Phylogeny and biogeography of Chinese and Australasian Polystichum ferns as inferred from chloroplast trnL-F and rps4-trnS sequence data

Polystichum, one of the largest genera of ferns, occurs worldwide with the greatest diversity in southwest China and adjacent regions. Although there have been studies of Chinese Polystichum on its traditional classification, geographic distributions, and even a few on its molecular systematics, its relationships to other species outside China remain little known. Here, we investigated the phylogeny and biogeography of the Polystichum species from China and Australasia. The evolutionary relationships among 42 Polystichum species found in China (29 taxa) and Australasia (13 taxa) were inferred from phylogenetic analyses of two chloroplast DNA sequence data sets: rps4-trnS and trnL-F intergenic spacers. The divergence time between Chinese and Australasian Polystichum was estimated. The results indicated that the Australasian species comprise a monophyletic group that is nested within the Chinese diversity, and that the New Zealand species are likewise a monophyletic group nested within the Australasian species. The divergence time estimates suggested that Chinese Polystichum migrated into Australasia from around 40 Ma ago, and from there to New Zealand from about 14 Ma. The diversification of the New Zealand Polystichum species began about 10 Ma. These results indicated that Polystichum probably originated in eastern Asia and migrated into Australasia: first into Australia and then into New Zealand.     

The mycorrhizal status of Welwitschia mirabilis

This is the first report of the mycorrhizal status of Welwitschia mirabilis, a gymnosperm endemic to the Namib Desert. Like all other gymnosperms except the Pinaceae and Gnetaceae, W. mirabilis is associated with vesicular-arbuscular mycorrhizal (VAM) fungi. Mycorrhizal colonization of roots and the diversity and abundance of VAM species were determined at seven sites. Six sites received annual rainfall of 0–100 mm, varying widely from year to year. The seventh site experienced more predictable annual rainfall of 150–200 mm. Perennial vegetation was sparse at the six low-rainfall sites. Dry annual grasses from previous rain events were present at only three of these six sites and mean mycorrhizal colonization levels of W. mirabilis at these three sites were as high as 18%. W. mirabilis was not mycorrhizal at sites where grasses were absent. The seventh site, receiving higher rainfall, supported small trees and annual grasses in addition to W. mirabilis. Mycorrhizal colonization levels of W. mirabilis at this site were significantly higher than at the other six sites, closely paralleling those of the surrounding annual grasses. The mycorrhizal flora of W. mirabilis consisted of four Glomus species. These taxa were not unique to W. mirabilis, having been found with Stipagrostis and Cladoraphis grasses throughout the Namib and Kalahari deserts.     

Within-population variation in localized and integrated responses of Trifolium repens to biotically patchy environments

Summary Genets of Trifolium repens (white clover) were collected from three patches of old permanent pasture dominated by Agrostis capillaris, Holcus lanatus or Lolium perenne. Plants derived from the genets were grown with plants of one grass species present on one side of each T. repens, and a different grass species on the other side, in all combinations of two of the three grasses. Different modules (a node with its associated internode, leaf, and axillary bud) on the same clover plant responded independently to the microenvironment provided by their own neighbouring grasses. In contrast, all apical meristems on the plant reacted similarly, showing a unified response and integrating the effects of the different microenvironments experienced by the whole clover plant. This is consistent with what is known both physiologically about the nutrition of meristems and modules, and ecologically about the exploratory growth habit of the species. Averaged over all associated grasses, there was no significant variation in the final dry weight of the different clover genets but these differed in their growth habit response to different grasses. In response to Agrostis as a neighbour, each meristem of T. repens rapidly produced many small modules. New modules were produced more slowly and were larger when Holcus or Lolium was the neighbour. The same pattern of differences occurred among clovers sampled from different backgrounds. Either genetic differences paralleled plastic responses, or plastic changes in phenotype that developed in response to different neighbours in the field persisted in the greenhouse. Plants taken from backgrounds of different grass species showed different responses to growing with those grass species. The differences were manifest primarily in a positive leading diagonal effect of Holcus or not-Holcus. They were the result primarily of differences in the dry weight per module and the probability of development of the axillary bud into a branch. This confirms earlier results, and implicates the central importance of branching as a means of local response to the microenvironment.     

The nucleotide sequence of five ribosomal protein genes from the cyanelles ofCyanophora paradoxa: Implications concerning the phylogenetic relationship between cyanelles and chloroplasts

Summary The nucleotide sequences of the ribosomal protein genesrps18, rps19, rpl2, rpl33, and partial sequence ofrpl22 from cyanelles, the photosynthetic organelles of the protistCyanophora paradoxa, have been determined. These genes form two clusters oriented in opposite and divergent directions. One cluster contains therpl33 andrps18 genes; the other contains therpl2, rps19, andrpl22 genes, in that order. Phylogenetic trees were constructed from both the DNA sequences and the deduced protein sequences of cyanelles,Euglena gracilis and land plant chloroplasts, andEscherichia coli, using parsimony or maximum likelihood methods. In addition, a phylogenetic tree was built from a distance matrix comparing the number of nucleotide substitutions per site. The phylogeny inferred from all these methods suggests that cyanelles fall within the chloroplast line of evolution and that the evolutionary distances between cyanelles and land plant chloroplasts are shorter than betweenE. gracilis chloroplasts and land plant chloroplasts.     

Germination and seed water status of four grasses on moss-dominated biological soil crusts from arid lands

Biological soil crusts dominated by drought-tolerant mosses are commonly found through arid and semiarid steppe communities of the northern Great Basin of North America. We conducted growth chamber experiments to investigate the effects of these crusts on the germination of four grasses: Festuca idahoensis, Festuca ovina, Elymus wawawaiensis and Bromus tectorum. For each of these species, we recorded germination time courses on bare soil and two types of biological soil crusts; one composed predominantly of the tall moss Tortula ruralis and the other dominated by the short moss Bryum argenteum. On the short-moss crust, the final germination percentage was about half of that on bare soil. Also, the mean germination time was 4 days longer on short-mosses than on bare soil. In contrast to the short-moss crust, the tall-moss crust did not reduce the final germination percentage but increased the mean germination time. Similar results were observed in the four grasses studied. To investigate the mechanism by which moss crusts affected germination, we analyzed the water status of seeds on bare soil and moss crusts. Six days after seeding, the water content of seeds on bare soil was approximately twice that of seeds on tall- or short-moss crust. Analysis of the time course of changes in seed weight and water potential in Bromus tectorum revealed that overtime seeds on tall mosses reached higher water content than those on short mosses. The increase in the water content of seeds on tall mosses occurred as the seeds gradually fell through the moss canopy. Taken together, our results indicate that biological soil crusts with distinct structural characteristics can have different effects on seed germination. Furthermore, this study revealed that a biological soil crust dominated by short mosses had a negative effect on seed water status and significantly reduced seed germination.     

Phylogeny of Chinese <Emphasis Type="Italic">Polystichum</Emphasis> (Dryopteridaceae) based on chloroplast DNA sequence data (<Emphasis Type="Italic">trnL-F</Emphasis> and <Emphasis Type="Italic">rps4-trnS</Emphasis>)

Polystichum is one of the largest and most taxonomically complex fern genera in China. The evolutionary relationships of Chinese Polystichum and related genera, and the relationship between our Polystichum phylogeny and ecogeographic distribution, were tested by the use of DNA sequence data. Fifty-one species of Polystichum and 21 species in allied genera were sequenced for the plastid intergenic spacers rps4-trnS and trnL-F. Maximum parsimony and Bayesian phylogenetic analyses of both individual and combined data sets showed that Chinese Polystichum as commonly recognized was paraphyletic: one clade (the CCPC clade) included Cyrtomidictyum lepidocaulon, two Cyrtogonellum species, three Cyrtomium species, and a small number of Polystichum species usually occurring on limestone. A second clade, Polystichum sensu stricto, included the remainder of the Polystichum species; these often occur on non-limestone substrates. The remaining Cyrtomium species formed the third clade. Three subclades resolved within Polystichum sensu stricto (s.s.) clade do not correspond with recent sectional classifications, and we outline the issues relevant to a new classification for the genus. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Molecular phylogeny of Armillaria from the Patagonian Andes

A number of species in the plant pathogen genus Armillaria are known from South America where they cause root rot disease on a wide variety of hosts. Knowledge pertaining to phylogenetic relationships of these species with those of other Armillaria species is almost non-existent. In addition, very few cultures representing these species are available, making DNA-based phylogenetic analyses impossible. The aim of this study was to characterise a collection of Armillaria isolates from the Patagonian Andes using DNA sequences and to determine their phylogenetic relationships with other Armillaria species. DNA sequences were obtained from the internal transcribed regions (ITS1, 5.8S and ITS4) and ribosomal large subunit (LSU) gene and used in phylogenetic analyses. Phylogenetic trees generated from the sequences separated the Armillaria isolates into four lineages. Lineages I and II represented A. novae-zelandiae and A. luteobubalina, respectively. Isolates belonging to A. novae-zelandiae from Malaysia, New Zealand, Australia and South America showed considerable intra-clade sub-structure. Lineages III and IV are probably distinct species and are most closely related to A. hinnulea and an unnamed species isolated from New Zealand and Kenya. This is the first comprehensive study of the phylogenetic relationships of Armillaria species from Patagonia and it provides a foundation for future research in this region.     

青藏高原东缘林线杜鹃-岷江冷杉原始林的空间格局

为深入理解高山林线原始林中优势树种的空间结构特征和种间关系,以青藏高原东缘林线杜鹃-岷江冷杉原始林1 hm²样地调查数据为基础,采用成对相关函数g(r)函数,分析了优势种岷江冷杉(Abies faxoniana)和凝毛杜鹃(Rhododendron agglutinatum)各径级的空间分布格局和各径级间的空间关联性。结果表明:岷江冷杉和凝毛杜鹃径级分布连续,呈倒"J"型,均为进展种群。小尺度上,对于岷江冷杉活立木(小树+中树+大树)、小树、中树为显著聚集分布,大树为均匀分布,死树则为随机分布;凝毛杜鹃活立木(小树+中树+大树)、小树、中树、大树、死树均为显著聚集分布。小尺度上随径级增大岷江冷杉的分布格局从聚集分布趋于均匀分布。岷江冷杉大树与其小树的空间关联验证了Janzen-Connell假说中的距离制约效应。通过验证接受了随机死亡假说,发现种内的密度制约效应不明显。两个树种的枯立木对凝毛杜鹃小树均表现为排斥关系,而对岷江冷杉小树表现为相互独立的关系。两个优势种总体表现为相互独立,但种间不同径级间的空间关联性各异。     

<Emphasis Type="Italic">Lecomtedoxa plumosa</Emphasis> (Sapotaceae), a new tree species from Korup National Park,Cameroon

Summary   Lecomtedoxa plumosa Burgt (Sapotaceae), a new tree species from the southern part of Korup National Park in Cameroon, is described and illustrated. The flowers show the characteristics of the genus Lecomtedoxa: for example the staminodes are free and placed alternately to the stamens and corolla lobes. The leaves of the new species are clearly different from other Lecomtedoxa spp., but they look similar to the leaves of Gluema ivorensis, especially to those of the collections from Cameroon. In total 26 trees ≥ 10 cm dbh were found. The largest trees found were 36 m high and 74 cm dbh. The trees grow in primary rain forest, in clusters of up to 10 trees on 2 ha, mixed with many other tree species. The seed dispersal is ballistic. The conservation status of the species is assessed as Endangered, EN D.     

Host plants of someRhinanthoideae (Scrophulariaceae) of eastern North America

Twenty three species in 11 genera were examined in the field to determine hosts. OnlyStriga asiatica andSeymeria cassioides have a narrow host range being restricted to grasses and pines, respectively. These are the only species which cause pronounced and sometimes serious host damage. The other species attach to a great diversity of hosts.     

Roots,soil water and crop yield: tree crop interactions in a semi-arid agroforestry system in Kenya

Variations in soil water, crop yield and fine roots of 3–4 year-old Grevillea robusta Cunn. and Gliricidia sepium (Jacq.) Walp. growing in association with maize (Zea mays L.) were examined in semiarid Kenya during the long rains of 1996 and 1997. Even although tree roots penetrated more deeply than maize roots, maximum root length densities for both tree species and maize occurred in the top 200 mm of the soil profile where soil moisture was frequently recharged by rains. Populations of roots in plots containing trees were dominated by tree roots at the beginning of the growing season but because tree roots died and maize root length increased during the cropping season, amounts of tree and maize roots were similar at the end of the season. Thus, there was evidence of temporal separation of root activity between species, but there was no spatial separation of the rooting zones of the trees and crops within that part of the soil profile occupied by crop roots. Tree root length density declined with increasing distances from rows of trees and with depth in the soil profile. Although Grevillea trees were largest, plots containing G. sepium trees always contained more tree roots than plots containing G. robusta trees and Gliricidia was more competitive with maize than Grevillea. Overall, Gliricidia reduced crop yield by about 50% and Grevillea by about 40% relative to crop yield in control plots lacking trees and reductions of crop yield were greatest close to trees. There was less soil moisture in plots containing trees than in control plots. Such difference between control plots and plots containing trees were maximal at the end of the dry season and there was always less soil moisture close to trees than elsewhere in the plots. Plots containing Gliricidia trees contained less soil water than plots containing Grevillea trees.     

Multi-proxy evidence for competition between savanna woody species

Coexistence of trees and grasses in savannas should be possible if competition between the woody and the grassy components is less intense than the competition within each component. Although several studies have investigated competition between trees and grasses, little is known about tree–tree interactions. We used a multi-proxy approach to examine the spatial pattern of Acacia mellifera and other savanna woody species in a semi-arid savanna in South Africa. Spatial analysis of the point patterns of young and reproductively mature shrubs detected decreasing aggregation with size/age over all spatial scales. This indicated the prevalence of competition although the overall spatial shrub pattern was aggregated. In contrast to point pattern statistics that detect changes only when competition has led to the death of the inferior competitor, we also applied methods identifying the competitive effect on sizes of individual trees. Competition should lead to a negative spatial autocorrelation in size, which we observed in half of the studied cases. Quantile regressions show that nearest-neighbour distance increased steeply with combined size of the target shrub and its neighbours indicating strong competitive effects. The medians of the distributions of maximum root lengths of A. mellifera, of the scale of regular patterns, and of negative autocorrelations were not significantly different, suggesting that overlapping root systems mediate competitive interactions. A competitor removal experiment did not lead to increased shrub sizes, which may be due to the limited duration of the experiment. From the nearest neighbour and autocorrelation analyses, we conclude that competition had a strong impact on growth rates of savanna woody species. Competition-induced mortality only becomes obvious when analysing the shift towards less aggregated spatial patterns when shrubs become reproductively mature. As the overall clustered spatial pattern masks the perceptible effect of competition, a time component should always be included in spatial pattern-based inference of competition.     

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     

Occurrence of the marbled rose-chafer (Protaetia lugubris Herbst, Coleoptera, Cetoniidae) in rural avenues in northern poland

The occurrence of Protaetia lugubris, an endangered species developing in hollow trees, was studied in a network of rural avenues in northern Poland. We detected 1002 trees from nine species with hollows suitable for beetle development (25% of all trees inspected). Among them, 74 trees (7.4%) from seven species were occupied by P. lugubris. The distribution of P. lugubris was random with respect to tree species identity. The beetle preferred trees above 200 cm in circumference with a tendency towards higher occupancies of the bigger trees having circumferences above 300 cm. P. lugubris did not show any significant preferences according to hollow entrance area, exposition and road surface type. Our results indicate that P. lugubris is a generalist species colonizing all suitable hollows. Its occurrence indicates suitable conditions for many other species associated with tree cavities and decaying wood.     

Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s.s.

The taxonomy of Bambusoideae is in a state of flux and phylogenetic studies are required to help resolve systematic issues. Over 60 taxa, representing all subtribes of Bambuseae and related non-bambusoid grasses were sampled. A combined analysis of five plastid DNA regions, trnL intron, trnL-F intergenic spacer, atpB-rbcL intergenic spacer, rps16 intron, and matK, was used to study the phylogenetic relationships among the bamboos in general and the woody bamboos in particular. Within the BEP clade (Bambusoideae s.s., Ehrhartoideae, Pooideae), Pooideae were resolved as sister to Bambusoideae s.s. Tribe Bambuseae, the woody bamboos, as currently recognized were not monophyletic because Olyreae, the herbaceous bamboos, were sister to tropical Bambuseae. Temperate Bambuseae were sister to the group consisting of tropical Bambuseae and Olyreae. Thus, the temperate Bambuseae would be better treated as their own tribe Arundinarieae than as a subgroup of Bambuseae. Within the tropical Bambuseae, neotropical Bambuseae were sister to the palaeotropical and Austral Bambuseae. In addition, Melocanninae were found to be sister to the remaining palaeotropical and Austral Bambuseae. We discuss phylogenetic and morphological patterns of diversification and interpret them in a biogeographic context.     

Extensive Reorganization of the Plastid Genome of <Emphasis Type="Italic">Trifolium subterraneum</Emphasis> (Fabaceae) Is Associated with Numerous Repeated Sequences and Novel DNA Insertions

The plastid genome of Trifolium subterraneum is 144,763 bp, about 20 kb longer than those of closely related legumes, which also lost one copy of the large inverted repeat (IR). The genome has undergone extensive genomic reconfiguration, including the loss of six genes (accD, infA, rpl22, rps16, rps18, and ycf1) and two introns (clpP and rps12) and numerous gene order changes, attributable to 14–18 inversions. All endpoints of rearranged gene clusters are flanked by repeated sequences, tRNAs, or pseudogenes. One unusual feature of the Trifolium subterraneum genome is the large number of dispersed repeats, which comprise 19.5% (ca. 28 kb) of the genome (versus about 4% for other angiosperms) and account for part of the increase in genome size. Nine genes (psbT, rbcL, clpP, rps3, rpl23, atpB, psbN, trnI-cau, and ycf3) have also been duplicated either partially or completely. rpl23 is the most highly duplicated gene, with portions of this gene duplicated six times. Comparisons of the Trifolium plastid genome with the Plant Repeat Database and searches for flanking inverted repeats suggest that the high incidence of dispersed repeats and rearrangements is not likely the result of transposition. Trifolium has 19.5 kb of unique DNA distributed among 160 fragments ranging in size from 30 to 494 bp, greatly surpassing the other five sequenced legume plastid genomes in novel DNA content. At least some of this unique DNA may represent horizontal transfer from bacterial genomes. These unusual features provide direction for the development of more complex models of plastid genome evolution. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Generation of transgenic Lolium temulentum plants by Agrobacterium tumefaciens-mediated transformation

Lolium temulentum L. (Darnel ryegrass) has been proposed to be used as a model species for functional genomics studies in forage and turf grasses, because it is a self-fertile, diploid species with a short life cycle and is closely related to other grasses. Embryogenic calluses were induced from mature embryos of a double haploid line developed through anther culture. The calluses were broken up into small pieces and used for Agrobacterium tumefaciens-mediated transformation. A. tumefaciens strain EHA105 harboring pCAMBIA1301 and pCAMBIA1305.2 vectors were used to infect embryogenic callus pieces. Hygromycin was used as a selection agent in stable transformation experiments. Hygromycin resistant calluses were obtained after 4–6 weeks of selection and transgenic plants were produced in 10–13 weeks after Agrobacterium-mediated transformation. Fertile plants were readily obtained after transferring the transgenics to the greenhouse. Transgenic nature of the regenerated plants was demonstrated by Polymerase chain reaction (PCR), Southern hybridization analysis, and GUS staining. Progeny analysis showed Mendelian inheritance of the transgenes. The transformation system provides a valuable tool for functionality tests of candidate genes in forage and turf grasses.     

Occurrence of Larca lata H.J. Hansen (Pseudoscorpionida: Garypidae) and Allochernes wideri C.L. Koch (Pseudoscorpionida: Chernetidae) in tree hollows in relation to habitat quality and density

Many beetles associated with old trees are on national red lists, but pseudoscorpions living in similar habitats have received little attention. This study reports the habitat and occurrence patterns of two species of pseudoscorpions living in hollow trees. Their occurrence has been assessed by sieving wood mould from 274 oaks in southeastern Sweden and from museum specimens collected in Sweden. Larca lata is confined to hollow oaks with a large girth and a plentiful supply of wood mould. Allochernes wideri is much less particular about wood mould volume, trunk diameter and tree species. Larca lata inhabits hollow trunks with characteristics that are typical of very old trees, whereas A. wideri predominantly occurs in trunks in an earlier stage of hollow formation. Larca lata was almost exclusively found in larger assemblages of hollow oaks, which suggests long-term survival may be difficult when the network of suitable hollow trees is too sparse. Larca lata is a rare species in Europe and probably vulnerable to extinction, since it is dependent on a habitat which has declined severely in the last few centuries.