The Fish Speciation Genome Project (P. I.: Iria Fernandez-Silva) seeks to address key evolutionary questions pertaining to the evolution of reef fishes.

In traditional speciation models geographic isolation is a prerequisite for the evolution of reproductive barriers and species boundaries. However, coral reef fishes and other marine organisms defy this view, because geographic barriers in the oceans are scarce and their initial life stages (eggs and larvae) can drift with oceanic currents over vast geographic areas. Yet, coral reefs are incredibly diverse and harbor over 25% of the marine species.

Our work is a multidisciplinary approach to investigate the genomic architecture of lineage divergence and the role of gene flow in speciation. We also aim to investigate the prevalence of hybridization and genomic introgression in coral reef fishes and its consequences for the calibration of molecular clocks and phylogeographic inference. The recent discovery of two hybrid zones in the tropical Indo-Pacific highlights the need for a thorough examination of reticulate evolution in this group.

Centropyge angelfishes

We are combining ecological and genomic data from Indo-Pacific pygmy angelfishes of the Centropyge flavissima complex: C. flavissima, C. vrolikii, and C. eibli.

Species in this complex are delineated by color and have overlapping geographic distribution. Phylogenetic analyses reveal three deep mtDNA lineages that conform not to species designation, but to geographic regions, highlighting the role of introgression in the evolution of this group. Where the species ranges overlap, hybrids with intermediate coloration define two hybrid zones.

The comparison of genomes of pygmy angelfishes that are only distinguishable in the base of color and hybrids that display a range of intermediate colorations will also provide insights into the genetic control of this trait, for which nothing is virtually known, in spite of its prominent role in the diversification of reef fishes.

Marie Curie Actions logo

This project is funded by a Marie Curie Action (European Research Council) to Dr. Iria Fernandez-Silva and is a partnership between the California Academy of Sciences and the University of Vigo. We also work with collaborators at Curtin University and the Hawaii Institute of Marine Biology.

Academy Contributors

Research Associate
Luiz Rocha
Curator and Follett Chair of Ichthyology
in Sao Tome
Associate Curator and Director of the Center for Comparative Genomics

Other Contributors

Dr. David Posada (University of Vigo, Spain), Dr. J-P Hobbs (Curtin University, Australia), Dr. Joseph DiBattista (Curtin University, Australia)


The FishSpeciationGenome Project team

Dr. Iria Fernandez-Silva
Marie Curie Research Fellow
California Academy of Sciences – University of Vigo
 - Project leader

Dr. David Posada
“Phylogenomics” group leader
University of Vigo, Spain
​ - Phylogenomics and molecular evolution

Dr. Luiz Rocha​
Curator of Ichthyology
California Academy of Sciences, USA
 - Evolution of coral reef fishes

Dr. Brian Simison
Director of the Center for Comparative Genomics
California Academy of Sciences, USA
 - Computational genomics and genome sequencing

Jim Henderson
Research Associate
California Academy of Sciences
 - Genome assembly and computational genomics

Dr. J-P Hobbs
Curtin University
 - Coral reef fish ecology and hybridization

Dr. Joseph DiBattista
Curtin University
​ - Phylogeography and evolution of coral reef fishes