DOI: 10.5281/zenodo.15127876
title: Images and landmark data of Neotoma lower dentition for: Fox and Blois (2025). "A geometric morphometric approach to identifying recent and fossil woodrat molars with remarks on late Pleistocene Neotoma macrotis from Rancho La Brea".

description: Woodrats of the genus Neotoma are an important study system for ecological and paleoecological research. However, paleontological studies are often hindered by the difficulty of identifying woodrat remains to species. We address this limitation by using 2D landmark-based geometric morphometrics to classify 199 lower first molars (m1s) of five extant western North American Neotoma species (N. albigula, N. cinerea, N. fuscipes, N. lepida, and N. macrotis) collected throughout California. We then use discriminant analysis of principal components (DAPC) models to identify late Pleistocene fossils of unknown species from the Rancho La Brea Tar Pits in Los Angeles, CA. DAPC correctly identifies ~85-90% of extant individuals to species, with most misclassifications occurring between sister taxa N. fuscipes and N. macrotis. Most fossil m1s are classified as N. macrotis by DAPC, which may be the first confirmation of N. macrotis in the fossil record. We show that landmark-based geometric morphometric analyses are generally effective at differentiating m1s of extant Neotoma species in California and they are an auspicious method for unknown fossil identification. Further applications of this method across a broader range of geographic locations and species will better contextualize its utility.
description: This file contains images and landmark coordinates of Neotoma lower dentition analyzed in Fox and Blois (2025) “A geometric morphometric approach to identifying recent and fossil woodrat molars with remarks on late Pleistocene Neotoma macrotis from Rancho La Brea”. The file contains three subfolders: "All Images", "Recent CA Neotoma", and "Unknowns". Each subfolder, described further below, contains .jpg specimen images and .tps files of 2D landmark coordinate data. All .tps files were built and combined in TpsUtil 32 (Rohlf, 2018a) with coordinate data digitized in TpsDig 2.32 (Rohlf, 2018b). Please see the manuscript text for a description of analyzes performed. Input data, analytical code, and output data/figures can be found in the Software section below, and at: https://github.com/bloispaleolab/Neotoma.m1.GM

The "All Images" folder contains images of all specimens analyzed and referenced in the manuscript (n = 229). It also contains two .tps files with landmark coordinate data obtained from lower first molars (m1s) of all specimens. These “Neotoma_combined_R1” and “Neotoma_combined_R2” files represent both landmarking repetitions of five extant Neotoma species from California (n = 199) combined with recent Neotoma cinerea specimens from Idaho and South Dakota (n = 13) and late Pleistocene fossil specimens from Project 23 deposits at Rancho La Brea (n = 16). Images and .tps files for each of those groups are also saved separately in the folders described below. Image files are named starting with genus and species first letter abbreviations (NX), then catalog number, then element (L= lower (mandible), LR = lower right (dentary)). Specimens are from the Museum of Vertebrate Zoology (MVZ) unless prefixed with P23 (Los Angeles County Museum of Paleontology, Rancho La Brea, Project 23) or SDSM (South Dakota School of Mines and Technology, Museum of Geology). For example, “NA_10467LR” = MVZ 10467 Neotoma albigula right dentary.

The “Recent CA Neotoma” folder contains images of recent Neotoma specimens from MVZ collected in California (n = 199). These images were obtained in November 2018 using a Dino-Lite Edge AM4815ZTL digital microscope. The folder also contains four .tps files: “Neotoma_extant_R1”, “Neotoma_extant_R2”, “WearVetted_R1”, and “WearVetted_R2”. The “Neotoma_extant” files contain landmark coordinate data for all 199 specimens. Twenty-eight of those specimens with very worn and nearly unworn molars were removed from the “WearVetted” files to evaluate wear-stage effects on tooth morphology. See manuscript Supplementary Table 1 for the list of removed specimens.

The “Unknowns” folder contains two subfolders: “East N.cinerea” and “LACMP23”. The “East N.cinerea” subfolder contains images of 12 Neotoma cinerea specimens from western South Dakota sampled from the SDSM Recent Vertebrates Collection (SDSM-SD-XXXXXX), and one specimen from Idaho sampled from MVZ (filename = “UCMVZ-ID-NC-51944L”). The SDSM specimens were photographed in November 2024 with a Dino-Lite Edge Plus AM4917MZT digital microscope and the MVZ specimen was photographed in November 2018 with a Dino-Lite Edge AM4815ZTL digital microscope. In this subfolder there is one .tps file with landmark coordinate data of all 13 specimens: “East_NC”. The “LACMP23” subfolder contains images of 16 late Pleistocene fossil m1s, and dentaries with m1s, from several Project 23 deposits at Rancho La Brea (P23_XXXXX). See manuscript Table 4 for the deposits each specimen was sampled from. Project 23 specimens were photographed between January and August of 2019 with a Dino-Lite Edge AM4815ZTL digital microscope. Left fossil elements were flipped to imitate right elements for analysis. This subfolder also contains one .tps file with landmark coordinate data of all 16 fossil specimens: “LACMP23”.

References:

Rohlf, F.J., 2018a. TpsUtil version 1.76. Ecology & Evolution: (program), New York: Suny at Stony Brook.

Rohlf, F.J., 2018b. TpsDig version 2.31. Ecology & Evolution: (program), New York: Suny at Stony Brook.