EAGER: New Methods for Genomic Analysis of Noninvasive Samples

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The objective of this study is to develop novel methods for generating and analyzing genome-scale data from biological samples that have been collected in a noninvasive manner. Noninvasive samples are often the only type of biological sample available for natural populations, especially in endangered or threatened species, but they yield tiny quantities of low-quality DNA. Noninvasive genetic analysis techniques have changed little in the past twenty years, meaning that the genomic revolution has not yet arrived for species for which only noninvasive samples are available. This study will address this problem by producing new lab protocols for increasing and purifying the DNA yield from noninvasive samples to a level appropriate for genomic analysis, and by developing new software to analyze the resulting genomic data. It will validate these approaches by comparing genomic data from noninvasive samples to data from high-quality DNA samples, using data for a known pedigree from the well-studied wild baboons of the Amboseli basin in East Africa. This project will result in a major leap forward in tools for studying the genomics of many different species and sample types. Publicly available protocols and software will be released, which can be used to investigate evolutionary and population history in species for which such studies were previously impossible. It will also provide societal benefits in the form of tools for assessing the conservation status of vulnerable species. Finally, both graduate and undergraduate students will be trained as collaborators on the project.