Developing Methods for Access to High Quality Genome Sequences from Wild Ape Populations

Modern evolutionary study of wild ape populations requires the collection of genomic DNA from individuals living in their natural habitat. In order to be maximally useful, these samples must be robust enough for the amplification and subsequent assembly of genomic sequences, which are driving much of modern evolutionary research. Additionally, conservation efforts require that these samples be collected with zero intervention on the study species, because all great apes are now critically endangered. Consequently, the conventional method for genomic DNA collection has been extraction from cells present in fecal samples. However, this approach presents multiple difficulties to investigators, including extensive contamination of sequences from gut microbiota and limited storage time. The purpose of this study is to explore alternative procedures of noninvasive DNA collection to overcome these challenges. Specifically, the study looks at DNA extraction from hair follicle cells and from cells present in urine. These sources of genomic information confer a number of advantages over feces, such as smaller volumes of collection, much lower levels of microbial contamination, and relative ease of storage and transport. In this study, a method for isolating genomic DNA from chimpanzee (Pan troglodytes) hair follicle cells is developed and tested for limit of detection using a decreasing number of hairs per extraction. Validation of the method is then established through the determination of the frequency of polymorphisms due genomic amplification error by comparing sequences obtained from three identically handled samples. After laying out the next steps of development for this method, the study also suggests a similar investigation for samples derived from urine. The overall aim of these studies is a future incorporation of these procedures into the suite of DNA collection techniques available to researchers working with natural populations of great apes and other mammals.