When divergence occurs in the presence of gene flow, there can arise an interesting dynamic in which selection against gene flow, at sites associated with population-specific adaptations or genetic ...incompatibilities, can cause net gene flow to vary across the genome. Loci linked to sites under selection may experience reduced gene flow and may experience genetic bottlenecks by the action of nearby selective sweeps. Data from histories such as these may be poorly fitted by conventional neutral model approaches to demographic inference, which treat all loci as equally subject to forces of genetic drift and gene flow. To allow for demographic inference in the face of such histories, as well as the identification of loci affected by selection, we developed an isolation-with-migration model that explicitly provides for variation among genomic regions in migration rates and/or rates of genetic drift. The method allows for loci to fall into any of multiple groups, each characterized by a different set of parameters, thus relaxing the assumption that all loci share the same demography. By grouping loci, the method can be applied to data with multiple loci and still have tractable dimensionality and statistical power. We studied the performance of the method using simulated data, and we applied the method to study the divergence of two subspecies of European rabbits (Oryctolagus cuniculus).
Machining: State-of-the-Art 2022 Silva, Francisco J. G.; Fernandes, Filipe; Sousa, Vitor F. C.
Metals (Basel ),
06/2023, Volume:
13, Issue:
6
Journal Article
Peer reviewed
Open access
Although additive manufacturing is gaining prominence in the market, many applications require very high levels of precision, which are currently not attainable by additive manufacturing ...
Divergent host use has long been suspected to drive population differentiation and speciation in plant‐feeding insects. Evaluating the contribution of divergent host use to genetic differentiation ...can be difficult, however, as dispersal limitation and population structure may also influence patterns of genetic variation. In this study, we use double‐digest restriction‐associated DNA (ddRAD) sequencing to test the hypothesis that divergent host use contributes to genetic differentiation among populations of the redheaded pine sawfly (Neodiprion lecontei), a widespread pest that uses multiple Pinus hosts throughout its range in eastern North America. Because this species has a broad range and specializes on host plants known to have migrated extensively during the Pleistocene, we first assess overall genetic structure using model‐based and model‐free clustering methods and identify three geographically distinct genetic clusters. Next, using a composite‐likelihood approach based on the site frequency spectrum and a novel strategy for maximizing the utility of linked RAD markers, we infer the population topology and date divergence to the Pleistocene. Based on existing knowledge of Pinus refugia, estimated demographic parameters and patterns of diversity among sawfly populations, we propose a Pleistocene divergence scenario for N. lecontei. Finally, using Mantel and partial Mantel tests, we identify a significant relationship between genetic distance and geography in all clusters, and between genetic distance and host use in two of three clusters. Overall, our results indicate that Pleistocene isolation, dispersal limitation and ecological divergence all contribute to genomewide differentiation in this species and support the hypothesis that host use is a common driver of population divergence in host‐specialized insects.
Full text
Available for:
BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Next‐generation sequencing of pooled samples (Pool‐seq) is a popular method to assess genome‐wide diversity patterns in natural and experimental populations. However, Pool‐seq is associated with ...specific sources of noise, such as unequal individual contributions. Consequently, using Pool‐seq for the reconstruction of evolutionary history has remained underexplored. Here we describe a novel Approximate Bayesian Computation (ABC) method to infer demographic history, explicitly modelling Pool‐seq sources of error. By jointly modelling Pool‐seq data, demographic history and the effects of selection due to barrier loci, we obtain estimates of demographic history parameters accounting for technical errors associated with Pool‐seq. Our ABC approach is computationally efficient as it relies on simulating subsets of loci (rather than the whole‐genome) and on using relative summary statistics and relative model parameters. Our simulation study results indicate Pool‐seq data allows distinction between general scenarios of ecotype formation (single versus parallel origin) and to infer relevant demographic parameters (e.g. effective sizes and split times). We exemplify the application of our method to Pool‐seq data from the rocky‐shore gastropod Littorina saxatilis, sampled on a narrow geographical scale at two Swedish locations where two ecotypes (Wave and Crab) are found. Our model choice and parameter estimates show that ecotypes formed before colonization of the two locations (i.e. single origin) and are maintained despite gene flow. These results indicate that demographic modelling and inference can be successful based on pool‐sequencing using ABC, contributing to the development of suitable null models that allow for a better understanding of the genetic basis of divergent adaptation.
Full text
Available for:
BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
One of the most critical factors in producing plastic injection molds is the cost estimation of machining services, which significantly affects the final mold price. These services’ costs are ...determined according to the machining time, which is usually a long and expensive operation. If it is considered that the injection mold parts are all different, it can be understood that the correct and quick estimation of machining times is of great importance for a company’s success. This article presents a proposal to apply artificial neural networks in machining time estimation for standard injection mold parts. For this purpose, a large set of parts was considered to shape the artificial intelligence model, and machining times were calculated to collect enough data for training the neural networks. The influences of the network architecture, input data, and the variables used in the network’s training were studied to find the neural network with greatest prediction accuracy. The application of neural networks in this work proved to be a quick and efficient way to predict cutting times with a percent error of 2.52% in the best case. The present work can strongly contribute to the research in this and similar sectors, as recent research does not usually focus on the direct prediction of machining times relating to overall production cost. This tool can be used in a quick and efficient manner to obtain information on the total machining cost of mold parts, with the possibility of being applied to other industry sectors.
Cultural practices can deeply influence genetic diversity patterns. The Neolithic transitions that took place at different times and locations around the world led to major cultural and demographic ...changes that influenced and therefore left their marks on human genetic diversity patterns. Several studies on the European Neolithic transition suggest that mitochondrial DNA (mtDNA) and Y-chromosome data can exhibit different patterns, which could be owing to different demographic histories for females and males. Archaeological and anthropological data suggest that the transition from hunter–gatherers (HGs) to farmers' societies is probably associated with changes in social organization, particularly in post-marital residence (PMR) rules (i.e. patrilocality, matrilocality or bilocality). The movements of humans and genes associated with these rules can be seen as sex-biased short-range migrations. We developed a new individual-based simulation approach to explore the genetic consequences of 45 different scenarios, where we varied the patterns of PMR and admixture between HGs and farmers. We recorded mtDNA and Y-chromosome data and analysed their diversity patterns within and between populations, through time and space. We also collected published mtDNA and Y-chromosome data from European and Near-Eastern populations in order to identify the scenarios that would best explain them. We show that: (i) different PMR systems can lead to different patterns of genetic diversity and differentiation, (ii) asymmetries between mtDNA and Y-chromosome can be owing to different behaviours between males and females, but also to different mutations rates, and (iii) patrilocality in farmers explains the present patterns of genetic diversity better than matrilocality or bilocality. Moreover, we found that (iv) the genetic diversity of farmers change depending on the HGs PMR rules even though they are assumed to disappear more than 5000 years ago in our simulations.
Full text
Available for:
BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
Evidence for ancient interspecific gene flow through hybridization has been reported in many animal and plant taxa based on genetic markers. The study of genomic patterns of closely related species ...with allopatric distributions allows the assessment of the relative importance of vicariant isolating events and past gene flow. Here, we investigated the role of gene flow in the evolutionary history of four closely related freshwater fish species with currently allopatric distributions in western Iberian rivers-Squalius carolitertii, S. pyrenaicus, S. torgalensis and S. aradensis-using a population genomics dataset of 23,562 SNPs from 48 individuals, obtained through genotyping by sequencing (GBS). We uncovered a species tree with two well-differentiated clades: (i) S. carolitertii and S. pyrenaicus; and (ii) S. torgalensis and S. aradensis. By using D-statistics and demographic modelling based on the site frequency spectrum, comparing alternative demographic scenarios of hybrid origin, secondary contact and isolation, we found that the S. pyrenaicus North lineage is likely the result of an ancient hybridization event between S. carolitertii (contributing ~84%) and S. pyrenaicus South lineage (contributing ~16%), consistent with a hybrid speciation scenario. Furthermore, in the hybrid lineage, we identify outlier loci potentially affected by selection favouring genes from each parental lineage at different genomic regions. Our results suggest that ancient hybridization can affect speciation and that freshwater fish species currently in allopatry are useful to study these processes.
Full text
Available for:
EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Due to the automotive industry’s strict demands, customers submit constant production pressure, leading to the adoption of new methodologies, techniques, and management ideas. The goal is always to ...minimise losses and waste. These demands also affect the maintenance department, which has to keep the balance between machines’ availability for production and ensuring that the machines’ proper running conditions translate into excellent-quality products. Thus, continuous improvement and correct management of maintenance activities are crucial for a company to maintain effective production, without defects, breakdowns, and accidents. Nevertheless, some maintenance activities should also prevent the degradation of equipment conditions in order to produce high-quality products. This paper presents an improvement of maintenance activities conducted on equipment that produces large tires. The main problems and technical difficulties of Machine Tolerance Check (MTC) activities are explored by analysing existing documents, internal knowledge, and changes to working methods. We discuss the implementation of the SMED (Single-Minute Exchange of Die) methodology in calibration procedures, as this method is commonly applied to machines’ setups to reduce downtime. At the end of the study, a 31% decrease in the duration of machine tolerance check activities was achieved, which led to a significant increase in the equipment’s availability.
The circadian clock is a biological timing system that improves the ability of organisms to deal with environmental fluctuations. At the molecular level it consists of a network of ...transcription-translation feedback loops, involving genes that activate (bmal and clock - positive loop) and repress expression (cryptochrome (cry) and period (per) - negative loop). This is regulated by daily alternations of light but can also be affected by temperature. Fish, as ectothermic, depend on the environmental temperature and thus are good models to study its integration within the circadian system. Here, we studied the molecular evolution of circadian genes in four Squalius freshwater fish species, distributed across Western Iberian rivers affected by two climatic types with different environmental conditions (e.g., light and temperature). S. carolitertii and S. pyrenaicus inhabit the colder northern region under Atlantic climate type, while S. torgalensis, S. aradensis and some populations of S. pyrenaicus inhabit the warmer southern region affected by summer droughts, under Mediterranean climate type.
We identified 16 circadian-core genes in the Squalius species using a comparative transcriptomics approach. We detected evidence of positive selection in 12 of these genes using methods based on dN/dS. Positive selection was mainly found in cry and per genes of the negative loop, with 55 putatively adaptive substitutions, 16 located on protein domains. Evidence for positive selection is predominant in southern populations affected by the Mediterranean climate type. By predicting protein features we found that changes at sites under positive selection can impact protein thermostability by changing their aliphatic index and isoelectric point. Additionally, in nine genes, the phylogenetic clustering of species that belong to different clades but inhabit southern basins with similar environmental conditions indicated evolutionary convergence. We found evidence for increased nonsynonymous substitution rate in convergent lineages, likely due to positive selection at 27 sites, mostly in cry genes.
Our results support that temperature may be a selective pressure driving the evolution of genes involved in the circadian system. By integrating sequence-based functional protein prediction with dN/dS-based methods to detect selection we uncovered adaptive convergence in the southern populations, probably related to their similar thermal conditions.
Inconel 718 is a highly valued material in the aerospace and nuclear industries due to the fact of its exceptional properties. However, the processing of this material is quite difficult, especially ...through machining processes. Machining this material results in rapid tool wear, even when low material removal rates are considered. In this study, instrumented turning experiments were employed to evaluate the machinability of Inconel 718 alloy using PCBN tools while assessing the usage of two distinct binder phases, TiN and TiC, for those cutting tools. It was found that the tool life was highly sensitive to the cutting speeds but also affected by the workpiece mechanical properties. At lower cutting speeds, notch wear significantly impacted the tool integrity, whereas at higher cutting speeds, flank wear was the primary failure mode of the tool. The flank wear of the tools with TiN-based binder outperformed TiC by almost 30%, presenting a more consistent behavior when machining.
PDF
