Dataset supporting Domestication during restoration: Unintentional selection during eight generations of wild seed propagation reduces herkogamy, dichogamy, and heterozygosity in Clarkia pulchella

Abstract

Seed production on native seed farms has increased to meet the rising demand for plant material for restoration. However, few studies have tested whether cultivation of wild populations imposes selection and elicits evolutionary change that aligns with process of crop domestication, and those that have report mixed results. Here we show that eight generations of propagation resulted in floral and genomic change in Clarkia pulchella Pursh (Onagraceae) compared to the wild source populations. Both herkogamy and dichogamy i.e., the physical and temporal separation of male and female flower parts, respectively) were significantly decreased between cultivated and wild populations. To determine if these changes resulted in the loss of heterozygosity and overall levels of genetic diversity, we examined >6,500 SNPs derived from RAD-seq data from 46 wild and 47 farmed samples. We show that mean and median heterozygosity of the farmed samples was 81.7% and 61.9% less than that of the wild samples, respectively. This was strongly driven by a loss of alleles, resulting in more than double the number of SNPs with a heterozygosity of zero. This reduction in genetic diversity was significant whether the farmed samples were compared to the pooled wild samples or to a single population. This suggests cultivation of wild populations may be having similar effects to the early stages of crop domestication. We discuss these results in the context of native seed farming and measures that can retain the genetic integrity of wild population during the process of seed increase for restoration. (Genomic data stored in GenBank)