The rise of angiosperms has been regarded as a trigger for the Cretaceous revolution of terrestrial ecosystems. However, the timeframe of the rise angiosperm-dominated herbaceous floras (ADHFs) is lacking. Here, we used the buttercup family (Ranunculaceae) as a proxy to provide insights into the rise of ADHFs. An integration of phylogenetic, molecular dating, ancestral state inferring and diversification analytical methods was used to infer the early evolutionary history of Ranunculaceae. We found that Ranunculaceae became differentiated in forests between about 108–90 Ma. Diversification rates markedly elevated during the Campanian, mainly resulted from the rapid divergence of the non-forest lineages, but did not change across the Cretaceous-Paleogene boundary. Our data for Ranunculaceae indicate that forest-dwelling ADHFs may have appeared almost simultaneously with angiosperm-dominated forests during the mid-Cretaceous, whereas non-forest ADHFs arose later, by the end of the Cretaceous terrestrial revolution. Furthermore, ADHFs were relatively unaffected by the Cretaceous-Paleogene mass extinction.

Understanding which factors have driven the evolutionary success of a group is a fundamental question in biology. Angiosperms are the most successful group in plants and have radiated and adapted to various habitats. Among angiosperms, legumes are a good example for such successful radiation and adaptation. We here investigated how the interplay of past climate changes, geographical expansion and habit shifts has promoted diversification of the phaseoloid legumes, one of the largest clades in the Leguminosae. Using a comprehensive genus-level phylogeny from three plastid markers, we estimate divergence times, infer habit shifts, test the phylogenetic and temporal diversification heterogeneity, and reconstruct ancestral biogeographical ranges. We found that the phaseoloid lineages underwent twice dramatic accumulation. During the Late Oligocene, at least six woody clades rapidly diverged, perhaps in response to the Late Oligocene warming and aridity, and a result of rapidly exploiting new ecological opportunities in Asia, Africa and Australia. The most speciose lineage is herbaceous and began to rapidly diversify since the Early Miocene, which was likely ascribed to arid climates, along with the expansion of seasonally dry tropical forests in Africa, Asia, and America. The phaseoloid group provides an excellent case supporting the idea that the interplay of ecological opportunities and key innovations drives the evolutionary success.

Caves are home to unique and fragile biotas with high levels of endemism. However, little is known about how the biotic colonization of caves has developed over time, especially in caves from middle and low latitudes. Subtropical East Asia holds the world's largest karst landform with numerous ancient caves, which harbor a high diversity of cave-dwelling organisms and are regarded as a biodiversity hotspot. Here, we assess the temporal dynamics of biotic colonization of subtropical East Asian caves through a multi-taxon analysis with representatives of green plants, animals, and fungi. We then investigate the consequences of paleonviromental changes on the colonization dynamics of these caves in combination with reconstructions of vegetation, temperature, and precipitation. We discover that 88% of cave colonization events occurred after the Oligocene-Miocene boundary, and organisms from the surrounding forest were a major source for subtropical East Asian cave biodiversity. Biotic colonization of subtropical East Asian caves during the Neogene was subject to periods of acceleration and decrease, in conjunction with large-scale, seasonal climatic changes and evolution of local forests. This study highlights the long-term evolutionary interaction between surface and cave biotas; our climate-vegetation-relict model proposed for the subtropical East Asian cave biota may help explain the evolutionary origins of other mid-latitude subterranean biotas.

Correct combination of plastid (cp) and nuclear (nr) DNA data for plant phylogenetic reconstructions is not a new issue, but with an increasing number of nrDNA loci being used, it is of ever greater practical concern. For accurately reconstructing the phylogeny and evolutionary history of plant groups, correct treatment of phylogenetic incongruence is a vital step in the proper analysis of cpDNA and nrDNA data. We first evaluated the current status of analyzing cpDNA and nrDNA data by searching all articles published in the journal Systematic Botany between 2005 and 2011. Many studies combining cpDNA and nrDNA data did not rigorously assess the combinability of the data sets, or did not address in detail possible reasons for incongruence between the two data sets. By reviewing various methods, we outline a procedure to more accurately analyze and/or combine cpDNA and nrDNA data, which includes four steps: identifying significant incongruence, determining conflicting taxa, providing possible interpretations for incongruence, and reconstructing the phylogeny after treating incongruence. Particular attention is given to explanation of the cause of incongruence. We hope that our procedure will help raise awareness of the importance of rigorous analysis and help identify the cause of incongruence before combining cpDNA and nrDNA data.