Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s.s.

The taxonomy of Bambusoideae is in a state of flux and phylogenetic studies are required to help resolve systematic issues. Over 60 taxa, representing all subtribes of Bambuseae and related non-bambusoid grasses were sampled. A combined analysis of five plastid DNA regions, trnL intron, trnL-F intergenic spacer, atpB-rbcL intergenic spacer, rps16 intron, and matK, was used to study the phylogenetic relationships among the bamboos in general and the woody bamboos in particular. Within the BEP clade (Bambusoideae s.s., Ehrhartoideae, Pooideae), Pooideae were resolved as sister to Bambusoideae s.s. Tribe Bambuseae, the woody bamboos, as currently recognized were not monophyletic because Olyreae, the herbaceous bamboos, were sister to tropical Bambuseae. Temperate Bambuseae were sister to the group consisting of tropical Bambuseae and Olyreae. Thus, the temperate Bambuseae would be better treated as their own tribe Arundinarieae than as a subgroup of Bambuseae. Within the tropical Bambuseae, neotropical Bambuseae were sister to the palaeotropical and Austral Bambuseae. In addition, Melocanninae were found to be sister to the remaining palaeotropical and Austral Bambuseae. We discuss phylogenetic and morphological patterns of diversification and interpret them in a biogeographic context.     

竹亚科系统学和生物地理学研究进展及存在的问题

对近年来在竹亚科作为一个单系类群的界定、其系统位置的确定、内部系统演化趋势以及地理分布和起源方面研究所取得的进展进行了评述。竹亚科作为一个单系类群仅包括了木本的竹族（Bambuseae)和一个草本的莪利竹族（Olyreae),其中莪利竹族分布在新几内亚的伊里安竹（Buergersiochloa)处于Olyreae最基部。禾本科12个亚科中除了3个亚科为基部类群以外,其余9个亚科分成PACCAD（包括黍亚科,狭义的芦竹亚科,广义的虎尾草亚科,假淡竹叶亚科,三芒草亚科和扁芒草亚科）和BOP单系分支（包括竹亚科,稻亚科和早熟禾亚科）。在BOP支中,竹亚科与早熟禾亚科相近缘,共同组成稻亚科的姐妹群。竹亚科分成草本和木本两个单系类群,木本竹子又分成热带和温带支系,热带支系进一步分成新世界热带和旧世界热带两个单系类群。从现有的化石证据和基部类群的地理分布推断,竹亚科很可能起源于晚白垩纪的冈瓦纳古陆。最后,本文就竹亚科研究尚存在的问题做了初步探讨。     

Phylogeny of the grass family (Poaceae) from rpl16 intron sequence data

DNA sequence data from the chloroplast noncoding rpl16 intron are used to address phylogenetic relationships among the major lineages of the grass family, with particular emphasis on the highly heterogeneous subfamily Bambusoideae and the basal lineages. Thirty-five grass sequences representing all six currently recognized major groups of the family and one outgroup sequence were analyzed using both parsimony and distance methods. The phylogenetic analyses indicated: (1) Puelia, a traditionally isolated bambusoid genus, is the most basal lineage in the BOP clade (Bambusoideae, Oryzoideae, and Pooideae); (2) the bambusoid clade is a sister group to the pooid clade; and (3) the monophyletic oryzoid clade is well separated from the bambusoid clade. The study further confirmed the recognition of two primary groups in the grass family: the BOP clade and the PACC clade (Panicoideae, Arundinoideae, Chloridoideae, and Centothecoideae); it also provided further evidence that the traditional subfamily Bambusoideae is highly heterogeneous and phylogenetically unacceptable. The data support Streptochaeteae, Anomochloeae, and Phareae as the most basal lineages among the extant grasses. Within the BOP clade, oryzoids and pooids are confirmed as two monophyletic clades, but the bambusoid clade, including only the woody bamboo tribe Bambuseae and the herbaceous bamboo tribe Olyreae, is relatively weakly supported. The study also indicated that the chloroplast noncoding region sequence data could be useful in phylogenetic analysis at relatively high taxonomic levels.     

Phylogenetic structure in the grass family (Poaceae) as inferred from chloroplast DNA restriction site variation

A cladistic analysis of chloroplast DNA restriction site variation among representatives of all subfamilies of the grass family (Poaceae), using Joinvillea (Joinvilleaceae) as the outgroup, placed most genera into two major clades. The first of these groups corresponds to a broadly circumscribed subfamily Pooideae that includes all sampled representatives of Ampelodesmeae, Aveneae, Brachypodieae, Bromeae, Diarrheneae, Meliceae, Poeae, Stipeae, and Triticeae. The second major clade includes all sampled representatives of four subfamilies (Panicoideae [tribes Andropogoneae and Paniceae], Arundinoideae [Arundineae], Chloridoideae [Eragrostideae], and Centothecoideae [Centotheceae]). Within this group (the “PACC” clade), the Panicoideae are resolved as monophyletic and as the sister group of the clade that comprises the other three subfamilies. Within the latter group, Danthonia (Arundinoideae) and Eragroslis (Chloridoideae) are resolved as a stable monophyletic group that excludes Phragmites (Arundinoideae); this structure is inconsistent with the Arundinoideae being monophyletic as currently circumscribed. The PACC clade is placed within a more inclusive though unstable clade that includes the woody Bambusoideae (Bambuseae) plus several disparate tribes of herbaceous grasses of uncertain affinity that are often recognized as herbaceous Bambusoideae (Brachyelytreae, Nardeae, Olyreae, Oryzeae, and Phareae). Among eight most-parsimonious trees resolved by the analysis, four include a monophyletic Bambusoideae sensu lato (comprising Bambuseae and all five of these herbaceous tribes) as the sister group of the PACC clade; in the other four trees these bambusoid elements are not resolved as monophyletic, and the PACC clade is nested among these tribes. These results are consistent with those of previous analyses that resolve a basal or near-basal branch within the family between Pooideae and all other grasses. However, resolution by the present analysis of the PACC clade, which includes Centothecoideae, Chloridoideae, and Panicoideae, but excludes Bambusoideae, is inconsistent with the results of previous analyses that place Bambusoideae and Panicoideae in a monophyletic group that excludes Centothecoideae and Chloridoideae.     

Use of flowering gene <Emphasis Type="Italic">FLOWERING LOCUS T</Emphasis> (<Emphasis Type="Italic">FT</Emphasis>) homologs in the phylogenetic analysis of bambusoid and early diverging grasses

A nuclear gene, FLOWERING LOCUS T (FT) homolog, was cloned from Phyllostachys meyeri as PmFT. Its putative copy number was estimated as four by Southern blot analysis, and the two copies were completely sequenced. Twenty-seven FT homolog sequences of bambusoid and early diverging grasses comprised 172-bp exons, and 357- to 785-bp introns exhibited 0-58.9% pairwise divergence with six modal levels. Parsimony analyses of the FT homologs rooted at Pharus virescens produced six equally parsimonious trees. In the strict consensus tree, five clades were resolved; they were affected by divergence of the intron region rather than exon region. The basal clade was Puelioideae, followed by Olyreae clade including Oryza sativa. Streptogyneae clade combined the Olyreae clade with terminal sister clades of the Bambuseae, i.e., pantropical bamboos and East Asiatic temperate bamboos. The global topology suggested that FT homologs are significant for resolving the tribe level. However, the phylogeny of FT homologs does not resolve monophyly in Bambusoideae because of intercalary positioning by Streptogyneae clade. We discussed the role of FT homologs in controlling the inflorescence architecture and position of Streptogyneae in the bamboo phylogeny.     

Dawyck Botanic Garden: the Heron Wood cryptogamic project

Background: Arundinarieae are a large tribe of temperate woody bamboos for which phylogenetics are poorly understood because of limited taxon sampling and lack of informative characters.

Aims: This study assessed phylogenetic relationships, origins and classification of Arundinarieae.

Methods: DNA sequences (plastid trnL-F; nuclear ITS) were used for parsimony and Bayesian inference including 41 woody bamboo taxa. Divergence dates were estimated using a relaxed Bayesian clock.

Results: Arundinarieae were monophyletic but their molecular divergence was low compared to the tropical Bambuseae. Ancestors of the Arundinarieae lineage were estimated to have diverged from the other bamboos 23 (15–30) million years ago (Mya). However, the Arundinarieae radiation occurred 10 (6–16) Mya compared to 18 (11–25) Mya for the tropical Bambuseae. Some groups could be defined within Arundinarieae, but they do not correspond to recognised subtribes such as Arundinariinae or Shibataeinae.

Conclusions: Arundinarieae are a relatively ancient bambusoid lineage that underwent a rapid radiation in the late Miocene. The radiation coincides with the continental collision of the Indo-Australian and Eurasian Plates. Arundinarieae are distributed primarily in East Asia and the Himalayas to northern Southeast Asia. It is unknown whether they were present in Asia long before their radiation, but we believe recent dispersal is a more likely scenario.     

High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae)

Background

Bambusoideae is the only subfamily that contains woody members in the grass family, Poaceae. In phylogenetic analyses, Bambusoideae, Pooideae and Ehrhartoideae formed the BEP clade, yet the internal relationships of this clade are controversial. The distinctive life history (infrequent flowering and predominance of asexual reproduction) of woody bamboos makes them an interesting but taxonomically difficult group. Phylogenetic analyses based on large DNA fragments could only provide a moderate resolution of woody bamboo relationships, although a robust phylogenetic tree is needed to elucidate their evolutionary history. Phylogenomics is an alternative choice for resolving difficult phylogenies.

Methodology/Principal Findings

Here we present the complete nucleotide sequences of six woody bamboo chloroplast (cp) genomes using Illumina sequencing. These genomes are similar to those of other grasses and rather conservative in evolution. We constructed a phylogeny of Poaceae from 24 complete cp genomes including 21 grass species. Within the BEP clade, we found strong support for a sister relationship between Bambusoideae and Pooideae. In a substantial improvement over prior studies, all six nodes within Bambusoideae were supported with ≥0.95 posterior probability from Bayesian inference and 5/6 nodes resolved with 100% bootstrap support in maximum parsimony and maximum likelihood analyses. We found that repeats in the cp genome could provide phylogenetic information, while caution is needed when using indels in phylogenetic analyses based on few selected genes. We also identified relatively rapidly evolving cp genome regions that have the potential to be used for further phylogenetic study in Bambusoideae.

Conclusions/Significance

The cp genome of Bambusoideae evolved slowly, and phylogenomics based on whole cp genome could be used to resolve major relationships within the subfamily. The difficulty in resolving the diversification among three clades of temperate woody bamboos, even with complete cp genome sequences, suggests that these lineages may have diverged very rapidly.     

The contribution of foliar micromorphology and anatomy to the circumscription of species within the <Emphasis Type="Italic">Chusquea ramosissima</Emphasis> informal group (Poaceae,Bambusoideae, Bambuseae)

Chusquea is a diverse but monophyletic genus of Neotropical woody bamboos from primarily montane forests that comprises four well-supported lineages: subg. Magnifoliae, subg. Platonia, subg. Rettbergia, and the Euchusquea clade (comprising subg. Swallenochloa and subg. Chusquea). However, the relationships among clades or taxa within the Euchusquea clade inferred from molecular data are mostly not congruent with those inferred from morphological evidence, consequently limiting our ability to understand species relationships. In this study we generated foliar micromorphological and anatomical data for the Chusquea ramosissima informal group (Chusquea ramosissima, C. tenella, and C. tenuiglumis), and for the putative new species from Bolivia in this group, in order to test the value of these types of data for defining species and to seek potential synapomorphies for this group. Our results demonstrate that epidermal features, mainly with regard to the stomatal apparatus, proved to be more valuable in distinguishing species than anatomical characters. The presence of horizontally elongated silica cells over the veins and adaxial arm cells with invaginations from the abaxial side was shared by all the studied species but is not unique to this group. The type of trichomes, shape of silica bodies, type of arm cells, and midrib structure may be useful to lesser degree. All four species exhibited intraspecific variation in development of the papillae on the long cells. Support for the recognition of the new species from Bolivia is provided by micromorphological characters. An identification key based on leaf blade features is provided for the four studied species.     

巴西竹类生物多样性

巴西是全球生物多样性最丰富的地区,其竹类多样性也极为丰富。结合现存资料及野外调查,对巴西全境的竹类分布格局进行了讨论。巴西全国有原生竹亚科植物256种(含2亚种及3变种),北部地区草本竹类(莪莉竹族)最丰富,有61种,而东南部地区木本竹类(箣竹族)最丰富,有96种。偏穗竹属(Merostachys)(43种)和丘斯夸竹属(Chusquea)(45种)是最常见的属,并是最具潜在经济利用的竹类。属种的特有性分别高达32.4%和68.8%。特有属有11个,分别为莪莉竹族的双药莪利草竹属(Diandrolyra)、独焰草竹属(Eremitis)、小百瑞草竹属(Parianella)、赖茨草竹属(Reitzia)、苏克蕾草竹属(Sucrea)和箣竹族的南美梨藤竹属(Alvimia)、离枝竹属(Apoclada)、密穗竹属(Athroostachys)、卡姆巴珠瓦竹属(Cambajuva)、菲尔盖拉斯竹属(Filgueirasia)、无枝竹属(Glaziophyton)。     

Una nueva especie de Chusquea (Poaceae: Bambusoideae) de la Cordillera de Mérida, Venezuela

A new species of woody bamboo (Poaceae: Bambusoideae),Chusquea guirigayensis, is described and illustrated. This species is placed inChusquea sect.Swallenochloa (McClure) L. G. Clark because of its shrubby habit, short waxy internodes, intravaginal branching, and linearly arranged subsidiary buds/branches. In addition, we discuss related species, and describe the ecology and distribution of the new species. Separate keys based on sterile and fertile material of the Venezuelan species ofC. sect.Swallenochloa are provided.     

A molecular phylogenetic and fruit evolutionary analysis of the major groups of the paleotropical woody bamboos (Gramineae: Bambusoideae) based on nuclear ITS, GBSSI gene and plastid trnL-F DNA sequences

This study presented the first molecular phylogenetic analysis of the major clades of woody bamboos of the Old World tropics based on nuclear and chloroplast sequences (ITS, GBSSI and trnL-F). Sequence data from 53 species, representing 17 paleotropical woody bamboo genera, were analyzed using the maximum parsimony and Bayesian inference methods. All examined ingroup taxa were clustered into two clades, i.e., the Bambusinae+Dinochloa clade and the Melocanninae clade. The former clade included Bambusa, Bonia, Dendrocalamus, Dendrocalamopsis, Dinochloa, Gigantochloa, Molecalamus, Neomicrocalamus, Neosinocalamus, Oxytenanthera s. str. (sensu stricto), Racemobambos and Thyrsostachys. The Melocanninae clade consisted of Cephalostachyum, Leptocanna (better treated as part of Cephalostachyum), Melocanna, Pseudostachyum and Schizostachyum s. str. The subtribe Racemobambosinae and tribes Dendrocalameae and Oxytenanthereae were not supported and may be better placed in subtribe Bambusinae. The ovary characters seemed to be good criteria to distinguish these two clades. The reconstruction of ancestral fruit characters indicated that the bacoid caryopsis, namely, fleshy or berry-like fruits, was found to be scattered in three lineages of the examined paleotropical woody bamboos. Fruit characters are thus not reliable indicators of phylogeny and bacoid caryopsis likely represents a specialization for particular ecological conditions.     

Phylogenetic analysis of the subfamily Alpinioideae (Zingiberaceae), particularly Etlingera Giseke, based on nuclear and plastid DNA

Parsimony analyses based on DNA sequence data of the plastid group II intron rps16 and the internal transcribed spacer (ITS) were performed in order to examine the relationship of the pantropical subfamily Alpinioideae in Zingiberaceae (Zingiberales). Special emphasis was given to the large genus Etlingera placed in the tribe Alpinieae. A total of 50 taxa were included in the analysis. The strict consensus tree obtained by combining all data (280 parsimony informative characters of ITS, rps16, and coded indels) is well resolved with strongly supported clades. The subfamily Alpinioideae (excluding Pommereschea and Rhynchanthus) is strongly supported as monophyletic. The basal part of the tree is unresolved but a clade containing the derived genera of Alpinieae (Geocharis, Amomum, Hornstedtia, and Etlingera) is strongly supported. The establishment of Etlingera as the inclusive name for Achasma, Geanthus, and Nicolaia is also strongly supported: Etlingera is monophyletic with Hornstedtia as sister group.     

Molecular phylogeny of the arthrostylidioid bamboos (Poaceae: Bambusoideae: Bambuseae: Arthrostylidiinae) and new genus Didymogonyx

We present the first multi-locus chloroplast phylogeny of Arthrostylidiinae, a subtribe of neotropical woody bamboos. The morphological diversity of Arthrostylidiinae makes its taxonomy difficult and prior molecular analyses of bamboos have lacked breadth of sampling within the subtribe, leaving internal relationships uncertain. We sampled 51 taxa, chosen to span the range of taxonomic diversity and morphology, and analyzed a combined chloroplast DNA dataset with six chloroplast regions: ndhF, trnD-trnT, trnC-rpoB, rps16-trnQ, trnT-trnL, and rpl16. A consensus of maximum parsimony and Bayesian inference analyses reveals monophyly of the Arthrostylidiinae and four moderately supported lineages within it. Six previously recognized genera were monophyletic, three polyphyletic, and two monotypic; Rhipidocladum sect. Didymogonyx is here raised to generic status. When mapped onto our topology, many of the morphological characters show homoplasy.     

Tribal and intergeneric relationships of Mesechiteae (Apocynoideae, Apocynaceae): evidence from three noncoding plastid DNA regions and morphology

The Neotropical tribe Mesechiteae (Apocynaceae) is currently considered to include nine genera: Allomarkgrafia, Galactophora, Macrosiphonia, Mandevilla, Mesechites, Quiotania, Secondatia, Telosiphonia, and Tintinnabularia. Tribal and intergeneric relationships, however, are in dispute. To test the monophyly of the tribe and evaluate intratribal relationships, a maximum parsimony analysis was conducted based on DNA sequences from the plastid rpl16 intron, rps16 intron, and trnS-G intergenic spacer region as well as morphological data for 23 taxa of Mesechiteae and 11 taxa from other tribes of Apocynoideae. Mesechiteae, as currently circumscribed, was found to be polyphyletic. Only removal of Secondatia and Galactophora and inclusion of Forsteronia rendered the tribe monophyletic. Thus defined, Mesechiteae forms a strongly supported clade including seven genera in three subclades: the Mesechites subclade (comprising Tintinnabularia, Allomarkgrafia, and Mesechites), the Forsteronia subclade (containing only Forsteronia) and the Mandevilla subclade (comprising Macrosiphonia, Mandevilla, and Telosiphonia). Allomarkgrafia is nested in Mesechites. Macrosiphonia and Telosiphonia form two distinct monophyletic clades. Both, however, are nested in Mandevilla. Results suggest upholding the following genera in Mesechiteae: Allomarkgrafia, Forsteronia, Mandevilla, Mesechites, and Tintinnabularia. The status of Quiotania could not be evaluated.     

57 Systematics of hydropuntia montagne (gracilariaceae,gracilariales, rhodophyta) based on comparative morphology and rbcL sequence analysis

The taxonomic validity of the genus Hydropuntia Montagne (1843) (including Polycavernosa) within the Gracilariaceae (Gracilariales, Rhodophyta) is controversial. Morphological characters that define species of Hydropuntia are said to be variable and to overlap with those of Gracilaria. Here we present a global phylogenetic study of the family based on a Bayesian analysis of a large rbcL DNA sequence dataset indicating that the genus Hydropuntia forms a well supported monophyletic clade within the family, and recognize Hydropuntia as a genus distinct from Gracilaria. We also conducted smaller phylogenetic analyses in which thirty four Hydropuntia rbcL sequences resulted in two major clades within the genus, comprising a Caribbean clade and an Indo‐Pacific clade. Diagnostic reproductive stages that separate these two clades will be illustrated.     

Therps16 intron and the phylogeny of theRubioideae (Rubiaceae)

The phylogeny of the subfamilyRubioideae (Rubiaceae) was estimated from sequence variation in therps16 intron (cpDNA) in 143 ingroup and 5 outgroup taxa. The analysis largely confirms a recent one based onrbcL sequences, but branch support is often much stronger. Three of the traditional subfamilies are supported,Rubioideae, Cinchonoideae s. str., andIxoroideae s. l. while there is no support forAntirheoideae. TheRubioideae are the sister group of all otherRubiaceae and comprise the tribesAnthospermeae, Coccocypseleae, Cruckshanksieae, Coussareeae, Gaertnereae, Hedyotideae, Knoxieae, Morindeae, Ophiorrhizeae, Paederieae, Pauridiantheae, Perameae, Psychotrieae, Rubieae, Spermacoceae, Theligoneae, andUrophylleae. TheHamelieae andHillieae belong to theCinchonoideae. Rachicallis andSiemensia should be transferred from theHedyotideae to theCinchonoideae. ThePauridiantheae, Urophylleae, Ophiorrhizeae, andRaritebe form the basalmost subclade of theRubioideae. The second basalmost clade consists of the generaLasianthus andPerama. The third basalmost clade consists of the tribesCoussareeae, Coccocypseleae andCruckshanksieae, and the generaDeclieuxia andHindsia. The tribesKnoxieae, Anthospermeae, Argostemmateae, Paederieae, Theligoneae, Rubieae, Hedyotideae, andSpermacoceae are members of one clade. TheKnoxieae are monophyletic ifOtiophora, Otomeria, andPentas are included. The tribeAnthospermeae is supported as monophyletic, but its subtribes are not. ThePaederieae, together withTheligonum, form a paraphyletic grade basal to theRubieae. TheHedyotideae, includingSchismatoclada, form a grade at the base of theSpermacoceae. TheGaertnereae are monophyletic and distinct from thePsychotrieae. TheMorindeae are monophyletic and includeDamnacanthus andMitchella. Schradera is the sister group of theMorindeae. ThePsychotrieae are monophyletic when theGaertnereae, Lasianthus, andDeclieuxia are excluded. The recognition of a subtribeHydnophytineae leaves the rest of thePsychotrieae paraphyletic.Psychotria is paraphyletic with respect to all other genera of the tribe. Approximately 50 genera are here classified for the first time based on molecular data.     

Molecular phylogenetic analysis of all members of the genus Elminia confirms their presence within the Stenostiridae clade

The genus Elminia has had a jumbled taxonomic history, being placed among ‘old world flycatchers’ or ‘monarch flycatchers’, where it was for a long time lumped with Trochocercus. It was recently suggested that it might represent a deep clade in the large sylvioid radiation. Using one mitochondrial protein‐coding gene (ND2, 1041 bp) and one nuclear intron (myoglobin intron 2, 700 bp) DNA sequences, we obtained robust evidence for the phylogenetic placement of Elminia in the new family Stenostiridae, which is strongly supported by a synapomorphic insertion of one base in the nuclear myoglobin intron 2 sequence. Our analyses confirm the monophyly of Elminia and resolve relationships within this genus, but cannot confidently identify its sister‐taxon within the stenostirid clade. Two clades were strongly supported within the genus Elminia: one with the two fairy blue flycatchers and another with the three white‐tailed crested‐flycatchers. Within the first clade, Elminia longicauda appears non‐monophyletic but remains strongly related to E. albicauda. In the second clade, E. albiventris is sister to E. albonotata while the Dusky Crested Flycatcher (E. nigromitrata) appears in a basal position within this clade. According to our molecular dating, several geological events in western Africa and the Albertine Rift area seem to be related to the historical distribution of Elminia. Thus, the differentiation between E. albonotata and E. albiventris could be directly related to the tectonic history of these two regions. According to our molecular dating, at least one intercontinental dispersal event involving Culicicapa took place within the Stenostiridae clade at a time when the Middle East was forested.