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Overson RP, Johnson MG, Bechen LL, Kinosian SP, Douglas NA, Fant JB, Hoch PC, Levin RA, Moore MJ, Raguso RA, Wagner WL, Skogen KA, Wickett NJ. A phylogeny of the evening primrose family (Onagraceae) using a target enrichment approach with 303 nuclear loci. BMC Ecol Evol 2023; 23:66. [PMID: 37974080 PMCID: PMC10655384 DOI: 10.1186/s12862-023-02151-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/16/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The evening primrose family (Onagraceae) includes 664 species (803 taxa) with a center of diversity in the Americas, especially western North America. Ongoing research in Onagraceae includes exploring striking variation in floral morphology, scent composition, and breeding system, as well as the role of these traits in driving diversity among plants and their interacting pollinators and herbivores. However, these efforts are limited by the lack of a comprehensive, well-resolved phylogeny. Previous phylogenetic studies based on a few loci strongly support the monophyly of the family and the sister relationship of the two largest tribes but fail to resolve several key relationships. RESULTS We used a target enrichment approach to reconstruct the phylogeny of Onagraceae using 303 highly conserved, low-copy nuclear loci. We present a phylogeny for Onagraceae with 169 individuals representing 152 taxa sampled across the family, including extensive sampling within the largest tribe, Onagreae. Deep splits within the family are strongly supported, whereas relationships among closely related genera and species are characterized by extensive conflict among individual gene trees. CONCLUSIONS This phylogenetic resource will augment current research projects focused throughout the family in genomics, ecology, coevolutionary dynamics, biogeography, and the evolution of characters driving diversification in the family.
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Affiliation(s)
- Rick P Overson
- Arizona State University, PO Box 875502, Tempe, AZ, 85287, USA
| | | | - Lindsey L Bechen
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd, Glencoe, IL, 60022, USA
- Whitehead Institute for Biomedical Research, 455 Main St, Cambridge, MA, 02142, USA
| | - Sylvia P Kinosian
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd, Glencoe, IL, 60022, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, PO Box 210088, Tucson, AZ, 85721, USA
| | - Norman A Douglas
- University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Jeremie B Fant
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd, Glencoe, IL, 60022, USA
- Northwestern University, 2205 Tech Dr, Evanston, IL, 60208, USA
| | - Peter C Hoch
- Missouri Botanical Garden, 4344 Shaw Blvd, St. Louis, MO, 63110, USA
| | | | | | | | - Warren L Wagner
- Smithsonian Institution, MRC-166, PO Box 37012, Washington, DC, 20013, USA
| | - Krissa A Skogen
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd, Glencoe, IL, 60022, USA
- Northwestern University, 2205 Tech Dr, Evanston, IL, 60208, USA
- Clemson University, 132 Long Hall, Clemson, SC, 29634, USA
| | - Norman J Wickett
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd, Glencoe, IL, 60022, USA.
- Northwestern University, 2205 Tech Dr, Evanston, IL, 60208, USA.
- Clemson University, 132 Long Hall, Clemson, SC, 29634, USA.
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Kariñho-Betancourt E, Carlson D, Hollister J, Fischer A, Greiner S, Johnson MTJ. The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): A comparative transcriptomics approach. PLoS One 2022; 17:e0269307. [PMID: 35749399 PMCID: PMC9231714 DOI: 10.1371/journal.pone.0269307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 05/18/2022] [Indexed: 12/02/2022] Open
Abstract
The plant genus Oenothera has played an important role in the study of plant evolution of genomes and plant defense and reproduction. Here, we build on the 1kp transcriptomic dataset by creating 44 new transcriptomes and analyzing a total of 63 transcriptomes to present a large-scale comparative study across 29 Oenothera species. Our dataset included 30.4 million reads per individual and 2.3 million transcripts on average. We used this transcriptome resource to examine genome-wide evolutionary patterns and functional diversification by searching for orthologous genes and performed gene family evolution analysis. We found wide heterogeneity in gene family evolution across the genus, with section Oenothera exhibiting the most pronounced evolutionary changes. Overall, more significant gene family expansions occurred than contractions. We also analyzed the molecular evolution of phenolic metabolism by retrieving proteins annotated for phenolic enzymatic complexes. We identified 1,568 phenolic genes arranged into 83 multigene families that varied widely across the genus. All taxa experienced rapid phenolic evolution (fast rate of genomic turnover) involving 33 gene families, which exhibited large expansions, gaining about 2-fold more genes than they lost. Upstream enzymes phenylalanine ammonia-lyase (PAL) and 4-coumaroyl: CoA ligase (4CL) accounted for most of the significant expansions and contractions. Our results suggest that adaptive and neutral evolutionary processes have contributed to Oenothera diversification and rapid gene family evolution.
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Affiliation(s)
- Eunice Kariñho-Betancourt
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
- * E-mail: (EKB); (MTJJ)
| | - David Carlson
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Jessie Hollister
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Axel Fischer
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Stephan Greiner
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Marc T. J. Johnson
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
- * E-mail: (EKB); (MTJJ)
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Agrawal AA, Hastings AP, Maron JL. Evolution and seed dormancy shape plant genotypic structure through a successional cycle. Proc Natl Acad Sci U S A 2021; 118:e2026212118. [PMID: 34400497 PMCID: PMC8403902 DOI: 10.1073/pnas.2026212118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dormancy has repeatedly evolved in plants, animals, and microbes and is hypothesized to facilitate persistence in the face of environmental change. Yet previous experiments have not tracked demography and trait evolution spanning a full successional cycle to ask whether early bouts of natural selection are later reinforced or erased during periods of population dormancy. In addition, it is unclear how well short-term measures of fitness predict long-term genotypic success for species with dormancy. Here, we address these issues using experimental field populations of the plant Oenothera biennis, which evolved over five generations in plots exposed to or protected from insect herbivory. While populations existed above ground, there was rapid evolution of defensive and life-history traits, but populations lost genetic diversity and crashed as succession proceeded. After >5 y of seed dormancy, we triggered germination from the seedbank and genotyped >3,000 colonizers. Resurrected populations showed restored genetic diversity that reduced earlier responses to selection and pushed population phenotypes toward the starting conditions of a decade earlier. Nonetheless, four defense and life-history traits remained differentiated in populations with insect suppression compared with controls. These findings capture key missing elements of evolution during ecological cycles and demonstrate the impact of dormancy on future evolutionary responses to environmental change.
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Affiliation(s)
- Anurag A Agrawal
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853;
| | - Amy P Hastings
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853
| | - John L Maron
- Division of Biological Sciences, University of Montana, Missoula, MT 59803
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