L'eficiència de la selecció natural

Des del Departament de Genètica i Microbiologia de la Universitat Autònoma de Barcelona, s'ha pogut aprofundir una mica més en l'estudi del canvi evolutiu de les espècies. Partint de la teoria quasi neutra de l'evolució molecular, que emfatitza la importància del factor aleatori de les mutacions genètiques que no aporten beneficis a l'espècie, s'ha demostrat que es pot predir l'eficiència de la selecció natural segons el tamany de la població. Per arribar a aquesta conclusió, l'estudi s'ha realitzat a partir d'anàlisis estadístiques d'una base de dades de diferents espècies de Drosophila, tenint en compte la seva diversitat nucleotídica.Desde el Departamento de Genética y Microbiología de la Universitat Autònoma de Barcelona, se ha podido profundizar un poco más en el estudio del cambio evolutivo de las especies. Partiendo de la teoría casi neutra de la evolución molecular, que enfatiza la importancia del factor aleatorio de las mutaciones genéticas que no aportan beneficios a la especie, se ha demostrado que se puede predecir la eficiencia de la selección natural según el tamaño de la población. Para llegar a esta conclusión, el estudio se ha realizado a partir de análisis estadísticos de una base de datos de diferentes especies de Drosophila, teniendo en cuenta su diversidad nucleotídica

Exploring the Phenotypic Space and the Evolutionary History of a Natural Mutation in Drosophila melanogaster

A major challenge of modern Biology is elucidating the functional consequences of natural mutations. Although we have a good understanding of the effects of laboratory-induced mutations on the molecular- and organismal-level phenotypes, the study of natural mutations has lagged behind. In this work, we explore the phenotypic space and the evolutionary history of a previously identified adaptive transposable element insertion. We first combined several tests that capture different signatures of selection to show that there is evidence of positive selection in the regions flanking FBti0019386 insertion. We then explored several phenotypes related to known phenotypic effects of nearby genes, and having plausible connections to fitness variation in nature. We found that flies with FBti0019386 insertion had a shorter developmental time and were more sensitive to stress, which are likely to be the adaptive effect and the cost of selection of this mutation, respectively. Interestingly, these phenotypic effects are not consistent with a role of FBti0019386 in temperate adaptation as has been previously suggested. Indeed, a global analysis of the population frequency of FBti0019386 showed that climatic variables explain well the FBti0019386 frequency patterns only in Australia. Finally, although FBti0019386 insertion could be inducing the formation of heterochromatin by recruiting HP1a (Heterochromatin Protein 1a) protein, the insertion is associated with upregulation of sra in adult females. Overall, our integrative approach allowed us to shed light on the evolutionary history, the relevant fitness effects, and the likely molecular mechanisms of an adaptive mutation and highlights the complexity of natural genetic variants.A.U. is an FPI fellow (BES-2012-052999) and J.G. is a Ramón y Cajal fellow (RYC-2010-07306). This work was supported by grants from the European Comission (Marie Curie CIG PCIG-2011-293860) and from the Spanish Government (Fundamental Research Projects Grant BFU-2011-24397) to J.G.Peer reviewe

Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes

[Background] The rise of the primate lineage is accompanied by an outstanding emergence of microRNAs, small non-coding RNAs with a prominent role in gene regulation. In spite of their biological importance little is known about the way in which natural selection has influenced microRNAs in the human lineage. To study the recent evolutionary history of human microRNAs and to analyze the signatures of natural selection in genomic regions harbouring microRNAs we have investigated the nucleotide substitution rates of 1,872 human microRNAs in the human and chimpanzee lineages.[Results] We produced a depurated set of microRNA alignments of human, chimpanzee and orang-utan orthologs combining BLAT and liftOver and selected 1,214 microRNA precursors presenting optimal secondary structures. We classified microRNAs in categories depending on their genomic organization, duplication status and conservation along evolution. We compared substitution rates of the aligned microRNAs between human and chimpanzee using Tajima’s Relative Rate Test taking orang-utan as out-group and found several microRNAs with particularly high substitution rates in either the human or chimpanzee branches. We fitted different models of natural selection on these orthologous microRNA alignments and compared them using a likelihood ratio test that uses ancestral repeats and microRNA flanking regions as neutral sequences. We found that although a large fraction of human microRNAs is highly conserved among the three species studied, significant differences in rates of molecular evolution exist among microRNA categories. Particularly, primate-specific microRNAs, which are enriched in isolated and single copy microRNAs, more than doubled substitution rates of those belonging to older, non primate-specific microRNA families.[Conclusions] Our results corroborate the remarkable conservation of microRNAs, a proxy of their functional relevance, and indicate that a subset of human microRNAs undergo nucleotide substitutions at higher rates, which may be suggestive of the action of positive selection.This work was supported by the Ministerio de Ciencia e Innovación, España (BFU2012-38236, BFU2010-18477, BFU2009-06974, and CGL2009-09013), Direcció General de Recerca de la Generalitat de Catalunya” (2009SGR-1101, 2014SGR-866 and SGR2014-1311) and European Union Seventh Framework Programme (PIOF-GA-2009-236836 and PIRSES-GA-2013-612583). This publication has been cofinanced by FEDER —European Regional Development Fund “A way to build Europe.” MLV is funded by a Beca per a la Formació de Personal Investigador (FI) fellowship from the Agència de Gestió d’Ajuts Universitaris i de Recerca, Generalitat de Catalunya.Peer reviewe

Parity Broken Chiral Spin Dynamics in Ba3_3NbFe3_3Si2_2O14_{14}

The spin wave excitations emerging from the chiral helically modulated 120$^{\circ}$ magnetic order in a langasite Ba$_3$NbFe$_3$Si$_2$O$_{14}$ enantiopure crystal were investigated by unpolarized and polarized inelastic neutron scattering. A dynamical fingerprint of the chiral ground state is obtained, singularized by (i) spectral weight asymmetries answerable to the structural chirality and (ii) a full chirality of the spin correlations observed over the whole energy spectrum. The intrinsic chiral nature of the spin waves elementary excitations is shown in absence of macroscopic time reversal symmetry breaking

State-of-the-art of data analyses in environmental DNA approaches towards its applicability to sustainable fisheries management

An increasing number of studies using marine environmental DNA (eDNA) approaches are showing its potential application in marine fisheries management by helping and simplifying some of the labor-intensive traditional surveys required to assess exploited populations and ecosystem status. eDNA approaches (i.e. metabarcoding and targeted) can support to ecosystem-based fisheries management by providing information on species composition; surveillance of invasive, rare and/or endangered species; and providing estimates of species abundance. Due to these potential uses in fisheries and conservation sciences, the number of studies applying eDNA approaches in marine habitats has expanded in the very last few years. However, a lack of consistency across studies when applying pipelines for data analyses, makes results difficult to compare among them. Such lack of consistency is partially caused by poor knowledge in the management of raw sequences data, and analytical methods allowing comparative results. Hence, we review here the essential steps of eDNA data processing and analyses to get sound, reproducible, and comparable results, providing a set of bioinformatics tools useful for each step. Altogether this review presents the state of the art of eDNA data analyses towards a comprehensive application in fisheries management promoting sustainability

Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

Gazave, Elodie et al.Copy number variants (CNVs) are increasingly acknowledged as an important source of evolutionary novelties in the human lineage. However, our understanding of their significance is still hindered by the lack of primate CNV data. We performed intraspecific comparative genomic hybridizations to identify loci harboring copy number variants in each of the four great apes: bonobos, chimpanzees, gorillas, and orangutans. For the first time, we could analyze differences in CNV location and frequency in these four species, and compare them with human CNVs and primate segmental duplication (SD) maps. In addition, for bonobo and gorilla, patterns of CNV and nucleotide diversity were studied in the same individuals. We show that CNVs have been subject to different selective pressures in different lineages.Evidence for purifying selection is stronger in gorilla CNVs overlapping genes, while positive selection appears to have driven the fixation of structural variants in the orangutan lineage. In contrast, chimpanzees and bonobos present high levels of common structural polymorphism, which is indicative of relaxed purifying selection together with the higher mutation rates induced by the known burst of segmental duplication in the ancestor of the African apes. Indeed, the impact of the duplication burst is noticeable by the fact that bonobo and chimpanzee share more CNVs with gorilla than expected. Finally, we identified a number of interesting genomic regions that present high-frequency CNVs in all great apes, while containing only very rare or even pathogenic structural variants in humans.Financial support was provided by a Beatriu de Pinos postdoctoral Grant to E.G., the Spanish Ministry of Science and Innovation (Grant BFU2009-13409-02-02toA.N.),and the Spanish National Institute for Bioinformatics (INB, www.inab.org).Peer reviewe

Declining Population Sizes and Loss of Genetic Diversity in Commercial Fishes: A Simple Method for a First Diagnostic

Exploited fish species may have or are experiencing declines in population sizes coupled with changes in their environmental conditions owing to global change. Declining populations might lead to a decrease in genetic diversity, which in turn may produce losses of adaptive potential to face current and future environmental changes. Thus, this study aims to answer a simple, even naive question, given the complexity of the subject: Could we use a simple method to obtain information on the loss of genetic diversity in exploited fish species? We investigated the use of the levels of genetic diversity in the widely used genetic marker Cytochrome C Oxidase subunit I (COI) mitochondrial gene. Estimates of genetic diversity in COI were obtained for populations of seven fish species with different commercial importance from the East China Sea. These estimates were contrasted against large datasets of genetic diversity in COI for fish species (East-Asian N=118, and worldwide N=1425), and six control species with known biology and history. We found that estimates of genetic diversity in COI match the expectations from theoretical predictions and known declines by fishing pressures. Thus, the answer to our question is affirmative and we conclude that estimates of genetic diversity in COI provide an effective first diagnostic of the conservation status of exploited fish species.En prens

A step back on the conservation of a highly threatened species: opposite signs of recovery on Pinna nobilis population from Mar Menor lagoon

The endemic species Pinna nobilis is the most endangered Mediterranean bivalve, facing nearly extinction all over the Mediterranean Sea, hosting its last reservoirs in highly impacted coastal lagoons. Thus, knowledge about the populations' conservation status in these ecosystems is essential. In 2019, the Mar Menor lagoon’s population was considered as a highly vulnerable population (Nebot-Colomer et al., 2021) due to several ecological disasters. The present study represents a continuation of the previous work, which aims to evaluate the resilience of the population, by assessing its reproductive success and maintenance of the population. To do so, between 2019 to 2022, we installed between 23-45 larvae collectors, monitored 13 permanent individual’s plots, and conducted visual searches and censuses. Overall, densities remained stable over years, although the number of individuals alive monitored in permanent plots decrease each year. Moreover, none of the methodologies carried out detected the incorporation of recruits in the population. Our results pointed out to opposite signs of recovery of the species, increasing its vulnerability to future disturbances. Therefore, urgent management and conservation actions focused on restoring the ecosystem and protecting P. nobilis individuals are needed to avoid this population extinction

Degrees of freedom in social bonds of crested macaque females

Social bonds between group members can affect individual fitness and well-being. While the impact of bond strength is well studied, the consequences of bond predictability and equitability are often overlooked. Similarly, whether bonds reflect short-term contingencies and/or long-term social strategies remains understudied. We investigated these questions in female crested macaques (Macaca nigra), which display a tolerant social style within a nepotistic hierarchical social structure. We analysed the structure of dyadic social bonds by testing whether similarity within dyads - in kinship, dominance and age - predicted the strength, predictability and equitability of bonds. We then tested the value of social bonds by analysing the effect of their characteristics on three fitness-related behaviours: coalitionary support, feeding-in-proximity and aggression. We found that the bond characteristics of females differed substantially from those of other species with comparable data: bonds were of average strength, of moderate endurance and relatively balanced. Stronger bonds were more equitable but less predictable than weaker bonds. Closely-ranked females, but not kin or age peers, had stronger, more predictable and more equitable bonds than others. Coalitionary support was not related to any of the bond characteristics, feeding-in-proximity was positively associated with strength and predictability and aggression was positively linked to strength and equitability. These results highlight the complex picture of the benefits of social bonds in this species. They reflect the degrees of freedom tolerant macaque females can express in their social relationships within their stable social structure, a pattern that may not be given enough consideration in stable nepotistic hierarchical societies. Comparative research is necessary to establish whether these patterns are more general than previously thought or a specific feature of tolerant macaques. Investigating various characteristics of bonds together is paramount in order to appreciate the dynamics of social relationships and to better understand the social components of fitness

Polymer-stable magnesium nanocomposites prepared by laser ablation for efficient hydrogen storage

Hydrogen is a promising alternative energy carrier that can potentially facilitate the transition from fossil fuels to sources of clean energy because of its prominent advantages such as high energy density (142 MJ per kg), great variety of potential sources (for example water, biomass, organic matter), and low environmental impact (water is the sole combustion product). However, due to its light weight, the efficient storage of hydrogen is still an issue investigated intensely. Various solid media have been considered in that respect among which magnesium hydride stands out as a candidate offering distinct advantages. Recent theoretical work indicates that MgH2 becomes less thermodynamically stable as particle diameter decreases below 2 nm. Our DFT (density functional theory) modeling studies have shown that the smallest enthalpy change, corresponding to 2 unit-cell thickness (1.6 {\AA} Mg/3.0{\AA} MgH2) of the film, is 57.7 kJ/molMg. This enthalpy change is over 10 kJ per molMg smaller than that of the bulk. It is important to note that the range of enthalpy change for systems that are suitable for mobile storage applications is 15 to 24 kJ permolH at 298 K. The important key for the development of air/stable Mg/nanocrystals is the use of PMMA (polymethylmethacrylate) as an encapsulation agent. In our work we use laser ablation, a non-electrochemical method, for producing well dispersed nanoparticles without the presence of any long range aggregation. The observed improved hydrogenation characteristics of the polymer/stable Mg-nanoparticles are associated to the preparation procedure and in any case the polymer laser ablation is a new approach for the production of air/protected and inexpensive Mg/nanoparticles.Comment: Hydrogen Storage, Mg - Nanoparticles, Polymer Matrix Composites, Laser Ablation, to appear in International Journal of Hydrogen Energy, 201