Multivariate studies of Ipheion (Amaryllidaceae, Allioideae) and related genera

Ipheion, as recognized by Guaglianone (Darwiniana 17:159–242, 1972), is a small genus of the family Amaryllidaceae, subfamily Allioideae, tribe Gilliesieae endemic to South America. Since 1800, the species of Ipheion were treated under Beauverdia, Brodiaea, Milla, Nothoscordum, Tristagma or Triteleia. Nowadays, some species of Ipheion are treated as Tristagma and some other under Nothoscordum. In this paper, we analyzed the morphological variation among species of Ipheion and related genera using a numerical taxonomic approach based on overall similarity, to investigate the intergeneric and infrageneric variations to the circumscribed groups. Based on 141 operational taxonomic units and 51 morphological characters, multivariate analyses were performed. Results showed that Ipheion separated into two groups according to Guaglianone’s sectional treatment: Ipheion sect. Ipheion is morphologically more similar to the studied species of Tristagma, while I. sect. Hirtellum can be separated from Nothoscordum/Zoellnerallium and from Tristagma and allies. These a priori groupings were tested using discriminant and univariate analyses. Diagnostic characters were selected to differentiate groups. Previous taxonomic treatments are discussed and results are also evaluated using additional karyological and geographical data.     

Independent origins of coastal colonization in the tribe Athetini (Coleoptera,Staphylinidae)

Less than 1% of Staphylinidae are known to be confined to coastal habitats. To explore the origins of coastal colonization within the tribe Athetini Casey, we present a revised molecular phylogeny. The dataset comprised partial mitochondrial COI, COII, 16S rDNA, NADH1, partial nuclear 18S rDNA and 28S rDNA. We chose a total of 95 species in 51 genera, including 14 coastal species in eight genera and 21 outgroup species from other aleocharine tribes. The concatenated dataset was analysed simultaneously by both parsimony‐ and model‐based (Bayesian and maximum likelihood) methods. The tribe Athetini was not supported as a monophyletic group, but together with the tribes Tachyusini, Ecitocharini and Hygronomini did form a monophylum. The ecological association of species with a coastal habitat was mapped onto a phylogeny to assess the evolution of habitat specialization in the Athetini lineage. The results reveal that five independent origins of coastal colonization have occurred throughout the tribe Athetini: (a) Osakatheta + Adota minuta + coastal Atheta (Badura) (clade A); (b) Adota (clade B); (c) Pontomalota + Tarphiota + Thinusa (clade C); (d) Iotarphia (clade D); and (e) Psammostiba (clade E). The low species number of the coastal Athetini compared with the entire Athetini lineage indicates that coastal habitats are harsh environments and so only a few species were able to colonize this habitat. The following changes in classification are proposed: (a) Ad. minuta Lee and Ahn is removed from the genus Adota and tentatively included in Atheta (Badura); (b) The genus Saphocallus Sharp is transferred from Athetini to Geostibini.     

New chromosome counts and evidence of polyploidy in Haageocereus and related genera in tribe Trichocereeae and other tribes of Cactaceae

Chromosome numbers for a total of 54 individuals representing 13 genera and 40 species of Cactaceae, mostly in tribe Trichocereeae, are reported. Five additional taxa examined belong to subfamily Opuntioideae and other tribes of Cactoideae (Browningieae, Pachycereeae, Notocacteae, and Cereeae). Among Trichocereeae, counts for 35 taxa in eight genera are reported, with half of these (17 species) for the genus Haageocereus. These are the first chromosome numbers reported for 36 of the 40 taxa examined, as well as the first counts for the genus Haageocereus. Both diploid and polyploid counts were obtained. Twenty nine species were diploid with 2n=2x=22. Polyploid counts were obtained from the genera Espostoa, Cleistocactus, Haageocereus, and Weberbauerocereus; we detected one triploid (2n=3x=33), nine tetraploids (2n=4x=44), one hexaploid (2n=6x=66), and three octoploids (2n=8x=88). In two cases, different counts were recorded for different individuals of the same species (Espostoa lanata, with 2n=22, 44, and 66; and Weberbauerocereus rauhii, with 2n=44 and 88). These are the first reported polyploid counts for Haageocereus, Cleistocactus, and Espostoa. Our counts support the hypothesis that polyploidy and hybridization have played prominent roles in the evolution of Haageocereus, Weberbauerocereus, and other Trichocereeae.     

Distribution of 5S and 35S rRNA gene sites in 34 Chenopodium species (Amaranthaceae)

Studies on Chenopodium chromosomes are scarce and restricted mainly to chromosome number estimation. To extend our knowledge on karyotype structure of the genus, the organization of 5S and 35S rRNA genes in Chenopodium chromosomes was studied. The rDNA sites were predominantly located at chromosomal termini, except in a few species where 5S rDNA sites were interstitial. The majority of the diploid species possessed one pair each of 35S and 5S rDNA sites located on separate chromosomes. Slightly higher diversity in rDNA site number was observed in polyploid accessions. One or two pairs of 35S rDNA sites were observed in tetraploids and hexaploids. Tetraploid species had two, four or six sites and hexaploid species had six or eight sites of 5S rDNA, respectively. These data indicate that, in the evolution of some polyploid species, there has been a tendency to reduce the number of rDNA sites. Additionally, polymorphism in rDNA site number was observed. Possible mechanisms of rDNA locus evolution are discussed. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ??, ??–??.     

Major structural genomic alterations can be associated with hybrid speciation in Aegilops markgrafii (Triticeae)

During evolutionary history many grasses from the tribe Triticeae have undergone interspecific hybridization, resulting in allopolyploidy; whereas homoploid hybrid speciation was found only in rye. Homoeologous chromosomes within the Triticeae preserved cross‐species macrocolinearity, except for a few species with rearranged genomes. Aegilops markgrafii, a diploid wild relative of wheat (2n = 2x = 14), has a highly asymmetrical karyotype that is indicative of chromosome rearrangements. Molecular cytogenetics and next‐generation sequencing were used to explore the genome organization. Fluorescence in situ hybridization with a set of wheat cDNAs allowed the macrostructure and cross‐genome homoeology of the Ae. markgrafii chromosomes to be established. Two chromosomes maintained colinearity, whereas the remaining were highly rearranged as a result of inversions and inter‐ and intrachromosomal translocations. We used sets of barley and wheat orthologous gene sequences to compare discrete parts of the Ae. markgrafii genome involved in the rearrangements. Analysis of sequence identity profiles and phylogenic relationships grouped chromosome blocks into two distinct clusters. Chromosome painting revealed the distribution of transposable elements and differentiated chromosome blocks into two groups consistent with the sequence analyses. These data suggest that introgressive hybridization accompanied by gross chromosome rearrangements might have had an impact on karyotype evolution and homoploid speciation in Ae. markgrafii.     

A phylogenetically informed search for an alternative Macrostomum model species,with notes on taxonomy,mating behavior,karyology, and genome size

The free-living flatworm Macrostomum lignano is used as a model in a range of research fields—including aging, bioadhesion, stem cells, and sexual selection—culminating in the establishment of genome assemblies and transgenics. However, the Macrostomum community has run into a roadblock following the discovery of an unusual genome organization in M. lignano, which could now impair the development of additional resources and tools. Briefly, M. lignano has undergone a whole-genome duplication, followed by rediploidization into a 2n = 8 karyotype (distinct from the canonical 2n = 6 karyotype in the genus). Although this karyotype appears visually diploid, it is in fact a hidden tetraploid (with rarer 2n = 9 and 2n = 10 individuals being pentaploid and hexaploid, respectively). Here, we report on a phylogenetically informed search for close relatives of M. lignano, aimed at uncovering alternative Macrostomum models with the canonical karyotype and a simple genome organization. We taxonomically describe three new species: the first, Macrostomum janickei n. sp., is the closest known relative of M. lignano and shares its derived genome organization; the second, Macrostomum mirumnovem n. sp., has an even more unusual genome organization, with a highly variable karyotype based on a 2n = 9 base pattern; and the third, Macrostomum cliftonensis n. sp., does not only show the canonical 2n = 6 karyotype, but also performs well under standard laboratory culture conditions and fulfills many other requirements. M. cliftonensis is a viable candidate for replacing M. lignano as the primary Macrostomum model, being outcrossing and having an estimated haploid genome size of only 231 Mbp.     

Phylogeny of Adramini (Diptera,Tephritidae) based on integrative evidence

Species of the tribe Adramini (Tephritidae: Trypetinae) are usually slender, and some specific species have eyes borne at the ends of their long stalks. This tribe is mainly distributed in the tropics and subtropics of the Afrotropical, Oriental and Australasian Regions; relatively few species occur in the Palearctic and Nearctic Regions. The phylogeny of the tribe Adramini is presented here based on analysis of morphological and molecular information (DNA sequences of nuclear 28S rDNA, mitochondrial COI and COII, and 16S rDNA genes) for its representative species in most genera. Three monophyletic groups (Adrama‐com‐group, Pelmatops‐com‐group and Dimeringophrys‐com‐group) were discovered in the combined morphological and molecular tree. The results showed moderate support for the monophyly of Adramini and strong support for most of its genera. However, Euphranta appears to be polyphyletic. Sapadrama, Celidodacus and Euphranta are basal taxon, and Coelopacidia, Soita and Trypanophion are closely related to the stalk‐eyed fruit flies (Pelmatops + Pseudopelmatops). A hypothesis regarding the morphology–function relationships for two main groups of Adramini (Adrama‐group and Pelmatops‐group) with different evolving probabilities is inferred. Sapadrama is proposed be removed from Adramini; a new genus, Ichneumonomacula Chen gen. n. and a new species Ichneumonmacula wangyongi Chen sp. n., are recognized and described, and a key to recognize the genera of Adramini around the world is provided.     

Diverse evolutionary pathways shaped 5S rDNA of species of tribe Anemoneae (Ranunculaceae) and reveal phylogenetic signal

Anemone sensu lato (including Pulsatilla and Hepatica), tribe Anemoneae (Ranunculaceae), is arranged into two subgenera, Anemone and Anemonidium, with basic chromosome numbers x = 8 and x = 7, respectively. We elucidated the level of divergence of 5S rDNA unit arrays between the subgenera, determined intra‐individual and interspecific sequence variation and tested 5S rDNA phylogenetic signal in revealing the origin of polyploid species. High intra‐individual nucleotide diversity and the presence of 5S rDNA unit array length variants and pseudogenes indicate that weak homogenization forces have shaped 5S rDNA in the investigated species. Our results show that 5S rDNA evolved through two major changes: diversification of 5S rDNA into two lineages, one with long (subgenus Anemone) and one with short 5S rDNA unit arrays (subgenus Anemonidium); and subsequent contraction and expansion of 5S rDNA unit arrays. Phylogenetic analysis based on 5S rDNA supports the hypothesis that A. parviflora could be a parental species and donor of the subgenome D to the allopolyploids A. multifida (BBDD) and A. baldensis (AABBDD). In A. baldensis interlocus exchange possibly occurred, followed by subsequent replacement of the 5S rDNA from subgenome D with those from subgenome B. Here we present evidence that both models, concerted and birth‐and‐death evolution, were probably involved in the evolution of the 5S rDNA multigene family in subgenera Anemone and Anemonidium.     

Chromosome evolution in ground beetles: localization of the rDNA loci in the tribe Harpalini (Coleoptera,Carabidae)

The pattern of localization of the ribosomal genes was studied by means of fluorescence in situ hybridization in 39 species of the tribe Harpalini. Most of them show one pair of autosomes carrying the ribosomal genes in a distal position of a single chromosome arm. This pattern is hypothesized to be ancestral for the whole tribe. Both, chromosome number and the number and localization of rDNA loci, show little variation and are therefore of little phylogenetic value. Only in the subtribe Ditomina is there enough variation to characterize phyletic relationships. The stability of rDNA loci is even higher than the constancy of chromosome number, as most species of Ditomina (genera Dixus, Eocarterus, Carterus, Odontocarus and Ditomus) have the usual pair of autosomes with rDNA loci, in spite of remarkable differences in the diploid number. Only Dixus sphaerocephalus and Dixus clypeatus have two autosomal pairs with a fluorescent signal. These results do not support the hypothesis that the high chromosome numbers found within Ditomina are the result of polyploid change from the ancestral 2n = 37 karyotype of the tribe Harpalini. Chromosomal translocations or the presence of mobile genetic elements are plausible sources of the few cases of intraspecific polymorphism in the rDNA loci found in species of Harpalus.     

In vitro induction and identification of tetraploid plants of <Emphasis Type="Italic">Paulownia tomentosa</Emphasis>

Polyploidization is a major trend in plant evolution that has many advantages over diploid. In particular, the enlargement and lower fertility of polyploids are very attractive traits in forest tree breeding programs. We report here a system for the in vitro induction and identification of tetraploid plants of Paulownia tomentosa induced by colchicine treatment. Embryonic calluses derived from placentas were transferred to liquid Murashige and Skoog (MS) medium containing different concentrations of colchicine (0.01, 0.05, or 0.1%) and incubated for 24, 48, or 72 h on an orbital shaker at 110 rpm. The best result in terms of the production of tetraploid plantlets was obtained in the 48 h + 0.05% colchicine treatment, with more than 100 tetraploid plantlets being produced. The ploidy level of plantlets was verified by chromosome counts, flow cytometry, and morphology. The chromosome number of tetraploids was 2n = 4x = 80 and that of diploid plantlets was 2n = 2x = 40. The relative fluorescence intensity of tetraploids was twofold higher than that of diploids. The tetraploid and diploid plantlets differed significantly in leaf shape, with those of the former being round and those of the latter pentagonal. The mean length of the stomata was longer in tetraploid plants than diploid plants, and stomatal frequency was reduced with the increased ploidy level. The tetraploids had large floral organs that were easily distinguishable from those of diploid plants.     

Karyotype variation in 11 species of the Vernonieae Cass. tribe (Asteraceae Bercht. & J. Presl)

The Vernonieae tribe presents strong taxonomic delimitation problems as it is considered one of the most complex groups of the Asteraceae family, comprising approximately 1100 species distributed across 129 genera. In this study, a comparative analysis of the Vernonieae species was performed to understand the events involved in the chromosome evolution of these species and to further deduce their taxonomy. The representatives were cytogenetically characterized via analyses of morphology, karyotype asymmetry and differential staining with fluorochromes CMA and DAPI as well as FISH. According to morphometric data, all species showed symmetrical karyotypes with prevailing metacentric chromosomes, even in species belonging to different genera. Variability in diploid chromosome number was detected (2n = 18 to 2n = 60), and chromosome sizes were observed to be between 1.00 and 4.09 μm. Additionally, variation in the pattern of heterochromatin was observed mainly in relation to CMA⁺ bands, in which the number varied from 4 to 16 heterochromatic regions. Only one species, Vernonia scorpioides, presented positive DAPI bands, which were located in the terminal position in most of the chromosomes. The differences in the sizes and quantities of heterochromatic bands may be related to small structural rearrangements during karyotype evolution of the Vernonieae tribe.     

Cytogeography and chromosomal variation of the endemic East Asian herb Lycoris radiata

Information on the spatial distribution of cytotypes and karyotype variation in plants is critical for studies of the origin and evolution of polyploid complexes. Here, the spatial distribution of cytological races and intraspecific variation in the karyotype of Lycoris radiata, an endemic species to East Asia, is investigated. Conventional karyotype analysis methods were used to determine ploidy level and karyotypical characteristics in 2,420 individuals from 114 populations of L. radiata nearly covering the whole distribution areas in China. Of 114 populations studied, 52 (45.61%), 58 (50.88%), and 4 (3.51%) are diploid, triploid, and mixoploid populations, respectively, with 1,224, 1,195, and 1 individuals being diploid, triploid, and tetraploid, respectively. The triploid possesses a much wider distribution range than the diploid, with the former almost occupying the entire range of this complex species in East Asia and the latter distributing in the middle and east regions of China. Triploids tend to occur at high altitudes, and the relationship between the ploidy and altitude is significantly positive but low (r² = 0.103, p < 0.01). About 98.6% of examined bulbs have a common karyotype consisting of 22 or 33 acrocentric (A) chromosomes. Some aberrant chromosomes which should be generated from A‐type chromosome have been found including metacentrics (m), small metacentrics (m′), and B‐type chromosome. The results can provide a fundamental cytogeographic data for further studies on the evolutionary origins and adaptive divergences of polyploids, especially the triploid, within L. radiata using molecular and/or ecological methods in the future.     

The effect of chemical and biological treatment on root and crown rot disease caused by Phytophthora cryptogea Pethybr. & Lafferty in Gerbera

Phytophthora root and crown rot (Phytophthora cryptogea) on gerbera is difficult to manage because most gerbera cultivars are susceptible to P. cryptogea. This study was conducted in order to determine the in vivo (pot experiment) efficacy of some fungicides and biofungicides. In pot experiments, fungicides were applied 7 days after inoculation with P. cryptogea, while biofungicide was applied 7 days before inoculation. In this study, soil drenches of five fungicides were tested. “Ametoctradin+dimethomorph (100 ml/day),” “mandipropamid+difenoconazole (60 ml/day),” “propamocarb+fosetyl‐Al (200 ml/day),” “mancozeb+metalaxyl‐M (250 g/day)” and “azoxystrobin+difenoconazole (100 ml/day)” active substances were used. Similarly, one biofungicide Bacillus amyloliquefaciens syn. MBI 600 (50 g/100 L) was applied by soil drenching. Efficacy of treatments was assessed according to the percentage of the root system which was visibly rotten at the end of the experiment. Root and crown rot severity was rated on a scale of 0 = 0% root system necrotic, 1 = 1%‐25% necrotic, 2 = 26%‐50% necrotic, 3 = 51%‐75% necrotic and 4 = 76%‐100% necrotic from 12 to 21 days. In this experiment, “azoxystrobin 200 g/L + difenoconazole 125 g/L” exhibited the highest efficacy against P. cryptogea with a ratio of 43.75%. The other fungicides and biofungicides ametoctradin 300 g/L + dimethomorph 225 g/L, mandipropamid 250 g/L + difenoconazole 250 g/L, propamocarb 530 g/L + fosety‐Al 310 g/L, mancozeb 64%+metalaxyl‐M 4% and Bacillus amyloliquefaciens syn. MBI 600 11% were ineffective. Importance should be given to management strategies of P. cryptogea of and more experiments should be carried out for a better understanding of the use of registered fungicides and biofungicides.     

Chromosome banding and FISH with rDNA probe in the diploid and tetraploid loach Misgurnus anguillicaudatus

The chromosomes of the diploid and tetraploid loach Misgurnus anguillicaudatus were analyzed by staining with Ag, chromomycin A₃ (CMA₃)/distamycin A (DA), and DA/4′,6-diamidino-2-phenylindole (DAPI), and using fluorescence in situ hybridization (FISH) with 5.8S + 28S rDNA as a probe. Nucleolus organizer regions (NORs) were mapped to the telomeric region of the short arms of the largest (first) metacentric chromosome pair in the diploid loach with 2n = 50 and the homologous quartet in the tetraploid loach with 4n = 100. The NORs were positive at the same region of the first metacentric chromosome for Ag and CMA₃/DA stainings, but negative for DA/DAPI staining. Four signals at the homologs within the same quartet suggest the duplication of the entire genome from diploid to tetraploid status. However, a size difference was detected between the rDNA signals by FISH and CMA₃ banding.     

Molecular phylogeny and taxonomy of the genus Chaetophora (Chlorophyceae,Chlorophyta), including descriptions of Chaetophoropsis aershanensis gen. et sp. nov.

The broadly defined genus Chaetophora consisted of species with minute, uniseriate branching filaments enveloped in soft or firm mucilage forming macroscopic growths that are spherical, hemispherical, and tubercular or arbuscular, growing epiphytically on freshwater aquatic plants and other submerged surfaces in standing or fast‐flowing water. Recent molecular analyses clearly showed that this genus was polyphyletic. In this study, eight strains of Chaetophora and three strains of Stigeoclonium were identified and successfully cultured. In combination with the morphological data, a concatenated data set of four markers (18S + 5.8S + ITS2+ partial 28S rDNA) was also used to determine their taxonomic relationships and phylogenetic positions. The molecular analysis resolved the broadly defined Chaetophora to at least two genera. Species with a globose thallus of genus Chaetophora formed a separate monophyletic clade, which clearly separated from, a type of lobe‐form Chaetophora species. Therefore, we propose to erect a new genus, Chaetophoropsis, which includes all globose species of the Chaetophora. Chaetophoropsis aershanensis was determined to be a new species, based on its special characteristic of profuse long rhizoids. Stigeoclonium polyrhizum, as the closest relative to Chaetophoropsis, revealed its distant relationships to other species of Stigeoclonium. A globose thallus with a thick, soft mucilage matrix, and special rhizoidal branches lent further support to the placement of S. polyrhizum in the genus Chaetophoropsis and had the closest relationship to C. aershanensis. Taxonomic diversity was proven by distinctive morphological differences and by phylogenetic divergence in the broadly defined Chaetophora identified herein.     

Cytogenetic evidences on the evolutionary relationships between the tetraploids of the section <Emphasis Type="Italic">Rhizomatosae</Emphasis> and related diploid species (<Emphasis Type="Italic">Arachis</Emphasis>, Leguminosae)

Rhizomatosae is a taxonomic section of the South American genus Arachis, whose diagnostic character is the presence of rhizomes in all its species. This section is of particular evolutionary interest because it has three polyploid (A. pseudovillosa, A. nitida and A. glabrata, 2n?=?4x?=?40) and only one diploid (A. burkartii, 2n?=?2x?=?20) species. The phylogenetic relationships of these species as well as the polyploidy nature and the origin of the tetraploids are still controversial. The present study provides an exhaustive analysis of the karyotypes of all rhizomatous species and six closely related diploid species of the sections Erectoides and Procumbentes by cytogenetic mapping of DAPI/CMA heterochromatin bands and 5S and 18–26S rDNA loci. Chromosome banding showed variation in the DAPI heterochromatin distribution pattern, which, together with the number and distribution of rDNA loci, allowed the characterization of all species studied here. The bulk of chromosomal markers suggest that the three rhizomatous tetraploid species constitute a natural group and may have at least one common diploid ancestor. The cytogenetic data of the diploid species analyzed evidenced that the only rhizomatous diploid species—A. burkartii—has a karyotype pattern different from those of the rhizomatous tetraploids, showing that it is not likely the genome donor of the tetraploids and the non-monophyletic nature of the section Rhizomatosae. Thus, the tetraploid species should be excluded from the R genome, which should remain exclusively for A. burkartii. Instead, the karyotype features of these tetraploids are compatible with those of different species of the sections Erectoides and Procumbentes (E genome species), suggesting the hypothesis of multiple origins of these tetraploids. In addition, the polyploid nature and the group of diploid species closer to the tetraploids are discussed.