Diploid \u3ci\u3eAllium ramosum\u3c/i\u3e from East Mongolia: A Missing Link for the Origin of the Crop Species \u3ci\u3eA. tuberosum\u3c/i\u3e?

In eastern Mongolia, a diploid close relative of the tetraploid (4x) crop species Allium tuberosum and its closest wild relative A. ramosum (4x) was found and characterized by karyotype analysis and with molecular marker techniques. An earlier analyses revealed A. ramosum to be sister of the crop but excluded it as its progenitor. At that time a putative diploid cytotype of A. ramosum was hypothesized as a potential progenitor taxon of the tetraploids. New phylogenetic analyses of chloroplast and nuclear DNA sequences including the recently found cytotype (A. aff. tuberosum) together with A. tuberosum and A. ramosum accessions revealed a sister group relationship of both species, with A. aff. tuberosum having sequences very similar or identical with A. ramosum. Two fingerprint analyses (RAPD, SCoT) resulted in phylogenetic trees where aff. tuberosum grouped basal to A. ramosum, although the two taxa are morphologically and ecologically clearly differentiated. We conclude that East Mongolian aff. tuberosum is not the progenitor of A. tuberosum but that it might belong to a stock of ancient lineages that gave rise to both tetraploid taxa

Phylogeny and New Intrageneric Classification of Allium (Alliaceae) Based on Nuclear Ribosomal DNA ITS Sequences

The internal transcribed spacer region (ITS) of nuclear ribosomal DNA was sequenced from 195 representative species of Allium, two species of Nothoscordum, and one species each of lpheion, Dichelostemma, and Tulbaghia. Within the Allium species the lengths of the ITS regions were in a range from 612 to 661 base pairs and pairwise genetic distances reached up to 46%. The ITS data supported the inclusion of Nectaroscordum, Caloscordum, and Milula into Allium. Subgenera Rhizirideum and Allium, as well as sects. Reticulatobulbosa and Oreiprason were non-monophyletic taxa. Based on the phylogenetic relations, a new classification of genus Allium consisting of 15 monophyletic subgenera is presented. Sections Microscordum, Anguinum, Porphyroprason, Vvedenskya, Butomissa, Cyathophora, and Reticulatobulbosa are raised to subgeneric rank. Sections Austromontana N. Friesen, Eduardia N. Friesen, Mediasia F. O. Khassanov, S. C. Yengalycheva et N. Friesen, Nigrimontana N. Friesen, Falcatifolia N. Friesen, and Condensatum N. Friesen are newly described. Series Daghestanica, Pallasia, and Scabriscapa, as well as subsects. Eremoprasum, Longivaginata, and Sikkimensia are raised to sectional rank. A taxonomic conspectus of Allium at sectional level is given

Oligocene niche shift, Miocene diversification – cold tolerance and accelerated speciation rates in the St. John’s Worts (Hypericum, Hypericaceae)

Background: Our aim is to understand the evolution of species-rich plant groups that shifted from tropical into cold/temperate biomes. It is well known that climate affects evolutionary processes, such as how fast species diversify, species range shifts, and species distributions. Many plant lineages may have gone extinct in the Northern Hemisphere due to Late Eocene climate cooling, while some tropical lineages may have adapted to temperate conditions and radiated; the hyper-diverse and geographically widespread genus Hypericum is one of these. Results: To investigate the effect of macroecological niche shifts on evolutionary success we combine historical biogeography with analyses of diversification dynamics and climatic niche shifts in a phylogenetic framework. Hypericum evolved cold tolerance c. 30 million years ago, and successfully colonized all ice-free continents, where today ~500 species exist. The other members of Hypericaceae stayed in their tropical habitats and evolved into ~120 species. We identified a 15–20 million year lag between the initial change in temperature preference in Hypericum and subsequent diversification rate shifts in the Miocene. Conclusions: Contrary to the dramatic niche shift early in the evolution of Hypericum most extant species occur in temperate climates including high elevations in the tropics. These cold/temperate niches are a distinctive characteristic of Hypericum. We conclude that the initial release from an evolutionary constraint (from tropical to temperate climates) is an important novelty in Hypericum. However, the initial shift in the adaptive landscape into colder climates appears to be a precondition, and may not be directly related to increased diversification rates. Instead, subsequent events of mountain formation and further climate cooling may better explain distribution patterns and species-richness in Hypericum. These findings exemplify important macroevolutionary patterns of plant diversification during large-scale global climate change

Genomic, karyological and morphological changes of South American garlics (Ipheion) provide insights into mechanisms of speciation in the Pampean region

Speciation proceeds through mechanisms that promote reproductive isolation and shape the extent of genetic variation in natural populations, and thus its study is essential to understand the evolutionary processes leading to increased biodiversity. Chromosomal rearrangements are known to facilitate reproductive isolation by hybrid sterility and favour speciation events. The genus Ipheion (Amaryllidaceae, Allioideae) is unique as its species exhibit a remarkable karyological variability but lack population-level genetic data. To unveil the diversification processes acting upon the formation of new lineages within Ipheion in the Pampas of South America, we combined morphology and karyology approaches with genotyping-by-sequencing. Our phylogenomic and population genomics results supported the taxonomic division of Ipheion into three morphological and genetically well-differentiated groups. The origin of Ipheion uniflorum was traced back to its current southern distribution area in the southern Pampean region (in Argentina), from where it had expanded to the north reaching Uruguay. Our results further suggested that chromosome rearrangements and ploidy shifts had triggered speciation events, first during the origin of I. uniflorum and later during its subsequent diversification into I. recurvifolium and I. tweedieanum, in both cases reinforced by extrinsic factors and biogeographical settings. The current study illustrates the analytical power of multidisciplinary approaches integrating phylo- and population genomics with classic analyses to reveal evolutionary processes in plants.Fil: Sassone, Agostina Belén. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; Argentina. Leibniz Institute of Plant Genetics and Crop Plant Research; AlemaniaFil: Hojsgaard, Diego H.. Leibniz Institute of Plant Genetics and Crop Plant Research; AlemaniaFil: Giussani, Liliana Mónica. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Brassac, Jonathan. Leibniz Institute of Plant Genetics and Crop Plant Research; AlemaniaFil: Blattner, Frank R.. Leibniz Institute of Plant Genetics and Crop Plant Research; Alemani

Annual report 2015

Accessions considered in the study. Overview of the material considered in this study. For all materials, the GenBank identifier, the accession and species name as used in this study (Species) as well as their species synonyms used in the donor seed banks or in the NCBI GenBank (Material source/Reference) are provided. The genome symbol, and the country of origin, where the material was originally collected are given. The ploidy level measured in the scope of this study and the information if a herbarium voucher could be deposited in the herbarium of IPK Gatersleben (GAT) is given. Genomic formulas of tetraploids and hexploids are given as “female x male parent”. The genomes of Aegilops taxa follow Kilian et al. [74] and Li et al. [84]. Genome denominations for Hordeum follow Blattner [107] and Bernhardt [12] for the remaining taxa. (XLS 84 kb

Progenitor-Derivative Relationships of Hordeum Polyploids (Poaceae, Triticeae) Inferred from Sequences of TOPO6, a Nuclear Low-Copy Gene Region

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

Statistical properties of DNA sequences revisited: the role of inverse bilateral symmetry in bacterial chromosomes

Herein it is shown that in order to study the statistical properties of DNA sequences in bacterial chromosomes it suffices to consider only one half of the chromosome because they are similar to its corresponding complementary sequence in the other half. This is due to the inverse bilateral symmetry of bacterial chromosomes. Contrary to the classical result that DNA coding regions of bacterial genomes are purely uncorrelated random sequences, here it is shown, via a renormalization group approach, that DNA random fluctuations of single bases are modulated by log-periodic variations. Distance series of triplets display long-range correlations in each half of the intact chromosome and in intronless protein-coding sequences, or both long-range correlations and log-periodic modulations along the whole chromosome. Hence scaling analyses of distance series of DNA sequences have to consider the functional units of bacterial chromosomes.Comment: 27 pages, 9 figure