A Study of phylogenetic trees versus networks to objectively identify haplogroups in mitochondrial dna

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Title: A Study of phylogenetic trees versus networks to objectively identify haplogroups in mitochondrial dna
Author: Ruda, Melissa
Abstract: Mitochondrial DNA is important in the studies of population, medicine, migration, and forensics, as well as a few other disciplines. Further insight on grouping mtDNA sequences could give insight on identifying genetic variation that causes susceptibility to disease, more personalized medicines, or more effective forensic analysis. Mitochondrial DNA is currently grouped into haplogroups determined from phylogenetic tree analysis. Phylogenetic tree analysis may not be the optimal solution for mtDNA because they work better for data above the species level, to show population relationships, not sequences that only differ by a few nucleotides. To compare both analysis, sample data was obtained from Phylotree.org (van Oven & Kayser, 2009). The sequences were run through Clustal W (Latkin et al., 2007) for a multi sequence alignment. The results were then used to create a Neighbor-Joining phylogenetic tree in PAUP* 4.0 (David Swofford, 1993). The results where then compared to a phylogenetic network created using SplitsTree4 (D. H. Huson and D. Bryant 2006). The groupings in the network were compared to the groupings in the tree as well as what would be expected based on haplogroups. Even though the results were similar, the phylogenetic network did give a slightly more thorough result.
Record URI: http://hdl.handle.net/1850/14569
Date: 2011-08-02

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