Thomas J Givnish1, Alejandro Zuluaga2, Daniel Spalink3, Marybel Soto Gomez4, Vivienne K Y Lam4, Jeffrey M Saarela5, Chodon Sass6, William J D Iles7, Danilo José Lima de Sousa8, James Leebens-Mack9, J Chris Pires10, Wendy B Zomlefer9, Maria A Gandolfo11, Jerrold I Davis11, Dennis W Stevenson12, Claude dePamphilis13, Chelsea D Specht11, Sean W Graham4, Craig F Barrett14, Cécile Ané1,15. 1. Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA. 2. Departamento de Biologia, Universidad del Valle, Cali, Colombia. 3. Department of Ecosystem Science, Texas A&M University, College Station, Texas, 77840, USA. 4. Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada. 5. Canadian Museum of Nature, Ottawa, ON, K1P 6P4, Canada. 6. The University and Jepson Herbarium, University of California-Berkeley, Berkeley, California, 94720, USA. 7. Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, 48109, USA. 8. Departamento de Ciéncias Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, 44036-900, Brazil. 9. Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA. 10. Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, 65211, USA. 11. School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA. 12. New York Botanical Garden, New York, New York, 10458, USA. 13. Department of Biology, Pennsylvania State University, University Park, Pennsylvania, 16802, USA. 14. Department of Biology, West Virginia University, Morgantown, West Virginia, 26506, USA. 15. Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
Abstract
PREMISE OF THE STUDY: We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot-wide divergence times and rates of species diversification. METHODS: We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth. KEY RESULTS: Phylogenomic analyses shift the placement of 16 families in relation to earlier studies based on four plastid genes, add seven families, date the divergence between monocots and eudicots+Ceratophyllum at 136 Mya, successfully place all mycoheterotrophic taxa examined, and support recognizing Taccaceae and Thismiaceae as separate families and Arecales and Dasypogonales as separate orders. Only 45% of interfamilial divergences occurred after the Cretaceous. 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. Branch ascertainment and support across monocots increase with gene number and branch length, and decrease with relative branch depth. Analysis of entire plastomes in Zingiberales quantifies the importance of non-coding regions in identifying and supporting short, deep branches. CONCLUSIONS: We provide the first resolved, well-supported monocot phylogeny and timeline spanning all families, and quantify the significant contribution of plastome-scale data to resolving short, deep branches. We outline a new functional model for the evolution of monocots and their diagnostic morphological traits from submersed aquatic ancestors, supported by convergent evolution of many of these traits in aquatic Hydatellaceae (Nymphaeales).
PREMISE OF THE STUDY: We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot-wide divergence times and rates of species diversification. METHODS: We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth. KEY RESULTS: Phylogenomic analyses shift the placement of 16 families in relation to earlier studies based on four plastid genes, add seven families, date the divergence between monocots and eudicots+Ceratophyllum at 136 Mya, successfully place all mycoheterotrophic taxa examined, and support recognizing Taccaceae and Thismiaceae as separate families and Arecales and Dasypogonales as separate orders. Only 45% of interfamilial divergences occurred after the Cretaceous. 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. Branch ascertainment and support across monocots increase with gene number and branch length, and decrease with relative branch depth. Analysis of entire plastomes in Zingiberales quantifies the importance of non-coding regions in identifying and supporting short, deep branches. CONCLUSIONS: We provide the first resolved, well-supported monocot phylogeny and timeline spanning all families, and quantify the significant contribution of plastome-scale data to resolving short, deep branches. We outline a new functional model for the evolution of monocots and their diagnostic morphological traits from submersed aquatic ancestors, supported by convergent evolution of many of these traits in aquatic Hydatellaceae (Nymphaeales).
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