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.