on insemination. Male phallic glans tissues were artificially inflated to expand into their copulatory state, allowing the examination and quantification of structural changes at the gross and tissue levels. Digital reconstruction of MRI stacks yielded three-dimensional tissue compartment specific glans models of the inflated state. Silicone molds of female cloacae and oviducts in conjunction with dissection and diceCT analysis allowed us to assess internal geometry and infer how male and female features interact in copulo. We observed glans expansion within the female proctodeum would result in a copulatory lock limiting deeper intromission or retraction. Intromission and subsequent creation of the copulatory lock produces extensive clitoral compression, providing a possible mechanism for female assessment of male copulatory performance. Further, glans expansion forms a distal lumen that positions the glans tip in or near the vaginal openings. A coiled, muscular vagina provides a possible mechanism for postcopulatory sexual selection by excluding semen. Together, the complex male-female interaction supports evidence for cryptic selection by female choice, which can act as a driver of genital coevolution.

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.

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.

Australia's prehistoric 'swamp king': revision of the Plio-Pleistocene crocodylian genus Pallimnarchus de Vis, 1886

The crocodylian fossil record from the Cenozoic of Australasia is notable for its rich taxonomic diversity, and is primarily represented by members of the clade Mekosuchinae. Reports of crocodylian fossils from Australia date back to the late nineteenth century. In 1886, Charles Walter de Vis proposed the name Pallimnarchus pollens for crocodylian fossils from southeast Queensland-the first binomen given to an extinct crocodylian taxon from Australia. Pallimnarchus has come to be regarded as a large, broad-snouted crocodylian from Australia's Plio-Pleistocene, and numerous specimens, few of which are sufficiently complete, have been assigned to it by several authors throughout the twentieth century. In the late 1990s, the genus was expanded to include a second species, Pallimnarchus gracilis. Unfortunately, the original syntype series described as Pallimnarchus pollens is very fragmentary and derives from more than one taxon, while a large part of the subsequently selected lectotype specimen is missing. Because descriptions and illustrations of the complete lectotype do not reveal any autapomorphic features, we propose that Pallimnarchus pollens should be regarded as a nomen dubium. Following this decision, the fossil material previously referred to Pallimnarchus is of uncertain taxonomic placement. A partial skull, formerly assigned to Pallimnarchus pollens and known as 'Geoff Vincent's specimen', possesses many features of diagnostic value and is therefore used as basis to erect a new genus and species-Paludirex vincenti gen. et sp. nov. A comprehensive description is given for the osteology of 'Geoff Vincent's specimen' as well as aspects of its palaeoneurology, the latter being a first for an extinct Australian crocodyliform. The newly named genus is characterized by a unique combination of premaxillary features such as a distinctive arching of the anterior alveolar processes of the premaxillae, a peculiar arrangement of the first two premaxillary alveoli and a large size disparity between the 3rd and 4th premaxillary alveoli. These features presently allow formal recognition of two species within the genus, Paludirex vincenti and Paludirex gracilis comb. nov., with the former having comparatively more robust rostral proportions than the latter. The Paludirex vincenti holotype comes from the Pliocene Chinchilla Sand of the Darling Downs, south-eastern Queensland, whereas the material assigned to Paludirex gracilis is from the Pleistocene of Terrace Site Local Fauna, Riversleigh, northwest Queensland. Phylogenetic analyses recover Paludirex vincenti as a mekosuchine, although further cladistic assessments are needed to better understand the relationships within the clade.