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Abstract Geometric morphometrics is a powerful tool for studying fish body shape; however, body posture can be a hindrance to these analyses. Here I introduce new R language tools for correcting multiple types of bending of 3D data based on the TPS suite (geometric morphometric software) “unbend specimens” methodology. In a sample dataset of darters, these R tools adequately accounted for posture artifacts otherwise evident across multiple principal component axes. I hope these new tools will facilitate the incorporation of 3D landmark data into the comparative analysis of fish body shape. 

Abstract Fish skulls are often highly kinetic, with multiple linkage and lever systems powered by a diverse suite of muscles. Comparative analysis of the evolution of soft-tissue structures in the fish skull is often limited under traditional approaches, while new imaging techniques like diceCT (diffusible iodine-based contrast-enhanced computed tomography) allow for high-resolution imaging of muscles in situ. Darters (Percidae: Etheostomatinae) are a diminutive and species-rich clade of lotic freshwater fishes, which show diverse head shapes believed to be associated with different foraging strategies. We used diceCT to sample all major cranial adductors and abductors responsible for movement of the jaw, hyoid, operculum, and suspensorium from 29 species. We applied comparative phylogenetic approaches to analyse the evolutionary trends in muscle size across the clade. We found two major patterns: (i) darter cranial muscles show fundamental trade-offs relating to investment in musculature, as well as buccal expansion vs. biting attributes; early divergence in muscle size appears to be associated with shifts in habitat use and foraging; (ii) darter adductor mandibulae show high variation in architecture (fibre orientation, divisions). This study highlights how new imaging techniques can provide novel insights into the anatomy of even well-sampled/represented clades. 

Synopsis Contrast enhanced computed-tomography imaging like diffusible iodine-based contrast-enhanced computed tomography (diceCT) can provide detailed information on muscle architecture important to comparative analyses of functional morphology, using non-destructive approaches. However, manual segmentation of muscle fascicles/fibers is time-consuming, and automated approaches are at times inaccessible and unaffordable. Here, we introduce GoodFibes, an R package for reconstructing muscle architecture in 3D from diceCT image stacks. GoodFibes uses textural analysis of image grayscale values to track straight or curved fiber paths through a muscle image stack. Accessory functions provide quality checking, fiber merging, and 3D visualization and export capabilities. We demonstrate the utility and effectiveness of GoodFibes using two datasets, from an ant and bat diceCT scans. In both cases, GoodFibes provides reliable measurements of mean fiber length compared to traditional approaches, and is as effective as currently available software packages. This open-source, free to use software package will help to improve access to tools in the analysis of muscle fiber anatomy using diceCT scans. The flexible and transparent R-language environment allows other users to build on the functions described here and permits direct statistical analysis of the resulting fiber metrics. We hope that this will increase the number of comparative and evolutionary studies incorporating these rich and functionally important datasets. 

Abstract Allometry, the relationship between anatomical proportions and body size, may either limit or facilitate the diversification of morphology. We examined the impact of allometry in darter fish morphology, which displays a variety of trophic morphologies. This study aimed to address (a) whether there was significant variation in darter head allometry, (b) if allometry contributed to head shape diversity in adults, and (c) if darters show head shape modularity associated with allometry. We used geometric morphometrics to quantify head shape across 10 different species and test for heterogeneity in allometric slopes. In addition, we quantified the degree of modularity between the preorbital and postorbital regions of the darter head, both before and after correction for body size. We found that different species have unique allometric slopes, particularly among theSimopercasubgenus, and that closely related darter species tend to show ontogenetic divergence, contributing to the diversity of head shapes observed in adults. We suggest that such a pattern may result from the similarity of juvenile diets due to gape limitation. We also found that several species show significant modularity in head shape but that modularity was evolutionarily labile and only sometimes impacted by head shape allometry. Overall, our work suggests that ontogenetic shape development may have been important to the evolution of head shape in darters, particularly in the evolution of foraging traits and microhabitat.