Proyecto Primates Protocols Main Menu (para español presione aquí)

Version 2009-01-01

Welcome to the Proyecto Primates Protocol Site! In the following pages you will find detailed information on the different protocols that are being used for data collection, as well as protocols that are necessary for the management of the project and for collecting samples both in Yasuní National Park, Ecuador and in Formosa, Argentina. Anyone working in collaboration with Dr. Anthony Di Fiore and Dr. Eduardo Fernandez-Duque needs to read and follow these protocols. It is the information contained in the protocols that you are responsible for following, not the information passed on to you by other colleagues, students, assistants or even Dr. Di Fiore or Dr. Fernandez-Duque (since even we sometimes cannot remember everything that is included here). If you notice a discrepancy between something that we you and what is written here in the protocols, please bring that to our attention so that we can correct the protocols accordingly.

The protocols included here are divided into several different sections, not all of which need to be read by everyone on the project. For example, if you are not collecting phenological data or are not involved in processing captured animals, you need not read those particular protocols. However EVERYONE must read (and regularly REREAD) the basic information included following the Table below, as well as the PROJECT AND DATA MANAGEMENT protocols and the relevant BEHAVIORAL DATA and ECOLOGICAL DATA protocols for the project(s) you are affiliated with.

Position on Data Property and Signature Page Monogamous Primates Climatological Data Collection Darting and Capturing Fecal Samples for Hormone Extraction
Institutional Liability Release and Signature Page Ateline Primates Fruit Morphology Data Collection Processing Captured Animals Fecal Samples for DNA Extraction
Safety in the Forest Phenological Data Collection Urine Samples for Hormone Extraction
Flagging, Trail Maintenance, and Mapping Plant Voucher Specimens
Laboratory Maintenance and Equipment Care Plant Nutrient Samples
Data Management Salt Lick Camera and Video Camera Traps
Protocol and Database Change Log







A protocol consists of a detailed description of the methods used to collect data. The reality is that, no matter what anyone might say, no one can read a published scientific paper and precisely replicate the described methods, because the methods published in articles are not sufficiently detailed to allow that. But, everyone should be able to replicate the methods of a study by following the “protocol” used for the study. The use of protocols is common in laboratory settings, where it is important to have explicit instructions. For example, a protocol would indicate if you should centrifuge a reaction for 10 or 12 seconds. Although protocols do not appear to be used that often by field biologists, we are convinced that they are extraordinarily useful.

The secret to checking if a protocol is complete and ready to be followed is to “visualize” the entire data collection process: close your eyes, think about what you are going to do step by step, and make sure the protocol details that process precisely. For example, you are watching an animal and the alarm on your watch beeps: What do you see? What data you write down? In formulating a protocol, you need to be very explicit and leave little in doubt or ambiguous about what data an observer should be recording. Never think, “It’s obvious”! Instead, try to leave a minimum of things open to the interpretation of the observer.

In this project, you will be part of one of the first studies (we think THE first study!) where researchers are trying to collect truly comparable data on four different species of primates in two different countries with a set of unified protocols. The emphasis of our protocol is on the QUALITY of the data we aim to collect, not the quantity.


Our sampling procedure is designed so that all data can be collected by a single person. There is a lot of different kinds of data to collect, and we expect it to be collected, recorded, and entered into the computer in a very specific way, so you MUST reread all the protocols pertinent to your work once a month during the first week of the month to make sure you remember everything you need to be doing.

Our protocols have been designed to ensure that the collection of CERTAIN kinds of data is done in an exactly comparable manner for all primate species being studied both in Ecuador and Argentina. There is another set of data that are being collected so that they are totally comparable for the four monogamous species under investigation. Clearly, it is impossible to collect ALL kinds of data using comparable methods, given, for example, the nocturnal habits of owl monkeys and the intrinsic habitat differences between the Amazonian rainforest and the gallery forest of the Argentine Gran Chaco. Nonetheless, our aim is that certain kinds of data, and the analyses to be performed on these data, will be COMPLETELY comparable.

To accomplish this goal, is of paramount importance that the protocols take precedence over what other students, assistants, or even the senior researchers may say. You are responsible for reading the protocols and following them. You must not assume that what you are being told is correct!


There are a great number of different types of data that you will be recording in the field and/or laboratory. The data we are collecting is organized in a hierarchical or nested fashion. All “inner level” data pertain to corresponding higher levels, but not all “higher level” data have associated “inner level” data. In the table above, we have included all of the different protocols that you may need to become familiar depending on the specifics of your work. Regardless of the kind of data you will be collecting, however, there are three key types of data (and associated data record numbers) that are extremely important. These data are collected by everyone, and the relevant data record numbers need to be entered consistently everywhere. These numbers are OBSERVER SAMPLE NUMBERS, AVISTAJE NUMBERS and FOCAL SAMPLE NUMBERS. In Ecuador, the GROUP SCAN NUMBER is treated the same; we have not yet implemented group scans in Argentina. All of these numbers are entered directly on the PALM DATA RECORDERS if you are collecting data on a PDA. If you are collecting data on paper (which you should only be doing if your Palm Data Recorder is not working) you MUST write the OS, AV, and FS numbers in ALL PERTINENT PLACES in your DATA BOOKS (i.e., all observer data should have the OS number listed; avistaje data should have both the OS and AV numbers listed; and focal samples should have OS, AV, and FS numbers listed). Detailed instructions for each of these types of data follow below.




OBSERVER SAMPLES serve to organize almost all of the data being collected by each individual person on this project and also give us an idea of how observers are spending their time. This constitutes the highest level of organization of the main Proyecto Primates Database, and EVERY person affiliated with Proyecto Primates in Ecuador or Proyecto Mirikiná in Formsa must fill out an Observer Sample record for each day you are associated with the project. Ideally, we would like this data for everyone who works on the project for more than a few days (e.g., volunteers, SIT students) because this data can be used in grant applications (e.g., NSF) to QUANTIFY the Broader Impacts of our work in terms of training students, etc.

The use of OBSERVER SAMPLES to organize your data collection is simple and MANDATORY – these data MUST be collected each and every day, and there is no excuse for not doing it. The desktop and Palm databases have been organized so that this information must be included. Almost everything else present in these databases is pegged to a particular OBSERVER SAMPLE. OBSERVER SAMPLES are collected into the PP Observer Samples database on the Palm Data Recorder or into the Observer Samples section of your data book if collecting data on paper.

You will enter OBSERVER SAMPLES for every day you are associated with the project. This forms the “highest” level of organization of our data.
Every Observer Sample MUST have the following fields filled out when entered into the main Proyecto Primates Database:
Important Notes:

These data provide an overview of how various members of the project team are spending their time. These data are to be collected in the PP Obs Act Data Database on the Palm Data Recorder (or in the Observer Activity Data section of your Data Book if collecting data on paper) and entered into the Observer Activity Subform of the main Proyecto Primates Database. You should note when you begin and end various types of field and camp activities. The main aim in collecting this kind of data is so that we can see how long particular kinds of data collection activities take (e.g., phenological monitoring, mapping) and so that we can estimate the total number of OBSERVER HOURS spent in the forest. Note that we are asking for very general information on observer activities and have tried to make entering these data as simple as possible.

Important Notes:


The majority of the data you will collect in the field are organized around AVISTAJES (“sightings”) or encounters, either with your focal group of animals or with other groups or species. These data are to be collected in the PP Avistajes database on the Palm Data Recorder (or in the Avistajes section of your Data Book if collecting data on paper) and entered into the Avistajes Subform of the main Proyecto Primates Database.

You must collect AVISTAJE data EVERY TIME you encounter monkeys of any species, no matter whether you collect any other kind of data on them that day. This includes the animals you see while doing any field work activity. Every separate encounter you have within a given observer-day in the field constitutes a new AVISTAJE. For example, suppose you are with a group of sakis in the morning and you go back to camp for lunch (which should be rare!) or heavy rains force you to stop data collection. If you then return to the same group and do more sampling in the afternoon, the afternoon sampling session is considered a new AVISTAJE (since your original encounter “ended”) and the session should get a new number when the data are entered into the main Proyecto Primates Database.

How much data you will collect and the time spent in collecting AVISTAJE data will depend on the situation. For example, in Ecuador, if you are working on the "Monogamous Primate Project", AVISTAJE data should be collected as completely as possible for Pithecia, Aotus, and Callicebus. For other taxa, you must record at least the time and location of your encounter. Additional information may or may not be collected, depending on how it will interfere with your current activity.
For each Avistaje, ALL of the following fields MUST be filled in when entered into the main Proyecto Primates Database:
IMPORTANT NOTES: If you are entering data only on the Palm Data Recorder, it is especially important to review your Avistaje data immediately after you have transferred it to make sure you have entered EVERYTHING that needs to be entered (i.e., that none of the required fields are blank or contain odd pieces of information. Do not simply upload and forget about it! Do this BEFORE you delete the data from your Palm. Please be sure to follow in detail the protocol for How to Upload Data from the Palm.

For each AVISTAJE there will be a number of additional types of data you will be collecting, including Demography and Census Data, Ranging Data, Marked Trees Data , Feeding Bouts Data, Focal Samples Data, Group Scan Data, Juvenile Ad Libitum Data, and Other Ad Libitum Data. These are recorded in different databases on the Palm Data Recorder (or in separate places in your Data Book, if you are collecting data on paper). In the main Proyecto Primates Database, the Avistajes Subform has multiple Tabs that address each of the different kinds of data.

Demography and Census Data Tab

Ranging Data Tab

Throughout a follow, you will record the location of the group being observed every 20 minutes – on the hour and at 20 and 40 min past the hour – even if those points fall during a FOCAL SAMPLE or GROUP SCAN (see below). If you cannot take the position during a FOCAL SAMPLE or GROUP SCAN, try to remember where you were and take the position after the end of the sample or scan.

Some of the ranging data are recorded with the AVISTAJE for the group you are following since the AVISTAJE asks for the time and position where you first encounter monkeys and where you leave or lose them. The additional data on group locations recorded during a follow are collected in the PP Ranging Data database on the Palm Data Recorder or in the Ranging Data section of your Data Book if you are taking data on paper.

Positions should always be noted as distances and angles from reference points on the trails and transects or trees that have already been mapped. Whenever you can, it is better to take a position using a trail point rather than a tree as a reference point, but a nearby tree is better than a much further trail point.

If taking data on paper, all location data should be recorded in your Data Book in the form of “Distance, Compass Angle, Reference Point”. Do NOT record location data in any other way! Use the codes “m” for meters and “d” for degrees without inserting spaces after the commas. Example: “09:20 20m,250d,AV-05-021”.

You should practice estimating distances as you walk on the trails, which are marked at regular intervals. Count your paces for 25 meters and then use that to guide your distance estimates. You will get pretty good at estimating distances of up to 40 or 50 meters using your paces! From time to time, bring out the laser range finder and check yourself!

For each ranging point that you record, you must also record a Ranging Data Comment, qualitatively classifying each ranging data point as one of the following:
We cannot stress enough how absolutely critical the accurate and systematic collection of the ranging data is for this project. You should not be missing more than a few ranging points in any given full day follow. Be especially conscientious of writing down the CORRECT tree number if you use a tree as a mapping point. It is very easy to accidentally invert two digits or to assume you know the tree number without looking at the metal tag, but this causes a lot of problems if you are wrong, because such errors are VERY HARD to correct post hoc. If you are far away from a reference point or simply cannot stop to take the ranging data, and especially you are in a seldom used part of the group’s range or far away from trails, the ranging data are especially important. In this case, you may need to put up a temporary flag with the date and time and find your way back to that spot on a different day to map it. When you do this, be sure to go back and enter it IN THE CORRECT PLACE on the Palm Data Recorder or write it in the APPROPRIATE PLACE in your Data Book. Please do this sparingly, however, and REMOVE the temporary flagging once you go back to map the point.

Ranging data should be entered as follows:
REMEMBER, the goal is to automate the assignment of actual X and Y coordinates to your ranging points... we cannot look up the X and Y values for a reference point that does not exist in the database (or that cannot be found), thus the above conventions are ESSENTIAL to successfully search the database for reference point location.

Note that you can also use a GPS point as a reference point. To do so, enter “GPS ” plus a two digit code for the particular GPS used (e.g., “MM” for Mike Montague, “YS” for Yukiko Shimooka), plus the name or time you assign to the point on the GPS (e.g., “GPS MM SS0007" or "GPS YS1 11:54"). If you do this, however, you MUST be sure to download your GPS data properly and append it to the ‘GPS Points All’ table in the main Proyecto Primates Database and be sure to fill out the remaining fields in that table appropriately.  This means noting some measure of the precision of the GPS point (either the DOP or the average error) and whether the point was taken with 2D or 3D navigation.

Additionally, you will use the 0, 20, and 40 minute ranging data points to keep an informal running record of weather conditions, which we can use to examine the relationship between weather variables and particular behaviors such as army ant foraging by saki monkeys. There are two different weather variables to record at the 20 minute point: Light/Rain conditions and Wind conditions. Light/Rain should be classified on a scale representing the degree of cloud cover and rain: “Rain”, “Drizzle”, “Cloudy”, “Partly Cloudy”, “Slightly Cloudy”, “Full Sun” and “Mostly Cloudy” for daytime observations, “Clear Night”, “Moon Visible”, “Moon Partially Visible”, “Moon Not Visible” and “Dark” for nighttime observations. Wind condition is classified on a 3-point scale: “No Wind”, “Slight Breeze”, and “Windy”.

In Ecuador, for some projects, you will also use the ranging data points to note down several other pieces of information: the Group Speed, the Group Spread, whether the group is associated with another primate species, and, if so, the distance between the closest members of the two taxa. You will also note the average Group Height in the canopy at which the animals you are following are seen and the average Canopy Height in the forest at that location. For both, height categories are given in 5m increments (e.g., 0 to 5m, 5 to 10m, etc.).

Marked Trees Tab

To continue gathering data on the diets and ecological strategies of the taxa we are studying, we mark and map the locations of feeding trees and we estimate the time spent in feeding patches of various species. Thus, each time you find your target taxon feeding in a food patch, you will mark the tree and record a number of pieces of data concerning the feeding source. These data are recorded in the PP Marked Trees database on the Palm Data Recorder or in the Marked Trees section of your Data Book if you are taking data on paper.

You only need to mark only patches fed in by a group or individual monkey for more than five “group-feeding” minutes (i.e., “major” food sources: those fed in by a single animal for 5 minutes, or by several animals for a total of 5 “monkey minutes” over the course of the day). You should train your ears to listen for the sound of falling fruits and you should get in the habit of looking at your watch when you first hear fruits dropping in order to accurately assess whether or not to mark a patch.

You will mark with plastic tape all those trees used for foraging as described above plus trees that you know the animals sleep in (sakis, titis, and owl monkeys all reuse at least several sleeping trees). Mark sleeping and feeding trees (or the trunk supporting the feeding source in the case of epiphytes, hemiepiphytes, lianas, vines, or bromeliads) in the following way.
To mark the tree, write the tree number on PINK FLAGGING TAPE (please ONLY use pink!) and tie the tape around the tree, preferably UNDER (rather than around) any lianas hanging down or attached to the trunk. You should also write the date (in “mmm yy” format) and the initials “PP” for “Proyecto Primates” on the tape, and you should write on the tape “Sleep” if the tree is a sleeping tree or the Life Form of the feeding source if the tree is a feeding tree. Finally, you should write the tree number on a metal “write-on” or engravable tag that you then put on the tree with an aluminum nail. Go over the engraving with a black sharpie marker to make the number stand out at a distance. Do not hammer the nail all the way in; you should leave about an inch or so of shaft exposed on the nail to allow the tree to grow without swallowing the tag.

Note that if you are marking a liana or other epiphytic plant that spans several trees, you need only tag the trunk that supports the bulk of the liana. In Ecuador, every new life form marked on a given trunk should be tagged as a different number. For example, say one day the titi monkeys eat fruit from a tree that you tag as “CD-05-104” and then they eat, a few days later, from a liana in the same tree crown, the liana should get a NEW TAG NUMBER. Similarly, if multiple species eat from the same life form, you should put up a tag and tape for each species. Thus, a given tree may be marked with 2 or more metal tags and pink flags. If you do record a new number for a previously marked tree, enter all the other tags separated by slashes (and with a slash at the end) in the “AKA” section of the marked tree table in the database. Also note in this section any numbers on the metal tags from other projects (e.g., "FT" tree numbers from Abigail Derby's work on howler monkeys; the numbers from Mark Mulligan and collaborators' HERB projects).

The following data about each tree must be also noted on the PP Marked Trees database on Palm Data Recorder or in the Marked Trees section of your Data Book if you collect data on paper.
Some additional useful definitions for tree measurements, even if not prompted to enter them in the databases:

Feeding Bouts Tab

Additionally, for each marked tree – and for feeding sources that you are unable to mark – you will record feeding bout data in the PP Feeding Bouts database on the Palm Data Recorder (or in the Feeding Bouts section of your Data Book if collecting data on paper) for all bouts greater than five “monkey minutes”. You need not worry about recording bout data for bouts lasting less than five minutes.

For each feeding bout, note the time (to the nearest minute) at which the first feeder(s) entered the tree and began feeding (e.g., if recording data on paper, you would note “10:45 BE AV-05-001” for “Begin Eat AV-05-001 at 10:45”) and when the last feeder(s) finished feeding (e.g., “11:15 EE AV-05-001” for “End Eat AV-05-001 at 11:15”).

If you are following some animals and arrive at a food patch where animals are already feeding, score your arrival time as “BE Late” (“begin eat late”) or check the box “Late?” on the Palm Data Recorder. If you need to leave a tree before the last feeders have left (e.g., if your focal animal leaves the feeding patch while others are still eating), record the ending time as “EE Early” (“end eat early”) or check the box “Early?” on the Palm Data Recorder. If you miss a BE or EE time, score it as “Not Recorded”, but please be aware that this is a code of last resort, introduced to deal with when observers forgot to collect data that they were supposed to collect.

With the BE and EE times, we can calculate a minimum number of minutes that the group spent feeding in a particular patch. If the animals stop feeding in a patch for more than five minutes, and they return to the same tree, record another set of BE and EE times.

If the animals are feeding but you do not know from which tree you may record it as PA-05-XXX, meaning the monkeys are having a feeding bout but you cannot be sure on which tree, therefore you cannot mark it. Also, record the maximum number of individuals that you see feeding in the patch simultaneously (e.g., using the Max Feeders field popup menu on the Palm Data Recorder). For certain portions of the "Ateline Primate Project", you will also keep a running tally of the number of feeders in the tree each minute; to do this, use the Feeding Rec button on the Palm Data Recorder or note these data in the Feeding Bouts section of your Data Book.

If the food item is one that you do not recognize or that you have not collected previously, MAKE A COLLECTION of both the leaves and the fruit of the plant (note 
what collections you have made in the PP Marked Trees database on the Palm Data Recorder or in the Marked Trees section of your Data Book and in the main Proyecto Primates Database; you will enter specific information on the collection in the Plant Collections section of the main database later). It is important to do these collections to allow us to identify the plants being eaten. To make collections, look carefully at the tree through binoculars to get a good idea of the appearance of the leaves and fruits and then look for these on the ground under the tree. Carry plastic bags with you at all times to shove these collections into until you get back to the lab. In Argentina, if you cannot identify the species, write down in the last page of the Avistaje yellow book the information on the tree so that the Botanist David Iriart can identify the tree when he goes to Formosa. In Ecuador, when you return to the lab with your collection, process the samples according to the Plant Voucher Specimens protocol.

Finally, if the Feeding Bout is not in a marked tree, you should enter location data for the bout in the same format we use for all location data (XXm,Xxdeg,Loc Pto Ref).

Focal Samples Tabs and Focal Data

Behavioral data collected during focal samples are collected into different Palm Data Recorder databases, depending on the project you are associated with.  For the "Monogamous Primates Project", these include the databases PP Mono Foc Samples and PP Mono Focal Data.  For the "Ateline Primates Project", these inclue the databases PP Atel Foc Samples, PP Atel Focal Data, PP Juv Foc Samples, and PP Juv Focal Data .  If you are collecting data on paper, these data would go in the Focal Data section of your Data Book if collecting data on paper. Detailed information on how to collect these data is included in other protocols. Here, we simply note some key points regarding how data must be entered.

When completing FOCAL SAMPLES:
When completing FOCAL DATA:
Group Scan Tab

The priority for data collection is to collect focal samples. However, this is not always possible as often the animals are difficult to see or (especially for the monogamous primate project) disappear into the tops of trees for stretches of time. In order to have a better idea of how the animals are spending their time, we started, in Ecuador in summer 2007, to implement GROUP SCANS every 10 minutes (i.e., at 0, 10, 20, 30, 40, and 50 minutes past the hour) AT TIMES WHEN YOU ARE NOT IN THE MIDST OF A FOCAL. Again, the PRIORITY is focal samples, but at any 10 minute point during the day when you cannot, for some reason, do a focal, you should be doing a group scan.
For the "Monogamous Primates Project", we have discontinued this practice as of December 2008.

Behavioral data collected during groups scans are collected into the PP Mono Group Scans or PP Atel Group Scans databases on the Palm Data Recorder (depending on which project you are affiliated with) or are noted in the Group Scans section of your Data Book if collecting data on paper.

For the group scan procedure, you should look at each visible member of the group, count off 5 seconds in your head, and record its predominant behavior(s) (using the codes in the relevant ethogram), nearest neighbor(s), and distance(s) to its nearest neighbor(s) (record data for all nearest neighbors if more than one are present in the nearest neighbor category). When recording NN data during group scans, for any individual who has an INFANT in contact record NN data for BOTH THE INFANT AND THE NEXT NEAREST NEIGHBER. Thus, for a female carrying an infant whose next nearest neighbor is an adult male 5 to 10 meters away, you would note for NN: INF/AM/ and for NN Dist: CON/5-10m/. You should also check the appropriate checkbox indicating whether or not a scanned animal is carrying an infant.

Juvenile (Nursing and Feeding) Ad Lib Data and Other Ad Lib Data Tabs

In these tabs you will enter data pertaining to observations that may have happened outside of FOCAL SAMPLES or GROUP SCANS or that were not amenable to the systematic data collection. JUVENILE NURSING AD LIB and JUVENILE FEEDING AD LIB DATA are collected as part of the "Ateline Primates Project", while OTHER AD LIB DATA are collected for all projects. The data are collected into the PP Ad Lib, PP Nursing Bouts, and PP Juv Forage Bouts databases on the Palm Data Recorder or in the Ad Lib Data section of your Data Book if collecting data on paper.


This subform, accessed from the OBSERVER SAMPLES form, is used to enter data on PHENOLOGICAL PATTERNS in the forest (see the Phenological Data Collection protocol). These data are collected in the PP Phenology database on the Palm Data Recorders.


This subform, accessed from the 
OBSERVER SAMPLES form, is used to enter MAPPING DATA for trails and transects around the site (see the Flagging, Trail Maintenance, and Mapping protocol). These data are collected in the PP Mapping database on the Palm Data Recorders.


This subform, accessed from the 
OBSERVER SAMPLES form, is used to enter data on any BIOLOGICAL SAMPLES you collect (see the protocols for Plant Voucher Specimens, Plant Nutrient Samples, Fecal Samples for DNA Extraction, Fecal Samples for Hormone Extraction, and Urine Samples for Hormone Extraction). These data are collected into the PP Biol Samples database on the Palm Data Recorders.


This subform, accessed from the 
OBSERVER SAMPLES form, is used to enter data on darted and captured individuals (see the protocols for Darting and Capturing and for Processing Captured Animals). These data are collected into the PP Capt Measurements and PP Capture Data databases on the Palm Data Recorders.