One of the analysis that I like to do when trying to understand the function of a specific gene is to recapitulate its evolution since the last common ancestor between zebrafish and humans. This brings a problem: from which species do I have to search and download data to convincingly fill the gap on this divergence times? How many data points do we need to bridge a 400 million year gap, including (at least) one full whole-genome duplication?

Species Tree from
Species tree created with TimeTree

While there are countless publications with phylogenetic trees made with the sequences from zebrafish, mouse, humans, and either chicken or frogs, I found these datasets to be skewed towards tetrapods, with insufficient fish species coverage and usually lead to wrong conclusions.

As of 2018, this is the list of species that have a sequenced genome (at least partially) and I use in phylogenetic and reconciliation analysis focused on investigating genetic evolution between zebrafish and mammals:

Last common taxonomySpecies
EutelestomiLatimeria, lungfishes & Tetrapods
NeopterygiiLepisosteus oculatus
TeleosteiAnguilla anguilla
OsteoglossocephalaiScleropages formosus, Paramormyrops kingsleyae
ClupeocephalaGreat majority of fishes with sequenced genome:
Takifugu, Tetraodon, Oryzias, Gasterosteus, Peocilia, Xiphophorus, ...
OtomorphaClupea harengus
OtophysiAstyanax mexicanus, Electrophorus electricus, Ictalurus punctatus,
Pygocentrus nattereri
CyprinidaeCyprinus carpio, Squalius pyrenaicus, Sinocyclocheilus rhinocerous,
anshuiensis, and grahami, Leuciscus waleckii, Pimephales promelas
DanioDanio rerio

I often use sequences from lampreys and sharks to root the trees; the coealacanth and lungfishes help in joining the tetrapod and often diverging fish lineages; and the spotted gar is the only non-teleost fish with sequenced genome that I know of, which is useful to pinpoint duplications emerging from the whole genome duplication.