Center for Comparative Genomics

Current CCG Lab Projects

Flowering 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.

 

Marcela Alvear, Academy Curator Dr. Frank Almeda, and Dr. Darin Penneys are studying the evolutionary relationships of the genus Monochaetum. This genus is restricted to the neotropics in montane habitats in Mexico, Central America, extending into the northern Andes in South America and reaching the Guayana Highlands. The Tropical Andes are a notable center of diversity for Monochaetum. This study is a thorough morphological and molecular investigation of the genus in order to determine the evolutionary relationships within this group, its position in the large family, and to understand its biogeographic history and diversification patterns.

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.

Spiders

Anthea Carmichael  is currently working with 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.

Frogs

Xenophrys Wilkinson

Anna Sellas is working with Dr. Jeff Wilkinson of the Department of Herpetology using DNA sequences to understand the evolutionary relationships and delimit several potentially new species of frogs from Myanmar in the genera Ansonia, Polypedates, and Xenophrys. This work will add to the extensive amount of research (87 papers and 23 new species described at present) from the NSF funded Amphibian and Reptile Diversity of Myanmar Project.

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.

 

Research Assistants Chris Grace and Tinya Hoang are using molecular forensic techniques to elucidate the trade patterns of dried seahorses that are used in traditional Chinese medicine. They are currently sequencing DNA from illegally traded seahorses that were confiscated by the U.S. Fish and Wildlife Service at San Francisco International Airport. Genetic data will be used to identify what species of seahorses are being collected and from where they have originated.

Barnacles

Dr. 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.

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.

Turtles

In collaboration with Dr. James Parham of the California State University at Bakersfield, Anna Sellas and Dr. Brian Simison are investigating the genetic impact of invasions and hybridization in slider turtle populations of the US and Caribbean using DNA sequence and microsatellite data.

Sharks & Rays

Anna Sellas along with collaborators Kim Bassos-Hull from Mote Marine Laboratory and Kevin Feldheim from the Field Museum of Natural History are using nuclear and mitochondrial DNA data to investigate the population structure of spotted eagle rays (Aetobatus narinari) in the Gulf of Mexico.

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.

 

Dr. Rebecca Johnson is using molecular data to help elucidate evolutionary relationships in the chromodorid nudibranchs.  With over 300 described species, chromodorids are one of the most diverse (and colorful) Molluscan clades.  She is using the resulting hypotheses of relationships to better understand the evolution of color pattern and mimicry.  She is also interested in eastern Pacific intertidal invertebrates.

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.

 

Dr. Jerome Fuchs is currently working with Dr. David Mindell on a species level phylogeny of the worldwide distributed family Falconidae using a combination of mitochondrial and nuclear loci.  They primarily aim to reconstruct the biogeographic history of the family and understand how they diversified during their evolutionary history.

 

Drs. Jack Dumbacher, Jerome Fuchs, and David Mindell are collaborating with Drs. Joseph DeRisi and Amy Kistler at UCSF to screen wild populations of birds for known and unknown viruses.  They are testing the utility of ViroChip microarray technology, designed in the lab of Dr. DeRisi at UCSF, for the discovery of pathogens in wild bird populations. Technician Zach Hanna is currently applying viral screening techniques in the CCG lab to bird genetic samples from Papua New Guinea islands and several localities in California to describe and understand the role of viruses in natural populations.

Snakes

Ana Lisette Arellano, a 2009 SSI intern and currently PhD candidate at the University of Colorado, is working with Dr. Bob Drewes on the genetic relationships of two snake populations (Lamprophis) on the Gulf of Guinea Islands of São Tomé and Príncipe. Having determined that the two populations are genetically distinct from one another, Arellano, Drewes and two European collaborators are now establishing their relationship to African mainland species.