Julia A Clarke

University of Texas at Austin | UT

A second K/Pg boundary interval in the northern sector of the Antarctic Peninsula on Vega Island has been proposed, yet current temporal resolution of these strata prohibits direct testing of this hypothesis. To not only test for the existence of a K/Pg boundary on Vega Island but also provide increased age resolution for the associated vertebrate...

Reptile eggshell ensures water and gas exchange during incubation and plays a key role in reproductive success. The diversity of reptilian incubation and life history strategies has led to many clade-specific structural adaptations of their eggshell, which have been studied in extant taxa (i.e. birds, crocodilians, turtles, and lepidosaurs). Most s...

Significance The controversy over the taxonomic identity of the eggs exploited by Australia’s first people around 50,000 y ago is resolved. The birds that laid these eggs are extinct, and distinguishing between two main candidates, a giant flightless “mihirung” Genyornis and a large megapode Progura , had proven impossible using morphological and g...

Although an increasing number of studies are combining skeletal and neural morphology data in a phylogenetic context, most studies do not include extinct taxa due to the rarity of preserved endocasts. The early Eocene avifauna of the Fur Formation of Denmark presents an excellent opportunity for further study of extinct osteological and endocranial...

The globally distributed extinct clade Enantiornithes comprises the most diverse early radiation of birds in the Mesozoic with species exhibiting a wide range of body sizes, morphologies, and ecologies. The fossil of a new enantiornithine bird, Brevirostruavis macrohyoideus gen. et sp. nov., from the Lower Cretaceous Jiufotang Formation in Liaoning...

Of the more than 6,000 members of the most speciose avian clade, Passeriformes (perching birds), only the five species of dippers (Cinclidae, Cinclus) use their wings to swim underwater. Among nonpasserine wing‐propelled divers (alcids, diving petrels, penguins, and plotopterids), convergent evolution of morphological characteristics related to thi...

Carotenoids are pigments responsible for most bright yellow, red, and orange hues in birds. Their distribution has been investigated in avian plumage, but the evolution of their expression in skin and other integumentary structures has not been approached in detail. Here, we investigate the expression of carotenoid‐consistent coloration across tiss...

Birds today are the most diverse clade of terrestrial vertebrates, and understanding why extant birds (Aves) alone among dinosaurs survived the Cretaceous-Paleogene mass extinction is crucial to reconstructing the history of life. Hypotheses proposed to explain this pattern demand identification of traits unique to Aves. However, this identificatio...

While the state of the art has been described for recording bird songs and calls, there are no described best practices for collecting and preserving the avian vocal organ, the syrinx. In addition to skins and skeletal preparations, field collection of tissues for DNA sequencing has become a common practice. Protocols for such tissue collection oft...

Birds share an array of unique characteristics among extant land vertebrates. Among these, external and microstructural characteristics of extant bird eggs have been linked to changes in reproductive strategy that arose among non‐avian theropod dinosaurs. More recently, differences in egg proportions recovered in crown birds relative to other dinos...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Carotenoids are among the most ubiquitous pigments that produce bright colors in animals, and create most of the vibrant yellows, oranges, and reds in living birds. While they are comparatively well characterized in the plumage of many species, these pigments are also common in avian bare parts (e.g. skin, beak) but their phylogenetic distribution...

A recent study by Norell et al. (2020) described new egg specimens for two dinosaur species, identified as the first soft-shelled dinosaur eggs. The authors used phylogenetic comparative methods to reconstruct eggshell type in a sample of reptiles, and identified the eggs of dinosaurs and archosaurs as ancestrally soft-shelled, with three independe...

The stem lineage relationships and early phenotypic evolution of Charadriiformes (shorebirds) and Gruiformes (rails, cranes, and allies) remain unresolved. It is still debated whether these clades are sister-taxa. New phylogenetic analyses incorporating Paleogene fossils have the potential to reveal the evolutionary connections of these two specios...

Egg size and structure reflect important constraints on the reproductive and life-history characteristics of vertebrates. More than two-thirds of all extant amniotes lay eggs. During the Mesozoic era (around 250 million to 65 million years ago), body sizes reached extremes; nevertheless, the largest known egg belongs to the only recently extinct el...

Synthesizing data from three years of mixed methods classroom design research, this study reports on a model for a disciplinarily diverse course-based research experience (CBRE) to enhance university-based science learning. By emphasizing disciplinary mixing, mentorship and peer feedback, the experience develops scientific skills, identities and di...

One of the two lineages of extant birds resulting from its deepest split, Palaeognathae, has been reported not to exhibit structural coloration in feathers, affecting inferences of ancestral coloration mechanisms in extant birds. Structural coloration in facial skin and eggshells has been shown in this lineage, but has not been reported in feathers...

Relative brain sizes in birds can rival those of primates, but large-scale patterns and drivers of avian brain evolution remain elusive. Here, we explore the evolution of the fundamental brain-body scaling relationship across the origin and evolution of birds. Using a comprehensive dataset sampling> 2,000 modern birds, fossil birds, and theropod di...

Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization—the conversion of specimen data into accessible digital content—has greatly expanded the use of NHC collections across a diversity of disciplines....

Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well...

The middle-late Eocene of Antarctica was characterized by dramatic change as the continent became isolated from the other southern landmasses and the Antarctic Circumpolar Current formed. These events were crucial to the formation of the permanent Antarctic ice cap, affecting both regional and global climate change. Our best insight into how life i...

The Magallanes-Austral foreland basin preserves an important record of orogenesis and landscape evolution in the Patagonian Andes of Chile and Argentina. Throughout the retroarc foreland basin, a regional disconformity with little to no angular discordance separates Upper Cretaceous–lower Paleocene strata from overlying deposits of diachronous Eoce...

Numerous skeletal remains recovered in situ from the late early to middle Paleocene Takatika Grit of Chatham Island, New Zealand, are among the oldest known fossils attributed to the penguin clade (Aves, Sphenisciformes). They represent a new medium-sized taxon, for which we erect a new genus and species, and a second, notably larger form. These ne...

Background The lake deposits of the informal Ruby Paper Shale unit, part of the Renova Formation of Montana, have yielded abundant plant fossils that document Late Eocene – Early Oligocene global cooling in western North America. A nearly complete small bird with feather impressions was recovered from this unit in in 1959, but has only been informa...

There has been much discussion over whether basal birds (e.g. Archaeopteryx and Confuciusornis) exhibited active flight. A recent study of barb angles has suggested they likely could not but instead may have exhibited a gliding phase. Pennaceous primary flight feathers were proposed to show significant shifts in barb angle values of relevance to th...

Despite having one of the most robust fossil records within core-gruiform birds (rails, cranes, and allies), the biogeographic history of Gruidae (cranes) and key drivers of diversification within this group remain largely unknown. The Eogruidae of Eurasia represent some of the earliest known crane-like fossils. Here, we present description of a ne...

Cape Marsh, located on the eastern end of Robertson Island to the east of the Antarctic Peninsula, exposes an isolated outcrop of Late Cretaceous sedimentary strata. The outcrop is approximately 120 km southwest of the much better-studied exposures of similar age on and around James Ross Island (JRI); as such, its remoteness has complicated both lo...

Numerous isolated and associated skeletal remains recovered in situ from the late early to middle Paleocene Takatika Grit of Chatham Island, New Zealand, represent some of the oldest known penguin fossils (Aves: Sphenisciformes). Among these remains we recognise a new medium-sized taxon, and another notably larger form. The new penguins, as well as...

The Magallanes-Austral foreland basin records orogenesis and landscape evolution in the Patagonian Andes of Chile and Argentina. Throughout the retroarc foreland basin, a regional disconformity separates Upper Cretaceous-lower Paleocene strata from overlying diachronous Eocene-Miocene deposits. We present new data from a fossiliferous mixed marine/...

Although the fossil record of non-avian dinosaurs from the Cretaceous of Antarctica is the poorest of any continent, fossils representing at least five major taxonomic groups (Ankylosauria, early-diverging Ornithopoda, Hadrosauridae, Titanosauria, and Theropoda) have been recovered. All come from Upper Cretaceous (Coniacian–Maastrichtian) marine an...

The fossil record of birds from Antarctica is concentrated in the James Ross Basin, located in northeast of the Antarctic Peninsula. Birds are here represented by an extensive Paleogene record of penguins (Sphenisciformes) and Cretaceous-Paleogene record of Anseriformes, followed by other groups with a minor representation (Procellariiformes, Falco...

Understanding of the Asian early Paleogene avifauna is limited relative to that of North American and European avifauna of the same period. While major patterns of mammalian faunal exchange among these three regions across the Paleocene/Eocene boundary have been described, much less is known about the dynamics of bird diversity over the same time i...

Osmoregulation in birds is complicated, with different organs acting concurrently to regulate this physiological process. Of particular interest is how the urinary excretions of birds can remove excess nitrogen while minimizing the need for dietary water and balancing the physiological demands of oviparity. It has long been concluded from chemical...

The ability to fly has been lost in many groups of birds. A comparison of the wing structures and genomes of flighted and non-flighted species of steamer duck highlights a possible mechanism for the loss of flight. Genomes of flighted and flightless steamer ducks compared. Falkland Flightless Steamerduck 'steaming' on water

Lithornithids are volant stem palaeognaths from the Paleocene‐Eocene. Except for these taxa and the extant neotropical tinamous, all other known extinct and extant palaeognaths are flightless. Investigation of properties of the lithornithid wing and its implications for inference of flight style informs understood locomotor diversity within Palaeog...

Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization–the conversion of specimen data into accessible digital content–has greatly expanded the use of NHC collections across a diversity of disciplines....

Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization–the conversion of specimen data into accessible digital content–has greatly expanded the use of NHC collections across a diversity of disciplines....

The giant carnivorous phorusrhacid bird Phorusrhacos longissimus (Aves, Cariamiformes) was first described in 1887 by Florentino Ameghino on the basis of a jaw fragment. The majority of a skull of the species still encased in crumbling rock was preserved only long enough for illustrations to be made by Carlos Ameghino in the field and for a brief d...

In 2006, a partial avian femur (South Dakota School of Mines and Technology (SDSM) 78247) from the Upper Cretaceous (Maastrichtian) Sandwich Bluff Member of the López de Bertodano Formation of Sandwich Bluff on Vega Island of the northern Antarctic Peninsula was briefly reported as that of a cariamiform-a clade that includes extant and volant South...

Palaeognathae is an extant clade of birds with body masses ranging over several orders of magnitude of kilograms, including the largest-yet described terrestrial avian species. Most studies have suggested flight loss and increasing body size began early in its evolutionary history, prior to the divergence of the major extant lineages. However, rece...

1.Phenotypic data is crucial for understanding genotype–phenotype relationships, assessing the tree of life, and revealing trends in trait diversity over time. Large‐scale description of whole organisms for quantitative analyses (phenomics) presents several challenges, and technological advances in the collection of genomic data outpace those for p...

Natural history museums are unique spaces for interdisciplinary research and for educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they provide a place-based window to focus on integration of science and discovery, as well...

Natural history museums are unique spaces for interdisciplinary research and for educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they provide a place-based window to focus on integration of science and discovery, as well...

A core question in evolutionary biology is whether convergent phenotypic evolution is driven by convergent molecular changes in proteins or regulatory regions. We combined phylogenomic, developmental, and epigenomic analysis of 11 new genomes of paleognathous birds, including an extinct moa, to show that convergent evolution of regulatory regions,...

Metabolism links organisms to their environment through its effects on thermoregulation, feeding behaviour and energetics. Genes involved in metabolic processes have known pleiotropic effects on some melanic colour traits. Understanding links between physiology and melanic colour is critical for understanding the role of, and potential constraints...

The recently extinct Malagasy elephant birds (Palaeognathae, Aepyornithiformes) included the largest birds that ever lived. Elephant bird neuroanatomy is understudied but can shed light on the lifestyle of these enigmatic birds. Palaeoneurological studies can provide clues to the ecologies and behaviours of extinct birds because avian brain shape i...

Integumentary patterns and colors can differentiate species, sexes, and life changes and can inform on habitat and ecology. However, they are rarely preserved in the fossil record. Here, we report on an extremely well-preserved specimen of the Cretaceous bird Confuciusornis with unprecedented complexity, including small spots on the wings, crest, a...

Iodine staining combined with X-ray computed tomography (CT) has become a core approach in anatomy, offering three-dimensional and essentially non-destructive imaging of soft tissues. Although there have been rapid advances in methodologies and techniques, the mechanisms underlying diffusible iodine contrast-enhanced CT are not yet fully understood...

In its most basic conception, a novelty is simply something new. However, when many previously proposed evolutionary novelties have been illuminated by genetic, developmental, and fossil data, they have refined and narrowed our concept of biological "newness." For example, they show that these novelties can occur at one or multiple levels of biolog...

Penguins exhibit an array of derived feather features and color-producing mechanisms, including distinct melanosome morphologies and beta-keratin nanofibers that produce blue structural color. Several morphologies have been proposed to have hydrodynamic or insulatory functions. An understanding of the distribution of these morphologies over the bod...

Zygodactylidae are an extinct lineage of perching birds characterized by distinct morphologies of the foot and wing elements. Although the clade has a complex taxonomic history, current hypotheses place Zygodactylidae as the sister taxon to Passeriformes (i.e., songbirds). Given the rather sparse fossil record of early passeriforms, the description...

Morphological Character Scorings.

The tongue, with fleshy, muscular, and bony components, is an innovation of the earliest land-dwelling vertebrates with key functions in both feeding and respiration. Here, we bring together evidence from preserved hyoid elements from dinosaurs and outgroup archosaurs, including pterosaurs, with enhanced contrast x-ray computed tomography data from...

Major morphological evolution of bony hyoid traits in bird-line archosaurs with new data obtained from Avialae, Palaeognathae, and Neognathae. The hyoid elements are labeled as abbreviation, pg-paraglossal, bh-basihyal, cb-ceratobranchial, ep-epibranchial. Bony hyoid characters include: (1) origin of the narrow, arrow-shaped basihyal (not always mi...

Material of extinct taxa examined. Published specimens are indicated with an associated reference. (DOCX)

Homologous muscles proposed across reptilians and examined in this project. Muscles experiencing major shifts, or considered as neomorphs of birds, are indicated in bold face; dash lines indicate it is not present. All proposed homologies were reviewed from previous studies and new proposed homologies are indicated with an asterisk (*). (DOCX)

Character list used to reconstruct the major transitions of hyolingual evolution with Archosaria. (DOCX)

Data matrix (character list and coding). (DOCX)

Parsimony-based ancestral state reconstruction of hyoid features summarized in Fig 3 and the supplemental tables. Characters numbers correspond to states described in Supplemental Data Files 1, 2: the character descriptions and matrix. (JPG)

Skulls of basal archosaurs and non-avian dinosaurs with associated hyoids evaluated. a, Euparkeria capensis (SAM 5867); b, Jeholosaurus shangyuanensis (IVPP V12530); c, Gongbusaurus wucaiwanensis. (IVPP 14559); d, Massospondylus carinatus (cast, BP/1/4934); e, Syntarsus kayentakatae (MNA V2623); f, Similicaudipteryx yixianensis (STM22-6); g, Sinosa...

Avialan skulls with associated hyoid elements preserved. a, Confuciusornis sanctus (IVPP 13175); b, Confuciusornis sp. (STM 13–6); c, Rapaxavis pani (DNHM D2522); d, Sulcavis geeorum (BMNH ph 000805); e, Longusunguis kurochkini (IVPP V17864); f, Yanornis martini (IVPP V12558); g and h, photograph and line drawing of Hongshanornis sp. (STM 7–56). Th...

This mixed methods study maps and characterizes assemblages of support in the context of a novel course-based undergraduate research experience (CURE). The CURE blends graduates and undergraduates and features a curricular emphasis on research mentorship, writing and antidisciplinarity. We find that explicit attendance to mentorship may contribute...

Modifications to the upper vocal tract involving hyper-elongated tracheae have evolved many times within crown birds, and their evolution has been linked to a ‘size exaggeration’ hypothesis in acoustic signaling and communication, whereby smaller-sized birds can produce louder sounds. A fossil skeleton of a new extinct species of wildfowl (Gallifor...