Tropical mountains are hot spots of biodiversity and endemism, but the evolutionary origins of their unique biotas are poorly understood. In varying degrees, local and regional extinction, long-distance colonization, and local recruitment may all contribute to the exceptional character of these communities. Also, it is debated whether mountain endemics mostly originate from local lowland taxa, or from lineages that reach the mountain by long-range dispersal from cool localities elsewhere. Here we investigate the evolutionary routes to endemism by sampling an entire tropical mountain biota on the 4,095-metre-high Mount Kinabalu in Sabah, East Malaysia. We discover that most of its unique biodiversity is younger than the mountain itself (6 million years), and comprises a mix of immigrant pre-adapted lineages and descendants from local lowland ancestors, although substantial shifts from lower to higher vegetation zones in this latter group were rare. These insights could improve forecasts of the likelihood of extinction and 'evolutionary rescue' in montane biodiversity hot spots under climate change scenarios.

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Biogeographical analysis addresses two distinct problems: the reconstruction of Earth history and of taxon history. For the reconstruction of Earth history, an analogy between taxa and areas is often assumed. Uncritical acceptance of this analogy has led to methods for the reconstruction of taxon history being inappropriately used for the reconstruction of Earth history. A biogeographical protocol is proposed which does not rely on this analogy. This protocol resolves the historical sequence of vicariance events, not the relations between areas. The protocol is illustrated with the analysis of three examples.

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We inferred the classification of the Paleotropical climbing fern genus Arthropteris and its close relative Psammiosorus, a monotypic genus endemic to Madagascar. The classification of these ferns has until now been poorly understood. To address this, we sampled more than half of the species diversity covering the whole range of the genus including the outlying occurrence at the Juan Fernández Islands. To reconstruct phylogenetic relationships, we obtained DNA sequences from up to six plastid genome regions, including coding and non–coding regions, for these two genera and representatives of all families of the eupolypod I clade, with an emphasis on the Tectariaceae. These data were analyzed using maximum parsimony, maximum likelihood, and Bayesian inference. We also obtained divergence time estimates. Three questions were addressed. (1) We established that Arthropteris and Psammiosorus form a well–supported clade representing a separate taxon based on their morphological distinctiveness, phylogenetic relationships, and separation since the Eocene from other accepted families of eupolypod ferns. (2) Psammiosorus was found to be nested within Arthropteris. (3) Our analyses supported recognition of a previously doubted species endemic to the karst regions of southern China and northern Vietnam. As a consequence of our results, we describe the new family Arthropteridaceae and introduce the new combination Arthropteris paucivenia for the Madagascan endemic previously treated under Psammiosorus.