Data for Ecomorphological diversity of Australian tadpoles
datasetposted on 12.11.2018 by Emma Sherratt, Marion Anstis, J Scott Keogh
Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
Landmark and semilandmark coordinate data (2-dimensional) for tadpole body shape of 187 species of Australian frogs, and 17 species of worldwide frogs. To accompany: Sherratt, Anstis and Keogh 2018 Ecomorphological diversity of Australian tadpoles, Ecology & Evolution.
Data are provided as raw landmark coordinates, and after unbending using the quadratic approach in tpsUtil v.1.74 (unbent using the landmarks identified in "Unbend_tadpole_tail_eye.nts"). Sliding semilandmarks can be done during generalized Procrustes superimposition using the landmarks identified in "Curve_sliding_for_GPA.csv" - for use with R package geomorph.
# Read in data
tadpoles <- readland.tps("187spp_Australia_raw_coords_unbent.tps", specID = "ID")
# PAUSE: Negative landmark coordinates have been identified. Should they be considered as NAs? (y/n) n
# Perform GPA with minimising bending energy
curve.sliding <- as.matrix(read.csv("Curve_sliding_for_GPA.csv", header=TRUE))
tad.gpa <- gpagen(tadpoles, curves=curve.sliding, ProcD=F)
Landmarks and semilandmarks defined as: 1, centre of the eye; 2, centre of the external nares; 3, point where the upper labium contacts the head/body in lateral view; 4, point where the lower labium contacts the head/body in lateral view; 5, intersection of the head/body and tail on the ventral side, anterior to the vent; 6, intersection of the ventral edge if the tail muscle and the head/body; 7, intersection of the dorsal edge if the tail muscle and the head/body; 8, tip of the tail; 9, point on the dorsal fin closest to landmark 7 (superficially denotes the intersection of the head/body and tail regions); 10–17, equally-spaced semilandmarks marking the curve of the dorsal aspect of the head/body when viewed laterally; 18–27, equally-spaced semilandmarks marking the curve of the dorsal aspect of the tail fin when viewed laterally; 28–37, equally-spaced semilandmarks marking the curve of the ventral aspect of the tail fin when viewed laterally; 38–45, equally-spaced semilandmarks marking the curve of the ventral aspect of the head/body when viewed laterally; 46–55, equally-spaced semilandmarks marking the curve of the notochord. Landmark configuration has been straightened from the eye to the tip of the tail along the notochord in order to standardise all specimens’ configurations (see Methods for details).