Field Course: Genomics in the Jungle III - Herpetofauna of the Amazon
Join Our Molecular Bio Blitz!
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.
- 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.
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 instructor’s grade and issue credit for the course. For more details on obtaining credit or deciding if credit is for you, please email us at firstname.lastname@example.org
The United States 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 eventually. However, this system has little to no meaning outside the US itself, and thus, when we offer credits, we are primarily targeting those students within the US to whom this is relevant. Course credit is therefore only available to students in the US, or possibly countries like Canada, who can transfer credits from US Universities to their institutions to 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 US university system if you come from a country in which this system is itself not recognized. Furthermore, there is no requirement for US 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 university? Please consult your advisor and confirm this before signing up, because this is not the responsibility of either the university or Field Projects International
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, 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 one of 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, participants would receive all but 1.5% of fees already paid. The 1.5% represents the credit processing fees charged to FPI for accepting online payments.
Canceling for reasons not related to COVID-19:
- 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
- Transportation between Puerto Maldonado and the field station
- Structured field activities and classroom instruction for participants, and the provision of specialized equipment and supplies necessary to conduct training and research activities.
Program fees to NOT include:
- Flights from your home to Puerto Maldonado
- Health or travel insurance
- 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. There will 3 available for Peruvian citizens, and 1 available for non-Peruvians.
Apply here before June 1st.
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 (strongly recommended)
- COVID-19 (if you have trouble getting this, please contact us.)
If you have the flu shot for the year, all the better. Find a travel clinic and get your shots EARLY.
Currently, Peru requires inbound international passengers on commercial flights to have either a negative real-time COVID-19 molecular (RT-PCR), negative antigen test result, or a medical certificate of epidemiological discharge that is no more than 72 hours old after being issued and before boarding the plane. All passengers must also complete an affidavit of health (found here: https://e-notificacion.migraciones.gob.pe/dj-salud/). These requirements may change, so we advise you to contact your airline days prior your flight to gather the proper documentation and regularly consult the airport website for the latest guidance: https://www.lima-airport.com/eng/for-passengers/covid-19-protocol/arrival-protocol (in English) and https://www.lima-airport.com/esp/para-pasajeros/protocolo-covid-19/antes-de-viajar (in Spanish).
Regarding the 14-day quarantine for all visitors in Peru, travellers are able to quarantine at their final destination if they get there within 24 hours after landing in Lima. The field station where we work can serve as this site, as they meet all government-approved COVID protocols, and have the capacity to maintain social distance between all visitors.
Our Peruvian partners who operate the field station can optionally send an additional ‘letter of invitation’ in Spanish, to be shown at customs, which states that the field station will serve as a quarantine location. To receive this letter, let us know well in advance. They can personalize the letter, send it to you electronically, then you can print it at home before travelling.
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. They will have protocols for isolating symptomatic guests, arranging 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.
According to the U.S. State Department website, you must show proof of a negative COVID-19 test taken within 3 calendar days prior to boarding a flight bound for the United States, and sign an attestation confirming this. The test must be either NAAT (nucleic acid amplification tests such as PCR or LAMP), or it can be a viral antigen test. These tests reflect your current status, whereas an antibody test does not.
Currently, we recommend getting a molecular test at a clinic in Lima (molecular tests are currently not available in Puerto Maldonado, only rapid antigen tests). We recommend getting a molecular COVID test at UniLabs, located in Miraflores (about a 35 minute drive from the airport in Lima). You must purchase the test online, then they send you an e-ticket for confirmation. These tests cost around 145 soles (~$40), and the results should arrive within 12 hours. Plan on staying in Lima for one night to assure you get test results in time for your flight.
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 procedures pamphlet prior to departing for the field site, and may be required to complete a short online training on our website.