Characterizing Nuclear genes of Mitochdonrial origin in avian clades
Restricted (Penn State Only)
- Author:
- Kumar, Balaji
- Graduate Program:
- Biology
- Degree:
- Master of Science
- Document Type:
- Master Thesis
- Date of Defense:
- February 22, 2023
- Committee Members:
- David Toews, Thesis Advisor/Co-Advisor
Zachary A Szpiech, Committee Member
Stephen Schaeffer, Professor in Charge/Director of Graduate Studies - Keywords:
- Nuclear genes of mitochondrial origin
Phylogenetics
Evolution
Bioinformatics - Abstract:
- Structural variation and single nucleotide polymorphisms (SNPs), play a significant role in phenotypic evolution, functional innovation, ecological differentiation, and speciation. The goal of this research is to investigate a relatively understudied class of structural variation, focused specifically on NUclear genes of MiTochondrial origin (NUMTs). NUMTs are mitochondrial DNA fragments inserted into chromosomes during DNA double-strand break repair. NUMTs were detected and annotated in two clades of Parulid warblers, using whole genome short read resequencing data, which were mapped to the Setophaga coronata reference genome. We found 1065 unique loci where NUMTs inserted. On average, every species had 217 NUMT loci with a total NUMT content of 88 kb, with a few exceptions. We found that NUMTs originated uniformly across the mitogenome, including the D-loop. We found that larger NUMTs were fewer in number than smaller NUMTs, most likely due to selection against large insertions. We reconstructed NUMT ancestral states on the Lovette tree, using maximum parsimony and found that the majority, 634 out of the uniquely resolved 730 NUMTs, inserted recently, prior to divergence from their sister species. Of these, 468 NUMTs were found to be synapomorphic insertions. A total of 35 NUMTs were inserted before divergence of Setophaga and Vermivora. We found evidence of a few rare NUMTs that were deleted, post insertion. We used NUMTs as binary markers and reconstructed phylogenetic relationships using parsimony. NUMTs recapitulated multiple sister species relationships, similar to the accepted species tree, but differed in topology, possibly due to pseudogenization, deletion and other mutations of NUMTs leading to loss of phylogenetic signal over time. Our analysis shed new light on the evolution of NUMTs in these avian clades.