Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement

Here, we report a comprehensive paleogenomic study of archaeological and ethnographic sunflower remains that provides significant new insights into the process of domestication of this important crop. DNA from both ancient and historic contexts yielded high proportions of endogenous DNA, and althoug...

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Bibliographic Details
Published in:Evolutionary applications 2019-01, Vol.12 (1), p.38-53
Main Authors: Wales, Nathan, Akman, Melis, Watson, Ray H. B., Sánchez Barreiro, Fátima, Smith, Bruce D., Gremillion, Kristen J., Gilbert, M. Thomas P., Blackman, Benjamin K.
Format: Article
Language:English
Subjects:
ancient DNA
archaeobotany
Archaeological sites
Breeding
Crop improvement
Crops
Cultivars
Deoxyribonucleic acid
DNA
Domestication
genetic bottleneck
Genetic diversity
Haplotypes
Helianthus
Helianthus annuus
Minority & ethnic groups
Mitochondria
Nucleotide sequence
paleogenomics
plant evolution
Special Issue Original
Species
sunflower
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Summary:Here, we report a comprehensive paleogenomic study of archaeological and ethnographic sunflower remains that provides significant new insights into the process of domestication of this important crop. DNA from both ancient and historic contexts yielded high proportions of endogenous DNA, and although archaeological DNA was found to be highly degraded, it still provided sufficient coverage to analyze genetic changes over time. Shotgun sequencing data from specimens from the Eden's Bluff archaeological site in Arkansas yielded organellar DNA sequence from specimens up to 3,100 years old. Their sequences match those of modern cultivated sunflowers and are consistent with an early domestication bottleneck in this species. Our findings also suggest that recent breeding of sunflowers has led to a loss of genetic diversity that was present only a century ago in Native American landraces. These breeding episodes also left a profound signature on the mitochondrial and plastid haplotypes in cultivars, as two types were intentionally introduced from other Helianthus species for crop improvement. These findings gained from ancient and historic sunflower specimens underscore how future in‐depth gene‐based analyses can advance our understanding of the pace and targets of selection during the domestication of sunflower and other crop species.
ISSN:1752-4571
1752-4571
DOI:10.1111/eva.12594