Phylogenetic relationships and genetic diversity among members of theFestuca-Lolium complex (Poaceae) based on ITS sequence data

There have been few DNA sequencebased studies of phylogenetic relationships within theFestuca-Lolium complex. Here we infer the phylogeny of 31Festuca-Lolium taxa with a dataset of 116 ITS sequences. The results are consistent with previous studies that resolved two majorFestuca clades: one clade of fine fescues and another clade that containsLolium and associatedFestuca species. This study is unique in suggesting a third, basalFestuca clade, but support for the basal position of this group is low. Extensive sampling permitted investigation of the effects of lineage sorting and reticulate events on the evolution of the complex. Roughly half of the taxa show evidence of lineage sorting or reticulation, and the monophyly ofLolium has likely been obscured by reticulate events. Overall, polyploid species harbor higher levels of ITS sequence diversity than diploids; ITS sequence variants may provide clues to the identity of allopolyploid parents.     

Microsporogenesis and meiotic abnormalities in the hybrid complex of Phlomis composita (Lamiaceae)

The extent of chromosome structural differences such as permanent translocations and paracentric inversions has been studied in the hybrid complex of Phlomis composita and its putative parental taxa P. lychnitis and P. crinita . They are detected as meiotic abnormalities during microsporogenesis. In total, 117 plants from 19 populations in Andalusia (southern Spain) and Levante (eastern Spain) were studied for ploidy level, chromosome clumping, multivalent or univalent formation, late bivalent disjunction with bridges, chromatin bridges and fragments, irregular polysporads and variable pollen size. All individuals had the diploid chromosome number 2 n  = 20, with no significant difference in the frequencies of the above meiotic abnormalities either at taxon or population levels. However, very different frequencies were observed on the regional scale between populations in Andalusia and Levante. The results are discussed within the theoretical framework of homoploid hybrid or recombinational speciation.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 143 , 79−85.     

Systematic studies on some species of the genus Artemisia: biomolecular analysis

ABSTRACT

The internal transcribed spacers (ITS) of the ribosomal DNA gene of 11 taxa of the genus Artemisia were sequenced and compared with other 14 species taken from GenBank. The aims of this study are to clarify phylogenetic relationships for 25 taxa within the genus Artemisia, and to highlight the phylogenetic position of some species of geobotanical interest from the Alps or from other European areas. The results support the monophyly of the genus Artemisia, and the presence of the five main clades, corresponding to the morphologically based sections, Absinthium, Artemisia, Seriphidium, Dracunculus and Tridentatae. Only A. annua and A. genipi are not classified in the section in which they were traditionally included: A. annua is assigned to Seriphidium and not Artemisia, and A. genipi to Absinthium and not Artemisia. The basal structure of the tree differed in the 45 equally parsimonious MP trees, and thus appeared as a polytomy in the consensus tree. This does not allow us to completely solve the relationships among the clades. The molecular data are complementary with the morphological and biogeographical information and all are essential to draw valid conclusions on the relative closeness of the various taxa.     

Multiple diploid hybrid speciation of the Canary Island endemicArgyranthemum sundingii (Asteraceae)

There are several well-documented examples of multiple hybrid origins of polyploid species. Herein we report the first, to our knowledge, explicit example of a species that most probably has originated recurrently by diploid hybrid speciation. Genetic relationships and stabilization of twoArgyranthemum populations of putative hybrid origin on Tenerife, the Canary Islands, were investigated using chromosomal, morphometric, and fertility analyses of cultivated progeny families and artificial F₁ and F₂ hybrids. These data were compared to a recently published chloroplast DNA phylogeny of the genus, in which the same populations were included. The results suggest that the two populations must be referred to a single species,A. sundingii, which is diploid, fully fertile, genetically stabilized, and occurs in an ecologically intermediate habitat opened by deforestation, and that this species has originated at least twice following local hybridization in two valleys. The same parental species were involved in each origin; the montaneA. broussonetii and the coastalA. frutescens. The montane species was the chloroplast donor in one of the valleys and the coastal species in the other.     

Increasing evidence of the role of gene flow in animal evolution: hybrid speciation in the yellow-rumped warbler complex

In this issue of Molecular Ecology, Brelsford et al. (2011) present strong evidence for a case of hybrid speciation within the yellow-rumped warbler complex. Although homoploid hybrid speciation has now been documented in many animals (Mallet 2007), it seems rare in tetrapods (Mavárez & Linares 2008) and it has barely even been mentioned in birds (Price 2008). Brelsford and colleagues thus present the first detailed molecular evidence suggesting that hybrid speciation can occur in birds. Brelsford et al. (2011) posit that Audubon's warbler (Dendroica auduboni) constitutes a hybrid species originating from the admixture of two distinct parental lineages, represented today by myrtle warbler (D. coronata) and black-fronted warbler (D. nigrifrons). The authors present three major lines of molecular evidence suggesting that this is not simply a case of a hybrid swarm or limited introgression.     

New specific primers for amplification of the Internal Transcribed Spacer region in Clitellata (Annelida)

Nuclear molecular evidence, for example, the rapidly evolving Internal Transcribed Spacer region (ITS), integrated with maternally inherited (mitochondrial) COI barcodes, has provided new insights into the diversity of clitellate annelids. PCR amplification and sequencing of ITS, however, are often hampered by poor specificity of primers used. Therefore, new clitellate‐specific primers for amplifying the whole ITS region (ITS: 29F/1084R) and a part of it (ITS2: 606F/1082R) were developed on the basis of a collection of previously published ITS sequences with flanking rDNA coding regions. The specificity of these and other ITS primers used for clitellates were then tested in silico by evaluating their mismatches with all assembled and annotated sequences (STD, version r127) from EMBL, and the new primers were also tested in vitro for a taxonomically broad sample of clitellate species (71 specimens representing 11 families). The in silico analyses showed that the newly designed primers have a better performance than the universal ones when amplifying clitellate ITS sequences. In vitro PCR and sequencing using the new primers were successful, in particular, for the 606F/1082R pair, which worked well for 65 of the 71 specimens. Thus, using this pair for amplifying the ITS2 will facilitate further molecular systematic investigation of various clitellates. The other pair (29F/1084R), will be a useful complement to existing ITS primers, when amplifying ITS as a whole.     

Molecular evidence for double maternal origins of the diploid hybrid Hippophae goniocarpa (Elaeagnaceae)

Homoploid hybrid plant species are rare, and the mechanisms of their speciation are largely unknown, especially for homoploid hybrid tree species. Two contrasting hypotheses have been proposed to explain the origin of Hippophae goniocarpa: (1) it is a diploid hybrid originating from H. rhamnoides ssp. sinensis × H. neurocarpa ssp. neurocarpa, and (2) it originated via marginal differentiation from H. rhamnoides ssp. sinensis. Regardless of which of these hypotheses is true (if either), previous studies have suggested that H. rhamnoides ssp. sinensis is the only maternal donor for this hybrid species. In this study, we aim to elucidate the maternal composition of H. goniocarpa and to test the two hypotheses. For this purpose, we sequenced the maternal chloroplast DNA trnL‐F region of 75 individuals representing H. goniocarpa, H. rhamnoides ssp. sinensis, and H. neurocarpa ssp. neurocarpa in two co‐occurring sites of the taxa. Seven haplotypes were identified from three taxonomic units, and their phylogenetic relationships were further constructed by means of maximum parsimony, maximum likelihood, and network analyses. These seven haplotypes clustered into two distinct, highly divergent lineages. Two haplotypes from one lineage were found in H. rhamnoides ssp. sinensis, and five (representing the other lineage) in H. neurocarpa ssp. neurocarpa. Hippophae goniocarpa shared four common haplotypes from both lineages, but the haplotypes detected from the two populations differed to some extent, and in each case were identical to local haplotypes of the putative parental species. Thus, both H. rhamnoides ssp. sinensis and H. neurocarpa ssp. neurocarpa appear to have together contributed to the maternal establishment of H. goniocarpa. These results clearly demonstrate that the marginal origin hypothesis should be rejected, and support the hybrid origin hypothesis. Hippophae goniocarpa exhibits a sympatric distribution with its two parent species, without occupying new niches or displaying complete ecological isolation. However, this species has effectively developed reproductive isolation from its sympatric parent species. Our preliminary results suggest that H. goniocarpa may provide a useful model system for studying diploid hybrid speciation in trees. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 156 , 111–118.     

The use of ribosomal ITS to determine phylogenetic relationships within Sorghum

 For the first time, a combined analysis of the ITS1 regions of all twenty-five Sorghum species has been undertaken. Parsimony analysis revealed a distinct lineage of Sorghum consisting of the cultivated species and their progenitors plus S. angustum, S. brachypodum, S. ecarinatum, S. macrospermum, S. laxiflorum and Saccharum officinarum. A second unsupported lineage consists of the Parasorghum and Stiposorghum species S. grande, S. leiocladum, S. nitidum, S. purpureosericeum, S. timorense, S. versicolor, S. amplum, S. bulbosum, S. interjectum, S. plumosum, S. stipoideum and the African grass Cleistachne sorghoides. Three Australian endemic species, S. angustum, S. brachypodum and S. ecarinatum, are closely related to S. bicolor, with S. angustum showing no difference to S. bicolor in ITS1 sequence. Sorghum macrospermum and S. laxiflorum form a strong clade within the Eusorghum branch indicating closer relationships to this group than to any of the Parasorghum or Stiposorghum species. Saccharum officinarum has shown closer relationships to Sorghum than to Zea mays, while the close relationship of Cleistachne sorghoides to Sorghum has been confirmed. These relationships between Sorghum species provide an important guide for plant breeders to exploit the wider Sorghum genepool through crosses between wild and cultivated species in an effort to improve sorghum production. Received April 30, 2001 Accepted July 10, 2001     

Genome organization in diploid hybrid species of Argyranthemum (Asteraceae) in the Canary Islands

Two diploid species of hybrid origin, Argyranthemum lemsii and A. sundingii , have been described from different valleys in the Anaga peninsula, north-east Tenerife. They have previously been shown to originate from hybridization between the same parental species, the montane A. broussonetii and the coastal A. frutescens , A. broussonetii being the chloroplast donor in one valley and A. frutescens in the other. The specific status of the two hybrid species has been questioned. In this study we used karyotype analysis, FISH, and GISH to address the question of multiple diploid hybrid speciation. GISH did not discriminate clearly between the parental genomes, but differential labelling was observed in separate hybrid populations, indicating different chromosomal rearrangements in different valleys. Small karyotype differences and local loss of rDNA were also observed. Thus separate origins of the same hybrid combination in different valleys in Tenerife have been verified. Our results add some support to the recognition of two species of hybrid origin, but the case serves to illustrate some of the many problems connected with the species concept in plants.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 141 , 491–501.     

Genetic structure of the rare and endangered moss <Emphasis Type="Italic">Campylopus oerstedianus</Emphasis> (Dicranaceae) in Europe

The genetic structure, diversity and phylogeography of the moss species Campylopus oerstedianus in Europe was studied, based on the ITS region of the nrDNA of nine selected European populations. Although this species is only known in sterile stage, long-distance dispersal and gene flow among populations seem to be present within Europe. High levels of genetic differentiation between the investigated Greek population and the western European populations indicate a long lasting isolation. The populations from France and Switzerland root together and supposedly have a common origin. From the French populations, the one from the Pyrenees is the most basal one and the populations in the Massif Central and the Vosges Mts can be derived from it. This indicates relatively recent dispersal of the species from the Mediterranean to the north, in spite of the lack of sporophytes and the fact that the type of the dispersed propagules and their vectors are not obvious.     

Development of methods for detection and Agrobacterium-mediated transformation of the sterile,endophytic fungus Muscodor albus

Symbiotic endophytes, unlike plant pathogens, do not usually induce visible host response. This may constraint the researcher's decision whether a plant has been successfully infected by the endophyte. In order to properly study the establishment, development and progress of an endophyte in the host plant and host-endophyte interactions, methods for the identification and localization of endophytic microorganisms are needed. Towards this aim, we focused at two levels: (A) We constructed M. albus-specific primers for polymerase chain reaction (PCR). In vitro, these primers specifically detected only M. albus strains and not isolates of related fungi (such as Daldinia sp. and a Xylariaceae sp.). (B) For direct visualization of the fungi, we inserted a reporter gene (gfp) into M. albus hyphae using Agrobacterium-mediated transformation. Since M. albus is a sterile fungus (i.e., without spores or fungal fruiting bodies), we used chopped fungal mycelium for the transformation procedure. We transformed three different isolates of M. albus using Agrobacterium-mediated transformation. Fifty-nine different transformants were collected with a transformation efficacy of 0.0004–0.0026%. Although PCR-based detection and direct visualization of the transformants in planta were unsuccessful, all tested transformants (with one exception) exhibited similar biological activity to their cognate wild type. This work provides a significant step forward in molecular research of the relationships between this endophytic genus and their hosts.     

The Application of Sequence Analysis of rDNA Fragment to the Systematic Study of the Subfamily Cyrtandroideae (Gesneriaceae)

A molecular phylogeny of the subfamily Cyrtandroideae represented by five genera of four tribes was constructed using sequence analysis of the internal transcribed spacers (ITS) and partial 5.8 S rRNA gene (3’end) of nuclear ribosomal DNA. Direct PCR sequencing method was used in the study. The sequences of ITS-1 in the five species range from 234 bp to 258 bp in size and those of ITS-2 from 218 bp to 246 bp. The ITS-1 (258 bp) and ITS-2 (218 bp) of Whytockia bijieensis differ greatly from those of the other species in size, sequence and G + C content, and therefore the tribe Klugieae represented by W. bijieensis may have diverged from the ancestor of the subfamily Cyrtandroideae at a very early time. In PAUP analysis, W. bijieensis was used as the functional outgroup, and only one most parsimonious Fitch tree was obtained through exhaustive search. The tree has 353 steps, with CI = 0. 932 and RI = 0. 529. In the tree, Chirita crassifolia is basal to a monophyletic group comprising Cyrtandra umbellifera, Briggisia longipes and Anna mollifolia, and the monophyletic group is strongly supported by the bootstrap value (97). The tribes Trichosporeae and Cyrtandreae represented respectively by Anna mollifolia and Cyrtandra urnbellifera both evolved from the tribe Didymorcarpeae, which can explain why many intermediate taxa exist among the three tribes. According to this, the present authors suggest that the tribe Trichosporeae and the tribe Cyrtandreae be merged with the tribeDidymocarpeae.     

Molecular phylogenetics of Vanda and related genera (Orchidaceae)

The genus Vanda and its affiliated taxa are a diverse group of horticulturally important species of orchids occurring mainly in South‐East Asia, for which generic limits are poorly defined. Here, we present a molecular study using sequence data from three plastid DNA regions. It is shown that Vanda s.l. forms a clade containing approximately 73 species, including the previously accepted genera Ascocentrum, Euanthe, Christensonia, Neofinetia and Trudelia, and the species Aerides flabellata. Resolution of the phylogenetic relationships of species in Vanda s.l. is relatively poor, but existing morphological classifications for Vanda are incongruent with the results produced. Some novel species relationships are revealed, and a new morphological sectional classification is proposed based on support for these groupings and corresponding morphological characters shared by taxa and their geographical distributions. The putative occurrence of multiple pollination syndromes in this group of taxa, combined with complex biogeographical history of the South‐East Asian region, is discussed in the context of these results. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 549–572.     

Molecular genetic and quantitative trait divergence associated with recent homoploid hybrid speciation: a study of Senecio squalidus (Asteraceae)

Hybridization is increasingly seen as a trigger for rapid evolution and speciation. To quantify and qualify divergence associated with recent homoploid hybrid speciation, we compared quantitative trait (QT) and molecular genetic variation between the homoploid hybrid species Senecio squalidus and its parental species, S. aethnensis and S. chrysanthemifolius, and also their naturally occurring Sicilian hybrids. S. squalidus originated and became invasive in the United Kingdom following the introduction of hybrid plants from Mount Etna, Sicily, about 300 years ago. We recorded considerable molecular genetic differentiation between S. squalidus and its parents and their Sicilian hybrids in terms of both reduced genetic diversity and altered allele frequencies, potentially due to the genetic bottleneck associated with introduction to the United Kingdom. S. squalidus is also distinct from its parents and Sicilian hybrids for QTs, but less so than for molecular genetic markers. We suggest that this is due to resilience of polygenic QTs to changes in allele frequency or lack of selection for hybrid niche divergence in geographic isolation. While S. squalidus is intermediate or parental-like for most QTs, some trangressively distinct traits were observed, which might indicate emerging local adaptation in its invasive range. This study emphasizes the important contribution of founder events and geographic isolation to successful homoploid hybrid speciation.     

Molecular reexamination of korean umbelliferae based on internal transcribed spacer sequences of rDNA:Ligusticum tenuissimum (Nakai) Kitagawa andLibanotis coreana (Wolff) kitagawa

The taxonomic status ofLigusticum tenuissimum (Nakai) Kitagawa andLibanotis coreana (Wolff) Kitagawa has been controversial in Korea. We examined their phylogenetic relationships by comparing the internal transcribed spacer (=ITS) sequences of the nuclear ribosomal RNA gene (=rDNA) with another seven species in the Korean Umbelliferae. Our results support the legitimacy of the nomenclatural combination withL. tenuissimum Kitagawa rather than withAngelica tenuissima Nakai. We also suggest usingL coreana (Wolff) Kitagawa instead ofSeseli coreanum Wolff becauseL. coreana has been completely separated from most taxa of the genusSeseli. In addition, we have confirmed at least three phylogenetic lines in the genusLigusticum. One is the core group ofLigusticum that comprisesL tenuissimum and four other species. This clade includes theLigusticum hultenii line andLigusticum scothicum, known as an anomaly ofLigusticum. The second clade is composed ofLigusticum physospermifolium withSeseli monatum, which indicates the polyphyly ofLigusticum. The third line isLigusticum acutilobum, clustered as a sister grade ofDystaenia.     

基于ITS序列分析探讨杜鹃属映山红亚属的组间关系

以叶状苞亚属的叶状苞杜鹃为外类群,以杜鹃属映山红亚属（subg.Tsutsusi)2组12种杜鹃和羊踯躅亚属（subg.Pentanthera）3种4种杜鹃的ITS区（包括5.8S rDNA)的序列了系统学分析。3个亚属的ITS区序长度范围为642－645bp。排序后ITS区的序列长度为653个位点,gap做缺失处理时,变异位点和信息位点分别占6．58％和3．68％。运用PAUP4．0软件分析,获得15个最简树,步长为75,一致性指数（CI）和维持性指数（RI）值分别为0．9333和0．9515,利用15个最简约树获取严格一致树,结果表明：1）映山红亚属为一单系类群,其内部支持率为81％;2）不支持将R.ashiroi独立成假映山红组,也不支持将R.tashiroi并入映山红组,而支持将R.tashiroi并入轮生叶组中的观点;3）支持将R.tsusiophyllum并入映山红组中的观点;4）大字杜鹃的系统位置还需进一步的研究。     

Genetic diversity and distribution patterns of diploid and polyploid hybrid water frog populations (Pelophylax esculentus complex) across Europe

Polyploidization is a rare yet sometimes successful way for animals to rapidly create geno‐ and phenotypes that may colonize new habitats and quickly adapt to environmental changes. In this study, we use water frogs of the Pelophylax esculentus complex, comprising two species (Pelophylax lessonae, genotype LL; Pelophylax ridibundus, RR) and various diploid (LR) and triploid (LLR, LRR) hybrid forms, summarized as P. esculentus, as a model for studying recent hybridization and polyploidization in the context of speciation. Specifically, we compared the geographic distribution and genetic diversity of diploid and triploid hybrids across Europe to understand their origin, maintenance and potential role in hybrid speciation. We found that different hybrid and parental genotypes are not evenly distributed across Europe. Rather, their genetic diversity is structured by latitude and longitude and the presence/absence of parental species but not of triploids. Highest genetic diversity was observed in central and eastern Europe, the lowest in the northwestern parts of Europe. This gradient can be explained by the decrease in genetic diversity during postglacial expansion from southeastern glacial refuge areas. Genealogical relationships calculated on the basis of microsatellite data clearly indicate that hybrids are of multiple origin and include a huge variety of parental genomes. Water frogs in mixed‐ploidy populations without any parental species (i.e. all‐hybrid populations) can be viewed as evolutionary units that may be on their way towards hybrid speciation. Maintenance of such all‐hybrid populations requires a continuous exchange of genomes between diploids and triploids, but scenarios for alternative evolutionary trajectories are discussed.     

Genetic variation relevant for the conservation of the narrow endemic Senecio carbonensis (Asteraceae) from the southern Andes

We studied morphological variation, reproductive biology and genetic structure of Senecio carbonensis, a narrow endemic from high elevations of the southern Andes, and compared it to Senecio peteroanus, a closely related widespread congeneric species. Using ANOVAs and discriminant analysis we showed that populations of S. carbonensis were more similar to each other in their morphology, had comparatively limited reproductive capacity and presented lower plant density and more reduced plant cover than populations of S. peteroanus. Similar high genetic variation was found at the population and species level in both species, based on isozyme variation at 14 and 11 putative gene loci that were resolved in S. carbonensis and S. peteroanus, respectively. The two species were genetically distinct. However, the small genetic distance between populations of each species suggests that either they were recently founded and that genetic drift did not have time to promote divergence, or that its effects are masked by significant current gene flow. These results show that ecological and reproductive characteristics of S. carbonensis may limit its extension and abundance. In contrast, high genetic variation at the population level is probably favored by self‐incompatibility. Despite the restricted geographical distribution and low plant density of S. carbonensis populations, genetic characteristics do not seem to be limiting their long‐term persistence. This information suggests that populations of S. carbonensis are not at risk of extinction as a result of genetic factors, although it is important to study and monitor population dynamics to further assess the degree of recruitment through time.     

Patterns of genetic,phenotypic, and acoustic variation across a chiffchaff (Phylloscopus collybita abietinus/tristis) hybrid zone

Characterizing patterns of evolution of genetic and phenotypic divergence between incipient species is essential to understand how evolution of reproductive isolation proceeds. Hybrid zones are excellent for studying such processes, as they provide opportunities to assess trait variation in individuals with mixed genetic background and to quantify gene flow across different genomic regions. Here, we combine plumage, song, mtDNA and whole‐genome sequence data and analyze variation across a sympatric zone between the European and the Siberian chiffchaff (Phylloscopus collybita abietinus/tristis) to study how gene exchange between the lineages affects trait variation. Our results show that chiffchaff within the sympatric region show more extensive trait variation than allopatric birds, with a large proportion of individuals exhibiting intermediate phenotypic characters. The genomic differentiation between the subspecies is lower in sympatry than in allopatry and sympatric birds have a mix of genetic ancestry indicating extensive ongoing and past gene flow. Patterns of phenotypic and genetic variation also vary between regions within the hybrid zone, potentially reflecting differences in population densities, age of secondary contact, or differences in mate recognition or mate preference. The genomic data support the presence of two distinct genetic clades corresponding to allopatric abietinus and tristis and that genetic admixture is the force underlying trait variation in the sympatric region—the previously described subspecies (“fulvescens”) from the region is therefore not likely a distinct taxon. In addition, we conclude that subspecies identification based on appearance is uncertain as an individual with an apparently distinct phenotype can have a considerable proportion of the genome composed of mixed alleles, or even a major part of the genome introgressed from the other subspecies. Our results provide insights into the dynamics of admixture across subspecies boundaries and have implications for understanding speciation processes and for the identification of specific chiffchaff individuals based on phenotypic characters.