Genomics in the Jungle
Participate: Genomics in the Jungle
Quick Facts
- Timing: July 30 - August 13, 2024
- Duration: 2 weeks
- Language: Primarily English (Spanish assistance provided)
- Location: Estación Biological Rio Los Amigos, Madre de Dios, Peru
- Enrollment Deadline: June 30th
- Program Fee: $2490 for non-Peruvians; $760 for Peruvians living in Peru (Fee includes food + lodging + instruction at the field station. Fee DOES NOT include travel or accommodation in Puerto Maldonado)
- Pandemic Contingencies: If this program is cancelled by FPI for issues beyond our control, all fees paid will be refunded, minus a 1.5% credit card processing fee.
- More information in the FAQ below the program description.
NOTE
Each year this course attempts to tackle a new application of field genomics, in addition to our core efforts to better describe biodiversity through molecular classification and metagenomics. Specialty topics are typically announced at the end of the spring university semester.
PROGRAM DETAILS
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 option to participate remotely in a 1-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 core 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 [tentative]
- To complete a robust bioinformatics pipeline for amplicon sequence data clean-up and classification
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 vertebrate and eDNA sample collection, and molecular research. These lectures will be given by course instructors to enhance the participants’ understanding of local habitat and wildlife in the region, basic survey methods, as well as the uses of DNA for scientific research and applied conservation genetics from high throughput sequencing.
Lectures will cover (but are not limited to) the following topics:
- Review of Neotropical vertebrates: birds, mammals, reptiles, amphibians
- A review of wildlife forensics
- Regional topics in wildlife conservation and environmental health
- Introduction to genetics and genomics: basis of genetic research, background, and applications
- Genetic methodologies for field researchers with a focus on portable sequencing
- Nanopore adaptive sequencing protocol
- Analysis of sequence data: a crash course in bioinformatics
By the end of this program students will have basic competence in the following activities:
- Forest navigation and use of a compass and GPS
- Sample collection
- Biological sample storage
- DNA tissue extraction, PCR, gel electrophoresis
- Nanopore sequencing library preparation, including multiplexing strategies
- Nanopore sequence analysis
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. As a co-founder of Field Projects International, 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.
Read more about her work here.
Dr. Gideon Erkenswick co-founded Field Projects International and has spent over 12 years working in the Neotropics leading research programs focused on primate behavior, disease ecology, and mark-recapture. He completed a doctorate in biology at the University of Missouri-St. Louis (UMSL) in molecular disease ecology in 2017 and a postdoctoral research position on pathogen-host dynamics and gene regulation at Washington University in St. Louis School of Medicine in 2022. Gideon currently directs the global In Situ Laboratory Initiative (ISL) that aims to expand genetic research infrastructure and capacity for disease surveillance, biodiversity characterization, and wildlife population monitoring to key ecoregions in Asia Pacific, East Africa, and South America.
Read more about his work here.
Dr. Stefan Prost is Assistant Professor for Biodiversity Genomics at the University of Oulu in Finland. His group focuses on conservation and environmental genomics, in situ biodiversity monitoring and wildlife forensics. He has been using nanopore sequencing since 2015 and has developed both laboratory protocols as well as bioinformatic analyses software tools for this technology. Together with Aaron Pomerantz and other colleagues, he was among the first to try DNA barcoding with the MinION in a remote location (in the Ecuadorian jungle). Since then, he has used this technology for chromosome-level genome assemblies of several non-model organisms, DNA and metabarcoding, metagenomics, SNP typing and also validated the MinION for wildlife forensic case work. A core aspect of his work is local capacity building. Mini and Gideon (from FPI), Aaron Pomerantz and Stefan developed the ‘Genomics in the Jungle’ courses.
Dr. Jenny Chen is a computational genomicist interested in investigating biology by analyzing genomics data from species across the tree of life. She is interested in developing computational tools to understand how genetic evolution gives rise to phenotypic evolution. She received her PhD from MIT and is currently a postdoctoral fellow at Harvard University. Jenny took the first Genomics in the Jungle course in 2018 and works with Gideon on developing tools for viral genomics surveillance.
Learn more about Jenny’s research here.
Who we are looking for:
- Participants who have an interest in the natural history or ecology, conservation biology, and conservation genetics
- Participants with an interest in genetic laboratory techniques 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 advanced training in biology. Our course is structured to accommodate people from a variety of backgrounds: from novice students to those with much more experience.
- 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 2024. These are intended to foster better comprehension and discussion of course topics and should be read ahead of the course start date.
- Download the previous course syllabus for 2023 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.
A Slice of Genomics-in-the-Jungle Life!
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 or contact us at info[at]fieldprojects[dot]org.
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[at]fieldprojects[dot]org
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.
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.
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.
No, you do not need previous research experience. This field course is designed for participants at all levels. In past courses we have accomodated undergraduates, graduate students, post-doctoral researchers, and professors simultaneously. We maintain a low participant:instructor ratio for this reason, to give useful instruction to each participant. We also find that diverse course participants enriches the experience for everyone.
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.
Our cancellation policy is:
- 30 days or more before your start date: 45% of the program final fee refunded. Please note that the down payment is not refundable.
- Less than 30 days from your start date: no refund is possible
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.
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 (no exceptions)
- Rabies pre-exposure series (only for those in programs involving wildlife handling of mammals.)
If you have the flu shot for the year, all the better. Find a travel clinic and get your shots EARLY.
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.
Our programs will proceed as planned unless global travel restrictions prevent our team from reaching the field site, or the field site is shut down.
In the event of an ongoing pandemic quarantine and testing protocols will be observed to ensure that no one exposes another team member or animal the infectious agent. In addition to our programs protocols, all persons will have to comply with national travel regulations. During COVID-19, out field station qualified as a quaruntine site, since it met all government-approved COVID protocols, and has the capacity to maintain social distance between all visitors.
Our enhanced protocols in laboratory and 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 masks, N95 masks, and gloves during specific activities.
Participants will receive detailed instructions on our procedures prior to departing for the field site.
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 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.
