The Afromontane and Afroalpine areas constitute some of the main biodiversity hotspots of Africa. They are particularly rich in plant endemics, but the biogeographic origins and evolutionary processes leading to this outstanding diversity are poorly understood. We performed phylogenomic and biogeographic analyses of one of the most species-rich plant genera in these mountains, Helichrysum (Compositae-Gnaphalieae). Most previous studies have focused on Afroalpine elements of Eurasian origin, and the southern African origin of Helichrysum provides an interesting counterexample. We obtained a comprehensive nuclear dataset from 304 species (≈50% of the genus) using target-enrichment with the Compositae1061 probe set. Summary-coalescent and concatenation approaches combined with paralog recovery yielded congruent, well-resolved phylogenies. Ancestral range estimations revealed that Helichrysum originated in arid southern Africa, whereas the southern African grasslands were the source of most lineages that dispersed within and outside Africa. Colonization of the tropical Afromontane and Afroalpine areas occurred repeatedly throughout the Miocene–Pliocene. This timing coincides with mountain uplift and the onset of glacial cycles, which together may have facilitated both speciation and intermountain gene flow, contributing to the evolution of the Afroalpine flora.

The floras on the highest mountains in tropical eastern Africa are among the most unique floras in the world. Despite the exceptionally high concentration of endemic species, these floras remain understudied from an evolutionary point of view. In this study, we focus on the Carduus-Cirsium group (subtribe Carduinae) to unravel the evolutionary relationships of the species endemic to the tropical Afromontane and Afroalpine floras, aiming to improve the systematics of the group. We applied the Hyb-Seq approach using the Compositae1061 probe set on 190 samples (159 species), encompassing representatives of all genera of Carduinae. We used two recently developed pipelines that enabled the processing of raw sequence reads, identification of paralogous sequences and segregation into orthologous alignments. After the implementation of a missing data filter, we retained sequences from 986 nuclear loci and 177 plastid regions. Phylogenomic analyses were conducted using both concatenated and summary-coalescence methods. The resulting phylogenies were highly resolved and revealed three distinct evolutionary lineages consisting of the African species traditionally referred to as Carduus and Cirsium. Consequently, we propose the three new genera Afrocarduus, Afrocirsium and Nuriaea; the latter did notably not belong to the Carduus-Cirsium group. We detected some incongruences between the phylogenies based on concatenation vs. coalescence and on nuclear vs. plastid datasets, likely attributable to incomplete lineage sorting and/or hybridization.

Colonization and diversification processes are responsible for the distinctiveness of island biotas, with Madagascar standing out as abiodiversity hotspot exceptionally rich in species and endemism. Regardless of its significance, the evolutionary history and diversification drivers of Madagascar's flora remain understudied. Here we focus on Helichrysum (Compositae, Gnaphalieae) to investigate the evolutionary and biogeographic origins of the Malagasy flora. We inferred a highly resolved phylogeny based on target-enrichment data from 327 species (including 51 % of Malagasy endemics) and conducted ancestral range estimation analyses. Our results revealed at least six trans-oceanic dispersal events from different African regions to Madagascar during the Pliocene. In this process, biome conservatism prevailed, as evidenced by similarities between Malagasy lineages and their African relatives. The southern African grasslands, known to be the center of diversification and the main source of African Helichrysum lineages, played a key role in the colonization of Madagascar as the ancestral source area of at least three clades. The Tropical Afromontane region was revealed as the source of at least two montane Malagasy lineages that substantially radiated in-situ. Finally, a dispersal event from southwestern Africa led to a lineage represented by a single species adapted to the island's southwestern arid conditions. The main radiations of Helichrysum in Madagascar's mountains occurred within the last 2 My, coinciding with a transition towards cooler and drier conditions and the expansion of open habitats, likely driven by a combination of geographic and ecological speciation. Overall, our findings highlight the affinities between the montane floras of continental Africa and Madagascar.

Aim: We investigated the biogeographic history and diversification dynamics of Afrocarduus , an Afromontane–Afroalpine genus endemic to eastern Africa. We aimed to assess the roles of geographic isolation, habitat transitions, and ecological speciation in shaping current diversity. Location: The Afromontane and Afroalpine regions of East Africa and Ethiopia are situated along the Great Rift Valley system. Taxon: Afrocarduus (Compositae: Carduinae), a genus comprising 18 endemic species. Methods: We conducted a comprehensive taxonomic and geographic sampling of Afrocarduus , generating data from 489 nuclear loci. Phylogenomic and biogeographic ancestral estimation analyses were performed to infer the evolutionary history and historical biogeography of the genus. Results: Afrocarduus originated in the Afromontane zone of eastern Africa during the Late Miocene (~10.7 Ma), with major diversification events occurring in the Early Pleistocene (~2.3 Ma). Most dispersal events occurred between neighbouring massifs, though occasional long‐distance dispersal between disjunct mountain systems was detected. The Turkana Depression and the Great Rift Valley have acted as major biogeographic barriers. Phylogenetic structure shows distinct clades occupying different regions. Ecological divergence between Afromontane and Afroalpine environments contributed to speciation, with at least six independent adaptations to Afroalpine conditions and multiple cases of ecological reversal. Stem loss, a trait associated with alpine habitats, evolved convergently in two clades. Closely related species often segregate by elevation or microhabitat within the same massif. Main Conclusions: The diversification of Afrocarduus has been shaped by a combination of historical climate change, geographic isolation, and ecological adaptation. Our results emphasise the importance of ecological speciation and habitat transitions in Afrotemperate plant evolution and highlight the need for further research on understudied Afromontane taxa, especially under the threat of ongoing climate change.

Climate change poses a significant threat to the Afrotemperate flora of the Eastern Afromontane Biodiversity Hotspot, particularly to species confined to high-elevation ecosystems such as those found on the African sky islands. This study evaluates the vulnerability of tropical Afroalpine and Afromontane Helichrysum taxa (Compositae) by assessing their climatic niches and predicting future shifts in distribution, range fragmentation, and altitudinal limits under climate change scenarios. Occurrence records for 14 taxa (eight Afroalpine and six Afromontane) were obtained from recent field campaigns, biodiversity databases and herbaria. Ensemble ecological niche models were developed combining Generalized Linear Models, Generalized Boosting Models, and Random Forest. Taxon-specific bioclimatic variables were selected after correlation analyses. The models were calibrated using current climate data and projected using the PSL-CM6A-LR and MRI-ESM2.0 climate models with both low- and high-emission scenarios. The results show that most Afrotemperate taxa currently occupy only a portion of their climatically suitable habitat, often in geographically distant areas. Future projections indicate significant range contractions and increased fragmentation. Afroalpine taxa could lose 50–66% of their suitable habitat, while Afromontane taxa could decline by 53–79%. Suitable areas were estimated to shift upwards in elevation, with limited potential for colonization of new areas, and with no significant latitudinal or longitudinal shifts. These findings represent the first continental-scale assessment of the impact of climate change on the Afrotemperate flora using ecological niche modelling. The projected climate-induced range losses and increased habitat fragmentation, in particular combined with increasing anthropogenic pressure in this region, highlight the urgent need for targeted conservation actions.

Summary: Gynomonoecy has evolved repeatedly in Asteraceae, suggesting selective advantages for species whose capitula combine pistillate and bisexual flowers. Theories invoking conspicuous peripheral flowers and achene heteromorphism do not account for gynomonoecy in the southern African‐centred genus Helichrysum , which lacks both these features. We investigated whether gynomonoecy is associated with changes in capitulum architecture in South African Helichrysum , focusing on flower packing density and achene size. We compared flower packing density and achene size between hermaphroditic and gynomonoecious Helichrysum species using phylogenetic generalised least squares and reconstructed ancestral sexual systems using a well‐sampled, time‐calibrated phylogeny. Gynomonoecious species produced nearly twice as many flowers per unit receptacle area as hermaphroditic species and had subtly but significantly smaller achenes. Ancestral‐state reconstruction strongly supported hermaphroditism as ancestral, with gynomonoecy originating independently 18 times. Our results provide the first phylogenetically informed evidence within a single Asteraceae genus that shifts to gynomonoecy correlate with shifts in capitulum architecture. The association between gynomonoecy, denser flower packing, and reduced achene size is consistent with the hypothesis that accentuated resource gradients within capitula and priority access to resources by first‐maturing peripheral flowers may have favoured the evolution of gynomonoecy.