CCG Projects

Academy curator Dr. Dave Blackburn uses molecular phylogenetic methods to understand the diversity and evolution of African frogs, including phylogeography of lowland forest frogs, species-level phylogenies of genera such as Cardioglossa and Hylarana, diversity of North African water frogs, and species discovery in other frog lineages. Each project involves collaborators from the United States, Europe and Africa. For more information, visit the amphibians and reptiles of Central Africa project page.

Postdoctoral researcher Edward Stanley is using genetic data to investigate the systematics and evolution of African reptiles and amphibians. In particular he is interested in studying patterns of morphology, ecology and phylogenetics in the Cordylidae, a family of lizards endemic to Sub-Saharan Africa. One additional, exciting aspect of this work utilizes cutting edge CT scanning technology to quantify and analyze the staggering morphological variation displayed by the members of the family. For more information, visit the digital imaging project page.

University of California, Berkeley, PhD candidate, Zach Hanna, is working with Academy curator Jack Dumbacher to study the processes of hybridization and gene introgression in native Spotted Owls and invasive Barred Owls in the western U.S. They are working on a whole genome project of the Northern Spotted Owl using low-coverage whole genome sequencing efforts to track movement of genetic material between the two owl species.

PhD candidate Moises Bernal and Academy curator Luiz Rocha are using massively parallel sequencing to elucidate the evolutionary history of grunts (genus Haemulon). Sister species of this genus have completely overlapping distributions and some of them show evidence of hybridization, making this group an interesting model for the study of speciation.

Former CCG Laboratory and Collections Manager Anna Sellas, along with collaborators Kim Hull and Dr. Bob Hueter (Mote Marine Laboratory) are using nuclear and mitochondrial DNA data to investigate the population structure and migration patterns of spotted eagle rays in the Gulf of Mexico and northern Caribbean Sea. For more information about this project, visit the spotted eagle ray conservation page.

In collaboration with Dr. James Parham of California State University, Fullerton, Dr. Brian Simison is investigating the genetic impact of invasive species and hybridization in slider turtle populations of the United States and Caribbean using modern genomic techniques such as Restriction Site Associated DNA sequencing. For more information about this project, visit the turtle evolutionary genomics page.

For her Master's project Elizabeth Carlen is working with Academy curator Dr. Jack Dumbacher on the evolution of giant sengis (genus Rhynchocyon). She is using DNA sequences of mitochondrial and nuclear regions to reconstruct the molecular phylogeny of this genus.

Academy curator Peter Fritsch and Boni Cruz are studying the evolution of the sweetleaf family (Symplocaceae), a flowering plant group of ca. 340 species that grows mainly in the tropical regions on the lands bordering the Pacific Rim. By combining data from DNA sequences and fossils, these researchers have been able to track the origin and spread of this group over geological time. They were able to infer that the family originated in the Northern Hemisphere, most likely Europe, in the early Age of Mammals (Cenozoic), and then moved south to the tropics as climates subsequently dried and cooled later in this period. This provides an example of how modern tools for evolutionary biology can provide insights on how plants responded to ancient changes in climate. 

Postdoctoral researcher Darko Cotoras is working on a collaborative project between the California Academy of Sciences (Dr. Charles Griswold and Dr. Brian Simison) and the Paleogenomics lab at UC Santa Cruz (Dr. Beth Shapiro and Dr. Ed Green) studying the diversification patterns and biogeography of Tetragnatha spiders on different archipelagos from the Pacific Ocean. The project seeks to generate a phylogenomic reconstruction using a targeted enrichment approach, as well as improves and optimizes DNA extraction methods for museum specimens.

Cerise Chen is working for Academy curator Dr. Dave Kavanaugh sequencing DNA from the basal grade of carabid beetles in order to reconstruct the phylogenetic relationships among the supertribe Nebriitae, including the so-called “ice beetles”. These data will be used to compare phylogenetic hypotheses previously developed using morphological data.

Academy research associate and University of Nevada PhD candidate, Joshua Hallas, is collaborating with Academy researchers on understanding the 2015 bloom of Hopkin's rose, Okenia rosacea, along the California and Oregon coast. This species of nudibranch has rarely been observed in the colder waters of northern California, however, the warmer waters of 2015 may have allowed this species to expand its range as far north as central Oregon. Employing population genomic techniques, they hope to understand how changing water temperatures might have effected population structure and this sea slug's dispersal ability.

Academy Research Fellow Dr. Durrell Kapan and his collaborators have sequenced complete genomes of several species of Heliconius butterflies and are using comparative genomics to understand the role of natural selection and hybridization in rapid speciation.

Academy curator, Dr. Shannon Bennett, and post-doctoral researcher, James Angus Chandler, are using high throughput DNA sequencing to understand the drivers of diversification of pathogenic microbes, such as mosquito-borne infectious diseases. She is sequencing viruses, vectors and hosts and measuring virus copy number to determine patterns of genetic mutations related to epidemic potential and to explore within-host diversity of viruses.

Academy Researcher Christina Piotrowski is investigating the taxonomy and biogeography of marine scaleworm taxa (Polychaeta: Polynoidae and Iphionidae) using molecular and morphological phylogenetics. Molecular datasets reveal higher than expected levels of genetic diversity within currently accepted scaleworm taxa which supplement morphological data towards establishing realistic taxonomic boundaries.