Polymorphism data

Microsatellite and nucleotide sequence data sets, used in the polymorphism study and the ABC analysis. ReadMe files describing the data are included in the directories

Scripts and reference tables of the ABC analysis

Contains the scripts needed to perform the simulations with ABCtoolbox and fastsimcoal for the ABC analysis, and the reference tables for each simulated model. ReadMe files are included in the directories

DNA sequences (cytb gene)

DNA sequences (cytb gene

DNA sequences (CesA3 gene, short fragment)

DNA sequences (CesA3 gene, short fragment

Genetic data (gene haplotypes and microsatellite genotypes) and geographic sampling locations for each isolate

Genetic data (gene haplotypes and microsatellite genotypes) and geographic sampling locations for the 108 Plasmopara viticola isolates. Column description: Isolate_ID: unique isolate identifier Lat: latitude in decimal degrees Long: longitude in decimal degrees Wine_region: region of origin Trait_data: indicates whether quantitative traits were recorded for this isolate (see the « PV_trait_data.txt » file) Fungicide_category: resistance to CAA and QoI fungicides cytb_hap: cytochrome b haplotype. Names follow Chen et al. 2007 CesA3_short_hap1 & 2: CesA3 (short fragment) haplotypes CesA3_long_hap1 & 2: CesA3 (long fragment) haplotypes The last 23 columns give the allele sizes for the amplified microsatellite loci (1 column per locus, each allele is coded by a 3 digit number). Missing data are encoded by "999"

DNA sequences (CesA3 gene; long fragment)

Note that North-American isolates have IDs beginning with MS

Microsatellite_data

microsatellite genotypes for the individuals of our stud

Sorghum SSR

Dataset with the 321 sorghum samples and the 16 SSRs. The variety, site and farmer ID where the plant was collected are provided

Pearl millet SSR

Dataset of the 286 pearl millet samples and the 10 SSRs. The variety, site and farm where the plant was collected are provided

Maintenance and expansion of genetic and trait variation following domestication in a clonal crop

Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade‐off, we characterize the domestication and contemporary genetic diversity of Enset (Ensete ventricosum), an indigenous African relative of bananas (Musa) and a principal starch staple for 20 million Ethiopians. Wild enset reproduction occurs strictly by sexual outcrossing, but for cultivation, it is propagated clonally and associated with diversification and specialization into hundreds of named landraces. We applied tGBS sequencing to generate genome‐wide genotypes for 192 accessions from across enset's cultivated distribution, and surveyed 1340 farmers on enset agronomic traits. Overall, reduced heterozygosity in the domesticated lineage was consistent with a domestication bottleneck that retained 37% of wild diversity. However, an excess of putatively deleterious missense mutations at low frequency present as heterozygotes suggested an accumulation of mutational load in clonal domesticated lineages. Our evidence indicates that the major domesticated lineages initially arose through historic sexual recombination associated with a domestication bottleneck, followed by the amplification of favourable genotypes through an extended period of clonal propagation. Among domesticated lineages, we found a significant phylogenetic signal for multiple farmer‐identified food, nutrition and disease resistance traits and little evidence of contemporary recombination. The development of future‐climate adapted genotypes may require crop breeding, but outcrossing risks exposing deleterious alleles as homozygotes. This trade‐off may partly explain the ubiquity and persistence of clonal propagation over recent centuries of comparative climate stability.</p