[ECOLOG-L] Genomics in the Amazon: Field Course

[Mrinalini Erkenswick Watsa]

Course application link: http://bit.ly/2DjiOWx Application deadline: May 1, 2018 Scholarships available: http://bit.ly/2F50wGf Course Description Biological research is turning to genetic research methods for a deeper look into the factors that encode behavior and physiology. We use genetic techniques to determine species delimitations, define populations, understand mating systems, explain behavioral differences in foraging efficiency, screen for disease, conduct paternity studies, evaluate immune status and functioning, and explore microbiome diversity… and these are just a few examples of the full breadth of the field as applied to wildlife biology. The field of genetics is revolutionizing biological research, and in the past few years we have even witnessed the successful deployment of instruments that enable molecular work to be conducted ‘on-the-fly’ and in the field. These new tools are minimizing the hassles and barriers associated with transporting samples around the world to distant labs that possess the equipment and resources to extract, amplify, and sequence DNA. In many ways, this new technology is democratizing wildlife research by empowering field scientists all around the world with genetic tools to directly advance their research and conservation initiatives. This course will take you to the Peruvian Amazon, where you will learn how field research is conducted, assist in sample collection, and then actually extract, amplify, sequence, and interpret genetic data to answer several practical research questions about wildlife ecology and natural history. It will take place at the Inkaterra Field Guides Station, which is the site of the Green Lab, the world’s first tropical rainforest molecular genetics laboratory. You will go from sample collection to sequence analysis directly in the rainforest. This course is will provide an introduction to next-generation primatologists and biologists, who will gain not only the skills requisite for field research but the technical know-how to employ genetic research tools in the field. Research Topics In this course, we will focus on three specific cases in which cutting-edge genomics can help us solve mysteries common to wildlife research in the field. The ultimate goal of all of these projects will be to use a MinION, a USB-sized powerful sequencer that is revolutionizing how we do genomics in some of the craziest places on the planet. The MinION has been used to: *do whole-genome sequencing to identify species with PCRs in under 40 minutes and whole genome amplification in under 100 minutes *conduct real-time DNA sequencing in a remote rainforest by a course instructor *sequence DNA offline in the Antarctic and even on the International Space Station in outerspace! We will study three specific cases (class size and time permitting): *DNA fingerprinting *The effects of captivity on microbiome diversity *Environmental DNA We will try to answer a few additional questions with all case studies: *Can we use the What’s In My Pot (WIMP) workflow to accurately classify these species to a reference database in real-time for all of the case studies? *How many different kinds of samples can we multiplex at one go on a MinION? *Does the choice of DNA extraction kit affect the outcome? *Does the length of time we let the MinION run affect the accuracy of our species identifications? Course Highlights: *Explore one of the most biodiverse areas in the world – lowland Amazon rainforest. *Hike over a quarter of a mile on the iconic Inkaterra Rainforest Canopy Walkway, 98 feet above the ground. *Track three (or more!) primate species to noninvasively collect biological samples for DNA barcoding in the lab *Identify plants by morphological characteristics and DNA barcoding techniques *Visit a wildlife rehabilitation center to collect biological samples from captive exotic animals for comparison to the microbiomes of their wild counterparts *Manage a molecular genetics field laboratory in the Peruvian Amazon’s first such venture *Conduct parasitological screening in wild and captive primates *Visit Colpa Chuncho, a spectacular clay lick located within the 1000+ square-mile Tambopata National Reserve that attracts large numbers of several bird species, including scarlet macaws and toucans *Stay on after the field course and visit iconic archaeological sites such as Machhu Picchu. Course application link: http://bit.ly/2DjiOWx Application deadline: May 1, 2018 Scholarships available: http://bit.ly/2F50wGf