DOI: 10.5061/dryad.0000000bz
title: Exploring the use of the South African Nest Record Scheme to detect changes in phenology: A case study using four well represented species

description: Phenological changes are one of the most well recognised responses of
 organisms to climate change. The ability to detect phenological change
 often relies on long-term datasets, which are scarce in the global south.
 As the adaptive capacity of species is highly variable, it is important to
 improve our understanding of how species in southern hemisphere systems
 may be responding to climate change through shifts in their annual cycles.
 Citizen science projects, like bird Nest Record Schemes, offer valuable
 long-term data, although data quality can pose challenges, affecting their
 use in research. We investigated the suitability of the South African Nest
 Record Scheme for estimating lay dates and preliminary exploration of
 phenological shifts in four well-represented species. Firstly, this study
 explored the composition of nest records for each species, specifically
 the proportion of single- to multi-visit cards. Secondly, we explored the
 accuracy of single-visit cards in estimating lay dates compared to highly
 accurate multi-visit cards. Lastly, we compared analytical approaches to
 test for possible shifts in lay dates. For all species, a high proportion
 of records consisted of single-visits, however, our analysis suggested
 that both single- and multi-visit records mostly produced similar lay date
 estimates. This indicates that both single- and multi-visit records could
 be used for estimations of lay dates. Various analytical approaches were
 used to test whether different combinations of single- and multi-visit
 records exhibited the same trends. The different models showed a high
 degree of consistency in shifts of lay dates over time. However, a mixed
 model approach using all records, with card identity as a random term, was
 the most efficient and sensitive to assess shifts in lay dates. This study
 highlights the usefulness of the South African Nest Record Scheme in being
 able to detect phenological shifts in a region which is understudied in
 this regard.
description: We selected 6146 unique record cards from the period 1950-1999
 for four common bird species (two passerines and two columbids) from the
 SANRS, with the most digitally available records at the time of this
 study. Details of the data and the sample sizes per species are summarised
 in Table 1. Nest record data were checked row by row for accuracy. Most
 records gave only a place name and region, so we assigned co-ordinates to
 each record using Google Earth and Google Maps search engines. Locations
 were assigned to the nearest plausible central point given the available
 information on each card. Records were excluded if they contained
 ambiguous information (missing dates, unclear type of breeding activity,
 unknown location) or were thought to be a repeat card of a previous nest
 record. For each species we calculated the start, peak and length of the
 egg-laying period for both single-visit and multi-visit records using the
 estimated lay dates. The start of egg-laying was defined as the 5th
 percentile of the distribution of all lay dates of a species, the peak of
 egg-laying as the median, and the length of egg-laying as the number of
 days between the 5th and 95th percentiles. We also calculated the
 proportion of multi-visit cards for each species. All statistical analyses
 were completed in R version 4.2.2.
description: # Exploring the use of the South African Nest Record Scheme to detect
 changes in phenology: A case study using four well represented species
 Dataset DOI: [10.5061/dryad.0000000bz](10.5061/dryad.0000000bz) ##
 Description of the data and file structure The dataset contains
 information from the South African Nest Record Scheme for four bird
 species. Each row represents an observation from a record card, where
 cards have multiple visits/observations the card number (cardno) is the
 same. The data is in a CSV format. Each species has its own CSV file. The
 Metadata file will explain each variable/column of the data. This data is
 part of a greater database, and certain filtering has been applied. This
 dataset represents only records from South Africa during the years
 1950-1999. ## Variable definitions | Variable | Description | Variable
 Types | Units | Source | | :------------------ |
 :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | :------------- | :-------------- | :---------------------------------------------- | | cardno | A unique identifier for each record card. The first three numbers reflect the species number according to Roberts' Birds of Southern Africa 7th Edition and the following numbers indicate the individual card number. | ID | | | | scientific family | Family-level taxonomy according to Roberts' Birds of Southern Africa 7th Edition | categorical | | Roberts' Birds of Southern Africa 7th Edition | | scientific name | Species scientific taxonomy according to Roberts' Birds of Southern Africa 7th Edition | categorical | | Roberts' Birds of Southern Africa 7th Edition | | species name | Species common name according to Roberts' Birds of Southern Africa 7th Edition | categorical | | Roberts' Birds of Southern Africa 7th Edition | | year | The year of the associated data collection for a card | | yyyy | | | date | The full date of the associated date collection for a card | date | dd/mm/yyyy | | | day | The day of the associated data collection for a card | | dd  | | | month | The month of the associated data collection for a card | | mm  | | | stage | B= birds seen building nest or partaking in copulation behaviour; Sitting= bird seen sitting on the nest but unable to count eggs or chicks; INC = bird seen incubating, eggs present;INC\Y = bird seen on nest, eggs and chicks present; Y= bird seen at nest, young present | categorical | | | | eggs | The number of eggs in the nest | discrete | | | | young | The number of young present at the nest | discrete | | | | hatch date | The exact date of the first egg to hatch if/when available from observer notes | date | dd/mm/yyyy | | | lay date | The exact date of the first egg laid in the nest if/when available from observer notes | date | dd/mm/yyyy | | | egg.i | The average number of days between egg laying according to Roberts | discrete | | | | inc.p | The average number of days for incubation according to Roberts | discrete | | | | nest.p | The average number of days after hatching before young fledge according to Roberts | discrete | | | | locality | The nearest identifiable and traceable location to which the data was collected. Information presented here is based on data submitted by the observers, with some corrections where old locality assignments have been updated.  | categorical | | | | town | The nearest town to which the data was collected | categorical | | | | province | The province in which the data was collected | categorical | | | | country | The country in which the data was collected | categorical | | | | latitude | The latitude of where the data was collected | continuous | decimal degrees | | | longitude | The longitude of where the data was collected | continuous | decimal degrees | | ## Code/Software All analyses were conducted in R Studio using R Version 4.4.0. The script details the packages used and the detailed methods for analyses.  ## Empty cells There may be empty cells in the columns 'eggs', 'young', 'hatch date', and 'lay date'. For the first two columns, empty cells indicate that the nest was recorded as having only eggs or only young on that visit, not both, and so if the 'eggs' column contains a number then the cell for 'young' will be empty and vice versa.  If the 'stage' column has the code 'Sitting' then both 'eggs' and 'young' will be empty as the exact number of eggs or young was not determined on that visit.  For 'hatch date' and 'lay date', not all next records have visits from the exact day of first egg lay or first egg hatch. Therefore this is only present when the observer of the card was present on the exact lay date or hatch day and specifies as such.