Abstract Detail



Phylogenomics

Kates, Heather [1], Johnson, Matthew [2], Gardner, Elliot [3], Zerega, Nyree [4], Wickett, Norman [5].

Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus.

Untapped information about allelic diversity within populations and individuals (i.e. heterozygosity) could improve phylogenetic resolution and accuracy. Many phylogenetic reconstructions ignore heterozygosity because it is difficult to assemble allele sequences and combine allelic data across unlinked loci and it is unclear how reconstruction methods accommodate variable sequences. We present a novel method for assembling allele sequences from target enriched Illumina sequencing libraries and perform supermatrix phylogeny reconstruction and species tree estimation of Artocarpus based on three methods of accounting for heterozygous sequences. We characterize the extent to which highly heterozygous sequences impeded phylogeny reconstruction and determine whether the use of allele sequences improves phylogenetic resolution or decreases topological uncertainty. We show here that it is possible to infer phased alleles from target enriched Illumina libraries. We find that highly heterozygous sequences do not contribute disproportionately to poor phylogenetic resolution and that the use of allele sequences for phylogeny reconstruction does not have a clear effect on phylogenetic resolution or topological consistency.We provide a framework for inferring phased alleles from target enrichment data and for assessing the contribution of allelic diversity to phylogenetic reconstruction. 


1 - University of Florida, PO Box 117800, Gainesville, FL, 32611-7800, United States
2 - Texas Tech University, Biological Sciences, 2901 Main Street, Ms3131, Lubbock, TX, 79409, United States
3 - Northwestern University / Chicago Botanic Garden, Plant Science, 1000 Lake Cook Road, Glencoe, IL, 60022.0, United States
4 - Northwestern University And The Chicago Botanic Garden, Plant Biology And Conservation, 2205 Tech Drive, Hogan 2-144, Evanston, IL, 60202, United States
5 - Chicago Botanic Garden, 1000 Lake Cook Rd., Glencoe, IL, 60022, United States

Keywords:
Targeted Sequence Capture
Hyb-Seq
heterozygosity
allelic sequence data
Phylogenomics methods.

Presentation Type: Oral Paper
Number:
Abstract ID:639
Candidate for Awards:None


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