Computational protocol: Morphological divergence and flow-induced phenotypic plasticity in a native fish from anthropogenically altered stream habitats

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Protocol publication

[…] Body shape variation of field-collected and mesocosm-reared specimens was quantified using geometric morphometric analyses (Zelditch et al. ) with tps software (http://life.bio.sunysb.edu/morph/) and R (R Development Core Team ). The lateral left side of each individual was photographed (Canon PowerShot A1100) with a reference scale, and the order of photographs randomized (to reduce potential biases associated with the sequence specimens were subjected to landmark demarcation), and set 11 homologous landmarks on each photograph using tpsDig2 software (Fig. ; Rohlf ). We rescaled landmark coordinates using the reference scale, and aligned landmark coordinates using a General Procrustes Analysis (GPA) to remove the effects of scale, translation, and rotation on shape variation for each group separately (i.e., field-collected and mesocosm-reared individuals). Relative warps (hereafter referred to as shape variables) for each group were calculated (n = 18) but because some shape variables often do not explain an appreciable amount of variation (Rohlf ), we only retained shape variables that explained more than 3% of the variation in shape for each dataset (retained variables explained >89.0% of the variance in each data set). Variation in shape was visualized using thin-plate spline transformation grids in tpsRegr (Rohlf ). […]

Pipeline specifications

Software tools TpsDIG, TpsRegr
Application Macroscope & basic digital camera imaging
Organisms Homo sapiens