Training Program: Biodiversity Monitoring



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Quick Facts

Program Background

The Madre de Dios (MDD) region of Peru is part of the Tropical Andes Biodiversity Hotspot, which includes the Andes mountains and the adjacent lowlands of Ecuador, Colombia, Peru, Venezuela, and Bolivia, and some portions of northern Argentina and Chile. Within the hotspot, the MDD has been designated Peru’s “biodiversity capital” by law, with over 50% of it protected either in a private conservation concession or as a regional protected area. A 2018 assessment of the MDD revealed the following statistics: 6809 plant, 1212 bird, 272 fish, 256 mammal, 183 amphibian, and 143 reptile species. The indigenous groups living in this region most certainly have valuable knowledge of these species, and likely more that are new to science, but even among those documented by scientists, there is much yet to be learned. The Los Amigos Conservation Hub where this study takes place is within the Los Amigos Conservation Concession, established in 2000.

Figure: Overall Neotropical primate species richness compared to primate richness in the Amazon basin. The red-to-yellow gradient color indicates high-to-low richness of primates that are endemic to the Amazon. (a) A west-eastern gradient from the Andes mountains toward the Atlantic Ocean is observed, where the main tributaries of the Amazon river delimit the distribution of several primate species. (b) The Amazon hosts the higher gridded richness of primates in the Neotropics. Figure adopted from: Sales, L., Ribeiro, B.R., Chapman, C.A. and Loyola, R., 2020. Multiple dimensions of climate change on the distribution of Amazon primates. Perspectives in Ecology and Conservation

A very small proportion of these animals have their DNA sequenced, with records saved in global biodiversity databases. Even fewer still have complete genomes assembled. The primary reasons for this are a) a disparity in the rate of development of sequencing technologies and the accessibility of these technologies globally – while one end of the spectrum races ahead, it leaves several others behind; b) high costs to conducting genomic studies; c) the difficulty of acquiring biological samples from so many species animals and d), the need to export specimens out of the MDD region for analysis.

All of this is about to change, and necessarily so, for two reasons: 

  1. Biodiversity loss is at a critical level in the region. A recent study found that between 1993 and 2013, forest cover was converted to agriculture by 470%, to mining areas by 938%, and urban areas expanded into agricultural land by 187%. This was inspired in part by the lagging economic development of the MDD region, which stimulated several programs to encourage infrastructure building and job development. In 2010 for example, the Interoceanic Highway that connects the Pacific ports of Peru with Brazil was completed, which has encouraged immigration, economic development, and the growth of many secondary roads. Unfortunately, as in many places globally, the balance between development and conservation is a delicate one, not easily maintained.
  2. Sequencing has just become smaller, more efficient, and less costly with the advent of portable nanopore sequencers produced by Oxford Nanopore Technologies. In conjunction with dozens of other pieces of equipment that now have slimmer more field-friendly versions on the market, field genomics is fast-approaching a reality instead of a dream.

Goals of This Program

In this program in 2021, we have a single simple mandate: to conduct large-scale biodiversity screens of mammals in the region, which will be used to develop genetic and genomic resources and tools for more targeted population monitoring of focal species in the future.

This program is an off-shoot of In Situ Labs, and to this end, it program will:

  1. Implement a site-specific eDNA monitoring program as a model for future large-scale monitoring. Samples handled here include water and soil.
  2. Trial rapid-tests for critical species in specific environments, such as anacondas and giant river otters.
  3. Coordinate morphometric and DNA barcoding based species identification for all animals screened by the various handling programs on site.
  4. Coordinate hair-snare monitoring and conduct biological sampling of medium-sized mammals. Samples include footprints, hair, and feces from (we hope!) tayras, short-eared dogs, peccary, coati, olingos, kinkajous, armadillos, and margays.
  5. Conduct multiple bioblitzes for rapid biodiversity inventorying. Current taxonomic groups include reptiles/amphibians and insects.

Training and Activities

In this program, you will gain the following skills:

  • Field sampling for environmental DNA screening programs
  • GPS navigation training for off-trail navigation
  • Sample biobanking under field conditions
  • Species identification using morphometrics, high-quality photographic imagery
  • Basic laboratory skills including: DNA extraction, PCR amplification, electrophoresis and indexing
  • Advanced laboratory skills including library prep and portable nanopore-based sequencing.
  • DNA barcoding including submission to BOLD databases
  • Bioinformatics pipeline executions for field genomics
  • Sample coordination during field anesthetizations of mid-sized mammals by veterinarians.

Who Should Join our Field Team?

  • Those with a keen interest in biodiversity conservation and conservation genomics
  • Lovers of Latin names and taxonomic identification
  • Those with prior laboratory skills eager to transpose these to a cutting-edge field laboratory.

Who Can Apply?

We are currently recruiting participants with the following qualities. If you are uncertain if you are eligible don’t rule out the program, please contact us to confirm.

Minimum Requirements:

  • You must be at least 18 years of age by the time the training program begins (no upper age-limit)
  • A letter of recommendation from a source that can substantiate the participant’s experience and skills
  • Previous lab experience in molecular biology is required. Pipetting, PCR and gel electrophoresis experience at a minimum.
  • Must be able to carry at least a 20 lb back pack during field expeditions
  • Fluency in spreadsheet management via Excel.
  • A vaccine to COVID-19 (see FAQ below for details)
  • Participants must be in good physical condition, with the capability to walk 4 miles a day

Preferred Requirements:

  • Ideal participants will be biology majors, have taken anatomy- and morphology-based courses, and/or demonstrate a strong interest in natural history.
  • Genomics experience is not required, you will gain this on this program, but prior laboratory experience is welcomed.
  • Participants will not be discriminated against for medical conditions they might have, if we determine that being on this project will not pose an immediate risk to their health
  • Participants must be willing to maintain long hours in the field and the laboratory, with every effort made to balance this across the program.
  • Participants must be reliable – when a team is assigned to work with a group of animals, days of planning go into the execution of the protocol. Carelessness and tardiness on the part of the participant could jeopardize the entire project.
  • Participants must be detail-oriented; our job is to track species across several capture programs
  • Due to the nature of the work and weather constraints, participants MUST be willing to be flexible about their schedules

The biodiversity monitoring program is co-led by Dr. Gideon Erkenswick and Dr. Mrinalini Watsa in conjunction with the In Situ Lab Initiative.

 

Frequently Asked Questions

1. Apply online here. You will need a CV/resume and two references.

2. Once we hear from your references, we will schedule an interview with the principal investigator of your desired project

3. If accepted, you will be notified within 1 week

4. Upon acceptance, gain student access to online training modules to get prepared before you arrive.

5. Turn in medical info, vaccination record, liability waivers, etc.

6. See you in the field!

All start dates could be delayed 2-4 weeks if it is significantly more likely that participants will be able to get vaccines by that time. This decision will be made in the Spring, with final dates decided April 15. 

DO NOT buy flights until April 16 and the program dates are confirmed.

We will not take more than 1 week’s reservation fee at the time of recruitment.

Learn more about FPI and COVID-19 HERE.

Yes. This is the best way for us to ensure the safety of all participants, staff, and partners.  We cannot guarantee the health status of everyone you will encounter, so vaccines are mandatory to protect you and others you come into contact with. 

We will require proof that you have completed the full course of vaccine shots before arriving in Peru. 

If you think you will have trouble getting the vaccine in time within your country, please contact us.

Learn more about FPI and COVID-19 HERE.

Bear in mind that we require other shots as well:

  • Typhoid (all programs)
  • Yellow Fever (all programs)
  • Tetanus (all programs)
  • Rabies (Wildlife Health and Primate Monitoring programs only)

In order to train our research teams, it is necessary that everyone arrives on specific start dates. However, for some programs we are able to provide multiple start dates in order to accommodate the varying schedules of our research assistants. Note: this is not offered for all of our programs, so please pay attention to the specific start times for each program.  If you REALLY cannot make a particular start date, don’t abandon hope – email us and we can do our best to accommodate you!

There are pretty firm minimum requirements for each program (3- to 6-week commitments). These are firm because each research assistant must be trained, during which time the data they collect cannot be relied upon entirely. Anything less than the minimum time is deemed insufficient for the research assistant to contribute real data to the project. However, for most programs, you are welcome to apply for stays that are longer than the minimum period – in fact, we really do recommend and love it when you do!

Our courses have fewer enrollment requirements, and we strongly encourage anyone to apply. The research assistantships are more competitive, and there are fewer positions available.

You absolutely can apply to both a field course and an RAship program if the dates will line up! In fact, if you are accepted into the research assistantship, you can attend a field course for a lower fee (typically a $400 discount)

No, you do not need previous research experience. These are training programs designed for participants at all levels. It can be hard to acquire field experience, so we balance our teams with veteran researchers and those new to the world of field research. We seek bright and enthusiastic candidates with the right temperament to work in this challenging environment. 

The cost to participate includes lodging and all meals at the field station, transportation between Puerto Maldonado and the field station, specialized training for candidates accepted into the program, and the provision of equipment and supplies necessary to conduct this research.

A large majority of the fees paid to our training programs cover lodging fees 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.

We are now able to offer a peer-to-peer fundraising program for research assistants. Once accepted, you would be able to create a shareable profile on our platform. This is a team-based initiative, so half of your raised funds will go toward your own program fees, while the other half will go into pool to be split evenly among all program participants who had at least 5 donors. More details will be available during (and after) your interview. If you require help with the cost of the program, there are other options that you might pursue as well. You could start by contacting the Office of Undergraduate Research of your school, or request professional development support from your employer. Here you can explore what is available through your college/place-of-work, as well as through external funding sources. Many universities have SURF (Summer Undergraduate Research Fellowship) programs, which may provide stipends for students to pursue independent research. Please note that if you do find any kind of research-related funding — as many RAs have in the past — it will need to be applied for in conjunction with us, on research projects that we approve. In this case, one of our principal investigators will consult with you about developing a project that is feasible.

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. 

Some candidates may have an opportunity to win a grant that will fund their research assistantship site fees and travel. However, the grant requires them to submit a research proposal. If this is your situation, we may be able to work with you on a proposal. Contact us at info(at)fieldprojects.org and we can help you structure one. We cannot accommodate completely independent projects, but we can assist you with finding a subset of our samples or data that has not yet been full used, which you could develop further with supervision.

Yes, you can. We do not give co-authorship for collecting data alone, but we offer interested students the opportunity to work on data analyses after the summer research program, that could lead to co-authorship in the future. Many of our former field team members have gone on to become research collaborators.

Once you make your payment towards the program, we will go ahead and book your stay at the field station, which requires us to pay in advance and provides no refunds. We also block your spot and reject other applicants based on your being on the team; thus cancellations can affect team recruitment quite strongly. Nevertheless, we do recognize that circumstances sometimes demand cancellations – so we do the best that we can, given the restrictions we are under.

Here is our cancellation policy: 

  • 45 days before your start date: 45% refunded
  • Less than 45 days from your start date: no refund is possible
If you have extenuating circumstances, or applied closer than 45 days to your start date, please contact us to confirm your specific cancellation policy.

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