Showing papers in "Journal of Systematics and Evolution in 2008"
TL;DR: Thorough taxon sampling is one of the most practical ways to improve the accuracy of phylogenetic estimates, as well as the accuracyof biological inferences that are based on these phylogenetic trees.
Abstract: Appropriate and extensive taxon sampling is one of the most important determinants of accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary processes obtained from phyloge- netic analyses is improved significantly by thorough taxon sampling efforts. Many recent efforts to improve phylogenetic estimates have focused instead on increasing sequence length or the number of overall characters in the analysis, and this often does have a beneficial effect on the accuracy of phylogenetic analyses. However, phylogenetic analyses of few taxa (but each represented by many characters) can be subject to strong systematic biases, which in turn produce high measures of repeatability (such as bootstrap proportions) in support of incor- rect or misleading phylogenetic results. Thus, it is important for phylogeneticists to consider both the sampling of taxa, as well as the sampling of characters, in designing phylogenetic studies. Taxon sampling also improves estimates of evolutionary parameters derived from phylogenetic trees, and is thus important for improved applica- tions of phylogenetic analyses. Analysis of sensitivity to taxon inclusion, the possible effects of long-branch attraction, and sensitivity of parameter estimation for model-based methods should be a part of any careful and thorough phylogenetic analysis. Furthermore, recent improvements in phylogenetic algorithms and in computa- tional power have removed many constraints on analyzing large, thoroughly sampled data sets. Thorough taxon sampling is thus one of the most practical ways to improve the accuracy of phylogenetic estimates, as well as the accuracy of biological inferences that are based on these phylogenetic trees.
527 citations
TL;DR: The identity of the major groups of eukaryotes, some of their important, defining or simply interesting features and the pro- posed relationships of these groups to each other are outlined.
Abstract: Our understanding of eukaryote biology is dominated by the study of land plants, animals and fungi. However, these are only three isolated fragments of the full diversity of extant eukaryotes. The majority of eukaryotes, in terms of major taxa and probably also sheer numbers of cells, consists of exclusively or predominantly unicellular lineages. A surprising number of these lineages are poorly characterized. Nonetheless, they are fundamental to our understanding of eukaryote biology and the underlying forces that shaped it. This article consists of an overview of the current state of our understanding of the eukaryote tree. This includes the identity of the major groups of eukaryotes, some of their important, defining or simply interesting features and the proposed relationships of these groups to each other.
212 citations
TL;DR: Simulation results suggest that highly incomplete taxa can be safely included in many Bayesian phylogenetic analyses, as long as the overall number of characters in the analysis is large.
Abstract: The effect of missing data on phylogenetic methods is a potentially important issue in our attempts to reconstruct the Tree of Life. If missing data are truly problematic, then it may be unwise to include species in an analysis that lack data for some characters (incomplete taxa) or to include characters that lack data for some species. Given the difficulty of obtaining data from all characters for all taxa (e.g., fossils), missing data might seriously impede efforts to reconstruct a comprehensive phylogeny that includes all species. Fortunately, recent simulations and empirical analyses suggest that missing data cells are not themselves problematic, and that in- complete taxa can be accurately placed as long as the overall number of characters in the analysis is large. How- ever, these studies have so far only been conducted on parsimony, likelihood, and neighbor-joining methods. Although Bayesian phylogenetic methods have become widely used in recent years, the effects of missing data on Bayesian analysis have not been adequately studied. Here, we conduct simulations to test whether Bayesian analyses can accurately place incomplete taxa despite extensive missing data. In agreement with previous studies of other methods, we find that Bayesian analyses can accurately reconstruct the position of highly incomplete taxa (i.e., 95% missing data), as long as the overall number of characters in the analysis is large. These results suggest that highly incomplete taxa can be safely included in many Bayesian phylogenetic analyses. The impact of missing data is a potentially im- portant issue in phylogenetic analyses, particularly if the goal is to reconstruct a comprehensive Tree of Life that includes both fossil and living taxa. Missing data are often encountered when combining data from two or more different genes, when some of the taxa have sequence data available for one gene but not the other. If the taxa lacking data for a gene are included in the combined analysis, then the characters associated with this gene are typically coded as missing or unknown (often denoted with a "?"). Similarly, missing data are often encountered in analyses that include fossil taxa, when certain taxa must be scored as unknown for certain characters because the relevant features have not been adequately preserved. Concerns about missing data may often deter- mine what characters and taxa will be included in an analysis (Wiens, 2006), even if this is not always stated explicitly by researchers. For example, if missing data are considered to be problematic, then one should only include species that have complete data for all characters or else only include characters that have complete data for all species. Thus, one may have to reduce the number of taxa or characters in an
160 citations
TL;DR: P phylogenetic results will facilitate evolutionary developmental studies of these key traits of the plant life cycle, multicellularity, and gravitropism, which will help to gain mechanistic understanding on how plants adapted to environmental challenges when they colonized the land during one of the major transitions in evolution of life.
Abstract: Charophytic algae and land plants together make up a monophyletic group, streptophytes, which represents one of the main lineages of multicellular eukaryotes and has contributed greatly to the change of the environment on earth in the Phanerozoic Eon. Significant progress has been made to understand phylogenetic relationships among members of this group by phylogenetic studies of morphological and molecular data over the last twenty-five years. Mesostigma viride is now regarded as among the earliest diverging unicellular organisms in streptophytes. Characeae are the sister group to land plants. Liverworts represent the first diverging lineage of land plants. Hornworts and lycophytes are extant representatives of bryophytes and vascular plants, respectively, when early land plants changed from gametophyte to sporophyte as the dominant generation in the life cycle. Equisetum, Psilotaceae, and ferns constitute the monophyletic group of monilophytes, which are sister to seed plants. Gnetales are related to conifers, not to angiosperms as previously thought. Amborella, Nymphaeales, Hydatellaceae, Illiciales, Trimeniaceae, and Austrobaileya represent the earliest diverging lineages of extant angiosperms. These phylogenetic results, together with recent progress on elucidating genetic and developmental aspects of the plant life cycle, multicellularity, and gravitropism, will facilitate evolutionary developmental studies of these key traits, which will help us to gain mechanistic understanding on how plants adapted to environmental challenges when they colonized the land during one of the major transitions in evolution of life.
86 citations
TL;DR: Both ITS and ndhF data sets suggest that the formerly recognized genus Pygeum is polyphyletic and that the distinction of the subgenera Padus and Laurocerasus is not supported, and the biogeographic interactions of the temperate and tropical members in the Padus/Laurocersasus/Maddenia alliance includingPygeum are shown to be highly dynamic and complex.
Abstract: Sequences of the chloroplast ndhF gene and the nuclear ribosomal ITS regions are employed to reconstruct the phylogeny of Prunus (Rosaceae), and evaluate the classification schemes of this genus. The two data sets are congruent in that the genera Prunus s.l. and Maddenia form a monophyletic group, with Maddenia nested within Prunus. However, the ndhF data set is incongruent with the ITS data supporting two major groups within Prunus: one consisting of subgenera Laurocerasus (including Pygeum) and Padus as well as the genus Maddenia and another of subgenera Amygdalus, Cerasus, and Prunus. The ITS data, on the other hand, support a clade composed of subgenera Amygdalus and Prunus and Prunus sect. Microcerasus in addition to a paraphyletic grade of subgenera Laurocerasus and Padus (and the genus Maddenia) taxa. In general, the subgeneric classifications of Prunus s.l. are not supported. The ITS and ndhF phylogenies differ mainly in interspecific relationships and the relative position of the Padus/Laurocerasus group. Both ITS and ndhF data sets suggest that the formerly recognized genus Pygeum is polyphyletic and that the distinction of the subgenera Padus and Laurocerasus is not supported. The biogeographic interactions of the temperate and tropical members in the Padus/Laurocerasus/Maddenia alliance including Pygeum are shown to be highly dynamic and complex.
72 citations
TL;DR: In this early synthesis of the understanding of the phylogenetic relationships of Cypriniformes, all types of data have contributed historically to improving the understanding, but not all analyses are complementary in taxon sampling, thus precluding directUnderstanding of the impact ofTaxon sampling on achieving accurate phylogenetic inferences.
Abstract: The phylogenetic relationships of species are fundamental to any biological investigation, including all evolutionary studies. Accurate inferences of sister group relationships provide the researcher with an historical framework within which the attributes or geographic origin of species (or supraspecific groups) evolved. Taken out of this phylogenetic context, interpretations of evolutionary processes or origins, geographic distributions, or speciation rates and mechanisms, are subject to nothing less than a biological experiment without controls. Cypriniformes is the most diverse clade of freshwater fishes with estimates of diversity of nearly 3,500 species. These fishes display an amazing array of morphological, ecological, behavioral, and geographic diversity and offer a tremendous opportunity to enhance our understanding of the biotic and abiotic factors associated with diversification and adaptation to environments. Given the nearly global distribution of these fishes, they serve as an important model group for a plethora of biological investigations, including indicator species for future cli- matic changes. The occurrence of the zebrafish, Danio rerio, in this order makes this clade a critical component in understanding and predicting the relationship between mutagenesis and phenotypic expressions in vertebrates, including humans. With the tremendous diversity in Cypriniformes, our understanding of their phylogenetic relationships has not proceeded at an acceptable rate, despite a plethora of morphological and more recent mo- lecular studies. Most studies are pre-Hennigian in origin or include relatively small numbers of taxa. Given that analyses of small numbers of taxa for molecular characters can be compromised by peculiarities of long-branch attraction and nodal-density effect, it is critical that significant progress in our understanding of the relationships of these important fishes occurs with increasing sampling of species to mitigate these potential problems. The recent Cypriniformes Tree of Life initiative is an effort to achieve this goal with morphological and molecular (mitochondrial and nuclear) data. In this early synthesis of our understanding of the phylogenetic relationships of these fishes, all types of data have contributed historically to improving our understanding, but not all analyses are complementary in taxon sampling, thus precluding direct understanding of the impact of taxon sampling on achieving accurate phylogenetic inferences. However, recent molecular studies do provide some insight and in some instances taxon sampling can be implicated as a variable that can influence sister group relationships. Other instances may also exist but without inclusion of more taxa for both mitochondrial and nuclear genes, one cannot distinguish between inferences being dictated by taxon sampling or the origins of the molecular data.
69 citations
TL;DR: It is suggested that fruit evolution was driven at least in part by dispersal agents abundant in particular habitats, including desert and plains and North American plains and prairies.
Abstract: Success of flowering plants is greatly dependent on effective seed dispersal Specific fruit types aid different mechanisms of seed dispersal However, little is known about what evolutionary forces have driven the diversification of fruit types and whether there were phylogenetic constraints on fruit evolution among angio- sperm lineages To address these questions, we first surveyed the orders and families of angiosperms for fruit types and found no clear association between fruit types and major angiosperm lineages, suggesting there was little phylogenetic constraint on fruit evolution at this level We then surveyed fruit types found in two contrasting habitats: an open habitat including the Indian desert and North American plains and prairies, and a closed forest habitat of Australian tropical forest The majority of genera in the survey of tropical forests in Australia were fleshy fruit trees, whereas the majority of genera in the survey of prairies and plains in central North America were herbs with capsules and achenes Both capsules and achenes are frequently dispersed by wind in the open, arid habitat, whereas fleshy fruits are generally dispersed by animals Since desert and plains tend to provide continuous wind to aid dispersal and there are more abundant mammal and bird dispersers in the closed forest, this survey suggests that fruit evolution was driven at least in part by dispersal agents abundant in particular habitats
62 citations
TL;DR: The analysis of a dataset of 55 animal species and 102 proteins shows that standard site-homogeneous model inference is sensitive to long-branch attraction artifact, whereas the site-heterogeneous CAT model is less so and the resulting tree is in excellent agreement with the new animal phylogeny, confirming that "simple" organisms like platyhelminths and nematodes are not necessarily of basal emergence.
Abstract: Phylogenomics, the inference of phylogenetic trees using genome-scale data, is becoming the rule for resolving difficult parts of the tree of life. Its promise resides in the large amount of information available, which should eliminate stochastic error. However, systematic error, which is due to limitations of reconstruction meth- ods, is becoming more apparent. We will illustrate, using animal phylogeny as a case study, the three most effi- cient approaches to avoid the pitfalls of phylogenomics: (1) using a dense taxon sampling, (2) using probabilistic methods with complex models of sequence evolution that more accurately detect multiple substitutions, and (3) removing the fastest evolving part of the data (e.g., species and positions). The analysis of a dataset of 55 animal species and 102 proteins (25712 amino acid positions) shows that standard site-homogeneous model inference is sensitive to long-branch attraction artifact, whereas the site-heterogeneous CAT model is less so. The latter model correctly locates three very fast evolving species, the appendicularian tunicate Oikopleura, the acoel Convoluta and the myxozoan Buddenbrockia. Overall, the resulting tree is in excellent agreement with the new animal phylogeny, confirming that "simple" organisms like platyhelminths and nematodes are not necessarily of basal emergence. This further emphasizes the importance of secondary simplification in animals, and for organismal evolution in general.
49 citations
TL;DR: Examination of chloroplast trnL-trnF and rps16 sequence variation of Primula secundiflora, a relatively common alpine perennial endemic to this region, suggested a special phylogeographic pattern may have resulted from a combination of both climatic oscillation and complex topology of HM.
Abstract: The Hengduan Mountains (HM) and adjacent regions have been suggested as the important refugia of the temperate plants during the glacial stages. However, it remains unknown how the HM endemic species can respond to the climatic oscillations. In this study, we examined the chloroplast trnL-trnF and rps16 sequence variation of Primula secundiflora, a relatively common alpine perennial endemic to this region. Sequence data were obtained from 109 individuals of 11 populations covering the entire distribution range of the species. A total of 15 haplotypes were recovered and only one of them is commonly shared by three populations while the others are respectively fixed in the single population. The total diversity (HT=0.966) is high while the within-population diversity (HS=0.178) is low. Despite the high uniformity of the intraspecific morphology, an analysis of molecular variance (AMOVA) revealed a high level of genetic differentiation (97.65%) among populations. The higher NST (0.982) than GST (0.816) (P<0.05) suggested a distinctly phylogeographical pattern. Phylogenetic analyses of haplotypes identified four major clusters of the recovered haplotypes: three clades in the north, and the other one in the south. The isolated distribution of clades suggested multiple refugia of this species during the glacial stages. We failed to detect the interglacial or postglacial range expansion of this species as revealed for the other temper- ate plants. However, the low intra-population diversity suggested that most of the populations should have ex- perienced the in situ shrink-expansion cycles during the climatic oscillations. This inference was further supported by the nested clade analysis, which indicated that restricted gene flow with isolation by distance and allopatric fragmentation were likely the major processes that shaped the present-day spatial distribution of haplotypes in this species. Such a special phylogeographic pattern may have resulted from a combination of both climatic oscillation and complex topology of HM.
49 citations
TL;DR: Phylogenetics of Chilopsis and Catalpa (Bignoniaceae) was elucidated based on sequences of chloro- plast ndhF and the nrDNA ITS region and supported section Macrocatalpa of the West Indies and section Catalpa of eastern Asian and North American continents.
Abstract: Phylogenetics of Chilopsis and Catalpa (Bignoniaceae) was elucidated based on sequences of chloro- plast ndhF and the nrDNA ITS region. In Bignoniaceae, Chilopsis and Catalpa are most closely related as sister genera. Our data supported section Macrocatalpa of the West Indies and section Catalpa of eastern Asian and North American continents. Within section Catalpa, Catalpa ovata of eastern Asia form a clade with North American species, C. speciosa and C. bignonioides, while the other eastern Asian species comprise a clade where C. duclouxii is sister to the clade of C. bungei and C. fargesii. The Caribbean species of Catalpa diverged early from the continental species. More studies are needed to test whether the phylogenetic pattern is common in eastern Asian-North American disjunct genera with species in the West Indies. Catalpa Scop. (Bignoniaceae), an intercontinen- tal disjunct genus, consists of ten species, with two species in eastern North America (ENA), four in eastern Asia (EAS), and four in the West Indies (WI) (Li, 1952; Paclt, 1952; Gentry, 1992). Species of Catalpa are semievergreen or deciduous trees with opposite or whorled leaves. Their bisexual flowers are arranged in a raceme or panicle, and have two fertile stamens, a 2-lipped corolla, and tetrad pollen grains (Gentry, 1992). Four semievergreen species of section Macrocatalpa Griseb. are distributed in the WI, including C. brevipes Urban, C. longissima Sims, C. macrocarpa Ekman, and C. purpurea Griseb. (Man- ning, 2000). Species of section Catalpa are deciduous and disjunctly distributed between EAS and ENA. Catalpa bignonioides Walter, or the southern catalpa, has an original distribution in northern Florida and southwestern Georgia to southern Alabama and eastern Mississippi (Duncan & Duncan, 1988), Lou- isiana (Little, 1979), or easternmost Texas (Weniger, 1996). Catalpa speciosa Warder ex Engelm., the western catalpa, is native to the Mississippi River drainage basin from central Illinois and Indiana to northeastern Arkansas, western Tennessee (Beillman 1946; Little, 1979), and Louisiana (Burk & McMaster, 1988; Duncan & Duncan, 1988; Thomas & Allen, 1996). Both species have spread to other areas as a result of their cultivation as garden or lawn trees (Beillmann, 1946). Catalpa ovata G. Don is distrib- uted in central and northern China. Its young leaves are edible, while the extract of mature leaves and barks has been used as pesticide and in traditional Chinese medicine (Wang, 1990). Catalpa bungei C. A. Mey. and C. fargesii Bureau are distributed in central to southwestern China, and the latter has a glabrous form, namely, C. fargesii f. duclouxii (Don) Gilmour (Gilmour, 1936; =C. duclouxii Dode). Ca- talpa tibetica Forrest is endemic to southwestern China and shares creamy-yellow flowers with C. ovata (Forrest, 1921). Catalpa shares many reproductive characters
45 citations
TL;DR: This method of plant identification was rapid and highly specific when tested against DNA of several closely related species and was able to amplify specific markers from mixed DNA samples.
Abstract: Phyllanthus amarus Schum. & Thonn. has been widely used in traditional medicine in Thailand as an antipyretic, a diuretic, to treat liver diseases and viral infections. Two closely related species, P. debilis L. and P. urinaria Klein ex Willd., with different and less effective medicinal properties, are less commonly used. These three species are similar in morphology and often occur in overlapping populations in nature. The latter two species can easily be mistaken for P. amarus and collected for medicinal uses, which can lead to undesirable results. DNA fingerprints of these species were obtained using RAPD-PCR techniques. RAPD markers specific for each species were identified. Primers for highly specific sequence-characterized-amplified-regions (SCAR) were then designed from nucleotide sequences of specific RAPD markers. These primers efficiently amplified SCAR markers of 408, 501 and 319 bp unique to P. amarus, P. debilis and P. urinaria respectively. This method of plant identification was rapid and highly specific when tested against DNA of several closely related species and was able to amplify specific markers from mixed DNA samples.
TL;DR: Seventeen species, one subspecies and one variety of Dioscorea sect.
Abstract: Seventeen species, one subspecies and one variety of Dioscorea sect. Stenophora Uline were investi- gated for their phylogenetic relationships based on a sequence analysis of chloroplast matK and rbcL genes and trnL-F intergenic spacer by maximum parsimony and maximum likelihood methods. The results showed that: (a) sect. Stenophora was a strongly supported monophyletic group; (b) D. rockii, D. membranacea, D. banzhuana, and D. simulans formed a moderately supported monophyletic group, and D. prazeri was weakly supported to be sister to this group; (c) D. althaeoides and D. nipponica ssp. nipponica formed a moderately supported clade, and D. nipponica ssp. rosthornii was not a member of this clade; (d) D. zingiberensis and D. sinoparviflora showed a moderate to strong sister relationship; and (e) D. collettii var. hypoglauca and D. collettii var. collettii were sister to each other, but with only weak support.
Journal Article•
TL;DR: A newly developed discipline, phylogenomics, is introduced and its power and great potential in resolving difficult phylogenetic problems are demonstrated using the recent phylogenomic study of Oryza as an example.
Abstract: With more and more sequence data available, it has been a widespread practice to apply multiple genes to reconstruct phylogenies at different hierarchical levels.The phenomenon of conflicting gene trees has accordingly become a remarkable and difficult problem.It is increasingly understood that the difference between gene tree and species tree and the causes behind should be fully appreciated in molecular phylogenetic studies.In this paper, we have explored the major causes resulting in conflicting gene trees, including stochastic errors, systematic errors and biological factors.We also introduced a newly developed discipline, phylogenomics, and demonstrated its power and great potential in resolving difficult phylogenetic problems using our recent phylogenomic study of Oryza as an example.Furthermore, we discussed some strategies and approaches in elucidating conflicting gene trees and provided some suggestions and recommendations for molecular phylogenetic studies using multiple genes.
TL;DR: Molecular data demonstrated clearly that there indeed existed natural hybridization between S. alba and S. grif- fithii, and that S.griffithii was the maternal parent in this hybridization event.
Abstract: Interspecific hybridization has been frequently observed in the mangrove genus Sonneratia. However, no natural hybridization has been reported between Sonneratia alba and S. griffithii to date, despite their overlap- ping distribution in the coast of Andaman Sea. In this study, cysteine proteinase inhibitor gene (cpi) from the nuclear genome, and two intergenic spacers (trnL-trnF and trnV-trnM) from the chloroplast genome, were se- quenced to determine whether natural hybridization took place between the two species. Our results revealed two distinct types of cpi sequences from the putative hybrid matching those acquired from S. griffithii and S. alba, respectively. Sequencing of the chloroplast trnL-trnF and trnV-trnM regions showed that S. alba differed from S. griffithii by one nucleotide in each region, and the putative hybrid had the identical sequences with S. griffithii. Molecular data demonstrated clearly that there indeed existed natural hybridization between S. alba and S. grif- fithii, and that S. griffithii was the maternal parent in this hybridization event.
TL;DR: In this paper, 129 leaf samples from 35 species and one variety of the Chinese Epimedium(Berberidaceae), most of which were placed under subgen.Epimingium and sect.Diphyllon, were analyzed by HPLC method and suggested to be the most primitive type.
Abstract: In this paper, 129 leaf samples from 35 species and one variety of the Chinese Epimedium(Berberidaceae), most of which were placed under subgen.Epimedium and sect.Diphyllon, were analyzed by HPLC method.The HPLC chromatogram profiles of all the samples for icariin and similar compounds were achieved, sorted and analyzed.According to the second peak group(named as\"ABCI\"peak group) characters, chromaograms were divided into four main types and nine subtypes.By correlation analysis with flower morphology, II-3 was suggested to be the most primitive type;II-1, IV and I-3 were primitive and closely related to II-3;I-1 was basic type;I-2, I-4, Ⅲ and II-2 were derived types.The HPLC chromatogram type division corresponds to W.T.Stearn's classification on sect.Diphyllon with four series in 2002.
TL;DR: The nuclear ribosomal ITS region and the chloroplast trnL-trnF (trnLF) intergenic region were se- quenced for 45 accessions of Paranephelius and six accessions for Pseudonoseris, the two genera of the subtribe Paraphheliinae distributed in the alpine regions of the Andes.
Abstract: The nuclear ribosomal ITS region and the chloroplast trnL-trnF (trnLF) intergenic region were se- quenced for 45 accessions of Paranephelius and six accessions of Pseudonoseris, the two genera of the subtribe Paranepheliinae (Liabeae, Asteraceae) distributed in the alpine regions of the Andes. This data set was used to estimate relationships between these genera and within each genus to aid in evaluating morphological variation and classification. Our results with both ITS and trnLF markers support the monophyly of subtribe Paranephelii- nae, and place Pseudonoseris discolor as the first diverged taxon sister to the clade containing Paranephelius. Pseudonoseris szyszylowiczii exhibited intraspecific divergence supporting intergeneric hybridization between Pseudonoseris and Paranephelius. Within Paranephelius, genetic divergence is low and not adequate to fully resolve phylogenetic relationships at the species level, but two genetically and morphologically recognizable groups were revealed by the ITS data. Several accessions possessing multiple ITS sequences represent putative hybrids between the two groups. These putative hybrids have caused some taxonomic confusion and difficulties in establishing species boundaries in Paranephelius. The divergence time estimates based on ITS sequences indi- cated that the stem of subtribe Paranepheliinae dates to 13 million years ago, but the diversification of the crown clade of the extant members began in the early Pleistocene or late Pliocene, perhaps associated with the uplift of the Andes and the climatic changes of global cooling.
TL;DR: The results showed that the Hengduan Mountains might represent one of the frequency and diversity centers for Bupleurum, and suggested to raise B. stenophyllum to species rank based on the combined evidence from morphology, karyology, pollen morphology, and the ITS phylogenetic tree.
Abstract: Hengduan Mountains are the diversity center for the genus Bupleurum of Apiaceae in China. This paper reports chromosome numbers of six species and two varieties of Bupleurum, and for four species and two varieties their chromosome numbers are reported for the first time. The phylogeny of Bupleurum was investigated based on the ITS region of the nuclear ribosomal DNA (nrDNA) of 14 taxa from the Hengduan Mountains, 3 taxa from the North China (Hebei and Heilongjiang), and 16 taxa from Africa and the Mediterranean region. Varia- tions in chromosome numbers and the ITS sequences were used to infer phylogenetic relationships between Bupleurum species in Hengduan Mountains. The results showed that the Hengduan Mountains might represent one of the frequency and diversity centers for Bupleurum. The ancestors of Bupleurum species in the Hengduan Mountains may be related to the woody B. fruticosum in North Africa, or the species in the western Mediterranean region. It is postulated that the ancestral population migrated into Hengduan Mountains through the Middle East and the Caucasus. Furthermore, the neo-endemic B. mundtii in South Africa appeared to be a close relative of the species in the Hengduan Mountains. In the trend of basic chromosome number evolution, x = 8 should be regarded as the ancestral basic number, while x = 6, 7 as the derived ones. The Bupleurum species in the Hengduan Moun- tains have been undergoing changes in the basic chromosome numbers or the ploidy level. The ITS phylogenetic tree showed that the Chinese species were divided into two clades: one with the basic chromosome number x = 8, and the other with x = 6, 7. The results rejected the previous infrageneric classification of Bupleurum in China. We further suggested to raise B. marginatum var. stenophyllum to species rank based on the combined evidence from morphology, karyology, pollen morphology, and the ITS phylogenetic tree.
TL;DR: A tentative systematic arrangement focused on the Chinese lycophytes and monilophytes at the family level is presented and the relationships of all major lineages recovered in the rbcL phylogeny generally agree with those reconstructed in the studies that focused on these clades individually and had more extensive ingroup taxon sampling and/or character sampling.
Abstract: Recent phylogenetic studies have revealed that the traditional concept of pteridophytes which includes lycopods and ferns should be revised and a new classification of the extant monilophytes has just been published by Smith et al. China is very rich in plant diversity, with representatives of most important major groups of the lycophytes and monilophytes. Here we present the recent progress in phylogenetic analyses of lycophytes and monilophytes with a focus on relationships among the Chinese taxa. We conducted a phylogenetic analysis using sequence data of the chloroplast rbcL gene of 184 species (179 genera) representing 62 of a total of 63 families recognized by R. C. Ching. The relationships of all major lineages recovered in the rbcL phylogeny generally agree with those reconstructed in the studies that focused on these clades individually and had more extensive ingroup taxon sampling and/or character sampling. A tentative systematic arrangement focused on the Chinese lycophytes and monilophytes at the family level is presented.
TL;DR: Two new species of Curcuma, C. Sudmoon and C. zedoaroides, with rhizomes traditionally used for many decades as cobra-bite antidotes are described and illustrated.
Abstract: Two new species of Curcuma, C. sattayasaii A. Chaveerach & R. Sudmoon and C. zedoaroides A. Chaveerach & T. Tanee with rhizomes traditionally used for many decades as cobra-bite antidotes are described and illustrated. Curcuma sattayasaii is similar to C. longa L., but differs in rhizome horizontally branching on ground; coma bracts pinkish-white or pinkish-pale green; corolla pale yellow with orange tip; labellum pale orange with an orange central band; anther crest very short, broadly ovate, wider than long. Curcuma zedoaroides is similar to C. zedoaria (Christm.) Roscoe, but differs in rhizome branching pattern; the protruding secondary rhizomes curved down; blades oblong to oblong-lanceolate; peduncle glabrous; fertile and coma bracts glabrous; corolla lobes pale yellow to white, lateral lobe ovate, dorsal lobe broadly ovate. The new taxa have been found in
TL;DR: Three species and one variety of cryptomonad flagellates belonging to three genera were observed with the scanning electron microscope in sea water samples from Tolo Harbor (Hong Kong), Changjiang River Estuary and Xiamen Harbor and this is the first record of the genus Hemiselmis Parke in the China Sea.
Abstract: Three species and one variety of cryptomonad flagellates belonging to three genera were observed with the scanning electron microscope in sea water samples from Tolo Harbor (Hong Kong), Changjiang River Estuary and Xiamen Harbor. They are Hemiselmis sp. Novarino, Plagioselmis prolonga Butcher ex Novarino, Lucas & Morrall, Plagioselmis prolonga var. nordica Novarino, Lucas & Morrall and Teleaulax acuta (Butcher) Hill. The taxonomic characteristics, ecological habit and distribution of the above species are described and the LM and SEM photographs of the species are also presented. This is the first record of the genus Hemiselmis Parke in the China Sea, and the species Plagioselmis prolonga and Teleaulax acuta have records of producing blooms in the China Sea.
TL;DR: Floral organogenesis of three species of the genus Jatropha L. of the family Euphorbiaceae, viz., J curcas L., J podagrica Hook and J gossypifolia, was studied with scanning electron microscope.
Abstract: Floral organogenesis of three species of the genus Jatropha L. of the family Euphorbiaceae, viz., J. curcas L., J podagrica Hook. and J gossypifolia L., was studied with scanning electron microscope (SEM). The first sepal primordium is initiated in non-median abaxial position and the second one in median adaxial position. Five sepal primordia arise in a 2/5 sequence on the periphery of the floral apex and are initiated anticlockwise or clockwise in different floral buds of the same species. Five petal primordia initiate simultaneously. There are dicyclic stamens in male flowers with the outer whorl of stamens opposite to the petals (obdiplostemony) and inner whorl opposite to the sepals. Two types of stamen development exist in the genus. In J curcas, belonging to subgen. Curcas, five stamen primordia of the outer whorl arise simultaneously at first and then five of the inner whorl initiate simultaneously. In J podagrica and J gossypifolia, belonging to subgen. Jatropha, eight to nine stamen primordia of the two whorls arise simultaneously. In the female flowers, three carpel primordia appear simultaneously. The flowers of these three species are unisexual. In the female flowers, the ovary bulges and the stamens degenerate, whereas in the male flowers, the stamens grow normally but the ovary is absent. The division of the genus with subgenera is supported by the stamen development.
TL;DR: The aim of this study is to settle its true identity and to update the description and the literature history of M. aurantiaca from 1893 to the present.
Abstract: Since the initial description, the name Musa aurantiaca Baker (1893) has been unclear to most botanists. The aim of this study is to settle its true identity and to update the description. The plant is distributed in the regions of Upper Assam and Arunachal Pradesh, India, Northern Myanmar and Tibet, China where it occurs commonly but it is not mentioned in Chinese literature at all. In this paper, the authors also review the description and the literature history of M. aurantiaca from 1893 to the present. Musa aurantiaca Baker is typified here.
TL;DR: It is shown that ants of Formicidae, Leptothoras sp.
Abstract: Ant-plant interaction is widespread, common and diverse in terrestrial ecosystems, but ants acting as pollinators are uncommon. Here we present a study conducted in Huanglong Nature Reserve, Sichuan, China, showing that ants of Formicidae, Leptothoras sp. and Paratrechina sp., are principle pollinators of Neottia listeroides (Orchidaceae). The two ant species accounted for dominant floral visitors and transferred most pollinia in the orchid, compared to the role of other insect visitors. The flowering period of N. listeroides in the studied population lasted about 40 days, and most flowers were open from 15th to 26th July. The flower has an open nectariferous furrow on the surface of the labellum which ran down the centre to the bifurcation of the labellum, and produced the minute amount of nectar. While an ant arrived at the base of the labellum following the nectariferous furrow, it could not touch the crest of the rostellum and withdraw the pollinia until it raised its head upwards. Pollinia were often attached to the top of the ant head by the viscid fluid exuded from the touched crest of the rostellum. After being touched the rostellum bent down instantly and blocked the stigma, and then slowly recovered to its original position. The backward movement of the rostellum lasted 17–24 h (21.4±2.1 h, n=42). The temporary inaccessibility of the stigma decreased self-pollination resulting from revisiting of ants. Breeding system experiments showed that this orchid is self-compatible but not autogamous, and that pollination success was dependent on pollinators. The fruit set was 19.77% under natural conditions, indicating that the efficiency of this ant-pollination system is low relative to the high frequency of visitation of ants. The low pollination success of N. listeroides was considered as a result of poor match in morphology between flowers and ants. Moreover, the interaction between N. listeroides and these two ants in Huanglong Valley was suggested as a casual case in a specific period.
TL;DR: Sequences of the nuclear nitrate reductase (Nia) were used to test the naturalness of the two genera of Coryloideae, indicating that Carpinus is paraphyletic, and Ostrya has evolved from within Car pinus.
Abstract: Coryloideae consists of four genera: Corylus, Ostryopsis, Carpinus, and Ostrya. While both molecular and non-molecular data support the close relationship of Carpinus and Ostrya, the monophyly of the two genera has remained controversial. In this study, sequences of the nuclear nitrate reductase (Nia) were used to test the naturalness of the two genera. Ostrya species form a robust clade, supporting the monophyly of the genus. The clade, however, is located between Carpinus cordata and the remaining species of Carpinus, indicating that Carpinus is paraphyletic, and Ostrya has evolved from within Carpinus. Within Carpinus, section Distegocarpus is polyphyletic, whereas section Carpinus is a clade where subsections Polyneurae and Carpinus are more closely related to each other than either is to subsection Monbeigianae.
TL;DR: An origin for the vertebrate meiotic SMC1 in the most recent common ancestor since the divergence from invertebrate animals is supported and the analysis indicates that the SMC paralogs have been stably maintained at very low copy numbers, even after segmental (genome-wide) duplications.
Abstract: Members of the Structural Maintenance of Chromosome (SMC) family have long been of interest to molecular and evolutionary biologists for their role in chromosome structural dynamics, particularly sister chromatid cohesion, condensation, and DNA repair. SMC and related proteins are found in all major groups of living organisms and share a common structure of conserved N and C globular domains separated from the conserved hinge domain by long coiled-coil regions. In eukaryotes there are six paralogous proteins that form three heterodimeric pairs, whereas in prokaryotes there is only one SMC protein that homodimerizes. From recently completed genome sequences, we have identified SMC genes from 34 eukaryotes that have not been described in previous reports. Our phylogenetic analysis of these and previously identified SMC genes supports an origin for the vertebrate meiotic SMC1 in the most recent common ancestor since the divergence from invertebrate animals. Additionally, we have identified duplicate copies due to segmental duplications for some of the SMC paralogs in plants and yeast, mainly SMC2 and SMC6, and detected evidence that duplicates of other paralogs were lost, suggesting differential evolution for these genes. Our analysis indicates that the SMC paralogs have been stably maintained at very low copy numbers, even after segmental (genome-wide) duplications. It is possible that such low copy numbers might be selected during eukaryotic evolution, although other possibilities are not ruled out.