Drift Shape Research Articles

Climate Adaptation and Drift Shape the Genomes of Two Eel-Goby Sister Species Endemic to Contrasting Latitude.

Deciphering the role of climate adaptation in generating genetic divergence and hence speciation is a central question in evolution. Comparisons of genomes of closely related species spanning selective climate gradients are particularly informative in discerning the signatures of selection and thereby providing valuable information concerning the role of climate adaptation in speciation. Here we re-sequenced 99 genomes of the two sister eel-goby species Odontamblyopus lacepedii and O. rebecca, which are endemic to tidal mudflats spanning contrasting latitude gradients, to estimate the influence of divergent climate selection on shaping genome-wide patterns of divergence. The results indicated that genome-wide differentiation between the two species was evident (genome-wide FST = 0.313). Against a background of high baseline genomic divergence, 588 and 1202 elevated divergent loci were detected to be widespread throughout their genomes, as opposed to focused within small islands of genomic regions. These patterns of divergence may arise from divergent climate selection in addition to genetic drift acting through past glacial segregation (1.46 million years ago). We identified several candidate genes that exhibited elevated divergence between the two species, including genes associated with substance metabolism, energy production, and response to environmental cues, all putative candidates closely linked to thermal adaptation expected from the latitude gradient. Interestingly, several candidates related to gamete recognition and time of puberty, and also exhibited elevated divergence, indicating their possible role in pre-zygote isolation and speciation of the two species. Our results would expand our knowledge on the roles of latitude climate adaptation and genetic drift in generating and maintaining biodiversity in marine teleosts.

Numerical study on snow erosion and deposition around an embankment with a snow fence under snowfall conditions

Snow drift which usually occurs in conjunction with snowfall can significantly alter the distribution pattern of snow cover around roads creating travel hazards for vehicles. To study the snow distribution around a road and evaluate the snow prevention efficiency of snow fence, based on the theories of two-phase flow and snowdrift erosion and deposition, a numerical model is developed. The model includes snowfall during snow drift, spatial distribution characteristics of wind speed and snow phase volume fraction, and dynamic changes of snow drift shape on the ground during drifting. We simulate the distribution characteristics of snowdrift around an embankment without and with the protection of a snow fence and under the conditions of no snowfall and snowfall. The results indicate that snow deposition is greatest on the leeward side of the embankment in comparison to the windward side of the embankment and takes a longer time to reach equilibrium. On the leeward side of the embankment, the snow accumulation rate under the condition of snow falling is higher than that under the condition of no snow falling. Nonetheless, the two conditions both suggest that installation of the snow fence intercepts a large amount of snow behind the snow fence, decreases the snow phase volume fraction near the ground, and reduces the snowdrift accumulation on the leeward side of the embankment within a certain period.

Fixation and effective size in a haploid–diploid population with asexual reproduction

The majority of population genetic theory assumes fully haploid or diploid organisms with obligate sexuality, despite complex life cycles with alternating generations being commonly observed. To reveal how natural selection and genetic drift shape the evolution of haploid–diploid populations, we analyze a stochastic genetic model for populations that consist of a mixture of haploid and diploid individuals, allowing for asexual reproduction and niche separation between haploid and diploid stages. Applying a diffusion approximation, we derive the fixation probability and describe its dependence on the reproductive values of haploid and diploid stages, which depend strongly on the extent of asexual reproduction in each phase and on the ecological differences between them.

Stability of Deep Underground Mine Drift through Complex Geology Conditions in Quang Ninh Coal Area

The stability of deep underground mine drifts is pivotal to sustainable, safe mining in underground coal mines. The main objective of this research is to determine the stability and drifting safety issues in 500-m-deep deep underground mine drift through complex geology in the Quang Ninh coal area. The laboratory experimentation and field measurements were used to analyze the large deformations and failure characteristics of the surrounding rock, the influence factors of safe excavation and stability of deep underground mine drift, and to study the stability control countermeasures. This study also shows the main factors influencing the stability and drifting safety include complex geology zones, high in situ stress, poor mechanical properties and engineering performance of the argillaceous rock mass. According to the field study, the groutability of cement-matrix materials in the argillaceous rock in the complex geology zones were extremely poor, and deformations and failure of the surrounding rock were characterized by dramatic initial deformation, high long-term creep rate, obviously asymmetric deformations and failure, the rebound of roof displacements, overall loosened deformations of deep surrounding rock on a large scale, and high sensitivity to engineering disturbance and water immersion. Various geo-hazards occurred during the underground mine drift excavation, including roof collapse, groundwater inrush. Control techniques are proposed and should be adopted to ensure drifting safety and to control the stability of deep underground mine drift through complex geology zones, including choice of reasonable drift shape, reasonable support type, steel sets, regional strata reinforcement technique such as ground surface pre-grouting, primary enhanced control measures, grouting reinforcement technique, and secondary enclosed support measures for long-term stability, which are critical for ensuring the sustainable development of the underground coal mine.

Two perturbation formulations of the nonlinear dynamics of a cable excited by a boundary motion

A nonlinear cable excited by an inclined boundary motion, termed as cable's moving boundary problem, is attacked by two different perturbation approaches, i.e., the boundary modulation formulation and the quasi-static drift formulation. The former transforms the boundary motion into a weak modulation on cable's high-order dynamics, while the latter introduces a hybrid mode expansion using an empirical drift shape function. In both formulations, the inclined boundary motion induces three different excitation effects, i.e., longitudinal direct, vertical boundary kinematic, and high-order parametric, all of which being characterized by the parametric modulation factors. Detailed comparative studies indicate that the modulation factors in the two formulations are exactly equivalent to each other only if a new drift shape function, well defined in the boundary modulation formulation, is used for the quasi-static drift formulation. In contrast, the empirical shape functions lead only to an approximate equivalence for intermediate/large boundary motion inclinations. Moreover, for small inclinations, the two formulations induce possible quantitative and qualitative differences. The approximate analytical framework is validated and shown to be computationally efficient, by comparison with the finite difference method.

Using a comparative approach to investigate the relationship between landscape and genetic connectivity among woodland salamander populations

For many amphibian species, reduced landscape connectivity results in reduced genetic connectivity among populations. However, large effective population sizes (Ne) slow the rate of genetic drift, causing subdivided populations to remain genetically similar despite little gene flow among them. Therefore, it is important to address the combined effects of Ne and matrix permeability to quantify the relative importance of gene flow and genetic drift on isolated amphibian populations. We applied a landscape genetic approach to investigate how patterns of gene flow (m), Ne (inferred via θ) and genetic differentiation differ among Eastern Red-backed Salamander (Plethodon cinereus) populations in a fragmented landscape (n = 4) compared to a continuous forest (n = 4). We assayed a panel of 10 microsatellite markers for population genetic analyses. Additionally, we constructed and validated a distribution model to generate resistance surfaces for examining the relationship between landscape connectivity, m, θ, and genetic differentiation (FST) using maximum-likelihood population-effects models (MLPE). Populations in continuous habitat were undifferentiated, whereas fragmented populations exhibited genetic structure driven by a single population. Results of the MLPE models in the fragmented landscape revealed spatial variation in θ as the best predictor of pairwise FST, followed by estimates of m, suggesting migration-drift interactions have a stronger influence on genetic differentiation than matrix permeability. Moreover, model coefficients for landscape resistance were comparable between landscapes. Overall, our results provide insight as to how the interaction of gene flow and genetic drift shapes population structure for a dispersal-limited species within a predominately anthropogenic landscape.

Molecular footprint of Medawar's mutation accumulation process in mammalian aging.

Medawar's mutation accumulation hypothesis explains aging by the declining force of natural selection with age: Slightly deleterious germline mutations expressed in old age can drift to fixation and thereby lead to aging‐related phenotypes. Although widely cited, empirical evidence for this hypothesis has remained limited. Here, we test one of its predictions that genes relatively highly expressed in old adults should be under weaker purifying selection than genes relatively highly expressed in young adults. Combining 66 transcriptome datasets (including 16 tissues from five mammalian species) with sequence conservation estimates across mammals, here we report that the overall conservation level of expressed genes is lower at old age compared to young adulthood. This age‐related decrease in transcriptome conservation (ADICT) is systematically observed in diverse mammalian tissues, including the brain, liver, lung, and artery, but not in others, most notably in the muscle and heart. Where observed, ADICT is driven partly by poorly conserved genes being up‐regulated during aging. In general, the more often a gene is found up‐regulated with age among tissues and species, the lower its evolutionary conservation. Poorly conserved and up‐regulated genes have overlapping functional properties that include responses to age‐associated tissue damage, such as apoptosis and inflammation. Meanwhile, these genes do not appear to be under positive selection. Hence, genes contributing to old age phenotypes are found to harbor an excess of slightly deleterious alleles, at least in certain tissues. This supports the notion that genetic drift shapes aging in multicellular organisms, consistent with Medawar's mutation accumulation hypothesis.

Combining hydrodynamic modelling with genetics: can passive larval drift shape the genetic structure of Baltic Mytilus populations?

While secondary contact between Mytilus edulis and Mytilus trossulus in North America results in mosaic hybrid zone formation, both species form a hybrid swarm in the Baltic. Despite pervasive gene flow, Baltic Mytilus species maintain substantial genetic and phenotypic differentiation. Exploring mechanisms underlying the contrasting genetic composition in Baltic Mytilus species will allow insights into processes such as speciation or adaptation to extremely low salinity. Previous studies in the Baltic indicated that only weak interspecific reproductive barriers exist and discussed the putative role of adaptation to environmental conditions. Using a combination of hydrodynamic modelling and multilocus genotyping, we investigate how oceanographic conditions influence passive larval dispersal and hybrid swarm formation in the Baltic. By combining our analyses with previous knowledge, we show a genetic transition of Baltic Mytilus species along longitude 12°-13°E, that is a virtual line between Malmö (Sweden) and Stralsund (Germany). Although larval transport only occurs over short distances (10-30km), limited larval dispersal could not explain the position of this genetic transition zone. Instead, the genetic transition zone is located at the area of maximum salinity change (15-10psu). Thus, we argue that selection results in weak reproductive barriers and local adaptation. This scenario could maintain genetic and phenotypic differences between Baltic Mytilus species despite pervasive introgressive hybridization.

Measuring microbial fitness in a field reciprocal transplant experiment.

Microbial fitness is easy to measure in the laboratory, but difficult to measure in the field. Laboratory fitness assays make use of controlled conditions and genetically modified organisms, neither of which are available in the field. Among other applications, fitness assays can help researchers detect adaptation to different habitats or locations. We designed a competitive fitness assay to detect adaptation of Saccharomyces paradoxus isolates to the habitat they were isolated from (oak or larch leaf litter). The assay accurately measures relative fitness by tracking genotype frequency changes in the field using digital droplet PCR (DDPCR). We expected locally adapted S.paradoxus strains to increase in frequency over time when growing on the leaf litter type from which they were isolated. The DDPCR assay successfully detected fitness differences among S.paradoxus strains, but did not find a tendency for strains to be adapted to the habitat they were isolated from. Instead, we found that the natural alleles of the hexose transport gene we used to distinguish S.paradoxus strains had significant effects on fitness. The origin of a strain also affected its fitness: strains isolated from oak litter were generally fitter than strains from larch litter. Our results suggest that dispersal limitation and genetic drift shape S.paradoxus populations in the forest more than local selection does, although further research is needed to confirm this. Tracking genotype frequency changes using DDPCR is a practical and accurate microbial fitness assay for natural environments.

Fishing for drifts: detecting buoyancy changes of a top marine predator using a step-wise filtering method.

ABSTRACTIn southern elephant seals (Mirounga leonina), fasting- and foraging-related fluctuations in body composition are reflected by buoyancy changes. Such buoyancy changes can be monitored by measuring changes in the rate at which a seal drifts passively through the water column, i.e. when all active swimming motion ceases. Here, we present an improved knowledge-based method for detecting buoyancy changes from compressed and abstracted dive profiles received through telemetry. By step-wise filtering of the dive data, the developed algorithm identifies fragments of dives that correspond to times when animals drift. In the dive records of 11 southern elephant seals from South Georgia, this filtering method identified 0.8–2.2% of all dives as drift dives, indicating large individual variation in drift diving behaviour. The obtained drift rate time series exhibit that, at the beginning of each migration, all individuals were strongly negatively buoyant. Over the following 75–150 days, the buoyancy of all individuals peaked close to or at neutral buoyancy, indicative of a seal's foraging success. Independent verification with visually inspected detailed high-resolution dive data confirmed that this method is capable of reliably detecting buoyancy changes in the dive records of drift diving species using abstracted data. This also affirms that abstracted dive profiles convey the geometric shape of drift dives in sufficient detail for them to be identified. Further, it suggests that, using this step-wise filtering method, buoyancy changes could be detected even in old datasets with compressed dive information, for which conventional drift dive classification previously failed.

Dynamics in microbial communities: unraveling mechanisms to identify principles.

Diversity begets higher-order properties such as functional stability and robustness in microbial communities, but principles that inform conceptual (and eventually predictive) models of community dynamics are lacking. Recent work has shown that selection as well as dispersal and drift shape communities, but the mechanistic bases for assembly of communities and the forces that maintain their function in the face of environmental perturbation are not well understood. Conceptually, some interactions among community members could generate endogenous dynamics in composition, even in the absence of environmental changes. These endogenous dynamics are further perturbed by exogenous forcing factors to produce a richer network of community interactions and it is this 'system' that is the basis for higher-order community properties. Elucidation of principles that follow from this conceptual model requires identifying the mechanisms that (a) optimize diversity within a community and (b) impart community stability. The network of interactions between organisms can be an important element by providing a buffer against disturbance beyond the effect of functional redundancy, as alternative pathways with different combinations of microbes can be recruited to fulfill specific functions.

The roles of genetic drift and natural selection in quantitative trait divergence along an altitudinal gradient in Arabidopsis thaliana.

Understanding how natural selection and genetic drift shape biological variation is a central topic in biology, yet our understanding of the agents of natural selection and their target traits is limited. We investigated to what extent selection along an altitudinal gradient or genetic drift contributed to variation in ecologically relevant traits in Arabidopsis thaliana. We collected seeds from 8 to 14 individuals from each of 14 A. thaliana populations originating from sites between 800 and 2700 m above sea level in the Swiss Alps. Seed families were grown with and without vernalization, corresponding to winter-annual and summer-annual life histories, respectively. We analyzed putatively neutral genetic divergence between these populations using 24 simple sequence repeat markers. We measured seven traits related to growth, phenology and leaf morphology that are rarely reported in A. thaliana and performed analyses of altitudinal clines, as well as overall QST-FST comparisons and correlation analyses among pair-wise QST, FST and altitude of origin differences. Multivariate analyses suggested adaptive differentiation along altitude in the entire suite of traits, particularly when expressed in the summer-annual life history. Of the individual traits, a decrease in rosette leaf number in the vegetative state and an increase in leaf succulence with increasing altitude could be attributed to adaptive divergence. Interestingly, these patterns relate well to common within- and between-species trends of smaller plant size and thicker leaves at high altitude. Our results thus offer exciting possibilities to unravel the underlying mechanisms for these conspicuous trends using the model species A. thaliana.

Verification of Structural Health Assessment Method Using Full-Scale Collapse Test of Four-Story Steel Building

In this paper, the health status of a full-scale four-story steel building is investigated using the data of collapse test at the E-defense in Hyogo Prefecture, Japan. We extracted the features such as hysteretic characteristics, story drift angle, natural frequency and shapes using only the acceleration data of the collapse test. We evaluated the reliability and the correlation of the features with structural damage. Moreover, we proposed the preferred index for the damage detection.

Prediction and follow-up of failure and fallouts in footwall drifts in the Kiirunavaara mine

A likely result of changes in rock stresses due to progressing mining is an increased number of compressive stress–induced failures. This paper presents the results from numerical analysis and observations of stress-induced fallouts in footwall drifts in the Kiirunavaara underground mine. A brittle-plastic “cohesion-softening friction-hardening” (CSFH) material model was used for simulating brittle fallouts. To account for mining-induced stress changes, the local model stress boundary conditions were extracted from a global model. The rock mass properties were based on field observations in the footwall drifts as well as on results from laboratory testing. A multi-stage analysis was carried out to gradually change the stresses to simulate mining progress. A parametric study was conducted in which strength properties, location, and shape of the footwall drift were varied. Yielded elements and maximum shear strain were used as damage and fallout indicators. The modelling results were sensitive to the shape of the drift. The location of the predicted fallouts was in good agreement with the location of observed fallouts for the case in which the drift roof was simulated flatter than the theoretical cross section. The results indicate that the true shape of the drift is different from the planned one.

Modelling the evolutionary dynamics of viruses within their hosts: a case study using high-throughput sequencing.

Uncovering how natural selection and genetic drift shape the evolutionary dynamics of virus populations within their hosts can pave the way to a better understanding of virus emergence. Mathematical models already play a leading role in these studies and are intended to predict future emergences. Here, using high-throughput sequencing, we analyzed the within-host population dynamics of four Potato virus Y (PVY) variants differing at most by two substitutions involved in pathogenicity properties. Model selection procedures were used to compare experimental results to six hypotheses regarding competitiveness and intensity of genetic drift experienced by viruses during host plant colonization. Results indicated that the frequencies of variants were well described using Lotka-Volterra models where the competition coefficients βij exerted by variant j on variant i are equal to their fitness ratio, rj/ri. Statistical inference allowed the estimation of the effect of each mutation on fitness, revealing slight (s = −0.45%) and high (s = −13.2%) fitness costs and a negative epistasis between them. Results also indicated that only 1 to 4 infectious units initiated the population of one apical leaf. The between-host variances of the variant frequencies were described using Dirichlet-multinomial distributions whose scale parameters, closely related to the fixation index F ST, were shown to vary with time. The genetic differentiation of virus populations among plants increased from 0 to 10 days post-inoculation and then decreased until 35 days. Overall, this study showed that mathematical models can accurately describe both selection and genetic drift processes shaping the evolutionary dynamics of viruses within their hosts.

Longevity, calling effort, and metabolic rate in two populations of cricket

Intraspecific variation in a resting metabolic rate (RMR) is likely to be an important determinant of energetic-resource use and may influence the resources subsequently available for allocation to traits not directly associated with somatic maintenance. The influence of RMR on resource availability could be especially important for condition-dependent sexual traits, such as cricket calls, that are themselves energetically costly to produce. RMR may also be associated with longevity, either negatively because individuals with a high RMR burn resources faster and die young, or positively as individuals with high RMR are more able to accrue resources to fuel survival. Additionally, the associations between RMR and other characters may vary across populations if differential selection or drift shapes these traits. Here we tested for differences in RMR, body mass, calling effort, and longevity in two populations of cricket Gryllodes sigillatus and then evaluated the potential influence of RMR on calling and longevity. We find that RMR, calling effort, and longevity varied across populations, but mass did not. Controlling for population and mass, RMR was not significantly associated with calling effort, but was negatively associated with longevity. These findings suggest that male crickets that live fast die young.

The population genomics of begomoviruses: global scale population structure and gene flow.

BackgroundThe rapidly growing availability of diverse full genome sequences from across the world is increasing the feasibility of studying the large-scale population processes that underly observable pattern of virus diversity. In particular, characterizing the genetic structure of virus populations could potentially reveal much about how factors such as geographical distributions, host ranges and gene flow between populations combine to produce the discontinuous patterns of genetic diversity that we perceive as distinct virus species. Among the richest and most diverse full genome datasets that are available is that for the dicotyledonous plant infecting genus, Begomovirus, in the Family Geminiviridae. The begomoviruses all share the same whitefly vector, are highly recombinogenic and are distributed throughout tropical and subtropical regions where they seriously threaten the food security of the world's poorest people.ResultsWe focus here on using a model-based population genetic approach to identify the genetically distinct sub-populations within the global begomovirus meta-population. We demonstrate the existence of at least seven major sub-populations that can further be sub-divided into as many as thirty four significantly differentiated and genetically cohesive minor sub-populations. Using the population structure framework revealed in the present study, we further explored the extent of gene flow and recombination between genetic populations.ConclusionsAlthough geographical barriers are apparently the most significant underlying cause of the seven major population sub-divisions, within the framework of these sub-divisions, we explore patterns of gene flow to reveal that both host range differences and genetic barriers to recombination have probably been major contributors to the minor population sub-divisions that we have identified. We believe that the global Begomovirus population structure revealed here could facilitate population genetics studies into how central parameters of population genetics namely selection, recombination, mutation, gene flow, and genetic drift shape the global begomovirus diversity.

Evolution Is a Quantitative Science

Evolutionary genetics is a mature field of endeavour, and some of biology’s greatest minds have contributed to the theory of population genetics. Initially, they faced a problem, in that following the rediscovery of Mendel’s results in the early years of the 20th century, some saw an unbridgeable gulf between the sudden changes in appearance seen in the mutant forms of peas studied by Mendel, and the gradual and subtle changes to evolving populations envisaged by Darwin. The socalled Neo-Darwinian synthesis linked these ideas by considering the likely effect of Darwinian natural selection on variations in Mendelian genes, variations which would not necessarily have major effects on organisms’ phenotypes. Unusually, for biology, this theory was developed, primarily by Fisher, Haldane and Wright, prior to the existence of data sets to which it could realistically be applied. As a result, the second half of the 20th century saw evolutionary geneticists’ struggle to produce data to test theory. They were especially interested in polymorphisms— discrete genetic variations where the rarer type still has an appreciable frequency in the population. So they studied visible polymorphisms, such as the colours and banding patterns of snails, and polymorphisms in the charges of soluble enzymes, until, finally, abundant DNA sequence data became available in the last years of the century. Now, a resurgence of interest in evolutionary genetics can be predicted, since we will have, through the 1,000 genomes project, for example, data sets detailing population genetic variation genome-wide in many species. We need the tools of evolutionary genetics to describe and explain this variation. What does the variation tell us about population sizes in the past, and rates of gene flow between subpopulations? Which parts of the genome have been subject to purifying and adaptive natural selection, and how strong has this selection been? Recent advances in population genetic theory, in particular, incorporating knowledge that chromosomes include linked sites that are subject to different forces such as selected versus neutral sites, create powerful methods that can help in answering these questions. For these and other reasons, a strong grounding in evolutionary genetics must be included in all bioinformatics and genomics courses. Educators will find that foundation in Elements of Evolutionary Genetics, by Brian and Deborah Charlesworth. This thorough and accurate textbook represents a remarkable achievement. The rigour of the approach is impeccable throughout, and the text makes clear just how many areas of biology, such as sex, genome structure, migration and population variation, and adaptive evolution itself, can be understood only through the application of formal models in which evolutionary processes are considered in a precise way. Most telling, however, is the consistently quantitative approach to data and their interpretation. While a full appreciation of the book will require some mathematical understanding, the steps required are clearly dealt with in appendices, and the reader is helped by problems in each chapter. Space precludes a full description of such a major work. The focus shies away from the changes to the genetic material over long-term evolution, and methods in building phylogenetic trees, etc., but rather concentrates on evolutionary change at the genetic level over the short term, exploring how mutation, migration, natural selection, and random drift shape the genetic variation within and between populations and how data can give insight into the underlying evolutionary forces that are at play. Following descriptions of the measurement of genetic variation—the theory of quantitative genetics and the theory of population genetics as it can be applied to infinite populations—the sampling effects that create genetic drift and determine levels of neutral variation are described. The expected variation between populations, the consequences and causes of sex and recombination, and the interpretation of genome structure in population genetic terms, all of which are found in the second half of the book, represent areas of particular recent interest. All have been investigated at the theoretical level and much of this theory has been contributed by Brian and Deborah Charlesworth themselves. An example is the expected, and observed, evolution of sex chromosomes. If a single chromosome, such as the mammalian Y chromosome, determines sex, its presence as a sole copy in the cell prevents it from ever undergoing recombination. The lack of recombination will attenuate the power Charlesworth B, Charlesworth D (2010) Elements of evolutionary genetics. Greenwood Village, Colorado: Roberts & Co. 734p ISBN (hardback) 978-0-98151942-5 US$80.00. doi:10.1371/journal.pbio.1000381.g001

Desaturation and structure relationships around drifts excavated in the well-compacted Tournemire's argillite (Aveyron, France)

This study aimed to explore the relationships between the extension of rock desaturation and the Excavation Damaged Zone (EDZ) subsequent to the excavation of a century-old tunnel and of recent drifts (1996 and 2003) at the Tournemire Underground Research Laboratory (URL) located in the Aveyron county (South of the Massif Central, France). The other objective of this work was to assess the impact of desaturation on the hydraulic head profile measured around the tunnel. One section was selected per drift. Two boreholes were drilled for each section: one parallel and one inclined (45°) with respect to the bedding. For each borehole, we performed on-site drill core mapping, petrophysical measurements, pneumatic and hydraulic tests by means of a Modular Mini-Packer System (MMPS). Results indicate that the EDZ around drifts is mainly a combination of unloading joints, mimicking the drift shape, and of desaturation cracks, parallel to the bedding. The EDZ extension around the tunnel is twice to three times that of the drifts of 1996 and 2003 and is essentially composed of unloading joints resulting from the mechanical response of the rock. The masonery covering the tunnel walls is assumed to have protected the rock from seasonal variations of air humidity, thus limiting (without excluding) the formation of desaturation cracks. The EDZ extension deduced from core mapping is in agreement with that deduced from pneumatic tests with permeabilities several orders of magnitude greater than in the undisturbed zone. Degrees of saturation for the three sections range between 0.9 and 1 in the EDZ area and reach 1 in the undamaged zone. The head profile deduced from measurements recorded since 2002 indicates the occurrence of an Excavation disturbed Zone (EdZ) of about 40 m around the tunnel. This EdZ is likely due to the existence of sub-atmospheric water pressures clearly seen in the first meter around the tunnel. We have tried to quantify the impact of the tunnel since its excavation on saturation degree and on hydraulic heads. The simulation was performed by considering, as a first approach, the absence of fracturing in the EDZ. A constant suction of − 3300 m, deduced from the mean annual values of relative humidity and temperature measured in the tunnel atmosphere since 2002, was applied at the tunnel wall. The degrees of saturation simulated around the tunnel are underestimated in the EDZ area and consistent to experimental data in the unfractured zone. The modelling of hydraulic heads is overestimated in the horizontal direction and is in the domain of experimental values in the vertical direction, but the lack of intermediate data cannot enable us to conclude on this consistency. This study demonstrated the role played by fracturing on the distribution of petrophysical parameters and of heads around drifts and the century-old tunnel. It has also demonstrated the necessity of coupling mechanic and hydraulic calculations by considering capillary forces.

Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia.

Wigglesworthia glossinidia brevipalpis, the obligate bacterial endosymbiont of the tsetse fly Glossina brevipalpis, is characterized by extreme genome reduction and AT nucleotide composition bias. Here, multivariate statistical analyses are used to test the hypothesis that mutational bias and genetic drift shape synonymous codon usage and amino acid usage of Wigglesworthia. The results show that synonymous codon usage patterns vary little across the genome and do not distinguish genes of putative high and low expression levels, thus indicating a lack of translational selection. Extreme AT composition bias across the genome also drives relative amino acid usage, but predicted high-expression genes (ribosomal proteins and chaperonins) use GC-rich amino acids more frequently than do low-expression genes. The levels and configuration of amino acid differences between Wigglesworthia and Escherichia coli were compared to test the hypothesis that the relatively GC-rich amino acid profiles of high-expression genes reflect greater amino acid conservation at these loci. This hypothesis is supported by reduced levels of protein divergence at predicted high-expression Wigglesworthia genes and similar configurations of amino acid changes across expression categories. Combined, the results suggest that codon and amino acid usage in the Wigglesworthia genome reflect a strong AT mutational bias and elevated levels of genetic drift, consistent with expected effects of an endosymbiotic lifestyle and repeated population bottlenecks. However, these impacts of mutation and drift are apparently attenuated by selection on amino acid composition at high-expression genes.