These sequence data (fasta+gap alignment) were used to reconstruct the phlogenetic trees presented in Kates et al. 2017 Evolutionary and domestication history of Cucurbita (pumpkin and squash) species inferred from 44 nuclear loci. Sequences were amplified using Fluidigm Access Array and sequenced using Illumina MiSeq. Each sequence name includes information on taxon, sample, and geographic origin. There are two alignments for each genetic locus: alignments are named "alleles" or "ambiguity" to identify whether the sequences were assembled as allelic sequences or with ambiguity codes in the case of heterozygosity. See Kates et al. 2017 for details.