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Kanapeckas KL, Vigueira CC, Ortiz A, Gettler KA, Burgos NR, Fischer AJ, Lawton-Rauh AL. Escape to Ferality: The Endoferal Origin of Weedy Rice from Crop Rice through De-Domestication. PLoS One 2016; 11:e0162676. [PMID: 27661982 PMCID: PMC5035073 DOI: 10.1371/journal.pone.0162676] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 08/26/2016] [Indexed: 11/30/2022] Open
Abstract
Domestication is the hallmark of evolution and civilization and harnesses biodiversity through selection for specific traits. In regions where domesticated lines are grown near wild relatives, congeneric sources of aggressive weedy genotypes cause major economic losses. Thus, the origins of weedy genotypes where no congeneric species occur raise questions regarding management effectiveness and evolutionary mechanisms responsible for weedy population success. Since eradication in the 1970s, California growers avoided weedy rice through continuous flood culture and zero-tolerance guidelines, preventing the import, presence, and movement of weedy seeds. In 2003, after decades of no reported presence in California, a weedy rice population was confirmed in dry-seeded fields. Our objectives were to identify the origins and establishment of this population and pinpoint possible phenotypes involved. We show that California weedy rice is derived from a different genetic source among a broad range of AA genome Oryzas and is most recently diverged from O. sativa temperate japonica cultivated in California. In contrast, other weedy rice ecotypes in North America (Southern US) originate from weedy genotypes from China near wild Oryza, and are derived through existing crop-wild relative crosses. Analyses of morphological data show that California weedy rice subgroups have phenotypes like medium-grain or gourmet cultivars, but have colored pericarp, seed shattering, and awns like wild relatives, suggesting that reversion to non-domestic or wild-like traits can occur following domestication, despite apparent fixation of domestication alleles. Additionally, these results indicate that preventive methods focused on incoming weed sources through contamination may miss burgeoning weedy genotypes that rapidly adapt, establish, and proliferate. Investigating the common and unique evolutionary mechanisms underlying global weed origins and subsequent interactions with crop relatives sheds light on how weeds evolve and addresses broader questions regarding the stability of selection during domestication and crop improvement.
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Affiliation(s)
- Kimberly L. Kanapeckas
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
- South Carolina Department of Natural Resources, Marine Resources Research Institute, Charleston, South Carolina, United States of America
| | - Cynthia C. Vigueira
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
- Department of Biology, High Point University, High Point, North Carolina, United States of America
| | - Aida Ortiz
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Kyle A. Gettler
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Nilda R. Burgos
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Albert J. Fischer
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Amy L. Lawton-Rauh
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
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Misiewicz TM, Fine PVA. Evidence for ecological divergence across a mosaic of soil types in an Amazonian tropical tree: Protium subserratum (Burseraceae). Mol Ecol 2014; 23:2543-58. [PMID: 24703227 DOI: 10.1111/mec.12746] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 03/20/2014] [Accepted: 03/28/2014] [Indexed: 11/29/2022]
Abstract
Soil heterogeneity is an important driver of divergent natural selection in plants. Neotropical forests have the highest tree diversity on earth, and frequently, soil specialist congeners are distributed parapatrically. While the role of edaphic heterogeneity in the origin and maintenance of tropical tree diversity is unknown, it has been posited that natural selection across the patchwork of soils in the Amazon rainforest is important in driving and maintaining tree diversity. We examined genetic and morphological differentiation among populations of the tropical tree Protium subserratum growing parapatrically on the mosaic of white-sand, brown-sand and clay soils found throughout western Amazonia. Nuclear microsatellites and leaf morphology were used to (i) quantify the extent of phenotypic and genetic divergence across habitat types, (ii) assess the importance of natural selection vs. drift in population divergence, (iii) determine the extent of hybridization and introgression across habitat types, (iv) estimate migration rates among populations. We found significant morphological variation correlated with soil type. Higher levels of genetic differentiation and lower migration rates were observed between adjacent populations found on different soil types than between geographically distant populations on the same soil type. PST -FST comparisons indicate a role for natural selection in population divergence among soil types. A small number of hybrids were detected suggesting that gene flow among soil specialist populations may occur at low frequencies. Our results suggest that edaphic specialization has occurred multiple times in P. subserratum and that divergent natural selection across edaphic boundaries may be a general mechanism promoting and maintaining Amazonian tree diversity.
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Affiliation(s)
- Tracy M Misiewicz
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
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Roy T, Chang TH, Lan T, Lindqvist C. Phylogeny and biogeography of New World Stachydeae (Lamiaceae) with emphasis on the origin and diversification of Hawaiian and South American taxa. Mol Phylogenet Evol 2013; 69:218-38. [DOI: 10.1016/j.ympev.2013.05.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/25/2013] [Accepted: 05/30/2013] [Indexed: 12/15/2022]
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Lawton-Rauh A. Demographic processes shaping genetic variation. CURRENT OPINION IN PLANT BIOLOGY 2008; 11:103-109. [PMID: 18353707 DOI: 10.1016/j.pbi.2008.02.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2008] [Revised: 02/14/2008] [Accepted: 02/15/2008] [Indexed: 05/26/2023]
Abstract
Demographic processes modulate genome-wide levels and patterns of genetic variation via impacting effective population size independently of natural selection. Such processes include the perturbation of population distributions from external events shaping habitat landscape and internal factors shaping the probability of contemporaneous alleles in a population (coalescence). Several patterns have recently emerged: spatial and temporal heterogeneity in population structure have different influences on the persistence of new mutations and genetic variation, multi-locus analyses indicate that gene flow continues to occur during speciation and the incorporation of demographic processes into models of molecular evolution and association genetics approaches has improved statistical power to detect deviations from neutral-equilibrium expectations and decreased false positive rates.
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Affiliation(s)
- Amy Lawton-Rauh
- Department of Genetics and Biochemistry, Clemson University, 100 Jordan Hall, Clemson, SC 29634-0318, USA.
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