We performed principal component analysis (PCA) on 5,365 present-day northwestern Europeans, from Ireland to Sweden, and projected our ancient genomes onto this genetic variation (Fig. 2). For present-day variation, PC1 and PC2 broadly reflect geography, forming a V-shaped pattern from Scandinavians via individuals from northern Germany and the Netherlands towards those from Britain and Ireland. We highlight the position of individuals from present-day England (Fig. 2a), which follow a clinal distribution defined by the western British and Irish (WBI; which includes Irish, Northern Irish, Scottish and Welsh) at one extreme and overlapping present-day Dutch at the other extreme. The ancient genomes fall onto a slightly separate cline, with most of the early medieval individuals from Dutch, German and Danish sites plotting on top of present-day continental northern Europeans (CNEs; northern Germans and Danish), whereas Bronze and Iron Age individuals from Britain and Ireland cluster together with WBI (Fig. 2b). Of note, in contrast to the preceding Bronze and Iron Age individuals from Britain and Ireland, the majority of the early medieval samples from England (England EMA) plot together with the ancient individuals from the continental North Sea area along with the present-day CNEs. The divergence between prehistoric and early medieval individuals from England is also seen in the distribution of genetic distances (FST) as well as shared alleles (F4) on both the population (Extended Data Fig. 1) and the individual scale (Supplementary Fig. 3.3). We notice that the individuals from early medieval English sites are distinctly heterogeneous in the first two PCs and cover the full extent of the cline between the Bronze and Iron Age cluster and the early medieval cluster.
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Our three-way population model for present-day England supports a view of post-Roman English genetic history as punctuated by gene flow processes from at least two major sources: first, the attested arrival of CNE ancestry during the Early Middle Ages from northern Germany, the Netherlands and Denmark, and second, the arrival of ancestry related to France IA. Although we cannot precisely date the order of those arrivals, at least substantial amounts of France IA-related ancestry seem to be absent in northern and eastern England during the Early Middle Ages and therefore must have arrived there subsequently. In other parts of England, however, it may have entered together with CNE ancestry or even earlier. Notably in southern England, namely, Eastry, Apple Down and Rookery Hill, several early medieval individuals already exhibit France IA-related ancestry, which probably results, at least in part, from localized mobility between the south of England and the Frankish areas of Europe during the Early Middle Ages (Extended Data Fig. 8a). Indeed, Frankish material culture is evident in these regions, particularly in Kent and Sussex58,59,60. Admixture from this second source is, therefore, unlikely to have resulted from a single discrete wave. More plausibly, it resulted from pulses of immigration or continuous gene flow between eastern England and its neighbouring regions.
Domesticated materials with well-known wild relatives provide an experimental system to reveal how human selection during cultivation affects genetic composition and adaptation to novel environments. In this paper, our goal was to elucidate how two geographically distinct domestication events modified the structure and level of genetic diversity in common bean. Specifically, we analyzed the genome-wide genetic composition at 26, mostly unlinked microsatellite loci in 349 accessions of wild and domesticated common bean from the Andean and Mesoamerican gene pools. Using a model-based approach, implemented in the software STRUCTURE, we identified nine wild or domesticated populations in common bean, including four of Andean and four of Mesoamerican origins. The ninth population was the putative wild ancestor of the species, which was classified as a Mesoamerican population. A neighbor-joining analysis and a principal coordinate analysis confirmed genetic relationships among accessions and populations observed with the STRUCTURE analysis. Geographic and genetic distances in wild populations were congruent with the exception of a few putative hybrids identified in this study, suggesting a predominant effect of isolation by distance. Domesticated common bean populations possessed lower genetic diversity, higher F ST, and generally higher linkage disequilibrium (LD) than wild populations in both gene pools; their geographic distributions were less correlated with genetic distance, probably reflecting seed-based gene flow after domestication. The LD was reduced when analyzed in separate Andean and Mesoamerican germplasm samples. The Andean domesticated race Nueva Granada had the highest F ST value and widest geographic distribution compared to other domesticated races, suggesting a very recent origin or a selection event, presumably associated with a determinate growth habit, which predominates in this race.
The genus Phaseolus, and more specifically its economically most important species, the common bean or Phaseolus vulgaris L. (2n = 2x = 22), provides interesting features to study the process of plant domestication. Of the 70-odd species that have been recognized in the genus (Freytag and Debouck 2002), 5 have been domesticated and a few additional species show signs of incipient domestication (Delgado-Salinas et al. 2006). Domestication in common bean took place in two, already diverged ancestral gene pools distributed from northern Mexico to Colombia (Mesoamerican gene pool), on the one hand, and from southern Peru to northwestern Argentina (Andean gene pool), on the other (Gepts et al. 1986; Koenig and Gepts 1989; Khairallah et al. 1990, 1992; Koinange and Gepts 1992; Freyre et al. 1996). The two domestications led to two distinct domesticated gene pools (Singh et al. 1991b, c; Becerra Velásquez and Gepts 1994), in part because they arose from two already diverged gene pools just mentioned but also because of further selection under domestication. One consequence of this selection was the appearance of ecogeographic races in each of the two domesticated gene pools (Singh et al. 1991a; Beebe et al. 2000; Díaz and Blair 2006). Partial reproductive isolation has been identified between them, both in wild (Koinange and Gepts 1992) and domesticated populations (Gepts and Bliss 1985), suggesting that P. vulgaris may be in the process of incipient speciation.
The existence of the Andean and Mesoamerican gene pools in common bean and the multiple domestications associated with them is a unique situation among crops, rice being an exception (Vitte et al. 2004; Londo et al. 2006). The existence of these two gene pools raises a number of questions such as the origin and relationships between these two gene pools, the qualitative and quantitative differences in genetic diversity between them, the respective levels of linkage disequilibrium, and the extent to which different loci have been the subject of selection during and after the two major domestications in the species. The first question has been answered with the discovery in the 1980s of a missing link, namely wild P. vulgaris populations in Ecuador and northern Peru (Debouck et al. 1993). Based on a DNA sequence analysis of the genes for phaseolin seed protein, this segment of bean germplasm is actually the putative ancestor of the species (Kami et al. 1995). This segment also shows chloroplast DNA (cpDNA) haplotypes that closely resemble the putative ancestral cpDNA haplotype of the species (Chacón et al. 2007). From the core area on the western slope of the Andes in Ecuador and northern Peru, wild beans were dispersed northwards (to Colombia, Central America, and Mexico) and southwards (southern Peru, Bolivia, and Argentina) resulting in the Mesoamerican and Andean gene pools, respectively. The alpha-amylase inhibitor (Gepts et al. 1999) and internal transcribed spacer (Chacón et al. 2005) sequence data independently suggest that the split between Andean and Mesoamerican gene pools took place some 0.5 million years ago.
In the research reported here, we broadened the scope of earlier research on the organization of genetic diversity in common bean using microsatellite markers by examining a larger plant sample (n = 349), which included both wild and domesticated accessions from the Andean and Mesoamerican gene pools. Microsatellite markers are more polymorphic (Blair et al. 2006) than markers used earlier to characterize genetic diversity such as phaseolin seed protein (Gepts et al. 1986), allozymes (Koenig and Gepts 1989; Singh et al. 1991c), RFLP (Becerra Velásquez and Gepts 1994), and RAPD (Freyre et al. 1996). They are also more widely distributed in the bean genome (Freyre et al. 1998; Blair et al. 2003). In common bean, around 400 microsatellite markers have been developed and mapped (Yu et al. 2000; Gaitán-Solís et al. 2002; Blair et al. 2003; Masi et al. 2003; Yaish and Pérez de la Vega 2003; Guerra-Sanz 2004; Caixeta et al. 2005; Buso et al. 2006). However, population studies with microsatellites in common bean so far have been performed only in a small number of landraces or breeding lines or they have focused on certain geographic regions (Métais et al. 2002; Blair et al. 2006; Díaz and Blair 2006). Thus, an analysis of population structure among wild and domesticated accessions from Andean and Mesoamerican gene pool using microsatellites could yield significant additional insights into the organization of genetic diversity of common bean.
Specifically, we sought to determine how the two domestication processes in common bean had affected genetic diversity and differentiation in the two major gene pools (Andean vs. Mesoamerican), in their respective wild and domesticated components, and among the different domesticated ecogeographic races. We also sought to determine the level of multilocus associations (Hedrick et al. 1978) across and within gene pools and races as a prelude to future linkage disequilibrium (LD; Gupta et al. 2005) and association mapping studies (Zhu et al. 2008). 2ff7e9595c
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