An interactive pipeline for multitrait evolutionary analysis in a phylogenetic framework

Comparative phylogenetic studies based on 2D image data can reveal macroevolutionary patterns and processes by integrating phylogenetic and ecological analyses. The advent of high-throughput imaging facilities has led to the accumulation of large image datasets; however, large-scale data extraction and analysis using these resources can be labour- and computation-intensive. Moreover, there are few standardized methods to analyse multitrait image-based data in a phylogenetic framework. Several packages in the R statistical environment offer utilities for processing and analysing large-scale image data. Techniques for the comparative phylogenetic analysis of multitrait data have also been introduced in other packages. However, most of these approaches are specialized for discrete purposes, and there is a lack of streamlined and efficient methodological pipelines integrating features across packages. Here, we present multEvol, an interactive pipeline for the extraction and phylogenetic analysis of shape and colour pattern data from 2D images in the R statistical computing environment. Using this pipeline, shape outlines and colour pattern data for multiple colours can be extracted, visualised, and compared in a phylogenetic framework. Using various utilities provided in the phytools, RNiftyReg, Momocs, patternize, convevol, and geiger packages, we introduce an interactive interface that allows user inputs for iterative data extraction. This pipeline provides an efficient method for the bulk processing of images of biological specimens from museum collections. As such, it has potential applications in the large-scale morphometric analysis of museum specimens to reveal macroevolutionary patterns in ecology, evolution and integrative biology.