Abstract Detail

Phylogenomics

Givnish, Thomas J [1], Zuluaga-Trochez, Alejandro [2], Spalink, Daniel [3], Graham, Sean [4], Barrett, Craig [5], Soto Gomez, Marybel [6], Lam, Vivienne [7], Saarela, Jeffery [8], Sass, Chodon [9], LIma, Danilo [10], Leebens-Mack, Jim [11], Pires, Joseph Chris [12], Zomlefer, Wendy [13], Gandolfo, Maria A [14], Davis, Jerrold [15], Stevenson, Dennis [16], Specht, Chelsea [17].

Monocot plastid phylogenomics, timeline, and the power of multi-gene analyses.

Over the past decade, plastome-scale DNA sequence data have clarified several relationships among monocots that were unresolved or weakly supported by analyses that use only one or a few plastid genes, or are hampered by inadequate taxon sampling. Here we present the first plastome phylogeny to encompass all 77 monocot families, based on 77 plastid genes scored across 545 monocots and 22 outgroups. We calibrated this phylogeny against time using 13 fossil and 7 secondary calibration priors, and estimated rates of net species diversification across all major lineages. Our phylogenomic data shift the placement of 16 families - or their equivalents under prior classifications - and add seven others compared with earlier analyses based on four plastid genes; successfully place all mycoheterotrophic taxa examined; estimate the divergence between monocots and eudicots + Ceratophyllum at 137 Mya; and support the recognition of monofamilial Dasypogonales and Arecales as separate orders based on their phenotypic distinctiveness and deep split 119 Mya, the most ancient divergence between any two monocot families or orders. Our analyses also support recognition of families Thismiaceae and Taccaceae, and successfully place several mycoheterophic taxa. Only 45% of branching events at the family level occurred after the Cretaceous, the most recent between Lapageriaceae and Philesiaceae at ca. 17.5 Mya. Net species diversification underwent four large-scale accelerations, in PACMAD-BOP Poaceae, Asparagales sister to Doryanthaceae, Orchidoideae-Epidendroideae, and Araceae sister to Lemnoideae, each associated with specific ecological/morphological shifts. We subsampled loci to determine the probability of identifying branches in the complete-data tree, as well as their bootstrap support, as a function of the number of genes sampled, branch length, and relative branch depth. Branch ascertainment and support increase with the number of genes sampled and branch length, and decrease with relative branch depth, quantifying the important contribution of plastome-scale data to resolving short, deep branches. Analysis of complete aligned plastomes in Zingiberales demonstrates the added importance of non-coding regions in identifying and supporting short, deep branches; even using complete aligned plastomes, support for the position of Heliconiaceae and Musaceae within Zingiberales is less than 100%.

1 - University Of Wisconsin-Madison, Department Of Botany, Birge Hall, 430 Lincoln Drive, Madison, WI, 53706, United States
2 - Universidad del Valle, Cali, Colombia
3 - University Of Utah, Department Of Biology, 257 South 1400 East, Salt Lake City, UT, 84112, United States
4 - University Of British Columbia, Department Of Botany, 3529 - 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
5 - West Virginia University, Morgantown, WV, 26506, USA
6 - Botany, 118-425 E11th Ave, Vancouver, BC, V5T 4K8, Canada
7 - University of British Columbia, Vancouver, BC, Canada
8 - Department Of Biological Sciences, Cw 405 Biological Sciences Center, Edmonton, AB, T6G 2 E9, Canada
9 - Plant And Microbial Biology, 111 Koshland Hall, Berkeley, CA, 94720, United States
10 - Universidade Estadual de Feira de Santana, Feira de Santana, Paria, Brazil
11 - University of Georgia, Plant Biology, Athens, GA
12 - University of Missouri, Biological Sciences, Columbia, MO, 65211
13 - University Of Georgia, Department Of Plant Biology, 2402 Miller Plant Sciences Building, 120 Carlton Street, Athens, GA, 30602, United States
14 - Cornell University, Plant Biology, 410 Mann Library Building, Plant Biology Section, SIPS, Cornell University, Ithaca, NY
15 - Cornell University, SIPS - Plant Biology, 412 Mann Library Building, Ithaca, NY, 14853, United States
16 - New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY, 10458.0, United States
17 - Cornell University, Ithaca, NY, USA

Keywords:
Commelinids
partitioned maximum likelihood
net rates of species diversification
mycoheterotrophy.

Presentation Type: Oral Paper
Session: 36, Phylogenomics III
Location: 107/Mayo Civic Center
Date: Wednesday, July 25th, 2018
Time: 8:15 AM
Number: 36002
Abstract ID:248
Candidate for Awards:None