Hide and seek shark teeth in Random Forests: machine learning applied to Scyliorhinus canicula populations

Abstract

Shark populations that are distributed alongside a latitudinal gradient often display body size differences at sexual maturity and vicariance patterns related to their number of tooth files. Previous works have demonstrated that Scyliorhinus canicula populations differ between the northeastern Atlantic Ocean and the Mediterranean Sea based on biological features and genetic analysis. In this study, we sample more than 3,000 teeth from 56 S. canicula specimens caught incidentally off Roscoff and Banyuls-sur-Mer. We investigate population differences based on tooth shape and form by using two approaches. Classification results show that the classical geometric morphometric framework is outperformed by an original Random Forests-based framework. Visually, both S. canicula populations share similar ontogenetic trends and timing of gynandric heterodonty emergence but the Atlantic population has bigger, blunter teeth, and less numerous accessory cusps than the Mediterranean population. According to the models, the populations are best differentiated based on their lateral tooth edges, which bear accessory cusps, and the tooth centroid sizes significantly improve classification performances. The differences observed are discussed in light of dietary and behavioural habits of the populations considered. The method proposed in this study could be further adapted to complement DNA analyses to identify shark species or populations based on tooth morphologies. This process would be of particular interest for fisheries management and identification of shark fossils.

A shark-inspired general model of tooth morphogenesis unveils developmental asymmetries in phenotype transitions

“…S1 ). Catshark cuspidity (cusp number) tends to increase from medial to distal teeth, which appears reminiscent of within-jaw cuspidity trends in other shark species and even in many mammals ( 21 , 39 , 40 , 52 , 53 ).…”

“…Next, we explored to which extent the model can help understand some of the natural variation of S. canicula dentition. In this species, tooth shapes vary both between populations, sexes, ages, and within jaws ( 40 , 52 ), comprising cusp numbers between 1 and 7, symmetrical and asymmetrical teeth, as well as different cusp heights and different height ratios between neighboring cusps in multicuspid teeth (cf. SI Appendix , Fig.…”

“…Such a developmental degeneracy may even facilitate the emergence of heterodonty, i.e., phenotypic variation within the same organism, as it increases the likelihood that existing patterning cues between different body parts will in some way connect to the tooth developmental program and produce the selected variation ( 85 ). In the case of Scyliorhinus , heterodont tooth shape transitions involving changes in cusp numbers correlate with age, sex, and jaw position ( 39 , 52 ). Yet, our theoretical results suggest that the mechanisms underlying each of those transitions may be different in each instance and that we should be careful when generalizing or inferring mechanistic hypotheses even within the same organism ( 89 ).…”

The sensory shark: high-quality morphological, genomic and transcriptomic data for the small-spotted catsharkScyliorhinus caniculareveal the molecular bases of sensory organ evolution in jawed vertebrates

“…The availability of two sets of genomic sequences and RNA-seq data coming from two populations of the small spotted catshark allowed to describe a population genomic landscape for the first time in this species. The identified outlier regions may contain the genetic bases of diverging morphotypes between Atlantic and Mediterranean populations (as identified in growth patterns or tooth shape (Berio et al 2022)). Further studies using genomic re-sequencing data and a larger sample size could delineate these with more confidence.…”