PhiPSII_data_Dryad

Quantum yield of photosystem II (PhiPSII) measured with a chlorophyll fluorometer using on the same tissue and under the same conditions used to measure NPQmax, qE, qI, and qZ

qEqZqI_data_Dryad

Raw chlorophyll fluorescence values (Fm, Fm'1, Fm'2), and values calculated for individual nonphotochemical quenching (NPQ) components (qE, qZ, qI). Data derived from the same tissues as used in NPQmax_data_Dryad.xlsx

concat_alllegume.fsa

Concatenated nucleotide alignments for 101 orthogroups used to estimate a species tree in RAxML. This is a multifasta file

DNA alignments

cDNA alignments for all gene families in the project, made using pal2nal. These are multifasta alignment files

CDS translations

Corresponding CDS sequences for the peptide translations. These are multifasta files

Legume pairs - ksplots

Putative paralog pairs estimated from Ks plots for multiple species from study. These were used to test for other WGD events (other than PWGD). This is a tab delimited file with the first and second columns being Ks plot identified putative paralogs and the third column being a designation for the putative event

trees - bipartitions

The RAxML bipartitions trees for the 3360 orthogroup alignments containing Glycine max. syntelogs. These are Newick tree files

alignments for other WGD tests

Alignments of orthogroups used to look at putative WGD events in data set. These are multifasta files

peptide translations

Peptide translations based on a blastx of the filtered Trinity assemblies to the 22 genome dataset (Amborella Genome Consortium, 2013) and conceptually translated using Genewise. These are multifasta files

RAxML_bipartitions.concat_alllegume.fsa.raxml.out

RAxML best tree with bootstrap values estimated from concatenation of 101 orthogroups alignments. This is a Newick tree file