Abstract Detail

Systematics Section/ASPT

Godden, Grant T. [1], Chamala, Srikar [2], Soltis, Douglas E. [3], SOLTIS, PAMELA S. [3].

85 Nuclear Genes Largely Resolve the Phylogeny of Lamiales.

Lamiales are one of the largest orders of flowering plants, with a worldwide distribution and more than 20,000 species from ca. 25 families. This hyper-diverse clade of life presents many exciting opportunities to investigate global patterns of radiation and to link these patterns to shifts in distribution, ecology, and phenotypic evolution. Unfortunately, comparative studies of Lamiales have proven somewhat intractable due to poor phylogenetic resolution. Progress has been made recently, however, with large-scale sampling of taxa and plastid genes (e.g., over 17,000 bp of aligned sequence data); our understanding of interfamilial relationships is now much improved. Nevertheless, phylogenies based solely on plastid data provide a very biased view of Lamiales evolution, and nuclear data have been largely underexplored in studies of this diverse order. To address this issue, we employed a novel pipeline and marker discovery tool, MarkerMiner 1.0, and 76 transcriptomes from the One Thousand Plants Project (1kp) to identify a large set of single-copy nuclear (SCN) loci for a phylogenetic investigation of Lamiales. Our sampling included accessions from 18 of the 25 families of Lamiales (i.e., Acanthaceae, Bignoniaceae, Byblidaceae, Calceolariaceae, Gesneriaceae, Gratiolaceae, Lamiaceae, Lentibulariaceae, Oleaceae, Orobanchaceae, Paulowniaceae, Pedaliaceae, Phrymaceae, Plantaginaceae, Schlegeliaceae, Scrophulariaceae, Tetrachondraceae, and Verbenaceae) and nine additional representative species from Boraginales, Gentianales, and Solanales. In all, 1,993 orthologous SCN loci were identified using our approach, of which we selected 85 commonly shared loci for concatenation and phylogenetic analysis. Our assembled supermatrix included over 116,000 bp of aligned sequence data, of which 50% of the total characters were parsimony-informative. Moreover, the topologies inferred from these data were fully resolved with strong support for the majority of clades. Our phylogenetic results—the first inferred with large-scale, multi-locus nuclear data—provide an alternative view of Lamiales evolution. They also demonstrate the enormous potential of SCN loci to resolve difficult phylogenetic problems and pave the way for future studies that employ gene tree-species tree reconciliation methods.

1 - University of Florida, Department of Biology and Florida Museum of Natural History, Dickinson Hall, Gainesville, FL, 32611-7800, USA
2 - University of Florida, Department of Biology, 407 Cancer and Genetics Research Complex, Gainesville, FL, 32611, USA
3 - University of Florida, Florida Museum of Natural History, PO Box 117800, Gainesville, FL, 32611, USA

Keywords:
Lamiales
single copy nuclear genes
phylogenomics
marker discovery
transcriptomes.

Presentation Type: Oral Paper:Papers for Sections
Session: 33
Location: River Fork/Grove
Date: Wednesday, July 30th, 2014
Time: 11:15 AM
Number: 33012
Abstract ID:874
Candidate for Awards:None