Origin and expansion of the allotetraploid Aegilops geniculata, a wild relative of wheat

Abstract

Summary• This study reconstructs the phylogeography of Aegilops geniculata, an allotetraploid relative of wheat, to discuss the impact of past climate changes and recent human activities (e.g. the early expansion of agriculture) on the genetic diversity of ruderal plant species.• We combined chloroplast DNA (cpDNA) sequencing, analysed using statistical parsimony network, with nonhierarchical K-means clustering of amplified fragment length polymorphism (AFLP) genotyping, to unravel patterns of genetic structure across the native range of Ae. geniculata. The AFLP dataset was further explored by measurement of the regional genetic diversity and the detection of isolation by distance patterns.• Both cpDNA and AFLP suggest an eastern Mediterranean origin of Ae. geniculata. Two lineages have spread independently over northern and southern Mediterranean areas. Northern populations show low genetic diversity but strong phylogeographical structure among the main peninsulas, indicating a major influence of glacial cycles. By contrast, low genetic structuring and a high genetic diversity are detected in southern Mediterranean populations. Finally, we highlight human-mediated dispersal resulting in substantial introgression between resident and migrant populations.• We have shown that the evolutionary trajectories of ruderal plants can be similar to those of wild species, but are interfered by human activities, promoting range expansions through increased long-distance dispersal and the creation of suitable habitats.

Comparative Phylogeography in a Specific and Obligate Pollination Antagonism

“…Nei genetic diversities [27] in Arum maculatum were calculated for samples having successfully amplified fragments with both AFLP primer pairs, applying a geographic moving window run on R 9.2.1 [28] as in Arrigo et al [29]. The method consists of the following steps: i) the region of study is defined by the most extreme sampled locations, ii) a grid of fixed cell size (in our case 75 km) and their associated centroids are calculated, iii) starting at each centroid a fixed maximum number of samples is randomly selected (three in our case) in a user-defined perimeter (150 km in this study), iv) Nei diversities are calculated for each centroid, v) points iii and iv are repeated 10,000 times, vi) mean values are calculated for each centroid.…”

“…This method applies Markov chain Monte Carlo (MCMC) searches to identify, given a K number of clusters, individual assignment probabilities that optimize Hardy-Weinberg equilibrium at the intra- and inter-cluster levels. Following recommendations of the authors [29], data was coded as diploid and recessive alleles as present. The most probable K was identified using the approach proposed by Pritchard et al [32].…”

The complex history of the olive tree: from Late Quaternary diversification of Mediterranean lineages to primary domestication in the northern Levant

“…A weighted by haplotype frequencies; R ¼ S 1/p i ) [18]. Spatial patterns of genetic diversity were inferred using a 'sliding window' [19].…”

Natural Pathways to Polyploidy in Plants and Consequences for Genome Reorganization

“…Multiple origin of polyploid species is now considered the rule rather than the exception [Soltis and Sol tis, 1999]. It has been demonstrated for several allopolyploids Abbott and Lowe, 2004;Soltis et al, 2004;Arrigo et al, 2010] and autopolyploids [Shore, 1991;Segraves et al, 1999;Soltis and Soltis, 1999;Parisod and Besnard, 2007], despite notable exceptions such as Arabidopsis suecica [Jakobsson et al, 2006] or Draba ladina [Widmer and Baltisberger, 1999]. Noticeably, multiple origins may occur over restricted geographical distributions and/or short evolutionary timescales as illustrated by the allopolyploid Tragopogon miscellus that formed at least 21 times independently during the last 50-60 years .…”