Total RNA was extracted from dissected heads of full-sib F1 lab reared embryos, larvae, or juvenile C. variegatus produced by breeding a single wild caught male and wild caught female. Heads were stored in RNA-later prior to RNA extraction. RNA was extracted using an ambion TRIzol Plus RNA Purification Kit. Illumina libraries were prepared for sequencing using an NEBNext Ultra Directional RNA Library Prep Kit for Illumina with NEBNext poly(A) magnetic beads for mRNA isolation. RNA was chemically fragmented following the NEB protocol, except that the time was reduced to produce insert sizes of approx. 250bp. Random primers were used to produce cDNA.

Illumina HiSeq 2500 sequencing; RNA-seq of Cyprinodon: embryonic head

Cyprinodon variegatus

Understanding the evolution of novel morphologies is fundamental to the study of evolution. Illumina RNAseq was used to investigate gene expression divergence and sequence divergence among incipient species of pupfish that vary in skull morphology.

RNAseq of Cyprinodon pupfishes

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Samples