Archaeogenetic Evidence of Ancient Nubian Barley Evolution from Six to Two-Row Indicates Local Adaptation

Abstract

BackgroundArchaeobotanical samples of barley (Hordeum vulgare L.) found at Qasr Ibrim display a two-row phenotype that is unique to the region of archaeological sites upriver of the first cataract of the Nile, characterised by the development of distinctive lateral bracts. The phenotype occurs throughout all strata at Qasr Ibrim, which range in age from 3000 to a few hundred years.Methodology and FindingsWe extracted ancient DNA from barley samples from the entire range of occupancy of the site, and studied the Vrs1 gene responsible for row number in extant barley. Surprisingly, we found a discord between the genotype and phenotype in all samples; all the barley had a genotype consistent with the six-row condition. These results indicate a six-row ancestry for the Qasr Ibrim barley, followed by a reassertion of the two-row condition. Modelling demonstrates that this sequence of evolutionary events requires a strong selection pressure.ConclusionsThe two-row phenotype at Qasr Ibrim is caused by a different mechanism to that in extant barley. The strength of selection required for this mechanism to prevail indicates that the barley became locally adapted in the region in response to a local selection pressure. The consistency of the genotype/phenotype discord over time supports a scenario of adoption of this barley type by successive cultures, rather than the importation of new barley varieties associated with individual cultures.

Sunflower domestication alleles support single domestication center in eastern North America

“…Furthermore, new sequencing technologies have made ancient DNA studies increasingly successful means of revealing genealogical and phenotypic characteristics of extinct lineages (4,8,(41)(42)(43)(44)(45)(46). Studies of these and newly identified domestication genes in DNA isolated from archaeological plant remains discovered in ENA and Mexico promise to yield even further insight into the timing and geography of sunflower domestication.…”

“…Patterns of sequence diversity around domestication alleles have yielded estimates of the strength of selection during domestication for several loci in rice and maize (5)(6)(7). In addition, the geographic distributions of domestication alleles in extant cultivated and wild germplasm have been used to assess how crops and crop alleles have spread from domestication centers and reveal whether convergent traits in independent lineages evolved from the same or unique suites of mutations (5,(8)(9)(10)(11).…”

“…In particular, if domesticated sunflower reached Mexico through trade routes from the North, we predicted that ENA and Mexican landraces would share the same haplotypes at these genes. If two independent domestication events occurred in isolation, it is highly unlikely these parallel events would have selected for the same causative mutations arising on the same haplotype backgrounds at multiple loci (8)(9)(10). In addition, the presence of the domesticated haplotype in ENA wild populations and its absence from wild Mexican populations would exclude the possibility of a parallel selective sweep from equivalent standing variation.…”

Ancient DNA in archaeological wheat grains: preservation conditions and the study of pre-Hispanic agriculture on the island of Gran Canaria (Spain)

“…Ancient DNA (aDNA) has been recovered from charred wheat grains from an Iron Age hillfort (Allaby et al, 1994) and a Neolithic lakeshore dwelling (Schlumbaum et al, 1998), from desiccated Egyptian barley (Palmer et al, 2009), sorghum (Deakin et al, 1998, radish (O'Donoghue et al, 1996), wheat (Blatter et al, 2002a) and maize (Freitas et al, 2003), as well as waterlogged Prunus (Pollmann et al, 2005), grape pips (Manen et al, 2003) and olive stones (Elbaum et al, 2005).…”

Diversity of North European oat analyzed by SSR, AFLP and DArT markers

“…Isolation of PCR-amplifiable DNA from 4,700-year-old maize (Goloubinoff et al 1993), 3,300-year-old emmer wheat (Allaby et al 1994) and 2,900-yearold barley (Palmer et al 2009) has been reported. Compared with these ancient materials, 120-year-old oat seeds are almost 'fresh', and indeed, the AFLP profiles between the museum and the genebank accessions were quite comparable, with no problems in data scoring.…”