A new phylogenetic analysis of Phytosauria (Archosauria: Pseudosuchia) with the application of continuous and geometric morphometric character coding

Variation in the sacrum of phytosaurs: New evidence from a partial skeleton of Machaeroprosopus mccauleyi

Phytosaurs are a group of Upper Triassic semi-aquatic archosauriform reptiles. Their variable skull morphology forms the foundation of our understanding of their relationships and paleoecology, while only a few studies have focused on demonstrating the existence of postcranial variation. The numbers of vertebrae in the sacrum are thought to vary from two, the plesiomorphic condition for archosauriforms, to three, with the addition of a sacralized dorsal (i.e., dorsosacral) vertebra. In this study, we demonstrate the presence of a sacralized first caudal (i.e., caudosacral) vertebra in a sacrum belonging to Machaeroprosopus mccauleyi. We rule out taphonomic distortion or pathology as explanations for the inclusion of this element in the sacrum, suggesting instead that it occurred through modifications of the same developmental processes that likely produced dorsosacral vertebrae in phytosaurs. Additionally, we show that a dorsosacral vertebra is common in phytosaur specimens from the Chinle Formation and Dockum Group of the southwestern United States and suggest that it may be widespread among phytosaurs. The addition of sacral vertebrae potentially aided adaptation to larger body sizes or more terrestrial lifestyles in certain taxa.

Cranial osteology and paleoneurology of Tarjadia ruthae: An erpetosuchid pseudosuchian from the Triassic Chañares Formation (late Ladinian-?early Carnian) of Argentina

Tarjadia ruthae is a quadrupedal terrestrial pseudosuchian from the Middle-early Upper Triassic of the Chañares Formation, La Rioja Province, Argentina. Originally, this species was identified as an indeterminate archosaur and later as a doswelliid archosauriform based on very fragmentary specimens characterized by the ornamentation of the skull roof and osteoderms. Additional specimens (including skulls and postcrania) recovered in the last decade show that Tarjadia is an erpetosuchid, an enigmatic pseudosuchian group composed of six species registered in Middle-Upper Triassic continental units of Tanzania, Germany, Scotland, North America, Brazil, and Argentina. Tarjadia ruthae from Argentina and Parringtonia gracilis from Tanzania are the best preserved and more abundant species. Although the monophyly of Erpetosuchidae is well supported, alternative high-level positions within Archosauria have been suggested, such as sister taxon to Crocodylomorpha, Aetosauria, or Ornithosuchidae. In order to improve the knowledge about the erpetosuchids, we performed a detailed description and paleoneurological reconstruction of the skull of Tarjadia ruthae, based on two articulated partial skulls (CRILAR-Pv 478 and CRILAR-Pv 495) and other fragmentary specimens. We analyzed the stratigraphic and geographic occurrence of historical and new specimens of Tarjadia and provided a new emended diagnosis (the same for the genus as for the species, due to monotypy) along with a comparative description of the cranial endocast. The skull of Tarjadia is robust, with a thick and strongly ornamented skull roof, triangular in dorsal view, with concave lateral margins at mid-length that form an abrupt widened posterior region. The external nares are the smallest openings of the skull. The antorbital fossa is deeply excavated and has a small heart-shaped fenestra with both lobes pointing anteriorly. The supratemporal fenestrae are as large and rounded as the orbits, and the infratemporal fenestrae are L-shaped with an extensive excavation along the jugal, quadratojugal and quadrate. The hemimandibles are low, slightly concave on the dentigerous region and strongly convex on the posterior region, conferring them a S-shaped profile in dorsal view. The external mandibular fenestra is small and elliptic, being twice longer than high. The maxillary dentition is restricted to the anterior to mid region of the rostrum. Since the braincase of both specimens is partially damaged, the dorsal surface of the brain could not be entirely reconstructed. As a result, the endocast is anteroposteriorly elongated and seemingly flat, and the cephalic flexure seems to be lower than expected for a suchian. The labyrinth is twice wider than high, the semicircular canals are remarkably straight, and the anterior canal is longer than the posterior one.

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.

What else is dentition telling us? A new specimen-level phylogeny of Mesotheriidae (Mammalia, Notoungulata)

Mesotheriidae (Panperissodactyla, Notoungulata) are an extinct clade (early Oligocene-Pleistocene) of small to medium-sized herbivorous mammals that were widely distributed in South America. Although two subfamilies traditionally have been recognized (Trachytheriinae and Mesotheriinae), recent cladistic analyses based on discrete characters have indicated that "Trachytheriinae" is a paraphyletic assemblage. Given the availability of a large number of specimens and the fact that dental characters are the most common characters used in mesotheriid phylogenies, we performed specimen-level cladistic analyses combining discrete, continuous and geometric morphometrics-based dental characters. The aim was to: (1) include new scored morphological characters to solve the phylogenetic relationships of Mesotheriidae; (2) compare the results of the upper and lower dentition analyses as different character partitions and in combination, to establish phylogenetic hypotheses; and (3) trace the evolution of dental traits. Phylogenetic analyses employing characters of associated upper and lower dentitions recovered one most parsimonious tree with Archaeohyracidae (outgroup) as the sister group of Pan-Mesotheriidae (= Mesotheriidae; converted clade name), this latter composed of trachytheriines (stem-mesotheriine) + Mesotheriinae (converted clade name). Within Mesotheriinae, we recovered two main lineages phylogenetically defined here as Bolivarini and Pampaini (new clade names). Analyses of isolated upper and lower dentition sub-datasets each resulted in one most parsimonious tree congruent with the associated dentition. Our study emphasizes the use of geometric morphometrics characters to resolve additional clades in phylogenetic analyses, provides information on the evolution of size and morphology of teeth, and exposes specimen assignment issues at a taxonomic level. The integration of osteological characters might be crucial to further understanding the evolution of Mesotheriidae.

A late-surviving phytosaur from the northern Atlantic rift reveals climate constraints on Triassic reptile biogeography

BACKGROUND

The origins of all major living reptile clades, including the one leading to birds, lie in the Triassic. Following the largest mass extinction in Earth's history at the end of the Permian, the earliest definite members of the three major living reptile clades, the turtles (Testudines), crocodylians and birds (Archosauria), and lizards, snakes, amphisbaenians, and Tuatara (Lepidosauria) appeared. Recent analyses of the Triassic reptile fossil record suggest that the earliest diversifications in all three of these clades were tightly controlled by abrupt paleoclimate fluctuations and concordant environmental changes. Yet, this has only been preliminarily tested using information from evolutionary trees. Phytosauria consists of superficially crocodylian-like archosaurs that either form the sister to the crown or are the earliest divergence on the crocodylian stem and are present throughout the Triassic, making this clade an excellent test case for examining this biogeographic hypothesis.

RESULTS

Here, I describe a new phytosaur, Jupijkam paleofluvialis gen. et sp. nov., from the Late Triassic of Nova Scotia, Canada, which at that time sat in northern Pangaea near the northern terminus of the great central Pangean rift. As one of the northernmost occurrences of Phytosauria, J. paleofluvialis provides critical new biogeographic data that enables revised estimations of phytosaur historical biogeography along phylogenies of this clade built under multiple methodologies. Reconstructions of phytosaur historical biogeography based on different phylogenies and biogeographic models suggest that phytosaurs originated in northern Pangaea, spread southward, and then dispersed back northward at least once more during the Late Triassic.

CONCLUSIONS

The results presented in this study link phytosaur biogeography to major changes to Triassic global climate and aridity. Together with the earliest dinosaurs and several other reptile lineages, phytosaur diversification and migration appear to have been restricted by the formation and loss of arid belts across the Pangean supercontinent.

Deep reptilian evolutionary roots of a major avian respiratory adaptation

Vertebral ribs of the anterior thorax in extant birds bear bony prongs called uncinate processes, which improve the mechanical advantage of mm. appendicocostales to move air through the immobile lung and pneumatic air sacs. Among non-avian archosaurs, broad, cartilaginous uncinate processes are present in extant crocodylians, and likely have a ventilatory function. Preserved ossified or calcified uncinate processes are known in several non-avian dinosaurs. However, whether other fossil archosaurs possessed cartilaginous uncinate processes has been unclear. Here, we establish osteological correlates for uncinate attachment to vertebral ribs in extant archosaurs, with which we inferred the presence of uncinate processes in at least 19 fossil archosaur taxa. An ancestral state reconstruction based on the infer distribution suggests that cartilaginous uncinate processes were plesiomorphically present in Dinosauria and arguably in Archosauria, indicating that uncinate processes, and presumably their ventilatory function, have a deep evolutionary history extending back well beyond the origin of birds.

Growth and limb bone histology of aetosaurs and phytosaurs from the Late Triassic Krasiejów locality (sw Poland) reveals strong environmental influence on growth pattern

The growth pattern of the Polish phytosaur Parasuchus cf. arenaceus and the aetosaur Stagonolepis olenkae (both Krasiejów; Norian) was studied. Results were compared to published data of other members of these two groups and to a new sample of the German (Heslach; Norian) phytosaur Nicrosaurus sp. All three herein studied taxa display lamellar-zonal bone consisting predominately of parallel-fibred tissue and on average a low to moderate vascular density. Towards the outer cortex the thickness of annuli increases in most samples and becomes distinctly wider than the zones. Therefore, most of the appositional growth in adults was achieved during phases of prolonged slow growth. All bones show a diffuse growth pattern, without well demarcated zones and annuli. Distinct lines of arrested growth (lag) are not identified in the Krasiejów sample, only the Nicrosaurus femur shows one distinct lag as do other taxa outside Krasiejów. Instead, the Krasiejów taxa display multiple rest lines and sub-cycles. Thus, identification and count of annual growth cycles remains difficult, the finally counted annual growth cycles range (two to six) is quite large despite the low size range of the samples. A correlation between age and bone length is not identified, indicating developmental plasticity. Although both are archosaurs, Stagonolepis and Parasuchus are phylogenetically not closely related, however, they show a very similar growth pattern, despite different life styles (terrestrial vs. semi-aquatic). Based on the new data, and previously histological studies from Krasiejów, the local environmental conditions were special and had a strong influence on the growth pattern.

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.

Relative tooth size, Bayesian inference, and Homo naledi

OBJECTIVES

Size-corrected tooth crown measurements were used to estimate phenetic affinities among Homo naledi (~335-236 ka) and 11 other Plio-Pleistocene and recent species. To assess further their efficacy, and identify dental evolutionary trends, the data were then quantitatively coded for phylogenetic analyses. Results from both methods contribute additional characterization of H. naledi relative to other hominins.

MATERIALS AND METHODS

After division by their geometric mean, scaled mesiodistal and buccolingual dimensions were used in tooth size apportionment analysis to compare H. naledi with Australopithecus africanus, A. afarensis, Paranthropus robustus, P. boisei, H. habilis, H. ergaster, H. erectus, H. heidelbergensis, H. neanderthalensis, H. sapiens, and Pan troglodytes. These data produce equivalently scaled samples unaffected by interspecific size differences. The data were then gap-weighted for Bayesian inference.

RESULTS

Congruence in interspecific relationships is evident between methods, and with many inferred from earlier systematic studies. However, the present results place H. naledi as a sister taxon to H. habilis, based on a symplesiomorphic pattern of relative tooth size. In the preferred Bayesian phylogram, H. naledi is nested within a clade comprising all Homo species, but it shares some characteristics with australopiths and, particularly, early Homo.

DISCUSSION

Phylogenetic analyses of relative tooth size yield information about evolutionary dental trends not previously reported in H. naledi and the other hominins. Moreover, with an appropriate model these data recovered plausible evolutionary relationships. Together, the findings support recent study suggesting H. naledi originated long before the geological date of the Dinaledi Chamber, from which the specimens under study were recovered.

A Different Perspective on Sex Dimorphism in the Adult Hermann's Tortoise: Geometric Morphometry

Eastern Hermann's tortoise (Testudo hermanni boettgeri) is a subspecies of Hermann's tortoise (Testudo hermanni) found in Albania. Gender determination is one of the crucial elements in determining the population dynamics in all species. Female and male adult tortoises look different, but these differences can be difficult to distinguish in captivity or when their sex indicators are deformed or injured. Therefore, the aim of this study was to use indirect and non-invasive methods such as geometric morphometric analysis to determine the sex of adult tortoises. For the geometric morphometry, 17 female and 23 male Hermann's tortoises were collected and photographed from the hills and mountains around the Tirana district of Albania between August and October 2019. Sexes were discriminated based on geometric morphometry, and plastron shape was a better indicator than carapace shape. In addition, abdominal, femoral and anal scutes on the plastron and the ratio of femoral to pectoral suture lengths were important for the sex distinction. Females had a larger plastron than males; this may have been supported by fecundity selection, because a large plastron suggests more volume in which to store eggs. The femoral and anal scutes were larger in male tortoises, and serve as a stronger base during mating. This study was conducted for adults only, and future studies are needed to determine if these indicators also apply to hatchlings and juveniles.

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.

The phylogenetic relationships of neosuchian crocodiles and their implications for the convergent evolution of the longirostrine condition

Since their origin in the Late Triassic, crocodylomorphs have had a long history of evolutionary change. Numerous studies examined their phylogeny, but none have attempted to unify their morphological characters into a single, combined dataset. Following a comprehensive review of published character sets, we present a new dataset for the crocodylomorph clade Neosuchia consisting of 569 morphological characters for 112 taxa. For the first time in crocodylian phylogenetic studies, quantitative variation was treated as continuous data (82 characters). To provide the best estimate of neosuchian relationships, and to investigate the origins of longirostry, these data were analysed using a variety of approaches. Our results show that equally weighted parsimony and Bayesian methods cluster unrelated longirostrine forms together, producing a topology that conflicts strongly with their stratigraphic distributions. By contrast, applying extended implied weighting improves stratigraphic congruence and removes longirostrine clustering. The resulting topologies resolve the major neosuchian clades, confirming several recent hypotheses regarding the phylogenetic placements of particular species (e.g. Baryphracta deponiae as a member of Diplocynodontinae) and groups (e.g. Tethysuchia as non-eusuchian neosuchians). The longirostrine condition arose at least three times independently by modification of the maxilla and premaxilla, accompanied by skull roof changes unique to each longirostrine clade.

Estimating the phylogeny of geoemydid turtles (Cryptodira) from landmark data: an assessment of different methods

BACKGROUND

In the last 20 years, a general picture of the evolutionary relationships between geoemydid turtles (ca. 70 species distributed over the Northern hemisphere) has emerged from the analysis of molecular data. However, there is a paucity of good traditional morphological characters that correlate with the phylogeny, which are essential for the robust integration of fossil and molecular data. Part of this problem might be due to intrinsic limitations of traditional discrete characters. Here, we explore the use of continuous data in the form of 3D coordinates of homologous landmarks on the turtle shell for phylogenetic inference and the phylogenetic placement of single species on a scaffold molecular tree. We focus on the performance yielded by sampling the carapace and/or plastral lobes and using various phylogenetic methods.

METHODS

We digitised the landmark coordinates of the carapace and plastron of 42 and 46 extant geoemydid species, respectively. The configurations were superimposed and we estimated the phylogenetic tree of geoemydids with landmark analysis under parsimony, traditional Farris parsimony, unweighted squared-change parsimony, maximum likelihood with a Brownian motion model, and neighbour-joining on a matrix of pairwise Procrustes distances. We assessed the performance of those analyses by comparing the trees against a reference phylogeny obtained from seven molecular markers. For comparisons between trees we used difference measures based on quartets and splits. We used the same reference tree to evaluate phylogenetic placement performance by a leave-one-out validation procedure.

RESULTS

Whatever method we used, similarity to the reference phylogeny was low. The carapace alone gave slightly better results than the plastron or the complete shell. Assessment of the potential for placement of single species on the reference tree with landmark data gave much better results, with similar accuracy and higher precision compared to the performance of discrete characters with parsimony.

Description and phylogenetic placement of a new marine species of phytosaur (Archosauriformes: Phytosauria) from the Late Triassic of Austria

Phytosaurs are a group of carnivorous, semi-aquatic archosaurian reptiles that attained an almost global distribution during the Late Triassic. We here describe a new species of the phytosaur genus Mystriosuchus from the Norian Dachstein Limestone of Austria, from a marine lagoonal depositional environment. The new Austrian material comprises remains of at least four individuals of similar size (c. 4 m in total length) found in association but disarticulated, and includes one complete and two partial skulls and postcrania. All of these specimens apparently represent a single taxon, which is distinguished by numerous anatomical features from the two previously named Mystriosuchus species. Maximum parsimony analysis of a comprehensive morphological dataset provides strong statistical support for the phylogenetic position of the new Austrian taxon in Mystriosuchus, as the sister taxon to a clade comprising M. planirostris and M. westphali. Histological analysis suggests that the Austrian phytosaur specimens represent individuals that were at least eight years old at time of death, but which had not yet reached skeletal maturity. Taphonomic and palaeoenvironmental data suggest that these phytosaurs were living in the marine lagoon in which they were preserved, providing the strongest evidence to date of marine adaptations in phytosaurs.