DOI: 10.5061/dryad.wh70rxwp9
title: Exploring the mechanisms of coordinated chick provisioning in the Manx shearwater (Puffinus puffinus)

description: Many species that provide care for their offspring in tandem with a
 partner coordinate their activities to maximise the efficiency of their
 investment. However, it is not well known exactly how this coordination is
 achieved. Manx shearwaters Puffinus puffinus are Procellariiform seabirds
 that exhibit a dual foraging strategy during chick provisioning in which
 long foraging trips to maintain condition are alternated with short,
 frequent trips to feed the offspring. This strategy is employed in a
 coordinated manner between the parents, with one making short trips while
 the other takes a single long trip. Previous work revealed that a
 complementary switch in foraging trip type is initiated by the parents
 following a synchronous visit to the nest. We used a combination of
 observational data and an experimental manipulation to examine the
 mechanisms that may underlie this behaviour. Specifically, we investigated
 the evidence that physical reunion is necessary to induce a switch in trip
 type, whether parents change their behaviour to maximise the probability
 of partner encounter, and whether indirect cues gained from the chick
 could inform a switch in behaviour. In our experimental approach, we
 manipulated the information adults had available to them by
 supplementarily feeding chicks to alter their begging behaviour. We found
 no support for the role of physical reunion or indirect cues in the
 coordination of care in this species. We discuss the possibility that the
 patterns of alternated provisioning observed during chick rearing in Manx
 shearwaters may emerge through entrainment during the well-coordinated
 incubation period preceding chick provisioning.
description: Overview This folder contains codes and data
 to reproduce both the main and supplementary results of the paper,
 published in the Journal of Avian Biology (2021). DOI:
 10.1111/jav.02881 There are 2 folders: "Data"
 and "Scripts". As this is a large and multi-year dataset that
 may be currently used by other members of the project or collaborators, we
 would appreciate if you could contact Natasha Gillies
 (gilliesne@gmail.com) if you would like to make use of the dataset. This
 will reduce duplication of effort, and ensure that we can give you any
 additional information that may be useful for analysis or
 interpretation. Data These are the
 datasets used in the analysis. In folder
 'Shapefiles', 8 shapefiles are given for the islands making up
 the possible rafting area of Manx shearwaters for which we had GPS. These
 data are used to analyse the location of rafting events for Supplementary
 Materials S3.  - MASH_exptMetadata.xlsx: meta data
 relating to the supplementary feeding experiment, where each row
 corresponds to one fed chick. The columns are:<br>     - nest -
 factor encoding nest identity;<br>     - time_in - time the chick
 was taken to lab for feeding;<br>     - mass_in - mass of chick
 prior to feeding;<br>     - mass_out - mass of chick following
 feeding;<br>     - time_out - time the chick was returned to the
 nest;<br>     - date - date of feeding;<br>     - feed_size -
 calculated feed size (mass_out - mass_in);<br>     - handling_time -
 calculated handling time (time_out - time_in). -
 MASH_fullDataset.csv: data, with each row corresponding to an RFID
 detection on a given night. This should be loaded into the **preamble.r**
 code for processing and then analysed in 'data-analysis.r'. The
 columns are: <br>     - burID - factor encoding nest
 identity;<br>     - date - date of recording;<br>     - ring -
 factor encoding individual identity;<br>     - loopID - factor for
 processing steps giving unique identity to a nest and night;<br>    
 - firstdet - date-time of first detection of individual on a given
 night;<br>     - lastdet - date-time of last detection of individual
 on a given night;<br>     - visitDur - duration (minutes) of
 parent's visit to nest (lastdet-firstdet);<br>     - prevVisit
 - time of departure for previous visit to nest;<br>     - pev_days -
 time (days) since previous visit;<br>     - chick_mass - mass (g) of
 chick taken during the day of the visit;<br>     - Sex - factor
 representing parent sex: "F" (female) or "M"
 (male);<br>     - incarcerated - factor for analysis of
 incarceration experiment (Supplementary Materials) giving ring of
 incarcerated parent;<br>     - group - factor representing which
 experiment the nest was involved with: 'control' (no
 manipulation), 'feeding_suc' (successful feeding),
 'feeding_fail' (unsuccesful feeding), 'inc_suc'
 (successful incarceration), 'inc_fail' (unsuccessful
 incarceration);<br>     - burrow - factor representing nest
 identity;<br>     - age - number of days since chick
 hatched;<br>     - year - either 2018 or 2019;<br>     -
 colSync - factor representing whether parents visited colony on same night
 ('YES') or not ('NO');<br>     - burSync -
 factor representing whether parents visited nest at same time
 ('YES') or not ('NO');<br>     - timebetween -
 time (minutes) between arrival of parents if they visited the colony on
 the same night - negative value indicates time spent at nest
 together;<br>     - ringYr - ID variable indicating individual
 identity and year;<br>     - tripLength - duration of foraging trip
 following departure from nest (hours);<br>     - trip_diff -
 difference in trip duration between trip following nest departure and trip
 preceding nest arrival (hours);<br>     - tripDays - tripLength
 converted to nearest day;<br>     - days_diff - difference in trip
 duration converted to nearest day;<br>     - abstrip - absolute
 value of hourly difference in trip duration (i.e. trip_diff);<br>  
   - absdays - absolute value of daily difference in trip duration (i.e.
 days_diff);<br>     - PREVtriptype - factor representing trip
 category ('short' or 'long') of trip preceding nest
 arrival;<br>     - NEXTtriptype - factor representing trip category
 ('short' or 'long') of trip following nest
 departure.  - MASH_gpsData.csv: GPS data to use in
 Supplementary Materials S3. The columns are:<br>     - date_time -
 date-time variable representing time of GPS fix;<br>     - longitude
 - longitude;<br>     - latitude - latitude;<br>     -
 dist_next - distance (km) to next GPS point;<br>     - calc_speed -
 speed (km/h);<br>     - ring - factor encoding individual
 identity;<br>     - burrow - factor encoding nest
 identity; <br>     - ID - factor encoding identity of
 trip;<br>     - ringID - factor encoding combined ring and year
 identity;<br>     - colony - factor encoding colony location, either
 'cp' (Copeland) or 'sk' (Skomer);<br>     -
 home_lat - latitude of colony;<br>     - home_lon - longitude of
 colony;<br>     - dist_home - distance to colony (km);<br>    
 - med_distance - medium distance from colony for trip;<br>     - TA
 - turning angle;<br>     - raft - factor encoding individual rafting
 events;<br>     - behaviour - factor encoding 'raft'
 versus 'fly' behaviour.  Scripts
 Before running any of the data analysis codes, the script
 preamble.r will process the dataset into relevant objects and subsets for
 analysis. Here are the main scripts in R to reproduce
 the results in the paper.  - data-analysis.r Code to
 run the models outlined in the paper, run a power analysis for our
 experiment, and produce all figures displayed in the paper with the
 exception of the schematic in Figure 2. -
 functions.r This script contains custom functions used in the analysis or
 when producing figures - power-analysis.r This script
 runs a power analysis for the experiment described in Supplementary
 Materials S1 -
 Supplementary-Materials_data-analysis.r Code to run the analyses and
 produce the results outlined in the Supplementary Materials