Field Course: Genomics in the Jungle V - Biodiversity of the Amazon
Each year this course tackles a different application of field genomics. In 2022, course participants focused on detecting animal trace DNA and eDNA sampling technique. THE 2023 COURSE WILL FOCUS ON GENETIC TECHNIQUES FOR DESCRIBING BIODIVERSITY, WITH PRACTICAL TRAINING ON SPECIES MOLECULAR CLASSIFCATION, METAGENOMICS, AND METAGENOMIC TARGET SEQUENCE ENRICHMENT.
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. In the past decade 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 eliminating the need for transporting samples around the world to distant labs that possess the equipment and resources to extract, amplify, and sequence DNA. This new technology is democratizing wildlife research by empowering field scientists with genetic tools to directly advance their research and conservation initiatives in situ.
We leave traces of our DNA everywhere – in the air, in water, in latrines, on our food, on the ground. Forensic scientists are dedicated to finding these traces we leave behind to solve mysteries and crimes. Conservation biologists can use the same techniques to detect species or even count individuals in a particular environment, which may be highly impactful for endangered species. In this course, the fifth in the series, we will focus on using molecular methods to describe biodiversity in three ways: standard species molecular classification technique (using widely accepted and documented mitochondrial gene markers), metagenomic technique intended to differentiate populations or unclear taxonomic groups, and metagenomic target enrichment utilizing Nanopore adaptive sequencing methodology. Participants will engage in noninvasive sampling of DNA from select vertebrate taxa (may include herpetofauna, small mammals, and birds) and water samples from relatively stagnant sources such as oxbow lakes, palm swamps, and clay-licks. Samples will be diverse, requiring the use of variable preservation and DNA extraction techniques. In addition to training in laboratory procedure, participants learn best-practice methods for data collection, sample organization, preservation, and preparation, processes that have been continually refined over a decade of field work at this location. Finally, while in the field participants complete a crash course in using essential bioinformatics tools for Nanopore sequence analysis, with the optional to participate remotely in a 1 to 2-day data discovery session approximately 3 weeks after the field program concludes.
This course combines training in molecular research techniques with a real-time sampling effort from Amazonian fauna 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, the Los Amigos Wildlife Conservation Laboratory. Course participants will assist experienced field biologists and geneticists in collecting samples and then carry out the full pipeline of DNA extraction, amplification, sequencing, and bioinformatic analysis for species identification and basic mitochondrial genome assembly.
Since the courses inception in 2018, this program has had 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 demonstrate to the broader scientific community and conservation stakeholders the utility and efficiencies of conducting DNA-based surveillance entirely in the field.
- To experience a pristine, faunaly intact, and highly diverse Neotropical ecosystem
- To execute best practices methods for noninvasive sample collection from Neotropical vertebrates and the environment
- To employ mitochondrial molecular markers to amplify DNA of local fauna from the samples collected for goal 2
- To compare species detected by DNA sequence against established lists of local fauna
- To carry-out metagenomics for full mitochondrial and/or microbial genome assembly
- To explore the utility of positive/negative Nanopore adaptive sequencing procedure
- To complete a robust bioinformatics pipeline for amplicon sequence data clean-up and classification
- To develop a short workflow for mitochondrial genome assembly from metagenomic sequence data
A Slice of Genomics-in-the-Jungle Life!
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 email@example.com
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.
- 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:
- Yellow Fever
- 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.