The evolutionary history of the Arabidopsis arenosa complex : diverse tetraploids mask the Western Carpathian center of species and genetic diversity

The Arabidopsis arenosa complex is closely related to the model plant Arabidopsis thaliana. Species and subspecies in the complex are mainly biennial, predominantly outcrossing, herbaceous, and with a distribution range covering most parts of latitudes and the eastern reaches of Europe. In this study we present the first comprehensive evolutionary history of the A. arenosa species complex, covering its natural range, by using chromosome counts, nuclear AFLP data, and a maternally inherited marker from the chloroplast genome [trnL intron (trnL) and trnL/F intergenic spacer (trnL/F-IGS) of tRNALeu and tRNAPhe, respectively]. We unravel the broad-scale cytogeographic and phylogeographic patterns of diploids and tetraploids. Diploid cytotypes were exclusively found on the Balkan Peninsula and in the Carpathians while tetraploid cytotypes were found throughout the remaining distribution range of the A. arenosa complex. Three centers of genetic diversity were identified: the Balkan Peninsula, the Carpathians, and the unglaciated Eastern and Southeastern Alps. All three could have served as long-term refugia during Pleistocene climate oscillations. We hypothesize that the Western Carpathians were and still are the cradle of speciation within the A. arenosa complex due to the high species number and genetic diversity and the concurrence of both cytotypes there

An Arabidopsis introgression zone studied at high spatio-temporal resolution: interglacial and multiple genetic contact exemplified using whole nuclear and plastid genomes

Background: Gene flow between species, across ploidal levels, and even between evolutionary lineages is a common phenomenon in the genus Arabidopsis. However, apart from two genetically fully stabilized allotetraploid species that have been investigated in detail, the extent and temporal dynamics of hybridization are not well understood. An introgression zone, with tetraploid A. arenosa introgressing into A. lyrata subsp. petraea in the Eastern Austrian Forealps and subsequent expansion towards pannonical lowlands, was described previously based on morphological observations as well as molecular data using microsatellite and plastid DNA markers. Here we investigate the spatio-temporal context of this suture zone, making use of the potential of next-generation sequencing and whole-genome data. By utilizing a combination of nuclear and plastid genomic data, the extent, direction and temporal dynamics of gene flow are elucidated in detail and Late Pleistocene evolutionary processes are resolved. Results: Analysis of nuclear genomic data significantly recognizes the clinal structure of the introgression zone, but also reveals that hybridization and introgression is more common and substantial than previously thought. Also tetraploid A. lyrata and A. arenosa subsp. borbasii from outside the previously defined suture zone show genomic signals of past introgression. A. lyrata is shown to serve usually as the maternal parent in these hybridizations, but one exception is identified from plastome-based phylogenetic reconstruction. Using plastid phylogenomics with secondary time calibration, the origin of A. lyrata and A. arenosa lineages is pre-dating the last three glaciation complexes (approx. 550,000 years ago). Hybridization and introgression followed during the last two glacial-interglacial periods (since approx. 300,000 years ago) with later secondary contact at the northern and southern border of the introgression zone during the Holocene. Conclusions: Footprints of adaptive introgression in the Northeastern Forealps are older than expected and predate the Last Glaciation Maximum. This correlates well with high genetic diversity found within areas that served as refuge area multiple times. Our data also provide some first hints that early introgressed and presumably preadapted populations account for successful and rapid postglacial re-colonization and range expansion

First Order Calculation of the Inclusive Cross Section pp to ZZ by Graviton Exchange in Large Extra Dimensions

We calculate the inclusive cross section of double Z-boson production within large extra dimensions at the Large Hadron Collider (LHC). Using perturbatively quantized gravity in the ADD model we perform a first order calculation of the graviton mediated contribution to the pp to ZZ cross section. At low energies (e.g. Tevatron) this additional contribution is very small, making it virtually unobservable, for a fundamental mass scale above 2500 GeV. At LHC energies however, the calculation indicates that the ZZ-production rate within the ADD model should differ significantly from the Standard Model if the new fundamental mass scale would be below 15000 GeV. A comparison with the observed production rate at the LHC might therefore provide direct hints on the number and structure of the extra dimensions.Comment: 7 pages, 7 figures, accepted for publication in Phys. Rev.

Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants

Background: Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR source for plants of economic relevance but their application to non-model species is still modest. Methods: Here, we explored the use of publicly available ESTs (GenBank at the National Center for Biotechnology Information-NCBI) for SSRs development in non-model plants, focusing on genera listed by the International Union for the Conservation of Nature (IUCN). We also search two model genera with fully annotated genomes for EST-SSRs, Arabidopsis and Oryza, and used them as controls for genome distribution analyses. Overall, we downloaded 16 031 555 sequences for 258 plant genera which were mined for SSRsand their primers with the help of QDD1. Genome distribution analyses in Oryza and Arabidopsis were done by blasting the sequences with SSR against the Oryza sativa and Arabidopsis thaliana reference genomes implemented in the Basal Local Alignment Tool (BLAST) of the NCBI website. Finally, we performed an empirical test to determine the performance of our EST-SSRs in a few individuals from four species of two eudicot genera, Trifolium and Centaurea. Results: We explored a total of 14 498 726 EST sequences from the dbEST database (NCBI) in 257 plant genera from the IUCN Red List. We identify a very large number (17 102) of ready-to-test EST-SSRs in most plant genera (193) at no cost. Overall, dinucleotide and trinucleotide repeats were the prevalent types but the abundance of the various types of repeat differed between taxonomic groups. Control genomes revealed that trinucleotide repeats were mostly located in coding regions while dinucleotide repeats were largely associated with untranslated regions. Our results from the empirical test revealed considerable amplification success and transferability between congenerics. Conclusions: The present work represents the first large-scale study developing SSRs by utilizing publicly accessible EST databases in threatened plants. Here we provide a very large number of ready-to-test EST-SSR (17 102) for 193 genera. The cross-species transferability suggests that the number of possible target species would be large. Since trinucleotide repeats are abundant and mainly linked to exons they might be useful in evolutionary and conservation studies. Altogether, our study highly supports the use of EST databases as an extremely affordable and fast alternative for SSR developing in threatened plants

Correction to: An Arabidopsis introgression zone studied at high spatio-temporal resolution: interglacial and multiple genetic contact exemplified using whole nuclear and plastid genomes

Upon publication of the original article [1], the authors had flagged that there was an error in Fig. 1c, as the key in this figure was displaying incorrectly. The colours had not displayed in the key in the final published article, and instead appear as plain white

The evolutionary history of the Arabidopsis lyrata complex: a hybrid in the amphi-Beringian area closes a large distribution gap and builds up a genetic barrier

<p>Abstract</p> <p>Background</p> <p>The genomes of higher plants are, on the majority, polyploid, and hybridisation is more frequent in plants than in animals. Both polyploidisation and hybridisation contribute to increased variability within species, and may transfer adaptations between species in a changing environment. Studying these aspects of evolution within a diversified species complex could help to clarify overall spatial and temporal patterns of plant speciation. The <it>Arabidopsis lyrata </it>complex, which is closely related to the model plant <it>Arabidopsis thaliana</it>, is a perennial, outcrossing, herbaceous species complex with a circumpolar distribution in the Northern Hemisphere as well as a disjunct Central European distribution in relictual habitats. This species complex comprises three species and four subspecies, mainly diploids but also several tetraploids, including one natural hybrid. The complex is ecologically, but not fully geographically, separated from members of the closely related species complex of <it>Arabidopsis halleri</it>, and the evolutionary histories of both species compexes have largely been influenced by Pleistocene climate oscillations.</p> <p>Results</p> <p>Using DNA sequence data from the nuclear encoded cytosolic phosphoglucoisomerase and Internal Transcribed Spacers 1 and 2 of the ribosomal DNA, as well as the <it>trn</it>L/F region from the chloroplast genome, we unravelled the phylogeography of the various taxonomic units of the <it>A. lyrata </it>complex. We demonstrate the existence of two major gene pools in Central Europe and Northern America. These two major gene pools are constructed from different taxonomic units. We also confirmed that <it>A. kamchatica </it>is the allotetraploid hybrid between <it>A. lyrata </it>and <it>A. halleri</it>, occupying the amphi-Beringian area in Eastern Asia and Northern America. This species closes the large distribution gap of the various other <it>A. lyrata </it>segregates. Furthermore, we revealed a threefold independent allopolyploid origin of this hybrid species in Japan, China, and Kamchatka.</p> <p>Conclusions</p> <p>Unglaciated parts of the Eastern Austrian Alps and arctic Eurasia, including Beringia, served as major glacial refugia of the Eurasian <it>A. lyrata </it>lineage, whereas <it>A. halleri </it>and its various subspecies probably survived in refuges in Central Europe and Eastern Asia with a large distribution gap in between. The North American <it>A. lyrata </it>lineage probably survived the glaciation in the southeast of North America. The dramatic climatic changes during glaciation and deglaciation cycles promoted not only secondary contact and formation of the allopolyploid hybrid <it>A. kamchatica</it>, but also provided the environment that allowed this species to fill a large geographic gap separating the two genetically different <it>A. lyrata </it>lineages from Eurasia and North America. With our example focusing on the evolutionary history of the <it>A. lyrata </it>species complex, we add substantial information to a broad evolutionary framework for future investigations within this emerging model system in molecular and evolutionary biology.</p

Averaging approach to phase coherence of uncoupled limit-cycle oscillators receiving common random impulses

Populations of uncoupled limit-cycle oscillators receiving common random impulses show various types of phase-coherent states, which are characterized by the distribution of phase differences between pairs of oscillators. We develop a theory to predict the stationary distribution of pairwise phase difference from the phase response curve, which quantitatively encapsulates the oscillator dynamics, via averaging of the Frobenius-Perron equation describing the impulse-driven oscillators. The validity of our theory is confirmed by direct numerical simulations using the FitzHugh-Nagumo neural oscillator receiving common Poisson impulses as an example

Positive selection and ancient duplications in the evolution of class B floral homeotic genes of orchids and grasses

<p>Abstract</p> <p>Background</p> <p>Positive selection is recognized as the prevalence of nonsynonymous over synonymous substitutions in a gene. Models of the functional evolution of duplicated genes consider neofunctionalization as key to the retention of paralogues. For instance, duplicate transcription factors are specifically retained in plant and animal genomes and both positive selection and transcriptional divergence appear to have played a role in their diversification. However, the relative impact of these two factors has not been systematically evaluated. Class B MADS-box genes, comprising <it>DEF</it>-like and <it>GLO</it>-like genes, encode developmental transcription factors essential for establishment of perianth and male organ identity in the flowers of angiosperms. Here, we contrast the role of positive selection and the known divergence in expression patterns of genes encoding class B-like MADS-box transcription factors from monocots, with emphasis on the family Orchidaceae and the order Poales. Although in the monocots these two groups are highly diverse and have a strongly canalized floral morphology, there is no information on the role of positive selection in the evolution of their distinctive flower morphologies. Published research shows that in Poales, class B-like genes are expressed in stamens and in lodicules, the perianth organs whose identity might also be specified by class B-like genes, like the identity of the inner tepals of their lily-like relatives. In orchids, however, the number and pattern of expression of class B-like genes have greatly diverged.</p> <p>Results</p> <p>The <it>DEF</it>-like genes from Orchidaceae form four well-supported, ancient clades of orthologues. In contrast, orchid <it>GLO</it>-like genes form a single clade of ancient orthologues and recent paralogues. <it>DEF</it>-like genes from orchid clade 2 (<it>OMADS3</it>-like genes) are under less stringent purifying selection than the other orchid <it>DEF</it>-like and <it>GLO</it>-like genes. In comparison with orchids, purifying selection was less stringent in <it>DEF</it>-like and <it>GLO</it>-like genes from Poales. Most importantly, positive selection took place before the major organ reduction and losses in the floral axis that eventually yielded the zygomorphic grass floret.</p> <p>Conclusion</p> <p>In <it>DEF</it>-like genes of Poales, positive selection on the region mediating interactions with other proteins or DNA could have triggered the evolution of the regulatory mechanisms behind the development of grass-specific reproductive structures. Orchidaceae show a different trend, where gene duplication and transcriptional divergence appear to have played a major role in the canalization and modularization of perianth development.</p

Interspecific and interploidal gene flow in Central European Arabidopsis (Brassicaceae)

Background Effects of polyploidisation on gene flow between natural populations are little known. Central European diploid and tetraploid populations of Arabidopsis arenosa and A. lyrata are here used to study interspecific and interploidal gene flow, using a combination of nuclear and plastid markers. Results Ploidal levels were confirmed by flow cytometry. Network analyses clearly separated diploids according to species. Tetraploids and diploids were highly intermingled within species, and some tetraploids intermingled with the other species, as well. Isolation with migration analyses suggested interspecific introgression from tetraploid A. arenosa to tetraploid A. lyrata and vice versa, and some interploidal gene flow, which was unidirectional from diploid to tetraploid in A. arenosa and bidirectional in A. lyrata. Conclusions Interspecific genetic isolation at diploid level combined with introgression at tetraploid level indicates that polyploidy may buffer against negative consequences of interspecific hybridisation. The role of introgression in polyploid systems may, however, differ between plant species, and even within the small genus Arabidopsis, we find very different evolutionary fates when it comes to introgression

The gravitational analogue to the hydrogen atom (A summer study at the borders of quantum mechanics and general relativity)

This article reports on a student summer project performed in 2006 at the University of Frankfurt. It is addressed to undergraduate students familiar with the basic principles of relativistic quantum mechanics and general relativity. The aim of the project was to study the Dirac equation in curved space time. To obtain the general relativistic Dirac equation we use the formulation of gravity as a gauge theory in the first part. After these general considerations we restrict the further discussion to the special case of the Schwarzschild metric. This setting corresponds to the hydrogen atom, with the electromagnetic field replaced by gravity. Although there is a singularity at the event horizon it turns out that a regular solution of the time independent Dirac equation exists. Finally the Dirac equation is solved numerically using suitable boundary conditions.Comment: 19 pages, 3 figure