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Mammal Research Team

Understanding the diversity, distribution, population dynamics, and optimal conservation strategies for forest-dwelling mammals in Amazonian Peru

Our neotropical mammal research in Peru, featuring our Lead Mammal Research Coordinator, Nadine Holmes. Video credit: Foggy Lens Productions

Mammal Team Objectives

The Mammal Research Team, headquartered in the city of Puerto Maldonado, is tasked with developing baseline datasets on the diversity and abundance of 45 species of non-volant mammals at numerous field sites across the Madre de Dios region of Amazonian Peru, and to monitor changes in these variables over timescales ranging from months to decades. By undertaking sampling throughout the year, in dry and wet seasons; across various habitat types, including floodplain and terra firme forest; and in contrasting land-use categories, such as reserves and national parks, native community forests, ecotourism concessions, Brazil nut forests, timber extraction zones, bushmeat extraction areas, and forests associated with agriculture and cattle ranching; and also by collating climate data at each study site, the team is able to determine the relative importance of each variable, understand the patterns and trends in diversity and abundance in time and space, and ultimately predict the current and future conservation status of mammals across the entire landscape.

Lowland Tapir seen by Fauna Forever Mammal Team

Lowland tapir (Tapirus terrestris) crossing a river

Photo: Tom Ambrose

Mammals - Patrick Collins checking track

Mammal team coordinator - Patrick Collins - identifying tracks. Photo: Patrick Collins

Common Paca Tracks seen during Fauna Forever Mammal Survey

Measuring the stride length of Common paca (Cuniculus paca) tracks. Photo: Chris Kirkby.

Methods Used

The sampling methods that the team uses to study mammal populations, and which are led by one or two mammal team coordinators, include unbounded line transects, camera traps, track traps, GPS-enabled species encounters mapping, and to a limited degree pitfall traplines for small rodents. The latter method (pitfall traps) is achieved in collaboration with the herpetofauna team. Each field site has 4-8 line transects (totalling 8-24 km in length) which are sampled in the early morning, late afternoon, and at night; 10-20 camera traps operating 24 hrs a day; 8-16 pitfall traps (site-dependent and managed by the Herpetofauna team); 15-30 track traps (site and season dependent); and the team is also equipped with 2-3 handheld GPS receivers to collect precise geographic coordinate data of mammal encounters and the location of key feeding trees in the case of focal primate group follows. Each week, sampling is undertaken on 4-6 mornings depending on weather conditions, alternating between line transects and primate follows, and similarly on 3-5 afternoons or evenings. Morning sampling begins at or just after dawn (5:30-6 am); afternoon sampling begins at 3:30 pm once the air temperature has dropped and diurnal mammal species activity levels increase; and the evening or nocturnal sampling begins at 8 pm. Sampling periods last anywhere between 3-5 hours depending on the method. While conducting an unbounded line transect, the team uses all their senses (visual, acoustic, smell) to locate and identify the presence of terrestrial and arboreal mammals on either side of the transect. Close scrutiny of the ground is also required in order to observe tracks, scats and other species-specific sign. When track traps are located on a transect, a couple of minutes are spent inspecting these too. All encounter and presence data is recorded in relation to its distance along a transect and frequently involves the use of a GPS. Straight-line and perpendicular distances between observers and animals are carefully measured to the nearest metre and recorded in the datasheets. When undertaking primate group follows, the team employs both continuous sampling (specifically of the geographic location of the primate group) as well as scan sampling, the latter of which is undertaken at 10-minute intervals to record the behaviour of each individual in the primate group. The continuous GPS data is used to map primate group home range size and shape, using GIS software. When a primate group begins feeding in a tree (on fruit or flowers), the team also records the location of this tree and takes fruit and flower samples back to camp to aid its identification. Understanding the diversity of food sources is important when planning primate conservation programs. Dung samples from primates and other mammal species may also be collected. Data analysis and visualisation programs that we use include R, SPSS, Distance, Mark, Estimates, and QGIS.

Summary of a Typical Day on the Mammal Team

Research days are split into a mixture of morning, afternoon, and nocturnal sampling sessions. On each research day, two sessions are usually completed, totalling 6-7 hrs of active field time and data input activities. On most mornings, sampling begins at or just after dawn (5:30-6 am), having already eaten a very early breakfast. Box breakfasts are also taken if the team is expected to take more than 1 hour to get to sample location. Line transect sampling and primate follows take between 3-5 hours. Upon completion, the team may check pitfall traps for rodents (alongside herpetofauna team members) and/or change out memory cards and batteries on one or more camera traps before heading back to the research station. On returning to camp, data from the session is entered into the laptop computers and the team shares and discusses any interesting encounters or behaviours observed in order to better understand the ecology of the species involved. Lunch is served at 1 pm, after which team members relax for a couple of hours during the hottest part of the day. At 3:30 pm, the late afternoon sampling session begins, lasting until sundown at 6 pm. This session may consist of line transects and track traps, downloading imagery from camera traps and/or relocating these, habitat monitoring within 0.05-ha modified Gentry plots. At some sites, afternoon sessions are also used to clean and mark transects, especially during the first few days of a visit to a new field site. The evening or nocturnal sessions, which are focused on line transect sampling, begin either at 6 pm or 8 pm and last last 2-3 hours, with team members using headlamps, powerful spotlights, and sometimes even sound recording equipment to sample nocturnal mammals as they move through the rainforest in total darkness. Daily schedules are subject to change at the discretion of the team coordinators and depending on current projects and weather. 

Field Course Internship

This option is for those people interested in learning or improving research techniques and related field skills for studying terrestrial and arboreal mammals in tropical habitats. We offer Beginner, Intermediate, Advanced and Master-level course segments in line transect sampling, camera trapping, track traps, species identification (especially via auditory cues, tracks, scats and other sign) and datasheet and database management methods. Each course segment is expected to take approximately 2 weeks for interns to complete, however this is not a set expectation as we understand individuals learn certain skills at different speeds. Progression to the next stage of the course will be at the discretion of the team's head research coordinator. Participants who successfully complete the full course (or the three most advanced segments), with an aptitude for bird research techniques will be considered for opportunities to join our Skilled Research Internship program or be considered for an Assistant Research Coordinator position.

1. Beginner Course Segment - Neotropical Non-volant Mammals

Duration: 2 weeks

Description: Participants will learn the basics of (i) how to set up and sample bounded and un-bounded line transects, and the theory behind distance sampling in general; (ii) how to set up and manage a camera trap array; (iii) how to set up and manage an array of track traps for both wet and dry season conditions; (iv) how to set up and manage pitfall trap lines for small rodents, including safe handling techniques and the morphological data to collect (e.g. weight); (v) techniques and resources for identifying mammal species, including vocalisations, smells, tracks, scats and other sign; (vi) efficient management of datasheets and digital databases; (vii) the basics of the main data analysis techniques used to assess mammal diversity, density and community structure; and (viii) the theory and practice behind the habitat variables that we collect in and around each line transect and other sampling stations (i.e. modified Gentry plots). Time spent on theoretical themes (60%) and time spent in the forest actively learning (40%).

Mouse Opossum see during Fauna Forever mammal transect

Mouse opossum observed on a nocturnal transect. 

Photo: Alex Markham

Squirrel Monkey seen during Fauna Forever Primate Survey

A Bolivian squirrel monkey (Saimiri boliviensis) having a scratch

Photo: Alex Markham

2. Intermediate Course Segment - Neotropical Non-volant Mammals

Duration: 2 weeks

Description: Participants will learn (i) to more accurately identify mammal species while in the forest, with a large emphasis on acoustic cues and tracks; (ii) to begin collecting accurate perpendicular distance and straight line observer-animal distances during encounters with mammals along line transects; (iii) to set up their own camera traps, download imagery and video, and identify animals with a degree of accuracy of at least 50%; (iv) to efficiently set up a pitfall trap line that uses four large 70-litre buckets and 30 metres of durable plastic fencing, and how to safely extract and properly hold rodents (while using gloves); (v) to record some of the morphological characteristics of captured rodents; (vi) to set up a wet season and dry season track trap, and effectively monitor it and identify species with at least 30% accuracy; (vii) to use handheld GPS equipment and use it to follow a focal primate group; (viii) to recognise the different primate behavioural traits that we monitor, such as grooming, aggression, alarm, feeding and so forth; (ix) to recognise the main tree species that primates and other mammal species relly on, especially palms and figs; (x) to enter data from each method into laptop computers, under close supervision, including data review techniques to catch errors and to increase the quality of the dataset; and (xi) to practise setting up vegetation plots and collecting habitat variable data, including techniques to analyse this information. Time spent on theoretical themes (40%) and time spent in the forest actively learning and practising skills (60%).

Fruit found during a Fauna Forever Primate Survey

A mature Mayna fruit commonly eaten by primates. Photo: Chris Kirkby

Fauna Forever Coordinator conducitng a primate survey in the Amazon

Mammal team coordinator - Holly O'Donnell - carefully searching for primates along a line transect in the forest. Photo: Holly O'Donnell

3. Advanced Course Segment - Neotropical Non-volant Mammals

Duration: 2 weeks

Description: Participants will learn (i) to more accurately identify mammal species while in the forest, with a large emphasis on acoustic cues, tracks, scats, smells, hair, foraging scrapings, and scratches on tree trunks; (ii) to manage all aspects of bounded and un-bounded line transect surveys; (iii) to manage all aspects of camera trap-based studies, including identifying species with 90% accuracy, and professionally using digital databases (e.g. CameraBase) for automatic analysis of collected imagery; (iv) to safely handle all rodent species captured in pitfall trap lines and to record all of the morphological characteristics of captured rodents and how best to analyse this data; (v) to manage all aspects of track trap surveys for all seasons and soil characteristics, and to identify tracks with an accuracy of at least 75%; (vi) to use all options available on handheld GPS equipment to follow focal primate groups through the forest in a safe and professional manner, with supervision; (vii) to recognise the different primate behavioural traits that we monitor with 90% accuracy, and to identify individual animals (especially alpha males) with ease; (viii) to recognise the 30 or so main tree species that primates and other mammal species relly on; (ix) to enter data from each method into laptop computers, under close supervision, including data review techniques to catch errors and to increase the quality of the dataset; (x) to analyse transect data using the Distance software to estimate species dansity and community structure; and (xi) to manage the collection of habitat data in modified Gentry plots, including more techniques to analyse this information. Time spent on theoretical themes (20%) and time spent in the forest actively learning and practising skills (80%).

Saddleback Tamarins seen during a Fauna Forever primate survey

A pair of Saddleback tamarins (Saguinus fuscicollis) scanning the foliage for insect prey. Photo: Jason Kopp

A mouse opossum found during Fauna Forever mammal surveys

A mouse opossum about to be released back into the forest. Photo: Holly O'Donnell

4. Master Course Segment - Neotropical Non-volant Mammals

Duration: 2 weeks

Description: Participants will improve all aspects of the knowledge and skills taught in earlier courses (see above) reaching a high degree of professionalism allowing them the ability to independently undertake all tasks related to the mammal research protocols with only very little supervision from our mammal team coordinators (with supervision focused only on health and safety, species identification, and data entry and checking processes). This course will also include a formal evaluation of theoretical knowledge and practical skills towards the end of the segment. Thus, participants who successfully complete this course will possess the skills necessary to be able to establish and develop their own mammal population monitoring projects in a variety of environments around the world. 

Nine-banded Armadillo found during a Fauna Forever mammal survey

A friendly Nine-banded armadillo (Dasypus novemcinctus).

Mammal interns collecting data during a Fauna Forever mammal survey

Two thesis project interns from the UK studying mammal tracks. Photo: Chris Kirkby

Thesis Project Internship

If you are a student looking to undertake an official thesis or dissertation project on Neotropical mammals in the Peruvian Amazon and would like to benefit from our expertise and know-how, this option we offer. You can find out more on the Thesis Project Internship page. We are able to offer support and advice to students regarding project design, implementation and data analysis, along with close supervision from our research coordinators. We have even identified some potential research questions that could be developed into thesis projects, although we are also open to ideas and questions from student applicants. Undergraduate level projects should ideally be planned to be undertaken over a minimum 6-week period. Any shorter and there is no guarantee, in our experience, that sufficient quality data would be collected. Our management team can also provide official supervision and reporting as may be required by colleges and universities. Due to the specific nature of each student's thesis project idea, final costs will be agreed following discussions with the Fauna Forever research team. ​​​

Camera Traps used during a Fauna Forever mammal survey

A camera trap - Bushnell Trophy Cam

Photo: Mas Mong Mo

Data collection during a Fauna Forever primate survey

Collecting mammal data during a line transect survey. Photo: Holly O'Donnell

© Jaguar image in header courtesy of Amanda Guercio

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