1,664 research outputs found
Maintenance of species boundaries despite ongoing gene flow in ragworts
No full textThe role of hybridization between diversifying species has been the focus of a huge amount of recent evolutionary research. While gene flow can prevent speciation or initiate species collapse, it can also generate new hybrid species. Similarly, while adaptive divergence can be wiped out by gene flow, new adaptive variation can be introduced via introgression. The relative frequency of these outcomes, and indeed the frequency of hybridization and introgression in general are largely unknown. One group of closely-related species with several documented cases of hybridization is the Mediterranean ragwort (genus: Senecio) species-complex. Examples of both polyploid and homoploid hybrid speciation are known in the clade, although their evolutionary relationships and the general frequency of introgressive hybridization among them remain unknown. Using a whole genome gene-space dataset comprising eight Senecio species we fully resolve the phylogeny of these species for the first time despite phylogenetic incongruence across the genome. Using a D-statistic approach, we demonstrate previously unknown cases of introgressive hybridization between multiple pairs of taxa across the species tree. This is an important step in establishing these species as a study system for diversification with gene flow, and suggests that introgressive hybridization may be a widespread and important process in plant evolution
Data from: The genomic bases of morphological divergence and reproductive isolation driven by ecological speciation in Senecio (Asteraceae)
No full textEcological speciation, driven by adaptation to contrasting environments, provides an attractive opportunity to study the formation of distinct species, and the role of selection and genomic divergence in this process. Here, we focus on a particularly clear-cut case of ecological speciation to reveal the genomic bases of reproductive isolation and morphological differences between closely related Senecio species, whose recent divergence within the last ~200,000 years was likely driven by the uplift of Mt. Etna (Sicily). These species form a hybrid zone, yet remain morphologically and ecologically distinct, despite active gene exchange. Here, we report a high-density genetic map of the Senecio genome and map hybrid breakdown to one large and several small quantitative trait loci (QTL). Loci under diversifying selection cluster in three 5 cM regions which are characterized by a significant increase in relative (F(ST)), but not absolute (d(XY)), interspecific differentiation. They also correspond to some of the regions of greatest marker density, possibly corresponding to 'cold-spots' of recombination, such as centromeres or chromosomal inversions. Morphological QTL for leaf and floral traits overlap these clusters. We also detected three genomic regions with significant transmission ratio distortion (TRD), possibly indicating accumulation of intrinsic genetic incompatibilities between these recently diverged species. One of the TRD regions overlapped with a cluster of high species differentiation, and another overlaps the large QTL for hybrid breakdown, indicating that divergence of these species may have occurred due to a complex interplay of ecological divergence and accumulation of intrinsic genetic incompatibilities.</span
Homomorphic plant sex chromosomes are coming of age
No full textSex chromosomes are a very peculiar part of the genome that have evolved independently in many groups of animals and plants (Bull ). Major research efforts have so far been focused on large heteromorphic sex chromosomes in a few animal and plant species (Chibalina and Filatov ; Zhou and Bachtrog ; Bellott et al. ; Hough et al. ; Zhou et al. ), while homomorphic (cytologically indistinguishable) sex chromosomes have largely been neglected. However, this situation is starting to change. In this issue, Geraldes et al. () describe a small (~100 kb long) sex-determining region on the homomorphic sex chromosomes of poplars (Populus trichocarpa and related species, Fig. ). All species in Populus and its sister genus Salix are dioecious, suggesting that dioecy and the sex chromosomes, if any, should be relatively old. Contrary to this expectation, Geraldes et al. () demonstrate that the sex-determining region in poplars is of very recent origin and probably evolved within the genus Populus only a few million years ago
Genomic divergence during speciation driven by adaptation to altitude
No full textEven though Darwin's "On the Origin of Species" implied selection being the main driver of species formation, the role of natural selection in speciation remains poorly understood. In particular, it remains unclear how selection at a few genes can lead to genome-wide divergence and the formation of distinct species. We used a particularly attractive clear-cut case of recent plant ecological speciation to investigate the demography and genomic bases of species formation driven by adaptation to contrasting conditions. High altitude Senecio aethnensis and low altitude Senecio chrysanthemifolius live at the extremes of a mountain slope on Mt. Etna, Sicily and form a hybrid zone at intermediate altitudes, but remain morphologically distinct. Genetic differentiation of these species was analysed at the DNA polymorphism and gene expression levels by high-throughput sequencing of transcriptomes from multiple individuals. Out of ca. 18,000 genes analysed, only a small number (90) displayed differential expression between the two species. These genes showed significantly elevated species differentiation (FST and Dxy), consistent with diversifying selection acting on these genes. Genome-wide genetic differentiation of the species is surprisingly low (FST = 0.19), while ca. 200 genes showed significantly higher (FDR < 1%; mean outlier FST > 0.6) interspecific differentiation and evidence for local adaptation. Diversifying selection at only a handful of loci may be enough for the formation and maintenance of taxonomically well-defined species, despite on-going gene flow. This provides an explanation of why many closely-related species (in plants in particular) remain phenotypically and ecologically distinct despite on-going hybridisation, a question that has long puzzled naturalists and geneticists alike
The genomic bases of morphological divergence and reproductive isolation driven by ecological speciation in Senecio(Asteraceae)
No full textEcological speciation, driven by adaptation to contrasting environments, provides an attractive opportunity to study the formation of distinct species, and the role of selection and genomic divergence in this process. Here, we focus on a particularly clear-cut case of ecological speciation to reveal the genomic bases of reproductive isolation and morphological differences between closely related Senecio species, whose recent divergence within the last ~200 000 years was likely driven by the uplift of Mt. Etna (Sicily). These species form a hybrid zone, yet remain morphologically and ecologically distinct, despite active gene exchange. Here, we report a high-density genetic map of the Senecio genome and map hybrid breakdown to one large and several small quantitative trait loci (QTL). Loci under diversifying selection cluster in three 5 cM regions which are characterized by a significant increase in relative (FST), but not absolute (dXY), interspecific differentiation. They also correspond to some of the regions of greatest marker density, possibly corresponding to ‘cold-spots’ of recombination, such as centromeres or chromosomal inversions. Morphological QTL for leaf and floral traits overlap these clusters. We also detected three genomic regions with significant transmission ratio distortion (TRD), possibly indicating accumulation of intrinsic genetic incompatibilities between these recently diverged species. One of the TRD regions overlapped with a cluster of high species differentiation, and another overlaps the large QTL for hybrid breakdown, indicating that divergence of these species may have occurred due to a complex interplay of ecological divergence and accumulation of intrinsic genetic incompatibilities
Writing the Time of Troubles, False Dmitry in Russian Literature (Book Review)
No full textThis book discusses the Time of Troubles (Smutnoe vremya) period and the pretenders who appeared after the killing of Ivan the Terrible’s legal heir, Ivan, leaving the Empire without leadership. The power struggle began immediately after the death of Tsar Ivan which brought the Rurikid dynasty to an end; rival boyars created a weak government and autocracy. The book discusses these issues and the representations of Dmitry, the son of Ivan the Terrible within the context of Russian literature. The absence of legitimate royal authority after the demise of the Rurikid dynasty in 1598 caused a dynastic crisis. This period known as the Time of Troubles was characterized by a dynastic struggle that nearly resulted in the shattering of the Muscovite state. It finally came to an end in 1613 with the appearance of the new dynasty, the Romanovs. The book consists of six chapter. In the Introduction the author states that she will examine the “protagonist”, Dmitry, within the context of Russian literature. She examines Dmitry both as a literary figure and a real historical one, and describes Dmitry as a “tabula rasa” because he died under mysterious circumstances with no credible witnesses to confirm how he died. In her book, the author conducts her research both chronologically and diachronically. Chapter I is an introductory chapter that provides information on the eighteenth and nineteenth-century Russian texts Tulupov’s Life of St. Dmitry, The Story of Grishka Otrepev and Tale of Recovery that illustrate the prehistory of Dmitry. The author compares seventeenth century text types and arrives at the conclusion that all three works express a political message and that all of them contain a hagiographical structure and explication. Chapter II examines Russia’s historical experience in the eighteenth century and its literary tradition. In this chapter, the author examines Sumarokov’s tragedy Dmitry the Pretender and Narezhny’s Dmitry the Pretender. The author compares the main causes of his usurpation and its interpretation in literary works of the seventeenth century and the eighteenth century, and concludes that the writers of the seventeenth century crafted quasi-literary, polemical, monological interpretations of the period and determined who was the sole man qualified to rule. Prose treatments of the Dmitry material were the most appropriate way to shape their literature. Eighteenth century writers, on the other hand, recognized a large number of candidates to the throne and their interpretation of the period was multifaceted; tragedy was the most popular literary genres. In Chapter III, the author examines the body of works discussing Dmitry and the Time of Troubles in the 1820s and 1830s: Alexander Pushkin’s Comedy about Tsar Boris and Grishka Otrepev, Faddey Bulgarin’s Dmitry the Pretender, Alexey Khomyakov’s Dmitry the Pretender, Mikhail Pogodin’s Historical Portrait of Dmitry the Pretender. She states that the writers of Russia’s early nineteenth century were fascinated with the Dmitry materials, and each writer depicted him as a man who lived among others and saw him as an alternative to the reigning autocracy. However, they later arrived at the conclusion that there was no viable alternative to the reigning autocracy. Chapter IV deals with two plays written in response to the Era of Great Reforms in 1866: Alexander Ostrovsky’s Dmitry the Pretender and Vasily Shuisky and Nikolay Chaev’s Dmitry the Pretender. She criticizes both authors’ works on a number of fronts, regarding all of them as being overly ambitious in that they attempt to treat too many unrelated issues, and that the miscellaneous political issues raised in these dramatic works have no clear connection to one another. In the Chapter V, the author states that Dmitry disappears from Russian novels and plays for a century and reappears after the demise of the Soviet Union. She examines Daniil Mordovtsev’s False Dmitry: A Historical Novel of the Time of Troubles, Vasily Avenarius’s In Service to the Tsarevich, Nikolay Alekseev’s The False Tsarevich and Alexey Suvorin’s Tsar Dmitry the Pretender and Tsarevna Xenya. The author concludes that each writer has presented his own interpretation of Dmitry and his era, that these works are clearly independent and any similarities among them are merely coincidental with no pattern to them. Since each writer has selected his own particular assortment of “facts”, the novels each follow their own unique line of development. On a more general note, the author argues that the collection of late nineteenth century works on the Time of Troubles should be interpreted in the context of both their local frame of reference and national pride in the country’s cultural heritage. However, in the Soviet period Dmitry’s disappearance was the result of the Soviets’ emphasis on shaping the nation’s future rather than linking present realities to the national past. In the Conclusion, the author points out that all of the works discussed simultaneously deal with two distinct periods in time – the time in which the works are set and the time in which they were composed. For seventeenth century writers, marking the passing of the old dynasty was important, but the establishment of a new dynasty was just as significant. In the two eighteenth century works that were examined, contemporary political issues were treated in the context of Dmitry’s era. Nineteenth century works more closely resemble seventeenth century works in that the contemporary relevance of the historical events these works deal with is their main focus. According to the author, as long as writers continue to deal with political issues in literature or the theater, the figure of Dmitry will remain a relevant character. This book is very well written source examining the Time of Troubles period, a period when there was no legal heir to run the state, when dynastic struggle began the process of bringing an end to the Rurik Dynasty and leading to a period pretenders. The author provides different interpretations for the “protagonist”, Dmitry, within the context of Russian literature. The author particularly examines different writers’ works in chronological order and discusses the legitimacy of Dmitry by comparing the treatments of the pretenders. This book should be of interest to anyone interested in the period of the Time of Troubles and usurpation and their interpretation in Russian literature
A multi-lepton search for new physics in 35pb⁻¹ proton-proton collisions at the LHC for a center of mass energy of √s = 7 TeV using the CMS detector
No full textThis thesis describes a model independent search for new physics with a decay signature of three or more leptons and missing transverse energy in 35pb⁻¹ of proton-proton collisions at the LHC at a center mass energy √s = 7 TeV using the CMS detector. Standard Model backgrounds are predicted using both simulations and collision data. The observed events are consistent with the Standard Model predictions. The results are interpreted using various supersymmetric models: gravity mediated symmetry breaking, gauge mediated symmetry breaking with slepton co-NLSP, and leptonic R-parity violating.Ph. D.Includes bibliographical referencesby Dmitry Hit
Speciation and adaptation of senecio
No full textSpeciation was thought to be initiated by geographical isolation only. However, more and more research has shown that there are other drivers of speciation, such as divergent selection, and that speciation could happen in the face of gene flow with mechanisms to maintain reproductive isolation. This thesis presents similar findings on a case of recent speciation with gene flow found on Mount Etna (Sicily), where closely related high- and low-elevation adapted species, Senecio aethnensis and S. chrysanthemifolius live and hybridise. I used different methods to examine the processes during their speciation and the maintenance of their reproductive isolation. Their homoploid hybrid species, S. squalidus, was also studied to explore various aspects of hybrid speciation. I started by exploring the demographic history of the two species, and revealed several crucial features during their speciation, including heterogenous gene flow, bidirectional gene flow and historical gene flow. Although a secondary contact scenario and a gene flow since divergence scenario could not be determined, the rest of the thesis focused on the evolutionary processes that happened during speciation. Cline analyses and genome scans revealed the presence of divergent selection and positive selection widespread across all linkage groups and that selective agents had various strengths and ages, supporting the multifarious selection hypothesis. These two analyses also provided a list of candidate genes that are related to adaptation to different elevations on Mount Etna, such as those regarding metal ions defence and UV response. In the final chapter of the thesis, I investigated hybrid breakdown using multiple F2 families. Not only was hybrid breakdown confirmed, new breakdown traits were discovered. I also uncovered phenotypic evidence of nucleocytoplasmic incompatibility in the system, and showed that the level of hybrid breakdown likely depended on the level of incompatibility between different S. aethnensis and S. chrysanthemifolius pairs. Last but not least, the hybrid species ex situ, S. squalidus, exhibited significant phenotypic differences from artificial F2 hybrids, hinting morphological novelties during its evolution and establishment in the UK. Overall, this thesis presents research on both the intrinsic and extrinsic mechanisms during the speciation of Etnean Senecio. At the same time, it illustrates the value of these young non-model systems in studying speciation and demonstrates that evolution of new traits for adaptation can happen very quickly
Outstanding Surgeon and Scientist Dmitry Alekseevich Arapov
No full textIn 2022, we are approaching 125 years since the birth of Dmitry Alekseevich Arapov, a prominent domestic surgeon, scientist, experimenter, organizer of the military medical services. Dmitry A. Arapov, one of the most prominent representatives of the S.S. Yudin scientific school, worked at the N.V. Sklifosovsky Research Institute for Emergency Medicine from 1929 till 1984. He quickly proved himself not only as an excellent doctor and a skilled surgeon, but also as a researcher, and soon became one of the closest students and associates of S.S. Yudin. Dmitry A. Arapov drafted as a field surgeon during the Soviet-Finnish war of 1939-1940, from the first to the last day he went through the Great Patriotic War, being the Head of the surgical service of the Northern Fleet in Polyarny. In this position, he significantly improved the system for providing emergency surgical care on ships and in naval hospitals, based on the experience gained over the years of work at the N.V. Sklifosovsky Research Institute for Emergency Medicine. From July 1950 Dmitry A. Arapov was Chief Surgeon of the USSR Navy, from May 1953 he was Deputy Chief surgeon of the Main Military Sanitary Directorate of the USSR Ministry of Defense, and from May 1955 again Chief Surgeon of the USSR Navy, until his retirement in October, 1968. At the same time, Dmitry A. Arapov did not leave his work at the N.V. Sklifosovsky Research Institute for Emergency Medicine until the last days of his life. Dmitry A. Arapov is the author of more than 200 research papers, including 14 monographs. Scientific interests of Dmitry A. Arapov went far beyond emergency surgery, to which he naturally paid most attention. His works are devoted to various issues of military and emergency surgery of the abdominal and thoracic organs, topical issues of burn injuries, surgical site infections, reconstructive surgery, neurosurgery, treatment of endocrine disorders, and anesthesiology and resuscitation. Also Dmitry A. Arapov successfully dealt with the problems of autotransfusion, blood reinfusion from the chest and abdomen, transfusion of fibrinolytic blood. The main directions of scientific research, laid down by Dmitry A. Arapov, are currently being continued at the Scientific Department of Emergency Surgery, Endoscopy and Intensive Care of the N.V. Sklifosovsky Research Institute for Emergency Medicine. Memory of Dmitry A. Arapov has been preserved to this day. To the 100th anniversary of the birth of D.A. Arapov, a scientific conference was held at our Institute. The naval hospital in the town of Polyarny, Murmansk region, was named after Dmitry A. Arapov, and in honor of D.A. Arapov, a memorial plaque was installed on its building. In the 70s of the twentieth century, People’s Artist of the USSR L.E. Kerbel created a sculpture of Dmitry A. Arapov, which was stored in the local history museum of the town of Polyarny. His bust portrait (by artist T.S. Smagina) is exhibited at the Scientific Department of Emergency Surgery, Endoscopy and Intensive Care of the N.V. Sklifosovsky Research Institute for Emergency Medicine. In addition, the N.V. Sklifosovsky Research Institute for Emergency Medicine owns an earlier portrait of Dmitry A. Arapov by artist F.S. Bulgak. We introduce these portraits into scientific circulation for the first time. We are confident that they will be able to tell contemporaries a lot about this scientist, surgeon and man who made a great contribution to surgery and military medicine, and rightfully entered the history of Russian medicine
Genome-wide analysis of selection in insects, mammals and fungi
No full textCharacterising and understanding factors that affect the rate of molecular evolution in proteins has played a major part in the development of evolutionary theory. The early analyses of amino acid substitutions stimulated the development of the neutral theory of molecular evolution, which later evolved into the nearly neutral theory. More recent work has lead to a better understanding of the role selection plays at the molecular level, but there is still limited understanding of how higher levels of protein organisation affect the way natural selection acts. The investigation of this question is the central aim of this thesis, which is addressed via the analysis of selective pressures in secondary protein structures in insects, mammals and fungi. The analyses for the first two groups were conducted using publically available datasets. To conduct the analyses in fungi, genome sequence data from the fungal genus Microbotryum (sequenced in our laboratory) was assembled and annotated, resulting in the development of a number of bioinformatics tools which are described here. The fungal, insect and mammalian datasets were interrogated with regard to a number of structural features, such as protein secondary structure, position of a site with regard to adaptively evolving sites, hydropathy and solvent-accessibility. These features were correlated with the signals of positive and purifying selection detected using phylogenetic maximum likelihood and Bayesian approaches. I conclude that all of the factors examined can have an effect on the rate of molecular evolution. In particular, disordered and hydrophilic regions of the protein are found to experience fewer physiochemical constraints and contain a higher proportion of adaptively evolving sites. It is also revealed that positively selected residues are ‘clustered’ together spatially, and these trends persist in the three taxa. Finally, I show that this variation in adaptive evolution is a result of both selective events and physiochemical constraint
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