Neil Shubin - US grants

The vertebrate limb arose approximately five hundred million years ago from the fins of advanced fish. Despite this enormous amount of time, the evolution of the limbs of vertebrate animals has been extremely regular--certain patterns frequently recur, other patterns are never encountered. Many workers have suggested that the mechanisms of development may limit the amount of evolutionary change possible in different species. This proposal focuses on the relationships between development and evolutionary diversity in the most primitive living group of limbed animals--salamanders. Comparative and experimental studies will enlighten the extent to which the evolutionary history of the salamander limb has been limited by developmental mechanisms. In particular, the relationship between body size, the timing of key developmental events, and evolutionary diversity will be analyzed. Comparative studies of developing and adult limbs will reveal the regularities seen in the evolution of the pattern of bony elements of the hands and feet of salamanders. Experimental studies will reveal the manner in which developmental mechanisms are responsible for these regularities. Many of the regularities seen on limb evolution may be related to the size of the developing embryo and larva. Changes in body size are an important trend in salamander evolution. Body size will be experimentally manipulated through both chemical and surgical treatments to explore the role of body size and the pattern of bones in salamander limbs. These studies will elucidate the role of an important constraint, body size, on salamander limb evolution.

The next generation of ecologists and organismal biologists will be called upon to link their basic-science focus with other skills necessary to solve major environmental and social problems. These skills--in public policy, environmental law, management, and scientific communication-- are severely lacking in our current graduate training. We propose a cross-disciplinary training program that will provide students with a rigorous introduction to the methods of environmental science and exposure to the tools necessary to apply the fruits of their research to attack major social and environmental issues. Before initiating their diqsertation research, students will complete a two year curriculum consisting of new lecture, seminar and field courses. Field and management courses will draw on personnel and resources of the Conservation Research Center of the Smithsonian Institution. Seminar courses on scientific communication, current environmental issues, and environmental law and policy will draw on faculty from other graduate schools at the University of Pennsylvania and other professionals actively involved with these issues. These courses, together with basic science research will provide trainees with exposure to the methods needed to affect scientific and social solutions to environmental problems.

Abstract

Collaborative Research: Biotic diversity and vertebrate evolution in
Late Devonian non-marine ecosystems of North America

Neil Shubin-EAR-0208377
Edward Daeschler-EAR-0207721

The Late Devonian (375-360 MYA) witnessed a burst of diversification of vertebrate life, including the origin of limbed vertebrates, and the elaboration of plants and invertebrates in terrestrial ecosystems. Accordingly, the description and analysis of Late Devonian vertebrates and ecosystems offers the ability to generate important data on the emergence of new taxa, new anatomical structures, new faunas, and new habitats during this critical moment of evolution. Our prior work (1993 to present) in the Late Devonian (Famennian Stage) Catskill Formation in Pennsylvania has produced well-preserved, highly diverse vertebrate assemblages from the same stratigraphic horizons as macrofossil plants, palynomorphs, arthropods, and bivalves. Exploratory work (1999-2000) in the Late Devonian (Frasnian Stage) Okse Bay Group in the Canadian Arctic has also revealed significantly fossiliferous units in this virtually unexplored region.
This project will document and interpret the diversity of the non-marine parts of these Late Devonian systems in eastern North America. The temporal range will cover the Frasnian and Famennian Stages of the Late Devonian, a critical window in evolution. Fieldwork in the Famennian-age Catskill Formation has taken a significant step; the Pennsylvania Department of Transportation has given permission to remove a large wedge of overburden from the Red Hill locality, source of two early tetrapod taxa and a very diverse fauna and flora. Fieldwork in the Frasnian-age Okse Bay Group in the Canadian Arctic will focus on areas now recognized for their fossil productivity. The first major goal is the recovery, preparation and description of Late Devonian fossil material. Ensuing investigation of the phylogenetic affinities and stratigraphic position of fossil assemblages will allow both intraformational and global comparisons of biotic diversity. Assessment of intraformational stratigraphic relationships will enable an understanding of the biotic diversity in different portions of the fluvial systems. These analyses will inform: 1) higher level phylogenetic hypotheses of gnathostome vertebrates, 2) biostratigraphic and biogeographic analysis of the distribution of the Late Devonian tetrapods and fish, and 3) paleobiological investigation of the elaboration of terrestrial and freshwater ecosystems.

Salamanders are one of the major groups of living amphibians. Unfortunately, very little is known about their early evolution because early salamander fossils have not been recovered. Indeed until now, only two species from the relevant time was known. We are now presented with an unusual opportunity to investigate major questions of salamander evolution and diversity. Over the past three years, we have recovered more than 800 superbly preserved salamander specimens from the earliest parts of salamander history. These sites, from northern China, contain a highly diverse and well preserved fauna of salamanders. Access to these sites has been granted and they can readily be quarried in an effort to recover even more specimens. The importance of these sites and this material lies in its age (these are among the earliest known salamanders), its abundance (hundreds of articulated skeletons can be collected from each site), its taxonomic diversity (several different families are present), its life-history diversity (many different parts of the life cycle are are all preserved), and its exceptional preservation (soft-tissue impressions are often present). Major goals of this project include: 1. to collect new fossils from and assess the relative age of the exceptional fossil-bearing units northern China, 2. to describe new fossil salamanders and revise known taxa, 3. to access the evolutionary and geographic history of fossil and Recent salamanders, and 4. to use the exquisite preservation of the new salamander material to address how morphological variation has evolved.

Collaborative Research:
Late Devonian Tetrapodomorph Fishes and the Origin of Tetrapods

Edward B. Daeschler, Acad. Nat. Sci. Philadelphia, EAR-0544093
Neil H. Shubin, Univ. Chicago, EAR-0544656

Abstract
Towards the end of the Devonian Period, between 385 and 360 million years ago, there were dramatic evolutionary changes to plants and animals living in freshwater habitats. This time interval witnessed the origin of limbed vertebrates (tetrapods), the diversification of fishes closely related to early tetrapods, and the elaboration of plant communities on land. PIs ongoing work in the Canadian Arctic (Ellesmere Island, Nunavut Territory) and Pennsylvania provide new evidence for understanding these monumentally important events. For example, a newly discovered site on Ellesmere Island includes numerous articulated fish that are one of the closest known relatives of limbed animals. In addition, 12 years of field study in the Catskill Formation in Pennsylvania has yielded abundant Late Devonian fossils notable for their taxonomic diversity and the quality of preservation of the vertebrates, plants, and arthropods. The biological diversity, environmental settings, and age of these North American systems serve as the basis for PIs proposed studies on the evolution of the earliest tetrapods and their lobe-finned fish precursors, and the development of the Late Devonian habitats that were a crucible for the evolutionary innovations in the Late Devonian.
With substantial collections already in hand and great potential for additional field discoveries, the goals for this project include: 1) additional fieldwork to discover new material of key taxa at the cusp of the fish-tetrapod transition, 2) exploration of promising areas that may produce the earliest tetrapod fossils, 3) fossil preparation including molding and casting of important specimens for worldwide distribution, 4) description and evolutionary analysis of early limbed animals and their fish relatives, 5) functional analyses of skeletal structures in elpistostegid fishes that will provide an understanding of the biological significance of changes at the fish-tetrapod transition, and 6) assessing the geographic and environmental conditions associated with the origin of tetrapods. This work will have a broad impact through outreach in educational and informal science learning venues, and via internet, print and broadcast media.

Non-mammalian synapsids represent the dominant group of terrestrial backboned animals (tetrapods) during the Permian and Early Triassic Periods, 300-245 million years ago. Non-mammalian synapsids have a very rich, temporally well-resolved fossil record by tetrapod standards. This project will use geometric morphometric analysis to study evolutionary patterns in the non-mammalian synapsids. Geometric morphometrics compare the positions of shared features, or landmarks, on specimens (e.g. suture boundaries between bones of the skull) to summarize morphological (shape) variation among individuals. Using a global dataset of non-mammalian synapsid specimens, the researchers will address questions of evolutionary rates and morphological trends associated with the radiation of the group.

The period of non-mammalian synapsid dominance was punctuated by the Permo-Triassic extinction, the greatest mass extinction in earth history, in which 95% of all species are estimated to have been lost. The researchers will examine synapsid faunas before and after the extinction to determine whether certain morphologies were preferentially lost, while others survived. These data can be used to identify potentially extinction-prone morphologies in other taxa. Early synapsids are also important because they represent the ancestors of mammals. Studying shape change over the course of synapsid history will provide important information on the evolutionary dynamics underlying mammal origins.

This Integrative Graduate Education and Research Traineeship (IGERT) project builds links broadly across Chicago's scientific community to develop an integrative training program for U.S. doctoral students in motor control and movement. To develop an integrative understanding of movement, it is necessary to address both the biology and the engineering of the systems involved and how they work together. Students from graduate programs at the University of Chicago and Northwestern University will obtain the biological and engineering backgrounds required to develop the integrative approach needed to take the field in new directions. Educational tools include a boot camp, a three-quarter common core curriculum, a discussion series, required laboratory rotations, and workshops and seminars at the Field Museum. The program will involve outreach to local Chicago-area schools, with training for students and faculty in the development and conduct of effective outreach. Mentoring of undergraduate students by IGERT graduate trainees will be done in close collaboration with local universities that primarily serve underrepresented minorities in the Chicago area. A trans-institutional website will highlight opportunities and results related to this program's IGERT goals and provide resources for teachers and students. IGERT is an NSF-wide program intended to meet the challenges of educating U.S. Ph.D. scientists and engineers with the interdisciplinary background, deep knowledge in a chosen discipline, and the technical, professional, and personal skills needed for the career demands of the future. The program is intended to catalyze a cultural change in graduate education by establishing innovative new models for graduate education and training in a fertile environment for collaborative research that transcends traditional disciplinary boundaries.

ABSTRACT

Project Title:
Collaborative Research: The Late Devonian Tetrapodomorph Tiktaalik roseae

PI: Edward B. Daeschler, Associate Curator of Vertebrate Zoology, Academy of Natural Sciences of Philadelphia, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103

PI: Neil H. Shubin, Robert R. Bensley Distinguished Professor, Department of Organismal Biology and Anatomy, 1027 East 57th Street, University of Chicago, Chicago, IL 60637


Tiktaalik roseae is a fossil fish from the Late Devonian Period (385-362 million-years-ago) that was discovered in 2004 on Ellesmere Island, Nunavut, Canada. This species is the finned animal that is most closely related to tetrapods (limbed vertebrates). As an intermediate form, T. roseae helps us to recognize the sequence of morphological changes across the fish-to-tetrapod transition and can teach us about the forces that were driving these important evolutionary changes. T. roseae was first described in 2006 and has provoked a great deal of interest among evolutionary biologists. To date, however, the only published reports on this species have been short papers in Nature. With continued study and documentation of the abundant and well-preserved material of T. roseae, we will fill the need for a detailed investigation of this important fossil at the cusp of the fish-to-tetrapod transition.

A primary contribution of this research will be a detailed publication on a wide range of topics about T. roseae. The core of this publication will be a thorough morphological description including extensive figures of many of the 50+ specimens. We will also investigate the internal structure of bones in the fins for the first time, further document the ancient environment where T. roseae lived, and produce new studies of the evolutionary tree across the fish-to-tetrapod transition. The other major contribution of this project will take advantage of the quality of T. roseae fossils to assess the functional anatomy of the fins and skull. Evaluation of the hypothesis that the fins were capable of body support will involve detailed analysis of joint structure and the relative motions possible between bones, fin rays, and scales of the front fin and shoulder. The second set of analyses will explore the relationship between skull architecture and different stresses and strains in the skull related to movement, breathing and feeding. At the conclusion of this study, all T. roseae specimens are to be returned to the Government of Nunavut, and so the timely publication of these data via print and websites is of particular importance.

The discovery and description of T. roseae has received considerable attention from educational organizations and media internationally; as a textbook transitional fossil it has become a powerful tool in the communication of evolution to the general public. The PIs have a record of public lectures and development of web-based educational resources. We will make use of this research project to further communicate the results of the work, as well as the scientific process, to a broad audience and thereby help people get a better grasp of how evolution works.

One of the most important discoveries from the rise of genomics is that animals, despite their staggering differences in shape and size, utilize a common set of genes. How does the incredible diversity of animal forms arise if animals all contain the same core genetic code? There is a growing body of evidence that changes in the time, location, and amount of gene expression is responsible for the evolution of structures. This project is aimed at determining how regulation of gene expression may have influenced the defining feature of limbs, which is the presence of the hand. Fish do not possess hands, but they possess all of the genes necessary to build one. Thus, the goal of this project is to identify the gene regulatory elements in zebrafish that drive gene expression in fins, and compare them to their counterparts in mouse. This knowledge will help us understand what aspects of fish fin development are ancient, and what aspects have evolved to be specific for building a hand.
As the hand is a ?new? feature of limbs that is not present in fins, this project will shed light on how novel features may originate during the evolutionary process. Investigating how genetic switches have influenced the fin to limb transition may provide a general model for how complex and unique features of animals have arisen. In addition, this project is collaboration with a lab in Seville, Spain. This type of collaboration between institutions is beneficial to the greater scientific community by promoting exchange of ideas and techniques in genetics, especially as genomics gets further integrated into evolutionary biology.

This project investigates how different types of shell shapes are encoded in snail embryos. Animal form is marvelously varied. This study addresses the question: what are the developmental mechanisms that produce such diversity? Snails have long been a model system for studying biological form. They have diverse shapes but are easy to measure due to their mathematically regular coiling and have been a major study group since Charles Darwin's famous voyage around the world. Darwin's approach to the study of animal form included investigations of patterns of change in the snail-rich fossil record (paleontology). Modern developmental biology uses molecular tools to understand how genes determine snail form. This project will determine the genetic and environmental interactions that may underlie a conspicuous pattern in paleontology, the repeated evolution of non-coiled shells from coiled ancestors. The researchers will combine computer imaging technology, genetic manipulation and paleontology to provide unparalleled precision in determining how both genes and their environment shape an organism through time. Broader societal impacts will result from this work due in part to the design and implementation of a workshop on visual literacy. This workshop will improve the ability of the researchers and the scientific community to understand and convey complex visual information to the public. The workshop materials will be posted online for increased access.

This project investigates the developmental basis of snail shell morphology and the transition from coiled to non-coiled shells in the emerging model system, the Common Slipper Shell (Crepidula fornicata). Specifically, it evaluates the hypothesis that simple modification in signaling patterns in a protein named decapentaplegic could be the basis for a pattern of non-coiled shell evolution. Other shell developmental genes also will be evaluated for the ability to affect shell patterning more generally. Genetic pathways influenced by changes in shell coiling will be manipulated in developing animals to isolate their individual effects on morphology. Detailed morphological data is required for this work. Scanning electron microscopy will be used to visualize the process of torsion and to assess morphological changes across the entire embryo in response to genetic perturbations. Computed tomography (CT scanning) will enable the use of 3-dimensional shape analysis of embryo and shell form with enhanced precision. The use of these computer-assisted technologies combined with molecular techniques will allow new insight into how paleontological patterns are formed.

This research will provide new insights into the relationships and history of sharks, fish and limbed animals. Understanding these relationships forms the backbone for both basic and applied science because fish often serve as models of human traits and diseases. Some of the main lines of evidence for these relationships come from fossils in rocks over 380 million years old that were originally deposited as ancient rivers and streams. Because rocks of this type and age are abundantly exposed along a number of the dry valleys and mountains of Antarctica, the investigation of these areas holds exceptional promise for discoveries that can have a broad impact. The fieldwork will involve geological mapping and assessment of the rocks with detailed reconnaissance for the fossils that they may hold. Fossil discoveries form the backbone for public communication of the methods and results of scientific research-- these studies will be used as vehicles for training of students at multiple levels as well as communication of science to the broader non-science citizen base.

The discovery, description, and analysis of Middle to Late Devonian (390-355 Million years ago) vertebrates and depositional environments provide important data on the emergence of novel anatomical structures, faunas, and habitats during a critical interval in the history of life and earth. Biological innovation during this time includes the early evolution of freshwater fish, the origins of major groups of vertebrates (e.g., sharks, lobe and ray-finned fish, tetrapods), and the expansion and elaboration of non-marine ecosystems. Accordingly, expanding our knowledge of vertebrate diversity during the Middle and Late Devonian will provide new evidence on the relationships of the major groups of vertebrates, the assembly of novelties that ultimately enabled tetrapods to invade land, the origin and early evolution of sharks and their relatives, and the assembly and expansion of non-marine ecosystems generally. The Aztec Siltstone of Antarctica Middle-Late Devonian; Givetian-Frasnian Stages) has exceptional potential to produce new paleontological evidence of these events and to illuminate the temporal, ecological, and geographic context in which they occurred. It is essentially fossiliferous throughout its known exposure range, something that is rare for Middle-Late Devonian non-marine rocks anywhere in the world. In addition, fine-grained meandering stream deposits are abundantly exposed in the Aztec Siltstone and are recognized as an important locus for the discovery of well-preserved Devonian fish, including stem tetrapods and their relatives. Given the exceedingly fossiliferous nature of the Aztec Siltstone, the large number of taxa known only from partial material, and the amount of promising exposure yet to be worked, a dedicated reconnaissance, collection, and research effort is designed to recover important new fossil material and embed it in a stratigraphic and sedimentological context. The first major objective of this study is the recovery, preparation, and description of Middle-Late Devonian fossil taxa. Ensuing investigation of the phylogenetic affinities, taphonomic occurrence, and stratigraphic position of fossil assemblages will allow both local and global comparisons of biotic diversity. These analyses will inform: 1) higher level phylogenetic hypotheses of jawed vertebrates, 2) biostratigraphic and biogeographic analysis of the distribution of the Middle-Late Devonian fish, and 3) paleobiological investigation of the elaboration of terrestrial and freshwater habitats. The broader impacts are derived from the utility of paleontology and Antarctic expeditionary science as educational tools with powerful narratives. Specific goals include affiliations with local urban secondary schools (using established relationships for broadening participation) and collegiate and graduate training. Wider dissemination of knowledge to the general public is a direct product of ongoing interactions with national and international media (print, television, internet).