Quaternary climatic oscillations had strong effects on Palearctic biodiversity. Although Transcaucasia is hypothesised to be a centre of diversity for many taxa, relatively few studies have investigated its potential role as such, or as a Pleistocene refugium. Using AFLP and sequence data (ITS, matK, trnL-F) from samples collected across the entire range of Microthlaspi perfoliatum, from the Iberian peninsula to Kazakhstan, and including the Mediterranean Basin and Central Europe, in this study it is examined how the interplay of Pleistocene climatic oscillations and historical demography may have shaped the current genetic structure of the species. The results of this study provide evidence that M. perfoliatum survived Pleistocene glaciation in five major refugia, Iberia, southwestern France, Italy, the Balkans and Anatolia/Transcaucasia and a sixth, unknown refugium in the disjunct distribution area in Central Asia. Our analyses support an ancient colonisation of M. perfoliatum towards the western and central Palearctic, perhaps, during the early Pleistocene or late Pliocene, likely starting from Transcaucasia. However, postglacial recolonisation of western and Central Europe has taken place from two distinct refugia, namely southwestern France/northern Italy, and Anatolia/Southern Balkans, respectively. The Iberian populations apparently did not contribute to postglacial recolonisation of Europe, perhaps because the Pyrenees acted as a significant barrier to dispersal. It is also conceivable that a rapidly expanding population from southwestern France and the southeastern part of the range effectively blocked the establishment of latecomers. The present study thus reveals a complex pattern of colonisation of Europe from Transcaucasia, with an interplay of climate and physical geography as main factors shaping the present-day genetic structure of M. perfoliatum.
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