DOI: 10.5061/dryad.kh1893277
title: Resource allocation underlies parental decision-making during incubation in the Manx shearwater

description: Examining resource allocation is fundamental to understanding the
 relationships between a species’ behaviour and its life history.
 Furthermore, for biparentally-caring animals, examining the relative
 investment decisions made by members of a breeding pair can give insight
 into the extent and nature of cooperative care. As a key measure of
 resource availability, examining body mass changes can help elucidate the
 ways in which parents balance their allocation. In birds, these trade-offs
 become particularly stark during incubation, as maintaining constant egg
 warming usually requires one parent to fast. This period therefore
 represents a key opportunity to investigate investment decisions. We took
 daily measurements of body mass from breeding Manx shearwaters, a
 biparentally-caring seabird, during incubation, and related this to
 measures of nest attendance and behaviour collected using field
 observations and miniaturised biologgers. We investigated how changes in
 body mass related to the decisions made at the nest and at sea, whether
 this differed between the sexes, and whether pair experience influenced
 incubation behaviour. We found that while body mass predicted the
 probability that incubating birds would choose to temporarily desert the
 nest, incubation shift duration was ultimately set by return of the
 foraging bird. The trip durations of foraging birds in turn were primarily
 dictated by their body mass reserves on departure from the nest. However,
 foragers appeared to account for the condition of the incubating partner,
 returning from sea earlier when their partner was in poor condition. Our
 results contribute to understanding the mechanisms by which individuals
 regulate both their own and their partner's incubation behaviour,
 with implications for interacting with fine-scale resource availability.
  
description: This repository contains codes and data to
 reproduce both the main and supplementary results of the paper, published
 in Ornithology (2022). There are 2 folders: "Data_inputs" 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. Scripts <strong>1_MASH-incubation_main-analysis.R</strong> This script contains all the code necessary to reproduce the main results and figures presented in the manuscript. <strong>2_MASH-incubation_functions.R</strong> This script contains additional functions to run the analyses in script 1. Data inputs There are 6 datasets used in the analysis. <strong>MASH2015-2019_daily-active-nests.csv</strong> Contains the number of active nests per day and year, and is used to define the simulated changeovers for the randomisation analysis. The columns are: <em>date</em> Date where active nests recorded <em>nburrows</em> Number of active nests <em>year</em> Year of recording <strong>MASH2015-2019_daily-foraging-data.csv</strong> Summarised activity for birds across individual foraging trips. The columns are: <em>ring</em> Individual ring identity of bird <em>stintID</em> Unique identity of individual stint <em>sex</em> Female (F) or male (M) <em>burrow</em> Identity of nest <em>start_mass</em> Mass (g) at beginning of foraging trip <em>year</em> Year of recording <em>end_mass</em> Mass (g) at end of foraging trip <em>foragetrip</em> Duration (days) of foraging trip <em>forageGain</em> Mass (g) gained across duration of foraging trip <em>neglect</em> Whether the trip followed neglect (YES) or not (NO) <em>prop_rest</em> Proportion of foraging trip spent resting <em>prop_flight</em> Proportion of foraging trip spent in flight <em>prop_forage</em> Proportion of foraging trip spent foraging <em>phase</em> What phase of the trip the bird was in, commuting (commute) or foraging (forage) <strong>MASH2015-2019_daily-mass-change.csv</strong> Contains daily mass changes for all birds for which mass data were collected. The columns are: <em>year</em> Year data was collected <em>ring</em> Individual identity of bird <em>sex</em> Female (F) or male (M) <em>stintID</em> Denotes unique identity of stint (within bird) <em>DSL</em> ‘Days Since Laying’, indicates time since egg was laid <em>stintday</em> Day of stint <em>mass_chg</em> Difference in mass (g) from previous day <em>mass_chgPer</em> Difference in mass (g) from previous day as a percentage of body mass <em>exp</em> Pair experience, unknown (UNKNOWN), newly formed (NEW) or experienced (EXP) <strong>MASH2015-2019_forage-data-by-trip.csv</strong> Contains summarised data from individual foraging trips. The columns are: <em>burrow</em> Individual identity of nest <em>year</em> Year data were collected <em>stintID</em> Denotes unique identity of stint (within bird) <em>ring</em> Individual identity of bird <em>sex</em> Female (F) or male (M) <em>start_mass</em> Mass of bird (g) at beginning of foraging trip <em>DSL</em> ‘Days Since Laying’, indicates time since egg was laid <em>foragetrip</em> Duration of foraging trip (days) <em>partnerincoming</em> Mass of returning partner (g) upon departure on foraging trip <em>exp</em> Pair experience, unknown (UNKNOWN), newly formed (NEW) or experienced (EXP) <strong>MASH2015-2019_incub-data-by-shift.csv</strong> Contains summarised data from individual incubation shifts. The columns are: <em>burrow</em> Individual identity of nest <em>year</em> Year data were collected <em>stintID</em> Denotes unique identity of stint (within bird) <em>start_date</em> Date that the incubation shift began <em>ring</em> Individual identity of bird <em>sex</em> Female (F) or male (M) <em>start_mass</em> Mass of bird (g) at beginning of foraging trip <em>burrowID</em> Denotes identity of nest within a given year <em>stintlength</em> Duration of incubation shift (days) <em>DSL</em> ‘Days Since Laying’, indicates time since egg was laid <em>end_mass</em> Mass of bird (g) at end of incubation shift <em>endsInNeglect</em> Whether bird neglected egg at end of stint (YES) or not (NO) <em>followsNeglect</em> Whether incubation shift commenced following neglect (YES) or not (NO) <em>exp</em> Pair experience, unknown (UNKNOWN), newly formed (NEW) or experienced (EXP) <em>whoFirst</em> Factor denoting whether the female (F) or male (M) took the first incubation shift. If the first incubation shift was not recorded for that nest, recorded as ‘nostart’ <strong>MASH2015-2019_nest-data.csv</strong> Contains summarised data for entire incubation attempts for each nest used in the study. The columns are: <em>year</em> Year the data were collected <em>burrow</em> Denotes individual identity of nest <em>outcome</em> Whether the incubation attempt was successful (HATCHED) or not (FAILED) <em>incDur</em> Total duration (days) from egg laying to egg hatching (or failure) <em>count.F</em> Number of incubation shifts taken by the female <em>count.M</em> Number of incubation shifts taken by the male <em>NO.BIRD</em> Number of days neither parent was recorded at the nest <em>femper</em> Proportion of incubation days taken by female <em>malper</em> Proportion of incubation days taken by male <em>exp</em> Pair experience, unknown (UNKNOWN), newly formed (NEW) or experienced (EXP) <em>julian</em> Lay date recorded as Julian date <em>whoFirst</em> Factor denoting whether the female (F) or male (M) took the first incubation shift. If the first incubation shift was not recorded for that nest, recorded as ‘nostart’