Extended Data Fig. 2: A schematic of the decision-making process for defining colonisation, single speciation and cladogenetic speciation.

Examples of the decision process for defining assembly processes. For each clade we combined two ancestral state reconstructions, shown here on two adjacent trees: one of elevational distribution (red and blue tip states) and the other of geographic distribution (yellow and green tip states). The ancestral state reconstructions were run on 35 Myr time slices of the phylogeny, with the state of stem node forced to be either low-elevation or non-EAS as relevant. a. A colonisation event is defined as the arrival of a lineage in the Alpine sky-islands. We consider that a sky-island species has originated via colonisation if its most recent common ancestor (MRCA) occurred at low elevations or in non-EAS regions, and its current distribution includes non-EAS regions, as illustrated by species D. b. We define a single speciation event as the generation of a new species due to a lineage splitting across the boundaries of the Alpine sky-islands. Species A, B, and D are all considered single-speciation species. Species A originated via single speciation as it has speciated across both elevational and geographic boundaries, its MRCA occurring at low elevations in non-EAS regions. Species B split across elevational boundaries, likely speciating during a transition from lower elevation zones to sky-islands within the EAS. Conversely, species D had a high-elevation ancestor, but likely underwent geographic divergence after arriving from a non-EAS mountain range. c. We define a cladogenetic speciation event as lineage splitting within the boundaries of the Alpine sky-island. In the left-hand example, species B, C, and D are considered a sky-island group that originated through cladogenetic speciation, as their MRCAs are all reconstructed to occur in the sky-islands and the EAS. In this scenario, species B is assumed to have originated in the sky-island and since extended its range to include non-EAS regions. Species E is not considered part of the group, as it does not occur in the sky-islands. Although species E has sky-island and EAS ancestors, its non-sky-island distribution suggests that speciation occurred across the treeline rather than within the sky-island boundaries. Species A is not included in the group as it does not have sky-island ancestry. In the right-hand example, all five species have sky-island ancestry. Non-EAS ancestry is reconstructed at the starred node however, suggesting that at this node lineage splitting did not occur in a sky-island context. Therefore, we circumscribe two groups, the first containing species A and B, and the second containing species D and E. Species C is then considered a single speciation event.