Genome-wide analysis of melanism, introgression, and aggression in eastern fox (Sciurus niger) and eastern grey (Sciurus carolinensis) squirrels
Presenter Type
UNO Graduate Student (Masters)
Major/Field of Study
Biology
Other
Biology
Advisor Information
James A. Wilson
Location
MBSC304 - G (Masters)
Presentation Type
Oral Presentation
Start Date
24-3-2023 9:00 AM
End Date
24-3-2023 10:15 AM
Abstract
This study examines the genetic basis of melanism in fox squirrels (Sciurus niger) in Omaha and Lincoln, Nebraska. Melanism can be attributed to variation in MC1R or ASIP. All melanistic fox squirrels (n = 8) sampled in this study were found to have a 24 base pair deletion in MC1R. No sampled melanistic squirrels had variation in ASIP. Both fox and gray squirrels in this study had haplotypes that could be placed into previously reported MC1R haplotype groupings. In addition, fox squirrels had wider variation in ASIP than was previously reported. Whole genome sequencing was done on seven sampled squirrels: two wild-type (rufus) fox squirrels, two melanistic fox squirrels, and three wild-type gray squirrels in order to better understand introgression between these species. The FST analysis to discover divergence between fox (n = 4) and gray squirrel (n = 3) populations showed that chromosome 2 had the highest number of consecutive windows with high FST. The average FST between fox and gray squirrels was 0.639. Melanistic fox squirrels (n = 2) had a lower measure of average FST when being compared to wild-type fox squirrels (n = 2, average FST = -0.0284,). The genome-wide nucleotide diversity (π) of gray squirrels was higher than that of fox squirrels (0.004 and 0.003, respectively). A genome-wide runs of homozygosity analysis found fox squirrels to be more inbred than gray squirrels. Additionally, melanistic squirrels were more inbred than their rufus counterparts. A gray squirrel (Sciurus carolinensis) genome was annotated and made publicly available as a reference sequence on the National Center for Biotechnology Information (NCBI) platform. RNA-seq data from this squirrel was analyzed to measure the expression of genes contributing to risk factors associated with aggression, with the highest rated gene, MAOA, found to express in various tissues. Additionally, CDH13, a gene that can contribute to aggression in tandem with MAOA, was found to be in close proximity (< 6 Mb) to MC1R. This gene needs further study to better understand its impact in relation to melanistic squirrels.
Scheduling
9:15-10:30 a.m., 10:45 a.m.-Noon
Genome-wide analysis of melanism, introgression, and aggression in eastern fox (Sciurus niger) and eastern grey (Sciurus carolinensis) squirrels
MBSC304 - G (Masters)
This study examines the genetic basis of melanism in fox squirrels (Sciurus niger) in Omaha and Lincoln, Nebraska. Melanism can be attributed to variation in MC1R or ASIP. All melanistic fox squirrels (n = 8) sampled in this study were found to have a 24 base pair deletion in MC1R. No sampled melanistic squirrels had variation in ASIP. Both fox and gray squirrels in this study had haplotypes that could be placed into previously reported MC1R haplotype groupings. In addition, fox squirrels had wider variation in ASIP than was previously reported. Whole genome sequencing was done on seven sampled squirrels: two wild-type (rufus) fox squirrels, two melanistic fox squirrels, and three wild-type gray squirrels in order to better understand introgression between these species. The FST analysis to discover divergence between fox (n = 4) and gray squirrel (n = 3) populations showed that chromosome 2 had the highest number of consecutive windows with high FST. The average FST between fox and gray squirrels was 0.639. Melanistic fox squirrels (n = 2) had a lower measure of average FST when being compared to wild-type fox squirrels (n = 2, average FST = -0.0284,). The genome-wide nucleotide diversity (π) of gray squirrels was higher than that of fox squirrels (0.004 and 0.003, respectively). A genome-wide runs of homozygosity analysis found fox squirrels to be more inbred than gray squirrels. Additionally, melanistic squirrels were more inbred than their rufus counterparts. A gray squirrel (Sciurus carolinensis) genome was annotated and made publicly available as a reference sequence on the National Center for Biotechnology Information (NCBI) platform. RNA-seq data from this squirrel was analyzed to measure the expression of genes contributing to risk factors associated with aggression, with the highest rated gene, MAOA, found to express in various tissues. Additionally, CDH13, a gene that can contribute to aggression in tandem with MAOA, was found to be in close proximity (< 6 Mb) to MC1R. This gene needs further study to better understand its impact in relation to melanistic squirrels.