Incongruences between nuclear and plastid phylogenies challenge the identification of correlates of diversification in Gentiana in the European Alpine System

Alpine Botany ◽

10.1007/s00035-021-00267-6 ◽

2021 ◽

Author(s):

Adrien Favre ◽

Juraj Paule ◽

Jana Ebersbach

Keyword(s):

Chromosome Numbers ◽

Complex Interaction ◽

Morphological Features ◽

Ancestral State ◽

Chromosomal Variation ◽

Divergence Dating ◽

Acting In Concert ◽

Alpine System ◽

Occurrence Records

AbstractMountains are reservoirs for a tremendous biodiversity which was fostered by a suite of factors acting in concert throughout evolutionary times. These factors can be climatic, geological, or biotic, but the way they combine through time to generate diversity remains unknown. Here, we investigate these factors as correlates of diversification of three closely related sections of Gentiana in the European Alpine System. Based upon phylogenetic approaches coupled with divergence dating and ancestral state reconstructions, we attempted to identify the role of bedrock preferences, chromosome numbers coupled with relative genome sizes estimates, as well as morphological features through time. We also investigated extant climatic preferences using a heavily curated set of occurrence records individually selected for superior precision, and quantified rates of climatic niche evolution in each section. We found that a number of phylogenetic incongruences derail the identification of correlates of diversification, yet a number of patterns persist regardless of the topology considered. All the studied correlates are likely to have contributed to the diversification of Gentiana in Europe, however, their respective importance varied through time and across clades. Chromosomal variation and divergence of climatic preferences appear to correlate with diversification throughout the evolution of European Gentiana (Oligocene to present), whereas shifts in bedrock preferences appear to have been more defining during recent diversification (Pliocene). Overall, a complex interaction among climatic, geological and biotic attributes appear to have supported the diversification of Gentiana across the mountains of Europe, which based upon phylogenetic as well as other evidence, was probably also bolstered by hybridization.

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The SOS Error-Prone DNA Polymerase V Mutasome and β-Sliding Clamp Acting in Concert on Undamaged DNA and during Translesion Synthesis

Cells ◽

10.3390/cells10051083 ◽

2021 ◽

Vol 10 (5) ◽

pp. 1083

Author(s):

Adhirath Sikand ◽

Malgorzata Jaszczur ◽

Linda B. Bloom ◽

Roger Woodgate ◽

Michael M. Cox ◽

...

Keyword(s):

Dna Synthesis ◽

Dna Polymerase ◽

Pathogenic Bacteria ◽

Fold Increase ◽

Translesion Dna Synthesis ◽

Sliding Clamp ◽

Pol V ◽

Dna Polymerase V ◽

Acting In Concert

In the mid 1970s, Miroslav Radman and Evelyn Witkin proposed that Escherichia coli must encode a specialized error-prone DNA polymerase (pol) to account for the 100-fold increase in mutations accompanying induction of the SOS regulon. By the late 1980s, genetic studies showed that SOS mutagenesis required the presence of two “UV mutagenesis” genes, umuC and umuD, along with recA. Guided by the genetics, decades of biochemical studies have defined the predicted error-prone DNA polymerase as an activated complex of these three gene products, assembled as a mutasome, pol V Mut = UmuD’2C-RecA-ATP. Here, we explore the role of the β-sliding processivity clamp on the efficiency of pol V Mut-catalyzed DNA synthesis on undamaged DNA and during translesion DNA synthesis (TLS). Primer elongation efficiencies and TLS were strongly enhanced in the presence of β. The results suggest that β may have two stabilizing roles: its canonical role in tethering the pol at a primer-3’-terminus, and a possible second role in inhibiting pol V Mut’s ATPase to reduce the rate of mutasome-DNA dissociation. The identification of umuC, umuD, and recA homologs in numerous strains of pathogenic bacteria and plasmids will ensure the long and productive continuation of the genetic and biochemical journey initiated by Radman and Witkin.

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The role of climatic and geological events in generating diversity in Ethiopian grass frogs (genus Ptychadena )

Royal Society Open Science ◽

10.1098/rsos.170021 ◽

2017 ◽

Vol 4 (8) ◽

pp. 170021 ◽

Cited By ~ 4

Author(s):

Megan L. Smith ◽

Brice P. Noonan ◽

Timothy J. Colston

Keyword(s):

Habitat Complexity ◽

Molecular Data ◽

Cryptic Diversity ◽

Horn Of Africa ◽

Climatic Fluctuations ◽

Divergence Dating ◽

Evolutionary Radiation ◽

Novel Taxa ◽

Climatic History

Ethiopia is a world biodiversity hotspot and harbours levels of biotic endemism unmatched in the Horn of Africa, largely due to topographic—and thus habitat—complexity, which results from a very active geological and climatic history. Among Ethiopian vertebrate fauna, amphibians harbour the highest levels of endemism, making amphibians a compelling system for the exploration of the impacts of Ethiopia's complex abiotic history on biotic diversification. Grass frogs of the genus Ptychadena are notably diverse in Ethiopia, where they have undergone an evolutionary radiation. We used molecular data and expanded taxon sampling to test for cryptic diversity and to explore diversification patterns in both the highland radiation and two widespread lowland Ptychadena . Species delimitation results support the presence of nine highland species and four lowland species in our dataset, and divergence dating suggests that both geologic events and climatic fluctuations played a complex and confounded role in the diversification of Ptychadena in Ethiopia. We rectify the taxonomy of the endemic P. neumanni species complex, elevating one formally synonymized name and describing three novel taxa. Finally, we describe two novel lowland Ptychadena species that occur in Ethiopia and may be more broadly distributed.

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Descending Dysploidy and Bidirectional Changes in Genome Size Accompanied Crepis (Asteraceae) Evolution

Genes ◽

10.3390/genes12091436 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1436

Author(s):

Magdalena Senderowicz ◽

Teresa Nowak ◽

Magdalena Rojek-Jelonek ◽

Maciej Bisaga ◽

Laszlo Papp ◽

...

Keyword(s):

Genome Size ◽

Dna Sequences ◽

Chromosome Numbers ◽

Karyotype Evolution ◽

Base Number ◽

Ancestral State ◽

Ancestral Genome ◽

Independent Events ◽

Karyotype Asymmetry ◽

Major Direction

The evolution of the karyotype and genome size was examined in species of Crepis sensu lato. The phylogenetic relationships, inferred from the plastid and nrITS DNA sequences, were used as a framework to infer the patterns of karyotype evolution. Five different base chromosome numbers (x = 3, 4, 5, 6, and 11) were observed. A phylogenetic analysis of the evolution of the chromosome numbers allowed the inference of x = 6 as the ancestral state and the descending dysploidy as the major direction of the chromosome base number evolution. The derived base chromosome numbers (x = 5, 4, and 3) were found to have originated independently and recurrently in the different lineages of the genus. A few independent events of increases in karyotype asymmetry were inferred to have accompanied the karyotype evolution in Crepis. The genome sizes of 33 Crepis species differed seven-fold and the ancestral genome size was reconstructed to be 1 C = 3.44 pg. Both decreases and increases in the genome size were inferred to have occurred within and between the lineages. The data suggest that, in addition to dysploidy, the amplification/elimination of various repetitive DNAs was likely involved in the genome and taxa differentiation in the genus.

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Understanding the evolution of phenotypical characters in the Micarea prasina group (Pilocarpaceae) and descriptions of six new species within the group

MycoKeys ◽

10.3897/mycokeys.57.33267 ◽

2019 ◽

Vol 57 ◽

pp. 1-30

Author(s):

Beata Guzow-Krzemińska ◽

Emmanuël Sérusiaux ◽

Pieter P. G. van den Boom ◽

A. Maarten Brand ◽

Annina Launis ◽

...

Keyword(s):

New Species ◽

Secondary Metabolites ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Its Rdna ◽

Ancestral State ◽

Secondary Substances ◽

Gyrophoric Acid

Six new Micarea species are described from Europe. Phylogenetic analyses, based on three loci, i.e. mtSSU rDNA, Mcm7 and ITS rDNA and ancestral state reconstructions, were used to evaluate infra-group divisions and the role of secondary metabolites and selected morphological characters on the taxonomy in the M.prasina group. Two main lineages were found within the group. The Micareamicrococca clade consists of twelve species, including the long-known M.micrococca and the newly described M.microsorediata, M.nigra and M.pauli. Within this clade, most species produce methoxymicareic acid, with the exceptions of M.levicula and M.viridileprosa producing gyrophoric acid. The M.prasina clade includes the newly described M.azorica closely related to M.prasina s.str., M.aeruginoprasina sp. nov. and M.isidioprasina sp. nov. The species within this clade are characterised by the production of micareic acid, with the exception of M.herbarum which lacks any detectable substances and M.subviridescens that produces prasinic acid. Based on our reconstructions, it was concluded that the ancestor of the M.prasina group probably had a thallus consisting of goniocysts, which were lost several times during evolution, while isidia and soredia evolved independently at multiple times. Our research supported the view that the ancestor of M.prasina group did not produce any secondary substances, but they were gained independently in different lineages, such as methoxymicareic acid which is restricted to M.micrococca and allied species or micareic acid present in the M.prasina clade.

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Clinical Teams

Essentials of Clinical Informatics ◽

10.1093/med/9780190855574.003.0021 ◽

2019 ◽

pp. 231-235

Author(s):

Mark E. Frisse ◽

Karl E. Misulis

Keyword(s):

Care Management ◽

Chronic Care ◽

Healthcare Delivery ◽

Clinical Informatics ◽

Care Plan ◽

Collaborative Activity ◽

Chronic Care Management ◽

Complex Interactions ◽

Acting In Concert

Healthcare delivery is a collaborative activity involving many individuals playing myriad roles. Clinical informatics often emphasizes the role of physicians, nurses, pharmacists, and other staff acting in concert to ensure that key clinical tasks are performed. Only recently have clinical informatics systems begun to model the complex interactions of the team supporting care in the home. Most posthospitalization care and most chronic care management require coordination across teams working from delivery organizations and both the formal and informal teams delivering care in the home. This degree of coordination requires targeted communication and maintenance of both a care record and a care plan.

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The application of omics techniques to understand the role of the gut microbiota in inflammatory bowel disease

Therapeutic Advances in Gastroenterology ◽

10.1177/1756284818822250 ◽

2019 ◽

Vol 12 ◽

pp. 175628481882225 ◽

Cited By ~ 14

Author(s):

Jonathan P. Segal ◽

Benjamin H. Mullish ◽

Mohammed Nabil Quraishi ◽

Animesh Acharjee ◽

Horace R. T. Williams ◽

...

Keyword(s):

Systems Biology ◽

Gut Microbiota ◽

Potential Role ◽

Intestinal Inflammation ◽

Clinical Care ◽

Complex Interaction ◽

Bowel Diseases ◽

Inflammatory Bowel ◽

Compositional Changes

The aetiopathogenesis of inflammatory bowel diseases (IBD) involves the complex interaction between a patient’s genetic predisposition, environment, gut microbiota and immune system. Currently, however, it is not known if the distinctive perturbations of the gut microbiota that appear to accompany both Crohn’s disease and ulcerative colitis are the cause of, or the result of, the intestinal inflammation that characterizes IBD. With the utilization of novel systems biology technologies, we can now begin to understand not only details about compositional changes in the gut microbiota in IBD, but increasingly also the alterations in microbiota function that accompany these. Technologies such as metagenomics, metataxomics, metatranscriptomics, metaproteomics and metabonomics are therefore allowing us a deeper understanding of the role of the microbiota in IBD. Furthermore, the integration of these systems biology technologies through advancing computational and statistical techniques are beginning to understand the microbiome interactions that both contribute to health and diseased states in IBD. This review aims to explore how such systems biology technologies are advancing our understanding of the gut microbiota, and their potential role in delineating the aetiology, development and clinical care of IBD.

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Language contact in Sardinian between the Middle and the Early Modern Ages

Lexicographica - International Annual for Lexicography / Internationales Jahrbuch für Lexikographie ◽

10.1515/lexi-2017-0012 ◽

2018 ◽

Vol 33 (1) ◽

pp. 225-254

Keyword(s):

Early Modern ◽

Language Contact ◽

Morphological Features ◽

Contact Processes ◽

The Relationship

AbstractThis paper describes the role of language contact in Sardinian lexical stratification, focusing on the Sardinian lexicon as well as on some morphological features. The major aim is to show the importance of the Sardinian lexicon for the understanding of the historical contact processes between Sardinian and other languages of the island and for the comprehension of the relationship between different varieties of Sardinian.

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Examining sexual offences through a sociological lens: A socio-cultural exploration of causal and desistance theories

European Journal of Probation ◽

10.1177/2066220316681899 ◽

2016 ◽

Vol 8 (3) ◽

pp. 170-184

Author(s):

Debbie Kyle

Keyword(s):

Psychological Factors ◽

Sexual Offending ◽

Complex Interaction ◽

Theoretical Argument ◽

Sexual Offences ◽

Cultural Elements ◽

Theoretical Approaches ◽

Offending Behaviour ◽

Criminological Theories

This article considers often contrasting theoretical approaches to sexual and non-sexual offending by comparing some influential accounts of the causes of sexual offending and examining the role of socio-cultural factors in the offending process. It also examines how desistance theories may be applied to this complex interaction between psychological factors and socio-cultural ones. The article concludes that there is a strong theoretical argument for substantial socio-cultural elements of sexual offending. It also argues that desistance theories may be applied for the same reason, but also because the causal and desistance process may be thought of as two separate processes. Moreover, and related to the second point, many criminological theories position offending behaviour not in the action that is considered a crime, but the fact that this action is a crime, meaning that both resistance to and desistance from sexual offending can be viewed in the context of general criminological theories.

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Football, Politics and Europe

The Hague Journal of Diplomacy ◽

10.1163/1871191x-12341261 ◽

2013 ◽

Vol 8 (3-4) ◽

pp. 333-340 ◽

Cited By ~ 1

Author(s):

William Gaillard

Keyword(s):

International Relations ◽

European Society ◽

Complex Interaction ◽

Institutional Governance ◽

History Of ◽

European Football

Summary This article examines the place of sports and football in European society and the complex interaction of the sports field and the football sub-field, which has its own codes of behaviour, its own institutional governance, its own ethics, its own judicial culture and its own language. Charting the history of European football and the Union of European Football Associations (UEFA), the author argues that unless one understands how the football habitus interact with the rest of European society, it is difficult to examine the role of sports and, in particular, football in international relations and diplomacy.

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