| Abstract Detail
Systematics Section/ASPT Schori, Melanie [1], Lin, Wei [2]. Analyzing Sequence Variation: Barcodes to Genomes. DNA barcoding and phylogenetic reconstructions both depend on molecular data that exhibit appropriate levels of variation. Ideally, within-species variation should be low, while between-species variation should be higher but not too high. However, intraspecific sequence variation of chloroplast gene regions is rarely discussed in the literature, and no appropriate analysis technique is widely used. We present a combination of analysis algorithms for assessing sequence variation in aligned datasets. The first, based on Hamming distance, calculates within- and between-species variation, and identifies sequences that are likely to be mislabeled. The second, which uses distribution distances, determines how many informative positions exist for distinguishing pairs of species. These results can then be pooled to assess genus-level variation for the gene region of interest. The algorithms can be applied to combined datasets and could be used to analyze genome-level alignments to identify regions with levels of variation suitable for phylogenetic analyses. Broader Impacts:
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1 - Ohio University, Environmental & Plant Biology, Porter Hall 315, Athens, OH, 45701, USA
2 - Ohio University, Mathematics, Morton Hall 527, Athens, OH, 45701, USA
Keywords:
Hamming distance
DNA barcoding
Phylogenetic analysis
Sequence variation
Intraspecific variation.
Presentation Type: Oral Paper:Papers for Sections
Session: 18
Location: Magnolia/Riverside Hilton
Date: Tuesday, July 30th, 2013
Time: 8:30 AM
Number: 18001
Abstract ID:238
Candidate for Awards:None |
