Дисертації з теми "Population genetics Mathematics"
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Herbots, Hilde Maria Jozefa Dominiek. "Stochastic models in population genetics : genealogy and genetic differentiation in structured populations." Thesis, Queen Mary, University of London, 1994. http://qmro.qmul.ac.uk/xmlui/handle/123456789/1482.
Повний текст джерелаLevin, Alex Ph D. (Alexander) Massachusetts Institute of Technology. "Graphs, matrices, and populations : linear algebraic techniques in theoretical computer science and population genetics." Thesis, Massachusetts Institute of Technology, 2013. http://hdl.handle.net/1721.1/83695.
Повний текст джерелаCataloged from PDF version of thesis.
Includes bibliographical references (pages 149-155).
In this thesis, we present several algorithmic results for problems in spectral graph theory and computational biology. The first part concerns the problem of spectral sparsification. It is known that every dense graph can be approximated in a strong sense by a sparse subgraph, known as a spectral sparsifier of the graph. Furthermore, researchers have recently developed efficient algorithms for computing such approximations. We show how to make these algorithms faster, and also give a substantial improvement in space efficiency. Since sparsification is an important first step in speeding up approximation algorithms for many graph problems, our results have numerous applications. In the second part of the thesis, we consider the problem of inferring human population history from genetic data. We give an efficient and principled algorithm for using single nucleotide polymorphism (SNP) data to infer admixture history of various populations, and apply it to show that Europeans have evidence of mixture with ancient Siberians. Finally, we turn to the problem of RNA secondary structure design. In this problem, we want to find RNA sequences that fold to a given secondary structure. We propose a novel global sampling approach, based on the recently developed RNAmutants algorithm, and show that it has numerous desirable properties when compared to existing solutions. Our method can prove useful for developing the next generation of RNA design algorithms.
by Alex Levin.
Ph.D.
Ishida, Yoichi. "Secret analogies mathematics, ecology, and evolution /." abstract and full text PDF (free order & download UNR users only), 2007. http://0-gateway.proquest.com.innopac.library.unr.edu/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:1442878.
Повний текст джерелаReich, David Emile. "Genetic analysis of human evolutionary history with implications for gene mapping." Thesis, University of Oxford, 1999. http://ora.ox.ac.uk/objects/uuid:9e3a3eb7-3cce-4494-82e8-8616fabed145.
Повний текст джерелаGjini, Erida. "Bridging between parasite genomic data and population processes : trypanosome dynamics and the antigenic archive." Thesis, University of Glasgow, 2012. http://theses.gla.ac.uk/3375/.
Повний текст джерелаLundy, Ian J. "Theoretical population genetics of spatially structured populations /." Title page, contents and summary only, 1997. http://web4.library.adelaide.edu.au/theses/09PH/09phl962.pdf.
Повний текст джерелаLoucoubar, Cheikh. "Statistical genetic analysis of infectious disease (malaria) phenotypes from a longitudinal study in a population with significant familial relationships." Phd thesis, Université René Descartes - Paris V, 2012. http://tel.archives-ouvertes.fr/tel-00685104.
Повний текст джерелаOlsson, Fredrik. "Inbreeding, Effective Population Sizes and Genetic Differentiation : A Mathematical Analysis of Structured Populations." Doctoral thesis, Stockholms universitet, Matematiska institutionen, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-115708.
Повний текст джерелаAt the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Submitted.
Xu, Yiyang. "Topics in population genetics and mathematical evolutionary biology." Thesis, University of Bristol, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.682366.
Повний текст джерелаMartin, Anna. "Mathematical modeling of seed bank dynamics in population genetics." Thesis, Uppsala universitet, Institutionen för informationsteknologi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-321191.
Повний текст джерелаAuton, Adam. "The estimation of recombination rates from population genetic data." Thesis, University of Oxford, 2007. http://ora.ox.ac.uk/objects/uuid:dc38045b-725d-4afc-8c76-94769db3534d.
Повний текст джерелаSester-Huss, Elisabeth Mariko [Verfasser], and Peter [Akademischer Betreuer] Pfaffelhuber. "Population genetic models with selection, fluctuating environments and population structure." Freiburg : Universität, 2020. http://d-nb.info/1206095830/34.
Повний текст джерелаJiang, Hongyu. "Population genetics genealogies under selection." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:141f4e19-d13a-409e-a7c7-aeaabd6b9b88.
Повний текст джерелаTran, Tat Dat. "Information Geometry and the Wright-Fisher model of Mathematical Population Genetics." Doctoral thesis, Universitätsbibliothek Leipzig, 2012. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-90508.
Повний текст джерелаKOT, MARK. "THE EFFECTS OF PARAMETRIC EXCITATION AND OF DISPERSAL ON THE DYNAMICS OF DISCRETE-TIME POPULATION MODELS." Diss., The University of Arizona, 1987. http://hdl.handle.net/10150/184074.
Повний текст джерелаLópez, de Rioja Víctor. "Population range expansions, with mathematical applications to interacting systems and ancient human genetics." Doctoral thesis, Universitat de Girona, 2019. http://hdl.handle.net/10803/667171.
Повний текст джерелаAquesta tesi estudia des d’un punt de analític i computacional, gràcies a les equacions de reacció-difusió, l’evolució espaciotemporal de diferents poblacions que interactuen entre elles. El primer article estudia la dinàmica del bacteriòfag T7 infectant el bacteri E. coli. Gràcies a la incorporació del temps de retard en els termes de difusió i reacció, així com de nous termes matemàtics amb sentit biològic, aconseguim uns resultats que s’ajusten millor a les velocitats de propagació. El segon article aplica diferents models matemàtics per entendre millor l’expansió del VSV en Glioblastomes. L'únic model capaç d'explicar de manera correcte el sistema té en compte el temps de retard per als processos de difusió i reacció. L’últim article explica la transició del Neolític a través d’Europa utilitzant mostres genètiques antigues i simulacions matemàtiques. Centrant-nos en l’haplogrup K, el model es construeix tenint en compte els dos mecanismes de difusió neolítica: dèmica i cultural. Les simulacions mostren que la transició és bàsicament dèmica, on només el 2% dels neolítics interaccionen culturalment
Lipson, Mark (Mark Israel). "New statistical genetic methods for elucidating the history and evolution of human populations." Thesis, Massachusetts Institute of Technology, 2014. http://hdl.handle.net/1721.1/89873.
Повний текст джерелаThis electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 165-173).
In the last few decades, the study of human history has been fundamentally changed by our ability to detect the signatures left within our genomes by adaptations, migrations, population size changes, and other processes. Rapid advances in DNA sequencing technology have now made it possible to interrogate these signals at unprecedented levels of detail, but extracting more complex information about the past from patterns of genetic variation requires new and more sophisticated models. This thesis presents a suite of sensitive and efficient statistical tools for learning about human history and evolution from large-scale genetic data. We focus first on the problem of admixture inference and describe two new methods for determining the dates, sources, and proportions of ancestral mixtures between diverged populations. These methods have already been applied to a number of important historical questions, in particular that of tracing the course of the Austronesian expansion in Southeast Asia. We also report a new approach for estimating the human mutation rate, a fundamental parameter in evolutionary genetics, and provide evidence that it is higher than has been proposed in recent pedigree-based studies.
by Mark Lipson.
Ph. D.
Arpin, Sheree. "Using Mathematical Models to Investigate Phenotypic Oscillations in Cichlid Fish: A Case of Frequency-dependent Selection." Diss., The University of Arizona, 2007. http://hdl.handle.net/10150/195981.
Повний текст джерелаPieper, Daniel [Verfasser], and Martin [Akademischer Betreuer] Hutzenthaler. "Many-demes limit for interacting diffusions with applications in population genetics / Daniel Pieper ; Betreuer: Martin Hutzenthaler." Duisburg, 2020. http://d-nb.info/1213245508/34.
Повний текст джерелаHustedt, Thiemo [Verfasser]. "The Moran model of population genetics : case studies with recombination and selection / Thiemo Hustedt. Fakultät für Mathematik." Bielefeld : Universitätsbibliothek Bielefeld, Hochschulschriften, 2012. http://d-nb.info/1024640523/34.
Повний текст джерелаForest, Marie. "Simultaneous estimation of population size changes and splits times using importance sampling." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:8c067a3d-44d5-468a-beb5-34c5830998c4.
Повний текст джерелаGayley, Todd Warwick. "Genetic models of two-phenotype frequency-dependent selection." Diss., The University of Arizona, 1989. http://hdl.handle.net/10150/184883.
Повний текст джерелаWittmann, Meike [Verfasser], and Dirk [Akademischer Betreuer] Metzler. "Stochastic models for the ecology and population genetics of introduced species / Meike Wittmann. Betreuer: Dirk Metzler." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2014. http://d-nb.info/1047062380/34.
Повний текст джерелаStraulino, Daniel. "Selection in a spatially structured population." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:3a20f7a3-27cd-4cbb-9e88-7ebb21ce4e0d.
Повний текст джерелаXifara, Dionysia-Kiara. "The detection, structure and uses of extended haplotype identity in population genetic data." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:9fabc91a-dd07-4deb-b722-f6b9110b34fb.
Повний текст джерелаGonzález, Casanova Soberón Adrián [Verfasser], Jochen [Akademischer Betreuer] Blath, Noemi [Akademischer Betreuer] Kurt, Jochen [Gutachter] Blath, Noemi [Gutachter] Kurt, and Anton [Gutachter] Wakolbinger. "The effect of latency in population genetics / Adrián González Casanova Soberón ; Gutachter: Jochen Blath, Noemi Kurt, Anton Wakolbinger ; Jochen Blath, Noemi Kurt." Berlin : Technische Universität Berlin, 2016. http://d-nb.info/1156013100/34.
Повний текст джерелаSiska, Veronika. "Human population history and its interplay with natural selection." Thesis, University of Cambridge, 2019. https://www.repository.cam.ac.uk/handle/1810/284164.
Повний текст джерелаTran, Tat Dat [Verfasser], Jürgen [Akademischer Betreuer] Jost, Jürgen [Gutachter] Jost, and Shun-ichi [Gutachter] Amari. "Information Geometry and the Wright-Fisher model of Mathematical Population Genetics / Tat Dat Tran ; Gutachter: Jürgen Jost, Shun-ichi Amari ; Betreuer: Jürgen Jost." Leipzig : Universitätsbibliothek Leipzig, 2012. http://d-nb.info/1238077277/34.
Повний текст джерелаHechter, Eliana. "On genetic variants underlying common disease." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:d883f20e-7dad-4216-8851-b006993832fd.
Повний текст джерелаBhatt, Samir. "Statistical analysis of natural selection in RNA virus populations." Thesis, University of Oxford, 2010. http://ora.ox.ac.uk/objects/uuid:64341c38-f09e-48ed-84e8-7ab9f171a753.
Повний текст джерелаDilthey, Alexander Tilo. "Statistical HLA type imputation from large and heterogeneous datasets." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:1bca18bf-b9d5-4777-b58e-a0dca4c9dbea.
Повний текст джерелаPereira, Renato Nunes. "Modelo hierárquico bayesiano na determinação de associação entre marcadores e QTL em uma população F2." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/11/11134/tde-25042012-161429/.
Повний текст джерелаThe objective of the mapping of quantitative trait loci (QTL) is to identify its position in the genome, ie, identify which chromosome is and what is its location in the chromosome, as well as to estimate their genetic eects. Since the location of QTL are not known a priori, markers are often used to assist in it mapping. Some markers may be closely linked to one or more QTL, and thus they may show a strong association with the phenotypic trait. The genetic eect of QTL and the phenotypic values of a quantitative trait are usually described by a linear model. Since the QTL locations are not known a priori, markers are used to represent them. Generally is used a large number of markers. These markers are used in the linear model to make the process of association and thus the model specied contains a large number of parameters to be estimated. However, it is expected that many of these parameters are not signicant, requiring a special treatment. In Bayesian estimation this problem is treated through structure priori distribution used. A parameter that is expected to assume the value zero (not signicant) is naturally specied by means of a distribution that put more weight at zero, bayesian shrinkage. This paper proposes the use of two models using priori distributions to shrinkage. One of the models is related to the use of priori distribution Laplace (bayesian Lasso) and the other with Horseshoe (Horseshoe Estimator). To evaluate the performance of the models to determine the association between markers and QTL, we performed a simulation study. We analyzed the association between markers and QTL using three phenotypic traits: grain yield, ear height and plant height. We compared the results obtained in this study with analyzes in the literature on the detection of markers associated with these characteristics. The computational implementation of the algorithms was done using the C language and executed the statistical package R. The program is implemented in C languages presented and made available. Due to the interaction between the programming languages C and R, it was possible execute the program in the environment R.
Gryspeirt, Aiko. "Impact des plantes Bt sur la biologie de Plodia interpunctella: évaluation de l'efficacité de la stratégie agricole "Haute dose - refuge" pour la gestion de la résistance des insectes ravageurs aux plantes Bt." Doctoral thesis, Universite Libre de Bruxelles, 2008. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210542.
Повний текст джерелаMon projet de recherche s’inscrit dans le cadre de l’évaluation de l'efficacité de cette stratégie et s’articule en deux phases :une phase expérimentale et une phase théorique. La première se concentre sur la caractérisation en laboratoire de l'impact des toxines Cry sur la biologie d'un ravageur. Cette phase constitue un support au volet théorique :la mise au point d’un modèle mathématique évaluant l'efficacité de la stratégie HD/R. L'originalité de ce projet repose entre autre sur l'interactivité entre ces deux volets.
Volet expérimental. Impact des toxines Cry sur la biologie de Plodia interpunctella. Nous évaluons séparément l'impact d'une gamme de concentrations de deux toxines Cry (CryXX et CryYY) sur une série de paramètres comportementaux et biologiques d'un insecte commun des denrées stockées: Plodia interpunctella (Hübner) (Lepidoptera :Pyralidae). Ces paramètres sont sélectionnés car leur variation pourrait avoir un impact sur l'efficacité de la stratégie HD/R dans le contrôle de la résistance. Il est donc pertinent de les quantifier pour intégrer dans le modèle des ordres de grandeur réalistes et générer des résultats qui ne sont pas uniquement basés sur des spéculations théoriques.
Volet théorique A. Efficacité de la stratégie HD/R pour des plantes Bt synthétisant une ou deux toxines simultanément. La stratégie 'HD/R' a été développée pour prévenir la résistance envers les plantes Bt synthétisant une seule toxine. Or, depuis 2003, de nouvelles variétés de coton Bt synthétisant simultanément deux toxines Cry sont commercialisées (BollgardII® et WidestrikeTM). Nous évaluons, grâce au modèle que nous avons développé, l'efficacité de cette stratégie lors d'une utilisation exclusive de plantes Bt synthétisant une ou deux toxines.
Volet théorique B. Impact du ralentissement du développement des insectes sur les plantes Bt sur l'efficacité de la stratégie HD/R. Le volet expérimental met en évidence un allongement de la durée du développement des larves se nourrissant sur une diète contaminée en toxine Cry. Ce ralentissement induit une séparation temporelle entre l'émergence des adultes de la zone Bt et de la zone refuge et perturbe une hypothèse principale de la stratégie HD/R: le croisement aléatoire entre adultes, indépendamment du génotype et de la zone d'origine. Dans ce troisième chapitre, nous étudions l'impact de la perturbation du croisement aléatoire sur l'efficacité de la stratégie HD/R. Nous testons également deux options pour optimiser la stratégie en cas d'asynchronie: l'utilisation de plantes Bt synthétisant une faible concentration en toxine (atténuant le décalage entre l'émergence des adultes) ou l'augmentation de la taille de la zone refuge (favorisant la survie des individus porteurs d'allèle de sensibilité et donc optimisant la dilution de la résistance à la génération suivante).
Ce travail s'intègre dans une problématique actuelle et utilise des outils de biologie théorique (théories de la dynamique et de la génétique des populations) ainsi que le développement d'un modèle mathématique. Il apporte des éléments de réponse et de réflexion sur l'optimisation de la gestion de la résistance des insectes mais c'est aussi une illustration de la complémentarité entre la biologie expérimentale et théorique.
/
On the market since 1996, genetically modified plants synthesizing an insecticidal toxin (Cry toxin) stemmed from Bacillus thuringiensis, called Bt plants, target several insect pests (Lepidoptera or Coleoptera). Bt crops cover increasingly larger areas and control important pest populations The Insect Resistance Management Strategy (IRM) strategy currently recommended in the U.S.A. to limit the development of resistant populations is the High Dose / Refuge zone (HD/R) strategy. This pre-emptive strategy requires a refuge zone composed by non-Bt plants, usable by the target insect and in close proximity of the Bt zone synthesizing a high toxin concentration.
My research project contributes to the effectiveness assessment of this HD/R strategy. It is structured on two main parts: an experimental, and a theoretical section. The first part characterizes the impact of Cry toxins on the biology of an insect pest. It is the basis of the theoretical part: the implementation of a mathematical model, which evaluates the effectiveness of the HD/R strategy.
The originality of this project is based on the interactivity of these two components.
Experimental section. Impact of the Cry toxins on the biology of Plodia interpunctella. We assess the impact of a range of concentrations of two Cry toxins (CryXX et CryYY) on several behavioural and biological parameters of a common pest of stored products: Plodia interpunctella (Hübner) (Lepidoptera :Pyralidae). These parameters are selected because their variation could influence the effectiveness of a HD/R strategy. So, it is important to quantify these parameters so that realistic values can be integrated in our model. The results of the model are thus not based on theoretical assumptions alone.
Theoretical section A. Effectiveness of a HD/R strategy with Bt plants synthesizing one or two toxins. Initially, the HD/R strategy has been developed to limit the resistance towards Bt plants synthesizing one toxin. However, since 2003, new Bt cotton varieties synthesize two toxins simultaneously (BollgardII® et WidestrikeTM). We assess, with our model, the effectiveness of this strategy for Bt plants synthesizing one or two toxins.
Theoretical section B. Impact of the slowing down of the insect development reared on Bt plants on the effectiveness of the HD/R strategy. The experimental part demonstrates that larvae reared on a Bt diet have a protracted development duration. The consequence of this is a temporal separation between adult emergence in the two zones (Bt zone and refuge zone). This could affect the main assumption of the HD/R strategy, i. e. random mating independently of the genotype and of the native zone. In this third chapter, we study the impact of random mating disruption on the effectiveness of a HD/R strategy. We test two options to optimise the strategy in case of asynchrony: the use of Bt plants synthesizing a lower toxin concentration (limiting emergence asynchrony) or increasing the refuge zone size (favouring the survival of insect carrying one or two susceptible allele and thus optimising the dilution of resistance at the next generation).
This work is applied to a current issue. It uses some of the tools of theoretical biology (theories of population dynamics and population genetics) and develops a mathematical model. It provides some responses and some elements of thought about insect resistance management. It is also an illustration of the complementarity between experimental and theoretical biology.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished
Blum, Michael G. B. "Statistique bayésienne et applications en génétique des populations." Habilitation à diriger des recherches, Université de Grenoble, 2012. http://tel.archives-ouvertes.fr/tel-00766196.
Повний текст джерелаBrown, Samuel David James. "Molecular systematics and colour variation of Carpophilus species (Coleoptera: Nitidulidae) of the South Pacific." Diss., Lincoln University, 2009. http://hdl.handle.net/10182/1430.
Повний текст джерелаViho, Agbélénko Goudjo. "Étude de modèles markoviens en génétique et calculs des temps d'absorption." Grenoble 1, 1996. http://www.theses.fr/1996GRE10121.
Повний текст джерелаErfmeier, Alexandra. "Ursachen des Invasionserfolges von Rhododendron ponticum L. auf den Britischen Inseln Einfluss von Habitat und Genotyp /." Doctoral thesis, [S.l. : s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=975033476.
Повний текст джерелаFischer, Stephan. "Modélisation de l'évolution de la taille des génomes et de leur densité en gènes par mutations locales et grands réarrangements chromosomiques." Phd thesis, INSA de Lyon, 2013. http://tel.archives-ouvertes.fr/tel-00924831.
Повний текст джерелаBrink-Spalink, Rebekka. "Stochastic Models in Population Genetics: The Impact of Selection and Recombination." Doctoral thesis, 2015. http://hdl.handle.net/11858/00-1735-0000-0022-5F9A-D.
Повний текст джерелаGiorgi, Elena Edi. "A mathematical growth model of the viral population in early HIV-1 infections." 2011. https://scholarworks.umass.edu/dissertations/AAI3482705.
Повний текст джерелаHeuer, Benjamin. "Convergence of the Genealogy of the Spatial Cannings Model." Doctoral thesis, 2016. http://hdl.handle.net/11858/00-1735-0000-002B-7CA9-7.
Повний текст джерелаGroeneveld, Linn Fenna. "Species delimitation, phylogeography and population genetics of the endemic Malagasy dwarf lemurs (genus Cheirogaleus)." Doctoral thesis, 2008. http://hdl.handle.net/11858/00-1735-0000-000D-F23D-6.
Повний текст джерелаSTUDENÁ, Lucie. "Aplikace matematických znalostí při výuce biologie." Master's thesis, 2018. http://www.nusl.cz/ntk/nusl-390973.
Повний текст джерелаAston, Christopher Eric. "Statistical models for multilocus structures." Phd thesis, 1985. http://hdl.handle.net/1885/141088.
Повний текст джерелаSteinrücken, Matthias [Verfasser]. "Multiple merger coalescents and population genetic inference / vorgelegt von Matthias Steinrücken." 2009. http://d-nb.info/998939536/34.
Повний текст джерелаAshander, Jaime. "Effects of parasite exchange between wild and farmed salmon." Master's thesis, 2010. http://hdl.handle.net/10048/1292.
Повний текст джерелаApplied Mathematics
Fehren-Schmitz, Lars. "Molekularanthropologische Untersuchungen zur präkolumbischen Besiedlungsgeschichte des südlichen Perus am Beispiel der Palpa-Region." Doctoral thesis, 2008. http://hdl.handle.net/11858/00-1735-0000-0006-AD06-F.
Повний текст джерелаWhale, John W. "Population genetic analysis of the black blow fly Phormia regina (Meigen) (Diptera: Calliphoridae)." Thesis, 2015. http://hdl.handle.net/1805/6722.
Повний текст джерелаThe black blow fly, Phormia regina (Diptera: Calliphoridae), is a widely abundant fly autochthonous to North America. Like many other Calliphorids, P. regina plays a key role in several disciplines particularly in estimating post-mortem intervals (PMI). The aim of this work was to better understand the population genetic structure of this important ecological species using microsatellites from populations collected in the U.S. during 2008 and 2013. Additionally, it sought to determine the effect of limited genetic diversity on a quantitative trait throughout immature development; larval length, a measurement used to estimate specimen age. Observed heterozygosity was lower than expected at five of the six loci and ranged from 0.529-0.880 compared to expected heterozygosity that ranged from 0.512-0.980, this is indicative of either inbreeding or the presence of null alleles. Kinship coefficients indicate that individuals within each sample are not strongly related to one another; values for the wild-caught populations ranged from 0.033-0.171 and a high proportion of the genetic variation (30%) can be found among samples within regions. The population structure of this species does not correlate well to geography; populations are different to one another resulting from a lack of gene flow irrespective of geographic distance, thus inferring temporal distance plays a greater role on the genetic variation of P. regina. Among colonized samples, flies lost much of their genetic diversity, ≥67% of alleles per locus were lost, and population samples became increasingly more related; kinship coefficient values increased from 0.036 for the wild-caught individuals to 0.261 among the F10 specimens. Colonized larvae also became shorter in length following repeated inbreeding events, with the longest recorded specimen in F1 18.75 mm in length while the longest larva measured in F11 was 1.5 mm shorter at 17.25 mm. This could have major implications in forensic entomology, as the largest specimen is often assumed to be the oldest on the corpse and is subsequently used to estimate a postmortem interval. The reduction in length ultimately resulted in a greater proportion of individuals of a similar length; the range of data became reduced. Consequently, the major reduction in genetic diversity indicates that the loss in the spread of length distributions of the larvae may have a genetic influence or control. Therefore, this data highlights the importance when undertaking either genetic or development studies, particularly of blow flies such as Phormia regina, that collections of specimens and populations take place not only from more than one geographic location, but more importantly from more than one temporal event.
Hao, Yangyang. "Computational modeling for identification of low-frequency single nucleotide variants." 2015. http://hdl.handle.net/1805/8891.
Повний текст джерелаReliable detection of low-frequency single nucleotide variants (SNVs) carries great significance in many applications. In cancer genetics, the frequencies of somatic variants from tumor biopsies tend to be low due to contamination with normal tissue and tumor heterogeneity. Circulating tumor DNA monitoring also faces the challenge of detecting low-frequency variants due to the small percentage of tumor DNA in blood. Moreover, in population genetics, although pooled sequencing is cost-effective compared with individual sequencing, pooling dilutes the signals of variants from any individual. Detection of low frequency variants is difficult and can be cofounded by multiple sources of errors, especially next-generation sequencing artifacts. Existing methods are limited in sensitivity and mainly focus on frequencies around 5%; most fail to consider differential, context-specific sequencing artifacts. To face this challenge, we developed a computational and experimental framework, RareVar, to reliably identify low-frequency SNVs from high-throughput sequencing data. For optimized performance, RareVar utilized a supervised learning framework to model artifacts originated from different components of a specific sequencing pipeline. This is enabled by a customized, comprehensive benchmark data enriched with known low-frequency SNVs from the sequencing pipeline of interest. Genomic-context-specific sequencing error model was trained on the benchmark data to characterize the systematic sequencing artifacts, to derive the position-specific detection limit for sensitive low-frequency SNV detection. Further, a machine-learning algorithm utilized sequencing quality features to refine SNV candidates for higher specificity. RareVar outperformed existing approaches, especially at 0.5% to 5% frequency. We further explored the influence of statistical modeling on position specific error modeling and showed zero-inflated negative binomial as the best-performed statistical distribution. When replicating analyses on an Illumina MiSeq benchmark dataset, our method seamlessly adapted to technologies with different biochemistries. RareVar enables sensitive detection of low-frequency SNVs across different sequencing platforms and will facilitate research and clinical applications such as pooled sequencing, cancer early detection, prognostic assessment, metastatic monitoring, and relapses or acquired resistance identification.
Mader, Felix. "Räumliche, GIS-gestützte Analyse von Linientransektstichproben." Doctoral thesis, 2007. http://hdl.handle.net/11858/00-1735-0000-0006-B626-D.
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