Sex chromosomes in meiotic, hemiclonal, clonal and polyploid hybrid vertebrates: along the ‘extended speciation continuum'

We review knowledge about the roles of sex chromosomes in vertebrate hybridization and speciation, exploring a gradient of divergences with increasing reproductive isolation (speciation continuum). Under early divergence, well-differentiated sex chromosomes in meiotic hybrids may cause Haldane-effects and introgress less easily than autosomes. Undifferentiated sex chromosomes are more susceptible to introgression and form multiple (or new) sex chromosome systems with hardly predictable dominance hierarchies. Under increased divergence, most vertebrates reach complete intrinsic reproductive isolation. Slightly earlier, some hybrids (linked in ‘the extended speciation continuum') exhibit aberrant gametogenesis, leading towards female clonality. This facilitates the evolution of various allodiploid and allopolyploid clonal (‘asexual’) hybrid vertebrates, where ‘asexuality' might be a form of intrinsic reproductive isolation. A comprehensive list of ‘asexual' hybrid vertebrates shows that they all evolved from parents with divergences that were greater than at the intraspecific level (K2P-distances of greater than 5–22% based on mtDNA). These ‘asexual' taxa inherited genetic sex determination by mostly undifferentiated sex chromosomes. Among the few known sex-determining systems in hybrid ‘asexuals', female heterogamety (ZW) occurred about twice as often as male heterogamety (XY). We hypothesize that pre-/meiotic aberrations in all-female ZW-hybrids present Haldane-effects promoting their evolution. Understanding the preconditions to produce various clonal or meiotic allopolyploids appears crucial for insights into the evolution of sex, ‘asexuality' and polyploidy. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.

Micron-scale phenomena observed in a turbulent laser-produced plasma

Turbulence is ubiquitous in the universe and in fluid dynamics. It influences a wide range of high energy density systems, from inertial confinement fusion to astrophysical-object evolution. Understanding this phenomenon is crucial, however, due to limitations in experimental and numerical methods in plasma systems, a complete description of the turbulent spectrum is still lacking. Here, we present the measurement of a turbulent spectrum down to micron scale in a laser-plasma experiment. We use an experimental platform, which couples a high power optical laser, an x-ray free-electron laser and a lithium fluoride crystal, to study the dynamics of a plasma flow with micrometric resolution (~1μm) over a large field of view (>1 mm2). After the evolution of a Rayleigh–Taylor unstable system, we obtain spectra, which are overall consistent with existing turbulent theory, but present unexpected features. This work paves the way towards a better understanding of numerous systems, as it allows the direct comparison of experimental results, theory and numerical simulations.

Presence of the Hmq system and production of 4-hydroxy-3-methyl-2-alkylquinolines is heterogeneously distributed between Burkholderia cepacia complex species and more prevalent among environmental than clinical isolates

Some Burkholderia cepacia complex (Bcc) strains have been reported to produce 4-hydroxy-3-methyl-2-alkylquinolines (HMAQs), analogous to the 4-hydroxy-2-alkylquinolines of Pseudomonas aeruginosa. Using in silico analyses, we previously showed that the hmqABCDEFG operon, which encodes enzymes involved in the biosynthesis of HMAQs, is carried by about one-third of Bcc strains, with considerable inter- and intra-species variability. In the present study, we investigated by PCR, using consensus primers, the distribution of hmqABCDEFG in a collection of 313 Bcc strains (222 of clinical and 91 of environmental origins) - belonging to 18 Bcc species. We confirmed that the distribution is species-specific, although not all strains within a species carry the hmqABCDEFG operon. Among the 30% of strains bearing the hmqABCDEFG operon, we measured the total HMAQs production and showed that 90% of environmental isolates and 68% of clinically isolated Bcc produce detectable levels of HMAQs when cultured in TSB medium. For the strains having the hmqABCDEFG operon but not producing HMAQs, we studied the transcription and showed that none expressed the hmqA gene under the specified culture conditions. Interestingly, the hmqABCDEFG operon is more prevalent among plant root environment species (e.g. B. ambifaria, B. cepacia) and absent in species commonly found in chronically colonized individuals with cystic fibrosis (e.g. B. cenocepacia, B. multivorans), suggesting that the Hmq system could play a role in niche adaptation by influencing rhizosphere microbial community and could have been lost through evolution. Understanding the Hmq system and its regulation will provide clues concerning the production of HMAQs and their functions in Bcc.

Challenges with conceptualizations of evolution in biology education

Evolution education is, by default, the domain of biology education, and as such, historical conceptions of evolutionary change drawn from the Modern Synthesis strongly influence our conceptualization of what evolution is and how evolutionary analyses are to be conducted. There is a surface logic to this influence, however, it abstracts out a robust interdisciplinary scientific discourse that has been particularly productive during the 21st century. The continued conceptualization of evolution from the idealized, gene-centric, Modern Synthesis model may be problematic in terms of evolution understanding and acceptance. In this article, we take a closer look at some examples of current discourse, standards, educational materials, and assessment tools of evolution education and point out a number of challenges regarding how our field tends to frame the evolutionary analysis of, especially, human-related traits of behavior, cognition, and culture.

Protein Structural Information and Evolutionary Landscape by In Vitro Evolution

Protein structure is tightly intertwined with function according to the laws of evolution. Understanding how structure determines function has been the aim of structural biology for decades. Here, we have wondered instead whether it is possible to exploit the function for which a protein was evolutionary selected to gain information on protein structure and on the landscape explored during the early stages of molecular and natural evolution. To answer to this question, we developed a new methodology, which we named CAMELS (Coupling Analysis by Molecular Evolution Library Sequencing), that is able to obtain the in vitro evolution of a protein from an artificial selection based on function. We were able to observe with CAMELS many features of the TEM-1 beta-lactamase local fold exclusively by generating and sequencing large libraries of mutational variants. We demonstrated that we can, whenever a functional phenotypic selection of a protein is available, sketch the structural and evolutionary landscape of a protein without utilizing purified proteins, collecting physical measurements, or relying on the pool of natural protein variants.

IDENTIFICAÇÃO DAS FEIÇÔES GRANÍTICAS DO MUNICÍPO DE IRAUÇUBA-CEARÁ

A exumação de rochas graníticas do Complexo Tamboril-Santa Quitéria, especificamente, na superfície de aplainamento do município de Irauçuba, Ceará, tem revelado uma grande variedade de feições geomorfológicas que se justificam por fatores litológicos e evidentes flutuações climáticas cenozoicas, comandadas, sobretudo, por morfogênese mecânica, associada a climas secos. São relevos residuais como, maciços, cristas, inselbergs, inselguebergs, lajedos e blocos saprolitizados (boulders) em diferentes graus de desenvolvimento que se sobressaem em meio à superfície erosiva rebaixada, regionalmente conhecida como depressão sertaneja. Nesse trabalho, foram identificadas diferentes formas de relevo granítico condicionadas, sobretudo por intempéries de subsuperfície, controladas por falhas e fraturas, e por remoção do regolito através da erosão superficial, além de eventos de esfoliação. Essas formas graníticas constituem peças fundamentais na compreensão da evolução paleoclimática do município de Irauçuba. Para a realização do presente trabalho foram usadas as seguintes metodologias: revisão bibliográfica, levantamento cartográfico e trabalho de campo.Palavras-chave: Feições graníticas; Superfícies de aplainamento; Erosão diferencial. ABSTRACTThe granitic rocks exhumation of Complexo Tamboril-Santa Quitéria, specifically, on the planing surface of Irauçuba county, Ceará, has revealed a great variety of geomorphological features that are justified by lithologic factors and evident Cenozoic climatic fluctuations, mainly, headed by mechanical morphogenesis, associated with dry climates. Residual reliefs like rocky massives, residual ridges, inselbergs and inselguebergs, slab stones and boulders in different degrees of development stand out in the middle of the lowered erosive surface, regionally known by “depressão sertaneja”. In this study, different forms of granite relief were identified, specially conditioned by subsurface erosion, controlled by geological faults and fractures, but also by regolith removal through surface erosion, plus exfoliation spheroidal events. These granitic features are fundamental in paleoclimatic evolution understanding of Irauçuba municipality. For the accomplishment of the present work the following methodology was used: bibliographical revision, cartographic survey and field work. For the accomplishment of the present work the following methodology was used: bibliographical revision, cartographic survey and field work.Keywords: Granitic features; Planing surface; Differential erosion.RESUMENLa exhumación de rocas graníticas del Complejo tamboril-Santa Quitéria, específicamente en la superficie de aplanado del municipio de Irauçuba, Ceará, ha revelado una gran variedad de rasgos geomorfológicos que se justifican por factores litológicos y evidentes fluctuaciones climáticas cenozoicas, comandadas principalmente por morfogénesis mecánica, asociada a climas secos. Son relieves residuales como, macizos, crestas, Inselbergs, inselguebergs, losas y bloques saprolitizados (Boulders) en diferentes grados de desarrollo que sobresalen en medio de la superficie erosiva rebajada, regionalmente conocida como depresión sertaneja. En este trabajo, se identificaron diferentes formas de relieve granítico condicionadas, principalmente por intemperies de subsuperficie, controladas por fallas y fracturas, y por eliminación del regolito a través de la erosión superficial, además de eventos de exfoliación. Estas formas graníticas constituyen piezas fundamentales en la comprensión de la evolución paleoclimática del municipio de Irauçuba. Para la realización del presente trabajo se utilizaron las siguientes metodologías: revisión bibliográfica, levantamiento cartográfico y trabajo de campo.Palabras clave: Facciones graníticas; Superficies de aplanado; Erosión diferencial.

MID TERM SIMULATION OF SUSPENDED SEDIMENT TRANSPORT AND BED EVOLUTION FOR THE PATOS LAGOON ESTUARY

Worldwide harbors are settled inside estuarine areas due the protection function of these environments against oceanic waves and therefore are subjected to the hydrodynamic processes that provide morphodynamic changes in sediment distribution and bed evolution. Understanding the dynamic of sediments and the bed evolution at estuaries is of crucial importance on maintenance of fairways and harbor docks. We modeled using the finite element technique 1005 days of hydro and morphodynamic of the Patos Lagoon estuary, in order to identify the critical deposition areas inside the Rio grande harbor fairway. Therefore, a hydrodynamic model, TELEMAC 3D, and a morphodynamic, Sisyphe, were applied in order to acquire the bed evolution and sediment distribution of the area using different data sources for the oceanic, atmospherical and continental boundary conditions. The results, present that clay is being deposited at deeper parts of the channel. Bed evolution results indicate siltation/erosion process where silt/clay is being deposited. Sedimentation rates were calculated based on the bed evolution results as well. The validation procedure showed good representation by the models of the physical aspects of the environment.

fuNTRp: Identifying protein positions for variation driven functional tuning

ABSTRACTEvaluating the impact of non-synonymous genetic variants is essential for uncovering disease associations and mechanisms of evolution. Understanding corresponding sequence changes is also fundamental for synthetic protein design and stability assessments. However, the performance gain of variant effect predictors observed in recent years is not in line with the increased complexity of new methods. One likely reason for this might be that most approaches use similar sets of gene/protein features for modeling variant effect, often emphasizing sequence conservation. While high levels of conservation highlight residues essential for protein activity, much of the in vivo observable variation is arguably weaker in its impact and, thus, requires evaluation at a higher level of resolution. Here we describe function Neutral/Toggle/Rheostat predictor (funtrp), a novel computational method that categorizes protein positions based on the position-specific expected range of mutational impacts: Neutral (weak/no effects), Rheostat (function-tuning positions), or Toggle (on/off switches). We show that position types do not correlate strongly with familiar protein features such as conservation or protein disorder. We also find that position type distribution varies across different protein functions. Finally, we demonstrate that position types reflect experimentally determined functional effects and can thus improve performance of existing variant effect predictors and suggest a way forward for the development of new ones.