An automated barcode tracking system for behavioural studies in birds

Abstract

121. Recent advances in technology allow researchers to automate the measurement of animal 13 behaviour. These methods have multiple advantages over direct observations and manual data 14 input as they reduce bias related to human perception and fatigue, and deliver more extensive 15 and complete data sets that enhance statistical power. One major challenge that automation 16 can overcome is the observation of many individuals at once, enabling whole-group or whole-17 population tracking. 18 2. We provide a detailed description for implementing an automated system for tracking birds. Our 19 system uses printed, machine-readable codes mounted on backpacks. This simple, yet robust, 20 tagging system can be used simultaneously on multiple individuals to provide data on bird 21 identity, position and directionality. Further, because our codes and backpacks are printed on 22 paper, they are very lightweight. 23 3. We describe the implementation of this automated system on two flocks of zebra finches. We 24 test different camera options, and describe their advantages and disadvantages. We show that 25 our method is reliable, relatively easy to implement and monitor, and with proper handling, has 26 proved to be safe for the birds over long periods of time. Further, we highlight how using single-27 . CC-BY-NC-ND 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/201590 doi: bioRxiv preprint first posted online Oct. 11, 2017; board computers to control the frequency and duration of image capture makes this system 28 affordable, flexible, and adaptable to a range of study systems. 29 4. The ability to automate the measurement of individual positions has the potential to 30 significantly increase the power of both observational and experimental studies. The system can 31 capture both detailed interactions (using video recordings) and repeated observations (e.g. once 32per second for the entire day) of individuals over long timescales (months or potentially years). 33This approach opens the door to tracking life-long relationships among individuals, while also 34 capturing fine-scale differences in behaviour. 35 36 Introduction 37

Feeder density enhances house finch disease transmission in experimental epidemics

“…Because our RFID approach detected only the time spent sitting on feeders and did not determine what birds were doing while at perches, sickness behaviours of index birds may have obscured any such differences in direct physical contact with feeder surfaces. Recent developments in tracking technology for captive birds now allow much more detailed data to be collected across entire aviaries [35]. These advances will allow capture of much finer detail on behavioural shifts associated with changing infection state.…”

Experimental disturbances reveal group-level costs of social instability

“…As outlined above, we predicted that disturbance events would lead colonies to become less efficient at depleting the food patch. Using fine-scale simultaneous tracking of all colony members [28], we then quantified changes in group-level social behaviours during foraging to identify mechanisms that could be responsible for a reduction in foraging efficiency. If social instability disrupts the social relationships among individuals (i.e.…”

Animal culture research should include avian nest construction

“…Thus, their social learning coupled with their proven tractability as a study system, together also positions zebra finches as a powerful model to investigate cultural processes associated with nest construction, and animal material technology in general. That two of the cutting-edge tracking tools [ 33 , 38 ], detailed above, were streamlined in zebra finches ( figure 2 a ), strengthens this suggestion, as does the documented flexibility to study the nest-construction behaviour of zebra finches in both laboratory and field conditions (recent empirical examples: [ 27 , 43 , 44 , 46 – 51 ]; figure 2 c ).…”

“…Cutting-edge backpack tracking tags (non-invasive harnesses mounted with unique, camera-detectable and software-readable barcodes that encode bird identity, position, and direction; figure 2 a ) should facilitate such social network mapping of the birds in the observer group in this make-believe scenario [ 32 – 34 ]; their dominance hierarchies might be mapped, for instance, using agonistic interactions—e.g. dyadic displacement data—extracted from barcodes detected at a filmed feeding period prior to nest construction ( sensu [ 33 ]; figure 2 a ). Thus, the data generated from the first imagined experiment could reveal nest-building birds' capacity for, and candidate social processes involved in, animal material culture.…”