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

Abstract

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.

Phylogeography and the Evolutionary History of Sunflower (Helianthus annuus L.): Wild Diversity and the Dynamics of Domestication

“…Overall, these results are consistent with the known history of cultivated sunflower, but many issues remain unresolved: specifically, the duration of the domestication bottleneck, and the tempo and mode of bottleneck-induced population declines. A genomic analysis of contemporary and archeological specimens (e.g., [94]) with recently developed methods designed to infer more granular changes in effective population size through time [95] may be useful in generating richer insights into the broad demographic patterns observed in this study.…”

Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners

“…Other examples demonstrate the importance of paleogenomic studies in domesticated taxa, including grapevine (Wales et al, 2016), barley (Mascher et al, 2016), sunflower (Wales et al, 2019), horses (Schubert et al, 2014), dogs (Frantz et al, 2016) and cats (Ottoni et al, 2017).…”

Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager

“…Ancient DNA (aDNA) has become a widely accepted source of biological data, helping to provide new perspectives for a range of fields including archaeology, cultural heritage, evolutionary biology, ecology, and palaeontology. The utilisation of short-read high-throughput sequencing has allowed the recovery of whole genomes and genome-wide data from a wide variety of sources, including (but not limited to), the skeletal remains of animals [1,2,3,4], modern and archaic humans [5,6,7,8], bacteria [9,10,11], viruses [12,13], plants [14,15], palaeofaeces [16,17], dental calculus [18,19], sediments [20,21], medical slides [22], parchment [23], and recently, ancient ‘chewing gum’ [24,25]. Improvement in laboratory protocols to increase yields of otherwise trace amounts of DNA has at the same time led to studies that can total hundreds of ancient individuals [26,27], spanning single [28] to thousands of organisms [18].…”