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  • MEDLINE/PubMed (NLM)  (13)
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  • 1
    Language: English
    In: Journal of Plant Research, 2008, Vol.121(3), pp.261-270
    Description: The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, ITS2) represents the most widely applied nuclear marker in eukaryotic phylogenetics. Although this region has been assumed to evolve in concert, the number of investigations revealing high degrees of intra-individual polymorphism connected with the presence of pseudogenes has risen. The 5.8S rDNA is the most important diagnostic marker for functionality of the ITS region. In Mammillaria , intra-individual 5.8S rDNA polymorphisms of up to 36% and up to nine different types have been found. Twenty-eight of 30 cloned genomic Mammillaria sequences were identified as putative pseudogenes. For the identification of pseudogenic ITS regions, in addition to formal tests based on substitution rates, we attempted to focus on functional features of the 5.8S rDNA (5.8S motif, secondary structure). The importance of functional data for the identification of pseudogenes is outlined and discussed. The identification of pseudogenes is essential, because they may cause erroneous phylogenies and taxonomic problems.
    Keywords: 5.8S rDNA ; Intra-individual variability ; Mammillaria ; Pseudogene ; Secondary structure
    ISSN: 0918-9440
    E-ISSN: 1618-0860
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  • 2
    Language: English
    In: Molecular Phylogenetics and Evolution, March 2013, Vol.66(3), pp.617-627
    Description: ► We provide the first exhaustive phylogeny of crocuses based on nuclear sequences. ► We reconstruct chromosome number evolution and polyploidization in . ► 8 out of 15 series of are monophyletic, as well as probably both sections. ► Chromosome numbers increased multiple times independently by polyploidization. ► Supernumerary B chromosomes evolved at least five times independently within consists of about 100 species distributed from western Europe and northern Africa to western China, with the center of diversity on the Balkan Peninsula and in Asia Minor. Our study focuses on clarifying phylogenetic relationships and chromosome number evolution within the genus using sequences of the chloroplast L-F region, the nuclear ribosomal DNA internal transcribed spacer (ITS) region, and a part of the nuclear single-copy gene . In a combined dataset of ITS and L-F sequences, 115 individuals representing 110 taxa from both subgenera and all sections and series of were analyzed with Bayesian phylogenetic inference. For 79 individuals representing 74 taxa were included, and for the majority of them PCR amplicons were cloned and up to eight clones per individual were sequenced to detect allopolyploidization events. species were included as outgroup in both analyses. Characteristics of seed surface structures were evaluated by scanning electron microscopy. Phylogenetic analysis of ITS/ L-F data resulted in a monophyletic genus , probably monophyletic sections and , and inferred monophyly for eight of the 15 series of the genus. The aggregate, thought to be consisting of closely related subspecies, was found to be polyphyletic, the taxa occurring within three major clades in the phylogenetic tree. Cloning of resulted in the detection of homoeologous copies in about one third of the taxa of section , indicating an allotetraploid origin of this section. Reconstruction of chromosome number evolution along the phylogenetic tree using a probabilistic and a parsimony approach arrived at partly contradictory results. Both analyses agreed however on the occurrence of multiple polyploidization and dysploidy events. B chromosomes evolved at least five times independently within the genus, preferentially in clades characterized by karyotype changes.
    Keywords: B Chromosome ; Chromosome Number ; Crocus ; Evolution ; Internal Transcribed Spacer (Its) ; Pcosat103 ; Phylogeny ; Trnl-F ; Seed Testa ; Whole Genome Duplication ; Biology
    ISSN: 1055-7903
    E-ISSN: 1095-9513
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  • 3
    In: PLoS ONE, 2016, Vol.11(4)
    Description: Most flowers display distinct colour patterns comprising two different areas. The peripheral large-area component of floral colour patterns attracts flower visitors from some distance and the central small-area component guides flower visitors towards landing sites. Whereas the peripheral colour is largely variable among species, the central colour, produced mostly by anthers and pollen or pollen mimicking floral guides, is predominantly yellow and UV-absorbing. This holds also for yellow flowers that regularly display a UV bull’s eye pattern. Here we show that yellow-flowering Crocus species are a noticeable exception, since yellow-flowering Crocus species–being entirely UV-absorbing–exhibit low colour contrast between yellow reproductive organs and yellow tepals. The elongated yellow or orange-yellow style of Crocus flowers is a stamen-mimicking structure promoting cross-pollination by facilitating flower visitors’ contact with the apical stigma before the flower visitors are touching the anthers. Since Crocus species possess either yellow, violet or white tepals, the colour contrast between the stamen-mimicking style and the tepals varies among species. In this study comprising 106 Crocus species, it was tested whether the style length of Crocus flowers is dependent on the corolla colour. The results show that members of the genus Crocus with yellow tepals have evolved independently up to twelve times in the genus Crocus and that yellow-flowering Crocus species possess shorter styles as compared to violet- and white-flowering ones. The manipulation of flower visitors by anther-mimicking elongated styles in Crocu s flowers is discussed.
    Keywords: Research Article ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Biology And Life Sciences ; Research And Analysis Methods ; Biology And Life Sciences
    E-ISSN: 1932-6203
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  • 4
    Language: English
    In: Molecular Phylogenetics and Evolution, October 2018, Vol.127, pp.891-897
    Description: Phylogenetic relationships among the taxa of series are still unclear, preventing the understanding of species diversity and the evolution of the important spice saffron ( ). Therefore, we analyzed sequences of two chloroplast ( L- F, K- K) and three nuclear (TOPO6, ribosomal DNA ETS and ITS) marker regions to infer phylogenetic relationships among all species belonging to series . Our phylogenetic analyses resolved the relationships among all taxa of the series. and the former subspecies appeared polyphyletic. The latter deserve elevating the subspecies to species rank, while for a detailed study of species boundaries is necessary. Multi-locus and also genome-wide single nucleotide polymorphism data obtained through genotyping-by-sequencing placed within with no indication that other species contributed to the evolution of the triploid. Our analyses thus made an autotriploid origin of from very likely.
    Keywords: Crocus Series Crocus ; Evolution ; GBS ; Multi-Locus Analysis ; Phylogeny ; Saffron ; Biology
    ISSN: 1055-7903
    E-ISSN: 1095-9513
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  • 5
    Language: English
    In: Molecular Phylogenetics and Evolution, 2006, Vol.41(3), pp.579-593
    Description: Molecular studies of 21 species of the large Cactaceae genus representing a variety of intrageneric taxonomic levels revealed a high degree of intra-individual polymorphism of the internal transcribed spacer region (ITS1, 5.8S rDNA, ITS2). Only a few of these ITS copies belong to apparently functional genes, whereas most are probably non-functional (pseudogenes). As a multiple gene family, the ITS region is subjected to concerted evolution. However, the high degree of intra-individual polymorphism of up to 36% in ITS1 and up to 35% in ITS2 suggests a non-concerted evolution of these loci in . Conserved angiosperm motifs of ITS1 and ITS2 were compared between genomic and cDNA ITS clones of . Some of these motifs (e.g., ITS1 motif 1, ‘TGGT’ within ITS2) in combination with the determination of GC-content, length comparisons of the spacers and ITS2 secondary structure (helices II and III) are helpful in the identification of pseudogene rDNA regions.
    Keywords: Internal Transcribed Spacer ; Non-Concerted Evolution ; Mammillaria ; Pseudogene ; Its Motifs ; Its2 Secondary Structure ; Biology
    ISSN: 1055-7903
    E-ISSN: 1095-9513
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  • 6
    Language: English
    In: PLoS ONE, June 2, 2017, Vol.12(6), p.e0178402
    Description: Cistanthe longiscapa is an endemic annual herb and characteristic element of the Chilean Atacama Desert. Principal threats are the destruction of its seed deposits by human activities and reduced germination rates due to the decreasing occurrence of precipitation events. To enable population genetic and phylogeographic analyses in this species we performed paired-end shotgun sequencing (2x100 bp) of genomic DNA on the Illumina HiSeq platform and identified microsatellite (SSR) loci in the resulting sequences. From 29 million quality-filtered read pairs we obtained 549,174 contigs (average length 614 bp; N50 = 904). Searching for SSRs revealed 10,336 loci with microsatellite motifs. Initially, we designed primers for 96 loci, which were tested for PCR amplification on three C. longiscapa individuals. Successfully amplifying loci were further tested on eight individuals to screen for length variation in the resulting amplicons, and the alleles were exemplarily sequenced to infer the basis for the observed length variation. Finally we arrived at 26 validated SSR loci for population studies in C. longiscapa, which resulted in 146 bi-allelic SSR markers in our test sample of eight individuals. The genomic sequences were also used to assemble the plastid genome of C. longiscapa, which provides an additional set of maternally inherited genetic markers.
    Keywords: Genomes -- Analysis ; Dna Sequencing -- Analysis ; Genetic Markers -- Analysis ; Genomics -- Analysis ; Dna -- Analysis
    ISSN: 1932-6203
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  • 7
    Language: English
    In: ZooKeys, Jan 6, 2014, Issue 367, p.65(20)
    Description: Detailed information on species' ecological niche characteristics that can be related to declines and extinctions is indispensable for a better understanding of the relationship between the occurrence and performance of wild species and their environment and, moreover, for an improved assessment of the impacts of global change. Knowledge on species characteristics such as habitat requirements is already available in the ecological literature for butterflies, but information about their climatic requirements is still lacking. Here we present a unique dataset on the climatic niche characteristics of 397 European butterflies representing 91% of the European species (see Appendix). These characteristics were obtained by combining detailed information on butterfly distributions in Europe (which also led to the 'Distribution Atlas of Butterflies in Europe') and the corresponding climatic conditions. The presented dataset comprises information for the position and breadth of the following climatic niche characteristics: mean annual temperature, range in annual temperature, growing degree days, annual precipitation sum, range in annual precipitation and soil water content. The climatic niche position is indicated by the median and mean value for each climate variable across a species' range, accompanied by the 95% confidence interval for the mean and the number of grid cells used for calculations. Climatic niche breadth is indicated by the standard deviation and the minimum and maximum values for each climatic variable across a species' range. Database compilation was based on high quality standards and the data are ready to use for a broad range of applications. It is already evident that the information provided in this dataset is of great relevance for basic and applied ecology. Based on the species temperature index (STI, i.e. the mean temperature value per species), the community temperature index (CTI, i.e. the average STI value across the species in a community) was recently adopted as an indicator of climate change impact on biodiversity by the pan-European framework supporting the Convention on Biological Diversity (Streamlining European Biodiversity Indicators 2010) and has already been used in several scientific publications. The application potential of this database ranges from theoretical aspects such as assessments of past niche evolution or analyses of trait interdependencies to the very applied aspects of measuring, monitoring and projecting historical, ongoing and potential future responses to climate change using butterflies as an indicator. Keywords: Climate change, climate warming, CTI, global change, global warming, modelling, risk, trend, STI, Europe, butterflies, Lepidoptera, Papilionidae, Pieridae, Lycaenidae, Riodinidae, Nymphalidae, Hesperiidae
    Keywords: Butterflies – Analysis ; Soil Moisture – Analysis ; Climate – Analysis ; Biodiversity – Analysis ; Niches (Ecology) – Analysis ; Global Warming – Analysis
    ISSN: 1313-2989
    E-ISSN: 13132970
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  • 8
    Language: English
    In: Molecular Phylogenetics and Evolution, July 2019, Vol.136, pp.14-20
    Description: , the saffron crocus, is the source of saffron, which is made from the dried stigmas of the plant. It is a male-sterile triploid lineage that ever since its origin has been propagated vegetatively. Its mode of evolution and area of origin are matters of long-lasting debates. Here we analyzed chloroplast genomes and genome-wide DNA polymorphisms obtained through genotyping-by-sequencing (GBS) to infer the parent and area of origin of . These data were complemented by genome size measurements and analyses of nuclear single-copy genes. We could place 99.3% of saffron GBS alleles in , a species occurring in southeastern mainland Greece and on Aegean islands, identifying it as the sole progenitor of the saffron crocus. Phylogenetic and population assignment analyses together with chloroplast polymorphisms indicated the population in the vicinity of Athens as most similar to . We conclude that the crop is an autotriploid that evolved in Attica by combining two different genotypes of . Triploid sterility and vegetative propagation prevented afterwards segregation of the favorable traits of saffron, resulting in worldwide cultivation of a unique clonal lineage.
    Keywords: Autotriploidy ; Crocus ; Crop Evolution ; Domestication ; Genotyping-By-Sequencing ; Saffron ; Biology
    ISSN: 1055-7903
    E-ISSN: 1095-9513
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  • 9
    In: Ecology and Evolution, May 2019, Vol.9(10), pp.5870-5890
    Description: The Irano‐Turanian (IT) floristic region is considered an important center of origin for many taxa. However, there is a lack of studies dealing with typical IT genera that also occur in neighboring areas. The species‐rich monocot genus Salisb. shows a center of diversity in IT region and a distribution in adjacent regions, therefore representing a good study object to investigate spatial and temporal relationships among IT region and its neighboring areas (East Asia, Euro‐Siberia, Himalaya, and Mediterranean). We aimed at (a) testing the origin of the genus and of its major lineages in the IT region, (b) reconstructing divergence times, and (c) reconstructing colonization events. To address these problems, sequences of the ribosomal DNA internal transcribed spacer (ITS) region of 418 individuals and chloroplast intergenic spacers sequences (A‐H, L‐F) of 497 individuals, representing 116 species from all sections of the genus and nearly its entire distribution area were analyzed. Divergence times were estimated under a random molecular clock based on nrITS phylogeny, which was the most complete data set regarding the representation of species and distribution areas. Ancestral distribution ranges were estimated for the nrITS data set as well as for a combined data set, revealing that most likely originated in southwestern Asia. This genus first diversified there starting in the Early Miocene. In the Middle Miocene, migrated to the Mediterranean and to East Asia, while migration into Euro‐Siberia took place in the Late Miocene. During the Pleistocene, the Arctic was colonized and the most widespread species, reached North America. The Mediterranean basin was colonized multiple times from southwestern Asia or Euro‐Siberia. Most of the currently existing species originated during the last 3 Ma. Divergence time estimation and ancestral range reconstructions were carried out for the species‐rich monocot genus (Liliaceae). Our study could demonstrate that the species‐rich Irano‐Turanian (IT) floristic region, a current centre of species diversity, is also the origin of the genus and of its major linages. Colonisation of adjacent areas started from the IT floristic region and benefit from periods of climatic changes creating dry habits. Therefore, our study supports that the IT region is an important source of taxa for adjacent areas of Euro‐Siberia.
    Keywords: Ancestral Area Reconstruction ; Biogeography ; Dated Phylogeny ; Gagea ; Irano‐Turanian Region ; Southwestern Asia
    ISSN: 2045-7758
    E-ISSN: 2045-7758
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  • 10
    In: Nature Communications, 2016, Vol.7
    Description: Impacts of climate change on individual species are increasingly well documented, but we lack understanding of how these effects propagate through ecological communities. Here we combine species distribution models with ecological network analyses to test potential impacts of climate change on 〉700 plant and animal species in pollination and seed-dispersal networks from central Europe. We discover that animal species that interact with a low diversity of plant species have narrow climatic niches and are most vulnerable to climate change. In contrast, biotic specialization of plants is not related to climatic niche breadth and vulnerability. A simulation model incorporating different scenarios of species coextinction and capacities for partner switches shows that projected plant extinctions under climate change are more likely to trigger animal coextinctions than vice versa. This result demonstrates that impacts of climate change on biodiversity can be amplified via extinction cascades from plants to animals in ecological networks.
    Keywords: Climate Change ; Ecosystem ; Extinction, Biological ; Plants -- Metabolism;
    ISSN: 2041-1723
    E-ISSN: 2041-1723
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