Field Course: Genomics in the Jungle III - Herpetofauna of the Amazon
Join Our Molecular Bio Blitz!
NOTE: This program concluded in August, 2021.
Please see our main Programs page for upcoming Genomics in the Jungle courses.
Quick Facts
- Timing: August 1 -15, 2021
- Duration: 2 weeks
- Language: English
- Location: Los Amigos Conservation Hub, Madre de Dios, Peru
- Enrollment Deadline: June 15, 2021
- Program Fee: $2400 for non-Peruvians; $700 for Peruvians living in Peru (Fee includes food + lodging, transportation to the field station from Puerto Maldonado and back. Fee does not include travel to Puerto Maldonado)
- Pandemic Contingencies: If this program is cancelled by FPI due to factors beyond our control, all fees paid will be refunded, minus a 1.5% credit card processing fee. More info in the FAQ below.
Biological research has turned to genetic research methods for a deeper look into the factors that encode behavior and physiology. We use genetic techniques to delimit species, 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 with genetic tools to directly advance their research and conservation initiatives. Hereptofauna in the region have been extensively surveyed and there are 86 reptilian and 98 amphibian species estimated to occur at this site. Documenting herpetofauna community stability in the face of habitat loss, global warming, and emergent disease is no easy task. A more complete DNA reference library sets the stage for the use of eDNA to document presence/absence for the multitude of species in the region.
This course combines training in molecular research techniques with a real-time survey of Amazonian herpetofauna (tropical amphibians and snakes) at the Los Amigos Conservation Hub that sits at the edge of a 300,000 hectare conservation concession of intact lowland tropical rainforest. The field station is equipped with an in-situ genetics laboratory. Course participants will assist experienced herpetologists conducting a methodical, rapid inventory of frogs and reptiles and then carry out the full pipeline DNA extraction, amplification, sequencing, and species identification with experienced molecular biologists.
This program has two primary goals.
- To assist participating scientists and conservationists to realize the powerful applications of field-based genetic and genomic methodologies in biodiversity monitoring
- To create a more complete DNA and photographic reference library of herpetofauna in this highly diverse habitat.
Program goals:
- To conduct a foot-survey of herpetofauna over a 5 square-kilometer area.
- To take biological specimens from both sexes of each target species.
- To create a high-quality photographic and videographic record of each species.
- To conduct a health screen including testing for Batrachochytrium dendrobatidis for each animal surveyed
- To test broadly for mercury toxicity in each animal.
- To extract and sequence multiple species-distinguishing genetic markers via nanopore-based sequencing for each animal surveyed.
- To submit sequences so obtained to the Barcode of Life Database.
This course will take students into the forest and laboratory for hands-on training but will also expect attendance of regular classroom-based lectures on topics relevant to herpetology and molecular research. These lectures will be given by course instructors to enhance the participant’s understanding of the natural history of herpetofauna in the region, basic survey methods, as well as DNA barcoding using high throughput sequencing.
Lectures will cover the following topics:
- Introduction to herpetology: amphibian and reptiles of the region, toxicology, disease
- Herpetological field sampling and data collection
- Herpetological conservation and management
- Introduction to genetics and genomics: basis of genetic research, background, and applications
- Genetic methodologies for field researchers
- Analysis of sequence data: a crash course in bioinformatics
- Ecotoxicology in the Madre de Dios region: guest lecture by Caroline Moore, Ph.D., D.V.M.
By the end of this program students will have basic competence in the following activities:
- Forest navigation and use of a compass and GPS
- Safe handling of amphibians and reptiles
- Differentiating herpetofauna based on morphological characters
- Biological sample collection and storage
- DNA tissue extraction, PCR, gel electrophoresis
- Nanopore sequencing library preparation
- Nanopore sequence analysis based on a highly multiplexed amplicon sequencing protocol
Jennifer Stabile began her career in herpetological research with the Central Florida Zoo in their Department of Herpetology. She is a lifelong herpetologist with prior experience from the Department of Herpetology of the Central Florida Zoo (CFZ), Medtoxin Venom Laboratories (Florida), and the Ashton Biodiversity Research & Preservation Institute. She has worked to prevent amphibian population declines across diverse landscapes, including collaborating with Proyecto Coqui, which monitors and attempts to breed endemic frogs to Puerto Rico. Jen’s prior research efforts have included studying the presence and prevalence of amphibian diseases, such as the amphibian chytrid fungus (Batrachochytrium dendrobatidis) and ranaviruses, with colleagues in Florida, New Mexico, and Texas. Jen also worked at the University California at Berkeley as a Science Educator for UC Berkeley’s EBAYS program, which involved teaching climate and energy science to underprivileged communities in the Bay area of California. She holds a Master’s of Science degree from the Department of Environmental Management at the University of San Francisco and has been a field course instructor with FPI since 2016. Jen is Conservation Section Editor of Herpetological Review, a scientific advisor for the Chiricahua Desert Museum, and current president of the International Herpetological Symposium. She is the first female president of this organization in its 40-year history.
Dr. Mrinalini Watsa began a love affair with the rainforest in the backyard of her home in India, virtually overrun with cobras, chameleons and even jackals. She has a PhD in biological anthropology from Washington University in Saint Louis, with a specialization in molecular genetics of vertebrates. She has managed a mark-recapture program with wild primates in Peru for more than a decade, and run both university and field molecular genetics laboratories in the US and Peru. Today she is a researcher with the San Diego Zoo Wildlife Alliance where her work focuses on field-based conservation genomics for species in Africa, Asia and the Neotropics.
Visit her full profile here or explore her website.
Dr. Gideon Erkenswick co-founded Field Projects International, and has spent more than 10 years working in the Neotropics leading research programs focused on primate behavior, disease ecology, and mark-recapture. For the past 4 years, he has also taught field courses in general tropical biology and primate behavior. Between 2011 and 2017 he completed a doctorate in biology at the University of Missouri-St. Louis (UMSL) that focused on parasite-host relationships from a diverse community of nonhuman primates using molecular genetics and genomics.
At UMSL Gideon also acquired formal classroom teaching experience in anatomy and physiology, comparative vertebrate anatomy, evolution, and organismal biology. Currently, in addition to his role as a senior research scientist for FPI and founder of the Green Lab, he works for the Infectious Diseases Division of the Washington University in St. Louis School of Medicine as a post-doctoral research associate.
Visit his full profile here or his website.
Timothy Paine has had a lifelong fascination with herpetology that has led him to explore some of the most remote places on earth in search of rare amphibians. Apart from his degree in biology, he began a path toward becoming a consummate naturalist by chasing after the many lizards and snakes of the Mojave desert in California. Tim recognized early on that the dialogue and public perception surrounding herpetofauna, and how they are normally documented in the wild, is not conducive to conservation. To address this, he has repeatedly involved himself with organizations that support or operate in areas of heightened amphibian diversity, including Tree Walkers International, Field Projects International (he currently serves as a director), and the Forman Rainforest Project. He created and presently maintains Amphibios.org, an online resource for sharing experience about travel, amphibian conservation, and hands-off wildlife photography. He has contributed to the scientific literature many new amphibian and snake species site records and is passionate about experiential research training in herpetology.
Dr. Stefan Prost works at the Natural History Museum in Vienna focusing on conservation genomics and wildlife forensics. He started working with the MinION in 2014 and is developing laboratory and bioinformatic tools for in situ DNA barcoding approaches. He has been using the platform in many areas of the world, such as Ecuador and Peru. His team recently validated the MinION for wildlife forensic case work. As a postdoctoral scholar at Stanford University, Stefan’s research focus is on genome architecture, comparative genomics and paleogenomics. He has worked on such diverse projects as creating the first complete mitochondrial genome of New Zealand’s first dogs, to real-time DNA barcoding of some rare herpetofauna (the recently re-discovered Jambato toad Atelopus ignescens, which was thought to be extinct for 28 years, a rare species of blind snake Trilepida guayaquilensis, and two undescribed species of Dipsas (snakes) using nanopore sequencing in the Ecuadorian rainforest. Stefan has co-instructed two field courses for FPI titled Genomics in the Jungle at the Inkaterra Green Lab during the summers of 2018 and 2019.
Who we are looking for:
- Participants who have an interest in the natural history of herpetofauna, particularly in the Amazon.
- Participants with an interest in genetic laboratory techniques, taxonomy, and/or DNA barcoding will enjoy this program
- If you like to merge the worlds of laboratory and field science, then this program is for you.
There are a few simple requirements to determine eligibility for this course:
- You must be at least 18 years of age at the time of the course.
- You must have medical insurance (including COVID-19 coverage), and provide proof of such insurance to us to complete your reservation.
- We have no citizenship requirements. Anyone is welcome to apply.
- You must obtain visas independently if necessary.
- You do not need any training in biology – our course is structured to accommodate people from a variety of backgrounds.
- Courses have a maximum capacity of 12 participants. If you are concerned that you will lose your spot, please contact us to confirm how many spots we have left.
- Peruvian nationals currently living in Peru will qualify for a reduced rate. These spots are limited.
- Course readings: Reading list to be announced in June 2021. These are intended to foster better comprehension and discussion of course topics and should be read ahead of the course start date.
- Syllabus: This document is being updated with new case study information and will be available for download by June 2021. The framework for the course will be similar to last year’s program (view last year’s syllabus HERE)
- Download our Sexual and Gender-Based Policy: HERE
- Download our Student Policy Manual: HERE

Read the paper from our first
Genomics in the Jungle field course
Watsa, M., Erkenswick, G.A., Pomerantz, A. and Prost, S., 2020. Portable sequencing as a teaching tool in conservation and biodiversity research. PLoS Biology, 18(4), p.e3000667.
Frequently Asked Questions
We meet up for this course in Puerto Maldonado, Peru, then head to the field station together as a group. If you have questions about what to bring, how to plan your travel, what the meals and lodging will be like at the field station, and more, then please visit this page.
If you don’t find the answers you are looking for on that page, please feel free to contact using the form at the bottom of this page.
Participants can acquire credit directly from their universities. You would provide your university with the course syllabus, and the school may decide to accept the instructors’ evaluation and issue credit for the course. For more details on obtaining credit or deciding if credit is for you, please email us at info@fieldprojects.org
The United States of America’s university system runs on credits – typically 2 to 4 per class. A student needs a certain number of credits to graduate with a Bachelors’ degree. However, this system has little to no meaning outside the USA itself, and thus, when we offer credits, we are primarily targeting those students within the USA to whom this is relevant. Course credit is therefore only available to students in the USA, or possibly countries like Canada, who can transfer credits from USA Universities to their institutions that will apply towards their degrees.
For all other students — and there have been plenty who have attended our courses — you receive many other benefits to taking the course, such as:
- A certificate from FPI showing that you attended and completed the course
- A detailed report of your performance and your final grade, which you can share with future employers or anyone else in any manner you wish to.
To be clear: You are not required to sign up for credits in the USA university system, whether or not you come from a country in which this system is recognized. Furthermore, there is no requirement for USA students to take this course for credit. Course credit is an optional item, and will incur credit fees from the university in question.
Questions to ask yourself before signing up for credit:
1. Will my university accept transfer credits from another institution? Please consult your advisor and confirm this before signing up.
2. Can I afford to take the course for credit? The credit costs are paid directly to the university while the course fee is paid to FPI. Both will be necessary before you can take the course for credit.
Apart from the valuable skills, knowledge, and experience that you will acquire, FPI encourages alumni to network, support, and collaborate with each other after the course is done. Also, our staff remains available for academic and career advice. Many of our alumni have returned as research assistants, and later even joined us as research collaborators, field team leaders, and instructors.
In addition to the specific training that will benefit those going into many fields, our courses also entail pushing yourself beyond your comfort zone and are challenging both mentally and physically. Furthermore, this is a chance to visit remote research stations in the most bio-diverse regions of the planet, and to learn about the incredible flora and fauna that you will see at every turn.
If FPI cancels a program due to complications related to COVID-19 or any other reason, participants would receive all but 1.5% of fees already paid. The 1.5% represents the third party credit processing fees charged to FPI for accepting online payments.
Cancellation Policy:
- 30 days or more before your start date: 45% refunded
- Less than 30 days from your start date: no refund is possible
Our cancellation policy specific to COVID-19:
- Before July 1st, if you cancel for a COVID-19 related reason, you will get all payments refunded, minus a 1.5% credit processing fee.
- After July 1st, FPI will have paid a large portion of your program fees to our field station partners, who provide your accommodations and meals the entire time you are on site. This means that those withdrawing due to COVID-19 after July 1st will be refunded all fees paid minus 6.5%. This portion is retained solely to cover our own credit processing fees, as well as the bank fees incurred by our partners at the Los Amigos Conservation Hub in Peru.
The cost to participate includes:
- Lodging and all meals at the field station
- Structured field activities and classroom instruction for participants, plus the provision of specialized equipment and supplies necessary to conduct training and research activities.
Program fees do NOT include:
- Any travel costs
- Lodging and meals in Puerto Maldonado
- Health or travel insurance
- Required vaccinations
- Binoculars or other personal field equipment
A large majority of the fees paid to our training programs cover lodging and food costs charged by the host field station. Importantly, at the Los Amigos Biological Station lodging fees not only support the cost of running and maintaining a remote field site, but contribute to the larger mission of their parent NGO (Association for the Conservation of the Amazon Basin) to protect conservation areas, monitor deforestation, maintain wildlife corridors, and more.
Limited, competitive scholarships are available through FPI. Each has specific criteria, including some specifically for Peruvian students and individuals who identify as Black. See our scholarships page for more details.
All participants are required to show proof of medical insurance before joining us in the field. Many travel insurance providers can assist with emergency medical coverage and emergency medical evacuation. Be certain that COVID-19 is covered in your plan.
You will have to provide proof of a normal vaccination record (as listed here by the CDC). For travel to Peru, we require that you also get the following vaccines:
- Typhoid
- Yellow Fever
- Tetanus
- COVID-19 + boosters
If you have the flu shot for the year, all the better. Find a travel clinic and get your shots EARLY.
Prior to arrival in Peru:
The official requirements of Peru have included a PCR testing requirement to enter the country in the past, but regardless of the governmental requirements at the time of your program, FPI requires all participants to have either a negative PCR test no more than 72 hours before boarding their plane.
After arrival in Peru:
In addition, FPI program participants will get a rapid test at a clinic in Puerto Maldonado before heading to the field station. This is arranged by us, and will cost approximately $25.
Participants are further required to bring a COVID-19 testing kit with them from home. These are generally free or low-cost. You will use one of the two tests a few days after arrival at the station, and save the other in case you develop symptoms during your stay.
NOTE: By maintaining these strict policies, we held our largest field season to date in 2021 with zero COVID-19 infections. This successfully kept program participants, FPI staff, other researchers and workers at the station, and the local wildlife safe.
Negative tests are not an official requirement for those arriving at the field station, but a strong recommendation. Researchers from different institutions and others who are not affiliated with FPI also use this field station, and while temperatures will be taken and screening questions will be asked of everyone, there is no guarantee that an asymptomatic or presymptomatic person won’t be present. This means that masks, social distancing, and other detailed protocols are especially important. In addition, this is why we require all non-Peruvian participants to get vaccinated.
The first signs of suspected symptoms or a temperature above 100 degrees Fahrenheit should be reported immediately to the field station managers and FPI senior scientists. You will be asked to use the testing kit that we require all participants to bring, There are also have protocols for isolating symptomatic guests, arranging additional viral testing, notifying those you have been in contact with, and evacuating you to the nearest hospital if necessary. (Note that travel to a hospital and any care there is at your own cost; make sure your insurance policy covers this.)
The nearest healthcare facilities are in Puerto Maldonado, which is approximately 4-5 hours downriver from our field site. In that city, our Peruvian partners have a recommended doctor certified by MINSA (the Ministry go Health). There are also other private and public healthcare options. The private facilities are more expensive (one of the reasons we require participants to have travel medical insurance), but they will likely be able to treat patients faster if public facilities are full.
The second option would be in Cusco, which is approximately 10 hours by car from Puerto Maldonado. There are more clinics in Cusco than Puerto Maldonado.
*While everyone will have their temperatures taken upon arrival by an infrared thermometer, we strongly suggest that participants bring their own thermometers in their first-aid kits, and check themselves daily.
If a person must leave the field station to get treatment and recover from COVID-19, they will be permitted to return after 7 days with a negative antigen test. A negative molecular test will let someone back to the station after 14 days.
The field station’s safety protocols apply to everybody: staff, researchers, guests, and visitors.
For every new person arriving at the field station, the science director will go over the COVID-protocol with them personally and explain to them about the mandatory use of face masks, hand sanitizer, table seating, and social distancing. There are planned spaces equipped for maximum distance between people.
People living or travelling together in a group for more than 14 days can share the same table at the commissary and will be treated as a “grupo de aislamiento,” keeping distance from other guests or groups. Room service and/or separate seating at different tables will be arranged for all others.
The field station also practices “cuarentena laboral.” This means that there are separate working areas, and you will be expected to avoid using workspaces and equipment that is designated for other individuals or groups.
Our enhanced protocols in laboratory or wildlife handling situations are designed to meet or exceed scientific best practices. They are drafted in conjunction with our Peruvian partners (Conservacion Amazonica), Peruvian authorities (SERFOR) and Institutional Animal Care and Use Committees (IACUC) of our affiliate research universities. Broadly speaking, they will involve strict use of face shields, N95 masks, and gloves. Participants will receive a detailed training on these procedures upon entry into our programs.