Twelve thousand recent limpets (Mollusca, Patellogastropoda) from a northeastern Pacific latitudinal gradient

Provided here is an image and 2D shape library of 12,035 Recent patellogastropod limpet (Mollusca, Patellogastropoda) shells collected from the northeastern Pacific along a latitudinal gradient ranging from Alaska to Baja, California. 2D outline coordinate data and morphometric measurements were generated using macroscopic high-throughput imaging methods (AutoMorph: https://github.com/HullLab/AutoMorph) developed in P.M. Hull’s lab at Yale University.

This dataset is composed of patellogastropoda from 1,256 University of California Museum of Paleontology (UCMP) sample lots (metadata.tar.gz: Table 1). These lots represent multi-species assemblages collected from 353 unique localities along the western coast of North America (metadata.tar.gz: Table 2), ranging from Cape Yakataga, Alaska, United States (60°06’11N) to Cabo San Lucas, Baja California, Mexico (22°89’56N).

Images and morphometric data are provided in 7 datasets:

1) boxed_full_images.zip: 1,256 full-lot (overview) images with boxed object identified by the segment module.

2) zstacks.zip: image stacks for each of the 1,256 sample lots processed by segment. These image stacks may potentially be used to generate individual 3D height maps.

3) 2d_edfs_labeled.zip: 12,035 individual extended-depth-of-focus (EDF) images produced by focus. A list of the individuals represented is provided in TableS1 in metadata.zip.

4) 2d_outlines.zip: 12,035 EDF images with 2D outline overlays for quality control.

5) 2d_coordinates.zip: 1,256 .csv files of the outline shape coordinates for all lots successfully processed with AutoMorph, including one file (all_coordinates_limpets.csv) with the coordinates for all 12,035 individuals extracted.

6) master_2d_measurements.csv: UCMP locality numbers, UCMP lot numbers, locality coordinates, object identification numbers output by AutoMorph, and morphometric data for all 12,035 individuals. Each individual has associated full-lot, individual EDF, 2D and outline images, as well as outline shape coordinates, all of which may be found in the .zip files listed above. Object identification numbers, which are used to link morphometric measurements with associated images, can be found in the column ‘object IDs’. Morphometric data provided includes major axis length, minor axis length, perimeter length, eccentricity, and rugosity, as well as aspect ratio and the height and width of the aspect rectangle. Locality coordinates are rounded to the nearest 0.1 degree to account for potential measurement uncertainty.

7) metadata.zip: A directory containing 5 tables in corresponding .xslx files. Table 1 provides UCMP specimen and locality numbers, site names, rounded coordinates, and the number of individuals per UCMP lot. Table 2 provides the number of species per site, with locality numbers and species names also provided. Table 3 provides information on the species’ range minima and maxima observed in the present dataset, as well as the number of individuals per species. Table 4 provides a comparison of hand measurements and AutoMorph outputs for 41 specimens, used for measurement validation. Table 5 provides locality information mismatches for three UCMP specimen lots. Table S1 provides a list of all objects included in the dataset, including an indication of which objects have known locality coordinates.

The dataset provided accompanies the manuscript “Twelve thousand Recent limpets (Mollusca, Patellogastropoda) from a northeastern Pacific latitudinal gradient” submitted to Scientific Data. This manuscript describes methods of data collection and contains important usage notes, and should thus be consulted before attempting to use the data provided here.

This work was funded by the American Chemical Society PRF Grant #55837-DNI8 and by support from Yale University.