College of Arts and Sciences

Speciation/DNA Barcoding

Speciation and DNA barcoding are unique projects that make use of the same sequence data. Thus, inferences can be made about both goals through the collection and phylogenetic analysis of sequences.


The taxonomy for the brown algae is highly unresolved and there is much to be studied in regards to speciation events. Understanding the evolutionary history of brown algae will help us better classify algae, understand the movement of algae between ocean basins, the shift from unicellular to multicellular, and the effect of flow regimes on evolution. Research on speciation events often requires more than one gene region to be able to make inferences about speciation events.

DNA Barcoding

DNA barcodes have been used successfully in studies on red, green and some brown algae. A DNA barcode is a short gene region that, once sequenced, gives a clear species identity. Choosing to identify species with molecular instead of morphological variation avoids problems with misidentification due to high rates of phenotypic plasticity. Effective DNA barcodes are about 700 base pairs and focus on one or a partial gene region.

Brian analyzes a gel.Eisenia arborea

Kelp forests are very productive ecosystems in temperate subtidal communities around the world. Past research suggests that water flow and hydrodynamic pressure differences between the shallow and deep subtidal zones may shape algal morphology. Eisenia arborea is an example of a kelp species with populations in the shallow subtidal and deep subtidal zones near Catalina Island, California, each with a distinct morphology. Whether the morphological differentiation is caused by phenotypic plasticity or genetic differences remains unclear. The goal of this research is to determine whether these populations are still one species adapted to two different environments or have diversified sufficiently to be considered two distinct species. Samples were collected from these two subtidal populations and DNA was extracted from all samples. Based on the difference in polysaccharide content from the total genomic DNA extractions; variation between these two populations were evident. Two gene regions, one nuclear (the 5’ end of LSU [Z fragment] and one mitochondrial (cox 1 5’) were amplified and sequenced. Phylogenetic analyses for the LSU Z fragment and cox 1 5’ gene region showed a significant amount of genetic variation. Both showed promise as DNA barcodes/markers to differentiate between individuals in the shallow or deep populations. Further sequencing and phylogenetic analyses of both gene regions for the two populations will be performed with exciting results to follow.

DNA Barcoding in Sargassum

Sargassum is one of the most ecologically important and widespread brown algal genera. The genus commonly forms either pelagic floating beds or large coastal stands in tropical to subtropical ocean basins around the world. However, there is still much to be discovered about its evolutionary history and phylogeny, but progress is hampered by the inability to identify species with 100% accuracy. Problems with identification are due to high rates of phenotypic plasticity and cryptic species as well as a lack of studies of Caribbean Sargassum species. This is especially true in coastal regions of Panama, where estimates of diversity are high with many potentially undiscovered species. The development of a DNA barcode for Sargassum would solve problems with traditional identification based on morphology and supply data for phylogenetic analysis. The goal of this project is to compare three gene regions for barcoding utility, and use the data to contribute to the resolution of Sargassum’s phylogeny. Twenty-one samples from the Caribbean Sea and the Pacific Ocean in areas surrounding Panama were obtained. Samples were extracted using a modified CTAB method and whole genome amplified using Genomiphi methods to archive DNA. Several gene regions were selected, amplified (e.g. LSU, rbcL and ITS-2) and sequenced. All 21 samples were successfully extracted and products of whole genome amplification were archived for future use. Master alignments for individual gene regions are being built for the genus using new and GenBank data. Phylogenetic analysis produced a Maximum Likelihood-Bootstrap tree that demonstrated the LSU fragment Z does not have enough variation to function as a barcode. Future directions for this study will focus on pairing LSU Z with another LSU fragment or other gene regions. 


Ascoseria is a unique species of algae that is endemic to the harsh conditions of Antartica. The order Ascosierales, like other brown algal orders, has a highly unresolved taxonomy. Ascoseira mirabilis exhibits different morphologies between areas with turbulent and quiet flow regimes. Whether differences in stipe length are due to phenotypic plasticity or adaptive evolutionary changes is unclear. Specimens were collected from three separate areas, total genomic DNA was extracted and amplification of the regions ITS-2 and rbcL was carried out. Sequences were aligned and phylogenetic analysis was carried out. Not enough variation was discovered in the gene regions to determine whether speciation had occurred between the two populations. Future studies will focus on several other gene regions as well as Radtag analysis.