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To elucidate the speciation mechanisms prevalent within hotspots of biodiversity, and the evolutionary processes behind the rise of their species-rich and endemic biota, we investigated the phylogeny of the giant fire-millipede genus  Aphistogoniulus  Silvestri, 1897, a Malagasy endemic. This study is the first comprehensive (molecular and morphological) phylogenetic study focusing on millipede (class Diplopoda) speciation on Madagascar. The morphological analysis is based on 35 morphological characters and incorporates ten described as well as two newly described species ( A. rubrodorsalis   n. sp.  and  A. jeekeli   n. sp. ) of  Aphistogoniulus . The molecular analysis is based on both mitochondrial (COI and 16S), and nuclear genes (complete 18S rDNA), together comprised of 3031 base pairs, which were successfully sequenced for 31 individual specimens and eight species of  Aphistogoniulus . In addition to the null-model (speciation by distance), two diversification models, mountain refugia and ecotone shift, were discovered to play a role in the speciation of soil arthropods on Madagascar. Mountain refugia were important in the speciation of the  A. cowani  clade, with three species occurring in the Andringitra and Ranomafana Mountains in the southeast ( A. cowani ), the Ambohijanahary and Ambohitantely Mountains in the mid-west ( A. sanguineus ), and the Marojejy Mountain in the northeast ( A. rubrodorsalis   n. sp. ). An ecotone shift from the eastern rainforest to the unique subarid spiny forest of Mahavelo was discovered in the  A. vampyrus  -  A. aridus  species-pair. In the monophyletic  A. diabolicus  clade, evidence for divergent evolution of sexual morphology was detected: species with greatly enlarged gonopods are sister-taxa to species with normal sized gonopods. Among the large-bodied Spirobolida genera of Madagascar,  Colossobolus  and  Sanguinobolus  were found to be close sister-genera to  Aphistogoniulus . Forest destruction has caused forest corridors between populations to disappear, which might limit the possible resolution of biogeographic analyses on Madagascar.

Mountain Refugia Play a Role in Soil Arthropod Speciation on Madagascar: A Case Study of the Endemic Giant Fire-Millipede Genus Aphistogoniulus