Phylogenetic relationships in the Neotropical tribe Hamelieae (Rubiaceae, Cinchonoideae) and comments on its generic limits
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Abstract Our molecular phylogenetic analyses shed some light on the evolutionary relationships within the Hamelieae tribe. Phylogenetic reconstructions based on Internal Transcribed Spacer and trnL‐F sequence data revealed the presence of three distinct evolutionary lineages. The first clade includes Hamelia and Syringantha , the second clade includes Deppea s.l. (including Bellizinca , Csapodya , and Edithea ), and the third clade includes Pinarophyllon , Deppeopsis , Hoffmannia , Pseudomiltemia , Plocaniophyllon , Omiltemia , and Renistipula . The phylogenetic analysis re‐evaluated some taxonomical combinations. The transfer of Deppeopsis taxa from Deppea s.l. is supported, but however, the monophyly of the genus is not. The transfer of Renistipula from Rondeletieae is also highly supported. Both Csapodya and Edithea species form a well‐defined group among Deppea s.l. with high posterior probabilities, allowing to reconsider the exclusion or integration of these taxa to Deppea .Keywords:
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Abstract Comprised of ~2000 spp., Piper is a major clade in the magnoliid angiosperms. Three major groups are recognized in Piper , i.e., the Neotropical, Asian and South Pacific. Unlike Neotropical Piper , relationships in the Paleotropical Piper remain enigmatic. This study evaluates the relationships within Paleotropical Piper by focusing sampling efforts in the Malesian region. This is the center of diversity of the genus in the Paleotropics, yet has been barely represented in previous phylogenetic studies. Eleven out of 14 infrageneric groups in Paleotropical Piper and 14% of the species were included in this study and their phylogenetic relationships were inferred based on nuclear (ITS, g3pdh) and chloroplast (trnL-F) regions. The goals were to test the monophyly of infrageneric groups, to examine how the main characters used to delimit these infrageneric groups have shaped classifications past and present, and to understand the origin of bisexual flowers and the shrubby habit in the predominantly dioecious Asian clade of climbers. The results show that the Asian clade is monophyletic in all phylogenies and the South Pacific clade is monophyletic in nuclear phylogenies. Within the Asian clade, species predominantly distributed west of Wallace’s Line (WWL) form a moderately/strongly supported clade in the ITS phylogeny, embedded within a grade of species from east of Wallace’s Line (EWL). The ITS phylogeny also resolves 12 and 5 clades in the WWL clade and the EWL grade, respectively. G3pdh and trnL-F phylogenies resolve some of the same clades, but some relationships among and within clades are incongruent. Almost no currently recognized infrageneric groups in Asian Piper are monophyletic. Most of the characters previously used to delimit infrageneric groups are homoplasious, including fruit type, bract type, direction of anther dehiscence, and number of anther valves. However, bract and fruit types are still of some value in that many clades in the Asian Piper are characterized by single bract and fruit types. In Paleotropical Piper , bisexual flowers have evolved numerous times in almost every clade, and shrubby habit has evolved at least six times, but is restricted to four clades in the WWL clade. The 17 clades resolved in this study are described along with their potential diagnostic characters.
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We have previously shown that many of the nef sequences from Korean HIV-1 subtype B carriers were grouped together in phylogenetic tree analyses. To determine whether this pattern was originated from either a single HIV-1–infected person or some biological pressure which directs the HIV-1 genomic mutation by the Korean specific immunological characters, we analyzed nef sequences from HIV-1–infected individuals with different time intervals. Thirty-two out of 46 analyzed patients formed a Korean monophyletic (KM) clade with 93% bootstrapping value. Eighteen patients' nef sequences were analyzed 1–9 years after first analysis. None of the patients shifted their clade from the first clustered clade (KM or non-KM), and all of the reanalyzed isolates were clustered close to the first analyzed clade. Isolates of the KM clade and non-KM clade in nef analysis showed the same pattern as in env analysis. Phylogenetic clustering evidences from both nef and C2/V3 trees strongly support the idea that introduction of the KM clade in subtype B strains originated from a common source. Thus, treatment and development of an AIDS vaccine may be somewhat easier than in other countries with multiple strains of HIV-1.
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Relationships among Halimolobos, Mancoa, Pennellia ,a ndSphaerocardamum have been controversial. Higher level studies, using cpDNA data from the chloroplast encoded ndhF and trnL intron, suggested that some species of these genera represent a monophyletic group: the halimolobine clade. The research presented here focuses on the halimolobine clade with denser intra and inter-specific sampling. The primary aims of the project were: (1) to further test the monophyly of the halimolobine clade; (2) to test the monophyly Halimolobos, Mancoa, Pennellia ,a ndSphaerocardamum; and (3) to study the evolution of morphological characters in the clade. Data were generated from the trnL-F region, nrDNA ITS, pistillata intron one, and 17 non-molecular characters. The difficulties associated with incorporating these data into simultaneous analyses are discussed and a strategy is presented. Separate and simultaneous analysis confirmed a monophyletic core group of halimolobine species. The strict consensus tree contained five well-supported halimolobine subclades: Sphaerocardamum, Pennellia plus Arabis tricornuta, Mancoa bracteata plus M. foliosa, a narrowly defined Halimolobos, and a clade consisting of a subset of Halimolobos and Mancoa species. Individual morphological characters vary in their utility for classification of the group. However, the majority of the characters provide some grouping information within the halimolobine clade.
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Phylogenetic Analysis of the nef Gene Reveals a Distinctive Monophyletic Clade in Korean HIV-1 Cases
To study the genetic variation of the HIV-1 strains prevalent in South Korea, we analyzed the nef sequences derived from 46 HIV-1-positive individuals living in various geographic regions in Korea. Phylogenetic analysis revealed four subtypes of HIV-1: A (3 patients), B (41 patients), D (1 patient), and a type that could not be clearly classified to any known subtype (1 patient). Thirty-five of the 41 Korean subtype B isolates formed a distinct monophyletic clade that is not related to any of the international sequences from the Los Alamos Database or GenBank as of June 1997. Indeed, the presence of unique conserved sequences was identified among the Korean isolates in this Korean subtype B group. The variations in the nucleotide sequences of a majority (32 of 35) subtype B samples within the Korean clade were 1.9% to 8.8%, and amino acid sequences varied from 3.9% to 15.5%. These results suggest that HIV-1 strains currently present in South Korea might have originated from a few sources or might be developing through a certain selective pressure. This is the first report on the molecular nature of the HIV-1 infection present in South Korea.This study examines the genetic variation of the HIV-1 strains prevalent in South Korea. It analyzes the nef sequences derived from 46 HIV-1 positive individuals living in various geographic regions of Korea. Phylogenetic analysis revealed four subtypes of HIV-1: A (3 patients), B (41 patients), D (1 patient), and a type that could not be clearly classified as any known subtype (1 patient). About 35 of the 41 Korean subtype B isolates formed a distinct monophyletic clade that is not related to any of the international sequences from the Los Alamos Database or GenBank as of June 1997. Indeed, the presence of unique conserved sequences was identified among the Korean isolates in this Korean subtype B group. The variations in the nucleotide sequences of a majority (32 of 35) of the subtype B isolates within the Korean clade were 3.9% to 15.5%. These results suggest that HIV-1 strains present in South Korea might have originated from a few sources or might be developing through a certain selective pressure.
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Ribosomal DNA sequence divergence in the internal transcribed spacer regions (ITS-1 and ITS-2) was examined for fourteen species and four subgenera (sixty-two clones) in the mosquito genus Culex (Diptera: Culicidae). A neighbour-joining tree produced with Kimura 2-parameter distances showed that each of the four subgenera was monophyletic at confidence probabilities of 70-99%. Culex (Lutzia) formed the sister group of Cx. (Culex). Two major clades, a Cx. pipiens complex-Cx. torrentium assemblage and a Cx. restuans-Cx. salinarius-Cx. erythrothorax assemblage, formed monophyletic groups. Cx. torrentium was closely related to members of the Cx. pipiens complex. Phylogenetic analysis of ITS-1 and ITS-2 sequences from members of the Cx. pipiens complex separated populations from northern latitudes and southern latitudes, but did not support the traditional taxa as monophyletic units.
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The SAR group (Stramenopila, Alveolata, Rhizaria) is one of the largest clades in the tree of eukaryotes and includes a great number of parasitic lineages. Rhizarian parasites are obligate and have devastating effects on commercially important plants and animals but despite this fact, our knowledge of their biology and evolution is limited. Here, we present rhizarian transcriptomes from all major parasitic lineages in order to elucidate their evolutionary relationships using a phylogenomic approach. Our results suggest that Ascetosporea, parasites of marine invertebrates, are sister to the novel clade Apofilosa. The phytomyxean plant parasites branch sister to the vampyrellid algal ectoparasites in the novel clade Phytorhiza. They also show that Ascetosporea + Apofilosa + Retaria + Filosa + Phytorhiza form a monophyletic clade, although the branching pattern within this clade is difficult to resolve and appears to be model-dependent. Our study does not support the monophyly of the rhizarian parasitic lineages (Endomyxa), suggesting independent origins for rhizarian animal and plant parasites.
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47 accessions of the Delosperma-clade are analyzed using ITS and four chloroplast markers. With two exceptions, Frithia pulchra and Delosperma esterhuyseniae, all accessions are retrieved in a single, unsupported Delosperma s.l. clade. The main Delosperma s.str. clade is well supported and falls in three subclades, one comprising the two Mestoklema accessions, the other two mainly Delosperma accessions, but also Corpuscularia and Ectotropis. These genera are therefore subsumed under Delosperma. Trichodiadema accessions are retrieved in several places inside the Delosperma s.l. clade. The East African-Arabian Delosperma species are monophyletic if D. alpina from the Drakensberg is included; but they are not monophyletic with the species from Madagascar and Réunion. The species of the Central Plateau of southern Africa are also monophyletic and sister to the East African-Arabian species. Two new species, Delosperma heidihartmanniae and D. melepoense, are here described in the East African-Arabian clade.
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Abstract We investigated morphological and DNA sequence data for studying the composition and phylogenetic relationships of the Lecointea clade sensu Herendeen and for testing its monophyly. Twenty nine representing 14 genera were analyzed, including all members of the Lecointea clade and some species of the genera Acosmium , Luetzelburgia , Sweetia , Vatairea and Vataireopsis . Ateleia herbert smithii , Bocoa mollis , and Myrocarpus frondosus were included as outgroup. Matrices were analyzed using maximum parsimony. Analyses of morphological data, chloroplast DNA trnL sequence data, and combined datasets resulted in similar tree topologies. The Lecointea clade sensu Herendeen, with the additional inclusion of Uribea , is monophyletic in all analyses. Exostyles and Harleyodendron belong to the Lecointea clade and not to the Vatairea clade as recently proposed by Pennington & al.
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