Search

Rapid evolutionary radiations are among the most challenging phylogenetic problems, wherein different types of data (e.g. morphology and molecular) or genetic markers (e.g. nuclear and organelle) often yield inconsistent results. The tribe Arundinarieae, that is, the temperate bamboos, is a clade of tetraploid originated 22 Ma and subsequently radiated in East Asia. Previous studies of Arundinarieae have found conflicting relationships and/or low support. Here, we obtain nuclear markers from ddRAD data for 213 Arundinarieae taxa and parallel sampling of chloroplast genomes from genome skimming for 147 taxa. We first assess the feasibility of using ddRAD-seq data for phylogenetic estimates of paleopolyploid and rapidly radiated lineages, optimize clustering thresholds, and analysis workflow for orthology identification. Reference-based ddRAD data assembly approaches perform well and yield strongly supported relationships that are generally concordant with morphology-based taxonomy. We recover five major lineages, two of which are notable (the pachymorph and leptomorph lineages), in that they correspond with distinct rhizome morphologies. By contrast, the phylogeny from chloroplast genomes differed significantly. Based on multiple lines of evidence, the ddRAD tree is favored as the best species tree estimation for temperate bamboos. Using a time-calibrated ddRAD tree, we find that Arundinarieae diversified rapidly around the mid-Miocene corresponding with intensification of the East Asian monsoon and the evolution of key innovations including the leptomorph rhizomes. Our results provide a highly resolved phylogeny of Arundinarieae, shed new light on the radiation and reticulate evolutionary history of this tribe, and provide an empirical example for the study of recalcitrant plant radiations. [Arundinarieae; ddRAD; paleopolyploid; genome skimming; rapid diversification; incongruence.] [ABSTRACT FROM AUTHOR]

Aim: The Hengduan Mountains (HDM) of southwest China is a biodiversity hotspot and harbours one of the world's richest temperate floras. However, the origin and evolution of its biota remain largely unresolved. Here we explore the impact of mountain uplift on the diversification process of biodiversity in this hotspot using alpine bamboos. Location: The HDM region, southwest China. Taxon: Alpine bamboos. Methods: We used ddRAD‐seq data from the most complete sampling of alpine bamboos undertaken to date (79% of the species diversity), to investigate their evolutionary history. The ancestral area of these bamboos was reconstructed using a time‐calibrated phylogeny in BioGeoBEARS and diversification rates were inferred using BAMM analyses. In addition, the impact of mountain uplift on the divergence of alpine bamboos was evaluated using trait‐dependent models of diversification. Results: The alpine bamboos were strongly supported as monophyletic, and the relationships within them were robustly resolved. Fargesia was found to be polyphyletic and Yushania was resolved as monophyletic. Alpine bamboos originated outside the HDM region during the late Miocene, and spread to this region in the Pliocene, undergoing a significant acceleration in net diversification, which is temporally congruent with the orogeny. The speciation rate increased with altitude and a high diversification rate, estimated to be 0.75 species per million years, was detected for alpine bamboos distributed in high elevations. Main Conclusions: Our study demonstrates that heterogeneous mountain habitats and geographical isolation of alpine bamboos, which have limited dispersal ability, are important drivers for their rapid diversification. This study also highlights the power of complementary analyses in revealing the link between species diversification and past geological changes. [ABSTRACT FROM AUTHOR]

Plant microRNAs (miRNAs) play important roles in various developmental and physiological processes ( e.g. seed germination, vegetative growth, flowering, seed production, and responses to abiotic or biotic stimuli) by targeting mRNAs for cleavage or translational repression at the post-transcriptional level. Bamboo flowering is an unusual physiological phenomenon relative to the typical graminaceous plants. In this study, we focused on the microRNAome of developing Dendrocalamus latiflorus inflorescences. Solexa high-throughput small RNA (sRNA) sequencing technology was used to sequence and quantify the miRNAs expressed during two phases of D. latiflorus flower development. A total of 118 conserved miRNAs and 47 novel miRNAs was identified in the developing flowers. The transcript levels of most of the miRNAs were similar between the two phases. However, five miRNAs showed distinct changes as the flowering developed, with the novel miRNA dla-miR18 in particular showing a large difference in transcript abundance between the two phases. Fifteen of the D. latiflorus miRNAs found in this study appeared likely to be specific to flower development. Moreover, 130 of the floral unigenes of D. latiflorus were determined to be putative targets of the miRNAs, and the miRNA cleavage sites of seven of these putative targets were validated by 5′-RACE. The results of this study provide the first broad survey of the microRNAomes of Bambusoideae and yield valuable insights into the potential roles of microRNAs in bamboo inflorescence development. Our findings represent a starting point for future functional research on the role of miRNA in the flower development in D. latiflorus and related species. [ABSTRACT FROM AUTHOR]

In flowering plants, three genomes (nuclear, mitochondrial, and plastid) coexist and intracellular horizontal transfer of DNA is prevalent, especially from the plastid to the mitochondrion genome. However, the plastid genomes are generally conserved in evolution and have long been considered immune to foreign DNA. Recently, the opposite direction of DNA transfer from the mitochondrial to the plastid genome has been reported in two eudicot lineages. Here we sequenced 6 plastid genomes of bamboos, three of which are neotropical woody species and three are herbaceous ones. Several unusual features were found, including the duplication of trnT-GGU and loss of one copy of rps19 due to contraction of inverted repeats (IRs). The most intriguing was the ~2.7 kb insertion in the plastid IR regions in the three herbaceous bamboos. Furthermore, the insertion was documented to be horizontally transferred from the mitochondrial to the plastid genome. Our study provided evidence of the mitochondrial-to-plastid DNA transfer in the monocots, demonstrating again that this rare event does occur in other angiosperm lineages. However, the mechanism underlying the transfer remains obscure, and more studies in other plants may elucidate it in the future. [ABSTRACT FROM AUTHOR]

In this paper we investigate the biogeography of the temperate woody bamboos (Arundinarieae) using a densely-sampled phylogenetic tree of Bambusoideae based on six plastid DNA loci, which corroborates the previously discovered 12 lineages (I–XII) and places Kuruna as sister to the Chimonocalamus clade. Biogeographic analyses revealed that the Arundinarieae diversified from an estimated 12 to 14 Mya, and this was followed by rapid radiation within the lineages, particularly lineages IV, V and VI, starting from c. 7–8 Mya. It is suggested that the late Miocene intensification of East Asian monsoon may have contributed to this burst of diversification. The possibilities of the extant Sri Lankan and African temperate bamboo lineages representing ‘basal elements’ could be excluded, indicating that there is no evidence to support the Indian or African route for migration of temperate bamboo ancestors to Asia. Radiations from eastern Asia to Africa, Sri Lanka, and to North America all are likely to have occurred during the Pliocene, to form the disjunct distribution of Arundinarieae we observe today. The two African lineages are inferred as being derived independently from Asian ancestors, either by overland migrations or long-distance dispersals. Beringian migration may explain the eastern Asian–eastern North American disjunction. [ABSTRACT FROM AUTHOR]