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

Nathan Wales*, Melis Akman, Ray H.B. Watson, Fátima Sánchez Barreiro, Bruce D. Smith, Kristen J. Gremillion, M. Thomas P. Gilbert, Benjamin K. Blackman

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
JournalEvolutionary applications
Early online date9 Jan 2018
Publication statusE-pub ahead of print - 9 Jan 2018

Bibliographical note

© 2018 The Authors


  • Helianthus annuus
  • Ancient DNA
  • Archaeobotany
  • Domestication
  • Genetic bottleneck
  • Paleogenomics
  • Plant evolution
  • Sunflower

Cite this