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Copetti D, Búrquez A, Bustamante E, Charboneau JLM, Childs KL, Eguiarte LE, Lee S, Liu TL, McMahon MM, Whiteman NK, Wing RA, Wojciechowski MF, Sanderson MJ. Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti. Proc Natl Acad Sci U S A 2017; 114:12003-12008. [PMID: 29078296 PMCID: PMC5692538 DOI: 10.1073/pnas.1706367114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae (Pachycereus, Lophocereus, and Stenocereus) and a more distant outgroup cactus, Pereskia We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed "hemiplasy." The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti.
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Affiliation(s)
- Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Alberto Búrquez
- Instituto de Ecología, Unidad Hermosillo, Universidad Nacional Autónoma de México, Hermosillo, Sonora, Mexico
| | - Enriquena Bustamante
- Instituto de Ecología, Unidad Hermosillo, Universidad Nacional Autónoma de México, Hermosillo, Sonora, Mexico
| | - Joseph L M Charboneau
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Seunghee Lee
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721
| | - Tiffany L Liu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824
| | | | - Noah K Whiteman
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | | | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721;
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