The tropical African legume Scorodophloeus clade includes two undescribed Hymenostegia segregate genera and Micklethwaitia,a rare,monospecific genus from Mozambique

Legume subfamily Caesalpinioideae accommodates approximately 2250 species in 171 genera which traditionally are placed in four tribes: Caesalpinieae, Cassieae, Cercideae and Detarieae. The monophyletic tribe Detarieae includes the Amherstieae subclade which contains about 55 genera. Our knowledge of the relationships among those genera is good in some cases but for many other genera phylogenetic relationships have been unclear. The non-monophyletic nature of at least two amherstioid genera, Cynometra and Hymenostegia has also complicated the picture. During the course of a multi-disciplinary study of Hymenostegia sensu lato, which includes phylogenetic analyses based on matK and trnL data, we have recovered the “Scorodophloeus clade”, an exclusively tropical African clade of four genera which includes the eponymous genus Scorodophloeus, two undescribed generic segregates of Hymenostegia sensu lato, and the previously unsampled rare monospecific genus Micklethwaitia from Mozambique. Zenkerella is suggested as a possible sister genus to the Scorodophloeus clade. A distribution map is presented of the seven species that belong to the Scorodophloeus clade.     

The phylogeny of the austral grass subfamily Danthonioideae: Evidence from multiple data sets

The grass subfamily Danthonioideae is one of the smaller in the family. We utilize DNA sequence data from three chloroplast regions (trnL, rpoC2 and rbcL) and one nuclear region (Internal Transcribed Spacer; ITS) both singly and in combination to elucidate the relationships of the genera in the subfamily. The topology retrieved by the ITS region is not congruent with that of the plastid data, but this conflict is not strongly supported. Nine well-supported clades are retrieved by all data sets. The relationships at the base of the subfamily are clearly established, comprising a series of three clades of Merxmuellera species. The earliest diverging clade probably does not belong in Danthonioideae. The other two clades are centered in the tropical African mountains and Cape mountains respectively. A clade of predominantly North and South American Danthonia species as well as D. archboldii from New Guinea is retrieved, but the African and Asian species of Danthonia are related to African species of Merxmuellera, thus rendering Danthonia polyphyletic. The relationships of the Danthonia clade remain equivocal, as do those of the two Cortaderia clades, the Pseudopentameris and Rytidosperma clades. Paseka Mafa was tragically killed in a vehicle accident in July 2001. This paper includes information he collected during the course of his MSc in Systematics and Biodiversity Science at the University of Cape Town.     

Phylogenetic relationships within Pappophoreae s.l. (Poaceae: Chloridoideae): Additional evidence based on ITS and trnL-F sequence data

Historically, Pappophoreae included the genera Cottea, Enneapogon, Kaokochloa, Pappophorum and Schmidtia. Some authors consider this tribe as a well-supported monophyletic group; while other evidences reveals Pappophoreae as polyphyletic, with Pappophorum separated from the rest of the tribe. When the latter happens, it can form a clade with Tridens flavus. Molecular phylogenetic analyses of the subfamily Chloridoideae have included few species of Pappophoreae; therefore, further research involving more representatives of this tribe is needed. With the aim of providing new evidence to help clarify the phylogenetic position of Pappophorum and its relationships with other genera of the tribe and the subfamily Chloridoideae, eight new sequences of ITS and trnL-F regions of Pappophoreae species were generated. These sequences were analyzed together with other available sequence data obtained from GenBank, using maximum parsimony and Bayesian inference, for individual (trnL-F or ITS) or combined trnL-F/ITS data sets. All analyses reveal that Pappophoreae is polyphyletic, with Pappophorum separated from the rest of the tribe forming a well-supported clade sister to Tridens flavus.     

Phylogenetics of tribe Sabiceeae (Ixoroideae,Rubiaceae) revisited,with a new subgeneric classification for Sabicea

Tribe Sabiceeae (Ixoroideae, Rubiaceae) has undergone recent taxonomical changes with the incorporation of the related genera Ecpoma, Pseudosabicea and Stipularia into the type genus Sabicea. We use phylogenetic analysis and morphological data to verify the relationships among members of the tribe, including the most comprehensive taxon sampling of the tribe to date with 74 of 145 species. Sequence data from the nuclear internal transcribed spacer (ITS) and three plastid markers (petD, rps16, trnT–F) were used to infer relationships among the members of the tribe. Individual analyses using maximum likelihood, parsimony and Bayesian approaches reveal several supported clades: the former genus Stipularia is resolved as a monophyletic unit, but Ecpoma is monophyletic only if Sabicea urbaniana and Sabicea xanthotricha are included (corresponding to Sabicea subgenus Stipulariopsis sensu Wernham). Pseudosabicea is biphyletic, with one clade corresponding to section Anisophyllae of Hallé (1964) and the other one to the other sections (Floribundae and Sphaericae) of the genus. Eleven morphological characteristics were recorded for all species studied and seven have been mapped onto the phylogenetic tree to study their evolution in the group and assess their value for the classification of Sabicea s.l. Finally, our study shows that a combination of diagnostic characteristics should be used to differentiate each group and we propose to recognise four subgenera in Sabicea.     

Molecular phylogeny of Macaranga, Mallotus, and related genera (Euphorbiaceae s.s.): insights from plastid and nuclear DNA sequence data

Macaranga and Mallotus (Euphorbiaceae s.s.) are two closely related, large paleo(sub)tropical genera. To investigate the phylogenetic relationships between and within them and to determine the position of related genera belonging to the subtribe Rottlerinae, we sequenced one plastid (trnL-F) and three nuclear (ITS, ncpGS, phyC) markers for species representative of these genera. The analyses demonstrated the monophyly of Macaranga and the paraphyly of Mallotus and revealed three highly supported main clades. The genera Cordemoya and Deuteromallotus and the Mallotus sections Hancea and Oliganthae form a basal Cordemoya s.l. clade. The two other clades, the Macaranga clade and the Mallotus s.s. clade (the latter with Coccoceras, Neotrewia, Octospermum, and Trewia), are sister groups. In the Macaranga clade, two basal lineages (comprising mostly sect. Pseudorottlera) and a crown group with three geographically homogenous main clades were identified. The phylogeny of the Mallotus s.s. clade is less clear because of internal conflict in all four data sets. Many of the sections and informal infrageneric groups of Macaranga and Mallotus do not appear to be monophyletic. In both the Macaranga and Mallotus s.s. clades, the African and/or Madagascan taxa are nested in Asian clades, suggesting migrations or dispersals from Asia to Africa and Madagascar.     

Cladistic analysis of Taxaceae s. l.

Taxaceae s. l. is a wider concept of classification treating five genera of Taxaceae s. str. and Cephalotaxus together. Cephalotaxus is morphologically very similar to the five genera of Taxaceae s. str. Various models of classification for six genera have already been published. However, the phylogenetic position and genuine relationships of these genera and species are still confusing. A cladistic analysis of Taxaceae s. l. has been carried out to resolve the problem existing in their phylogeny and to provide a new approach regarding the relationships of these six genera. Parsimony analyses were based on 28 characters and eight genera including two outgroups Agathis and Sciadopitys. The most parsimonious tree retained with branch length 38 and 194 rearrangement trials. Consistency index was 0.68 and retention index was 0.66. Principally, two main clades were found: one represented by Austrotaxus forming the base of the tree and another by the remaining five genera. Taxus + Pseudotaxus clade split after Austrotaxus, and Cephalotaxus was sister to Torreya + Amentotaxus clade. Taxus + Pseudotaxus clade was supported by the highest bootstrap value. Finally, cladistic analysis does not support existence of Cephalotaxaceae. Therefore, it would be better to classify Cephalotaxus within Taxaceae s. l. with the other five genera.     

Origin and early evolution of Ceropegieae (Apocynaceae-Asclepiadoideae)

The first-branching lineages of the tribe Ceropegieae, Anisotominae, Leptadeniinae, and Heterostemminae, are the focus of the present study. In the ingroup we molecularly analysed 34 samples from southern and (north)eastern Africa and Asia for the nuclear internal transcribed spacer (ITS) region, and five plastid markers (trnT-L, trnL-F and trnH-psbA intergenic spacers, trnL, and rps16 introns). Maximum Parsimony and Bayesian analyses were conducted for phylogenetic reconstruction and Bayesian binary MCMC (BBM) analysis as implemented in RASP for testing biogeographic inference. Sister to the well-known hyperdiverse subtribe Stapeliinae (around 700 species) are the Anisotominae, an African subtribe of c. 30 species, with the tropical Neoschumannia in sister-group position to the remaining genera, Anisotoma, Emplectanthus, Riocreuxia, and Sisyranthus. Emplectanthus is sequenced in full for the first time, and its monophyly as sister to Anisotoma is documented. As in Sisyranthus, new sequences in Riocreuxia, especially in Riocreuxia torulosa s.l., reveal very low genetic variation pointing to an actively radiating and speciating group, possibly in adaptation to pollinator pressure. Molecular and morphological data necessitate the transfer of Brachystelma natalense to Anisotoma, and the new combination Anisotoma natalensis is proposed. Leptadeniinae are sister to the Stapeliinae–Anisotominae clade. The position of the strictly Asian, rheophytic Pentasachme could be resolved as sister to the remaining genera of Leptadeniinae, Conomitra, Leptadenia, and Orthanthera. The position of the S Asian/Australasian wet forest lianas of the genus Heterostemma as sister to the remaining Ceropegieae is confirmed, indicating a humid Asian origin for this tribe known for its arid-adapted African succulents.     

Inclusion of Tenaris and Macropetalum in Brachystelma (Apocynaceae-Asclepiadoideae-Ceropegieae) inferred from non-coding nuclear and chloroplast DNA sequences

 The inclusion of Tenaris and Macropetalum in Brachystelma as proposed by Peckover in 1996 and contested by Victor and Nicholas in 1998 is supported by molecular studies. Parsimony analysis of sequence data from two non-coding molecular markers (ITS region of nrDNA and trnT-L and trnL-F spacers as well as the trnL intron of cpDNA) suggests a well-supported Brachystelma s.l. clade (including Tenaris and Macropetalum) with little internal resolution. The Brachystelma s.l. clade occupies a sistergroup position to the Ceropegia/stapeliad clade, and both clades together are sister to an Anisotoma/Sisyranthus/Neoschumannia clade. Received January 8, 2001 Accepted April 10, 2001     

Molecular phylogeny and taxonomic revision of the Philippine endemic Villaria Rolfe (Rubiaceae)

The little known Rubiaceae genus Villaria is endemic mostly to the coastal forests of the Philippines. Traditionally, it has been placed in the tribe Gardenieae. Later it was transferred to Octotropideae sensu Robbrecht and Puff. Villaria was placed among the ??primitive?? genera of the tribe, which are essentially characterized by large fruits, horizontal ovules and numerous seeds. Parsimony and Bayesian analyses of the combined plastid (rps16 and trnT-F) dataset strongly support the inclusion of Villaria in Octotropideae as well as monophyly of the genus. However, our molecular results do not conform to the current informal groups of the tribe delimited by fruit size, ovule position, number of seeds and exotesta thickenings. Instead, a close relationship between Villaria and two ??central genera?? (Hypobathrum and Pouchetia) is revealed for the first time. This clade is sister to a group comprising ??primitive?? (Fernelia), ??advanced?? (Kraussia and Polysphaeria) and ??central?? (Feretia) representatives. In addition, our combined tree strongly supports a sister taxa relationship between Canephora and Paragenipa. Villaria is characterized by unilocular ovaries, parietal placentation and strictly horizontal ovules. These features are unique within the Octotropideae. We recognize a total of five Villaria species, one new species (V. leytensis) is described here, and two species (V. philippinensis and V. rolfei) are transferred into synonymy with V. odorata. Each species is fully described, and a key to the species, a distribution map and illustrations are provided.     

Phylogeny of Carpinus and subfamily Coryloideae (Betulaceae) based on chloroplast and nuclear ribosomal sequence data

Phylogenetic studies were conducted for Carpinus and the subfamily Coryloideae (Betulaceae) using sequences of the chloroplast matK gene, the trnL-trnF region (trnL intron, and trnL [UAA] 3' exon-trnF [GAA] intergenic spacer) and the psbA-trnH intergenic spacer, and the nuclear ribosomal ITS regions. The combined analyses of the three chloroplast regions suggest that Coryloideae is monophyletic; Ostryopsis is sister to the Carpinus - Ostrya clade; Corylus is monophyletic and sister to the Ostrya - Carpinus - Ostryopsis clade; Ostrya is paraphyletic; and within Carpinus, species of sect. Carpinus from eastern Asia form a monophyletic group, whereas the positions of C. betulus from Europe and C. caroliniana from eastern North America are unresolved within the Carpinus clade. The cpDNA tree generated in this study is largely congruent with the previously published ITS results, but the ITS tree places Carpinus sect. Distegocarpus as sister to the Ostrya - Carpinus sect. Carpinus clade. Future work is needed to examine the relationships within the Ostrya - Carpinus clade, evaluate the generic status of Ostrya, and test the phylogenetic position of Ostryopsis.     

A settled sub-family for the orphan tree: The phylogenetic position of the endemic Colombian genus <Emphasis Type="Italic">Orphanodendron</Emphasis> in the Leguminosae

Orphanodendron is a taxonomically and geographically isolated South American genus of two species. When first described by Barneby and Grimes in 1990, the genus was placed in Leguminosae subfamily Caesalpinioideae, but that placement was doubted and the name Orphanodendron (Gr. orphanos, orphan + dendron, tree) was chosen to reflect the uncertain subfamilial relationship of the genus. In this study, nucleotide sequence data from five Orphanodendron specimens were added to 662 other, previously sampled, Leguminosae taxa representing all three currently recognized subfamilies (Caesalpinioideae, Mimosoideae and Papilionoideae) in a matK maximum parsimony analysis that resolved Orphanodendron as a member of the genistoid s.l. clade of subfamily Papilionoideae. Two additional Bayesian phylogenetic analyses with reduced taxon sampling of plastid (matK combined with trnL-F) and nuclear (ITS) loci strongly support the monophyly of Orphanodendron and unambiguously establish Orphanodendron as a member of the genistoid sensu lato clade. Although our plastid phylogenetic analysis finds relatively low support for a sister-group relationship with the African genus Camoensia, the nuclear-encoded ITS resolves Orphanodendron as sister to the Bowdichia clade with strong support and Camoensia as sister to other core genistoids. The phylogenetic resolution of Orphanodendron as a member of the genistoid s.l. legumes based on nuclear and plastid sequences will undoubtedly advance future evolutionary investigations of this Colombian endemic tropical tree genus.     

利用叶绿体基因组数据解析锦葵科梧桐亚科的系统位置和属间关系

分子系统学研究将传统梧桐科与锦葵科、木棉科和椴树科合并为广义锦葵科,并进一步分为9个亚科.然而,9个亚科之间的关系尚未完全明确,且梧桐亚科内的属间关系也未得到解决.为了明确梧桐亚科在锦葵科中的系统发育位置,厘清梧桐亚科内部属间系统发育关系,该研究对锦葵科8个亚科进行取样,共选取55个样本,基于叶绿体基因组数据,采用最大...     

Generic relationships among the baccate-fruited Amaryllidaceae (tribe Haemantheae) inferred from plastid and nuclear non-coding DNA sequences

Using sequences from the plastid trnL-F region and nrDNA ITS, we investigated the phylogeny of the fleshy-fruited African tribe Haemantheae of the Amaryllidaceae across 19 species representing all genera of the tribe. ITS and a combined matrix produce the most resolute and well-supported tree with parsimony analysis. Two main clades are resolved, one comprising the monophyletic rhizomatous genera Clivia and Cryptostephanus, and a larger clade that unites Haemanthus and Scadoxus as sister genera to an Apodolirion/Gethyllis subclade. One of four included Gethyllis species, G. lanuginosa, resolves as sister to Apodolirion with ITS. Relationships among the Clivia species are not in agreement with a previous published phylogeny. Biogeographic analysis using the divergence/vicariance method roots the tribe in Eastern South Africa, with several subsequent dispersals to the winter rainfall Western Cape region. Chromosomal change from an ancestral 2n=22 (characteristic of Clivia) is associated with each main clade. Reduction in number has occurred in all but Cryptostephanus, which has 2n=24 chromosomes. Increasing the sampling across all of the species in the tribe will allow a more detailed understanding of the biogeographic patterns inherent in the parsimony topology, which undoubtedly reflect Quaternary climatic changes in Southern Africa.     

Phylogenetic Framework for Trema (Celtidaceae)

We used ITS and trnL sequence data, analyzed separately and combined by MP, to explore species relationships and concepts in Trema (Celtidaceae), a pantropical genus of pioneer trees. Whether Trema is monophyletic or includes Parasponia is still unresolved. Three clades within Trema received moderate to high support, one from the New World and two from the Old World, but their relationships were not resolved. In the New World, specimens of T. micrantha formed two groups consistent with endocarp morphology. Group I, with smaller brown endocarps, is a highly supported clade sister to T. lamarckiana. Group II, with larger black endocarps, is poorly resolved with several subclades, including the highly supported T. integerrima clade. Both Old World clades contain Asian and African species, with three or more species in each region. Trema orientalis is not monophyletic: specimens from Africa formed a highly supported clade sister to T. africana, while those from Asia were sister to T. aspera from Australia.     

Phylogeny of the Southeast Asian endemic genus Neocinnamomum H. Liu (Lauraceae)

A phylogenetic analysis of Neocinnamomum H. Liu and related genera was conducted using psbA–trnH, trnK cpDNA regions, and the ITS nrDNA segment. Neocinnamomum was confirmed to be monophyletic, and an evolutionary series of inflorescence development within the genus was recognized. The compound thyrse seen in N. caudatum is reduced to the few- to many-flowered condensed inflorescences with a poorly defined branching system seen in most species and ultimately to the 1-flowered inflorescence seen in N. atjehense. Consensus network analysis (CNA) suggested that long-branch attraction is responsible for the observed close relationship between Neocinnamomum and Cassytha L. in a combined analysis of the complete data. In contrast, the sister relationship of Neocinnamomum and Caryodaphnopsis seen in the Bayesian analyses of the partial combined matrix was supported by CNA and is also supported by morphology and wood and bark anatomy. The close similarity of the compound thyrse of less derived Neocinnamomum species to the thyrsoid inflorescences of some Caryodaphnopsis species is also seen as strong support for their affinity.     

Molecular systematic study of Cardamine glechomifolia Levl. (Brassicaceae) using internal transcribed spacer sequence of nuclear ribosomal DNA (ITS) and chloroplast trnL and trnL-F sequences

The internal transcribed spacer (ITS) region of nuclear ribosomal DNA, trnL and trnL-F genes of Cardamine glechomifolia Levl. (family Brassicaceae) were sequenced and analyzed with the sequence of related Cardamine species retrieved from NCBI GenBank to detect pattern of evolutionary differentiation. All trees resulting from combined sequence analyses data of ITS, trnL and trnL-F gene resolve that C. glechomifolia – an endemic species to South Korea clade with Cardamine microzyga (100% bootstrap support). The evolutionary history was inferred using the Maximum Parsimony method. The consistency index is (0.588235), the retention index is (0.687500), and the composite index is 0.519622 (0.404412) for all sites and parsimony-informative sites (in parentheses). The result of the analysis using Maximum Parsimony was found congruence with Maximum Likelihood method and in Baseyan analysis.     

Phylogenetic split of Larix: evidence from paternally inherited cpDNA trnT-trnF region

A molecular phylogeny of Larix comprising 12 species was constructed from the sequence analysis of the paternally inherited cpDNA trnT-trnF region of 46 individuals. The most parsimonious tree split Larix into three sister clades: one clade was composed of two North American species, the other two were short-bracted and long-bracted species of Eurasia respectively except that L. sibirica was clustered in the long-bracted clade. The difference between the present cpDNA phylogeny and previous nrDNA ITS phylogeny in the position of L. sibirica seems to suggest that ancient cytoplasmic gene flow might exist between sections Larix and Multiserialis. The short-bracted L. laricina and long-bracted L. occidentalis have an identical sequence of the trnT-trnF region, which implies that the bract length divergence among North American larches might have occurred recently or chloroplast capture happened during the early differentiation of the two species. The cpDNA results also shed some light on the biogeography of Larix.     

Multi-gene region phylogenetic analyses suggest reticulate evolution and a clade of Australian origin among paleotropical woody bamboos (Poaceae: Bambusoideae: Bambuseae)

The paleotropical woody bamboo subtribe Bambusinae has not been satisfactorily circumscribed and remains a major taxonomic problem. Genera such as Holttumochloa, Mullerochloa and Temburongia have not been confidently assigned to this subtribe. The phylogenetic relationships among genera hitherto placed in or near the Bambusinae, together with the related subtribes Racemobambosinae and Melocanninae, were investigated using three chloroplast DNA markers (rps16-trnQ, trnC-rpoB and trnD-T intergenic spacers) and a nuclear DNA marker (granule-bound starch synthase I, GBSSI) for a sample of 51 ingroup species and 2 outgroup species. Phylogenetic analyses revealed four distinct lineages among the members of the currently recognized Bambusinae: (1) the Bambusa-Dendrocalamus-Gigantochloa (BDG) complex, (2) the Holttumochloa-Kinabaluchloa clade, (3) the Dinochloa-Mullerochloa-Neololeba-Sphaerobambos (DMNS) clade and (4) Temburongia simplex. The BDG complex, which comprises the core of the Bambusinae, appears to have a complex evolutionary history as indicated by incongruence between the cpDNA and the nuclear gene topologies. Introgressive hybridization and incomplete lineage sorting are possible underlying causes for this complexity. The distinction of the climbing-scrambling bamboo lineages from the core Bambusinae and Racemobambosinae suggests directions for investigating the possible existence of further subtribes with increased taxon and geographical sampling. Possible biogeographic scenarios associated with the Holttumochloa-Kinabaluchloa clade and the DMNS clade are discussed.