European hedgehogs, Erinaceus europaeus and E. concolor , are among the many European plant and animal taxa that have been subjected to cyclical restriction to glacial refugia and interglacial expansion. An analysis of 95 mitotypes, comprising partial cytochrome b and control region sequences, shows deep divergence between the two hedgehog species. Three europaeus and two concolor clades are clearly identified and are consistent with previously identified refugia for Europe: the Iberian peninsula, Italy, and the Balkans. The degree of mitochondrial divergence among these clades suggests pre-Pleistocene separation of the refugial populations. In contrast, analysis of two nuclear introns clearly separates the two concolor clades, as in the mitochondrial data, but cannot discriminate the three europaeus clades. This discrepancy between nuclear and mitochondrial data is attributed to historical differences in the refugial population size of europaeus and concolor . The geographical distribution of mitotypes is analysed using nested clade analysis. This method, by including unobserved ('missing') mitotypes, can identify mitotype groupings that remain undetected in conventional analyses. However, the application of nested clade analysis to the study of refugial populations may be hampered by such factors as the loss of haplotypes from the refugial areas by repeated contractions of the population and the recent time scale of colonization relative to mutation rate.

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For many European species, the mountains of the Alps and the Pyrenees have acted as significant barriers to northwards colonization from southern glacial refugia. To the east, the Caucasus Mountains would seem to have been a similar barrier to the white‐breasted hedgehog (Erinaceus concolor). A deep divergence among hedgehog mitochondrial sequences to the north and south of the Caucasus Mountains suggests two colonization routes, originating from separate refugial regions and divided by this mountain barrier. From a Balkan refugium, hedgehogs have colonized northwards into Russia and to the northern foothills of the Caucasus Mountains. The origins of hedgehogs colonizing the southern parts of the Caucasus are not entirely clear, although fossil and climatic data suggest a glacial refugium on the southern shores of the Black Sea. Divergence within the southern group indicates a long‐standing fragmentation within such a refugium or the presence of further cryptic refugia in Turkey and the Near East. The Caucasus barrier would seem to have been an important factor in structuring the late Pleistocene distribution of species.