Brian Tilston Smith - US grants

There are over 10,000 species of birds and they are found in nearly every terrestrial environment. This remarkable diversity has served as a critical component of enhancing public engagement with science and nature, as evidenced by the multi-billion dollar output generated by bird-watching activities in the US economy. Birds exhibit complex behaviors, elaborate physical characteristics, and impressive adaptations, which has made them a major focus of modern scientific research. In current research, birds are a model system for comparative studies on a range of fundamental topics in biology. However, the missing piece of this otherwise powerful comparative biology toolkit is an accurate and complete description of the evolutionary relationships (phylogeny) among all bird species, i.e., an avian tree of life. This project will collect DNA data to fill this gap by producing a complete tree of life for all bird species in order to test hypotheses regarding the origins, diversification, and dispersal of birds around the planet. A complete tree will be transformative to fields like ornithology and evolutionary biology. This project will help prepare the next-generation of biodiversity scientists by training undergraduate, graduate, and post-doctoral scientists, and also will include numerous public outreach components including exhibits and videos. Developing learning modules and working with teachers will help bring the research into the classroom, reaching a diversity of students in several states. Finally, the researchers will make all data collected from each bird immediately available to the scientific community and the public to enable broad-scale comparative analyses and integration with other avian data sets.

"Big trees" - comprehensive species-level phylogenies - are revolutionizing the field of evolutionary biology. This project will generate genome-wide markers for 8,000 species of birds and leverage data products from other NSF-supported studies to produce a phylogenetic hypothesis for all 10,560 bird species. A well-resolved, complete, time-calibrated, species-level phylogeny of birds will allow numerous challenging hypotheses to be tested, provide the conceptual foundation for a phylogenetic revision of bird taxonomy, and permit transformative analyses aimed at elucidating the processes that generate biological diversity. Specific hypotheses to be tested using phylogenies generated by this project include 1) Neoaves underwent a rapid radiation after the K-Pg mass extinction, 2) avian diversification has been shaped by the history of intercontinental dispersal, and 3) species tree methods outperform concatenation in phylogenetic analyses of genome-scale data.

Traditional museum specimens (e.g., skins, skeletons, dry- and fluid-preserved specimens), once considered poor sources of DNA, are now becoming recognized as a potential vast biological resource for historical DNA (hDNA), that provide an unparalleled record of biodiversity spanning the last 200 years. In particular, the advent of high-throughput sequencing platforms (using short DNA fragments) now provides a more efficient means of sampling the hDNA genome. However, hDNA?s potential has hardly yet been explored, with current procedures for DNA extraction often relying on approaches tested on few individuals and optimized for specific projects. Consequently, outcomes of most extraction efforts still often lead to unusable sequence data, or otherwise, high sequencing errors, missing data, and/or contamination. This project will develop efficient and open-source protocols for yielding usable genome-scale molecular data from typical traditional museum specimens, based on rigorous comparative experiments of existing and novel DNA extraction methods, using time-series collections at the American Museum of Natural History (AMNH). Broader societal impacts include conservation (using museum specimens to document historical trends in populations and emerging diseases), forensics (providing improved methods for accurate species identification of biological material), and genomics (documenting genetic change over the past 200 years).

Project outcomes will determine optimal tissue sources and extraction methods for hDNA, develop improved methods for reverse crosslinking of formalin-fixed DNA, and provide a deeper understanding of how DNA degrades due to exposure to formalin, alcohol, tissue buffers, and archival storage time. This project will also develop new approaches for bioinformatic processing of hDNA, to better detect contamination, evaluate the effects of hDNA on phylogenetic inference, and improve the utility of hDNA in all aspects of comparative biology. The application of reliable bioinformatic processing pipelines produced from this study will scale-up the availability of genetic research resources by at least 100-fold (e.g., at AMNH, 120,000 current DNA tissue samples compared to >20 million biological museum vouchers). The availability of DNA from historical museum specimens will also allow the genetics and epigenetics of extinct species and populations to be studied and provide exciting new opportunities to determine how genetic diversity has changed during the Anthropocene. Results of the project will be provided at https://www.amnh.org/research.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.