EVOLUTIONARY IMPLICATIONS OF INTRASPECIFIC CHLOROPLAST DNA VARIATION IN DWARF DANDELIONS (KRIGIA; ASTERACEAE)

Intraspecific chloroplast DNA polymorphisms were examined for 51 populations of seven species in the genus Krigia. A total of 1,100 restriction sites was surveyed and 46 of these were variable at the intraspecific level. Twenty-two of the variable sites were found within K. virginica, giving this species one of the highest levels of intraspecific chloroplast DNA divergence of any examined species. In contrast, no restriction site variation was detected within K. dandelion, K. wrightii, and K. occidentalis. Five polymorphisms were identified from the 16 populations of the K. cespitosa-gracilis complex, but no mutations distinguished the K. cespitosa and K. gracilis types. Krigia montana and K. biflora showed 11 and eight restriction site polymorphisms, respectively. The chloroplast genome of the hexaploid K. montana was derived from the diploid K. biflora rather than the tetraploid K. montana. High levels of polymorphism were found in species having different ploidy levels, such as K. virginica, K. biflora, and K. montana. Furthermore, most mutations found in these three species were recorded from the tetraploid lineages. As a result, evolutionary rates between different ploidy levels differ significantly. The chloroplast DNA restriction site data suggest that all surveyed populations of the autotetraploid K. virginica originated from a common ancestor. Our results also indicate that certain regions of the chloroplast genome have changed more rapidly than others and have the potential to resolve evolutionary questions at the population level.     

Comparisons of phylogenetic hypotheses among different data sets in dwarf dandelions (Krigia,Asteraceae): Additional information from internal transcribed spacer sequences of nuclear ribosomal DNA

The internal transcribed spacer (ITS) region of the 18 S–25 S nuclear ribosomal DNA repeat was sequenced from 19 populations of the tribeLactuceae, including all species of dwarf dandelion (Krigia) and five outgroup genera. The incidence of length changes and base substitutions was at least two times higher for ITS 1 than ITS 2. Interspecific sequence divergence withinKrigia averaged 9.62% (1.61%–15.19%) and 4.26% (0%–6.64%) in ITS 1 and ITS 2, respectively. Intergeneric sequence divergence ranged from 15.6% to 44.5% in ITS 1 and from 8.0% to 28.6% in ITS 2. High sequence divergence and homoplasy among genera of tribeLactuceae suggest that the phylogenetic utility of ITS sequence data is limited to interspecific studies or comparisons among closely related genera. Trees generated from ITS sequences are essentially identical to those from restriction site comparisons of the entire nuclear ribosomal (nr) DNA region. The degree of tree resolution differed depending on how gaps were treated in phylogenetic analyses. The ITS trees were congruent with the chloroplast DNA and morphological phylogenies in three major ways: 1) the sister group relationship betweenKrigia andPyrrhopappus; 2) the recognition of two monophyletic sections,Krigia andCymbia, in genusKrigia; and 3) the monophyly of theK. occidentalis-K. cespitosa clade in sect.Cymbia. However, the two nrDNA-based trees are not congruent with morphology/chloroplast DNA-based trees for the interspecific relationships in sect.Krigia. An average of 22.5% incongruence was observed among fourKrigia data sets. The relatively high degree of incongruence among data sets is due primarily to conflict between trees based on nrDNA and morphological/cpDNA data. The incongruence is probably due to the concerted evolution of nrDNA repeating units. The results fromKrigia and theLactuceae suggest that nrDNA data may have limited utility in phylogenetic studies of plants, especially in groups which exhibit high levels of sequence divergence. Our combined phylogenetic analysis as a total evidence shows the least conflict to each of the individual data sets.     

Phylogenetic and evolutionary implications of nuclear ribosomal DNA variation in dwarf dandelions (Krigia,Lactuceae, Asteraceae)

Restriction site and length variations of nrDNA were examined for 51 populations of seven species ofKrigia. The nrDNA repeat ranged in size from 8.7 to 9.6 kilobase (kb). The transcribed region, including the two ITSs, was 5.35 kb long in all examinedKrigia populations. In contrast, the size of the nontranscribed IGS varied from 3.35 to 4.25 kb. Eight different types of length-variations were identified among the 51 populations, including distinct nrDNA lengths in the tetraploid and diploid populations of bothK. biflora andK. virginica. However, a few variations were detected among populations of the same species or within a cytotype. All populations ofKrigia sect.Cymbia share a 600 bp insertion in IGS near the 18 S gene, and this feature suggests monophyly of the section. AllKrigia spp. had a conjugated type of subrepeat composed of approximately 75 basepairs (bp) and 125 bp. Base modifications in the gene coding regions were highly conserved among species. Forty-five restriction sites from 15 enzymes were mapped, 24 of which were variable among populations. Only four of the variable sites occurred in the rRNA coding region while 20 variable sites were detected in the noncoding regions. Collectively, 25 enzymes generated about 66 restriction sites in each nrDNA; this amounts to about 4.3% of the nrDNA repeat. A total of 50 restriction sites was variable, 28 of which were phylogenetically informative. Phylogenetic analyses of site mutations indicated that two sections ofKrigia, sect.Cymbia and sect.Krigia, are monophyletic. In addition, relationships among several species were congruent with other sources of data, such as cpDNA restriction site variation and morphology. Both length and restriction site variation supported an allopolyploid origin of the hexaploidK. montana. The average sequence divergence value inKrigia nrDNA was 40 times greater than that of the chloroplast DNA. The rapid evolution of nrDNA sequences was primarily due to changes of the IGS sequences.     

Comparative capitular morphology and anatomy of Coreopsis L. and bidens L. (compositae), including a review of generic boundaries

The capitular and floral morphology and anatomy ofBidens L. andCoreopsis L. were studied. All the North American species ofCoreopsis were studied. Selected species ofBidens from North and South America andCoreopsis from South America were included. The results were compared with previous observations on African species ofBidens (incl.Coreopsis). Emphasis was given to character states of the ray florets, paleae, stylearm apices, outer phyllaries, achenes, and pollen grains. Some of the character states are unique features ofCoreopsis, e.g., globular and elongately conical receptacles, deltoid outer phyllaries, truncate and indistinctly 3–5-dentate, 3–4-lobed ray florets, narrowly spathulate paleae, subulate paleae with linear-filiform upper half, hairy and apically 3-cleft paleae, truncate, convex or shallowly conical stylearm apices with the sweeping hairs limited to the area above the stigmatic surfaces and the orbicular to circular achenes. The cylindric setaceous pappus bristles so commonly encountered inBidens are unknown inCoreopsis. The pappus bristles inCoreopsis are paleaceous but similar, though thicker ones are also found in African species ofBidens (incl.Coreopsis) with winged achenes. Twin-celled hairs (setulae) with differing degrees of wall thickness are found on the achenes ofCoreopsis sect.Pseudoagarista (Mexico and South America),Coreopsis sect.Pugiopappus (California), AfricanBidens with winged achenes (e.g.,B. prestinaria, B. macroptera) and some North AmericanBidens (e.g.,B. aristosa). Similar sclerotic parenchyma make up the achenial wings of species in both genera. These may be interpreted as homologous structures, indicating the underlying similarity of these taxa and their derivation from a common ancestral stock.     

Novelties in spermacoceae (Rubiaceae) from Bolivia and Paraguay

One new Bolivian species (Borreria pazensis) and three new varieties (Borreria densiflora var.minima, Richardia, scabra var.chacoensis andStaelia virgata var.killeenii) are described and illustrated. The genusDiodella, with three species (D. apiculata comb. nov., D. radula comb. nov., andD. teres), is reported for the first time.Borreria limae, B. wunschmannii, B. scabiosoides var.scabiosoides, andB. scabiosoides var.anderssonii are also reported as new to Bolivia.     

Galatella anatolica sp. nov. (Asteraceae: Astereae) from Osmaniye,Turkey

Galatella anatolica Hamzao?lu & Budak sp. nov. (Asteraceae), collected from Osmaniye (Turkey) is here described as a new species. It is similar to G. angustissima (Tausch) Novopokr. in general habit. Both have stems with few branches and 1‐veined middle leaves, but are distinguished by involucral features, series of phyllaries, and lengths of disc florets, achenes and pappus.     

梭菌属分类研究进展:现状和展望

目前构成梭菌属的微生物在系统发育和表型特征上不一致。多相分类数据表明,梭菌属物种之间差异大。大量基于16S rRNA 基因的系统发育研究表明,梭菌属应被限定为梭菌属类群I,作为狭义梭菌属(Clostridium sensu stricto)。尽管有这方面认识,梭菌属新物种仍持续增加,这些新物种并不能与梭菌属类群I 和标准种丁酸梭菌(C. butryicum)形成一致分支,引发梭菌属分类上的混乱。本文明确了梭菌属物种的范围,即只包括模式种和梭菌属类群I。此外,4 个物种念珠状真杆菌(Eubacterium moniliforme)、旋舞真杆菌(Eubacterium tarantellae)、最大八叠球菌(Sarcina maxima)和胃八叠球菌(Sarcina ventriculi)应被调至梭菌属,分别命名为念珠状梭菌(Clostridium moniliforme)、旋舞梭菌(Clostridium tarantellae)、最大梭菌(Clostridium maximum)和胃梭菌(Clostridium ventriculi)。一个新属哈撒韦氏菌属(Hathewaya)被提议成立,3 个梭菌属物种溶组织梭菌(Clostridium histolyticum)、泥渣梭菌(Clostridium limosum)和解朊梭菌(Clostridiumproteolyticum)重新归为溶组织哈撒韦氏菌(Hathewaya histolytica)、泥渣哈撒韦氏菌(Hathewaya limosa)和解朊哈撒韦氏菌(Hathewaya proteolytica),其中Hathewaya histolytica 为模式种。     

Morphologic variation and classification of the North American Aristida purpurea complex (Gramineae)

The morphology of the Purpureae Group of North AmericanAristida is assessed by principal components and statistical analyses. Long considered a complex of about eight species, a mosaic of intergrading phenetic forms is revealed and the complex is reduced to one species with seven varieties. The taxa that are recognized areAristida purpurea var.purpurea, var.nealleyi (comb. nov.), var.curvifolia (comb. nov.), var.parishii (comb. nov.), var.wrightii (comb. nov.), var.fendleriana, and var.longiseta. A key and synopses for the varieties are provided.     

Recurved <Emphasis Type="Italic">Taraxacum</Emphasis> phyllaries function as a floral defense: experimental evidence and its implication for <Emphasis Type="Italic">Taraxacum</Emphasis> evolutionary history

Florivores directly decrease the reproductive success of plants by consuming pollen and seeds; thus, plants often have defense mechanisms against florivory. Here, we show that the recurved phyllaries of an agamospermous hybrid dandelion, Taraxacum japonicum × officinale, function as a physical barrier to slug florivory. We allowed Lehmannia valentiana, a European slug naturalized in Japan, to feed on eight pairs of the hybrid dandelion and T. japonicum, a Japanese species with erect phyllaries. Consequently, the slugs only damaged T. platycarpum flowers. The slugs either moved back from recurved phyllaries or spent more than twice as long on recurved than on erect phyllaries. When we removed the recurved phyllaries, the slugs stayed on hybrid and T. japonicum phyllaries for equal lengths of time. In addition to recurved outer phyllaries, the hybrid dandelion has erect inner phyllaries that are longer than those of T. japonicum, which effectively conceal the florets at night protecting them from slug florivory. Using the taxonomic literature, we have confirmed that recurved phyllaries evolved in many species in several parts of Europe, but are rare in East Asia. These findings suggest that European dandelions acquired recurved phyllaries as a defense mechanism under antagonistic coevolution with florivorous slugs, but this coevolution did not occur in East Asia.     

Comparative pappus micromorphology of edelweiss (Leontopodium,Gnaphalieae, Asteraceae) with implications for taxonomy,ecology and evolution

We analysed pappus characters in 31 of the c. 34 accepted Leontopodium spp. (edelweiss). Micromorphological pappus character states were useful for discriminating between individual species and intrageneric groups. The pappus differs in number, length, breadth, surface structure, colour and the tips of the bristles. Several features characterize single species, for example a unique fan‐like tip that is only found in L. franchetii. Leontopodium section Nobilia is supported by unusual pappus characters. Experimental evidence shows that the pappus of Leontopodium, previously thought to be caducous, is well suited for wind dispersal of the fruit. One clear trend is that species growing in sparsely vegetated, high‐altitude regions often have more numerous and longer pappus bristles, particularly on the female flowers.     

Variability of the inflorescence ofMicroseris laciniata (Compositae: Cichorieae)

Quantitative characters of the flowering head of a garden population ofMicroseris laciniata were scored during the second, third, and fourth season of growth. Number of achenes per head, number of phyllaries per head and the average number of pappus parts per achene in single heads show significant plant to plant variation. Achenes per head and pappus parts per achene were scored in identical plants in two subsequent seasons. The number of pappus parts per achene varies freely between five and ten. This contrasts with annual species ofMicroseris in which either five or ten pappus parts are found, depending on the species. In spite of a clear plant-specific average of pappus parts, both high and low pappus part determination can be demonstrated in all specimens. The number of pappus parts depends on the position of an achene on the receptacle, marginal achenes usually having fewer pappus parts than central ones. This gradient is not closely correlated with the position of an achene on the genetic spiral.     

DNA relatedness among saturn-spored yeasts assigned to the generaWilliopsis andPichia

Saturn-spored species assigned to the generaWilliopsis andPichia were compared from extent of nuclear DNA complementarity. Of thePichia spp., four were recognized as distinct taxa:P. dispora, P. saitoi, P. zaruensis andPichia sp. nov. AmongWilliopsis spp., the following were accepted:W. californica, W. mucosa comb. nov.,W. pratensis, W. saturnus var.saturnus, W. saturnus var.mrakii comb. nov.,W. saturnus var.sargentensis comb. nov.,W. saturnus var.subsufficiens comb. nov. andWilliopsis sp. nov. The newPichia andWilliopsis species are described elsewhere. Moderate (36–68%) DNA relatedness was detected between the formerPichia sargentensis and varieties ofW. saturnus again demonstrating that nitrate assimilation is not a reliable criterion for separating yeast species.     

Phylogenetic relationships of JapaneseAster (Asteraceae, Astereae) sensu lato based on chloroplast-DNA restriction site mutations

RFLPs of cpDNA were examined for 18 species ofAster, six species ofKalimeris, two species ofMiyamayomena and one species and one variety ofHeteropappus from Japan, using 16 restriction endonucleases. Approximately 275 restriction sites were surveyed, and a total of 74 restriction site mutations was detected, and 31 of these were phylogenetically informative. Sixteen most parsimonious trees constructed from Wagner parsimony analysis indicated the polyphyly ofKalimeris andMiyamayomena sensu Kitamura;K. miqueliana belongs to a different clade from the remaining species ofKalimeris, and two species ofMiyamayomena did not make a single clade. This result suggests that the shortening or loss of pappus have happened parallelly in different evolutionary lineages. We must be careful to assess the pappus character in taxonomy and phylogeny, and it is desirable to examine their phylogenetic relationships using a molecular data.     

Molecular phylogeny of interstitial Polycopidae ostracods (Crustacea) and descriptions of a new genus and four new species

Family Polycopidae is one of the more abundant and diverse taxa occurring in marine interstitial environments. Most of the interstitial polycopids are so far known from Japan and belong to the genus Parapolycope Klie, 1936. In this paper we describe another four new species from Japan. A new genus, K liecope gen. nov. is erected to include one new species K liecope mihoensis sp. nov. and one new combination Kliecope oligohalina (Tanaka & Tsukagoshi, 2010) comb. nov. Although the morphology of K liecope is similar to Parapolycope, the new genus has the following diagnostic characters: absence of an inward bulge on the antennular second podomere, presence of two setae bearing a sucker on the antennular third podomere, and absence of a dorsal seta on the basis of mandibula. Another three Parapolycope, P arapolycope setouchiensis sp. nov. , P arapolycope subtidalis sp. nov. , and P arapolycope miurensis sp. nov. are described as well. To test the phylogenetic relationship between the new genus and Parapolycope, we performed phylogenetic analyses based on the 14 18S rDNA sequences of interstitial Polycopidae species, 12 of which were newly obtained from our material. The 18S gene proved to be suitable for phylogenetic analyses in polycopids with high intraspecific or intrageneric resolution. Here we present trees obtained with maximum likelihood, maximum parsimony, and neighbour‐joining methods, and they support the divergence between Kliecope and Parapolycope with high bootstrap values. © 2014 The Linnean Society of London     

Taxonomic contributions to Hapalidiales (Corallinophycidae,Rhodophyta): Boreolithothamnion gen. nov., Lithothamnion redefined and with three new species and Roseolithon with new combinations

Phylogenetic analyses of rbcL gene sequences and of concatenated rbcL, psbA, and nuclear SSU rRNA gene sequences resolved the generitype of Lithothamnion, L. muelleri, in a clade with three other southern Australian species, L. kraftii sp. nov., L. saundersii sp. nov., and L. woelkerlingii sp. nov. Cold water boreal species currently classified in Lithothamnion and whose type specimens have been sequenced are transferred to Boreolithothamnion gen. nov., with B. glaciale comb. nov. as the generitype. The other species are B. giganteum comb. nov., B. phymatodeum comb. nov., and B. sonderi comb. nov., whose type specimens are newly sequenced, and B. lemoineae comb. nov., B. soriferum comb. nov., and B. tophiforme comb. nov., whose type specimens were already sequenced. Based on rbcL sequences from the type specimens of Lithothamnion crispatum, L. indicum, and L. superpositum, each is recognized as a distinct species and transferred to the recently described Roseolithon as R. crispatum comb. nov., R. indicum comb. nov., and R. superpositum com. nov., respectively. To correctly assign species to these three genera based only on morpho-anatomy, specimens must have multiporate conceptacles and some epithallial cells with flared walls. The discussion provides examples demonstrating that only with phylogenetic analyses of DNA sequences can the evolution of morpho-anatomical characters of non-geniculate corallines be understood and applied at the correct taxonomic rank. Finally, phylogenetic analyses of DNA sequences support recognition of the Hapalidiales as a distinct order characterized by having multiporate tetra/bisporangial conceptacles, and not as a suborder of Corallinales whose tetra/bisporangial conceptacles are uniporate.     

The phylogenetic relationship among Ectothiorhodospiraceae: a reevaluation of their taxonomy on the basis of 16S rDNA analyses

Sequences of the 16S rRNA gene were determined from all type strains of the recognized Ectothiorhodospira species and from a number of additional strains. For the first time, these data resolve the phylogenetic relationships of the Ectothiorhodospiraceae in detail, confirm the established species, and improve the classification of strains of uncertain affiliation. Two major groups that are recognized as separate genera were clearly established. The extremely halophilic species were removed from the genus Ectothiorhodospira and reassigned to the new genus Halorhodospira gen. nov., to recognize that the most halophilic eubacteria are species of this genus. These species are Halorhodospira halophila comb. nov., Halorhodospira halochloris comb. nov., and Halorhodospira abdelmalekii comb. nov. Among the slightly halophilic Ectothiorhodospira species, the classification of strains belonging to Ectothiorhodospira mobilis and Ectothiorhodospira shaposhnikovii was improved. Several strains that were tentatively identified as Ectothiorhodospira mobilis form a separate cluster on the basis of their 16S rDNA sequences and are recognized as two new species: Ectothiorhodospira haloalkaliphila sp. nov., which includes the most alkaliphilic strains originating from strongly alkaline soda lakes, and Ectothiorhodospira marina, describing isolates from the marine environment. Received: 12 October 1995 / Accepted: 1 December 1995     

Description of a new diatom genus Dorofeyukea gen. nov. with remarks on phylogeny of the family Stauroneidaceae

Type material of Navicula kotschyi was studied, and this species was transferred to Dorofeyukea gen. nov. as D. kotschyi comb. nov. Dorofeyukea was described on the basis of DNA sequence and morphological data. Additional species assigned to this genus that were previously included in Navicula include: D. ancisa comb. nov., D. grimmei comb. nov., D. ivatoensis comb. nov., D. orangiana comb. nov., D. rostellata comb. nov. & stat. nov., D. savannahiana comb. nov., D. tenuipunctata comb. nov., and D. texana comb. nov. All Dorofeyukea species share the same morphological features, including having a narrow stauroid fascia surrounded by 1–3 irregularly shortened striae, uniseriate, and weakly radiate striae, circular, or rectangular puncta in the striae that are covered internally by dome‐shaped hymenes, presence of a pseudoseptum at each apex and absence of septa. Partial DNA sequences of SSU and rbcL loci show Dorofeuykae belongs to the clade of stauroneioid diatoms together with Stauroneis, Prestauroneis, Craticula, Karayevia, Madinithidium, Fistulifera, Parlibellus, and, possibly, Schizostauron. A new species from the monoraphid genus Madinithidium, M. vietnamica sp. nov., was described based on valve and chloroplast morphology as well as DNA sequence data.