Analysing planktonic foraminiferal growth in three dimensions with foram3D: an R package for automated trait measurements from CT scans

Abstract

Foraminifera are one of the few taxa that preserve their entire ontogeny in their fossilised remains. Revealing this ontogeny through micro-computed tomography (CT) of fossil planktonic foraminifera has greatly improved our understanding of their life history and allows accurate quantification of total shell volume, growth rates and developmental constraints throughout an individual's life. Studies using CT scans currently mainly focus on chamber size, but the wealth of three-dimensional data generated by CT scans has the potential to reconstruct complete growth trajectories. Here we present an open-source R package to analyse growth in three-dimensional space. Using only the centroid xyz coordinates of every chamber, the functions determine the growth sequence and check that chambers are in the correct order. Once the order of growth has been verified, the functions calculate distances and angles between subsequent chambers, determine the total number of whorls and the number of chambers in the final whorl at the time each chamber was built, and, for the first time, quantify trochospirality. The applications of this package will enable repeatable analysis of large data sets and quantification of key taxonomic traits and ultimately provide new insights into the effects of ontogeny on evolution.