Evolution of endemism on a young tropical mountain.

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.

A bi-organellar phylogenomic study of Pandanales: inference of higher-order relationships and unusual rate-variation patterns.

We used a bi-organellar phylogenomic approach to address higher-order relationships in Pandanales, including the first molecular phylogenetic study of the panama-hat family, Cyclanthaceae. Our genus-level study of plastid and mitochondrial gene sets includes a comprehensive sampling of photosynthetic lineages across the order, and provides a framework for investigating clade ages, biogeographic hypotheses and organellar molecular evolution. Using multiple inference methods and both organellar genomes, we recovered mostly congruent and strongly supported relationships within and between families, including the placement of fully mycoheterotrophic Triuridaceae. Cyclanthaceae and Pandanaceae plastomes have slow substitution rates, contributing to weakly supported plastid-based relationships in Cyclanthaceae. While generally slowly evolving, mitochondrial genomes exhibit sporadic rate elevation across the order. However, we infer well-supported relationships even for slower evolving mitochondrial lineages in Cyclanthaceae. Clade age estimates across photosynthetic lineages are largely consistent with previous studies, are well correlated between the two organellar genomes (with slightly younger inferences from mitochondrial data), and support several biogeographic hypotheses. We show that rapidly evolving non-photosynthetic lineages may bias age estimates upwards at neighbouring photosynthetic nodes, even using a relaxed clock model. Finally, we uncovered new genome structural variants in photosynthetic taxa at plastid inverted repeat boundaries that show promise as interfamilial phylogenetic markers.

Evolution of mycoheterotrophy in Polygalaceae: The case of Epirixanthes.

PREMISE OF THE STUDY: The mycoheterotrophic lifestyle has enabled some plant lineages to obtain carbon from their mycorrhizal symbionts. The mycoheterotrophic genus Epirixanthes (Polygalaceae) consists of six species from tropical Asia. Although it is probably closely related to the chlorophyllous genus Salomonia and linked to arbuscular mycorrhizal fungi, lack of DNA sequence data has thus far prevented these hypotheses from being tested. Therefore, the evolutionary history of Epirixanthes remains largely unknown. METHODS: We reconstructed the phylogenetic relationships of Epirixanthes based on nuclear ITS and plastid matK data. Divergence times were inferred using a Bayesian relaxed clock approach, and we phylogenetically analyzed its mycorrhizal symbionts. We furthermore assigned these symbionts to operational taxonomic units, compared them with symbionts of other Polygalaceae, and measured their phylogenetic diversity. KEY RESULTS: We found that Epirixanthes is placed in tribe Polygaleae as sister to Salomonia. Epirixanthes has a Miocene-Oligocene stem age and grows exclusively in symbiosis with fungi of Glomeraceae. Salomonia and some Polygala species are linked to both Glomeraceae and Acaulosporaceae, resulting in higher phylogenetic diversity values. The majority of the symbionts of Epirixanthes are not found in Salomonia or Polygala, although a few shared fungal taxa are found. CONCLUSIONS: Epirixanthes forms a relatively young mycoheterotrophic lineage. The Oligocene-Miocene origin suggests its evolution was influenced by the environmental dynamics in Southeast Asia during this time. Although comparison of fungi from Epirixanthes with those from Salomonia and Polygala suggests some specialization, many other mycoheterotrophic plants are linked to a more narrow set of Glomeraceae.

New insights in the long-debated evolutionary history of Triuridaceae (Pandanales).

The mycoheterotrophic plant family Triuridaceae (Pandanales) is hypothesized to be an old family, mainly based on its pantropical distribution. The existence of fossils from the Upper Cretaceous, assigned to Triuridaceae may form additional support for a great age of the family, although the affinity of these fossils to Triuridaceae is questioned. Although the circumscription of Triuridaceae has never been problematic, probably due to its distinct morphological characters, its systematic relationship has been under debate since the family was described around 1840. The lack of synapomorphies suitable for resolving higher taxonomic relationships is a function of the family's reduced vegetative growth and the highly modified floral structures. Molecular studies have assigned Triuridaceae to Pandanales, but its exact phylogenetic position remains unknown. In the present study the phylogeny of the Pandanales was reconstructed using four molecular markers and the divergence age estimates were obtained with a relaxed molecular clock method. We found that Triuridaceae are monophyletic and most likely descent form the second major split in Pandanales. The relationships between the other Pandanales families (Cyclanthaceae, Pandanaceae, Stemonaceae and Velloziaceae) are otherwise in accordance with earlier studies. Velloziaceae are sister to the rest of the Pandanales, Stemonaceae are most likely sister to a clade consisting of Pandanaceae and Cyclanthaceae, and the latter two families are sister to each other. All currently recognized tribes within Triuridaceae are also monophyletic at current taxon sampling. We estimate that the family has a Cretaceous (or Lower Paleocene) stem age, which is in accordance with earlier predictions. This old age, along with elevated mutation rates indicated by long branch lengths and the family's mycoheterotrophic lifestyle, might account for the substantial morphological differences between Triuridaceae and its closest relatives.

Phylogenetic relationships of the mycoheterotrophic genus Voyria and the implications for the biogeographic history of Gentianaceae.

PREMISE OF THE STUDY: The angiosperm family Gentianaceae comprises over 1700 species in 91 genera. Gentianaceae are distributed worldwide, but most species occur in temperate zones. Phylogenetic studies demonstrate that the family consists of six monophyletic tribes. However, the phylogenetic position of the mycoheterotrophic genus Voyria, with a remarkable trans-Atlantic distribution, remained unknown. METHODS: We used nuclear ITS and 18S rDNA and mitochondrial apt1 and matR data to infer the phylogenetic position of Voyria in Gentianaceae. In addition, with Bayesian relaxed molecular clock analyses we obtained age estimates for the diversification of Voyria and Gentianaceae in general and used these results to reconstruct the ancestral areas associated with the early diversification events in Gentianaceae. KEY RESULTS: Our results demonstrate that Voyria is an early diverging lineage within Gentianaceae with no close relationships to other mycoheterotrophic Gentianaceae lineages. Voyria originated in the neotropics during the Early Eocene but only reached its current transoceanic distribution around the end of the Oligocene. The neotropics were an important area for the early diversification events in Gentianaceae, most of which occurred during the Eocene. CONCLUSIONS: Voyria is an old, phylogenetically isolated lineage within Gentianaceae, and the current distribution of the genus is indicative of the ancestral area in which the early diversification events of Gentianaceae occurred. In parallel with many other pantropical families, our results suggest that migration of tropical taxa through Laurasia during the Early Eocene has played an important role in shaping the current global distribution of Gentianaceae.