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Background  Recent studies have begun to reveal the complex evolutionary and biogeographic histories of mainland anoles in Central America, but the origins and relationships of many taxa remain poorly understood. One such group is the  Anolis (Norops) crassulus  species subgroup, which contains ten morphologically similar highland taxa, the majority of which have restricted distributions. The nominal taxon  A. crassulus  has a disjunct distribution from Chiapas, Mexico, through Guatemala, in the highlands of El Salvador, and in the Chortís Highlands of Honduras. We test the relationships of these species using multiple mitochondrial and nuclear loci in concatenated and multispecies coalescent frameworks, in an effort to both resolve long-standing taxonomic confusion and present new insights into the evolution and biogeography of these taxa.    Results  Sequences of multiple mitochondrial and nuclear loci were generated for eight of the ten species of the  Anolis crassulus  species subgroup. We analyzed phylogenetic relationships and estimated divergence times and ancestral ranges of the subgroup, recovering a monophyletic subgroup within  Anolis . Within the nominal taxon  Anolis crassulus,  we recovered multiple genetically distinct lineages corresponding to allopatric populations, and show that the Chortís Highland lineage split from the others over 13 MYA. Additionally, distinct mitochondrial lineages are present within the taxa  A. heteropholidotus  and  A. morazani,  and importantly, samples of  A. crassulus  and  A. sminthus  previously used in major anole phylogenetic analyses are not recovered as conspecific with those taxa .  We infer a Chortís Highland origin for the ancestor of this subgroup, and estimate cladogenesis of this subgroup began approximately 22 MYA.    Conclusions  Our results provide new insights into the evolution, biogeography, and timing of diversification of the  Anolis crassulus  species subgroup. The disjunctly distributed  Anolis crassulus    sensu    lato  represents several morphologically conserved, molecularly distinct anoles, and several other species in the subgroup contain multiple isolated lineages.    Electronic supplementary material  The online version of this article (doi: 10.1186/s12862-017-1115-8) contains supplementary material, which is available to authorized users.

Origins and biogeography of the Anolis crassulus subgroup (Squamata: Dactyloidae) in the highlands of Nuclear Central America