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PROJECTS: MICROARRAY-BASED GENOME SCANNING FOR FUNCTIONAL DIVERGENCE IN ACROPORA

Understanding the evolutionary origins and maintenance of biodiversity is one of the major challenges for conservation scientists. Preservation of genetic diversity is essential for effective management and our best option for anticipating changes in the future is to explore the changes that have taken place in the past. Novel genetic tools called microarray chips allow biologists to explore genetic variation at every sequenced gene in a genome. We are using microarray technology to perform a genome-wide survey of genes responsible for functional differentiation between two cross-fertile species of coral. Characterizing these genes will provide important information about the processes that have driven differentiation between these species.

With over 100 species spanning three ocean basins, Acropora is the most diverse and widespread genus of reef-building coral. Fossil records and genetic data place the genus' origin in the Paleocene, with relatively recent diversification associated with Plio-Pleistocene sea-level changes. Acropora is characterized by widespread reproductive compatibility between closely related species, large sympatric distributions and highly synchronized mass spawning events. These characteristics make Acropora an excellent system for studying how selection and gene flow interact to produce and maintain functional diversity among sympatric species.

Preliminary results along with previously published studies, suggest that although introgression is common between these species, not all regions of the genome are crossing species' borders at the same rate. According to Wu's genic view of the process of speciation, gene sharing can continue to occur freely over much of the genome in species that have recently diverged. However, functionally divergent genomic regions will be under selection against introgression. I contend that the pattern of incomplete introgression observed in Acropora is a result of incomplete speciation among these recently diverged species. A similar intermediate stage of speciation, with functional divergence present at only a portion of genomic regions, has been demonstrated for two cross-fertile species of oak.  The identification and characterization of these divergent loci in Acropora would allow for a thorough understanding of the diversifying forces that have acted on this taxon.

Acropora millepora is the most "genomically equipped" species in the genus with 10,247 publicly available gene sequences, or expressed sequence tags (ESTs). A. pulchra belongs to the same morphologically determined sub-group as A. millepora (the A. aspera group), and the two species have been shown to hybridize readily in vitro. Additionally, A. millepora and A. pulchra are morphologically easily distinguishable, which allows for unambiguous identification of individuals within natural populations. We study these two speciesto explore the process of speciation in corals by identifying and characterizing loci associated with functional divergence.

We are applying spotted cDNA microarrays designed from the A. millepora EST library to identify regions that are divergent between A. millepora and A. pulchra. Researchers at James Cook University and the Australian National University have already developed microarrays of this type for use in gene expression analyses, but these arrays have never been used with genomic DNA.  We competitively hybridize paired samples from the two species to each array, with each species bearing a distinct fluorescent dye. This allows independent visualization of the two samples on the same array. The A. millepora samples are near-perfect matches for the sequences on the microarray and therefore can be considered a baseline for comparison. The reduction in the degree of fluorescence of A. pulchra samples from the baseline indicate the degree of sequence divergence for a given gene between these two species.

"Species" are currently the major unit of protection in conservation management. Yet, the ecological meaning of the groups we define as species is still hotly contested. We are working to improve our understanding of the evolutionary role and ecological implications of distinct "species" in taxa that routinely exchange genetic information. Such taxa (e.g., plants, corals) are of particular conservation priority as they often form the structural foundations of complex ecosystems.

As an example, corals form the structural base of the oceans' most diverse and productive ecosystems. In addition to the inherent value of this biodiversity, coral reefs confer many direct economic benefits to humanity, which have been valued at US$30 billion annually. These benefits, termed ecosystem services, have been shown to be closely related to levels of ecosystem biodiversity, decreasing in productivity with a decline in species diversity. Twenty percent of the world's original coral reef habitat has already been damaged beyond repair and 50% of current reefs are severely threatened by anthropogenic impacts including the imminent threat of global climate change. This research will provide us with a more comprehensive understanding of the functional differentiation underlying coral diversity, and will open the doors for research on how this diversity will be impacted by changes in the future.

Hopkins Marine Station, Stanford University, 120 Ocean View Blvd., Pacific Grove, CA 93950