Yu-Xiao Zhang

Chloroplast phylogenomic analyses resolve deep-level relationships of an intractable bamboo tribe Arundinarieae (poaceae).

The temperate woody bamboos constitute a distinct tribe Arundinarieae (Poaceae: Bambusoideae) with high species diversity. Estimating phylogenetic relationships among the 11 major lineages of Arundinarieae has been particularly difficult, owing to a possible rapid radiation and the extremely low rate of sequence divergence. Here, we explore the use of chloroplast genome sequencing for phylogenetic inference. We sampled 25 species (22 temperate bamboos and 3 outgroups) for the complete genome representing eight major lineages of Arundinarieae in an attempt to resolve backbone relationships. Phylogenetic analyses of coding versus noncoding sequences, and of different regions of the genome (large single copy and small single copy, and inverted repeat regions) yielded no well-supported contradicting topologies but potential incongruence was found between the coding and noncoding sequences. The use of various data partitioning schemes in analysis of the complete sequences resulted in nearly identical topologies and node support values, although the partitioning schemes were decisively different from each other as to the fit to the data. Our full genomic data set substantially increased resolution along the backbone and provided strong support for most relationships despite the very short internodes and long branches in the tree. The inferred relationships were also robust to potential confounding factors (e.g., long-branch attraction) and received support from independent indels in the genome. We then added taxa from the three Arundinarieae lineages that were not included in the full-genome data set; each of these were sampled for more than 50% genome sequences. The resulting trees not only corroborated the reconstructed deep-level relationships but also largely resolved the phylogenetic placements of these three additional lineages. Furthermore, adding 129 additional taxa sampled for only eight chloroplast loci to the combined data set yielded almost identical relationships, albeit with low support values. We believe that the inferred phylogeny is robust to taxon sampling. Having resolved the deep-level relationships of Arundinarieae, we illuminate how chloroplast phylogenomics can be used for elucidating difficult phylogeny at low taxonomic levels in intractable plant groups.

Complex evolution in Arundinarieae (Poaceae: Bambusoideae): Incongruence between plastid and nuclear GBSSI gene phylogenies

The monophyly of tribe Arundinarieae (the temperate woody bamboos) has been unequivocally recovered in previous molecular phylogenetic studies. In a recent phylogenetic study, 10 major lineages in Arundinarieae were resolved based on eight non-coding plastid regions, which conflicted significantly with morphological classifications both at the subtribal and generic levels. Nevertheless, relationships among and within the 10 lineages remain unclear. In order to further unravel the evolutionary history of Arundinarieae, we used the nuclear GBSSI gene sequences along with those of eight plastid regions for phylogenetic reconstruction, with an emphasis on Chinese species. The results of the plastid analyses agreed with previous studies, whereas 13 primary clades revealed in the GBSSI phylogeny were better resolved at the generic level than the plastid phylogeny. Our analyses also revealed many inconsistencies between the plastid DNA and the nuclear GBSSI trees. These results implied that the nuclear genome and the plastid genome had different evolutionary trajectories. The patterns of incongruence suggested that lack of informative characters, incomplete lineage sorting, and/or hybridization (introgression) could be the causes. Seven putative hybrid species were hypothesized, four of which are discussed in detail on the basis of topological incongruence, chromosome numbers, morphology, and distribution patterns, and those taxa probably resulted from homoploid hybrid speciation. Overall, our study indicates that the tribe Arundinarieae has undergone a complex evolution.

The monophyly of Chimonocalamus and conflicting gene trees in Arundinarieae (Poaceae: Bambusoideae) inferred from four plastid and two nuclear markers

Arundinarieae is not only a taxonomically difficult group of bamboos, but also a troublesome one in molecular phylogenetics. In this study, the phylogeny of 50 species in Arundinarieae with an emphasis on Chimonocalamus was reconstructed, using four plastid regions (rpl32-trnL, trnT-trnL, rps16-trnQ and trnC-rpoB) and two nuclear genes (GBSSI and LEAFY). The plastid phylogeny was largely consistent with the previous studies, except that Ampelocalamus calcareus was newly recovered as lineage XI. The nuclear phylogeny of LEAFY had better resolution than the one of GBSSI. The close relationships among Ampelocalamus, Drepanostachyum and Himalayacalamus were retrieved by the nuclear datasets. Alpine Bashania, Chimonocalamus, Thamnocalamus, and species currently placed in Fargesia and Yushania formed a clade in the LEAFY and combined nuclear phylogenies. Some of the gene tree disparities revealed in previous studies were reconfirmed. Chimonocalamus was recovered as monophyletic by combining the nuclear genes, but as polyphyletic in plastid analyses. Insufficient informative characters, hybridization, plastid capture or incomplete plastid lineage sorting could be responsible for the incongruent phylogenetic positions of some species of Chimonocalamus.

Evidence for horizontal transfer of mitochondrial DNA to the plastid genome in a bamboo genus

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 ~2.7u2009kb 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.

Multi-locus plastid phylogenetic biogeography supports the Asian hypothesis of the temperate woody bamboos (Poaceae: Bambusoideae)

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 14Mya, and this was followed by rapid radiation within the lineages, particularly lineages IV, V and VI, starting from c. 7-8Mya. 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.

Identification of putative orthologous genes for the phylogenetic reconstruction of temperate woody bamboos (Poaceae: Bambusoideae)

The temperate woody bamboos (Arundinarieae) are highly diverse in morphology but lack a substantial amount of genetic variation. The taxonomy of this lineage is intractable, and the relationships within the tribe have not been well resolved. Recent studies indicated that this tribe could have a complex evolutionary history. Although phylogenetic studies of the tribe have been carried out, most of these phylogenetic reconstructions were based on plastid data, which provide lower phylogenetic resolution compared with nuclear data. In this study, we intended to identify a set of desirable nuclear genes for resolving the phylogeny of the temperate woody bamboos. Using two different methodologies, we identified 209 and 916 genes, respectively, as putative single copy orthologous genes. A total of 112 genes was successfully amplified and sequenced by next‐generation sequencing technologies in five species sampled from the tribe. As most of the genes exhibited intra‐individual allele heterozygotes, we investigated phylogenetic utility by reconstructing the phylogeny based on individual genes. Discordance among gene trees was observed and, to resolve the conflict, we performed a range of analyses using BUCKy and HybTree. While caution should be taken when inferring a phylogeny from multiple conflicting genes, our analysis indicated that 74 of the 112 investigated genes are potential markers for resolving the phylogeny of the temperate woody bamboos.

In search of the phylogenetic affinity of the temperate woody bamboos from Madagascar, with description of a new species (Bambusoideae, Poaceae)

Six temperate woody bamboos (Arundinarieae, Bambusoideae) from Madagascar were described in the genus Arundinaria during the 1920s to 1960s. However, recent phylogenetic studies imply that Arundinaria is restricted to North America, and taxonomic affiliation of the Malagasy temperate woody bamboos remained ambiguous. In search of phylogenetic affinity of these bamboos, herbarium observation, fieldwork, and molecular phylogenetic analysis have been carried out. Four of them and one potential new species were sampled for molecular phylogenetic analyses in the context of the tribe Arundinarieae. Maximum likelihood and Bayesian analyses indicated that those species were closely related to Oldeania alpina distributed in continental Africa, but not Arundinaria, Bergbambos, Fargesia (including Sinarundinaria), Thamnocalamus, or Yushania, in which they were placed at one time or another. On the grounds of molecular phylogeny, morphology, and phytogeography, the Malagasy temperate woody bamboos should be treated as members of the genus Oldeania. Arundinaria humbertii and A. ambositrensis are conspecific. A new species, Oldeania itremoensis, is described and illustrated. The other two temperate woody bamboo species in Madagascar not sampled in the molecular phylogeny are also transferred to Oldeania on the basis of morphology.

New distribution records of two bamboo species in Yunnan, China with description of the inflorescence for Melocalamus yunnanensis (Poaceae, Bambusoideae)

Abstract Ampelocalamus actinotrichus (Merrill & Chun) S. L. Chen, T. H. Wen & G. Y. Sheng and Neomicrocalamus prainii (Gamble) P. C. Keng are reported with new distribution records in southern and southeastern Yunnan, China, respectively. Ampelocalamus actinotrichus was previously recorded to be endemic to Hainan, China, and Neomicrocalamus prainii to be distributed in southern Tibet and western Yunnan in China, northeastern India, and Burma. The identities of individuals collected in southern and southeastern Yunnan of these two species are confirmed by molecular evidence. The new distribution record of Ampelocalamus actinotrichus provides a case at the species level for confirming floristic affinities of southern Yunnan and Hainan Island in south China. The disjunct distribution of Neomicrocalamus prainii in Yunnan is concordant with the ecogeographical diagonal line from northwestern Yunnan to southeastern Yunnan and this may imply a tropical origin of this species. In addition, the inflorescence of Melocalamus yunnanensis (T. H. Wen) T. P. Yi is described.

Pseudosasa xishuangbannaensis (Poaceae: Bambusoideae: Arundinarieae), a new species from Yunnan, China

Pseudosasa xishuangbannaensis is described and illustrated as a new species of Arundinarieae (the temperate woody bamboos) from southern Yunnan, China. It belongs to Pseudosasa subg. Sinicae. The new species is characterized by glabrous culm leaf sheaths with dense setae at the base, several to many spikelets, and 5–7 glumes, and it can be distinguished from closely related species by these morphological features and molecular evidence.

A new genus of temperate woody bamboos (Poaceae, Bambusoideae, Arundinarieae) from a limestone montane area of China

Abstract Ampelocalamuscalcareus is a climbing and slender bamboo, known from south Guizhou, China. This species grows in broadleaved forests of limestone montane areas. Recent molecular phylogenetic analyses demonstrated that A.calcareus was sister to all other lineages of the tribe Arundinarieae rather than a member of Ampelocalamus. The morphological features and habitats of A.calcareus and related genera including Ampelocalamus, Drepanostachyum and Himalayacalamus were compared and discussed. The characteristics of the branch complements, nodes and foliage leaves distinguish A.calcareus from morphologically similar taxa. On the basis of molecular and morphological evidence, we propose to establish a new genus, Hsuehochloa, to accommodate A.calcareus and to honour the late Chinese bamboo taxonomist Chi-Ju Hsueh (Ji-Ru Xue). In addition, we describe the inflorescence of Hsuehochloa for the first time.