Dental microwear scan and surface data from 15 wild sika deer populations

Dental microwear scan and surface data from 15 wild sika deer populations OverviewThis repository contains original scans, processed surfaces, and analysis files for 1,156 dental microwear scans from 293 sika deer (Cervus nippon) representing 15 wild populations in Japan. The dataset comprises 763 scans from 189 females and 393 scans from 104 males. These scans constitute the extant sika deer reference dataset analyzed by Kubo and Fujita (2021). This repository makes the scan and surface files available, organized by population and sex. The fossil Cervus astylodon data analyzed in that publication are not included here. Data acquisition and analysisDental surfaces were scanned using a VK-9700 confocal laser scanning microscope (Keyence, Japan). Surface preprocessing followed the procedure described in Kubo and Fujita (2021). The collection includes MountainsMap analysis documents and exported PDF reports associated with the processed surfaces. MountainsMap Imaging Topography (version 7.4.9286; Digital Surf, Besançon, France) was used for the archived female parameter-calculation documents. Details of specimen preparation, scanning, surface preprocessing, and the published analyses are provided in Kubo and Fujita (2021). Published scan-level parameter values are available in that article's Table S2. The archived analysis files are provided as supporting material; their displayed values in MNT documents should not be assumed to match the published table exactly if the software version is different. Dataset organizationFiles are organized by population and sex. Archive and folder names follow the convention Population_XX_F and Population_XX_M, where XX is the two-digit population number, F denotes females, and M denotes males. For example, Population_01_F.zip contains the female files for population 1, and Population_01_M.zip contains the male files for that population. Each population-and-sex folder contains four subfolders:- VK3: Original instrument scan files (.vk3).- SUR: Processed surface files (.sur).- MNT: MountainsMap analysis documents (.mnt).- PDF: Exported analysis reports (.pdf). The collection covers 15 populations and both sexes, giving 30 population-and-sex archives. The complete collection is expected to contain 1,152 VK3 files, four unprocessed SUR files supplied in place of unavailable VK3 files, 1,156 processed SUR files, 1,156 MNT documents, and 1,156 PDF reports, giving 4,624 scan-associated files in total. The common preprocessing template, Temp.mnt, is supplied separately and is not included in this count. For four scans from male specimens in the Hokkaido population, the original VK3 files were unavailable. Unprocessed surfaces were therefore exported in SUR format from archived MNT documents retaining the preprocessing history. These files are provided in Population_01_M/VK3/SUR_unprocessed/ as alternative source-surface data for those scans. They are distinct from the processed surfaces in the SUR subfolder. These exports preserve source-surface topography but are not original VK3 instrument files. File counts by population and sexThe table below lists the expected complete inventory. Source SUR denotes the unprocessed SUR files supplied in place of the four unavailable VK3 files. Processed SUR denotes surfaces in the SUR subfolder. Totals exclude the common Temp.mnt file and this README. Folder Individuals Scans VK3 Source SUR Processed SUR MNT PDF TotalPopulation_01_F 8 29 29 0 29 29 29 116Population_01_M 8 25 21 4 25 25 25 100Population_02_F 20 79 79 0 79 79 79 316Population_02_M 1 4 4 0 4 4 4 16Population_03_F 18 70 70 0 70 70 70 280Population_03_M 14 53 53 0 53 53 53 212Population_04_F 22 92 92 0 92 92 92 368Population_04_M 3 10 10 0 10 10 10 40Population_05_F 7 32 32 0 32 32 32 128Population_05_M 1 3 3 0 3 3 3 12Population_06_F 8 34 34 0 34 34 34 136Population_06_M 1 4 4 0 4 4 4 16Population_07_F 9 31 31 0 31 31 31 124Population_07_M 6 20 20 0 20 20 20 80Population_08_F 17 60 60 0 60 60 60 240Population_08_M 4 13 13 0 13 13 13 52Population_09_F 10 34 34 0 34 34 34 136Population_09_M 6 25 25 0 25 25 25 100Population_10_F 11 58 58 0 58 58 58 232Population_10_M 19 87 87 0 87 87 87 348Population_11_F 14 54 54 0 54 54 54 216Population_11_M 13 46 46 0 46 46 46 184Population_12_F 8 33 33 0 33 33 33 132Population_12_M 8 22 22 0 22 22 22 88Population_13_F 13 48 48 0 48 48 48 192Population_13_M 5 13 13 0 13 13 13 52Population_14_F 19 89 89 0 89 89 89 356Population_14_M 9 40 40 0 40 40 40 160Population_15_F 5 20 20 0 20 20 20 80Population_15_M 6 28 28 0 28 28 28 112Total 293 1156 1152 4 1156 1156 1156 4624 Population numbers01: Eastern Hokkaido (Hokkaido in Kubo and Fujita, 2021)02: Mt. Goyo03: Kinkazan Island04: Nikko05: Ashio06: Okutama07: Boso Peninsula08: Izu Peninsula09: Yamanashi10: Nara Park11: Shimane12: Yamaguchi13: Fukuoka14: Tsushima Island15: Yakushima Island Processing stages and file rolesVK3 files contain the original instrument scans before surface preprocessing in MountainsMap. SUR files contain processed surface topography. Temp.mnt documents the surface-preprocessing procedure used in Kubo and Fujita (2021) and is provided as a common procedural reference. The MNT documents and PDF reports record parameter calculations performed on processed SUR files and do not contain the preceding surface-preprocessing history. Temp.mnt is supplied as a procedural reference. Reprocessing the original VK3 files with this template has not been verified to reproduce the parameter values exactly when the MountainsMap software version is different. File naming and correspondenceFiles sharing the same filename stem refer to the same scan. For example:HKD-0401_Lm2_f10_Y1_X1.vk3HKD-0401_Lm2_f10_Y1_X1.surHKD-0401_Lm2_f10_Y1_X1.mntHKD-0401_Lm2_f10_Y1_X1.pdf In this example, HKD-0401 is the scan sample identifier, L indicates the left side, m2 indicates the second lower molar, f10 identifies the facet, and Y1_X1 identifies the scan location. Temporary processing prefixes, such as "Temp ---", have been removed from filenames where applicable to facilitate matching across formats. The full list of sika deer scans and their published texture parameter values are provided in Table S2 of Kubo and Fujita (2021). Corresponding files in this repository can be identified using the filename stem. Table S2 also contains Cervus astylodon data, which are outside the scope of this repository. Software and reuseThe parameter-calculation MNT documents were created using MountainsMap Imaging Topography version 7.4.9286 and require compatible MountainsMap software to open. VK3 files require software supporting the Keyence VK3 format. SUR files require software supporting the SUR format. PDF reports can be viewed with a standard PDF reader. For further analysis of processed surface topography, use the SUR files in the SUR subfolders and consult the corresponding MNT documents or PDF reports. Original VK3 files and Temp.mnt are provided for inspection of the source scans and exploration of alternative preprocessing procedures. Associated publicationKubo, M. O., and Fujita, M. (2021). Diets of Pleistocene insular dwarf deer revealed by dental microwear texture analysis. Palaeogeography, Palaeoclimatology, Palaeoecology, 562, 110098. https://doi.org/10.1016/j.palaeo.2020.110098