Inference of admixture and population size changes in structured populations with applications to conservation genetics

Tese de doutoramento, Biologia (Biologia Evolutiva), 2010, Universidade de Lisboa, Faculdade de CiênciasReconstructing the demographic history of populations with genetic data from present-day samples is a challenging inference problem. The general aim of this thesis is to determine whether major demographic events can be detected, quantified and dated using model-based inference approaches. The emphasis is on the study of admixture events and population size changes, which are relevant for conservation biology. Approximate Bayesian computation (ABC) methods were developed to make inference under models involving admixture. These methods were first implemented into a general and relatively simple model and later improved to deal with up to four populations and two admixture events. An ABC approach based onallele-frequencies was tested and compared in detail with a full-likelihood methods. Several aspects of theABC methodology were investigated in a simulation study, such as the choice of summary statistics anddistance metrics. The estimates obtained with the ABC approximated well the full-likelihood. Moreover, amodel choice procedure was developed to assess the relative probability of alternative admixture and populationsplit models. The results indicate that the ABC approach is able to identify with high probability thecorrect model. These methods have been implemented in a user-friendly software.The effect of population structure on estimates of population size change was also investigated. A simulationstudy was performed to assess the robustness of full-likelihood methods to deviations due to populationstructure. The results show a clear effect of population structure, leading to the detection of spurious bottlenecks,which depends on the sampling scheme and is stronger with limited gene-flow level, and higherscaled mutation rate.The methods developed and investigated here were applied to study two critically endangered freshwaterfish species, Iberochondrostoma lusitanicum and I. almacai. Results suggest that both species were highlystructured, and suffered recent population declines. The re-analysis of I. lusitanicum data with the ABCmethod developed suggested that the potential admixture events were likely due to shared polymorphism.Regarding the bottleneck signatures, the results suggest that the observed data cannot be explained by thepopulation structure alone, indicating that these species are undergoing a population decline.Overall, the results of this thesis may contribute to a better understanding of the potential and limitations of model-based inference methods using genetic data.The work presented in this dissertation was developed with the support of the Fundação para a Ciência e a Tecnologia:PhD Fellowship (SFRH/BD/22224/2005) and by the Projects Demographic and genetic responses to habitat fragmentationand habitat loss in large forest mammals (PTDC/BIA-BDE/71299/2006), GENESTREAM - Landscape genetics of freshwaterfishes: the geographical dimension of genetic diversity (PTDC/BIA-BDE/66519/2006), and Evolutionary processes in the originof Hotspots for Biodiversity': insights from southern Portuguese areas based on novel nuclear multilocus approaches in targetfreshwater fishes and amphibians (PTDC/BIA-BDE/69769/2006)

Recent Advances in Turning Processes Using Coated Tools—A Comprehensive Review

Turning continues to be the largest segment of the machining industry, which highlights the continued demand for turned parts and the overall improvement of the process. The turning process has seen quite an evolution, from basic lathes using solid tools, to complex CNC (Computer Numerical Control) multi-process machines, using, for the most part, coated inserts and coated tools. These coatings have proven to be a significant step in the production of high-quality parts and a higher tool life that have captivated the industry. Continuous improvement to turning coated tools has been made, with many researches focusing on the optimization of turning processes that use coated tools. In the present paper, a presentation of various recently published papers on this subject is going to be made, mentioning the various types of coatings that have recently been used in the turning process, the turning of hard to machine materials, such as titanium alloys and Inconel, as well as the interaction of these coatings with the turned surfaces, the wear patterns that these coatings suffer during the turning of materials and relating these wear mechanisms to the coated tool’s life expectancy. Some lubrication conditions present a more sustainable alternative to current methods used in the turning process; the employment of coated tool inserts under these conditions is a current popular research topic, as there is a focus on opting for more eco-friendly machining options.info:eu-repo/semantics/publishedVersio

Recent Advances on Coated Milling Tool Technology—A Comprehensive Review

The milling process is one of the most used processes in the manufacturing industry. Milling, as a process, as evolved, with new machines and methods being employed, in order to obtain the best results consistently. Milling tools have also seen quite an evolution, from the uncoated high-speed steel tool, to the now vastly used, coated tools. Information on the use of these coated tools in recent scientific researches was collected. The coatings that are currently being researched are going to be presented, highlighting some novel advances in the nanocomposite and diamond coatings area, as these coatings are seeing a growing use in the industry, with very satisfactory results, with performance and tool-life increase. Wear mechanism of various types of coatings are also a popular topic on recent research, as the cutting behavior of these coated tools provides valuable information on the tool’s-life. Furthermore, analysis of these mechanisms enables for the selection of the best coating type for the correct application. Recently, the employment of coated tools paired with sustainable lubrication methods as seen some use. As this presents the opportunity to enhance the coated tool’s and the process’s performance, obtaining better results, in terms of better tool-life and better surface finish quality, in a more sustainable fashionThis research was funded by ON-SURF Project, grant number NUP POCI-01-0247-FEDER-024521.info:eu-repo/semantics/publishedVersio

Rapid and predictable genome evolution across three hybrid ant populations

Hybridization is frequent in the wild but it is unclear when admixture events lead to predictable outcomes and if so, at what timescale. We show that selection led to correlated sorting of genetic variation rapidly after admixture in 3 hybrid Formica aquilonia × F. polyctena ant populations. Removal of ancestry from the species with the lowest effective population size happened in all populations, consistent with purging of deleterious load. This process was modulated by recombination rate variation and the density of functional sites. Moreover, haplotypes with signatures of positive selection in either species were more likely to fix in hybrids. These mechanisms led to mosaic genomes with comparable ancestry proportions. Our work demonstrates predictable evolution over short timescales after admixture in nature.info:eu-repo/semantics/publishedVersio

Rapid and predictable genome evolution across three hybrid ant populations

Funding Information: This work was supported by Academy of Finland (www.aka.fi) no. 328961 and HiLIFE (www2.helsinki.fi/en/helsinki-institute-of-lifescience) grants to JK. SHM was supported by a Royal Society University Research Fellowship URF \R1\180682 (www.royalsociety.org). VCS was supported by Fundação Ciência e Tecnologia CEECINST/00032/2018/CP1523/CT0008 and UIDB/00329/2020 grants (www.fct.pt). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank G. Barroso for assistance with iSMC, the SpecIAnt group for feedback, and CSC–IT Center for Science, Finland, for computational resources. This work was performed under the Global Ant Genomics Alliance. Publisher Copyright: Copyright: © 2022 Nouhaud et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Hybridization is frequent in the wild but it is unclear when admixture events lead to predictable outcomes and if so, at what timescale. We show that selection led to correlated sorting of genetic variation rapidly after admixture in 3 hybrid Formica aquilonia × F. polyctena ant populations. Removal of ancestry from the species with the lowest effective population size happened in all populations, consistent with purging of deleterious load. This process was modulated by recombination rate variation and the density of functional sites. Moreover, haplotypes with signatures of positive selection in either species were more likely to fix in hybrids. These mechanisms led to mosaic genomes with comparable ancestry proportions. Our work demonstrates predictable evolution over short timescales after admixture in nature.Peer reviewe

Adaptation and convergence in circadian‐related genes in Iberian freshwater fish

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.info:eu-repo/semantics/publishedVersio

Hybrid Manufacturing Processes Used in the Production of Complex Parts: A Comprehensive Review

Additive manufacturing is defined as a process based on the superposition of layers of materials in order to obtain 3D parts; however, the process does not allow achieve the adequate and necessary surface finishing. In addition, with the development of new materials with superior properties, some of them acquire high hardness and strength, consequently decreasing their ability to be machined. To overcome this shortcoming, a new technology assembling additive and subtractive processes, was developed and implemented. In this process, the additive methods are integrated into a single machine with subtractive processes, often called hybrid manufacturing. The additive manufacturing process is used to produce the part with high efficiency and flexibility, whilst machining is then triggered to give a good surface finishing and dimensional accuracy. With this, and without the need to transport the part from one machine to another, the manufacturing time of the part is reduced, as well as the production costs, since the waste of material is minimized, with the additive–subtractive integration. This work aimed to carry out an extensive literature review regarding additive manufacturing methods, such as binder blasting, directed energy deposition, material extrusion, material jetting, powder bed fusion, sheet laminating and vat polymerization, as well as machining processes, studying the additive-subtractive integration, in order to analyze recent developments in this area, the techniques used, and the results obtained. To perform this review, ScienceDirect, Web of Knowledge and Google Scholar were used as the main source of information because they are powerful search engines in science information. Specialized books have been also used, as well as several websites. The main keywords used in searching information were: “CNC machining”, “hybrid machining”, “hybrid manufacturing”, “additive manufacturing”, “high-speed machining” and “post-processing”. The conjunction of these keywords was crucial to filter the huge information currently available about additive manufacturing. The search was mainly focused on publications of the current century. The work intends to provide structured information on the research carried out about each one of the two considered processes (additive manufacturing and machining), and on how these developments can be taken into consideration in studies about hybrid machining, helping researchers to increase their knowledge in this field in a faster way. An outlook about the integration of these processes is also performed. Additionally, a SWOT analysis is also provided for additive manufacturing, machining and hybrid manufacturing processes, observing the aspects inherent to these technologies.The present work was done and funded under the scope of the projects ON-SURF (ANI | P2020 | POCI-01-0247-FEDER-024521 and MCTool21 “Manufacturing of cutting tools for the 21st century: from nano-scale material design to numerical process simulation” (ref.: “POCI-01-0247- FEDER-045940”) co-funded by Portugal 2020 and FEDER, through COMPETE 2020-Operational Programme for Competitiveness and Internationalisation. This work is also sponsored by FEDER National funds FCT under the project CEMMPRE ref. “UIDB/00285/2020”. F.J.G. Silva also thanks INEGI-Instituto de Ciência e Inovação em Engenharia Mecânica e Engenharia Indústria due to its support.info:eu-repo/semantics/publishedVersio

Build-Up an Economical Tool for Machining Operations Cost Estimation

Currently, there is a lack of affordable and simple tools for the estimation of these costs, especially for machining operations. This is particularly true for manufacturing SMEs, in which the cost estimation of machined parts is usually performed based only on required material for part production, or involves a time-consuming, non-standardized technical analysis. Therefore, a cost estimation tool was developed, based on the calculated machining times and amount of required material, based on the final drawing of the requested workpiece. The tool was developed primarily for milling machines, considering milling, drilling, and boring/threading operations. Regarding the considered materials, these were primarily aluminum alloys. However, some polymer materials were also considered. The tool first estimates the required time for total part production and then calculates the total cost. The total production time is estimated based on the required machining operations, as well as drawing, programming, and machine setup time. A part complexity level was also introduced, based on the number of details and operations required for each workpiece, which will inflate the estimated times. The estimation tool was tested in a company setting, comparing the estimated operation time values with the real ones, for a wide variety of parts of differing complexity. An average error of 14% for machining operation times was registered, which is quite satisfactory, as this time is the most impactful in terms of machining cost. However, there are still some problems regarding the accuracy in estimating finishing operation timesinfo:eu-repo/semantics/publishedVersio

Investigations on the Wear Performance of Coated Tools in Machining UNS S32101 Duplex Stainless Steel

Due to their high mechanical property values and corrosion resistance, duplex stainless steels (DSSs) are used for a wide variety of industrial applications. DSSs are also selected for applications that require, especially, high corrosion resistance and overall good mechanical properties, such as in the naval and oil-gas exploration industries. The obtention of components made from these materials is quite problematic, as DSSs are considered difficult-to-machine alloys. In this work, the developed wear during milling of the UNS S32101 DSS alloy is presented, employing four types of milling tools with different geometries and coatings. The influence of feed rate and cutting length variations on the tools’ wear and their performance was evaluated. The used tools had two and four flutes with different coatings: TiAlN, TiAlSiN and AlCrN. The cutting behavior of these tools was analyzed by collecting data regarding the cutting forces developed during machining and evaluating the machined surface quality for each tool. After testing, the tools were submitted to SEM analysis, enabling the identification of the wear mechanisms and quantification of flank wear, as well as identifying the early stages of the development of these mechanisms. A comparison of all the tested tools was made, determining that the TiAlSiN-coated tools produced highly satisfactory results, especially in terms of sustained flank wear.The present work was conducted and funded under the scope of the project ON-SURF (ANI|P2020|POCI-01-0247-FEDER-024521, co-funded by Portugal 2020 and FEDER, through the COMPETE 2020-Operational Programme for Competitiveness and Internationalisation. F.J.G. Silva thanks INEGI—Instituto de Ciência e Inovação em Engenharia Mecânica e Engenharia Indústria for its support. The authors would like to thank Rui Rocha from CEMUP (Porto, Portugal), due to his active collaboration in getting the best SEM pictures and helping with his critical analysis of some phenomena. The authors also would like to thank Ing. Ricardo Alexandre for his extremely important role in providing all the coatings through the TEandM company, and Eng. Nuno André for providing the substrate material and uncoated tools through the Inovatools company.info:eu-repo/semantics/publishedVersio

Using an Artificial Neural Network Approach to Predict Machining Time

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 sectorsinfo:eu-repo/semantics/publishedVersio