John J. Flynn, Ph.D. - US grants

Collaborative Research: Andean Fossil Mammals-Phylogenetic and Geologic Implications.

A grant has been awarded to Dr. John J. Flynn of the Field Museum of Natural History and Dr. Darin A. Croft of the University of Chicago to collect and study fossil mammals from the Andes Mountains of central Chile, and to carry out geological investigations of the region. This study will clarify poorly known aspects of South American mammal evolution, and help unravel the complex geologic history of the Andean mountain chain. Field collecting and reconnaissance will be undertaken to discover new localities and assemblages of fossil mammals of different ages. Once prepared, these fossils will be described in the scientific literature and analyzed in order to understand how factors such as climate change affect species diversity. The unusual occurrence of these fossils in volcanic rocks will enable the application of various "absolute" geologic dating methods, providing precise ages for these fossils and more accurate scientific analyses.

South America was an isolated continent for most of the last 80 million years. The highly peculiar mammals arising in response to this isolation have captured the interest of biologists and paleontologists for more than two centuries. Some 15 years ago Dr. Flynn and his colleagues unexpectedly discovered the first fossil mammals from this region of South America. By studying the fossil mammals, the team showed that the fossil-containing rocks were nearly 100 million years younger than previously assumed. This discovery has revolutionized understanding of the region's tectonic history. Moreover, this and other discoveries have helped to fill in important "missing chapters" in South American Mammal history, leading, for example, to the recent recognition of a new South American Land Mammal Age and evidence of the world's oldest grasslands. This project builds on earlier work, focusing on targeted geographic areas and particular groups of mammals (rodents, extinct plant eating forms, marsupials, etc.).

PaleoPortal has created a central, interactive entry point to vetted paleontology resources on the Internet for multiple audiences. Responsibilities for development delegated as appropriate to five institutions: UCMP, the American Museum, Bloomsburg University, the Paleontological Research Institute, and the Yale Peabody Museum. The focus will be on: Expanding and updating content by (1) bringing additional collections into the collections database, (2) adding research profiles and RSS feeds, (3) building how to modules on fossil preparation and collection management for smaller museums, and (4) including additional sites in our Famous Flora and Fauna feature. Deepening functionality with the addition of (1) interactive visualizations of large-scale patterns of floral/faunal distributions through time, and (2) a URL checker. Extending audience use by (1) developing an expanded teacher's guide for the site that targets K-12 teachers, (2) building a tool targeting informal science educators that would allow them to easily generate customized kiosk software and content based on PaleoPortal materials, and (3) making the database and the collections portal search software freely available in an effort to reach out to other institutions. The PaleoPortal provides direct access to paleontological information and resources, collections data, and images in an interactive, easy to navigate format. In addition, open access to the services and tools developed by this project will be added and include: (a) packaging and documentation of PaleoPortal distributed collections portal search software for distribution, and (b) a service allowing other projects and partner sites to access, manipulate, and display PaleoPortal content with their own design and functionality. The institutions represented in this collaborative effort have extensive experience and expertise in both research and education and in the integration of the two through the use of web-based technologies. PaleoPortal facilitates the sharing of paleontological research and resources and provides exposure to the geosciences in a format that integrates both biotic and abiotic components of Earth's history. During its development, this function has evolved to meet the needs of a broad and diverse paleontological community, which includes researchers, faculty, graduate students, undergraduate students, pre-college teachers, young people, and other non-scientist members of the public. It does so by providing access to data and information at different levels and through multiple interconnected pathways. The planned enhancements will further extend the use of the PaleoPortal by multiple audiences.

Wayne, Flynn, and collaborators propose to provide the most detailed examination to date of relationships within the vertebrate order that includes mammalian carnivores such as cats, dogs, weasels, raccoons and seals. This effort represents the first attempt to document the relationship of all species in a moderately diverse mammal order. The researchers will produce a comprehensive relationship tree of several hundred species using DNA sequences of 33 genes that will form the basis for testing ideas about how and when various traits influencing carnivore behavior, ecology and function have evolved and been shaped by natural selection. Additionally, the proposal supports collection of morphologic data on living and extinct carnivores that will be combined with the DNA sequence data to test key ideas about evolutionary history. Along with the public-financed genome sequencing of the dog and partial sequencing of the cat, this study will add a comparative database of carnivore sequence data and provide an evolutionary perspective that will add a new dimension to interpreting the significance of sequence differences in humans and other mammals.

This project includes support for extensive training and inter-institutional exchange of the next generation of systematists, including three post-doctoral scientists, several graduate students and dozens of undergraduates. Further, the consortium of investigators and institutions collaborating in this project (5 universities, two museums, one governmental laboratory, plus international collaborators) are well situated to more deeply immerse K-12 students and teachers, and the general public, in the approaches and results of systematic biology research. Finally, the scientists will develop a multi-layer web site with empirical and analytical information and a traveling museum exhibit using carnivores to illustrate fundamental concepts in systematics.

AToL: Collaborative Research: Resolving Mammalian Phylogeny with Genomic and Morphological Approaches

Novacek, Michael J., American Museum of Natural History, EF 0629811
Murphy, William J., Texas A & M Research Foundation, EF 0629849
O'Leary, Maureen A., SUNY Stony Brook, EF 0629836
Luo, Zhe-Xi, Carnegie Institute, EF 0629959
Springer, Mark, Univ. California, Riverside, EF 0629860

Abstract
Only a few of the myriad biological groups now thriving on this planet have fossil records that chronicle their evolutionary past. One of these few is Mammalia, known from about 5,000 extant species distributed among 1135 living genera, including our own human lineage, and more than 4,000 extinct genera, a four-to-one ratio of fossil genera to living genera that can hardly be matched elsewhere in the biota. Mammals display a spectacular range in size, form, and adaptations. They are closely linked to human health, welfare, and experience. No tree of all life could be regarded as complete without a comprehensive phylogeny of Mammalia. This conviction has inspired a surge of work in paleontology, comparative anatomy, and molecular biology. Despite these significant gains, many aspects of mammalian phylogeny are unresolved or highly controversial, even at some of the major branching points on the mammalian tree.
PIs propose to examine species exemplars for 135 extant families, the majority of some 350 extinct families, and to extend this sample to a generic-level data set of 500 extant and nearly 500 extinct genera for combined analysis of genes and morphology. Their molecular team will continue to sample taxa toward a goal of covering 95% of all living genera outside the murids (rats, mice, and kin) and sciurids (squirrels). For character evidence, PIs plan to sample 30Kb in gene sequences from 34 genes for at least one exemplar of all living families. For the larger generic-level phases of the project, they will sample at least 6Kb of sequence. Morphologists will collect a projected 2,000 characters. Completion of a broad scale phylogeny for mammals will provide a model system in evolutionary and comparative biology with numerous applications in conservation and wildlife management, human health, biomedicine, and other areas. In addition, PIs intend to compile an integrated and image rich database for mammalian characters and convert it into a powerful toolkit for conservation management, education, and outreach through training programs and web resources.

A grant has been awarded to the American Museum of Natural History under the direction of Dr. Jin Meng to upgrade the storage facilities and the database for the fossil mammal collection. The collection is one of the largest for fossil mammals and is heavily used by scientists. Many of the specimens were new to science when they were discovered. The project will allow the Museum to acquire new cabinets and heavy-duty shelving for the collection of Perrisodactyls (e. g., horses and rhinos) and other fossil mammals. The current cabinets and storage facilities consist of older equipment that does not adequately protect the specimens from temperature and humidity changes.

The data associated with the specimens will be entered into the AMNH database and become available to researchers and educators worldwide. Several teacher fellows will be recruited from New York public high schools to collaborate with research staff to prepare educational K-12 modules. The project will also support several undergraduate student interns, who will work with curators to re-house specimens and enter information into the database.

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5). The American Museum of Natural History REU Site will provide a research program for undergraduates during the summers of 2009-2013. Eight students will be selected each year to participate in an intensive 10-week research program in biological systematics and evolutionary questions. Systematics and evolution are central concepts in biological disciplines. Knowledge of the manner in which species are related to each other and the mechanisms by which they become distributed across the globe provide a framework (in evolutionary trees for example) for organizing and communicating ideas regarding biodiversity or comparative genomics. This program provides students with a coherent, hands-on introduction to research in systematics and comparative evolutionary biology, and serves a critical role in attracting, inspiring and educating undergraduate students in the fundamental importance of these biological disciplines. Students enrolled in the American Museum of Natural History (AMNH) REU program have at their disposal world-class collections of fishes, dinosaurs, reptiles, amphibians, mammals and invertebrates, as well as cutting edge research facilities in the Molecular Genomics laboratories and the museum's research library. Students are mentored by museum curators and projects variously include use of genetic, histological, anatomical or paleontological data and range from primary taxonomic to integrative phylogenetic studies. Students will also be provided opportunities to immerse themselves in the richness of New York City's cultural institutions and summer venues. Eight students will be selected for a 10 week summer program at the American Museum of Natural History REU program in Systematics and Evolutionary Biology. Additional information can be found at http://rggs.amnh.org/pages/academics_and_research/fellowship_opportunities, or by containing the Program Director, Dr. Mark E. Siddall at 212 769 5638; Siddall@amnh.org.

Carnivores (bears, wolves, lions, seals and relatives) are key predators in modern ecosystems. Understanding their evolutionary relationships is fundamental to interpreting other knowledge (biological, medical, ecological) derived from carnivore research. By developing the most comprehensive framework for interrelationships of living and fossil carnivores (>100 species) using 400 anatomical and over 30,000 genetic characteristics, and integrating novel 3-D imaging, mathematical, and engineering-derived computer modeling tools, this research will reconstruct carnivore evolutionary relationships and decipher their adaptations for critical ecosystem roles over time.

Analyzing how feeding function of skulls changed over time, and how species developed locomotion and cognitive specializations during major habitat transitions (land-to-water, tree-to-ground), this research will rigorously test previous hypotheses that these changes represent responses to significant environmental changes over the past 65 million years. This project will use cutting-edge research on these charismatic mammals to enrich museum exhibitions and create online multimedia (serving 5 million visitors [500,000 schoolchildren] and 12 million online learners annually). This project will also implement high school and college education and research training programs, including workshops, development of new graduate courses, training for three postdoctoral scientists, and instructional programs for dozens of high school students and undergraduate students.

The National Science Foundation (NSF) Graduate Research Fellowship Program (GRFP) is a highly competitive, federal fellowship program. GRFP helps ensure the vitality and diversity of the scientific and engineering workforce in the United States by recognizing and supporting outstanding graduate students who are pursuing research-based master's and doctoral degrees in fields within NSF's mission. GRFP provides three years of support for the graduate education of individuals who have demonstrated their potential for significant achievements in science and engineering research. The award to this GRFP institution supports NSF Graduate Fellows pursuing graduate education at the institution.

The horns, antlers, and other bony structures (cranial appendages) growing from the skulls of even-toed, hoofed mammals like deer, antelopes, and giraffes (the group of hoofed mammals called Pecora) are an evolutionary mystery. Cranial appendages are often used to determine how species are related to the different families of Pecora, because each family is distinguished by the presence of a specific type of appendage. When fossil species lack cranial appendages, it is difficult to assign them reliably to any particular family. These appendage-less fossil species could provide necessary information about the ancestral origins of cranial appendages in each family, but the inability to confidently place them in the context of pecoran evolutionary relationships precludes their use in studies of cranial appendage evolution. Prior studies have shown that variation in the way structures change as an animal grows can result in the origination of totally new structures. A better understanding of cranial appendage development will therefore provide much-needed context for hoofed mammal cranial appendage evolution and help resolve the question of their origins. It will also contribute to research on how skin and connective tissues contribute to bone growth and have implications for understanding pathways and patterns of skull development, with methods and results that are broadly applicable to skull and bone growth research in all vertebrates, including humans. This research will form the basis of a curriculum on genomic analyses and genetics for middle school students in the American Museum of Natural History's Lang Science Program, piloted with diverse groups of New York schoolchildren and available to teachers and schools across the country.

This project will test two competing hypotheses: 1) the broad range of distinctive cranial appendages observed in fossil and extant pecoran artiodactyls do not share a common evolutionary origin, 2) portions of cranial appendages, such as the permanent bone pedicles of antlers and the bone cores of horns, may be homologous across some or all of the appendage types in this clade. Samples will be collected from the cranial appendage forming tissues of at least three individuals each from the four extant cranial-appendage-bearing families of Pecora (Bovidae, Cervidae, Giraffidae, and Antilocapridae) and an appendage-less outgroup taxon from Tragulidae, at 3 developmental stages: birth, one month, and two months old. RNA will be isolated from these tissues and sequenced using next-generation sequencing technologies. Gene expression profiles sequenced from tissues at a second location on the body of each individual will provide a somatic control to estimate gene expression specifically related to cranial appendage growth (the cranial appendage transcriptome). These transcriptomes will be optimized onto a phylogeny to test for homology of the genes responsible for cranial appendage growth across and within age groups.