Title

Comparing McCloud River Sculpins’ FST using genomics and bioinformatics

Poster Number

09B

Lead Author Major

Biological Sciences

Lead Author Status

Junior

Second Author Major

Biological Sciences

Second Author Status

Freshman

Format

Poster Presentation

Faculty Mentor Name

Jason Baumsteiger

Faculty Mentor Email

jbaumsteiger@pacific.edu

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

This document is currently not available here.

Share

COinS
 
Apr 28th, 10:00 AM Apr 28th, 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.