Phylogenetic and biogeographic diversification of Rhus (Anacardiaceae) in the Northern Hemisphere

Sequences of internal transcribed spacers (ITS) of nuclear ribosomal DNA, the chloroplast ndhF gene, and chloroplast trnL-F regions (trnL intron, and trnL [UAA] 3' exon-trnF [GAA] intergenic spacer) were used for phylogenetic analyses of Rhus, a genus disjunctly distributed in Asia, Europe, Hawaii, North America, and Northern Central America. Both ITS and cpDNA data sets support the monophyly of Rhus. The monophyly of subgenus Rhus was suggested by the combined cpDNA and ITS data, and largely supported in the cpDNA data except that Rhus microphylla of subgenus Lobadium was nested within it. The monophyly of subgenus Lobadium was strongly supported in the ITS data, whereas the cpDNA data revealed two main clades within the subgenus, which formed a trichotomy with the clade of subgenus Rhus plus R. microphylla. The ITS and cpDNA trees differ in the positions of Rhus michauxii, R. microphylla, and Rhus rubifolia, and hybridization may have caused this discordance. Fossil evidence indicates that Rhus dates back to the early Eocene. The penalized likelihood method was used to estimate divergence times, with fossils of Rhus subgenus Lobadium, Pistacia and Toxicodendron used for age constraints. Rhus diverged from its closest relative at 49.1+/-2.1 million years ago (Ma), the split of subgenus Lobadium and subgenus Rhus was at 38.1+/-3.0 Ma. Rhus most likely migrated from North America into Asia via the Bering Land Bridge during the Late Eocene (33.8+/-3.1 Ma). Rhus coriaria from southern Europe and western Asia diverged from its relatives in eastern Asia at 24.4+/-3.2 Ma. The Hawaiian Rhus sandwicensis diverged from the Asian Rhus chinensis at 13.5+/-3.0 Ma. Subgenus Lobadium was inferred to be of North American origin. Taxa of subgenus Lobadium then migrated southward to Central America. Furthermore, we herein make the following three nomenclatural combinations: (1) Searsia leptodictya (Diels) T. S. Yi, A. J. Miller and J. Wen, comb. nov., (2) Searsia pyroides (A. Rich.) T. S. Yi, A. J. Miller and J. Wen, comb. nov., and (3) Searsia undulata (Jacq.) T. S. Yi, A. J. Miller and J. Wen, because our analyses support the segregation of Searsia from Rhus.     

Phylogenetic relationships in family Magnoliaceae inferred from ndhF sequences

The ndhF sequences of 99 taxa, representing all sections in extant Magnoliaceae, were analyzed to address phylogenetic questions in the family. Magnolia macrophylla and M. dealbata, North American species of Magnolia section Rytidospermum, are placed at the base in the subfamily Magnolioideae although its supporting value is low. In the remaining taxa, several distinctive lineages are recognized: (1) Magnolia, the biggest genus in the family, is not monophyletic; (2) Michelia, including section Maingola of Magnolia subgenus Magnolia, is closely related with Elmerrillia and sections Alcimandra and Aromadendron of Magnolia subgenus Magnolia; (3) the associates of Michelia are grouped with Magnolia subgenus Yulania and section Gynopodium of Magnolia subgenus Magnolia; (4) Pachylarnax forms a clade with sections Manglietiastrum and Gynopodium of Magnolia; (5) a well-supported Manglietia clade is recognized; (6) Caribbean species of section Theorhodon of Magnolia subgenus Magnolia, which are section Splendentes sensu Vázquez-Garcia, are closely allied with New World members of Magnolia subgenus Talauma; and (7) section Rytidospermum of Magnolia subgenus Magnolia and subgenus Talauma are polyphyletic. The separated clades in the molecular tree are considerably different from traditional taxonomic dispositions in the family. The molecular data strongly suggest that a taxonomic realignment of infrafamilial delimitations and compositions should be considered.     

Phylogenetic position of Dictyostelium inferred from multiple protein data sets

The phylogenetic position of Dictyostelium inferred from 18S rRNA data contradicts that from protein data. Protein trees always show the close affinity of Dictyostelium with animals, fungi, and plants, whereas in 18S rRNA trees the branching of Dictyostelium is placed at a position before the massive radiation of protist groups including the divergence of the three kingdoms. To settle this controversial issue and to determine the correct position of Dictyostelium, we inferred the phylogenetic relationship among Dictyostelium and the three kingdoms Animalia, Fungi, and Plantae by a maximum-likelihood method using 19 different protein data sets. It was shown at the significance level of 1 SE that the branching of Dictyostelium antedates the divergence of Animalia and Fungi, and Plantae is an outgroup of the Animalia-Fungi-Dictyostelium clade.Correspondence to: T. Miyata     

Phylogenetic relationships of the Magnoliaceae inferred from cpDNA matK sequences

The coding region of the matK gene was sequenced to infer the phylogeny of the family Magnoliaceae. Phylogenetic analyses of 21 matK sequences representing ten genera of Magnoliaceae and three outgroups suggest relationships among both subfamilies and genera. Monophyly of the subfamily Liriodendroideae (the genus Liriodendron) and the subfamily Magnolioideae is strongly supported, respectively. Within the subfamily Magnolioideae, three clades are formed: (1) the genus Magnlietia, (2) the subgenus Magnolia, and (3) the subgenus Yulania, with the genera Michelia, Paramichelia, Tsoongiodendron, Alcimandra, Kmeria, Parakmeria and Manglietiastrum. However, the genus Magnolia is shown to be a polyphyletic group, and the genus Michelia a paraphyletic group. Relatively low sequence divergences are detected among genera of the the subfamily Magnolioideae, ranging from 0.14% to 1.70%, especially in the tribe Micheliinae (0.14–0.98%). Molecular evidence from matK sequence data suggests that the phylogenetic positions and the delimitation of the eight genera Magnolia, Michelia, Tsoongiodendron, Paramichelia, Alcimandra, Kmeria, Parakmeria and Manglietiastrum need to be reconsidered. Received: 2 January 2000 / Accepted: 12 February 2000     

The branching order of mammuals: Phylogenetic trees inferred from nuclear and mitochrondrial molecular data

Summary In order to clarify some controverisal phylogenies such as those regarding the triplet of human, rodent, and cow and the evolutionary position of Lagompopha with respect to other mammals, we have analyzed both nuclear and mitochondrial genes using the stationary Markov model developed in our laboratory. We found that the two sets of genes give different results. In particular the mitochondrial tree showed rabbit linked first to rodents and the the rabbit-rodents branch linked to artiodactyls with human as the outgroup. The most favorite nuclear tree showed human linked first to artiocactlys and the human-artiocactyls branch linked to rabbit with rodents as the outgroup. The obvious questions, (1) which tree is the correct one, or (2) both trees can be incorrect, and (3) how can we explain such an evolutionary pattern, are discussed on the basis of our limited knowledge of factors that influence the clocklike behavior of biological macromolecules.     

Evolutionary and biogeographic patterns of the Badidae (Teleostei: Perciformes) inferred from mitochondrial and nuclear DNA sequence data

We reconstructed phylogenetic relationships of the family Badidae using both mitochondrial and nuclear nucleotide sequence data to address badid systematics and to evaluate the role of vicariant speciation on their evolution and current distribution. Phy-logenetic hypotheses were derived from complete cytochrome b (1,140 base pairs) sequences of 33 individuals representing 13 badid species, and using three species of Nandidae as outgroups. Additionally, we sequenced the nuclear RAG1 (1,473 base pairs) and Tmo-4C4 (511 base pairs) genes from each of the badid species and one representative of the outgroup. Our molecular data provide the first phylogenetic hypothesis of badid intrarelationships. Analysis of the mitochondrial and nuclear nucleotide sequence data sets resulted in well-supported trees, indicating a basal split between the genera Dario and Badis, and further supporting the division of the genus Badis into five species groups as suggested by a previous taxonomic revision of the Badidae. Within the genus Badis, mitochondrial and nuclear phylogenies differed in the relative position of B. kyar. We also used our molecular phylogeny to test a vicariant speciation hypothesis derived from geological evidence of large-scale changes in drainage patterns in the Miocene affecting the Irrawaddy- and Tsangpo-Brahmaputra drainages, in the southeastern Himalaya. Within both genera, Badis and Dario, we observed a divergence into Irrawaddy- and Tsangpo-Brahmaputra clades. Using a cytb substitution rate of 8.2 x 10(-9) (substitutions x base pair(-1) x year(-1), we tentatively date this vicariant event at the Oligocene-Miocene boundary (19-24Myr). It is concordant with a hypothesized paleo connection of the Tsangpo river with the Irrawaddy drainage that was most likely interrupted during Miocene orogenic events through tectonic uplifts in eastern Tibet. Our data, therefore, indicate a substantial role of vicariant-based speciation shaping the current distribution patterns of badids.     

Phylogenetic congruence and discordance among one morphological and three molecular data sets from Pontederiaceae

A morphological data set and three sources of data from the chloroplast genome (two genes and a restriction site survey) were used to reconstruct the phylogenetic history of the pickerelweed family Pontederiaceae. The chloroplast data converged towards a single tree, presumably the true chloroplast phylogeny of the family. Unrooted trees estimated from each of the three chloroplast data sets were identical or extremely similar in shape to each other and mostly robustly supported. There was no evidence of significant heterogeneity among the data sets, and the few topological differences seen among unrooted trees from each chloroplast data set are probably artifacts of sampling error on short branches. Despite well-documented differences in rates of evolution for different characters in individual data sets, equally weighted parsimony permits accurate reconstructions of chloroplast relationships in Pontederiaceae. A separate morphology-based data set yielded trees that were very different from the chloroplast trees. Although there was substantial support from the morphological evidence for several major clades supported by chloroplast trees, most of the conflicting phylogenetic structure on the morphology trees was not robust. Nonetheless, several statistical tests of incongruence indicate significant heterogeneity between molecules and morphology. The source of this apparent incongruence appears to be a low ratio of phylogenetic signal to noise in the morphological data.     

Phylogenetic relationships in Bulbostylis (Abildgaardieae: Cyperaceae) inferred from nuclear and plastid DNA sequence data

Previous molecular phylogenetic analyses of the family Cyperaceae based on rbcL sequences showed Bulbostylis as paraphyletic, with B. atrosanguinea and B. hispidula forming a clade with Nemum spadiceum. On the contrary, phylogenetic analyses of the tribe Abildgaardieae based on nuclear (ITS ribosomal region) and plastid sequences (trnL-F region) showed Bulbostylis as monophyletic, although they only incorporated four species of Bulbostylis and none of Nemum. In this work, we presented a phylogenetic hypothesis of Bulbostylis based on a comprehensive sampling, including species from different continents for the first time. New sequences of Abildgaardia, Crosslandia, Fimbristylis, and Nemum were included to test the monophyly of Bulbostylis. In total, 84 sequences of both ITS and trnL regions were generated. Analyses were performed using Bayesian inference, maximum likelihood, and parsimony. Ancestral state reconstruction was performed using ML, MCMC, and parsimony methods. In all analyses, Bulbostylis resulted paraphyletic as Nemum atracuminatum is nested within it. Most American species of Bulbostylis grouped together, but relationships amongst them appeared poorly resolved. Ancestral state reconstructions of native distribution suggest an African ancestor of Bulbostylis, with at least three introduction independent events of the species in America. Morphological diagnostic characters such as the ‘style base permanence or detachment from the ripe achene’, and the ‘micromorphological patterns of the achene surface’ are homoplastic in this phylogenetic context, and therefore unsuitable to propose infrageneric groupings within the Bulbostylis.     

Phylogenetic relationships among Syndermata inferred from nuclear and mitochondrial gene sequences

Phylogenetic relationships among Syndermata have been extensively debated, mainly because the sister-group of the Acanthocephala has not yet been clearly identified from analyses of morphological and molecular data. Here we conduct phylogenetic analyses on samples from the 4 classes of Acanthocephala (Archiacanthocephala, Eoacanthocephala, Polyacanthocephala, and Palaeacanthocephala) and the 3 Rotifera classes (Bdelloidea, Monogononta, and Seisonidea). We do so using small-subunit (SSU) and large-subunit (LSU) ribosomal DNA and cytochrome c oxidase subunit 1 (cox 1) sequences. These nuclear and mitochondrial DNA sequences were obtained for 27 acanthocephalans, 9 rotifers, and representatives of 6 phyla that were used as outgroups. Maximum parsimony (MP), maximum likelihood (ML), and Bayesian analyses were conducted on the nuclear rDNA(SSU+LSU) and the combined sequence dataset(SSU+LSU+cox 1 genes). Phylogenetic analyses of the combined rDNA and cox 1 data uniformly provided strong support for a clade including rotifers plus acanthocephalans (Syndermata). Strong support was also found for monophyly of Acanthocephala in analyses of the combined dataset or rDNA sequences alone. Within the Acanthocephala the monophyletic grouping of the representatives of each class was strongly supported. Our results depicted Archiacanthocephala as the sister-group to the remaining acanthocephalans. Analyses of the combined dataset recovered a sister-group relationship between Acanthocephala and Bdelloidea by parsimony, likelihood, and Bayesian methods. Support for this clade was generally strong. Alternative topologies that depicted a different rotifer sister-group of Acanthocephala (or monophyly of Rotifera) were significantly worse. In this paraphyletic assemblage of rotifers, the relative positions of Seisonidea and Monogononta to the clade Bdelloidea+Acanthocephala were inconsistent among trees based on different inference methods. These results indicate that Bdelloidea is the free-living sister-group to acanthocephalans, which should prove key for comparative investigations of the morphological, molecular, and ecological changes accompanying the evolution of parasitism.     

Phylogenetic relationships of Combretaceae inferred from nuclear and plastid DNA sequence data: implications for generic classification

The putative complexity of Combretaceae and lack of information on phylogenetic relationships within the family led us to explore relationships between genera of Combretaceae by means of combined analyses of plastid and nuclear sequences. We collected DNA sequence data from the nuclear ribosomal internal transcribed spacer region and plastid rbcL, psaA‐ycf3 spacer and psbA‐trnH spacer for 14 of the 17 genera of Combretaceae. The current classification of the family into two subfamilies, Strephonematoideae and Combretoideae, is corroborated. Within Combretoideae, division into two tribes, Laguncularieae and Combreteae, is strongly supported. Within Combreteae subtribe Terminaliinae, relationships between genera are largely unresolved. Terminalia is not supported as monophyletic and two groups were identified, one containing mainly African species and another of mostly Asian species. Pteleopsis, Buchenavia and Anogeissus are embedded within Terminalia, and we suggest that all genera of Terminaliinae, with the exception of Conocarpus, should be included in an expanded circumscrition of Terminalia. Within subtribe Combretinae, a clade formed by the two monotypic genera Guiera and Calycopteris is sister to the rest of the subtribe. Groupings in Combretinae are consistent with recent results based on morphological data. Combretum is currently divided into three subgenera: Apethalanthum, Cacoucia and Combretum. The last two were included in this study and supported as monophyletic if Quisqualis is included within subgenus Cacoucia. Meiostemon is sister to subgenus Combretum. We recommend that subgenus Combretum should be expanded to include Meiostemon and subgenus Cacoucia to include Quisqualis. The sectional classification within Combretum proposed in earlier morphological studies is confirmed except for the exclusion of C. imberbe from section Hypocrateropsis in a separate and monotypic section and the inclusion of C. zeyheri (section Spathulipetala) in section Macrostigmatea. In order to accommodate C. imberbe, a new section is suggested. The reinstatement of previously recognized sections Grandiflora and Trichopetala, both of which had been sunk into subgenus Cacoucia section Poivrea, is proposed. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 162 , 453–476.     

Phylogenetic relationships of the Aurantioideae inferred from chloroplast DNA sequence data

The tribes and subtribes of Aurantioideae, an economically important subfamily of the Rutaceae, have a controversial taxonomic history because of the lack of a phylogenetic framework. The rps16 and trnL-trnF sequences of the chloroplast were analyzed phylogenetically to construct an evolutionary history and evaluate the most recent classification system of Swingle and Reece (The Citrus Industry, volume 1 [1967]). Taxa representing tribes Citreae and Clauseneae and five of the six subtribes were sampled. Conflicts in the positions of some taxa between the rps16 and trnL-trnF trees are poorly supported. In all analyses, the Aurantioideae are monophyletic. The strict consensus tree of the combined analysis indicates that the two tribes along with the subtribes sampled are not monophyletic. The combined topology is not congruent with the widely used classification of Aurantioideae by Swingle and Reece. The tribes and subtribes are in need of revision.     

Phylogenetic signal in AFLP data sets

AFLP markers provide a potential source of phylogenetic information for molecular systematic studies. However, there are properties of restriction fragment data that limit phylogenetic interpretation of AFLPs. These are (a) possible nonindependence of fragments, (b) problems of homology assignment of fragments, (c) asymmetry in the probability of losing and gaining fragments, and (d) problems in distinguishing heterozygote from homozygote bands. In the present study, AFLP data sets of Lactuca s.l. were examined for the presence of phylogenetic signal. An indication of this signal was provided by carrying out tree length distribution skewness (g1) tests, permutation tail probability (PTP) tests, and relative apparent synapomorphy analysis (RASA). A measure of the support for internal branches in the optimal parsimony tree (MPT) was made using bootstrap, jackknife, and decay analysis. Finally, the extent of congruence in MPTs for AFLP and internal transcribed spacer (ITS)-1 data sets for the same taxa was made using the partition homogeneity test (PHT) and the Templeton test. These analytical studies suggested the presence of phylogenetic signal in the AFLP data sets, although some incongruence was found between AFLP and ITS MPTs. An extensive literature survey undertaken indicated that authors report a general congruence of AFLP and ITS tree topologies across a wide range of taxonomic groups, suggesting that the present results and conclusions have a general bearing. In these earlier studies and those for Lactuca s.l., AFLP markers have been found to be informative at somewhat lower taxonomic levels than ITS sequences. Tentative estimates are suggested for the levels of ITS sequence divergence over which AFLP profiles are likely to be phylogenetically informative.     

Phylogenetic relationships and evolution of Crassulaceae inferred from matK sequence data

Chloroplast gene matK sequence data were used to estimate the phylogeny of 112 species of Crassulaceae sampled from 33 genera and all six recognized subfamilies. Our analyses suggest that five of six subfamilies recognized in the most recent comprehensive classification of the family are not monophyletic. Instead, we recovered a basal split in Crassulaceae between the southern African CRASSULA: clade (Crassuloideae) and the rest of the family (Sedoideae). These results are compatible with recent studies of cpDNA restriction site analyses. Within Sedoideae, four subclades were also recovered: KALANCHOE:, Leucosedum, Acre, and AEONIUM:; evidence also exists for a TELEPHIUM: clade and SEMPERVIVUM: clade. The genus SEDUM: is highly polyphyletic with representatives spread throughout the large Sedoideae clade. Sympetaly and polymerous flowers have arisen multiple times in Crassulaceae and thus are not appropriate characters upon which to base subfamilial limits, as has been done in the past. One floral character, haplostemy, appears to be confined to the well-supported CRASSULA: clade. Our analyses suggest a southern African origin of the family, with subsequent dispersal northward into the Mediterranean region. From there, the family spread to Asia/eastern Europe and northern Europe; two separate lineages of European Crassulaceae subsequently dispersed to North America and underwent substantial diversification. Our analyses also suggest that the original base chromosome number in Crassulaceae is x = 8 and that polyploidy has played an important role in seven clades. Three of these clades are exclusively polyploid (SEMPERVIVUM: clade and two subclades within the KALANCHOE: and AEONIUM: clades), whereas four (Crassula, Telephium, Leucosedum, and ACRE: clades) comprise both diploid and polyploid taxa. Polyploidy is particularly rampant and cytological evolution especially complex in the ACRE: clade.     

Phylogenetic signal common to three data sets: Combining data which initially appear heterogeneous

This study makes use of three sources of data, morphology and two chloroplast DNA sequences,ndhF andrbcL, to resolve relationships in Gesneriaceae. Cladograms from each of the three data sets separately are not topologically congruent. Statistical indices suggest that each data set is congruent with thendhF data althoughrbcL and morphology are themselves incongruent. Consensus methods provide no resolution of taxonomic relationships when trees from the different data sets are combined. Combining data sets generally results in cladograms that are more fully resolved than each of the data sets analyzed separately and support for the clades increases based on higher decay index and bootstrap values. These results indicate that there is a phylogenetic signal common to each of the data sets, however, the noise (errors due to homoplasy, mis-scoring, etc.) unique to each data source masks this signal. In combining the data, the evidence for the common evolutionary history in each data set overcomes the noise and is apparent in the resulting trees.     

Phylogenetic relationships and generic affinity of Uncinula septata inferred from nuclear rDNA sequences

Based on 18S, 5.8S, and 28S rDNA sequences, the phylogenetic position of Uncinula septata within the Erysiphales has been inferred. Although appendages of the ascomata are uncinula like, i.e., unbranched with curved-coiled apices, U. septata is situated at the very base of the large Erysiphales cluster, far away from the pseudoidium clade (Erysiphe emend., including Microsphaera and Uncinula). Morphologically, U. septata differs from the species of Erysiphe sect. Uncinula (Uncinula) in having terminal, pluriseptate ascoma appendages, curved ascospores, and the absense of an anamorph. This species is a basal, tree-inhabiting powdery mildew with some additional ancestral characteristics, viz., uncinula-like appendages and 8-spored asci. The new genus Parauncinula with U. septata as the type species is proposed. Uncinula curvispora (U. septata var. curvispora) is tentatively maintained as a separate species, which is also assigned to Parauncinula.     

Phylogenetic relationships and natural hybridization in Triadica inferred from nuclear and chloroplast DNA analyses

Triadica (Euphorbiaceae) is a small genus endemic to East Asia and Southeast Asia, consisting of three species differentially adapted to heterogeneous habitats. To date, the phylogenetic relationships of this genus have not been resolved, and there has been no evidence for interspecific hybridization in Triadica. In this study, we sequenced the nrITS regions, two nuclear genes and a chloroplast gene to reconstruct the molecular phylogeny of Triadica and to test the hypothesis of natural hybridization between Triadica sebifera and Triadica cochinchinensis, and between T. sebifera and Tridica rotundifolia. Phylogenetic analysis showed that T. sebifera diverged first within this genus, and T. cochinchinensis and T. rotundifolia were sister species. Both of the two putative hybrids show chromatogram additivity at each of the two nuclear genes, providing convincing evidence for natural hybridization between T. sebifera and T. cochinchinensis, and between T. sebifera and T. rotundifolia. The chloroplast gene sequences of both hybrids were identical with that of T. sebifera, suggesting that T. sebifera was the maternal parent of the two hybrids. This is the first report of natural hybridization in Triadica, and the hybrids identified in this study should be a good starting point for further hybridization-based breeding in T. sebifera.     

Molecular phylogeny of Anaphalis (Asteraceae, Gnaphalieae) with biogeographic implications in the Northern Hemisphere

Anaphalis is the largest Asian genus in the tribe Gnaphalieae (Asteraceae) and has its greatest species diversity in the eastern Himalayas. The nuclear internal and external transcribed spacers were sequenced for Anaphalis species, with an emphasis on the eastern Himalayan taxa to examine the monophyly and construct the phylogenetic relationships of and within the genus. The results suggest that all species of Anaphalis are nested with Helichrysum, showing a close relationship with a Mediterranean–Asian group of Helichrysum. Although the monophyly of Anaphalis is only weakly supported, two clades within the genus are well recognized, each consisting of two subgroups. The inferred phylogenetic relationships within Anaphalis correspond to the shape of leaf base, rather than the morphology of the capitula and phyllaries that are usually used for species delimitation and classification in the genus. All four subgroups of Anaphalis are common and diversified in the eastern Himalayas with multiple dispersals out of this region. The sole North American species of Anaphalis is best hypothesized to be the result of long-distance dispersal or overland migration via Bering land bridge from Asia. Our analyses suggest that the extant distribution of Anaphalis has most likely resulted one radiation into the eastern Himalayas followed by repeated independent dispersals and/or radiations mostly into eastern Asia but also into the western Himalayas, North America, and southeast Asia.