CS-PHOC: weekly census counts of Southern Ocean phocids at Cape Shirreff, Livingston Island

Study Extent

This dataset describes the census counts of four Southern Ocean phocids (crabeater, leopard, southern elephant, and Weddell seals) at Cape Shirreff, Livingston Island (62.47° S, 60.77° W), beginning in 1997 and running through the time of publication.

Sampling

This dataset consists of census counts of four Southern Ocean phocids during the austral summer at Cape Shirreff, Livingston Island, from 1997 through the time of publication. Counts were performed by trained INACH or U.S. AMLR field biologists following a standardized sampling protocol. Count data were grouped and aggregated to provide a single, comparable count for each species for each census. Methods are further described in Woodman et al. (2024).

Quality Control

All event records were also reviewed and confirmed using the field notebook scans. All count records were screened for unreasonable values or duplicate entries via R code, either programmatically or visually through plots of the data. Duplicates were removed, and other data flagged by automated checks were validated using paper datasheets or scans of a technician’s field notebooks. Count records were also checked for consistency with regards to blank versus zero entries, ensuring that patterns in the data (i.e., when a particular count column should be NA vs zero) were consistent. Program directors were consulted about all observed patterns, as well as survey scope and techniques over the full timeseries. 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 scientificNameID. Event date and time were verified to be compliant with ISO 8601 standard.

Method steps

1. All data were collected at Cape Shirreff (62.47° S, 60.77° W) on the north shore of Livingston Island. Bounded by glaciers to the south, Cape Shirreff is approximately 3 km long and 1.5 km wide. The Cape Shirreff Phocid Census (CS-PHOC) surveys were conducted by INACH from 1997/98 to 2006/07. The U.S. AMLR Pinniped Research Program resumed these surveys in 2009/10, and, except for 2020/21 when the field season was canceled due to the COVID-19 pandemic, has performed them every season through the time of publication. Most CS-PHOC surveys were completed within one day, but occasionally spanned two or three days due to extenuating circumstances (e.g., weather).
2. The INACH and U.S. AMLR programs both followed the same overall census protocol, where trained field technicians surveyed all safely accessible regions of Cape Shirreff and recorded all live phocids. They collected counts of each species, as well as age class and sex when possible. While the full extent of the area surveyed varied slightly across and within seasons, core census locations were always surveyed. These core census locations span the vast majority of the coastline and phocid haul-out locations at Cape Shirreff, thereby ensuring that CS-PHOC counts are representative of phocid haul-out at Cape Shirreff during each census window. Locations were surveyed on foot, either by walking through haul-out locations, or using binoculars from a high vantage point when practical. Counts were recorded in field notebooks. After the census, data were either entered into a database or otherwise archived.
3. Entered data varied slightly across programs. Specifically, data from INACH surveys included explicit zero records when there were none of a particular phocid species at a location, while U.S. AMLR records did not include explicit zero records. After consultation with the U.S. AMLR program directors, explicit records with zeroes or missing codes as appropriate, were added to the U.S. AMLR data for core census locations for this dataset.
4. Data records were compiled from historical documents, field notebooks, Excel files, and a SQL Server database. INACH historical data (i.e., paper records, reports, Excel files) were consolidated into Excel files. These INACH files, along with historical U.S. AMLR Excel files, were imported into the U.S. AMLR Pinniped SQL Server database using R (R Core Team 2023). Once in the database, all data were read into R, where they were cleaned and standardized as follows. Location names and count types (i.e., age class and sex) were converted to standard names, and columns containing count data were aggregated to the lowest resolution across datasets. For instance, some seasons male and female pup counts were recorded separately, but during others only a single pup count was recorded. For this dataset, all pup counts were aggregated to a single, total pup count for each census record.
5. After cleaning, records were grouped and aggregated to provide a single, comparable count for each species for each census. Specifically, records were filtered for core census locations, and counts were summed after grouping by census and pinniped species. These core census location count values, along with counts for one other regularly-surveyed location, make up the published CS-PHOC dataset.

All phocids were identified to species level

1. Lobodon carcinophaga
   common name: Crabeater seal rank: species
2. Mirounga leonina
   common name: Southern elephant seal rank: species
3. Hydrurga leptonyx
   common name: Leopard seal rank: species
4. Leptonychotes weddellii
   common name: Weddell seal rank: species

Cape Shirreff, Livingston Island