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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 14 February 2017, Vol.114(7), pp.1726-1731
    Description: The movement of nuclear DNA from one vascular plant species to another in the absence of fertilization is thought to be rare. Here, nonnative rRNA gene [ribosomal DNA (rDNA)] copies were identified in a set of 16 diploid barley () species; their origin was traceable via their internal transcribed spacer (ITS) sequence to five distinct Panicoideae genera, a lineage that split from the Pooideae about 60 Mya. Phylogenetic, cytogenetic, and genomic analyses implied that the nonnative sequences were acquired between 1 and 5 Mya after a series of multiple events, with the result that some current sp. individuals harbor up to five different panicoid rDNA units in addition to the native rDNA copies. There was no evidence that any of the nonnative rDNA units were transcribed; some showed indications of having been silenced via pseudogenization. A single copy of a sp. rDNA unit present in had been interrupted by a native transposable element and was surrounded by about 70 kbp of mostly noncoding sequence of panicoid origin. The data suggest that horizontal gene transfer between vascular plants is not a rare event, that it is not necessarily restricted to one or a few genes only, and that it can be selectively neutral.
    Keywords: Hordeum ; Panicoideae ; Triticeae ; Horizontal Gene Transfer ; Transposable Elements ; Gene Transfer, Horizontal ; Phylogeny ; Cell Nucleus -- Genetics ; DNA, Ribosomal -- Genetics ; Poaceae -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    Language: English
    In: PLoS ONE, 2012, Vol.7(3), p.e33808
    Description: Polyploidization is a major mechanism of speciation in plants. Within the barley genus Hordeum , approximately half of the taxa are polyploids. While for diploid species a good hypothesis of phylogenetic relationships exists, there is little information available for the polyploids (4×, 6×) of Hordeum . Relationships among all 33 diploid and polyploid Hordeum species were analyzed with the low-copy nuclear marker region TOPO6 for 341 Hordeum individuals and eight outgroup species. PCR products were either directly sequenced or cloned and on average 12 clones per individual were included in phylogenetic analyses. In most diploid Hordeum species TOPO6 is probably a single-copy locus. Most sequences found in polyploid individuals phylogenetically cluster together with sequences derived from diploid species and thus allow the identification of parental taxa of polyploids. Four groups of sequences occurring only in polyploid taxa are interpreted as footprints of extinct diploid taxa, which contributed to allopolyploid evolution. Our analysis identifies three key species involved in the evolution of the American polyploids of the genus. ( i ) All but one of the American tetraploids have a TOPO6 copy originating from the Central Asian diploid H. roshevitzii , the second copy clustering with different American diploid species. ( ii ) All hexaploid species from the New World have a copy of an extinct close relative of H. californicum and ( iii ) possess the TOPO6 sequence pattern of tetraploid H. jubatum , each with an additional copy derived from different American diploids. Tetraploid H. bulbosum is an autopolyploid, while the assumed autopolyploid H. brevisubulatum (4×, 6×) was identified as allopolyploid throughout most of its distribution area. The use of a proof-reading DNA polymerase in PCR reduced the proportion of chimerical sequences in polyploids in comparison to Taq polymerase.
    Keywords: Research Article ; Agriculture ; Biology ; Plant Biology ; Evolutionary Biology
    E-ISSN: 1932-6203
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  • 3
    Language: English
    In: Molecular Phylogenetics and Evolution, 2010, Vol.55(2), pp.650-659
    Description: Wall barley ( ) occurs with three subspecies, naturally distributed from southern Central Asia through the Mediterranean region to northwestern Europe, but now is an invasive weed in many parts of the world. Subspecies is diploid, while subspp. and are tetraploids, the latter also occurring with a hexaploid cytotype. Earlier analyses were inconclusive regarding auto- or allopolyploid origins of subspp. and . We analyzed the phylogeny of the taxon group using amplified fragment length polymorphisms (AFLP), sequences of cloned PCR products of the nuclear ribosomal DNA internal transcribed spacer region (ITS), a part of the nuclear single-copy gene topoisomerase 6 (Topo6) spanning two introns, and sequences of the chloroplast L-F region together with length variation at six chloroplast microsatellite loci, including multiple individuals of each subspecies and cytotype, covering the entire natural distribution area of the species. Phylogenetic analyses with all used markers differentiate diploid and polyploids. Sequences of both nuclear regions indicated that diploid subsp. was involved in tetraploid formation together with a now extinct species belonging to the same genome group (Xu). Furthermore, AFLP and ITS analyses suggest that a third, though closely related extinct taxon contributed to hexaploid formation. No method was able to discern tetraploid subspp. and , which we attribute to the young age of subsp. . None of the used molecular markers revealed a strong geographic pattern of genetic variation that would allow comprehensive phylogeographic analysis, most probably due to the very effective seed dispersal of the taxa.
    Keywords: Aflp ; Allopolyploidy ; Chloroplast Trnl-F ; Evolution ; Hordeum Murinum ; Nrdna Internal Transcribed Spacer (Its) ; Phylogeography ; Polyploid Evolution ; Topoisomerase 6 (Topo6) ; Biology
    ISSN: 1055-7903
    E-ISSN: 1095-9513
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  • 4
    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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  • 5
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 2012, Vol.109(33), pp.13343-13346
    Description: Supernumerary B chromosomes are optional additions to the basic set of A chromosomes, and occur in all eukaryotic groups. They differ from the basic complement in morphology, pairing behavior, and inheritance and are not required for normal growth and development. The current view is that B chromosomes are parasitic elements comparable to selfish DNA, like transposons. In contrast to transposons, they are autonomously inherited independent of the host genome and have their own mechanisms of mitotic or meiotic drive. Although B chromosomes were first described a century ago, little is known about their origin and molecular makeup. The widely accepted view is that they are derived from fragments of A chromosomes and/or generated in response to interspecific hybridization. Through next-generation sequencing of sorted A and B chromosomes, we show that B chromosomes of rye are rich in gene-derived sequences, allowing us to trace their origin to fragments of A chromosomes, with the largest parts corresponding to rye chromosomes 3R and 7R. Compared with A chromosomes, B chromosomes were also found to accumulate large amounts of specific repeats and insertions of organellar DNA. The origin of rye B chromosomes occurred an estimated ∼1.1–1.3 Mya, overlapping in time with the onset of the genus Secale (1.7 Mya). We propose a comprehensive model of B chromosome evolution, including its origin by recombination of several A chromosomes followed by capturing of additional A-derived and organellar sequences and amplification of B-specific repeats. ; p. 13343-13346.
    Keywords: Models ; Chromosomes ; Transposons ; Meiotic Drive ; Dna ; Growth And Development ; Interspecific Hybridization ; Genome ; Secale ; Rye ; Evolution ; High-Throughput Nucleotide Sequencing
    ISSN: 0027-8424
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  • 6
    Language: English
    In: Molecular Phylogenetics and Evolution, January 2013, Vol.66(1), pp.1-16
    Description: ► A densely sampled phylogeny for the worldwide-distributed genus based on nrDNA ITS sequences. ► More than 40% of the c. 500 species sampled, considering almost all sections. splits into three large clades and two smaller grades, which are supported by morphology. ► Tree-like forms have evolved convergently in high elevation tropical habitats of Africa and South America. Phylogenetic hypotheses for the large cosmopolitan genus (St. John’s wort) have previously been based on morphology, and molecular studies have thus far included only a few species. In this study, we used 360 sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) for 206 species representing (incl. and ) and three other genera of Hypericaceae to generate an explicit phylogenetic hypothesis for the genus using parsimony and model-based methods. The results indicate that the small genus is nested in a clade within containing most of the New World species. Sister to is from Central America. Within , three large clades and two smaller grades were found; these are based on their general morphology, especially characters used previously in taxonomy of the genus. Relative to the most recent classification, around 60% of the sections of were monophyletic. We used a Bayesian approach to reconstruct ancestral states of selected morphological characters, which resulted in recognition of characters that support major clades within the genus and a revised interpretation of morphological evolution in . The shrubby habit represents the plesiomorphic state from which herbs evolved several times. Arborescent species have radiated convergently in high-elevation habitats in tropical Africa and South America.
    Keywords: Character Evolution ; Hypericaceae ; Internal Transcribed Spacer (Its) ; Phylogeny ; Thornea ; Triadenum ; Biology
    ISSN: 1055-7903
    E-ISSN: 1095-9513
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  • 7
    Language: English
    In: Plant Systematics and Evolution, 2016, Vol.302(2), pp.239-244
    Description: TOPO6 , a nuclear gene-marker region of subunit B of the plant homolog of archaean topoisomerase VI, occurs as single-copy locus in the haploid genome of most plant groups. The gene consists mainly of 19 exons and 18 introns, which provide conserved primer binding sites for PCR amplification in many angiosperm families combined with variable sequence stretches that can be explored in molecular systematics. Here intron/exon structure, sequence diversity, and a set of amplification primers are described to use TOPO6 as single-copy phylogenetic marker region in a wide range of plant taxa, either through PCR amplification or hybridization-based sequence capture.
    Keywords: Phylogenetic analysis ; Single-copy gene ; Topoisomerase IV B ; TOPO6 ; Universal primers
    ISSN: 0378-2697
    E-ISSN: 2199-6881
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  • 8
    Language: English
    In: PLoS ONE, 01 January 2016, Vol.11(3), p.e0149726
    Description: As a result of a taxonomic and phylogenetic revision of Astragalus section Hymenostegis we identified a new species of Astragalus from northwestern Iran, namely A. remotispicatus spec. nov., which is described and illustrated here. It is morphologically similar to A. karl-heinzii in possessing a lax inflorescence. Phylogenetic inference of the nuclear ribosomal DNA internal transcribed spacer (ITS) region support A. remotispicatus as a clearly distinct species within the lax-inflorescence group of this section. Also the placement of A. sciureus var. subsessilis was found to be wrong and this taxon should be treated as a synonym within A. kohrudicus.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 9
    In: Molecular Ecology, April 2010, Vol.19(7), pp.1423-1438
    Description: In this study, we explore the interplay of population demography with the evolution of ecological niches during or after speciation in . While large populations maintain a high level of standing genetic diversity, gene flow and recombination buffers against fast alterations in ecological adaptation. Small populations harbour lower allele diversity but can more easily shift to new niches if they initially survive under changed conditions. Thus, large populations should be more conservative regarding niche changes in comparison to small populations. We used environmental niche modelling together with phylogenetic, phylogeographic and population genetic analyses to infer the correlation of population demography with changes in ecological niche dimensions in 12 diploid species from the New World, forming four monophyletic groups. Our analyses found both shifts and conservatism in distinct niche dimensions within and among clades. Speciation due to vicariance resulted in three species with no pronounced climate niche differences, while species originating due to long‐distance dispersals or otherwise encountering genetic bottlenecks mostly revealed climate niche shifts. Niche convergence among clades indicates a niche‐filling pattern during the last 2 million years in South American . We provide evidence that species, which did not encounter population reductions mainly showed ecoclimatic niche conservatism, while major niche shifts occurred in species which have undergone population bottlenecks. Our data allow the conclusion that population demography influences adaptation and niche shifts or conservatism in South American species.
    Keywords: Environmental Niche Modelling ; Hordeum ; Niche Conservatism ; Niche Evolution ; Phylogeny ; Phylogeography ; Population Genetics ; Population Size
    ISSN: 0962-1083
    E-ISSN: 1365-294X
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  • 10
    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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