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Climate has a large impact on diversity and evolution of the world’s biota. The Eocene–Oligocene transition from tropical climate to cooler, drier environments was accompanied by global species turnover. A large number of Old World lacertid lizard lineages have diversified after the Eocene–Oligocene boundary. One of the most speciose reptile genera in the arid Palearctic,  Acanthodactylus , contains two sub-Saharan species with unresolved phylogenetic relationship and unknown climatic preferences. We here aim to understand how and when adaptation to arid conditions occurred in  Acanthodactylus  and when tropical habitats where entered .  Using whole mitogenomes from fresh and archival DNA and published sequences we recovered a well-supported  Acanthodactylus  phylogeny and underpinned the timing of diversification with environmental niche analyses of the sub-Saharan species  A. guineensis  and  A. boueti  in comparison to all arid  Acanthodactylus . We found that  A. guineensis  represents an old lineage that splits from a basal node in the Western clade, and  A. boueti  is a derived lineage and probably not its sister. Their long branches characterize them—and especially  A. guineensis —as lineages that may have persisted for a long time without further diversification or have undergone multiple extinctions. Environmental niche models verified the occurrence of  A. guineensis  and  A. boueti  in hot humid environments different from the other 42 arid  Acanthodactylus  species. While  A. guineensis  probably remained in tropical habitat from periods prior to the Eocene–Oligocene boundary,  A. boueti  entered tropical environments independently at a later period. Our results provide an important baseline for studying adaptation and the transition from humid to arid environments in Lacertidae.

Mitogenome analyses elucidate the evolutionary relationships of a probable Eocene wet tropics relic in the xerophilic lizard genus Acanthodactylus