Abstract
The Western Palearctic genus
Heremites
Gray, 1845 (Scincidae) has a long history of taxonomic uncertainty, with particularly unstable placement of the disjunct Hindu Kush populations reported from eastern Afghanistan and northwestern Pakistan. Herein this eastern population is reassessed using an integrative dataset combining broad mitochondrial screening, a six-locus phylogeny, and comparative morphology. Phylogenetic analyses recovered four main well-supported clades corresponding to
H. auratus
, the
H. septemtaeniatus
complex, the
H. vittatus
complex, and the Hindu Kush lineage. The Hindu Kush lineage is inferred to be deeply divergent and was recovered as sister to the clade comprising
H. auratus
and the
H. septemtaeniatus
complex, with an estimated split in the Late Miocene at approximately 10 Mya. This deep mitochondrial divergence is further supported by concordant structuring in the nuclear allele networks. Uncorrected p-distances further support its distinctiveness, with high mitochondrial divergence from western clades (15.2–15.8% in cyt
b
; 17.0–21.0% in ND2) and comparatively lower but consistent nuclear differentiation (1.17–2.59% in MC1R and 2.5–3.3% in RAG1). Multivariate analyses of morphometric, meristic, and categorical data separate the Hindu Kush lineage from
H. auratus
and the
H. septemtaeniatus
complex, supporting the genetic data. We therefore describe this eastern lineage as a new species, currently known from two foothill localities along the southern margin of the Hindu Kush, and discuss its biogeographic significance and the need for a further genus-wide integrative revision.