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 animal species 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.

Program Background

Long-term data on animal pathogens and parasites, as well as their health, are indicators of population and community wellbeing. Animal extractions from the wild, or changes to habitat or climate, can be reflected in metrics such as parasite/pathogen richness (unique number of species) or diversity (evenness of species distributions), and parameters such as animal weight or complete blood counts. In conjunction with our mark and recapture research programs, we have been safely collecting a variety of sample types for microscopic and molecular laboratory analysis to monitor wildlife disease and health since 2012 (see our publications page). These prior efforts have never seemed more important than they are today, as the world works toward overcoming a global pandemic. Only through longterm sampling programs can we tackle questions such as:

1. Is parasite species diversity changing and how fast?
2. To what extent are pathogens/parasites shared across multiple host species (e.g. in addition to bats, do monkeys, rodents, or marsupials harbor natural coronavirus infection)?
3. Which parasite/pathogens impact animal health?
4. Which humans diseases pose a risk to wildlife, and vice versa?

All of our research methods have been carefully practiced and refined by our senior scientists, and several wildlife veterinarians with whom we collaborate. Sampling protocols are comprehensive but put the comfort and safety of the animals above our own. For example, to ensure the maximum safety of the animals, we conduct all processing in the jungle, at the screening site. We limit the number of animals we screen each day. We begin each day very early, setting up our processing tents before dawn and closing them at an appropriate time to ensure that no animal is held overnight or for an entire day, depending on whether the animal is nocturnal or diurnal. Thus, we cause as minimal a disruption of their lives as is possible. Samples from this program are analyzed on site and at partner laboratories in the USA and Peru using microscopy and molecular techniques. Further on site training in field molecular genetics may be possible for participants.

High biosecurity standards and animal handling and sampling protocols are sanctioned by the Amazon Conservation Association, the Animal Care Committee of Washington University in St. Louis, and the Ministry of Agriculture and Forestry in Perú.

Noninvasive Sample Collecting

Some of the least studied mammals in the Amazon rainforest are unknown to us because of their cryptic nature. One does not get to track them or habituate them as easily as one can with most primates, for example. For them, we have to get clever. Our goal is to develop molecular tools to assist with population monitoring along with our partners, but to do so, we need to establish reliable ways of sampling from a single individual in the wild. Today, we can test for armadillos or tayras in general, but we cannot easily say how many of each exactly are present in an environment. This requires a single DNA sample, from a single animal, reliably collected and analysed before degradation in tropical environments.

Enter the hair snare – a simple, low-cost device that animals rub against, painlessly depositing a few hairs, after which the device will seal off the sample to keep it separate from the next such animal. By placement of “smart” snares at varying heights, accompanied with differing scent-lures, we will explore how to collect from cryptic animals such as tayras, capybaras, peccary, armidillos, etc. Our list is intentionally broad, because this has never been attempted on a large-scale before in the region. Who will come by? Only time and the inventiveness of this team will tell!

Smart Trap Technology

Broad-scale animal monitoring for wildlife health or biomonitoring is often restricted because safe animal handling standards require the frequent checking of trap lines. Often, days go by with no success, and the manual effort expended on trap monitoring is extremely high. We are developing systems that we can attach to existing hardware that will make each trapping event quick and efficient. Each trap will alert scientists a distance away, allowing them to quickly and efficiently process animals, as they are captured. Traps will also receive modifications to hold animals for a short period of time and then release them (in the case of small rodents and marsupials), then sealing off the entrance to protect fecal and hair samples deposited noninvasively inside. This will allow us to expand the area covered each night, reduce stress on animals, improve screening efficiencies and achieve project goals in a safer and more consistent manner.

Program Goals

In 2022, we will be conducting 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. To this end, we will:

1. Utilize eDNA monitoring techniques from 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 in various programs on site.
4. Monitor hair-snares 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. 

In addition, our ongoing disease and health surveillance efforts will continue to focus on primates, bats, small to medium-sized terrestrial mammals, and birds. Our interest in blood, gastrointestinal, and ectoparasites continues as well, as baseline data acquired from prior seasons provide our best measures of ecological change. Hosting multiple concomitant parasite/pathogen infections is the norm for wildlife, so we are monitoring for statistically significant changes in prevalence, richness, or abundance of infections.

In 2021, a molecular laboratory was established at our field site in coordination with the In Situ Labs Initiative, a field-based biosurveillance collaboration led by FPI. As a result, samples no longer need to be sent away from the collection site for analysis. There are enormous advantages to this, some of which you can read about here. We are now able to rely more heavily on the use of genetic techniques for detection and classification of parasites and pathogens.

Genetic methods have emerged as the most efficient, reliable, and now cost effective way of screening samples, and providing training opportunities in molecular research, especially where infrastructure is lacking is a core part of FPI’s educational programs. In addition, bacterial pathogen and RNA virus discovery will be added to our surveillance efforts, which will be highly informative to wildlife biologists, conservationists, and human health professionals in the Amazon region and worldwide.

Finally, in 2021 we also incorporated ecotoxicology into the research program. In the Madre de Dios department of Peru, where the Los Amigos Conservation Hub is located, the extent of gold mining increased by almost ten times between 1993 and 2013. As a result, mercury (an element commonly used to extract gold) is accumulating in the environment and its human and wildlife inhabitants at an extraordinary rate. Mercury accumulation is associated with neurological and reproductive dysfunction, and is noted to induce lasting, sometimes generational, epigenetic changes, and the full extent of harm it may be causing to the Amazon remains elusive. We are now analyzing all noninvasive tissues collected for methylmercury content, and especially look forward to achieving the analysis in the field where data can be put to immediate use.

Training and Activities

• Field sampling for environmental DNA screening programs
• GPS navigation training for off-trail navigation
• Sample biobanking under field conditions
• Species identification using morphometrics
• Sample coordination during field anesthetizations of mid-sized mammals by veterinarians.
• Best practices for personal safety and wellbeing while conducting field work in forest systems
• Non-invasive sample collection
• Animal tracking and safe capture-release techniques
• Safe animal handling procedure focused on bats, small mammals, and birds, including a number of opportunities to participate directly in collection events
• Sample collection, handling, labeling, and storage protocols, including the use of sterile technique to prevent self-contamination and preserve specimen integrity
• Animal health data collection and data management
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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; we must 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

We take great pride in being able to provide high quality research and training experiences to a diverse student body. The following list is not exhaustive and is intended to give a sense of the backgrounds of participants that have found great value in this program.

• One Health professionals or trainees
• Veterinarians, pre-veterinary students, veterinary technicians
• Public health students and professionals
• Individuals interested in ecological research
• 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.

Remote Animal Censusing

The “Naturechip” is an all-in-one camera trap, RFID tag reader, and weigh scale. It will be deployed in several use cases, beginning with tracking the microchipped primates in the study population. Typically, the wildlife handling team spends several weeks manually monitoring up to 11 sites at once to record primate habituation to baited sites. By modifying the Naturechip we plan to automate this process into a system that will alert scientists at camp at the arrival of the groups to each site, the ID of the group, as well as record detailed images for later analysis. This will free up our team to expand to new sites and operate with a smaller footprint. But the potential for this device is virtually limitless – one or more of its components could be used in long-term monitoring sites globally. One of the goals of this research program is to investigate other use-cases.