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Abstract Detail

Systematics Section/ASPT

Barrett, Craig [1], Baker, William [2], Comer, Jason [3], Conran, John [4], Lahmeyer, Sean Anthony [5], Leebens-Mack, James [3], Li, Jeff [6], Lim, Gwynne [7], Mayfield-Jones, Dustin [8], Medina, Jesus [1], Perez, Leticia [1], Pires, J. Chris [9], Santos, Cristian [10], Stevenson, Dennis [11], Zomlefer, Wendy [12], Davis, Jerrold [13].

Deep branch support and extensive variation in substitution rate in the commelinid monocots based on plastid genomes, with emphasis on the palms.

The commelinid monocots comprise a diverse clade of immense global importance, including four orders and one unplaced family: Arecales, Commelinales, Zingiberales, Poales, and Dasypogonaceae (endemic to Australia). Among the commelinid orders, Arecales (the palms) are important both ecologically and economically. Despite several multi-locus, phylogenetic studies of the palms, there remain areas of uncertainty in resolution and support among major clades and, moreover, support is tenuous for the placement of the palms among the commelinids. Also, the commelinids potentially represent a case of extreme heterogeneity in substitution rates across clades that has not been explicitly investigated in a phylogenetic context. To address questions of relationships, support, and substitution rates of palms and commelinid relatives, 38 complete plastome sequences representing the palms and four plastomes representing the four genera of Dasypogonaceae were generated via ‘genome skimming’ (Illumina). Protein-coding genes were extracted and combined with those from previous studies of monocots to produce an alignment of 75 genes by 132 taxa, representating 84 commelinids. Parsimony and Maximum Likelihood analyses (based on four model partitioning schemes) indicated moderate to robust Bootstrap support for Arecales as sister to Dasypogonaceae (81-91%), while support for (Zingiberales, Commelinales) as sister to Poales was slightly stronger (91-96%). Bootstrap support was 100% for all relationships among the five palm subfamilies (Calamoideae, (Nypoideae, (Coryphoideae, (Ceroxyloideae, Arecoideae)))), as well as for the monophyly of each, excluding the monotypic Nypoideae. Within the densely sampled subfamily Coryphoideae (the fan palms), relationships among all eight tribes received support of 99% or greater, and relationships among the diverse but problematic tribe Trachycarpeae also received strong support. Analyses of whole plastome alignments of the palms only (coding + non-coding regions) yielded identical relationships to those based on 75 genes, with strong support. Comparison of estimated branch lengths and model-based local clock analyses across commelinid orders provided evidence of extreme heterogeneity in substitution rates, with the Arecales having the slowest rates and Poales having the fastest (with much variation in the latter). Genome skimming and complete plastid genomes provide high support for relationships among the palms and commelinids, and strong evidence for rate variation among commelinid clades. Future genomic studies should include broad sampling across the nuclear genome to test hypotheses of relationships and rate heterogeneity based on whole plastomes, as well as phylogenetic tests of life history traits as potential explanatory variables for the observed rate heterogeneity among clades.

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1 - California State University, Los Angeles, Biological Sciences, Los Angeles, CA, 90032, USA
2 - Royal Botanic Gardens at Kew, Richmond, Surrey, UK
3 - University of Georgia, Department of Plant Biology, Athens, GA, 30602, USA
4 - The University Of Adelaide, ACEBB EEB/EES, Benham Bldg, DX650 312, Adelaide, N/A, SA 5005, Australia
5 - Huntington Botanical Garden, San Marino, CA, 91108, USA
6 - University of California, Riverside, Graduate Program in Genetics, Genomics, and Bioinformatics, Riverside, CA, 92521, USA
7 - Department Of Plant Biology, 6840 Route 96A, Ovid, NY, 14521, USA
8 - Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
9 - University of Missouri, Division of Biological Sciences, Columbia, MO, 65211, USA
10 - California State University, Los Angeles, Division of Biological Sciences, Los Angeles, CA, 90032, USA
11 - The NY Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA
12 - University Of Georgia, Department Of Plant Biology, 2052 Miller Plant Sciences Building, 120 Carlton Street, Athens, GA, 30602, USA
13 - Cornell University, Plant Biology And L.H. Bailey Hortorium, 412 Mann Library Building, Ithaca, NY, 14853-4301, USA

next generation sequencing
rate heterogeneity
branch support

Presentation Type: Oral Paper:Papers for Sections
Session: 50
Location: Salon 10/The Shaw Conference Centre
Date: Tuesday, July 28th, 2015
Time: 1:30 PM
Number: 50001
Abstract ID:722
Candidate for Awards:None

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