Data from: DNA sequencing of fish eggs and larvae reveals high species diversity and seasonal changes in spawning activity in the southeastern Gulf of California

Ichthyoplankton studies can provide valuable information on the species richness and spawning activity of fishes, complementing estimations done using trawls and diver surveys. Zooplankton samples were collected weekly between January and December 2014 in Cabo Pulmo National Park, Gulf of California, Mexico (n=48). Fish larvae and particularly eggs are difficult to identify morphologically, therefore the DNA barcoding method was employed to identify 4,388 specimens, resulting in 158 Operational Taxonomic Units (OTUs) corresponding to species. Scarus sp., Halichoeres dispilus, Xyrichtys mundiceps, Euthynnus lineatus, Ammodytoides gilli, Synodus lacertinus, Etrumeus acuminatus, Chanos chanos, Haemulon flaviguttatum, and Vinciguerria lucetia were the most abundant and frequent species recorded. Noteworthy species identified include rare mesopelagic species such as the giant oarfish (Regalecus glesne) and highly migratory and commercially important species such as black skipjack (Euthynnus lineatus) and yellowfin tuna (Thunnus albacares). Spawning activities showed distinct seasonal patterns with the highest abundance of ichthyoplankton recorded during spring, highest species richness during summer (90 OTUs) and lowest species richness during winter (28 OTUs). A total of seven OTUs were recorded throughout the year (4%), 11 OTUs during three seasons (7%), 36 OTUs in two seasons (23%) and 106 OTUs were recorded in only one season (66%). The study found eggs and/or larvae of 47 species that were not previously reported in Cabo Pulmo National Park. Results allow resource managers to compare shifting populations and spawning patterns of species that may be affected by both conservation efforts and broader oceanographic changes associated with climate change