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Background  Understanding the evolutionary history of morphologically cryptic species complexes is difficult, and made even more challenging when geographic distributions have been modified by human-mediated dispersal. This situation is common in the Mediterranean Basin where, aside from the environmental heterogeneity of the region, protracted human presence has obscured the biogeographic processes that shaped current diversity.  Loxosceles rufescens  (Araneae, Sicariidae) is an ideal example: native to the Mediterranean, the species has dispersed worldwide via cohabitation with humans. A previous study revealed considerable molecular diversity, suggesting cryptic species, but relationships among lineages did not correspond to geographic location.    Results  Delimitation analyses on cytochrome  c  oxidase subunit I identified 11 different evolutionary lineages, presenting two contrasting phylogeographic patterns: (1) lineages with well-structured populations in Morocco and Iberia, and (2) lineages lacking geographic structure across the Mediterranean Basin. Dating analyses placed main diversification events in the Pleistocene, and multiple Pleistocene refugia, identified using ecological niche modeling (ENM), are compatible with allopatric differentiation of lineages. Human-mediated transportation appears to have complicated the current biogeography of this medically important and synanthropic spider.    Conclusions  We integrated ecological niche models with phylogeographic analyses to elucidate the evolutionary history of  L. rufescens  in the Mediterranean Basin, with emphasis on the origins of mtDNA diversity. We found support for the hypothesis that northern Africa was the center of origin for  L. rufescens , and that current genetic diversity originated in allopatry, likely promoted by successive glaciations during the Pleistocene. We corroborated the scenario of multiple refugia within the Mediterranean, principally in northern Africa, combining results from eight atmosphere–ocean general circulation models (AOGCMs) with two different refugium-delimitation methodologies. ENM results were useful for providing general views of putative refugia, with fine-scale details depending on the level of stringency applied for agreement among models.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-014-0195-y) contains supplementary material, which is available to authorized users.

Ecological niche and phylogeography elucidate complex biogeographic patterns in Loxosceles rufescens (Araneae, Sicariidae) in the Mediterranean Basin