Contrasting patterns of DNA variation in natural populations of two related conifers, Cryptomeria japonica and Taxodium distichum (Cupressaceae sensu lato)

We investigated DNA variation within and between two closely related conifers, Cryptomeria japonica and Taxodium distichum, at nuclear loci encoding ferredoxin, glutamyl-tRNA reductase, lycopene beta cyclase, and phosphoribosylanthranilate transferase. Average nucleotide diversity at silent sites was estimated to be 0.0035 (SE 0.0012) in C. japonica and 0.0058 (SE 0.0006) in T. distichum. One population in C. japonica was differentiated from the others but generally there was not much differentiation among populations or varieties within the two species. However, the two species seemed to differ in frequency spectra of DNA polymorphisms. Excesses of intermediate-frequency variants were found in C. japonica, whereas excesses of both rare and high-frequency variants were found in T. distichum, which suggested different histories of population structures in the two species. Deviations from the standard neutral expectations in DNA polymorphisms were found by applications of neutrality tests. The results show that actions of selection to respective loci seem to differ between the two species, indicating differences of interaction among evolutionary factors.     

Amounts and patterns of nucleotide variation within and between two Japanese conifers, sugi (Cryptomeria japonica) and hinoki (Chamaecyparis obtusa) (Cupressaceae sensu lato)

Sugi (Cryptomeria japonica) and hinoki (Chamaecyparis obtusa) are the most important timber species in Japan. To quantify and compare the level of nucleotide variation in these species, we investigated their variation at ten nuclear loci. Average values of nucleotide diversity at synonymous sites (π _SYN) found in sugi and hinoki were 0.0038 and 0.0069, respectively. However, although the average value of nucleotide diversity was higher in hinoki than in sugi, their average values of haplotype diversity were similar. Deviations from the standard neutral model were detected at two loci in hinoki using Tajima’s D, Fay and Wu’s H, and Strobeck’s S statistics, which seem to be due to its historical population structure. Levels of divergence between the two species at synonymous sites of the ten genes ranged from 0.121 to 0.566 (0.28 on average). These values positively correlated with their guanine + cytosine contents at third-codon positions of synonymous sites (%GC3s).     

Cone and ovule development in Cunninghamia and Taiwania (Cupressaceae sensu lato) and its significance for conifer evolution

We examined the early developmental stages of the seed cones and seeds of two conifer genera, Cunninghamia and Taiwania, using scanning electron microscope (SEM) images of freshly collected material. In recent similar studies, these two taxa were not described. The present paper aims to fill that gap. Both genera appear to have features crucial to the understanding of the evolution of the cupressaceous cone, characteristic of the families Cupressaceae and Taxodiaceae, and provide further evidence for the need to merge these families. These features are: the ovuliferous scale in Cunninghamia develops as a small lobe with each of three ovules; in Taiwania these lobes are absent, but a small ridge could be a vestige of them. In neither of these two genera does an ovuliferous scale develop to maturity and only limited intercalary growth transforms the bracts, of which only their width and final shape distinguishes them from sterile leaves. Thus, the bracts, not the ovuliferous scales, form the mature cone in these two genera. This trend is continued in more derived genera of Cupressaceae. Another key extant taxon that has helped to elucidate the evolution of this type of conifer cone is Sciadopitys; similar studies have already been done on this genus, and we compared our findings to them. We also considered certain fossil Mesozoic conifer cones, which shed further light on the evolution of the cupressaceous cone. The evidence from these various genera strongly indicates that recently reconstructed phylogenies of gymnosperms based on molecular evidence from extant taxa do not reflect the evolution that actually happened. Such studies need to take into account nonmolecular evidence, as detailed here.     

Extended linkage disequilibrium in noncoding regions in a conifer, Cryptomeria japonica

We measured linkage disequilibrium in mostly noncoding regions of Cryptomeria japonica, a conifer belonging to Cupressaceae. Linkage disequilibrium was extensive and did not decay even at a distance of 100 kb. The average estimate of the population recombination rate per base pair was 1.55 × 10(-5) and was <1/70 of that in the coding regions. We discuss the impact of low recombination rates in a large part of the genome on association studies.     

Relationships within Cupressaceae sensu lato: a combined morphological and molecular approach

Parsimony analysis of matK and rbcL sequence data, together with a nonmolecular database, yielded a well-resolved phylogeny of Cupressaceae sensu lato. Monophyly of Cupressaceae sensu stricto is well supported, and separate northern and southern hemisphere subclades are resolved, with Tetraclinis within the northern subclade; there is no support for any of the tribes sensu Li. Taxodiaceae comprise five separate lineages. Chamaecyparis nootkatensis falls within Cupressus, clustering with a robust clade of New World species. Libocedrus Florin is paraphyletic and should incorporate Pilgerodendron. Evolution of several characters of wood and leaf anatomy and chemistry is discussed in light of this estimate of the phylogeny; numerous parallelisms are apparent. A new infrafamilial classification is proposed in which seven subfamilies are recognized: Callitroideae Saxton, Athrotaxidoideae Quinn, Cunninghamioideae (Sieb. & Zucc.) Quinn, Cupressoideae Rich. ex Sweet, Sequoioideae (Luerss.) Quinn, Taiwanioideae (Hayata) Quinn, Taxodioideae Endl. ex K. Koch. The rbcL sequence for Taxodium distichum is corrected, and the implications for a previously published estimate of the minimum rate of divergence of the gene since the Miocene are highlighted.     

Karyomorphology of Maianthemum sensu lato (Polygonatae, Ruscaceae)

We report results of karyotype analyses using nine species of Maianthemum from China. The species, except M. atropurpureum (with 2n=72), had 2n=36, and the results support the earlier suggestion that Maianthemum has x=18 with 2n=36 in most species. The species examined, however, showed marked differences in karyotype, particularly in the numbers of metacentric, submetacentric, and acrocentric chromosomes as well as in the number of satellites. In addition, we distinguished three different modes based on the number of clear gaps in chromosome length variation: unimodal, bimodal, and trimodal. The unimodal variation (with no gap) was found in M. dahuricum and M. atropurpureum, the bimodal variation (with one gap) in M. tatsienense, and the trimodal variation (with two gaps) in M. bifolium, M. forrestii, M. japonicum, M. henryi, M. purpureum, and M. lichiangense. In the trimodal variation, the positions of the two gaps may differ from species to species. In addition, the frequency of acrocentric chromosomes per complement was generally higher in the trimodal variation than in the unimodal and bimodal variations. Results of our analyses, which had not been clearly presented prior to this, may provide a better understanding of species evolution in the tribe Polygonatae.     

Persistence of Beauveria bassiana sensu lato and Metarhizium anisopliae sensu lato in Vermont (USA) forest soil

Persistence of granular formulations of Beauveria bassiana sensu lato, strains GHA726 and ERL1170, and Metarhizium anisopliae sensu lato, strains ERL824 and ERL701, applied to forest soil was documented. One formulation was prepared by producing fungi on millet and at application adding cooked, dried millet to provide additional nutrients for fungal growth. The other was made by producing fungi on corn starch ‘packing peanuts’, a biodegradable packaging material, adding additional packing peanuts as a nutrient base. The trial was conducted in three sites in a forest predominating in sugar maple (Acer saccharum) in Underhill, VT, USA. In each site, 33 dominant sugar maples were randomly selected. A 1-m² plot located 1 m from the bole of the tree was established. Soil samples were collected before application, and 1 h, 2, 4, 8, 12 and 16 wk post-application. Fungal levels were estimated based on number of colony-forming units (CFUs). A significant increase in CFUs was observed 2 wk post-application in plots treated with isolates GHA726, ERL1170 and ERL824 as a result of fungal reproduction on nutrients in the formulations. Evidence of greater persistence for the B. bassiana than the M. anisopliae isolates was observed, based on CFU levels over time. Isolates formulated with millet proliferated more than those on packing peanuts. Use of entomopathogenic fungi in forest soil has potential for managing soil-dwelling insect pests such as pear thrips, Taeniothrips inconsequens, and the black vine weevil, Otiorhynchus sulcatus, though the type of formulation and the specific isolate used must be selected carefully.     

Evolutionary history of the conifer root rot fungus Heterobasidion annosum sensu lato

We investigated two hypotheses for the origin of the root rot fungus Heterobasidion annosum species complex: (i) that geology has been an important factor for the speciation (ii) that co-evolutionary processes with the hosts drove the divergence of the pathogen species. The H. annosum species complex consists of five species: three occur in Europe, H. annosum s.s., Heterobasidion parviporum and Heterobasidion abietinum, and two in North America, Heterobasidion irregulare and Heterobasidion occidentale; all with different but partially overlapping host preferences. The evolution of the H. annosum species complex was studied using six partially sequenced genes, between 10 and 30 individuals of each species were analysed. Neighbour-joining trees were constructed for each gene, and a Bayesian tree was built for the combined data set. In addition, haplotype networks were constructed to illustrate the species relationships. For three of the genes, H. parviporum and H. abietinum share haplotypes supporting recent divergence and/or possible gene flow. We propose that the H. annosum species complex originated in Laurasia and that the H. annosum s.s./H. irregulare and H. parviporum/H. abietinum/H. occidentale ancestral species emerged between 45 and 60 Ma in the Palaearctic, well after the radiation of the host genera. Our data imply that H. irregulare and H. occidentale were colonizing North America via different routes. In conclusion, plate tectonics are likely to have been the main factor influencing Heterobasidion speciation and biogeography.     

Futures of Tropical Forests (sensu lato)

When net deforestation declines in the tropics, attention will be drawn to the composition and structure of the retained, restored, invaded, and created forests. At that point, the seemingly inexorable trends toward increased intensities of exploitation and management will be recognized as having taken their tolls of biodiversity and other forest values. Celebrations when a country passes this ‘forest transition’ will then be tempered by realization that what has been accepted as ‘forest’ spans the gamut from short‐rotation mono‐clonal stands of genetically engineered trees to fully protected old growth natural forest. With management intensification, climate change, species introductions, landscape fragmentation, fire, and shifts in economics and governance, forests will vary along gradients of biodiversity, novelty of composition, stature, permanence, and the relative roles of natural and anthropogenic forces. Management intensity will increase with the increased availability of financial capital associated with economic globalization, scarcity of wood and other forest products, demand for biofuels, improved governance (e.g., security of property rights), improved accessibility, and technological innovations that lead to new markets for forest products. In a few places, the trend toward land‐use intensification will be counterbalanced by recognition of the many benefits of natural and semi‐natural forests, especially where forest‐fate determiners are compensated for revenues foregone from not intensifying management. Land‐use practices informed by research designed and conducted by embedded scientists will help minimize the tradeoffs between the financial profits from forest management and the benefits of retention of biodiversity and the full range of environmental services.     

Chloroplast DNA restriction site variation and phylogenetic interrelationships of some genera of the Heliantheae sensu lato (Asteraceae)

Phylogenetic interrelationships of 12 genera of the Heliantheae s. lat., as well as two genera of the Anthemideae and Eupatorieae, were assessed by chloroplast DNA restriction site analysis. The 14 investigated species represented Guizotia, Helianthus, Melampodium, Rudbeckia, Sigesbeckia, Tridax , and Verbesina (Heliantheae s. str.), Helenium, Hymenoxys , and Palafoxia (Helenieae), Porophyllum (Tageteae), Coreopsis (Coreopsideae), Pleurocoronis (Eupatorieae), and Anthemis , (Anthemideae). Using 9 enzymes, 39 phylogenetically informative sites were found. Wagner parsimony analysis of the data yielded 10 equally parsimonious cladograms. Well supported relationships displayed by all cladograms included (1) a clade comprising all the genera (Heliantheae s. lat. and Eupatorieae) except Anthemis (Anthemideae), (2) a clade consisting of the genera of the Heliantheae s. str. with Pleurocoronis (Eupatorieae) nested among them, (3) a subclade of the former comprising Pleurocoronis, Guizotia , and Sigesbeckia , and (4) the generic pair of Helenium and Hymenoxys.     

Genetic variation is not concordant with morphological variation in the fern Asplenium hookerianum sensu lato (Aspleniaceae)

Species status cannot be adequately determined when partitions are based on only a single morphological character. For instance, the sympatry of plants with broad and narrow pinnules in the fern Asplenium hookerianum sensu lato from New Zealand creates the impression that two entities are present. The narrow-pinnuled plants are sometimes segregated as a distinct species, A. colensoi. However, this variation in pinnule morphology could equally be infraspecific, and only additional data can resolve this uncertainty. Analyses using AFLP DNA-fingerprinting and DNA sequencing of the chloroplast trnL-trnF region indicate that genetic variation in A. hookerianum sensu lato is not concordant with pinnule morphology. Consequently, the recognition of A. colensoi is not supported.     

广义竹叶青蛇属的系统学研究新进展

2004年以来,广义竹叶青蛇的系统学研究取得了较大的进展。本文对这近一年来的最新进展进行概括和报道。     

Prospects for genomic selection in conifer breeding: a simulation study of Cryptomeria japonica

Genomic selection (GS) can be a powerful technology in conifer breeding because conifers have long generation intervals, protracted evaluation times, and high costs of breeding inputs. To elucidate the potential of GS for conifer breeding, we simulated 60-year breeding programs in Cryptomeria japonica with and without GS. In conifers, the rapid decay of linkage disequilibrium (LD) can constitute a severe barrier to application of GS. For overcoming that barrier, we proposed an idea to leverage a seed orchard system, which has been used commonly in conifers, because some degree of LD exists in progenies derived from the limited number of elite trees in a seed orchard. The base population used for simulations consisted of progenies from 25 elite trees. Results show that GS breeding (GSB) done without model updating outperformed phenotypic selection breeding (PSB) during the first 30 years, but the genetic gain achieved over the 60 years was smaller in GSB than in PSB. However, GSB with model updating outperformed PSB over the 60 years. The genetic gain achieved over the 60 years of GSB with model updating was nearly twice that of PSB. Advantages of GSB over PSB prevailed, even for a low heritability polygenic trait. The number of markers necessary for efficient GS was a realistic level (e.g., one in every 1 cM), although higher marker density engendered higher accuracy of selection. These results suggest that GS can be useful in C. japonica breeding. Updating of the prediction model was, however, indispensable for attaining the large genetic gain.     

The function of intercellular spaces along the ray parenchyma in sapwood, intermediate wood, and heartwood of Cryptomeria japonica (Cupressaceae)

? Premise of the study: Intercellular spaces along ray parenchyma (ISRP) are common in many conifer xylems, but their function is uncertain because the in-situ structural network among ISRP, ray parenchyma, and tracheids has not been evaluated. Analysis of water distribution in ISRP from sapwood to heartwood is needed to elucidate the function of ISRP in sapwood, intermediate wood, and heartwood. ? Methods: We used cryo-scanning electron microscopy, x-ray photography, and water content measurement in xylem to analyze the presence of liquids in ISRP, ray parenchyma, and tracheids from sapwood to heartwood in Cryptomeria japonica (Cupressaceae). ? Key results: In sapwood, almost all ISRP were empty. "Cingulate-cavitated regions", which lose water along the tangential direction within one annual ring, formed in the earlywood tracheids, and their frequency increased toward the inner annual rings, whereas ray parenchyma cells were alive and not involved in the partial cavitation. In intermediate wood, almost all ISRP and earlywood tracheids and many of the ray cells were empty, and only some latewood tracheids retained liquid in their lumina. The ISRP were connected with tracheids via gas-filled ray parenchyma cells. ? Conclusions: The ISRP work as a pathway of gas for aspiration of ray parenchyma cells in sapwood. On the other hand, the occurrence of a gas network between ISRP, ray parenchyma, and tracheids facilitates cavitation of tracheids, resulting in the generation of low-moisture, intermediate wood.     

Leaf flavonoid patterns in the genus Tricyrtis (Tricyrtidaceae sensu stricto, Liliaceae sensu lato)

In a leaf flavonoid aglycone survey of 19 Tricyrtis species, the flavone lulcolin was detected in 16% of the taxa and the flavonols myricetin, qucrcetin, kaempfcrol and isorhamnetin in 32%, 63% and 68% and 58% of the sample, respectively. Kaempfcrol occurred more frequently than qucrcetin in sections Hirtae and Tricyrtis. Section Brachycyrtis was characterized by the presence of lulcolin, while flavoncs were absent from sections Flavae, Hirtae and Tricyrtis. Myricetin was found only in T J'ormosana and T. hirta (section Hirtae) and in T affirm and T. macropoda (section Tricyrtis). This is the first report of myricetin in Tricyrtis and in the Liliales. Also the co-occurrence of flavones and flavonols within the same plant, as in 7. ishiiana var. surugensis and T macrantha , is a rare event in this order. The flavonoid data are congruent with data from morphology, anatomy and molecular analysis in indicating the separation of section Brachycyrtis from the other three sections and in supporting a close relationship between sections Hirtae and Tricyrtis.     

A revision of Erythrochiton sensu lato (Cuspariinae,Rutaceae)

In the rutaceous subtribe Cuspariinae, species with relatively large, valvate, colored calyces have been assigned to Erythrochiton, but differences in arrangement of leaves, type of inflorescence, union of petals, of filaments, and of carpels, indument of corolla and testa, appendages of anthers, height of the intrastaminal disc, and exine of the pollen argue for the recognition of three genera. Erythrochiton s. str., characterized by often perennating inflorescences, connate, usually glabrous petals, free carpels, tomentulose seeds, and spinulose exine, consists of seven species of which four are new: E. fallax from the eastern flanks of the Andes from Colombia to Bolivia, E. odontoglossus from western Ecuador and adjacent Peru, E. trichanthus from eastern Peru, and E. gymnanthus from Costa Rica. The assignment to Toxosiphon of four species with woolly, coherent petals, connate carpels, glabrous seeds, and reticulate exine necessitates three new combinations: T. carinatus, T. macropodus, and T. trifoliatus. Recognition of a third unispecific genus with opposite simple leaves, sparsely pubescent, coherent, clawed petals, and spinulose exine requires a new genus name, Desmotes, and a new combination, D. incomparabilis.     

DNA sequence data reveal polyphyly of Brexioideae (Brexiaceae; Saxifragaceae sensu lato)

Previous molecular phylogenetic analyses have demonstrated that Saxifragaceae sensu lato are polyphyletic, with component lineages scattered throughout the eudicots. As part of our effort to elucidate the relationships of members of Engler and Prantl's Saxifragaceae s. l., we undertook a molecular systematic study of subfamily Brexioideae, which comprises three genera:Brexia, Ixerba, andRoussea. Not all taxonomic treatments have concurred, however, in placing these genera together. To elucidate relationships among these three genera as well as their relationships to other angiosperms we constructed large data sets ofrbcL, 18S rDNA, andrbcL + 18S rDNA sequences. Our phylogenetic analyses indicate clearly that Brexioideae are polyphyletic.Brexia is part of a celastroid clade that also includesParnassia, Lepuropetalon, and Celastraceae.Ixerba appears as sister to a large eurosid I clade;Roussea appears as part of Asterales. Molecular data, therefore, indicate that Brexioideae are a polyphyletic assemblage and component genera should ultimately be incorporated into other groups. Our studies continue to demonstrate the polyphyly not only Saxifragaceae s. l., but also of its constituent subfamilies.The first author would like to dedicate this paper to Kurt Schuchart, a good friend who passed away during this research.     

DNA relatedness among serovars ofListeria monocytogenes sensu lato

Sixty-six strains ofListeria monocytogenes (as defined in the eighth edition ofBergey's Manual of Determinative Bacteriology) were characterized by DNA relatedness. These strains formed five distinct DNA relatedness groups: (i)L. monocytogenes sensu stricto (30 strains) including the type spain ATCC 15313; (ii) serovar 5 strains (9 strains) corresponding to L. bulgarica; (iii) L. inocua (11 strains of serovars 6a, 6b, 4ab, and undesignated ones) including the reference strains; (iv) six strains of serovars 6a and 6b; (v) ten strains of various serovars. These five groups were clearly distinct fromL. grayi (4 strains) andL. murrayi (3 strains).     

Physical map of chloroplast DNA in sugi,Cryptomeria japonica

Summary To investigate the evolution of conifer species, we constructed a physical map of the chloroplast DNA of sugi, Cryptomeria japonica, with four restriction endonucleases, PstI, SalI, SacI and XhoI. The chloroplast genome of C. japonica was found to be a circular molecule with a total size of approximately 133 kb. This molecule lacked an inverted repeat. Twenty genes were localized on the physical map of C. japonica cpDNA by Southern hybridization. The chloroplast genome structure of C. japonica showed considerable rearrangements of the standard genome type found in vascular plants and differed markedly from that of tobacco. The difference was explicable by one deletion and five inversions. The chloroplast genome of C. japonica differed too from that of the genus Pinus which also lacks one of the inverted repeats. The results indicate that the conifer group originated monophyletically from an ancient lineage, and diverged independently after loss of an inverted repeat structure.     

Chloroplast DNA variation inAnemone s. lato (Ranunculaceae)

Chloroplast DNA of seven species belonging toAnemone (sectt.Omalocarpus, Anemonidium, andAnemonanthea),Hepatica, andPulsatilla have been analyzed by restriction enzymes. According to the dendrogram constructed, the sections ofAnemone and the generaHepatica andPulsatilla seem to be evolutionary approximately equidistant to each others. This supports the concept that these groups should be treated on a similar taxonomic level, either as genera or subgenera.