The role of European wild horses in horse domestication is poorly understood. While the fossil record for wild horses in Europe prior to horse domestication is scarce, there have been suggestions ...that wild populations from various European regions might have contributed to the gene pool of domestic horses. To distinguish between regions where domestic populations are mainly descended from local wild stock and those where horses were largely imported, we investigated patterns of genetic diversity in 24 European horse breeds typed at 12 microsatellite loci. The distribution of high levels of genetic diversity in Europe coincides with the distribution of predominantly open landscapes prior to domestication, as suggested by simulation-based vegetation reconstructions, with breeds from Iberia and the Caspian Sea region having significantly higher genetic diversity than breeds from central Europe and the UK, which were largely forested at the time the first domestic horses appear there. Our results suggest that not only the Eastern steppes, but also the Iberian Peninsula provided refugia for wild horses in the Holocene, and that the genetic contribution of these wild populations to local domestic stock may have been considerable. In contrast, the consistently low levels of diversity in central Europe and the UK suggest that domestic horses in these regions largely derive from horses that were imported from the Eastern refugium, the Iberian refugium, or both.
Selective breeding for speed in the racehorse has resulted in an unusually high frequency of the C-variant (g.66493737C/T) at the myostatin gene (MSTN) in cohorts of the Thoroughbred horse population ...that are best suited to sprint racing. Here we show using a combination of molecular- and pedigree-based approaches in 593 horses from 22 Eurasian and North-American horse populations, museum specimens from 12 historically important Thoroughbred stallions (b.1764-1930), 330 elite-performing modern Thoroughbreds and 42 samples from three other equid species that the T-allele was ancestral and there was a single introduction of the C-allele at the foundation stages of the Thoroughbred from a British-native mare. Furthermore, we show that although the C-allele was rare among the celebrated racehorses of the 18th and 19th centuries, it has proliferated recently in the population via the stallion Nearctic (b.1954), the sire of the most influential stallion of modern time, Northern Dancer (b.1961).
Broomcorn millet (Panicum miliaceum L.) is one of the world’s oldest cultivated cereals, with several lines of recent evidence indicating that it was grown in northern China from at least 10 000 cal ...bp. Additionally, a cluster of archaeobotanical records of P. miliaceum dated to at least 7000 cal bp exists in eastern Europe. These two centres of early records could either represent independent domestications or cross‐continental movement of this cereal that would predate that of any other crop by some 2 millennia. Here, we analysed genetic diversity among 98 landrace accessions from across Eurasia using 16 microsatellite loci, to explore phylogeographic structure in the Old World range of this historically important crop. The major genetic split in the data divided the accessions into an eastern and a western grouping with an approximate boundary in northwestern China. A substantial number of accessions belonging to the ‘western’ genetic group were also found in northeastern China. Further resolution subdivided the western and eastern genepools into 2 and 4 clusters respectively, each showing clear geographic patterning. The genetic data are consistent with both the single and multiple domestication centre hypotheses and add specific detail to what these hypotheses would entail regarding the spread of broomcorn millet. Discrepancies exist between the predictions from the genetic data and the current archaeobotanical record, highlighting priorities for investigation into early farming in Central Asia.
Gene resequencing and association analysis present new opportunities to study the evolution of adaptive traits in crop plants. Here we apply these tools to an extensive set of barley accessions to ...identify a component of the molecular basis of the flowering time adaptation, a trait critical to plant survival. Using an association-based study to relate variation in flowering time to sequence-based polymorphisms in the Ppd-H1 gene, we identify a causative polymorphism (SNP48) that accounts for the observed variation in barley flowering time. This polymorphism also shows latitude-dependent geographical distribution, consistent with the expected clinal variation in phenotype with the nonresponsive form predominating in the north. Networks, genealogies, and phylogenetic trees drawn for the Ppd-H1 haplotypes reveal population structure both in wild barley and in domesticated barley landraces. The spatial distribution of these population groups indicates that phylogeographical analysis of European landraces can provide information relevant to the Neolithic spread of barley cultivation and also has implications for the origins of domesticated barley, including those with the nonresponsive ppd-H1 phenotype. Haplotypes containing the nonresponsive version of SNP48 are present in wild barley accessions, indicating that the nonresponsive phenotype of European landraces originated in wild barley. The wild accessions whose nonresponsive haplotypes are most closely similar to those of landraces are found in Iran, within a region suggested as an area for domestication of barley east of the Fertile Crescent but which has previously been thought to have contributed relatively little to the diversity of European cultivars.
Wheat has been one of the most important crop in Eurasia since the Neolithic period. Understanding the spread of wheat cultivation is crucial to understanding the spread of agriculture as a whole and ...the interactions between prehistoric populations across the Eurasian continent. However, the routes by which wheat cultivation spread eastwards have been poorly understood to date, due to the scarcity of plant remains recovered from archaeological sites. Desiccated wheat grains excavated from the Xiaohe cemetery in Xinjiang, and dated to the early Bronze Age, show excellent DNA preservation. Here we present an ancient DNA (aDNA) analysis of wheat (
Triticum sp.) grains excavated from Xiaohe and provide the first definitive evidence for bread wheat in China during the Bronze Age. The nuclear ribosomal DNA internal transcribed spacer regions (ITS1 and ITS2) and the intergenic spacer region (IGS) were amplified. The IGS region within the D genome of wheat has a 71
bp insertion that is absent from corresponding regions in the A and B genomes. The results showed that the Xiaohe wheat showed most sequence similarity to hexaploid bread wheat (
Triticum aestivum), including the characteristic insertion into the D genome. The presence of bread wheat at the Xiaohe cemetery is discussed in relation to it having spread into Xinjiang by the Bronze Age, providing new insight into the origins of bread wheat in East Asia.
Historic DNA data have the potential to identify phenotypic information otherwise invisible in the historical, archaeological and palaeontological record. In order to determine whether a single ...nucleotide polymorphism typing protocol based on single based extension (SNaPshot™) could produce reliable phenotypic data from historic samples, we genotyped three coat colour markers for a sample of historic Thoroughbred horses for which both phenotypic and correct genotypic information were known from pedigree information in the General Stud Book. Experimental results were consistent with the pedigrees in all cases. Thus we demonstrate that historic DNA techniques can produce reliable phenotypic information from museum specimens.
Between ca. 6000 BC and ca. 500 BC, barley cultivation spread across the continent of Europe from the extreme south to the extreme north. Carbon-dating would suggest that this spread, and indeed the ...spread of crop cultivation generally, varied in its pace, with ‘delays’ at certain points along its route. Such delays in the spread of agriculture have been explained as resulting from the slow assimilation of agricultural practices by existing indigenous human populations or as the time taken for the crops to adapt to novel climatic conditions, such as altered temperature regimes and day-lengths. A mutant form of the photoperiod response gene, Ppd-H1, causes barley to be non-responsive to long days, while the wild-type responsive form allows plants to flower in response to long days. We sequenced this gene in 65 ‘historic’ barley accessions, from the late 19th and early 20th centuries, in order to explore the potential role of environmental adaptation in the spread of agriculture. We chose to use ‘historic’ material, to complement the richer patterns in extant genetic lines, by spreading the data range in both time and space. Our ‘historic’ barley data shows a latitudinal divide in the Ppd-H1 gene similar to that found in extant lines, but with clearer geographical resolution, and extending northwards into the Arctic Circle. We discuss the implications of our results in relation to the dynamics of agricultural spread across Europe.
Ancient DNA analyses are increasingly popular in archaeology. With the exception of Egypt, the African continent has been grossly understudied using these techniques. We review the state of ancient ...DNA research on Africa, ancient DNA analysis techniques, and common pitfalls in these studies. We provide recommendations for archaeologists interested in collecting and interpreting ancient DNA data. Les analyses archéologiques de l'ADN ancien sont de plus en plus populaires. À l'exception de l'Egypte, l'Afrique est très peu étudiée avec ces techniques. Nous résumons les techniques pour analyser l'ADN ancien, les problèmes de ces études et l'état de la recherche paléogénétique de l'Afrique. Nous offrons des recommendations pour obtenir et interpréter les données de l'ADN ancien.
Forensic and ancient DNA (aDNA) extracts are mixtures of endogenous aDNA, existing in more or less damaged state, and contaminant DNA. To obtain the true aDNA sequence, it is not sufficient to ...generate a single direct sequence of the mixture, even where the authentic aDNA is the most abundant (e.g. 25% or more) in the component mixture. Only bacterial cloning can elucidate the components of this mixture. We calculate the number of clones that need to be sampled (for various mixture ratios) in order to be confident (at various levels of confidence) to have identified the major component. We demonstrate that to be >95% confident of identifying the most abundant sequence present at 70% in the ancient sample, 20 clones must be sampled. We make recommendations and offer a free-access web-based program, which constructs the most reliable consensus sequence from the user's input clone sequences and analyses the confidence limits for each nucleotide position and for the whole consensus sequence. Accepted authentication methods must be employed in order to assess the authenticity and endogeneity of the resulting consensus sequences (e.g. quantification and replication by another laboratory, blind testing, amelogenin sex versus morphological sex, the effective use of controls, etc.) and determine whether they are indeed aDNA.
A number of widely grown varieties of Vitis vinifera ssp. sativa, the grape used for wine production, are known to have resulted from crosses between Pinot noir and Gouais blanc, although it is not ...known which was the maternal parent in these crosses. We have analysed microsatellites and a single nucleotide polymorphism (SNP) in chloroplast DNA from these two varieties and twelve progeny strains, including Chardonnay, Gamay noir and Aligoté. The results demonstrate that Gouais blanc was the maternal parent for nine of these strains, including Chardonnay, Gamay noir and Aligoté. This is a striking conclusion, as Gouais is generally considered a highly inferior variety, and its cultivation was banned for many years in parts of Europe.
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