Comparing McCloud River Sculpins’ FST using genomics and bioinformatics
Poster Number
09B
Format
Poster Presentation
Faculty Mentor Name
Jason Baumsteiger
Faculty Mentor Department
Biological Sciences
Abstract/Artist Statement
The goal of our research was to find how similar McCloud River Sculpin (Cottus) are to other locations throughout California. Sculpin are a type of benthic fish that live at the bottom of freshwater systems. Using SNPs (single-nucleotide polymorphisms) obtained after extracting and sequencing genomic data, we analyzed all samples and using bioinformatics, compared the allele frequency of collected sculpins. We then performed pairwise comparisons between the different locations and obtained differential FST values. FST values are measures of population differentiation due to genetic structure ranging from 0 (no difference) to 1 (significantly different). We wanted to know if sculpin from Hot Springs Creek (HSS) or the McCloud River (McC) are a distinct species/population or are similar to known species from nearby sites. These sites include: Prickly Sculpin from Putah Creek (Put), Pit Sculpin from the Pit River (Pit), and Riffle Sculpin from the Mokelumne (Mok), Merced (Mer), and Sacramento (Sac) Rivers. We found sculpins from the mouth of the McCloud River had a much higher value when compared with other locations on the McCloud River, but low FST values when all other McCloud locations are compared. This indicates individuals at the mouth are probably not the same species as the ones in the rest of the McCloud. The HSS population comparison with other locations resulted in high FST values, which indicates their population may not be related to any of the other locations sampled. Thus, by analyzing Fst values,we can conclude that sculpin at the mouth of the McCloud are a different species from other parts of the McCloud River and sculpin from HSS may be a different species altogether. Therefore, we need to protect and manage these sculpins differently than we have been currently.
Location
DeRosa University Center, Ballroom
Start Date
28-4-2018 10:00 AM
End Date
28-4-2018 12:00 PM
Comparing McCloud River Sculpins’ FST using genomics and bioinformatics
DeRosa University Center, Ballroom
The goal of our research was to find how similar McCloud River Sculpin (Cottus) are to other locations throughout California. Sculpin are a type of benthic fish that live at the bottom of freshwater systems. Using SNPs (single-nucleotide polymorphisms) obtained after extracting and sequencing genomic data, we analyzed all samples and using bioinformatics, compared the allele frequency of collected sculpins. We then performed pairwise comparisons between the different locations and obtained differential FST values. FST values are measures of population differentiation due to genetic structure ranging from 0 (no difference) to 1 (significantly different). We wanted to know if sculpin from Hot Springs Creek (HSS) or the McCloud River (McC) are a distinct species/population or are similar to known species from nearby sites. These sites include: Prickly Sculpin from Putah Creek (Put), Pit Sculpin from the Pit River (Pit), and Riffle Sculpin from the Mokelumne (Mok), Merced (Mer), and Sacramento (Sac) Rivers. We found sculpins from the mouth of the McCloud River had a much higher value when compared with other locations on the McCloud River, but low FST values when all other McCloud locations are compared. This indicates individuals at the mouth are probably not the same species as the ones in the rest of the McCloud. The HSS population comparison with other locations resulted in high FST values, which indicates their population may not be related to any of the other locations sampled. Thus, by analyzing Fst values,we can conclude that sculpin at the mouth of the McCloud are a different species from other parts of the McCloud River and sculpin from HSS may be a different species altogether. Therefore, we need to protect and manage these sculpins differently than we have been currently.