Marine & Environmental Sciences Faculty Articles
Revisiting the Phylogeny of Zoanthidea (Cnidaria: Anthozoa): Staggered Alignment of Hypervariable Sequences Improves Species Tree Inference
Document Type
Article
Publication Date
1-2018
Publication Title
Molecular Phylogenetics and Evolution
Keywords
Gene tree; Hypervariable sequences; Phylogeny-informed alignment; Species tree; Staggered alignment
ISSN
1055-7903
Volume
118
First Page
1
Last Page
12
Abstract
The recent rapid proliferation of novel taxon identification in the Zoanthidea has been accompanied by a parallel propagation of gene trees as a tool of species discovery, but not a corresponding increase in our understanding of phylogeny. This disparity is caused by the trade-off between the capabilities of automated DNA sequence alignment and data content of genes applied to phylogenetic inference in this group. Conserved genes or segments are easily aligned across the order, but produce poorly resolved trees; hypervariable genes or segments contain the evolutionary signal necessary for resolution and robust support, but sequence alignment is daunting. Staggered alignments are a form of phylogeny-informed sequence alignment composed of a mosaic of local and universal regions that allow phylogenetic inference to be applied to all nucleotides from both hypervariable and conserved gene segments. Comparisons between species tree phylogenies inferred from all data (staggered alignment) and hypervariable-excluded data (standard alignment) demonstrate improved confidence and greater topological agreement with other sources of data for the complete-data tree. This novel phylogeny is the most comprehensive to date (in terms of taxa and data) and can serve as an expandable tool for evolutionary hypothesis testing in the Zoanthidea. Spanish language abstract available in Text S1. Translation by L. O. Swain, DePaul University, Chicago, Illinois, 60604, USA.
Additional Comments
NSF grant #s: CBET-0937987, CBET-1240416, OCE-0550599
NSUWorks Citation
Timothy D. Swain. 2018. Revisiting the Phylogeny of Zoanthidea (Cnidaria: Anthozoa): Staggered Alignment of Hypervariable Sequences Improves Species Tree Inference .Molecular Phylogenetics and Evolution : 1 -12. https://nsuworks.nova.edu/occ_facarticles/1007.
ORCID ID
0000-0002-6485-6823
ResearcherID
M-7702-2013
DOI
10.1016/j.ympev.2017.09.008
Comments
©2017 Elsevier Inc.