Heterochrony structured theropod wing for flight and influenced its evolutionary paths

The theropod forewing evolution could have been shaped by changes in developmental timing, as seen for the skull. Theropods leading to birds suffered miniaturization with forelimb lengthening attributed to heterochrony (changes in developmental timing and/or rate) which has never been strictly tested. Using phylogenetic analysis of growth series shape-change, we detected paramorphism in the paravian node as an immature wing resembling adult early-diverging theropods. The coinciding development of pennaceous feathers, longer wings, and mobile shoulders in the paravian common ancestor demonstrates a major reorganization of the forelimb just before flight appeared. Once flight evolved, heterochrony continued influencing wing evolution and the rapid early diversification of avian flight styles. Our study extends the role of heterochrony to the wings of theropods, playing a central role in flight evolution.

Methods
Instructions to run sPASOS

Download sPASOS from: https://www.lillo.org.ar/phylogeny/spasos/
Download TNT from: https://www.lillo.org.ar/phylogeny/tnt/

sPASOS and TNT should be in the same folder

Open Windows Run command box
Copy the files tre_sPASOS.tre,tre_sPASOS_extended_data_Fig1.tre, and the output files previously generated hand_Pasos.tps, wing_Pasos.tps into the same folder as sPASOS or indicate the right path on the following commands.
Run the following command:

spasos -i hand_Pasos.tps -p 1 -t tre_sPASOS_main.tre -y -r 100
This will run PASOS for the hand configuration

Run the following command:

spasos -i wing_Pasos.tps -p 1 -t tre_sPASOS_main.tre -y -r 100
This will run PASOS for the forelimb configuration
These commands will open sPASOS and analyze the data in the .tps file with the phylogenetic hypothesis specified in the .tre file with a penalty of 1 (-p 1)and a resampling done 100 times (-y100). A decay index (-y) is also calculated.
(Fig. 2 - Phylogenetic hypothesis with PASOS heterochronic shift correspond to wing_Pasos_offset_tree and hand_Pasos_offset_tree)

copy the output files in your R script working directory 

to obtain the Extended Data Fig. 1 use the tree from tre_sPASOS_extended_data_Fig1.tre and the corresponding hand_Pasos_extended.tps and wing_Pasos_extended.tps files generated in the R script (See R script).