A re-evaluation of the domestication bottleneck from archaeogenomic evidence

Abstract

Domesticated crops show a reduced level of diversity that is commonly attributed to the "domestication bottleneck"; a drastic reduction in the population size associated with subsampling the wild progenitor species and the imposition of selection pressures associated with the domestication syndrome. A prediction of the domestication bottleneck is a sharp decline in genetic diversity early in the domestication process. Surprisingly, archaeological genomes of three major annual crops do not indicate that such a drop in diversity occurred early in the domestication process. In light of this observation, we revisit the general assumption of the domestication bottleneck concept in our current understanding of the evolutionary process of domestication.

Keywords: archaeogenomics; domestication; domestication bottleneck.

Figure 1

The conventional view of the domestication bottleneck

Figure 2

Mean population heterozygosity against population nucleotide diversity (π).(a) Maize populations defined by Swarts et al. (2017). (b) Barley pseudopopulations identified by cluster analysis of SNP matrix of Mascher et al. (2016). Remapped barley samples: subsample of wild accessions (FT), subsample of modern barley (BCC), and Yoram Cave ancient barley sample (Yoram Cave). Nucleotide diversity was conventionally calculated as number of pairwise differences divided by number of sites. Note in the maize data, total number of sites was unknown from GBS data so values are based on number of GBS sites reported in Swarts et al. (2017); hence, both He and π values are elevated

Figure 3

Direct estimates of genomic heterozygosity over time from modern and archaeogenomes. All heterozygosity estimates based on the number of heterozygous sites within a single genome. Modern wild progenitors taken as estimates of heterozygosity at the time of domestication. (a) Sorghum bicolor (data taken from Smith et al., 2018) (b) Zea mays of Northern Mexico and United States (data taken from Swarts et al., 2017). (c) Zea mays of central Mexico and South America (data taken from Swarts et al., 2017). (d) Hordeum vulgare (data taken from Mascher et al., 2016)