Cryptophytes are single celled protists found in all aquatic environments. Cryptophytes evolved from secondary endosymbiosis when an unknown eukaryote host engulfed a red alga symbiont. This merger provided cryptophytes the ability to harvest energy through photosynthesis. It also resulted in a four-genome system that includes the nuclear and mitochondrial genomes from the host and a second nuclear genome (nucleomorph) and plastid genome inherited from the symbiont. While Cryptophyta have long been recognized as a phylum consisting of two classes that include a heterotrophic group, Goniomonadea, and a mostly autotrophic group, Cryptophyceae, their exact phylogeny has been revised numerous times based on ultrastructural, biochemical, molecular and morpholgical data, and stillr emains unclear. In their new study titled "A three-genome ultraconserved element phylogeny of cryptophytes", Dr. Matthew Greenwold, former post-doc in the Dudycha lab and now Assistant Professor at the University of Texas at Tyler, and his collaborators Drs. Kristiaän Merritt, Tammi Richardson, and Jeff Dudycha, took advantage of  the different genomes (with potentially distinct evolutionary histories) of cryptophytes to perform a phylogenomic study of their early history. They produced a three-genome phylogeny of 91 strains of cryptophytes that led them to identify three major cryptophyte clades. Each of these major clades includes both freshwater and marine species, but subclades within these clades differ in degrees of niche conservatism. Altogether, their results demonstrate that classical taxonomy based on morphology does not consistently provide distinguishing features that reflect the evolutionary relationships of Cryptophyceae they ascertained from genomic data.