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null (Ed.)This article introduces an R package, dietr, which calculates fractional trophic levels from quantitative diet item and qualitative food item data following the routine implemented in TrophLab within the open source R environment. dietr is easy to use and can quickly calculate trophic levels for many diet records. In addition to calculating trophic levels following the TrophLab routines, users can also specify a taxonomic hierarchy and estimate trophic levels at multiple taxonomic levels in a single call of a function. Additionally, dietr works well with FishBase data obtained in R using rfishbase and comes with premade databases of prey trophic levels that users can utilize for estimating trophic levels. dietr can also calculate several prey electivity indices. I provide information on dietr’s performance and provide a use case example of how dietr can be used on an empirical dataset. Trophic levels for hundreds of specimens can be calculated in a few seconds and the flexibility of dietr’s input allows users to easily calculate trophic levels from their own data.more » « less
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Borstein, Samuel R.; Fordyce, James A.; O’Meara, Brian C.; Wainwright, Peter C.; McGee, Matthew D. (, Nature Ecology & Evolution)
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Kolmann, Matthew A.; Nagesan, Ramon S.; Andrews, James V.; Borstein, Samuel R.; Figueroa, Rodrigo Tinoco; Singer, Randal A.; Friedman, Matt; López‐Fernández, Hernán (, Journal of Fish Biology)Abstract Computed tomography (CT) scanning and other high‐throughput three‐dimensional (3D) visualization tools are transforming the ways we study morphology, ecology and evolutionary biology research beyond generating vast digital repositories of anatomical data. Contrast‐enhanced chemical staining methods, which render soft tissues radio‐opaque when coupled with CT scanning, encompass several approaches that are growing in popularity and versatility. Of these, the various diceCT techniques that use an iodine‐based solution like Lugol's have provided access to an array of morphological data sets spanning extant vertebrate lineages. This contribution outlines straightforward means for applying diceCT techniques to preserved museum specimens of cartilaginous and bony fishes, collectively representing half of vertebrate species diversity. This study contrasts the benefits of using either aqueous or ethylic Lugol's solutions and reports few differences between these methods with respect to the time required to achieve optimal tissue contrast. It also explores differences in minimum stain duration required for different body sizes and shapes and provides recommendations for staining specimens individually or in small batches. As reported by earlier studies, the authors note a decrease in pH during staining with either aqueous or ethylic Lugol's. Nonetheless, they could not replicate the drastic declines in pH reported elsewhere. They provide recommendations for researchers and collections staff on how to incorporate diceCT into existing curatorial practices, while offsetting risk to specimens. Finally, they outline how diceCT with Lugol's can aid ichthyologists of all kinds in visualizing anatomical structures of interest: from brains and gizzards to gas bladders and pharyngeal jaw muscles.more » « less
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