Center for Comparative Genomics

Current CCG Lab Projects

Plants

Melastomataceae are the 7th largest family of flowering plants, and are often among the most abundant and speciose groups in tropical forests worldwide. Dr. Darin Penneys is collecting DNA sequence data in order to elucidate phylogenetic relationships and revise the family-level classification. These data will also be useful for examining patterns of ecological and morphological character change.

 

Boni Cruz, Academy Curator Dr. Peter Fritsch, and colleagues from Wake Forest University are studying the evolution of the wintergreens, a flowering plant group within the heath family (Ericaceae). The group is represented in southeast Asia primarily by the genus Diplycosia. Fritsch went to Borneo to collect samples of this genus to estimate the relationships of this group to the larger Gaultheria group, which includes the classic wintergreen of the northeastern United States and salal in the western U.S.

 

Boni Cruz, in collaboration with Academy Curator Dr. Kim Steiner, uses molecular data to create phylogenies to understand the evolution of pollination systems in Nemesia, Diascia and Hemimeris (Scrophulariaceae) in southern Africa.

Beetles

Sophie Archambeault is working for Academy Curator Dr. Dave Kavanaugh sequencing DNA from the basal grade of carabid beetles. Dr. Kavanaugh is specifically interested in the phylogenetic relationships among the supertribe Nebriitae. These data will be used to make phylogenetic trees which will be compared to the existing trees created using morphological data.

 

Meghan Culpepper is a graduate student working with Dr. Dave Kavanaugh on beetle systematics. Her Master’s thesis project involves performing a thorough morphological and molecular phylogenetic analysis of the species comprising Scaphinotus subgenus Brennus in order to determine the evolutionary relationships within this group.

Seahorses & Seadragons

Beth Moore is the project coordinator for the Seahorse Research and Conservation Program. She is using genetics to study the evolutionary relationships of the fish family Syngnathidae, which includes seahorses, seadragons, pipehorses, and pipefish.

 

In collaboration with Dr. Sarah Cohen (SFSU) and Dr. Healy Hamilton (CAS), Mariana Padron is examining geographic patterns of genetic connectivity in two sympatric seahorse species from the Caribbean, Hippocampus reidi and H. erectus.

Spiders

Anthea Carmichael  is currently working for Dr. Charles Griswold sequencing DNA from Orsolobids, or Giant Goblin Spiders, found in Africa, South America, New Zealand, and Australia.  The resulting phylogeny will be dated and used to assess a variety of vicariance and dispersal scenarios.

Scaleworms

Chrissy Piotrowski uses molecular phylogenetics to study the taxonomy and biogeography of cryptic northeastern Pacific species of the intertidal polychaete scaleworm, Harmothoe “imbricata”.  First described in 1767, this species is reported from wide-ranging marine localities, yet members of this group have probably experienced convergent evolution of morphologies. Additionally, some populations have likely been transported and introduced to their current localities by human activity.

Barnacles

Bob Van Syoc is using DNA sequences generated in the lab to study barnacle phylogenetics and biogeography.  This sponge-inhabiting species from Madagascar has some intriguing morphological characteristics that allow the sponge host to grow up and around the barnacle shell.

Nudibranchs

For her Master's project at San Francisco State University, Kristen Roberts is studying the evolution of the aeolid nudibranch family Tergipedidae. She is using the DNA sequences of mitochondrial and nuclear genes to establish a molecular phylogeny of this family.

 

Jennifer Harris is investigating evolutionary relationships in polycerid nudibranchs. Juvenile and adult forms of Triopha maculata (formerly two separate species) and the potentially synonymous east coast Ancula gibbosa and west coast A. pacifica are of particular interest. She hopes molecular data will clarify morphological findings while contributing to the overall systematics of polycerid diversity.

Birds

Jean Carlos Mattos-Reano is currently working on his Master’s thesis project using ancient and modern DNA samples to investigate the phylogenetics of Southern and Northern Cassowaries (Casuarius casuarius and Casuarius unappendiculatus). Strong variation suggests that populations are isolated in different lowland basins, though the  subspecies boundaries remain unclear.

 

For her Master’s research, Hazel Thwin is conducting a molecular study of Fire-tailed Myzornis, Myzornis pyrrhoura, from the family Timaliidae. Hazel is a student of Academy Curator Dr. Jack Dumbacher.

Turtles

In collaboration with Dr. James Parham of the Field Museum of Natural History, Anna Sellas and Brian Simison are investigating the genetic impact of invasions and hybridization in slider turtle populations of the US and Carribean using DNA sequence and microsatellite data.

Mammals

From Dr. Ophir Klein's lab (UCSF), Cyril Charles and Vagan Mushegyan are working on sequencing DNA from various rodent species to investigate genotype/phenotype relationships and better understand rodent evolution.