Multiple optimality criteria support Ornithoscelida

Statistical evaluation of character support reveals the instability of higher-level dinosaur phylogeny

The interrelationships of the three major dinosaur clades (Theropoda, Sauropodomorpha, and Ornithischia) have come under increased scrutiny following the recovery of conflicting phylogenies by a large new character matrix and its extensively modified revision. Here, we use tools derived from recent phylogenomic studies to investigate the strength and causes of this conflict. Using maximum likelihood as an overarching framework, we examine the global support for alternative hypotheses as well as the distribution of phylogenetic signal among individual characters in both the original and rescored dataset. We find the three possible ways of resolving the relationships among the main dinosaur lineages (Saurischia, Ornithischiformes, and Ornithoscelida) to be statistically indistinguishable and supported by nearly equal numbers of characters in both matrices. While the changes made to the revised matrix increased the mean phylogenetic signal of individual characters, this amplified rather than reduced their conflict, resulting in greater sensitivity to character removal or coding changes and little overall improvement in the ability to discriminate between alternative topologies. We conclude that early dinosaur relationships are unlikely to be resolved without fundamental changes to both the quality of available datasets and the techniques used to analyze them.

Taxonomic, palaeobiological and evolutionary implications of a phylogenetic hypothesis for Ornithischia (Archosauria: Dinosauria)

The origin and evolutionary relationships of ornithischian dinosaurs are topics that have undergone a series of substantial revisions. At present there are several competing hypotheses concerning the relationship between Ornithischia and the other principal clades of Dinosauria. Some hypotheses have posited a tree topology within Dinosauria that imply a ‘ghost-lineage’ for Ornithischia (whose representatives make their first unambiguous appearance in the Hettangian) that extends through a substantial portion of Triassic time. In contrast, other hypotheses have placed conventionally Triassic dinosauromorph (stem-lineage Dinosauria) taxa within the clade Ornithischia. Recently, a large-scale phylogenetic analysis recovered an array of taxa, known as ‘silesaurids’, as a paraphyletic assemblage of taxa (referred to in this article using the informal terms silesaurs or silesaurians) on the branch leading to the clade Ornithischia. This latter hypothesis of relationships would account for the apparent absence of Triassic ornithischians, because stem-lineage ornithischians (silesaurs in this article) are exclusively Triassic. However, the analysis that produced this novel topology used a dataset that, in its original form, did not include all early representatives of Ornithischia (sensu lato), and did not incorporate all the anatomical characters that have been suggested to unite Ornithischia with other dinosaurian clades (Theropoda and Sauropodomorpha). Nor did the initial study go on to expand upon some important taxonomic, palaeobiological and evolutionary implications of a topology that links a paraphyletic array of silesaurs to the clade Ornithischia. The present article addresses these latter issues by expansion and re-analysis of the original dataset. The results find further support for the hypothesis that silesaurs comprise a paraphyletic grouping of taxa on the stem of Ornithischia and that successive silesaur taxa acquire anatomical characters anagenetically in a process that culminates in the assembly of what may be described as a ‘traditional’ ornithischian. The overall topology of the consensus tree remains but little changed from the original analysis, despite the addition of new taxa and characters. To provide stability to this area of the tree and to preserve the most important of the relevant taxonomic names, we suggest a revised taxonomic framework for ornithischians that is consistent with this new topology. We retain the name Ornithischia for the total-group (traditional Ornithischia and its stem-lineage), while we resuscitate a name originally proposed by Richard Owen, Prionodontia (= ‘coarse edged teeth’) for the clade containing only the so-called traditional ornithischian (= ‘bird-hipped’) dinosaurs. We also erect Parapredentata as a more exclusive subclade in Ornithischia. This novel taxonomic framework is intended to provide phylogenetic clarity and a degree of stability in Ornithischia and Dinosauria as further analyses and new data continue to refine and re-shape the tree. The data presented in this study represent a stage in our attempt to establish an early dinosaur dataset in which character definitions and character scores are agreed upon and used consistently.

Africa's oldest dinosaurs reveal early suppression of dinosaur distribution

The vertebrate lineages that would shape Mesozoic and Cenozoic terrestrial ecosystems originated across Triassic Pangaea^1-11. By the Late Triassic (Carnian stage, ~235 million years ago), cosmopolitan 'disaster faunas' (refs. ^12-14) had given way to highly endemic assemblages^12,13 on the supercontinent. Testing the tempo and mode of the establishment of this endemism is challenging-there were few geographic barriers to dispersal across Pangaea during the Late Triassic. Instead, palaeolatitudinal climate belts, and not continental boundaries, are proposed to have controlled distribution^15-18. During this time of high endemism, dinosaurs began to disperse and thus offer an opportunity to test the timing and drivers of this biogeographic pattern. Increased sampling can test this prediction: if dinosaurs initially dispersed under palaeolatitudinal-driven endemism, then an assemblage similar to those of South America^4,19-21 and India^19,22-including the earliest dinosaurs-should be present in Carnian deposits in south-central Africa. Here we report a new Carnian assemblage from Zimbabwe that includes Africa's oldest definitive dinosaurs, including a nearly complete skeleton of the sauropodomorph Mbiresaurus raathi gen. et sp. nov. This assemblage resembles other dinosaur-bearing Carnian assemblages, suggesting that a similar vertebrate fauna ranged high-latitude austral Pangaea. The distribution of the first dinosaurs is correlated with palaeolatitude-linked climatic barriers, and dinosaurian dispersal to the rest of the supercontinent was delayed until these barriers relaxed, suggesting that climatic controls influenced the initial composition of the terrestrial faunas that persist to this day.

Decelerated dinosaur skull evolution with the origin of birds

The evolutionary radiation of birds has produced incredible morphological variation, including a huge range of skull form and function. Investigating how this variation arose with respect to non-avian dinosaurs is key to understanding how birds achieved their remarkable success after the Cretaceous-Paleogene extinction event. Using a high-dimensional geometric morphometric approach, we quantified the shape of the skull in unprecedented detail across 354 extant and 37 extinct avian and non-avian dinosaurs. Comparative analyses reveal fundamental differences in how skull shape evolved in birds and non-avian dinosaurs. We find that the overall skull shape evolved faster in non-avian dinosaurs than in birds across all regions of the cranium. In birds, the anterior rostrum is the most rapidly evolving skull region, whereas more posterior regions-such as the parietal, squamosal, and quadrate-exhibited high rates in non-avian dinosaurs. These fast-evolving elements in dinosaurs are strongly associated with feeding biomechanics, forming the jaw joint and supporting the jaw adductor muscles. Rapid pulses of skull evolution coincide with changes to food acquisition strategies and diets, as well as the proliferation of bony skull ornaments. In contrast to the appendicular skeleton, which has been shown to evolve more rapidly in birds, avian cranial morphology is characterised by a striking deceleration in morphological evolution relative to non-avian dinosaurs. These results may be due to the reorganisation of skull structure in birds-including loss of a separate postorbital bone in adults and the emergence of new trade-offs with development and neurosensory demands. Taken together, the remarkable cranial shape diversity in birds was not a product of accelerated evolution from their non-avian relatives, despite their frequent portrayal as an icon of adaptive radiations.

Testing pterosaur ingroup relationships through broader sampling of avemetatarsalian taxa and characters and a range of phylogenetic analysis techniques

The pterosaurs first appear in the fossil record in the middle of the Late Triassic. Their earliest representatives are known from Northern Hemisphere localities but, by the end of the Jurassic Period, this clade of flying reptiles achieved a global distribution, as well as high levels of diversity and disparity. Our understanding of early pterosaur evolution and the fundamental interrelationships within Pterosauria has improved dramatically in recent decades. However, there is still debate about how the various pterosaur subgroups relate to one another and about which taxa comprise these. Many recent phylogenetic analyses, while sampling well from among the known Triassic and Early Jurassic pterosaurs, have not included many non-pterosaurian ornithodirans or other avemetatarsalians. Given the close relationship between these groups of archosaurs, the omission of other ornithodirans and avemetatarsalians has the potential to adversely affect the results of phylogenetic analyses, in terms of character optimisation and ingroup relationships recovered. This study has addressed this issue and tests the relationships between the early diverging pterosaur taxa following the addition of avemetatarsalian taxa and anatomical characters to an existing early pterosaur dataset. This study has, for the first time, included taxa that represent the aphanosaurs, lagerpetids, silesaurids and dinosaurs, in addition to early pterosaurs. Anatomical characters used in other recent studies of archosaurs and early dinosaurs have also been incorporated. By expanding the outgroup taxa and anatomical character coverage in this pterosaur dataset, better resolution between the taxa within certain early pterosaur subclades has been achieved and stronger support for some existing clades has been found; other purported clades of early pterosaurs have not been found in this analysis-for example there is no support for a monophyletic Eopterosauria or Eudimorphodontidae. Further support has been found for a sister-taxon relationship between Peteinosaurus zambelli and Macronychoptera, a clade here named Zambellisauria (clade nov.), as well as for a monophyletic and early diverging Preondactylia. Some analyses also support the existence of a clade that falls as sister-taxon to the zambellisaurs, here named Caviramidae (clade nov.). Furthermore, some support has been found for a monophyletic Austriadraconidae at the base of Pterosauria. Somewhat surprisingly, Lagerpetidae is recovered outside of Ornithodira sensu stricto, meaning that, based upon current definitions at least, pterosaurs fall within Dinosauromorpha in this analysis. However, fundamental ornithodiran interrelationships were not the focus of this study and this particular result should be treated with caution for now. However, these results do further highlight the need for broader taxon and character sampling in phylogenetic analyses, and the effects of outgroup choice on determining ingroup relationships.

Evolutionary Integration and Modularity in the Archosaur Cranium

Complex structures, like the vertebrate skull, are composed of numerous elements or traits that must develop and evolve in a coordinated manner to achieve multiple functions. The strength of association among phenotypic traits (i.e., integration), and their organization into highly-correlated, semi-independent subunits termed modules, is a result of the pleiotropic and genetic correlations that generate traits. As such, patterns of integration and modularity are thought to be key factors constraining or facilitating the evolution of phenotypic disparity by influencing the patterns of variation upon which selection can act. It is often hypothesized that selection can reshape patterns of integration, parceling single structures into multiple modules or merging ancestrally semi-independent traits into a strongly correlated unit. However, evolutionary shifts in patterns of trait integration are seldom assessed in a unified quantitative framework. Here, we quantify patterns of evolutionary integration among regions of the archosaur skull to investigate whether patterns of cranial integration are conserved or variable across this diverse group. Using high-dimensional geometric morphometric data from 3D surface scans and computed tomography scans of modern birds (n = 352), fossil non-avian dinosaurs (n = 27), and modern and fossil mesoeucrocodylians (n = 38), we demonstrate that some aspects of cranial integration are conserved across these taxonomic groups, despite their major differences in cranial form, function, and development. All three groups are highly modular and consistently exhibit high integration within the occipital region. However, there are also substantial divergences in correlation patterns. Birds uniquely exhibit high correlation between the pterygoid and quadrate, components of the cranial kinesis apparatus, whereas the non-avian dinosaur quadrate is more closely associated with the jugal and quadratojugal. Mesoeucrocodylians exhibit a slightly more integrated facial skeleton overall than the other grades. Overall, patterns of trait integration are shown to be stable among archosaurs, which is surprising given the cranial diversity exhibited by the clade. At the same time, evolutionary innovations such as cranial kinesis that reorganize the structure and function of complex traits can result in modifications of trait correlations and modularity.

Exploring the impact of morphology, multiple sequence alignment and choice of optimality criteria in phylogenetic inference: a case study with the Neotropical orb-weaving spider genus Wagneriana (Araneae: Araneidae)

We present a total evidence phylogenetic analysis of the Neotropical orb-weaving spider genus Wagneriana and discuss the phylogenetic impacts of methodological choices. We analysed 167 phenotypic characters and nine loci scored for 115 Wagneriana and outgroups, including 46 newly sequenced species. We compared total evidence analyses and molecular-only analyses to evaluate the impact of phenotypic evidence, and we performed analyses using the programs POY, TNT, RAxML, GARLI, IQ-TREE and MrBayes to evaluate the effects of multiple sequence alignment and optimality criteria. In all analyses, Wagneriana carimagua and Wagneriana uropygialis were nested in the genera Parawixia and Alpaida, respectively, and the remaining species of Wagneriana fell into three main clades, none of which formed a pair of sister taxa. However, sister-group relationships among the main clades and their internal relationships were strongly influenced by methodological choices. Alignment methods had comparable topological effects to those of optimality criteria in terms of ‘subtree pruning and regrafting’ moves. The inclusion of phenotypic evidence, 2.80–3.05% of the total evidence matrices, increased support irrespective of the optimality criterion used. The monophyly of some groups was recovered only after the addition of morphological characters. A new araneid genus, Popperaneus gen. nov., is erected, and Paraverrucosa is resurrected. Four new synonymies and seven new combinations are proposed.

Vertebral morphometrics and lung structure in non-avian dinosaurs

The lung-air sac system of modern birds is unique among vertebrates. However, debate surrounds whether an avian-style lung is restricted to birds or first appeared in their dinosaurian ancestors, as common osteological correlates for the respiratory system offer limited information on the lungs themselves. Here, we shed light on these issues by using axial morphology as a direct osteological correlate of lung structure, and quantifying vertebral shape using geometric morphometrics in birds, crocodilians and a wide range of dinosaurian taxa. Although fully avian lungs were a rather late innovation, we quantitatively show that non-avian dinosaurs and basal dinosauriforms possessed bird-like costovertebral joints and a furrowed thoracic ceiling. This would have immobilized the lung's dorsal surface, a structural prerequisite for a thinned blood-gas barrier and increased gas exchange potential. This could have permitted high levels of aerobic and metabolic activity in dinosaurs, even in the hypoxic conditions of the Mesozoic, contributing to their successful radiation.