RolandZimm/shark_heterodonty: Sharkheterodonty_release231224

This repository contains data used in the ongoing research project on shark heterodonty

Here, I share the following base data sets:

1. shark tooth half-outlines from 51 species, extracted from toothrows downloaded in 06-2021 from the j-elasmo data collection (http://naka.na.coocan.jp/) created and updated by Fumio Nakagawa. The folders containing outline data are named after the respective species, U/L for upper/lower jaw and numbers for relative individual tooth positions.
2. ecological data compiled about the species and their references.
3. NCBI genetic sequence references to create a phylogenetic tree of those species.
4. The Newick format of the used phylogenetic tree.
5. quantitative measurements and compiled ecological trait data for all species in a single plottable file: masterfile.data
6. CCA correlation strengths of complexity descriptors for different ecological traits: cancor.correlations.features2.all
7. PCA data points generated by discrete cos Fourier analysis: xx1.log
8. Files correlating genotypic and phenotypic distances
9. Additional statistical data and information connected to the results of this study
10. generative code: 10.1. compare_pairs.f90 : comparison of outline pairs using outline distance and shared area 10.2. outline_features.f90 : calculation of complexity-related outline-based features of tooth outlines 10.3. angle_complexities.f90 : calculation of angle-based shape complexity measures 10.4. heterodonties_per_species.f90 : calculation of mono- and dignathic heterodonty measures along toothrows. 10.5. geno_pheno_pval.f90 : ranks species pairs by genotypic distance, allowing to calculate p-values between sliding subsets.

These files relate to research results published as: Zimm, Roland, Vitoria Tobias-Santos, and Nicolas Goudemand. "Integration of multi-level dental diversity links macro-evolutionary patterns to ecological strategies across sharks." bioRxiv (2024): 2024-10. eventually to be published elsewhere attending peer review.

This version (1.2.) contains more data and generative code that can be used to apply morphometric measurements central to quantify heterodonty and shape complexity as well as correlate genotypic and phenotypic variation. Future releases may feature more interconnected and didactically annotated code files.

Any public use of this data shall include citation of this work as well as the j-elasmo morphological database.

Questions about this material may be directed to zimm.roland@gmail.com