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Exploring the mechanisms of coordinated chick provisioning in the Manx shearwater (Puffinus puffinus)

Citation

Gillies, Natasha et al. (2021), Exploring the mechanisms of coordinated chick provisioning in the Manx shearwater (Puffinus puffinus), Dryad, Dataset, https://doi.org/10.5061/dryad.wh70rxwp9

Abstract

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.

Usage Notes

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:
    - nest - factor encoding nest identity;
    - time_in - time the chick was taken to lab for feeding;
    - mass_in - mass of chick prior to feeding;
    - mass_out - mass of chick following feeding;
    - time_out - time the chick was returned to the nest;
    - date - date of feeding;
    - feed_size - calculated feed size (mass_out - mass_in);
    - 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: 
    - burID - factor encoding nest identity;
    - date - date of recording;
    - ring - factor encoding individual identity;
    - loopID - factor for processing steps giving unique identity to a nest and night;
    - firstdet - date-time of first detection of individual on a given night;
    - lastdet - date-time of last detection of individual on a given night;
    - visitDur - duration (minutes) of parent's visit to nest (lastdet-firstdet);
    - prevVisit - time of departure for previous visit to nest;
    - pev_days - time (days) since previous visit;
    - chick_mass - mass (g) of chick taken during the day of the visit;
    - Sex - factor representing parent sex: "F" (female) or "M" (male);
    - incarcerated - factor for analysis of incarceration experiment (Supplementary Materials) giving ring of incarcerated parent;
    - 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);
    - burrow - factor representing nest identity;
    - age - number of days since chick hatched;
    - year - either 2018 or 2019;
    - colSync - factor representing whether parents visited colony on same night ('YES') or not ('NO');
    - burSync - factor representing whether parents visited nest at same time ('YES') or not ('NO');
    - timebetween - time (minutes) between arrival of parents if they visited the colony on the same night - negative value indicates time spent at nest together;
    - ringYr - ID variable indicating individual identity and year;
    - tripLength - duration of foraging trip following departure from nest (hours);
    - trip_diff - difference in trip duration between trip following nest departure and trip preceding nest arrival (hours);
    - tripDays - tripLength converted to nearest day;
    - days_diff - difference in trip duration converted to nearest day;
    - abstrip - absolute value of hourly difference in trip duration (i.e. trip_diff);
    - absdays - absolute value of daily difference in trip duration (i.e. days_diff);
    - PREVtriptype - factor representing trip category ('short' or 'long') of trip preceding nest arrival;
    - 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:
    - date_time - date-time variable representing time of GPS fix;
    - longitude - longitude;
    - latitude - latitude;
    - dist_next - distance (km) to next GPS point;
    - calc_speed - speed (km/h);
    - ring - factor encoding individual identity;
    - burrow - factor encoding nest identity; 
    - ID - factor encoding identity of trip;
    - ringID - factor encoding combined ring and year identity;
    - colony - factor encoding colony location, either 'cp' (Copeland) or 'sk' (Skomer);
    - home_lat - latitude of colony;
    - home_lon - longitude of colony;
    - dist_home - distance to colony (km);
    - med_distance - medium distance from colony for trip;
    - TA - turning angle;
    - raft - factor encoding individual rafting events;
    - 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

Funding

Biotechnology and Biological Sciences Research Council, Award: BB/M011224/1