El Riego and Early Maize Agricultural Evolution

Benz, Bruce F.; Cheng, Li; Leavitt, Steven W.; Eastoe, C. J.

doi:10.1016/b978-012369364-8/50257-6

Cited by 12 publications

(22 citation statements)

References 13 publications

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“…Many domestication traits, alike maize traits, are polygenic and controlled by a number of loci with varying effect sizes [23]. Archaeological records of maize domestication traits show that adaptation took several thousand years [24]. Our example trait 1 matches this pattern, representing an adaptation time of almost 0.1N generations, equivalent to 10,000 years for a population similar to that of the wild ancestor of maize [22, Figure 6].…”

Section: Maize Domesticationmentioning

confidence: 60%

“…During the stationary phase before the shift and after reaching the new optimum we followed a Gaussian fitness function appropriate for a trait under stabilizing selection [14]. be observed when sudden changes in the environment favor a specific phenotype for invasive species [28] or in semi-artificial populations in agroecosystems and during domestication [24]. Truncation selection is also common in evolve and re-sequence experiments [29], crop populations [30] and during strong directional selection in natural populations [31].…”

Section: Model Choicementioning

confidence: 99%

“…We employ machine learning on genetic architecture matrices and find that demography and the effect size of new mutations have the largest influence on present day genetic architecture. After identifying general parameter importance, we use maize domestication as an example and investigate two diverging traits in a population that underwent a population bottleneck and exponential growth [22], showing how these traits adapt to the changing optimum and comparing our findings to archaeological and genetic data [23,24].…”

Section: Introduction Adaptationmentioning

confidence: 99%

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Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima

Stetter

Thornton

Ross‐Ibarra

2018

Preprint

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Understanding the genetic basis of phenotypic adaptation to changing environments is an essential goal of population and quantitative genetics. While technological advances now allow interrogation of genome-wide genotyping data in large panels, our understanding of the process of polygenic adaptation is still limited. To address this limitation, we use extensive forward-time simulation to explore the impacts of variation in demography, trait genetics, and selection on the rate and mode of adaptation and the resulting genetic architecture. We simulate a population adapting to an optimum shift, modeling sequence variation for 20 QTL for each of 12 different demographies for 100 different traits varying in the effect size distribution of new mutations, the strength of stabilizing selection, and the contribution of the genomic background. We then use random forest regression approaches to learn the relative importance of input parameters in determining a number of aspects of the process of adaptation including the speed of adaptation, the relative frequency of hard sweeps and sweeps from standing variation, or the final genetic architecture of the trait. We find that selective sweeps occur even for traits under relatively weak selection and where the genetic background explains most of the variation. Though most sweeps occur from variation segregating in the ancestral population, new mutations can be important for traits under strong stabilizing selection that undergo a large optimum shift. We also show that population bottlenecks and expansion impact overall genetic variation as well as the relative importance of sweeps from standing variation and the speed with which adaptation can occur. We then compare our results to two traits under selection during maize domestication, showing that our simulations qualitatively recapitulate differences between them.Overall, our results underscore the complex population genetics of individual loci in even relatively simple quantitative trait models, but provide a glimpse into the factors that drive this complexity and the potential of these approaches for understanding polygenic adaptation. Author summaryMany traits are controlled by a large number of genes, and environmental changes can lead to shifts in trait optima. How populations adapt to these shifts depends on a number of parameters including the genetic basis of the trait as well as population demography. We simulate a number of trait architectures and population histories to study the genetics of adaptation to distant trait optima.We find that selective sweeps occur even in traits under relatively weak selection and our machine learning analyses find that demography and the effect sizes of mutations have the largest influence on genetic variation after adaptation. Maize domestication is a well suited model for trait adaptation accompanied by demographic changes. We show how two example traits under a maize specific demography adapt to a distant optimum and demonstrate that polygenic adaptation is a well suited model for...

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Section: Maize Domesticationmentioning

confidence: 60%

Section: Model Choicementioning

confidence: 99%

Section: Introduction Adaptationmentioning

confidence: 99%

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Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima

Stetter

Thornton

Ross‐Ibarra

2018

Preprint

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“…It remains unclear when maize became productive enough to be a staple grain crop, and the small size of the earliest maize cobs from Oaxaca and Tehuacan have led some to hypothesize early nongrain use as a green vegetable (26) or stalk sugar to produce alcoholic beverages (27). Changes in maize cob size in the Tehuacan Valley (28) suggest that the transition to maize as a staple grain crop unfolded gradually (26,29). However, we know much less about this process in regions outside the known distribution of the two dominant teosinte subspecies in Mesoamerica, Z. mays ssp.…”

mentioning

confidence: 99%

High-precision chronology for Central American maize diversification from El Gigante rockshelter, Honduras

Kennett

Thakar

VanDerwarker

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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The first steps toward maize ( subspecies ) domestication occurred in the Balsas region of Mexico by ∼9,000 calendar years B.P. (cal B.P.), but it remains unclear when maize was productive enough to be a staple grain in the Americas. Molecular and microbotanical data provide a partial picture of the timing and nature of morphological change, with genetic data indicating that alleles for some domestication traits were not yet fixed by 5,300 cal B.P. in the highlands of Mexico. Here, we report 88 radiocarbon dates on the botanical remains from El Gigante rockshelter (Honduras) to establish a Bayesian chronology over the past ∼11,000 y spanning the transition to maize-based food production. Botanical remains are remarkably well preserved and include over 10,000 maize macrofossils. We directly dated 37 maize cobs to establish the appearance and local change of maize at the site. Cobs are common in deposits dating between 4,340 and 4,020 cal B.P., and again between 2,350 and 980 cal B.P. The earliest cobs appear robustly domesticated, having 10-14 rows, suggesting strong selection for increased yield. The later cobs are comparable to these earliest ones, but show clear emergence of diverse traits, including increased cob width, rachis segment length, and cupule width. Our results indicate that domesticated landraces of maize productive enough to be a staple grain existed in Central America by 4,300 cal B.P.

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“…Maize is commonly present in archaeological contexts in the Tehaucan Valley of Mexico by 3550 B.C. (Benz et al 2006), and it appears in northern Mexico and the American Southwest by about 2900 B.C. (Huckell 2006;Jaenicke-Despres and Smith 2006).…”

Section: Introductionmentioning

confidence: 99%

Factors Controlling Pre-Columbian and Early Historic Maize Productivity in the American Southwest, Part 1: The Southern Colorado Plateau and Rio Grande Regions

Benson

2010

J Archaeol Method Theory

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El Riego and Early Maize Agricultural Evolution

Cited by 12 publications

References 13 publications

Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima

Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima

High-precision chronology for Central American maize diversification from El Gigante rockshelter, Honduras

Factors Controlling Pre-Columbian and Early Historic Maize Productivity in the American Southwest, Part 1: The Southern Colorado Plateau and Rio Grande Regions

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