Diversification and paleobiology of early sharks

Primitive shark-like fishes (chondrichthyans) include the origins of modern sharks, rays and chimaeroids (rat fishes), early forms of which are much less well known than those of their bony relatives.  Modern sharks tend to be treated as primitive relics of an earlier era, although this sits uncomfortably with the alternative clichéd view of sharks as ultimate marine predators. Both notions rest on shaky foundations. Modern sharks are not especially similar to their early relatives, whose sometimes bizarre anatomy in certain respects converges on that of early bony fishes. The aim of the chondrichthyan project is to resolve early chondrichthyan phylogeny by means of using a wide variety of data, and to provide the basis for a renewed examination of basal jawed vertebrates as a whole.

Origin of cyclostomes and gnathostomes

Despite the recent series of high-profile papers, the earliest stages of vertebrate evolution remain as puzzling as ever. Archetypical ideas of the vertebrate body plan are primarily informed by select living groups of jawed vertebrates for convenience, as a result of model fitting, or by historical inertia. However, a great grade of jawless vertebrates encompasses spectacular diversity of morphologically disparate lineages — hagfish, lampreys, conodonts, enigmatic soft-bodied forms like the Cambrian myllokunmingiids, and multiple distinct radiations of ‘ostracoderms’ — and no single narrative seems to explain quite well how they fit to scenarios of character evolution toward the origin of jaw.

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Our recent contribution — a reconciliation of conflicting morphological and molecular evidence to support cylostomes, the natural group of hagfish and lampreys — brought stability to the base of the Vertebrata, but raised new questions we are now pursuing. In our new phylogeny, anaspids (an ostracoderm lineage) sit on the cyclostome stem, implying that the last common ancestor of all living vertebrates had a mineralized skeleton, only to be lost secondarily in cyclostomes. Other characters need to be scrutinized under new light: the evolution of inner ear, origins of vertebrae and paired fins, pharyngeal anatomy, and head-trunk differentiation. The momentum is building up for us to revisit long-held scenarios and models of early vertebrate evolution. Do lampreys serve as an appropriate outgroup to gnathostomes?  Do stem gnathostomes provide compelling evidence of character transitions from jawless to jawed vertebrates?  Are insights generated from development and fossil record congruent with each other?  How deep into invertebrates can ‘vertebrate’ traits be traced?  By addressing these questions, we are ultimately investigating what makes vertebrates vertebrates.

End-Devonian extinction/recovery

Origin of the modern vertebrate biota

It was only recently that the end-Devonian extinction (c.359 million years ago) was recognized as a major extinction event for vertebrates. This extinction eliminated many of the dominant groups at the time, and was followed by major diversifications among the survivors which include the origins of many modern vertebrate groups- rayfin fishes, sharks, and tetrapods. Research focuses include the timing of these radiations relative to the extinction and investigating the diversity and ecological impact of the extinction.

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Though paleontologists have understood mass extinctions for a long time now, much of what we know and understand about the end-Devonian extinction is very recent. For decades, the “Late Devonian mass extinction” was recognized as one of the five largest mass extinctions in Earth history, but considered to be an instance of low species origination instead of high species die-off. Crucial work by Lauren Sallan [Sallan and Coates 2010] was key in clarifying the story. The “Late Devonian” extinction was actually two separate events: an invertebrate extinction coincident with the Kellwasser event at the end of the Frasnian stage (c.372 million years ago) and a vertebrate extinction coincident with the Hagenberg event at the end of the Devonian (358 million years ago.) The end-Frasnian extinction was not a mass extinction for vertebrates, but it had catastrophic effects on invertebrates. During the Devonian, reef systems were more extensive than at any other point in Earth history; these were wiped out in the end-Frasnian extinction, and reef-building organisms did not fully recover for over 40 million years. The end-Devonian extinction eliminated the last of the ‘ostracoderm’ jawless fishes, placoderms (eg. Dunkleosteus), and many sarcopterygian (“lobe-finned”) fishes. Tetrapods, actinopterygian (“ray-finned”) and chondrichthyan fishes were the principal survivors, and their post-extinction radiations include the origins of numerous modern lineages. In this way, our modern vertebrate biota has its roots in the end-Devonian extinction.

The Hagenberg event is named after the global layer of black shale laid down at the end of the Devonian. At the end of the Devonian, the supercontinent Gondwana moved over the South Pole. This provided an easier place for ice to form, eventually reducing sea level [and blah blah something something anoxia] leading to the deposition of the Hagenberg shale.

Much fruitful work has been done on the end-Devonian extinction recently, particularly in clarifying the timing and mechanisms of the Hagenberg event. However, the full impact of this extinction has yet to be understood. It is not yet clear whether the extinction had the same effect in different environments, and on different groups of organisms. Also, while there has been some ecological work on the extinction aftermath, many areas and organisms have not been looked at yet, and the reef collapse at the end of the Frasnian has yet to be factored in.

Our research on the end-Devonian extinction focuses on understanding the post-Devonian world. Our morphological and phylogenetic work on chondrichthyans, actinopterygians, and tetrapods seeks to understand how the evolution of these groups was or was not impacted by the extinction. We are also becoming more interested in ecology, both in the origin of new morphologies and niches and changes at the ecosystem level. Through this week we aim to add to the ever-growing body of work on this crucial and under-studied interval in Earth history.

Resolving the bush at the base of the actinopterygian tree

The ray-finned fishes are the largest and most diverse group of living vertebrates, but little has been agreed about the timing and pattern of their early evolution. Collaborative research with Prince and Ho labs, and colleagues elsewhere, has resulted in a revised time-scale of their evolutionary history and raised major questions about the completeness of their fossil record. This work exemplifies OBA’s aim to promote integrative research, and uses a total-evidence approach combining fossils with molecular sequence data drawn from mitochondrial and nuclear genes. Fossil ray-finned fishes are probably the largest and least explored resource for the exploration of vertebrate historical biodiversity, and the potential for further research is considerable.

Phylogenetics and paleobiology of early tetrapods

Diversity, morphology, and evolution

Living tetrapods range from snakes to salamanders, humans to horny toads, and everything in-between. The origin of tetrapods in the Devonian period (c.375 . million years ago) is one of the classic questions of vertebrate evolutionary biology, encompassing phylogeny, anatomy, development, and ecology. Over the last decade, research has expanded beyond the origin of tetrapods to investigate when and how they made the water-land transition. Recent and ongoing work in the lab has focused on the phylogeny and comparative morphology of early tetrapods, particularly with regard to understanding the origin and divergence of the amphibian and amniote lineages.

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Tetrapods (four-limbed vertebrates with digits) originated in the Late Devonian period c.375 million years ago, and today encompass tens of thousands of species. Fossils of Devonian tetrapods and sarcopterygian (“lobe-finned”) fishes closely related to them have been known for over a century. However, the fish-tetrapod transition, as well as that between Devonian tetrapods and later Carboniferous and Permian forms was unclear for much of the 20th century. The re-analysis of Devonian tetrapods such as Acanthostega and the discovery of new ‘transitional forms’ like Tiktaalik has greatly helped our understanding of the origin of tetrapods. New discoveries have also helped populate the earlier part of tetrapod history in the Late Devonian and Early Carboniferous. Interdisciplinary work by lab members with international collaborators has also helped fill in ‘Romer’s Gap,’ a hiatus in the fossil record immediately after the end-Devonian extinction.

However, questions still remain. The age of the tetrapod crown group (amphibian/amniote split) have been broadly agreed upon for the last 15 years. But recent work, making use of new datasets and technologies, has produced very divergent phylogenetic hypotheses and crown group age estimates. At the same time, morphological studies, many of which have made extensive use of CT scanning, have both described new taxa and extracted new data from old fossils. It is clear that early tetrapods were more complex than previously considered.

Current lab research on tetrapods falls into several key areas. Our morphological work is focused on not only understanding individual tetrapod taxa, but also on establishing them within a broader comparative context, in order to better discern patterns of change (or lack thereof.) CT scanning and 3D surface scanning have allowed us to acquire information that would otherwise be impractical or inaccessible. Our phylogenetic work makes use of the resulting new information to build a new dataset and take a whole-evidence approach to tetrapod phylogeny, incorporating a rich sample of both characters and taxa. Finally, we are investigating tetrapod ecology from their origin in the Late Devonian through the Carboniferous. Coupled with the morphological and phylogenetic work, this will allow us to test various hypotheses about the influence of ecology on the origin of tetrapods, water-land transition, and amphibian/amniote split, as well as the establishment of terrestrial communities more broadly.

Evolution and development 

The lab has maintained a longstanding interest in the combination of evolutionary and comparative data with information gleaned from experimental molecular work to better understand the origin of key vertebrate features. Previous projects in this fascinating direction, exemplifying the Darwinian cluster’s integrative approach, have included the origin of the vertebrate vertebral column (with alumna Dr Kate Criswell) and the evolutionary origin and diversification of intriguing structures like the adipose fin (with Dr Tom Stewart, in collaboration with the Ho lab). Current projects include ongoing collaborations with zebrafish labs on campus to study the diversity and development of pelvic fins in teleosts as well as the anterior lateral line and its relationship with craniofacial development, particularly of th dermal skeleton. Recently, we have also been working with collaborators at Argonne national laboratories to utilize novel staining and high throughput imaging techniques to visualize ontogeny at very high resolutions and to enable 3D modeling of scan data as a complement to conventional histological approaches.