Antarctic Penguin Biogeography Project: Database of abundance and distribution for the Adélie, chinstrap, gentoo, emperor, macaroni, and king penguin south of 60 S

Christian Che-Castaldo1, Grant Humphries2, Heather Lynch1, Anton Van de Putte3

1 Stony Brook University, , United States; 2 Black Bawks Data Science, ; 3 , Belgium

Corresponding author(s): Christian Che-Castaldo (christian.che-castaldo@stonybrook.edu)Grant Humphries (grwhumphries@blackbawks.net)Heather Lynch (heather.lynch@stonybrook.edu), Anton Van de Putte (avandeputte@naturalsciences.be)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

Che-Castaldo C, Humphries G, Lynch H (2023): Antarctic Penguin Biogeography Project: Database of abundance and distribution for the Adélie, chinstrap, gentoo, emperor, macaroni, and king penguin south of 60 S. v1.2. Test Organization #1. Dataset/Samplingevent. https://ipt.gbif.org/resource?r=mapppd&v=1.2

Abstract

The Antarctic Penguin Biogeography Project is an effort to collate all known information about the distribution and abundance of Antarctic penguins through time and to make such data available to the scientific and management community. The core data product involves a series of structured tables with information on known breeding sites and surveys conducted at those sites from the earliest days of Antarctic exploration through to the present. This database, which is continuously updated as new information becomes available, provides a unified and comprehensive repository of information on Antarctic penguin biogeography that contributes to a growing suite of applications of value to the Antarctic community. One such application is the Mapping Application for Antarctic Penguins and Projected Dynamics (MAPPPD; www.penguinmap.com) - a browser-based search and visualization tool designed primarily for policymakers and other non-specialists (Humphries et al., 2017), and ‘mapppdr’, an R package developed to assist the Antarctic science community. The Antarctic Penguin Biogeography Project has been funded by the National Aeronautics and Space Administration (NASA), the Pew Fellowship for Marine Conservation, and the Institute for Advanced Computational Sciences at Stony Brook University.
Antarctic Penguin Biogeography Project: Database of abundance and distribution for the Adélie, chinstrap, gentoo, emperor, macaroni, and king penguin south of 60 S is an occurrence and sampling event type dataset published by SCAR-AntBIOS
This dataset contains records of Pygoscelis adeliae, Pygoscelis antarctica, Pygoscelis papua, Eudyptes chrysolophus, Aptenodytes patagonicus, and Aptenodytes forsteri annual nest, adult, and/or chick counts conducted during field expeditions or collected using remote sensing imagery, that were subsequently gathered by the Antarctic Penguin Biogeography Project from published and unpublished sources, at all known Antarctic penguin breeding colonies south of 60 S from 1892-11-01 to 2022-02-12.
The data is published as a standardized Darwin Core Archive and includes an event core and occurrence and eMoF extensions. 
This dataset is published by SCAR-AntOBIS under the license CC-BY 4.0. Please follow the guidelines from the SCAR and IPY Data Policies (https://www.scar.org/excom-meetings/xxxi-scar-delegates-2010-buenos-aires-argentina/4563-scar-xxxi-ip04b-scar-data-policy/file/) when using the data. If you have any questions regarding this dataset, please contact us via the contact information provided in the metadata or via data-biodiversity-aq@naturalsciences.be. Issues with dataset can be reported at https://github.com/biodiversity-aq/data-publication/
This dataset is part of the Antarctic Penguin Biogeography Project project funded by National Aeronautics and Space Administration (NASA), the Pew Fellowship for Marine Conservation, and the Institute for Advanced Computational Sciences at Stony Brook University.

Keywords: Samplingevent, OCEAN, SOUTHERN OCEAN, ANTARCTICA, BIRDS, PENGUINS, POPULATION ABUNDANCE, BIOGEOGRAPHY

General description

Purpose: To provide open access penguin population census data to the general public.

Project details

Project title: Antarctic Penguin Biogeography Project
Personnel: Christian Che-Castaldo, Heather Lynch, Grant Humphries
Funding: This project was initially funded by NASA Award NNX14AC32G under the NASA Ecosystem Forecasting program. Continued funding for database expansion and updating provided by NASA Award 80NSSC21K1027 under the Biodiversity program, a 2022 Pew Fellowship for Marine Conservation, and the Institute for Advanced Computational Science at Stony Brook University.

Data published through GBIF: https://ipt.gbif.org/resource?r=mapppd

Spatial coverage

General spatial coverage: Penguin breeding colonies located at or very near sea level distributed around the Antarctic continent and along the Antarctic Peninsula as well as on outlying islands in the Southern Ocean.
Coordinates: 77°42'36''S and 60°32'60''S Latitude; 157°41'60''W and 171°10'12''E Longitude 

Temporal coverage: November 1, 1892 - February 12, 2022

Methods

Method step description: 
- . 	Data contained within the core database include information collated from peer reviewed scientific manuscripts, expedition reports and other public data outside the scientific literature, management and policy documents, and private communications. These data contain information on breeding pairs of penguins only, and does not contain information on non-breeding distributions or sightings-at-sea. The fundamental unit of this database is the breeding “site”, which represents a population breeding on a single island or, in some cases, a discrete area of a larger landmass. In some cases, a geographically distributed population may be divided into multiple “sites” depending on the logistics of ground surveys, where each “site” can be accessed from a single landing location along the coastline. Rarely, several smaller nesting areas will be aggregated into a single “site” following historical precedent. Each site is associated with a unique four digit alphanumeric code, a name, and a specific geographic location. Note that several species may inhabit a single “site”. Data are ingested into the database manually and extensively checked against existing maps and records to ensure consistency. Because of the complexity of the geography and the different naming systems, site names may be changed between a published record and the database.
- . 	The database includes data on the number of nests (equivalently, breeding pairs), the number of chicks, or the number of total adults. If multiple measures are available (a count of nests and also a count of chicks), the database will include all data points as separate entries. Each data point is associated with information on the survey date, the survey method, an estimate of the accuracy of each data point, and a reference. In this database, we follow the five-point scale initially used by Croxall and Kirkwood (1979) and described in detail in Supplementary Materials 
1 to Che-Castaldo et al. (2017). If the original data source followed the Croxall and Kirkwood scale or reported an uncertainty that could be translated into that scale, our database includes that precision value. Where no information on uncertainty is provided, we estimate the precision based on information provided in the original account.
- . 	Some data are not eligible to be included in this database. Data that are collected at a spatial scale other than the “site” cannot be included. All data must be “site-wide” census estimates. In keeping with our commitment to open-source data, data that are not in the public domain or remain in private collections unavailable to the public are also not included in this database. Data that cannot be verified and/or cannot be unambiguously assigned to a “site” are not included. Data on the presence of breeding pairs absent a population estimate are included only when no survey data exist.
- . 	While traditional methods of surveying penguin colonies rely on the direct enumeration of penguin nests by ground-based researchers, more recent surveys have relied on various remote sensing methods. Remotely-piloted aircraft systems (RPAS; also known as drones, quadcopters, or unmanned aerial vehicles) take photographs from a low-altitude flight over the colony and yield photographs sufficient for the individual enumeration of nests, chicks, or adults. While the precision of such counts depends on the timing of the survey and the quality of the imagery, RPAS are capable of providing exceptionally precise counts and are often in the high accuracy category of N1. Satellite imagery can identify the areal extent of breeding colonies through the spectral properties of penguin guano and these estimates can be used to estimate the number of breeding pairs at a “site”. Because the precision of such estimates remains an active research question, all such estimates are assigned the lowest accuracy category of N5 (broadly defined as “order-of-magnitude”).
- . 	In some cases, data from a single location in a given year is published in multiple venues. However, it is difficult to know whether these multiple outlets represent one actual sampling event because the same event may be associated with different occurrence or abundance records between sources, either because earlier mistakes were corrected or because data were re-analyzed. It also can happen that a single site is surveyed multiple times by separate parties on the same day, arriving at different counts due to observation error. Our approach is to classify an event as a survey conducted at a specific site and time, using a specific sampling protocol, and reported in a specific publication (peer-reviewed article, policy document, thesis, or other type of report), dataset, or personal communication. From each event, there can be one or more occurrence or measurement records, depending on the number of species or life stages reported. In cases where we have information that data from a unique sampling event is published in multiple venues, we retain all records reported in publications and datasets, and drop duplicate records if the duplicate event is based on personal communication. We allow this potential duplication because 1) it is not clear which source is ultimately correct if counts differ between sources and 2) withholding records creates confusion with our end-users as to whether we have overlooked sources of data.
Study extent description: This dataset describes the abundance and distribution of six species of Antarctic breeding penguins (Adélie, gentoo, chinstrap, emperor, macaroni, king) at all sites south of 60 S. Data include all known historical data starting in 1979 and additional records as available prior to 1979.
Sampling description: This database includes all known records of penguin breeding abundance and distribution south of 60 S. Data sources include peer reviewed scientific manuscripts, expedition reports and other public datasets outside the scientific literature, management and policy documents, and private communications. Abundance estimates are derived primarily from direct ground counting, imagery collected by remotely-piloted aircraft systems, and satellite imagery. Additional data types include counts from aerial, ground, or vessel-based photographs.
Quality control description: - All records were validated.
- Coordinates were verified and plotted on map to verify the actual geographical location corresponds to its locality.
- All scientific names were checked for typo and matched to the species information backbone of Worlds Register of Marine Species (http://marinespecies.org/) and LSID were assigned to each taxa as scientificName.
- Event date and time were converted into ISO 8601 and verified with the field reports.

Datasets

Dataset description
Object name: Darwin Core Archive Antarctic Penguin Biogeography Project: Database of abundance and distribution for the Adélie, chinstrap, gentoo, emperor, macaroni, and king penguin south of 60 S
Character encoding: UTF-8
Format name: Darwin Core Archive format
Format version: 1.0
Distribution: https://ipt.gbif.org/archive.do?r=mapppd
Publication date of data: 2023-01-09
Language: English
Licences of use: Creative Commons Attribution (CC-BY) 4.0 License

Metadata language: English
Date of metadata creation: 2022-11-23
Hierarchy level: Dataset

References
Che-Castaldo, C., S. Jenouvrier, C. Youngflesh, K.T. Shoemaker, G. Humphries, P. McDowall, L. Landrum, M.M. Holland, Y. Li, R. Ji, and H.J. Lynch, “Pan-Antarctic analysis aggregating spatial estimates of Adélie penguin abundance reveals robust dynamics despite stochastic noise,” Nature Communications 8:832 (2017). https://doi.org/10.1038/s41467-017-00890-0
Croxall, J.P., and E. D. Kirkwood. The distribution of penguins on the Antarctic Peninsula and islands of the Scotia Sea. Cambridge: British Antarctic Survey, 1979.
Humphries, G., R. Naveen, M. Schwaller, C. Che-Castaldo, P. McDowall, M. Schrimpf, and H.J. Lynch, “Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD): Data and tools for dynamic management and decision support,” Polar Record 53, 2 (2017): 160–166. https://doi.org/10.1017/S0032247417000055.