Data from: Microallopatric speciation in southern African dung beetle genus <em>Macroderes</em> driven by Miocene aridification and ancestral flight loss

Southern Africa hosts a highly diverse array of dung beetles (Scarabaeidae: Scarabaeinae), the majority of which are endemic to the region. However, the historical drivers of this diversity remain largely unexplored. While each lineage exhibits a distinct diversification history, many remain poorly understood. To address this gap, we employed molecular phylogenetic analyses to investigate the evolutionary history of the flightless dung beetle genus Macroderes Westwood, which comprises 21 species with highly restricted distributions, collectively covering a relatively small geographic range. Specifically, we tested the hypothesis of monophyly of the genus Macroderes and inferred its hypothesised biogeographical history. Using biogeographical analyses and ancestral character reconstruction, we examined the genus's origins, environmental adaptations (semi-arid vs. moist habitats), and the emergence of flightlessness as an adaptive trait. Additionally, we explored how late Cenozoic aridification in southwestern Africa influenced the microallopatric speciation patterns observed today. Our findings indicate that Macroderes represents a monophyletic lineage, with its most recent common ancestor (MRCA) originating in the late Miocene (~8.44 mya; 95 % CI: 9.74–7.06 mya). The MRCA was flightless and associated with a semi-arid environment resembling the present-day Succulent Karoo biome of South Africa. This was followed by multiple southward colonization events from the Karoo into Fynbos. This repeated southward movement highlights the dynamic evolutionary history of Macroderes and the significant role of environmental transitions in shaping its lineage. Furthermore, our analyses suggest that intensified aridification in southwestern Africa played a pivotal role in the genus's diversification. The emergence of flightlessness appears intrinsically linked to semi-arid conditions, providing a compelling explanation for the genus's short-range endemicity. In summary, both aridification and flightlessness have been key drivers of the microallopatric speciation patterns observed within Macroderes.