Effect of a gap on gene flow between otherwise adjacent transgenic <Emphasis Type="Italic">Brassica napus</Emphasis> crops

The chloroplast DNA diversity of 33 accessions belonging to 16 species of five sections in Allium subgenus Rhizirideum was studied by analysing the sequence of three fragments: the trnL-F intergenic spacer, the rps 16 intron and rbcL (rubisco large subunit). The three sections Cepa, Schoenoprasum and Rhizirideum, representing the majority of the included species, each possess a separate clade after phylogenetic analysis. Exceptions to this general rule are the placement of Allium pskemense (section Cepa) connected to Allium senescens (section Rhizirideum) and Alium roylei, taking an intermediate position between sections Cepa and Schoenoprasum. Both species were located in their own section after nuclear DNA analysis. A range of crossing experiments has been carried out. The different position of A. roylei when comparing cpDNA and nDNA diversity was not confirmed with the production of hybrid seeds after crossing A. roylei with species other than those of section Cepa. The different position of A. pskemense in the cpDNA and the nDNA tree can not be compared to its crossability, since only a few crossing experiments are reported for this species. The hypothesis that a shorter distance between two species in a cpDNA tree compared to their distance in a nDNA tree will indicate interfertility at a certain level, is neither confirmed nor rejected by the currently available results.Communicated by R. Hagemann     

Incongruence among mitochondrial,chloroplast and nuclear gene trees in <Emphasis Type="Italic">Pinus</Emphasis> subgenus <Emphasis Type="Italic">Strobus</Emphasis> (Pinaceae)

Introgression has been considered to be one of main factors leading to phylogenetic incongruence among different datasets at lower taxonomic levels. In the plants of Pinaceae, the mtDNA, cpDNA, and nuclear DNA (nrDNA) may have different evolutionary histories through introgression because they are inherited maternally, paternally and biparentally, respectively. We compared mtDNA, cpDNA, and two low-copy nrDNA phylogenetic trees in the genus Pinus subgenus Strobus, in order to detect unknown past introgression events in this group. nrDNA trees were mostly congruent with the cpDNA tree, and supported the recent sectional and subsectional classification system. In contrast, mtDNA trees split the members of sect. Quinquefoliae into two groups that were not observed in the other gene trees. The factors constituting incongruence may be divided into the following two categories: the different splits within subsect. Strobus, and the non-monophyly of subsect. Gerardianae. The former was hypothesized to have been caused by the past introgression of cpDNA, mtDNA or both between Eurasian and North American species through Beringia. The latter was likely caused by the chimeric structure of the mtDNA sequence of P. bungeana, which might have originated through past hybridization, or through a horizontal transfer event and subsequent recombination. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Phylogeny of <Emphasis Type="Italic">Litsea</Emphasis> and related genera (Laureae-Lauraceae) based on analysis of <Emphasis Type="Italic">rpb2</Emphasis> gene sequences

The relationship between Litsea and related genera is currently unclear. Previous molecular studies on these taxa using cpDNA and nrITS were unable to produce well-resolved phylogenetic trees. In this study, we explored the potential of the rpb2 gene as a source of molecular information to better resolve the phylogenetic analysis. Although rpb2 was believed to be a single-copy gene, our cloning results showed that most species examined possessed several copies of these sequences. However, the genetic distance among copies from any one species was low, and these copies always formed monophyletic groups in our molecular trees. Our phylogenetic analyses of rpb2 data resulted in better resolved tree topologies compared to those based on cpDNA or nrITS data. Our results show that monophyly of the genus Litsea is supported only for section Litsea. As a genus, Litsea was shown to be polyphyletic. The genera Actinodaphne and Neolitsea were resolved as monophyletic groups in all analyses. They were also shown to be sisters and closer to the genus Lindera than to the genus Litsea. Our results also revealed that the genus Lindera is not a monophyletic group.     

Chloroplast DNA phylogeography of <Emphasis Type="Italic">Pedicularis</Emphasis> ser. <Emphasis Type="Italic">Gloriosae</Emphasis> (Orobanchaceae) in Japan

Phylogeographic analyses using chloroplast DNA (cpDNA) variation were performed for Pedicularis ser. Gloriosae (Orobanchaceae). Eighty-one plants of 18 populations of 6 species (P. gloriosa, P. iwatensis, P. nipponica, P. ochiaiana, P. sceptrum-carolinum and P. grandiflora) were analyzed. Fifteen distinct haplotypes were identified based on six cpDNA regions: the intergenic spacer between the trnT and trnL 3′exon, trnL 3′exon-trnF, atpB-rbcL, accD–psaI, the rpl16 intron and the trnK region (including the matK gene). Via phylogenetic analyses of the haplotypes, two continental species, P. sceptrum-carolinum and P. grandiflora, were placed at the most ancestral position in the trees. The former species is widely distributed in the Eurasian continent, and the latter is distributed in Far East Asia. Two robust major cpDNA clades (clades I and II) were revealed in the Japanese archipelago, although the statistical values of monophyly of these clades were weak. Clade I included the haplotypes (A-1, A-2, B-1, B-2 and J) of three species (P. gloriosa, P. iwatensis and P. ochiaiana), and Clade II included seven haplotypes (C-D, E-1, E-2 and F-H) of P. nipponica. These results suggest that this series originated on the Eurasian continent and that subsequently populations at the eastern edge of the continent differentiated into the two Japanese lineages. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Phylogeography and conservation genetics of Hygrophila pogonocalyx (Acanthaceae) based on atpB–rbcL noncoding spacer cpDNA

Genetic variation in the atpB–rbcL intergenic spacer region of chloroplast DNA (cpDNA) was investigated in Hygrophila pogonocalyx Hayata (Acanthaceae), an endangered and endemic species in Taiwan. In this aquatic species, seed dispersal from capsules via elasticity is constrained by gravity and is thereby confined within populations, resulting in limited gene flow between populations. In this study, a total of 849 bp of the cpDNA atpB–rbcL spacer were sequenced from eight populations of H. pogonocalyx. Nucleotide diversity in the cpDNA is low (=0.00343±0.00041). The distribution of genetic variation among populations agrees with an isolation-by-distance model. Two geographically correlated groups, the western and eastern regions, were identified in a neighbor-joining tree and a minimum-spanning network. Phylogeographical analyses based on the cpDNA network suggest that the present-day differentiation between western and eastern groups of H. pogonocalyx resulted from past fragmentation. The differentiation between eastern and western populations may be ascribed to isolation since the formation of the Central Mountain Range about 5 million years ago, which is consistent with the rate estimates based on a molecular clock of cpDNA.Huang JC and Wang WK equally contributed to this work.     

Phylogeny of the Madagascan endemic family Didiereaceae

A molecular phylogeny of the Didiereaceae was produced through parsimony analysis of chloroplastrpl16 intron andtrnL-trnF andtrnT-trnL intergenic spacer sequences of all eleven species of the Didiereaceae and several outgroup taxa from the Portulacaceae. Results indicated that: 1) the Didiereaceae were embedded within the Portulacaceae, withCalyptrotheca as the sister group of the family; 2) present generic limits were supported; 3)Alluaudiopsis was the most basal lineage; 4) at least two separate episodes of polyploidization within the genusAlluaudia had occurred, and 5) unusually low amounts of variation were present in rapidly evolving noncoding plastid sequences.     

Molecular phylogeny ofIva (Asteraceae,Heliantheae) based on chloroplast DNA restriction site variation

Iva s.str. (comprising ten species) was examined by cpDNA restriction site variation to determine phyletic relationships within the group. The results were compared with relationships proposed from other data. A total of 86 restriction site mutations was detected, 47 of which proved phylogenetically informative. A single most parsimonious tree was obtained using both Wagner and Dollo parsimony. The tree revealed three main lineages that are congruent with the three chromosome lineages (base numbers of x = 16, 17, 18). The monophyly of the x = 16 and 18 groups was supported strongly by molecular data, while the monophyly of x = 17 lineage was only supported moderately. Relationships among the three lineages indicate that the sect.Iva is paraphyletic because sect.Linearbractea is nested within it. Both morphological data and the secondary chemical data are in agreement with the proposed cpDNA phylogeny. Because of this agreement, sect.Iva is revised such that,I. axillaris was excluded and positioned within the newly proposed sect.Rhizoma. Patterns and rates of cpDNA evolution were also examined. The results indicated an uneven evolution in the chloroplast genome with different rates of cpDNA evolution in at least a few species ofIva. However, the evolutionary clock hypothesis can not be rejected within most of the lineages inIva.     

Speciation process of <Emphasis Type="Italic">Salvia isensis</Emphasis> (Lamiaceae), a species endemic to serpentine areas in the Ise-Tokai district,Japan, from the viewpoint of the contradictory phylogenetic trees generated from chloroplast and nuclear DNA

To understand the speciation process of Salvia isensis (Lamiaceae), a species endemic to a special environment (serpentine areas in the Ise-Tokai district, central Honshu, Japan), chloroplast DNA (cpDNA) and nuclear ribosomal DNA (nrDNA) were employed to analyze the phylogenetic relationships of S. isensis with related species in Japan. Allozymic polymorphisms were also used to analyze genetic relationships among Salvia species. A contradiction in the phylogenetic positions of species studied was detected when phylogenetic trees were constructed using cpDNA or nrDNA, i.e., S. isensis was a sister to the other species in phylogenetic trees generated from cpDNA, while S. japonica was a sister to the other species in the case of nrDNA. Genetic relationships between Salvia species estimated from allozymic polymorphisms did not contradict to the topology for nrDNA. Using the present results, the speciation process of S. isensis is discussed with regard to introgressive gene exchanges between related species. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

New species of <Emphasis Type="Italic">Eugenia</Emphasis> sect. <Emphasis Type="Italic">Racemosae</Emphasis> (Myrtaceae) from Brazilian Amazon Rainforest

Summary  The new species Eugenia pallidopunctata, E. caducibracteata, E. tenuiflora and E. breviracemosa from the Brazilian Amazon, all belonging to Eugenia sect. Racemosae (Myrtaceae), are described, illustrated and compared with their putative close relatives. Data on the geographic distribution and habitat are given for the new taxa, as well as illustrations.     

Geographic structuring of chloroplast DNA genotypes inTiarella trifoliata (Saxifragaceae)

Tiarella trifoliata comprises varietieslaciniata, trifoliata, andunifoliata, and is distributed from southeastern Alaska to northern California. We analyzed restriction site variation of chloroplast DNA (cpDNA) using 23 endonucleases in 76 populations representing the entire geographic range of the species and the three recognized varieties. We also employed comparative restriction site mapping of PCR-amplified chloroplast DNA fragments using 16 restriction endonucleases. This species exhibits low cpDNA restriction site variation. No differentiation is evident among varieties of this species based on cpDNA data; some plants of each variety were characterized by each of the two major cpDNA types detected. The two major cpDNA clades, which differ by only a single restriction site mutation, are geographically structured. A northern clade comprises populations from Alaska to central Oregon; most populations analyzed from southern Oregon and California form a southern clade. Populations that possess the typical northern cpDNA type also occur disjunctly to the south at high elevations in the Siskiyou—Klamath Mountain area of southern Oregon and northern California. Conversely, the southern cpDNA type is found disjunctly to the north in the Olympic Peninsula of Washington. Both geographic areas characterized by disjunct cytoplasms are considered glacial refugia.Tiarella trifoliata joins two other species,Tolmiea menziesii andTellima grandiflora, in having well-demarcated northern and southern cpDNA lineages. All three species have similar life-history traits and geographic distributions. We suggest that glaciation may have played a major role in the formation of the cpDNA discontinuities present in these three taxa. The pronounced relationship between cpDNA variation and geographic distribution suggests the potential applicability of intraspecific phylogeography to plants via the analysis of intraspecific cpDNA variation. These three examples also join a rapidly growing data base which indicates that cytoplasms are often geographically structured within species and species complexes.     

Phylogeny of Caragana (Fabaceae) based on DNA sequence data from rbcL, trnS–trnG, and ITS

Phylogenetic relationships of 48 species of Caragana (Fabaceae: tribe Hedysareae) and one representative each of Astragalus, Calophaca, Halimodendron, and Hedysarum are estimated from DNA sequences of the rbcL gene, trnS–trnG intron and spacer, and ITS region. At least one representative of all five sections and 12 series within Caragana are included. Analyses yielded strongly supported clades corresponding to sections Caragana, Bracteolatae, and Frutescentes. The species of section Jubatae are distributed among three strongly supported clades, i.e., one with the species of section Bracteolatae, another with two species of section Spinosae, and a third as sister to section Frutescentes. All but the last of these six clades are corroborated by at least one unambiguously traced morphological character. The placement of the other four species of section Spinosae are not well supported and lack unambiguous morphological synapomorphies, and the samples of Calophaca and Halimodendron nest within Caragana with weak support.     

The genus Setulipes (Marasmiaceae) in Madagascar and the Mascarenes, including a key to other African taxa

The authors report first records for the genus Setulipes in Madagascar, with the presence of Setulipes cf. hakgalensis and two new species, Setulipes funaliformis and S. moreaui, as well as a new species from Mauritius: S. mauritiensis. A key to these taxa, as well as to other African species, is supplied.     

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.     

The ontogenetic basis for floral diversity in <Emphasis Type="Italic">Agonis</Emphasis>, <Emphasis Type="Italic">Leptospermum</Emphasis> and <Emphasis Type="Italic">Kunzea</Emphasis> (Myrtaceae)

Floral development in three species each of Leptospermum and Kunzea, and one species of Agonis, is described and compared. Differences in the number of stamens and their arrangement in the flower at anthesis are determined by the growth dynamics of the bud. In Leptospermum, early expansion of the bud is predominantly in the axial direction and causes the stamen primordia to be initiated in antepetalous chevrons. In Kunzea, early expansion occurs predominantly in the lateral direction and successive iterations of stamen primordia are inserted alternately at more or less the same level. In both genera, further expansion in the lateral plane spreads the stamens into a ring around the hypanthium. Agonis flexuosa is similar to Leptospermum. Other variable factors include the timing at which stamen initiation commences (earlier in Leptospermum than Kunzea), the duration of stamen initiation (hence the total number of stamens produced – varies within genera), and very late differential expansion that forces stamens into secondary antesepalous groups in A. flexuosa and L. myrsinoides.The authors thank Dr H. Toelken for kindly providing some material and the impetus for this project. This research was supported by Australian Research Council grant AS19131815.     

IMI与K标本室中生于大戟科植物上链格孢属的种Ⅱ.大戟属,铁苋菜属和守宫木属上的种

本文系作者继大戟属(Euphorbia L.)、守宫木属(Sauropus B1.)和铁苋菜属(Acalypha L.)植物上链格孢属(Alternaria Nees)真菌研究(Zhang, 1995)之后,对生于大戟科(Euphorbiaceae)其它属植物上一些链格孢真菌种级分类单位评鉴结果的后续报道.内容包括:一个新种,巴豆生链格孢(A. croronicola T. Y.Zhang & J. C. David), Macrosporium compactum Cooke:对其模式标本(holotype)进行T订正、巴豆链格孢[A.crotonis kamal,Singh & Kumar]:提出关于新模式(neotype)标本的建议;对蓖麻链格孢[A. ricini(yoshii)Hansford]典型性状作了补充描述.此外,还在大戟科其它一些植物上检查到长极链格孢[A. longissima Deighton et MacGarvie]和细极链格孢[A. tenuissima(Nees ez Fr.) Wiltshire]。     

Characterization of the satellite DNA Msat-160 from the species <Emphasis Type="Italic">Chionomys</Emphasis><Emphasis Type="Italic">nivalis</Emphasis> (Rodentia,Arvicolinae)

The satellite DNA Msat-160 has been previously characterized in several species of the genus Microtus. Here we present the characterization of Msat-160 from Chionomys nivalis, a species with a very primitive karyotype. As in other Microtus species analyzed, C. nivalis Msat-160 is AT rich, has a monomer length of 160 bp, is undermethylated and is mainly located in all the pericentromeric heterochromatin of all autosomes and the X chromosome, but is completely absent from the Y chromosome. Hence, our results support the hypothesis that Msat-160 was initially distributed in the pericentromeric heterochromatin of all autosomes and the X chromosome. The taxonomic status of the genus Chionomys in relation to the genus Microtus is a very interesting issue, so we constructed phylogenetic dendrograms using Msat-160 sequences from several Microtus species. Although the results were not informative about this issue, the presence of Msat-160 in C. nivalis and Microtus species suggested that both genera are closely related and that this satellite DNA was present in the common ancestor. Studies of Msat-160 in different arvicoline species could help to determine the origin of this satellite and, perhaps, to establish the phylogenetic relationships of some arvicoline groups.     

Independent origins of tetraploid cryptic species in the fern <Emphasis Type="Italic">Ceratopteris thalictroides</Emphasis>

Ceratopteris thalictroides (L.) Brongn is a tetraploid fern species that contains at least three cryptic species, the south, the north and the third type. In this study we combined data from both chloroplast DNA (cpDNA) and nuclear DNA sequences of three diploid species and three cryptic species of C. thalictroides to unravel the origin of the cryptic species, particularly of the reticulate relationships among the diploid and tetraploid taxa in the genus Ceratopteris. Of the three diploid species examined, C. cornuta had cpDNA identical to that of the tetraploid third type plants, and this diploid species is a possible maternal ancestor of the tetraploid third type. Analysis of the homologue of the Arabidopsis thaliana LEAFY gene (CLFY1) identified ten alleles in the genus Ceratopteris, with six alleles found in C. thalictroides. The unrooted tree of the CLFY1 gene revealed four clusters. Each cryptic species showed fixed heterozygosity at the CLFY1 locus and had two alleles from different clusters of the CLFY1 tree. Consideration of the cpDNA sequences, CLFY1 genotypes of the cryptic species and CLFY1 gene tree in concert suggested that the cryptic species of C. thalictroides had originated through independent allopolyploidization events involving C. cornuta and two unknown hypothetical diploid species.     

台山含笑，广东木兰科一新种

报道了木兰科（Magnoliaceae）含笑属（Michelia L.）一新种：台山含笑（M. taishanensis Y. H. Tong,X. E. Ye,X. H. Ye & Yu Q. Chen）。该新种目前仅分布于我国广东台山市的北峰山,与广东含笑（M. guangdongensis Y. H. Yan,Q. W. Zeng & F. W. Xing）近缘,但其叶柄更纤细,叶背老时变无毛,雄蕊较多且较长,花丝白色,药隔短小而与后者区别。     

Detection of species within the Xerocomus subtomentosus complex in Europe using rDNA–ITS sequences

Identification of species within the boletoid genus Xerocomus has relied heavily upon the macromorphological features of the basidiomes. However, the phenotypic plasticity of these features has resulted in considerable confusion over the delimitation of taxa. In this study, we examined collections attributed to the X. subtomentosus complex in Europe using morphological and rDNA–ITS sequence data. In total, 45 European collections from a wide range of geographical areas and ecological conditions were included in the study. In spite of detecting considerable genetic variation, even within individual basidiomes of X. subtomentosus, molecular data, spore size, flesh colour, and the colour of the basal mycelium allow for the recognition of four distinct taxa: two correspond to X. subtomentosus (13 collections) and X. ferrugineus (20); one X. chrysonemus sp. nov. (10), to date only found in the UK, is described as new; and the existence of another taxon (two; Italy and UK) is noted but left undescribed owing to lack of material. Eight collections from North America were also included in the study, from which two taxa with a close affinity to X. ferrugineus were recognised.     

History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae)

How Quaternary climatic oscillations affected range distributions and intraspecific divergence of alpine plants on the Qinghai‐Tibetan Plateau (QTP) remains largely unknown. Here, we report a survey of chloroplast DNA (cpDNA) and nuclear ribosomal internal transcribed spacer (ITS) DNA variation aimed at exploring the phylogeographical history of the QTP alpine endemic Aconitum gymnandrum. We sequenced three cpDNA fragments (rpl20–rps12 intergenic spacer, the trnV intron and psbA‐trnH spacer) and also the nuclear (ITS) region in 245 individuals from 23 populations sampled throughout the species’ range. Two distinct lineages, with eastern and western geographical distributions respectively, were identified from a phylogenetic analysis of ITS sequence variation. Based on a fast substitution rate, these were estimated to have diverged from each other in the early Pleistocene approximately 1.45 Ma. The analysis of cpDNA variation identified nine chlorotypes that clustered into two major clades that were broadly congruent in geographical distribution with the two ITS lineages. The east–west split of cpDNA divergence was supported by an amova which partitioned approximately half of the total variance between these two groups of populations. Analysis of the spatial distribution of chlorotypes showed that each clade was subdivided into two groups of populations such that a total of four population groups existed in the species. It is suggested that these different groups derive from four independent glacial refugia that existed during the Last Glacial Maximum (LGM), and that three of these refugia were located at high altitude on the QTP platform itself at that time. Coalescent simulation of chlorotype genealogies supported both an early Pleistocene origin of the two main cpDNA clades and also the ‘four‐refugia’ hypothesis during the LGM. Two previous phylogeographical studies of QTP alpine plants indicated that such plants retreated to refugia at the eastern/south‐eastern plateau edge during the LGM and/or previous glacial maxima. However, the results for A. gymnandrum suggest that at least some of these cold‐tolerant species may have also survived centrally on the QTP platform throughout the Quaternary.