Citrullus_3D_GMM

3D geometric morphometric analysis using the R packages geomorph v4.0.0 and Morpho v2.8 for landmarks generated in Amira Software version 5.4.5
Code accompanies Wolcott et al. 2021, Plants, People, Planet.
Last updated 3 May 2021

_{^{Images show a subset of seeds and landmarks used to investigate 3D shape differences of modern and ancient watermelon seeds (To access micro-CT datasets and surfaces used for analysis, see our MorphoSource project page).}}

Archaeological research on the domestication history of watermelons has focused on seeds found at settlements where people either ate the sweet fruit pulp, the fat-rich seeds, or used the oil extracted from seeds. The earliest seeds assigned to Citrullus lanatus and C. colocynthis come from the Libyan archaeological site Uan Muhuggiag, but stratigraphic evidence suggested that it had been disturbed and contained younger intrusive material. We used 3D x-ray-micro-CT to investigate whether ancient Citrullus seeds can be reliably assigned to C. lanatus or C. colocynthis, using seeds from all but one extant species of Citrullus as well as seeds from Tutankhamun’s tomb at Thebes and from Uan Muhuggiag.

Steps

1. Generate surface files in Amira (see surface files and CT datasets in Morphosource)
2. Add landmarks to surface files in Amira (see all_lms.txt in this GitHub repository)
3. Do 3D GMM analysis (see analyze_landmarks_mac.R in this GitHub repository)

References

• geomorph. geomorph. GitHub.
• geomorph documentation on CRAN
• Adams and Otárola‐Castillo 2013. Geomorph: An r package for the collection and analysis of geometric morphometric shape data. Methods in Ecology and Evolution.
• Morpho. Morpho. GitHub.
• Morpho documentation on CRAN
• Schlager 2017. Morpho and Rvcg - Shape Analysis in R: R-Packages for Geometric Morphometrics, Shape Analysis and Surface Manipulations. Statistical Shape and Deformation Analysis: Methods, Implementation and Applications.
• Polly 2012a. Geometric morphometrics, an introduction - Day 2A. Department of Geological Sciences, Indiana University.
• Polly 2012b. A basic geometric morphometric analysis - Day 2B. Department of Geological Sciences, Indiana University.
• Jones 2018. Introduction to geomorph package. Uni Erlangen.