Academic literature on the topic 'Population genetics analyses'
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Journal articles on the topic "Population genetics analyses"
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Grünwald, N. J., S. E. Everhart, B. J. Knaus, and Z. N. Kamvar. "Best Practices for Population Genetic Analyses." Phytopathology® 107, no. 9 (September 2017): 1000–1010. http://dx.doi.org/10.1094/phyto-12-16-0425-rvw.
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Population genetic analysis is a powerful tool to understand how pathogens emerge and adapt. However, determining the genetic structure of populations requires complex knowledge on a range of subtle skills that are often not explicitly stated in book chapters or review articles on population genetics. What is a good sampling strategy? How many isolates should I sample? How do I include positive and negative controls in my molecular assays? What marker system should I use? This review will attempt to address many of these practical questions that are often not readily answered from reading books or reviews on the topic, but emerge from discussions with colleagues and from practical experience. A further complication for microbial or pathogen populations is the frequent observation of clonality or partial clonality. Clonality invariably makes analyses of population data difficult because many assumptions underlying the theory from which analysis methods were derived are often violated. This review provides practical guidance on how to navigate through the complex web of data analyses of pathogens that may violate typical population genetics assumptions. We also provide resources and examples for analysis in the R programming environment.
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Zhou, Chunbao, Xianyu Lang, Yangang Wang, and Chaodong Zhu. "gPGA: GPU Accelerated Population Genetics Analyses." PLOS ONE 10, no. 8 (August 6, 2015): e0135028. http://dx.doi.org/10.1371/journal.pone.0135028.
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Kadarmideen, Haja N., and Luc L. G. Janss. "Population and systems genetics analyses of cortisol in pigs divergently selected for stress." Physiological Genomics 29, no. 1 (March 2007): 57–65. http://dx.doi.org/10.1152/physiolgenomics.00144.2006.
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This study presents a systems genetic analysis on the physiology of cortisol in mice and pigs with an aim to show the potential of a comprehensive computational approach to quickly identify candidate genes and avoid a costly whole-genome quantitative trait locus (QTL) mapping. Population genetics analyses were performed on measurements of cortisol from a pig selection experiment. Expression QTL were mapped and gene networks were built using gene expressions for Crhr1 (corticotrophin-releasing hormone receptor) gene and single nucleotide polymorphisms from public mouse data. Results from mouse data were used to infer potential candidate regulatory genes involved in pig cortisol regulation, using a comparative or translational systems genetics approach. The pig data used were from a 10-yr divergent genetic selection experiment, providing data on 417 individuals. Population genetics analysis showed that cortisol is highly genetically determined with heritabilities of 0.40–0.70. Furthermore, a major gene with an additive effect of 86 ng/ml is segregating. Genetical-genomics investigations revealed two trans-acting eQTL for Crhr1 gene expression on chromosomes 2 and 13. Candidate gene search under trans-eQTL peaks yielded 63 genes for Crhr1 expression phenotypes. Functional links for Crhr1 genes with other genes/proteins in the gene network using mouse data were shown for the first 10 statistically significant genes involved. Results show translational or comparative systems genetics approaches reduce costs and time in large-scale genetics and “-omics” investigations. This is the first study to report a strong genetic basis for cortisol physiology using a systems approach.
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Spitze, K. "Population structure in Daphnia obtusa: quantitative genetic and allozymic variation." Genetics 135, no. 2 (October 1, 1993): 367–74. http://dx.doi.org/10.1093/genetics/135.2.367.
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Abstract Quantitative genetic analyses for body size and for life history characters within and among populations of Daphnia obtusa reveal substantial genetic variance at both hierarchical levels for all traits measured. Simultaneous allozymic analysis on the same population samples indicate a moderate degree of differentiation: GST = 0.28. No associations between electrophoretic genotype and phenotypic characters were found, providing support for the null hypothesis that the allozymic variants are effectively neutral. Therefore, GST can be used as the null hypothesis that neutral phenotypic evolution within populations led to the observed differentiation for the quantitative traits, which I call QST. The results of this study provide evidence that natural selection has promoted diversification for body size among populations, and has impeded diversification for relative fitness. Analyses of population differentiation for clutch size, age at reproduction, and growth rate indicate that neutral phenotypic evolution cannot be excluded as the cause.
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Pluzhnikov, Anna, Anna Di Rienzo, and Richard R. Hudson. "Inferences About Human Demography Based on Multilocus Analyses of Noncoding Sequences." Genetics 161, no. 3 (July 1, 2002): 1209–18. http://dx.doi.org/10.1093/genetics/161.3.1209.
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Abstract Data from 10 unlinked autosomal noncoding regions, resequenced in 15 individuals from each of three populations, were used in a multilocus analysis to test models of human demography. Each of the 10 regions consisted of ~2500 bp. The multilocus analysis, based on summary statistics (average and variance of Tajima's D and Fu and Li's D*), was used to test a family of models with recent population expansion. The African sample (Hausa of Cameroon) is compatible with a constant population size model and a range of models with recent expansion. For this population sample, we estimated confidence sets that showed the limited range of parameter values compatible with growth. For an exponential growth rate as low as 1 × 10−3/generation, population growth is unlikely to have started prior to 50,000 years ago. For higher growth rates, the onset of growth must be more recent. On the basis of the average value of Tajima's D, our sample from an Italian population was found to be incompatible with a constant population size model or any simple expansion model. In the Chinese sample, the variance of Tajima's D was too large to be compatible with the constant population size model or any simple expansion model.
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Walling, Grant A., Peter M. Visscher, Leif Andersson, Max F. Rothschild, Lizhen Wang, Gerhard Moser, Martien A. M. Groenen, et al. "Combined Analyses of Data From Quantitative Trait Loci Mapping Studies: Chromosome 4 Effects on Porcine Growth and Fatness." Genetics 155, no. 3 (July 1, 2000): 1369–78. http://dx.doi.org/10.1093/genetics/155.3.1369.
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Abstract For many species several similar QTL mapping populations have been produced and analyzed independently. Joint analysis of such data could be used to increase power to detect QTL and evaluate population differences. In this study, data were collated on almost 3000 pigs from seven different F2 crosses between Western commercial breeds and either the European wild boar or the Chinese Meishan breed. Genotypes were available for 31 markers on chromosome 4 (on average 8.3 markers per population). Data from three traits common to all populations (birth weight, mean backfat depth at slaughter or end of test, and growth rate from birth to slaughter or end of test) were analyzed for individual populations and jointly. A QTL influencing birth weight was detected in one individual population and in the combined data, with no significant interaction of the QTL effect with population. A QTL affecting backfat that had a significantly greater effect in wild boar than in Meishan crosses was detected. Some evidence for a QTL affecting growth rate was detected in all populations, with no significant differences between populations. This study is the largest F2 QTL analysis achieved in a livestock species and demonstrates the potential of joint analysis.
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Kimbeng, C. A., and E. T. Bingham. "Population improvement in lucerne (Medicago sativa L.): genetic analyses in original and improved populations." Australian Journal of Experimental Agriculture 39, no. 5 (1999): 549. http://dx.doi.org/10.1071/ea98155.
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Most quantitative genetics analyses are limited to the first (mean) and second (variance) degree statistics and their derivatives. Analyses based on third (skewness) and fourth (kurtosis) degree statistics can be useful especially for detecting and characterising the nature of gene interactions. Third and fourth degree statistics were analysed and used to interpret differences in forage yield among S1 families of lucerne derived from double-cross populations that were synthesised before (OGDC) and after (AGDC) improvement via inbreeding and selection. Higher levels of genetic load (deleterious alleles) were revealed in the OGDC population compared with the improved population. The analyses also revealed the importance of gene interaction for forage yield in lucerne. In the unselected OGDC population, interaction between alleles in repulsion phase linkages was more important, whereas, in the selected AGDC population, interaction between alleles linked in coupling phase assumed greater importance. The above results suggest that inbreeding and selection in lucerne can accumulate favourable alleles over generations of selection and result in population improvement. Skewness and kurtosis are relatively easy to compute and interpret and should serve as valuable tools in tetraploid quantitative genetics analyses.
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Gimbernat-Mayol, Julia, Albert Dominguez Mantes, Carlos D. Bustamante, Daniel Mas Montserrat, and Alexander G. Ioannidis. "Archetypal Analysis for population genetics." PLOS Computational Biology 18, no. 8 (August 25, 2022): e1010301. http://dx.doi.org/10.1371/journal.pcbi.1010301.
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The estimation of genetic clusters using genomic data has application from genome-wide association studies (GWAS) to demographic history to polygenic risk scores (PRS) and is expected to play an important role in the analyses of increasingly diverse, large-scale cohorts. However, existing methods are computationally-intensive, prohibitively so in the case of nationwide biobanks. Here we explore Archetypal Analysis as an efficient, unsupervised approach for identifying genetic clusters and for associating individuals with them. Such unsupervised approaches help avoid conflating socially constructed ethnic labels with genetic clusters by eliminating the need for exogenous training labels. We show that Archetypal Analysis yields similar cluster structure to existing unsupervised methods such as ADMIXTURE and provides interpretative advantages. More importantly, we show that since Archetypal Analysis can be used with lower-dimensional representations of genetic data, significant reductions in computational time and memory requirements are possible. When Archetypal Analysis is run in such a fashion, it takes several orders of magnitude less compute time than the current standard, ADMIXTURE. Finally, we demonstrate uses ranging across datasets from humans to canids.
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Guo, Yuxin, Zhiyu Xia, Wei Cui, Chong Chen, Xiaoye Jin, and Bofeng Zhu. "Joint Genetic Analyses of Mitochondrial and Y-Chromosome Molecular Markers for a Population from Northwest China." Genes 11, no. 5 (May 18, 2020): 564. http://dx.doi.org/10.3390/genes11050564.
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The genetic markers on mitochondria DNA (mtDNA) and Y-chromosome can be applied as a powerful tool in population genetics. We present a study to reveal the genetic background of Kyrgyz group, a Chinese ethnic group living in northwest China, and genetic polymorphisms of 60 loci on maternal inherited mtDNA and 24 loci on paternal inherited Y-chromosome short tandem repeats (Y-STRs) were investigated. The relationship between the two systems was tested, and the result indicated that they were statistically independent from each other. The genetic distances between Kyrgyz group and 11 reference populations for mtDNA, and 13 reference populations for Y-STRs were also calculated, respectively. The present results demonstrated that the Kyrgyz group was genetically closer to East Asian populations than European populations based on the mtDNA loci but the other way around for the Y-STRs. The genetic analyses could largely strengthen the understanding for the genetic background of the Kyrgyz group.
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Corander, Jukka, Patrik Waldmann, and Mikko J. Sillanpää. "Bayesian Analysis of Genetic Differentiation Between Populations." Genetics 163, no. 1 (January 1, 2003): 367–74. http://dx.doi.org/10.1093/genetics/163.1.367.
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Abstract We introduce a Bayesian method for estimating hidden population substructure using multilocus molecular markers and geographical information provided by the sampling design. The joint posterior distribution of the substructure and allele frequencies of the respective populations is available in an analytical form when the number of populations is small, whereas an approximation based on a Markov chain Monte Carlo simulation approach can be obtained for a moderate or large number of populations. Using the joint posterior distribution, posteriors can also be derived for any evolutionary population parameters, such as the traditional fixation indices. A major advantage compared to most earlier methods is that the number of populations is treated here as an unknown parameter. What is traditionally considered as two genetically distinct populations, either recently founded or connected by considerable gene flow, is here considered as one panmictic population with a certain probability based on marker data and prior information. Analyses of previously published data on the Moroccan argan tree (Argania spinosa) and of simulated data sets suggest that our method is capable of estimating a population substructure, while not artificially enforcing a substructure when it does not exist. The software (BAPS) used for the computations is freely available from http://www.rni.helsinki.fi/~mjs.
Dissertations / Theses on the topic "Population genetics analyses"
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Bycroft, Clare. "Genomic data analyses for population history and population health." Thesis, University of Oxford, 2017. https://ora.ox.ac.uk/objects/uuid:c8a76d94-ded6-4a16-b5af-09bbad6292a2.
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Many of the patterns of genetic variation we observe today have arisen via the complex dynamics of interactions and isolation of historic human populations. In this thesis, we focus on two important features of the genetics of populations that can be used to learn about human history: population structure and admixture. The Iberian peninsula has a complex demographic history, as well as rich linguistic and cultural diversity. However, previous studies using small genomic regions (such as Y-chromosome and mtDNA) as well as genome-wide data have so far detected limited genetic structure in Iberia. Larger datasets and powerful new statistical methods that exploit information in the correlation structure of nearby genetic markers have made it possible to detect and characterise genetic differentiation at fine geographic scales. We performed the largest and most comprehensive study of Spanish population structure to date by analysing genotyping array data for ~1,400 Spanish individuals genotyped at ~700,000 polymorphic loci. We show that at broad scales, the major axis of genetic differentiation in Spain runs from west to east, while there is remarkable genetic similarity in the north-south direction. Our analysis also reveals striking patterns of geographically-localised and subtle population structure within Spain at scales down to tens of kilometres. We developed and applied new approaches to show how this structure has arisen from a complex and regionally-varying mix of genetic isolation and recent gene-flow within and from outside of Iberia. To further explore the genetic impact of historical migrations and invasions of Iberia, we assembled a data set of 2,920 individuals (~300,000 markers) from Iberia and the surrounding regions of north Africa, Europe, and sub-Saharan Africa. Our admixture analysis implies that north African-like DNA in Iberia was mainly introduced in the earlier half (860 - 1120 CE) of the period of Muslim rule in Iberia, and we estimate that the closest modern-day equivalents to the initial migrants are located in Western Sahara. We also find that north African-like DNA in Iberia shows striking regional variation, with near-zero contributions in the Basque regions, low amounts (~3%) in the north east of Iberia, and as high as (~11%) in Galicia and Portugal. The UK Biobank project is a large prospective cohort study of ~500,000 individuals from across the United Kingdom, aged between 40-69 at recruitment. A rich variety of phenotypic and health-related information is available on each participant, making the resource unprecedented in its size and scope. Understanding the role that genetics plays in phenotypic variation, and its potential interactions with other factors, provides a critical route to a better understanding of human biology and population health. As such, a key component of the UK Biobank resource has been the collection of genome-wide genetic data (~805,000 markers) on every participant using purpose-designed genotyping arrays. These data are the focus of the second part of this thesis. In particular, we designed and implemented a quality control (QC) pipeline on behalf of the current and future use of this multi-purpose resource. Genotype data on this scale offers novel opportunities for assessing quality issues, although the wide range of ancestral backgrounds in the cohort also creates particular challenges. We also conducted a set of analyses that reveal properties of the genetic data, including population structure and familial relatedness, that can be important for downstream analyses. We find that cryptic relatedness is common among UK Biobank participants (~30% have at least one first cousin relative or closer), and a full range of human population structure is present in this cohort: from world-wide ancestral diversity to subtle population structure at sub-national geographic scales. Finally, we performed a genome-wide association scan on a well-studied and highly polygenic phenotype: standing height. This provided a further test of the effectiveness of our QC, as well as highlighting the potential of the resource to uncover novel regions of association.
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Campana, Michael Gray. "Diachonic DNA analyses of animal breeds and populations." Thesis, University of Cambridge, 2011. https://www.repository.cam.ac.uk/handle/1810/236764.
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Humans are dependent on the animals they raise and breed for food and secondary products. Archaeological and genetic investigations can provide critical insights into the history and development of these breeds and help understand human activities in the past. Furthermore, many well-adapted breeds are endangered and archaeological and genetic data can help inform future breed conservation choices. Utilising ancient DNA data could potentially permit detailed diachronic analyses of the development of animal breeds. Ancient DNA analyses have typically focussed on large-scale biogeographic patterns in time and space, such as the spread of domesticates or the movements of peoples. Few studies have attempted fine-scale diachronic analysis within single animal populations or breeds. This is largely due to restricted sample availability and the limited phylogenetic resolution provided by the mitochondrial genome, the most commonly used ancient DNA marker. In this thesis, I demonstrate that fine-scale diachronic analyses within single animal populations and breeds over short time scales are feasible. First, in order to address the limitations of sample size, I assessed three sample screening methods’ abilities (maximum mitochondrial DNA amplicon length, NanoDrop® spectrometry and collagen preservation) to select samples in which DNA was preserved and analysed the utility of parchment as a novel source of ancient and historic DNA. None of the screening methods accurately predicted DNA preservation, but collagen preservation was able to weed out extremely poorly preserved samples from further analysis. All but one of the tested parchments produced multiple sequences matching several different species. Parchment therefore was not appropriate for fine-scale diachronic analyses. Next, I assessed whether analysing the nuclear genome could permit fine-resolution diachronic genetic studies. Since single nucleotide polymorphisms are ideal candidate nuclear markers for diachronic DNA analyses, I assessed the accuracy of the nuclear SNP-typing methodology, SNaPshot™, by genotyping three coat colour markers for a sample of historic Thoroughbred horses for which both phenotypic and correct genotypic information were known from pedigree information in the General Stud Book. The SNaPshot™ protocol was found to provide accurate genotypic information in all cases. Finally, as a proof of method, I compared the diachronic information provided by the mitochondrial and nuclear genomes in Icelandic and Thoroughbred horses. Specifically, in the Icelandic horse, I analysed the mitochondrial D-loop and three coat colour genes in modern and historic populations. In the Icelandic horse, I found statistically significant evidence for genetic change in the mitochondrial genome over the last 150 years. I found no evidence for change in coat colour allele frequencies. Conversely, in the biased and small historic Thoroughbred dataset, the mitochondrial genome was insufficient to provide population-level information, but I was able to show that allele frequencies in the nuclear MSTN gene, a gene previously shown to influence racing performance, have changed significantly in the past century.
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Rohrer, Wendy L. "A biosystematic study of the rare plant Paronychia virginica Sprengel (Caryophyllaceae) employing morphometric and allozyme analyses." Thesis, Virginia Tech, 1997. http://hdl.handle.net/10919/46520.
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Paronychia virginica Spreng. (Caryophyllaceae) is a perennial evergreen herb of exposed, relatively xeric habitats. Approximately 10 mid-Appalachian populations remain in Virginia, West Virginia, and Maryland and are disjunct from populations located primarily in Texas, Oklahoma, and Arkansas. A study was conducted to test the hypothesis that eastern and western populations differ significantly and, therefore, represent at least two distinct taxa. Statistical analyses of 8 qualitative and 24 quantitative morphological characters indicated very highly significant (P < 0.001) variation between eastern and western populations of P. virginica. Characters differing most significantly included sepal pubescence, awn length, awn pubescence, awn curvature, length-width ratio of leaves, and shape of leaf apices. Starch gel electrophoresis was performed and six enzyme systems/nine loci (EST-2, EST-3, LAP, MDH-1, MDH-2, PGI, PGM-1, PGM-2, and SKDH) were identified as being consistently scorable and informative. Although gene flow between populations of P. virginica was shown to be restricted (mean FST = 0.353), populations are maintaining relatively high levels of genetic diversity. Genetic variability was quantified for each population and mean values for number of alleles per locus (A), percent loci polymorphic (P), and expected heterozygosity (HEXP) were found to be 1.95, 47.22%, and 0.204, respectively, exceeding those values reported for seed plants, widespread species, and endemic species. Hierarchical F statistics suggest higher levels of genetic variability within individual populations than among populations, regardless of geographic location. All statistically significant (P < 0.05) deviations from Hardy-Weinberg equilibrium indicated a deficiency in heterozygotes at the respective loci. Considering results from both the morphometric and allozyme analyses, the current author suggests recognizing two distinct subspecies, P. virginica subsp. virginica in the eastern U.S. and P. virginica subsp. scoparia in the south-central U.S. Conservation efforts should be focused on the maintenance of existing populations in both eastern and western regions of the U.S. in order to preserve the genetic and evolutionary potential of these taxa.Master of Science
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Robinson, Stacie Joy. "Landscape genetics of black bears (Ursus americanus) on the Kenai Peninsula, Alaska : phylogenetic, population genetic and spatial analyses /." PURL, 2007. http://www.arlis.org/docs/vol1/166237019.pdf.
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Flores, Bello André 1992. "Population genetic landscape of Basques." Doctoral thesis, Universitat Pompeu Fabra, 2019. http://hdl.handle.net/10803/668156.
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Basque people have been the focus of many studies in the last decades due to cultural and genetic characteristics that place them as an outlier population within the European landscape. Despite the existence of large amount of studies, several controversies exist in the population genetics field: their highest frequencies of Rh-negative, a strong genetic differentiation, a genetic substructure, and their connections with the main ancient European groups along history. Most of the previous studies focused on Basques have suffered from methodological flowbacks and weak study designs. In this thesis, these controversies are elucidated by using a more refined and accurate methodology, together with an exhaustive ethnolinguistic representation of the Basque population and surrounding groups. The main results show a high frequency of Rh-negative in agreement with previous studies, an internal genetic heterogeneity within Basques, together with a clear differentiation from the external populations, probably marked by a genetic continuity from the Bronze Age.La población vasca ha sido objeto de estudio durante las últimas décadas, debido a características culturales y genéticas que parecen definirlos como una población aislada dentro del contexto europeo. A pesar de la existencia de numerosos estudios, diversas controversias han surgido en el área de genética de poblaciones: una de las frecuencias más altas de Rh-negativo, una fuerte diferenciación genética, una subestructura poblacional y la relación con las principales poblaciones antiguas en Europa. Los estudios previos han estado sujetos a una metodología y un muestreo limitados. En esta tesis, se abordan dichas controversias con una metodología más refinada y precisa, además de una representación exhaustiva de la población vasca y de poblaciones circundantes desde un punto de vista etnolingüístico. Los principales resultados muestran: una alta frecuencia de Rh-negativo similar a la observada en trabajos anteriores, una heterogeneidad genética interna, junto con una clara diferenciación de las poblaciones externas, marcada posiblemente por una continuidad genética desde la Edad de Bronce.
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Kamps-Hughes, Nicholas. "Massively Parallel Sequencing-Based Analyses of Genome and Protein Function." Thesis, University of Oregon, 2015. http://hdl.handle.net/1794/19234.
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The advent of high-throughput DNA and RNA sequencing has made possible the assay of millions of nucleic acid molecules in parallel. This allows functional genomic elements to be identified from background in single-tube experiments. This dissertation discusses the development of two such functional screens as well as work implementing a third that was previously developed in my thesis laboratory.
Restriction-Associated DNA sequencing (RAD-Seq) is a complexity reduction sequencing method that allows the same subset of genomic sequence to be read across multiple samples. Differences in sample collection and data analysis allow manifold applications of RAD-Seq. Here we use RAD-Seq to identify mutant genes responsible for altered phenotypes in Caenorhabditis elegans and to identify hyper-invasive alleles in trout population admixtures.
Apart from acquiring genomic sequence data, massively-parallel sequencing can be used for counting applications that quantify activity across a large number of test molecules. This dissertation describes the development of a technique for simultaneously quantifying the activity of a restriction enzyme across all possible DNA substrates by linking digest of a sequenced genome to Illumina-sequencing in an unbiased fashion. Finally, a powerful approach to analyze transcriptional activation is described. This method quantifies output from millions of potential DNA transcriptional enhancers via RNA amplicon sequencing of covalently-linked randomer tags and is used in conjunction with RNA-Seq to provide a mechanistic view of hypoxic gene regulation in Drosophila.
This dissertation includes previously published, co-authored material
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Seshadri, Chitra. "Genome wide epigenetic analyses of Araptus attenuatus, a bark beetle." VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4167.
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Phylogeographic studies have relied on surveying neutral genetic variation in natural populations as a way of gaining better insights into the evolutionary processes shaping present day population demography. Recent emphasis on understanding putative adaptive variation have brought to light the role of epigenetic variation in influencing phenotypes and the mechanisms underlying local adaptation. While much is known about how methylation acts at specific loci to influence known phenotypes, there is little information on the spatial genetic structure of genome-wide patterns of methylation and the extent to which it can extend our understanding of both neutral and putatively adaptive processes. This research examines spatial genetic structure using paired nucleotide and methylation genetic markers in the Sonoran bark beetle, Araptus attenuatus, for which we have a considerable knowledge about its neutral demographic history, demography, and factors influencing ongoing genetic connectivity. Using the msAFLP approach, we attained 703 genetic markers. Of those, 297 were polymorphic in both nucleotide (SEQ) and methylation (METH) were assayed from 20 populations collected throughout the species range. Of the paired SEQ and METH locis, the METH were both more frequent (16% vs. 7%), maintained more diversity (Shannon IMeth = 0.361 vs. ISeq=0.272), and had more among-population genetic structure (ΦST; Meth = 0.035 vs. ΦST; Seq= 0.008) than their paired SEQ loci. Interpopulation genetic distance in both SEQ and METH markers were highly correlated, with 16% of the METH loci having sufficient signal to reconstruct phylogeographic history. Allele frequency variation at five loci (two SEQ and three METH) showed significant relationships with at-site bioclimatic variables suggesting the need for subsequent analysis addressing non-neutral evolution. These results suggest that methylation can be as informative as nucleotide variation when examining spatial genetic structure for phylogeography, connectivity, and, identifying putatively adaptive genetic variance.
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Wilches, Ricardo. "Evolution of genes related to temperature adaptation in Drosophila melanogaster as revealed by QTL and population genetics analyses." Diss., Ludwig-Maximilians-Universität München, 2014. http://nbn-resolving.de/urn:nbn:de:bvb:19-172396.
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The fixation of beneficial variants leaves genomic footprints characterized by a reduction of genetic variation at linked neutral sites and strong, localized allele frequency differentiation among subpopulations. In contrast, for phenotypic evolution the effect of adaptation on the genes controlling the trait is little understood. Theoretical work on polygenic selection suggests that fixations of beneficial alleles (causing selective sweeps) are less likely than small-to-moderate allele frequency shifts among subpopulations. This thesis encompasses three projects in which we have experimentally addressed the issue of selective sweeps vs. allele frequency shifts in the context of polygenic adaptation. We studied three X-linked QTL underlying variation in chill coma recovery time (CCRT), a proxy for cold tolerance, in Drosophila melanogaster from temperate (European) and tropical (African) environments. The analysis of these QTL was performed by means of selective sweep mapping and quantitative complementation tests coupled with expression assays.
While the results of the selective sweep mapping approach identified a gene (CG4491) that is unlikely to be affecting CCRT, quantitative and gene expression analyses revealed two linked candidate genes (brk and CG1677) that appear to differ in their evolutionary histories. We found that the difference in expression of the gene brk between populations affects CCRT variation. Cold tolerant flies from the temperate zone have a lower expression of this gene than cold sensitive flies from the tropics. We found that a likely cause of this difference is variation in a cis-regulatory element in the brk 5’ enhancer region. Sequence variants in this element exhibit moderate frequency differences between populations from temperate and tropical environments, forming two latitudinal clines: one from the equator to the north and another one in opposite direction to the south. In contrast, the other gene within the same QTL (CG1677), which is linked to brk, showed no measurable effect on cold tolerance but is a likely target of strong positive selection leading to a selective sweep in the European population.
These results are consistent with the aforementioned theoretical predictions about footprints of selection in polygenic adaptation. They are also proof of the conceptual bias incurred when identifying candidate genes within a QTL via selective sweep mapping, at least in naturally evolving populations. The challenge for the evolutionary genetics community in the coming years is to develop statistical tools that are as powerful and robust as those already available to map selective sweeps to identify sites in the genome where allele frequency shifts have occurred due to adaptive evolution at the phenotypic level.
Finally, the last section of the results is a report of a new population genetics dataset. It consists of a collection of 80 inbred lines from a natural D. melanogaster population in Sweden and 19 full genome sequences derived from this sample. We hope this material will provide us with further insight into the processes underlying adaptation to novel and stressful environments.
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Gersch, Jeffrey Walter. "Microsatellite, mitochondrial, and major histocompatibility complex analyses of genetic structure in the nurse shark, Ginglymostoma cirratum, in the western Atlantic Ocean." OpenSIUC, 2012. https://opensiuc.lib.siu.edu/theses/936.
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The nurse shark, Ginglymostoma cirratum, is a sedentary shark species that inhabits coral reefs in the tropical and subtropical Atlantic Ocean and along the western coast of the Americas in the Pacific Ocean. Nurse shark tissue samples were collected from the Bahamas, Belize, Brazil, and Dry Tortugas National Park in Florida. 186 individuals were genotyped at 11 microsatellite loci, the control region of the mitochondrial genome was sequenced in 190 individuals, and 89 individuals from the Bahamas, Belize, and Dry Tortugas were genotyped at the major histocompatibility complex (MHC) class IIα locus. An analysis of molecular variance (AMOVA) for the microsatellite loci indicated significant subdivision only between the Bahamas and Dry Tortugas populations. An AMOVA for the mitochondrial control region sequences indicated significant subdivision between all population pairs. The AMOVA for MHC class IIα locus indicated significant subdivision between two population pairs: the Bahamas population and the Dry Tortugas population and the Belize population and the Dry Tortugas population. The nurse shark has the lowest mitochondrial DNA nucleotide diversity (π=0.0125%) and haplotype diversity (h=0.2402) of any shark species to date. There were 14 MHC alleles from 39 polymorphic sites; ten were the same as published alleles (Kasahara et al. 1993; Ohta et al. 2000). This study was the first study to use MHC class IIα genes as a marker for population genetics in sharks. Our results showed that MHC class IIα locus behaves as a diploid locus and is a powerful tool for determining population genetic structure between populations.
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Awad, Lara. "Dynamique des forêts de sapin de Cilicie au Liban et changements globaux : apports des analyses palynologiques et génétiques." Thesis, Montpellier 2, 2014. http://www.theses.fr/2014MON20087/document.
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Le Liban est un pays qui constitue un carrefour des civilisations. Depuis le temps des pharaons, ses ressources forestières ont été exploitées, notamment pour le commerce du bois. Le Liban, connu pour son cèdre, possède une autre espèce emblématique, le sapin de Cilicie, dont les forêts sont en majorité non protégées. Historiquement, le bois de sapin a été exploité durant le Nouvel Empire égyptien ancien pour la construction des temples et des navires. Il représentait ainsi un signe de pouvoir du pharaon, en formant notamment la barque d'Amon. De même, le sapin a été coupé pour la construction du temple de Jérusalem, ainsi que des instruments de musique et de guerre. La fragmentation des sapinières au Liban n'est pas ancienne mais cette faible divergence se traduit cependant par un dème Nord-Est englobant 11 populations et un dème Sud-Ouest englobant 4 populations qui semblent être le résultat de deux processus démographiques consécutifs ou simultanés durant l'histoire du sapin au Liban. Le premier est un phénomène de migration en altitude en réponse à des changements dans l'environnement ou le climat. La reconstruction de la dynamique passée du sapin au Liban a montré que le sapin a subi des fluctuations importantes dans sa taille, depuis le Tardiglaciaire, il y a 14,000 ans. Notamment, le sapin a connu des périodes d'absence du registre pollinique qui pourrait être liées à la fragmentation anthropique de l'habitat ou à des extinctions locales ou contraction de l'aire de répartition. De même, il a connu des périodes d'expansion notamment au cours des événements de sécheresse dans le climat, notamment à 4090 cal. BP, à 5010 cal. BP et de 7800 à 8090 cal. BP. La richesse en allèles privés dans le dème Nord-Est indique la présence de plusieurs micro-refuges glaciaires de basses et de hautes altitudes, ainsi que des zones de suture issues de la recolonisation. Dans le dème Sud-Ouest, une recolonisation postglaciaire en altitude à partir du seul micro-refuge glaciaire détecté est probable. Le deuxième phénomène est lié à une migration asymétrique des populations génétiquement diversifiées du centre du dème vers les populations marginales génétiquement peu diversifiées. Ce processus, qui semblait être le résultat de la faible taille des populations cibles, pourrait permettre de retarder l'extinction des populations marginales, localement menacées. La superformance de la migration sur la dérive génétique et la dispersion sur des longues distances de 15 à 20 km constituent les effets médiateurs de ces processus démographiques. L'empreinte de cette dynamique démographique est une réduction historique de la taille effective des populations sur le long terme avec un signal ancien plutôt que récent, et une diversité génétique et richesse allélique basses. Cette diversité génétique semble être façonnée par les effets anthropiques ainsi que par les changements dans l'environnement ou le climat. La conservation in situ et ex situ de ces sapinières est nécessaire pour préserver leur patrimoine historique et génétiqueThe Lebanon is a country that constitutes a crossroads of civilizations. Back in the time of pharaohs, fir forests in Lebanon were exploited, particularly for the timber trade. Lebanon, known for its cedar, has another emblematic species, the Cilician fir, whose forests are in majority unprotected. Historically, the fir was used during the ancient Egyptian New Kingdom rule over Phoenicia for the construction of temples and ships. Notably, it represented a sign of power of the pharaoh, forming the sacred barque of Amun. Similarly, this tree was cut from Lebanon to build the temple of Jerusalem, as well as for making instruments of music and war. The fragmentation of the fir populations in Lebanon is not ancient but their low divergence, however, is marked by a Northeastern Ridge including 11 populations and a Southwestern Ridge including 4 populations that seem to be the result of two consecutive or simultaneous demographic processes during the history of fir in Lebanon. The first is a phenomenon of altitudinal migration in response to changes in the environment or climate. The reconstruction of the past dynamics of fir in Lebanon showed that it has undergone significant fluctuations in size, since the Late Glacial, 14,000 years ago. In particular, the tree has experienced periods of absence from the pollen record that could be related to anthropogenic habitat fragmentation or to local extinctions or contraction of the range of distribution. Similarly, there have been periods of expansion especially during periods of drought in the climate, at 4090 cal. BP, at 5010 cal. BP and between 7800 and 8090 cal. BP. The private allelic richness in the Northeastern Ridge indicated the presence of multiple glacial microrefugia of low and high elevations, as well as suture zones issues from recolonization. In the Southwestern Ridge, postglacial altitudinal recolonization from single microrefugial population is moslty probable. The second phenomenon is related to an asymmetric Northeast-Southwest migration from genetically diverse populations towards marginal and less genetically diverse populations. This process, which seems to be the result of the small size of the target populations, could help delay the extinction of marginal populations, locally threatened. The outperformance of migration over genetic drift and the dispersal over long distances of 15 to 20 km constitute the mediating effects of these demographic processes. The footprint of these population dynamics is a historic reduction in the effective population size on the long-term rather than on the short term, and weak genetic diversity and allelic richness. This genetic diversity seems to be shaped by anthropogenic effects as well as by changes in the environment or climate. In situ and ex situ conservation of fir populations in Lebanon is necessary to preserve their historical and genetic heritage
Books on the topic "Population genetics analyses"
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P, Altukhov I͡U. Population genetics--diversity and stability. Chur, Switzerland: Harwood Academic Publishers, 1990.
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A, Zhivotovskiĭ L., ed. Geneticheskie prot͡sessy v populi͡at͡sii͡akh. 2nd ed. Moskva: "Nauka", 1989.
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Pedigree analysis in human genetics. Baltimore: Johns Hopkins University Press, 1986.
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Genetic data analysis: Methods for discrete population genetic data. Sunderland, Mass: Sinauer Associates, 1990.
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Weir, B. S. Genetic data analysis II: Methods for discrete population genetic data. Sunderland, Mass: Sinauer Associates, 1996.
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R, Baverstock P., and Adams M. 1954-, eds. Allozyme electrophoresis: A handbook for animal systematicsand population studies. San Diego: Academic Press, 1990.
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Richardson, B. J. Allozyme electrophoresis: A handbook for animal systematics and population studies. San Diego: Academic Press, 1990.
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Käär, Pekka. Evolution of human life cycle: An analysis on historical human populations. Turku: Turun Yliopisto, 2001.
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Bherer, Claude. Caractérisation du pool génique de Lanaudière: Analyse démogénétique et étude épidemiogénétique de la névrite héréditaire NHSA2. Chicoutimi, Québec: GRIR, Université du Québec à Chicoutimi, 2008.
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Université du Québec à Chicoutimi. Groupe de recherche et d'intervention régionales., ed. Caractérisation du pool génique de Lanaudière: Analyse démogénétique et étude épidemiogénétique de la névrite héréditaire NHSA2. Chicoutimi, Québec: GRIR, Université du Québec à Chicoutimi, 2008.
Find full textBook chapters on the topic "Population genetics analyses"
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Kimura, Ryosuke. "Interpretations of Practical Population Genetics Analyses of Genome-Wide SNP Data on Human Demography." In Dynamics of Learning in Neanderthals and Modern Humans Volume 2, 105–17. Tokyo: Springer Japan, 2013. http://dx.doi.org/10.1007/978-4-431-54553-8_12.
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Pons, Jörn, Heiko Balzter, Andreas Langsdorf, and Wolfgang Köhler. "Population Genetics: Genetic Analysis and Modelling of Natural Populations." In Progress in Botany, 194–226. Berlin, Heidelberg: Springer Berlin Heidelberg, 1998. http://dx.doi.org/10.1007/978-3-642-80446-5_7.
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Edwards, J. H. "Haldane and the Analysis of Linkage." In Human Population Genetics, 153–64. Boston, MA: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4615-2970-5_11.
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Excoffier, L. "Analysis of Population Subdivision." In Handbook of Statistical Genetics, 980–1020. Chichester, UK: John Wiley & Sons, Ltd, 2008. http://dx.doi.org/10.1002/9780470061619.ch29.
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Vogler, George P., and D. C. Rao. "Path Analysis in Genetic Epidemiology: Theory and Applications." In Human Population Genetics, 291–304. Boston, MA: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4615-2970-5_19.
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Li, C. C. "Segregation Analysis Using the Properties of Binomial Data." In Human Population Genetics, 103–16. Boston, MA: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4615-2970-5_8.
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Ott, Jurg. "Recent Developments in the Theoretical Aspects of Linkage Analysis." In Human Population Genetics, 165–79. Boston, MA: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4615-2970-5_12.
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Zheng, Gang, Yaning Yang, Xiaofeng Zhu, and Robert C. Elston. "Population Structure." In Analysis of Genetic Association Studies, 259–86. Boston, MA: Springer US, 2012. http://dx.doi.org/10.1007/978-1-4614-2245-7_9.
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Chakraborty, Ranajit. "Analysis of Genetic Structure of Populations: Meaning, Methods, and Implications." In Human Population Genetics, 189–206. Boston, MA: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4615-2970-5_14.
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Elston, Robert C. "Some Recent Developments in the Theoretical Aspects of Segregation Analysis." In Human Population Genetics, 117–37. Boston, MA: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4615-2970-5_9.
Full textConference papers on the topic "Population genetics analyses"
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Smatti, Maria K., Yasser Al-Sarraj, Omar Albagha, and Hadi M. Yassine. "Host Genetic Variants Potentially Associated with SARS-Cov-2: A Multi-Population Analysis." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0298.
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Background: Clinical outcomes of Coronavirus Disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) showed enormous inter-individual and interpopulation differences, possibly due to host genetics differences. Earlier studies identified single nucleotide polymorphisms (SNPs) associated with SARS-CoV-1 in Eastern Asian (EAS) populations. In this report, we aimed at exploring the frequency of a set of genetic polymorphisms that could affect SARS-CoV-2 susceptibility or severity, including those that were previously associated with SARS-CoV-1. Methods: We extracted the list of SNPs that could potentially modulate SARS-CoV-2 from the genome wide association studies (GWAS) on SARS-CoV-1 and other viruses. We also collected the expression data of these SNPs from the expression quantitative trait loci (eQTLs) databases. Sequences from Qatar Genome Programme (QGP, n=6,054) and 1000Genome project were used to calculate and compare allelic frequencies (AF). Results: A total of 74 SNPs, located in 10 genes: ICAM3, IFN-γ, CCL2, CCL5, AHSG, MBL, Furin, TMPRSS2, IL4, and CD209 promoter, were identified. Analysis of Qatari genomes revealed significantly lower AF of risk variants linked to SARS-CoV-1 severity (CCL2, MBL, CCL5, AHSG, and IL4) compared to that of 1000Genome and/or the EAS population (up to 25-fold change). Conversely, SNPs in TMPRSS2, IFN-γ, ICAM3, and Furin were more common among Qataris (average 2-fold change). Inter-population analysis showed that the distribution of risk alleles among Europeans differs substantially from Africans and EASs. Remarkably, Africans seem to carry extremely lower frequencies of SARS-CoV-1 susceptibility alleles, reaching to 32-fold decrease compared to other populations. Conclusion: Multiple genetic variants, which could potentially modulate SARS-CoV-2 infection, are significantly variable between populations, with the lowest frequency observed among Africans. Our results highlight the importance of exploring population genetics to understand and predict COVID-19 outcomes. Indeed, further studies are needed to validate these findings as well as to identify new genetic determinants linked to SARS-CoV-2.
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A.Sh, Alimova, Vorobieva A.V., Gaidamachenko V.N., Golovinov I.V., Nebesikhina N.A., and Abrosimova E.B. "CHARACTERIZATION OF THE GENETIC DIVERSITY OF THE GREAT STURGEON (HUSO HUSO) IN THE AZOV-BLACK SEA BASYN BASED ON THE IDENTIFICATION OF MITOCHONDRIAL HAPLOTYPES." In II INTERNATIONAL SCIENTIFIC AND PRACTICAL CONFERENCE "DEVELOPMENT AND MODERN PROBLEMS OF AQUACULTURE" ("AQUACULTURE 2022" CONFERENCE). DSTU-Print, 2022. http://dx.doi.org/10.23947/aquaculture.2022.12-14.
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The article presents a study of genetic polymorphism of the natural population of the great sturgeon of the Azov-Black Sea basin using the analysis of the control region of mitochondrial DNA (D-loop) by capillary electrophoresis with the detection of a fluorescence signal. In the study, it was found that the two studied samples of the populations of the Black and Azov Seas do not have significant genetic differentiation among themselves (P<0.5). However, the overall genetic diversity in the natural population of the Azov-Black Sea basin in the period 2001-2010 was at a relatively high level.
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Chapman, Colin D., Kazuhiro Saitou, and Mark J. Jakiela. "Genetic Algorithms As an Approach to Configuration and Topology Design." In ASME 1993 Design Technical Conferences. American Society of Mechanical Engineers, 1993. http://dx.doi.org/10.1115/detc1993-0338.
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Abstract The Genetic Algorithm, a search and optimization technique based on the theory of natural selection, is applied to problems of structural topology optimization. Given a structure’s boundary conditions and maximum allowable design domain, a discretized design representation is created. Populations of genetic algorithm “chromosomes” are then mapped into the design representation, creating potentially optimal structure topologies. Utilizing genetics-based operators such as crossover and mutation, generations of increasingly-desirable structure topologies are created. In this paper, the use of the genetic algorithm (GA) in structural topology optimization is presented. An overview of the genetic algorithm will describe the genetics-based representations and operators used in a typical genetic algorithm search. After defining topology optimization and its relation to the broader area of structural optimization, a review of previous research in GA-based and non-GA-based structural optimization is provided. The design representations, and methods for mapping genetic algorithm “chromosomes” into structure topology representations, are then detailed. Several examples of genetic algorithm-based structural topology optimization are provided: we address the optimization of beam cross-section topologies and cantilevered plate topologies, and we also investigate efficient techniques for using finite element analysis in a genetic algorithm-based search. Finally, a description of potential future work in genetic algorithm-based structural topology optimization is offered.
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Lehrexwid, Per Kristian, and Pietro S. Oliveto. "Runtime analysis of population-based evolutionary algorithms." In GECCO '20: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2020. http://dx.doi.org/10.1145/3377929.3389890.
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Lehre, Per Kristian, and Pietro S. Oliveto. "Runtime analysis of population-based evolutionary algorithms." In GECCO '17: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2017. http://dx.doi.org/10.1145/3067695.3067714.
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Lehre, Per Kristian, and Pietro S. Oliveto. "Runtime Analysis of Population-based Evolutionary Algorithms." In GECCO '16: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2016. http://dx.doi.org/10.1145/2908961.2926976.
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Lehre, Per Kristian, and Pietro S. Oliveto. "Runtime analysis of population-based evolutionary algorithms." In GECCO '21: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2021. http://dx.doi.org/10.1145/3449726.3461423.
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Lehre, Per Kristian, and Pietro S. Oliveto. "Runtime analysis of population-based evolutionary algorithms." In GECCO '22: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2022. http://dx.doi.org/10.1145/3520304.3533658.
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Grignon, Pierre M., and Georges M. Fadel. "Multiobjective Optimization by Iterative Genetic Algorithm." In ASME 1999 Design Engineering Technical Conferences. American Society of Mechanical Engineers, 1999. http://dx.doi.org/10.1115/detc99/dac-8576.
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Abstract This paper presents a method to simultaneously produce multiple solutions to unconstrained multi-objective optimization problems. The proposed methodology uses populations of sets instead of populations of individuals and iterative calls to a Genetic Algorithm (IGA) to obtain a set of solutions spread across the Pareto set in the objective space. The superiority of such an approach to single run, conventional population Pareto GAs is shown. The various difficulties of the algorithm and the methods used to overcome them are detailed. Finally, the paper expands upon how this method can be used with or without user inputs, and shows an analysis of its performance by applying it to a succession of increasingly difficult problems, identifying its range of application.
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Đuretanović, Simona, Tijana Veličković, Aleksandra Milošković, Milena Radenković, Marijana Nikolić, Ivana Maguire, and Vladica Simić. "PRELIMINARY RESULTS REGARDING PHYLOGENY OF THE NOBLE CRAYFISH (DECAPODA, ASTACIDAE, „ASTACUS ASTACUS“) IN SERBIA." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac,, 2021. http://dx.doi.org/10.46793/iccbi21.222dj.
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The noble crayfish is one of the three autochthonous species that inhabit the freshwater ecosystems of Serbia, along with stone and Danube crayfish. The noble crayfish has a complex historical and genetic status shaped by geological events, habitat loss, pollution, translocations, and reintroductions of both autochthonous and allochthonous crayfish species. That led to the disruption of the species genetic structure, mixing, and loss of populations across Europe. According to recent data, its populations in the freshwater ecosystems of Serbia are significantly reduced, so it has the status of a "strictly protected species". The genetic structure of the species must be known for endangered species conservation. Unfortunately, there is lack of such data for the territory of Serbia, which due to its position on the Balkan Peninsula, was an important refuge during the glaciation period. In this paper, the genetic structure of seven crayfish populations in freshwater ecosystems of Serbia was examined. Analyzes were performed on the COI and 16S rRNA genes of mitochondrial DNA. The study results showed a significant diversity of COI and 16S rRNA haplotypes compared to already described haplotypes. Three haplotypes were detected, of which Hap26 is the most common and was detected in five studied populations. Haplotypes Hap47 and Hap49 were detected in one and two populations, respectively. The results obtained in this study, together with previously published morphometric data, represent a good starting point for further genetic and population research, which are the basis for the proposal of conservation measures.
Reports on the topic "Population genetics analyses"
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Sherman, Amir, Rebecca Grumet, Ron Ophir, Nurit Katzir, and Yiqun Weng. Whole genome approach for genetic analysis in cucumber: Fruit size as a test case. United States Department of Agriculture, December 2013. http://dx.doi.org/10.32747/2013.7594399.bard.
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The Cucurbitaceae family includes a broad array of economically and nutritionally important crop species that are consumed as vegetables, staple starches and desserts. Fruit of these species, and types within species, exhibit extensive diversity as evidenced by variation in size, shape, color, flavor, and others. Fruit size and shape are critical quality determinants that delineate uses and market classes and are key traits under selection in breeding programs. However, the underlying genetic bases for variation in fruit size remain to be determined. A few species the Cucurbitaceae family were sequenced during the time of this project (cucumber was already sequenced when the project started watermelon and melon sequence became available during the project) but functional genomic tools are still missing. This research program had three major goals: 1. Develop whole genome cucumber and melon SNP arrays. 2. Develop and characterize cucumber populations segregating for fruit size. 3. Combine genomic tools, segregating populations, and phenotypic characterization to identify loci associated with fruit size. As suggested by the reviewers the work concentrated mostly in cucumber and not both in cucumber and melon. In order to develop a SNP (single nucleotide polymorphism) array for cucumber, available and newly generated sequence from two cucumber cultivars with extreme differences in shape and size, pickling GY14 and Chinese long 9930, were analyzed for variation (SNPs). A large set of high quality SNPs was discovered between the two parents of the RILs population (GY14 and 9930) and used to design a custom SNP array with 35000 SNPs using Agilent technology. The array was validated using 9930, Gy14 and F1 progeny of the two parents. Several mapping populations were developed for linkage mapping of quantitative trait loci (QTL) for fruit size These includes 145 F3 families and 150 recombinant inbred line (RILs F7 or F8 (Gy14 X 9930) and third population contained 450 F2 plants from a cross between Gy14 and a wild plant from India. The main population that was used in this study is the RILs population of Gy14 X 9930. Phenotypic and morphological analyses of 9930, Gy14, and their segregating F2 and RIL progeny indicated that several, likely independent, factors influence cucumber fruit size and shape, including factors that act both pre-anthesis and post-pollination. These include: amount, rate, duration, and plane of cell division pre- and post-anthesis and orientation of cell expansion. Analysis of F2 and RIL progeny indicated that factors influencing fruit length were largely determined pre-anthesis, while fruit diameter was more strongly influenced by environment and growth factors post-anthesis. These results suggest involvement of multiple genetically segregating factors expected to map independently onto the cucumber genome. Using the SNP array and the phenotypic data two major QTLs for fruit size of cucumber were mapped in very high accuracy (around 300 Kb) with large set of markers that should facilitate identification and cloning of major genes that contribute to fruit size in cucumber. In addition, a highly accurate haplotype map of all RILS was created to allow fine mapping of other traits segregating in this population. A detailed cucumber genetic map with 6000 markers was also established (currently the most detailed genetic map of cucumber). The integration of genetics physiology and genomic approaches in this project yielded new major infrastructure tools that can be used for understanding fruit size and many other traits of importance in cucumber. The SNP array and genetic population with an ultra-fine map can be used for future breeding efforts, high resolution mapping and cloning of traits of interest that segregate in this population. The genetic map that was developed can be used for other breeding efforts in other populations. The study of fruit development that was done during this project will be important in dissecting function of genes that that contribute to the fruit size QTLs. The SNP array can be used as tool for mapping different traits in cucumber. The development of the tools and knowledge will thus promote genetic improvement of cucumber and related cucurbits.
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Joel, Daniel M., Steven J. Knapp, and Yaakov Tadmor. Genomic Approaches for Understanding Virulence and Resistance in the Sunflower-Orobanche Host-Parasite Interaction. United States Department of Agriculture, August 2011. http://dx.doi.org/10.32747/2011.7592655.bard.
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Oroginal Objectives: (i) identify DNA markers linked to the avirulence (Avr) locus and locate the Avr locus through genetic mapping with an inter-race Orobanche cumana population; (ii) develop high-throughput fingerprint DNA markers for genotypingO. cumana races; (iii) identify nucleotide binding domain leucine rich repeat (NB-LRR) genes encoding R proteins conferring resistance to O. cumana in sunflower; (iv) increase the resolution of the chromosomal segment harboring Or₅ and related R genes through genetic and physical mapping in previously and newly developed mapping populations of sunflower; and (v) develop high-throughput DNA markers for rapidly and efficiently identifying and transferring sunflower R genes through marker-assisted selection. Revisions made during the course of project: Following changes in O. cumana race distribution in Israel, the newly arrived virulent race H was chosen for further analysis. HA412-HO, which was primarily chosen as a susceptible sunflower cultivar, was more resistant to the new parasite populations than var. Shemesh, thus we shifted sunflower research into analyzing the resistance of HA412-HO. We exceeded the deliverables for Objectives #3-5 by securing funding for complete physical and high-density genetic mapping of the sunflower genome, in addition to producing a complete draft sequence of the sunflower genome. We discovered limited diversity between the parents of the O. cumana population developed for the mapping study. Hence, the developed DNA marker resources were insufficient to support genetic map construction. This objective was beyond the scale and scope of the funding. This objective is challenging enough to be the entire focus of follow up studies. Background to the topic: O. cumana, an obligate parasitic weed, is one of the most economically important and damaging diseases of sunflower, causes significant yield losses in susceptible genotypes, and threatens production in Israel and many other countries. Breeding for resistance has been crucial for protecting sunflower from O. cumana, and problematic because new races of the pathogen continually emerge, necessitating discovery and deployment of new R genes. The process is challenging because of the uncertainty in identifying races in a genetically diverse parasite. Major conclusions, solutions, achievements: We developed a small collection of SSR markers for genetic mapping in O. cumana and completed a diversity study to lay the ground for objective #1. Because DNA sequencing and SNPgenotyping technology dramatically advanced during the course of the study, we recommend shifting future work to SNP discovery and mapping using array-based approaches, instead of SSR markers. We completed a pilot study using a 96-SNP array, but it was not large enough to support genetic mapping in O.cumana. The development of further SNPs was beyond the scope of the grant. However, the collection of SSR markers was ideal for genetic diversity analysis, which indicated that O. cumanapopulations in Israel considerably differ frompopulations in other Mediterranean countries. We supplied physical and genetic mapping resources for identifying R-genes in sunflower responsible for resistance to O. cumana. Several thousand mapped SNP markers and a complete draft of the sunflower genome sequence are powerful tools for identifying additional candidate genes and understanding the genomic architecture of O. cumana-resistanceanddisease-resistance genes. Implications: The OrobancheSSR markers have utility in sunflower breeding and genetics programs, as well as a tool for understanding the heterogeneity of races in the field and for geographically mapping of pathotypes.The segregating populations of both Orobanche and sunflower hybrids are now available for QTL analyses.
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Lers, Amnon, Majid R. Foolad, and Haya Friedman. genetic basis for postharvest chilling tolerance in tomato fruit. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7600014.bard.
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ABSTRACT Postharvest losses of fresh produce are estimated globally to be around 30%. Reducing these losses is considered a major solution to ensure global food security. Storage at low temperatures is an efficient practice to prolong postharvest performance of crops with minimal negative impact on produce quality or human health and the environment. However, many fresh produce commodities are susceptible to chilling temperatures, and the application of cold storage is limited as it would cause physiological chilling injury (CI) leading to reduced produce quality. Further, the primary CI becomes a preferred site for pathogens leading to decay and massive produce losses. Thus, chilling sensitive crops should be stored at higher minimal temperatures, which curtails their marketing life and in some cases necessitates the use of other storage strategies. Development of new knowledge about the biological basis for chilling tolerance in fruits and vegetables should allow development of both new varieties more tolerant to cold, and more efficient postharvest storage treatments and storage conditions. In order to improve the agricultural performance of modern crop varieties, including tomato, there is great potential in introgression of marker-defined genomic regions from wild species onto the background of elite breeding lines. To exploit this potential for improving tomato fruit chilling tolerance during postharvest storage, we have used in this research a recombinant inbred line (RIL) population derived from a cross between the red-fruited tomato wild species SolanumpimpinellifoliumL. accession LA2093 and an advanced Solanum lycopersicumL. tomato breeding line NCEBR-1, developed in the laboratory of the US co-PI. The original specific objectives were: 1) Screening of RIL population resulting from the cross NCEBR1 X LA2093 for fruit chilling response during postharvest storage and estimation of its heritability; 2) Perform a transcriptopmic and bioinformatics analysis for the two parental lines following exposure to chilling storage. During the course of the project, we learned that we could measure greater differences in chilling responses among specific RILs compared to that observed between the two parental lines, and thus we decided not to perform transcriptomic analysis and instead invest our efforts more on characterization of the RILs. Performing the transcriptomic analysis for several RILs, which significantly differ in their chilling tolerance/sensitivity, at a later stage could result with more significant insights. The RIL population, (172 lines), was used in field experiment in which fruits were examined for chilling sensitivity by determining CI severity. Following the field experiments, including 4 harvest days and CI measurements, two extreme tails of the response distribution, each consisting of 11 RILs exhibiting either high sensitivity or tolerance to chilling stress, were identified and were further examined for chilling response in greenhouse experiments. Across the RILs, we found significant (P < 0.01) correlation between field and greenhouse grown plants in fruit CI. Two groups of 5 RILs, whose fruits exhibited reproducible chilling tolerant/sensitive phenotypes in both field and greenhouse experiments, were selected for further analyses. Numerous genetic, physiological, biochemical and molecular variations were investigated in response to postharvest chilling stress in the selected RILs. We confirmed the differential response of the parental lines of the RIL population to chilling stress, and examined the extent of variation in the RIL population in response to chilling treatment. We determined parameters which would be useful for further characterization of chilling response in the RIL population. These included chlorophyll fluorescence Fv/Fm, water loss, total non-enzymatic potential of antioxidant activity, ascorbate and proline content, and expression of LeCBF1 gene, known to be associated with cold acclimation. These parameters could be used in continuation studies for the identification and genetic mapping of loci contributing to chilling tolerance in this population, and identifying genetic markers associated with chilling tolerance in tomato. Once genetic markers associated with chilling tolerance are identified, the trait could be transferred to different genetic background via marker-assisted selection (MAS) and breeding. The collaborative research established in this program has resulted in new information and insights in this area of research and the collaboration will be continued to obtain further insights into the genetic, molecular biology and physiology of postharvest chilling tolerance in tomato fruit. The US Co-PI, developed the RIL population that was used for screening and measurement of the relevant chilling stress responses and conducted statistical analyses of the data. Because we were not able to grow the RIL population under field conditions in two successive generations, we could not estimate heritability of response to chilling temperatures. However, we plan to continue the research, grow the RIL progeny in the field again, and determine heritability of chilling tolerance in a near future. The IS and US investigators interacted regularly and plan to continue and expand on this study, since combing the expertise of the Co-PI in genetics and breeding with that of the PI in postharvest physiology and molecular biology will have great impact on this line of research, given the significant findings of this one-year feasibility project.
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Bogoliubov, A. G., and C. Loehle. A theoretical analysis of population genetics of plants on restored habitats. Office of Scientific and Technical Information (OSTI), July 1997. http://dx.doi.org/10.2172/505323.
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Bogoliubov, A. G., and C. Loehle. A theoretical analysis of population genetics of plants on restored habitats. Office of Scientific and Technical Information (OSTI), February 1995. http://dx.doi.org/10.2172/26698.
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Комарова, Олена Володимирівна, and Альберт Армаїсович Азарян. Computer Simulation of Biological Processes at the High School. CEUR Workshop Proceedings (CEUR-WS.org), 2018. http://dx.doi.org/10.31812/123456789/2695.
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Abstract. Research goals: the necessity of study in high school of the law of Hardy – Weinberg as one of the fundamental genetic laws was justified. The peculiarities of using the method of model experiment in the study of the genetic and evolutionary processes in populations with the use of computer technology. Object of research: computer simulation of population genetic structure. Subject of research: computer simulation of genetic and evolutionary processes in ideal and real populations. Research methods: pedagogical experiment (survey), analysis of scientific publications on the use of the high school method of modelling genetic and evolutionary processes in populations, computer simulation. Results of the research: a web page for processing by the pupils of the modelling results of genetic and evolutionary processes in populations was created.
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Комарова, Олена Володимирівна, and Альберт Арамаїсович Азарян. Computer Simulation of Biological Processes at the High School. CEUR-WS.org, 2018. http://dx.doi.org/10.31812/123456789/2656.
Full textAbstract:
Research goals: the necessity of study in high school of the law of Hardy – Weinberg as one of the fundamental genetic laws was justified. The peculiarities of using the method of model experiment in the study of the genetic and evolutionary processes in populations with the use of computer technology. Object of research: computer simulation of population genetic structure. Subject of research: computer simulation of genetic and evolutionary processes in ideal and real populations. Research methods: pedagogical experiment (survey), analysis of scientific publications on the use of the high school method of modelling genetic and evolutionary processes in populations, computer simulation. Results of the research: a web page for processing by the pupils of the modelling results of genetic and evolutionary processes in populations was created.
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Breiman, Adina, Jan Dvorak, Abraham Korol, and Eduard Akhunov. Population Genomics and Association Mapping of Disease Resistance Genes in Israeli Populations of Wild Relatives of Wheat, Triticum dicoccoides and Aegilops speltoides. United States Department of Agriculture, December 2011. http://dx.doi.org/10.32747/2011.7697121.bard.
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Wheat is the most widely grown crop on earth, together with rice it is second to maize in total global tonnage. One of the emerging threats to wheat is stripe (yellow) rust, especially in North Africa, West and Central Asia and North America. The most efficient way to control plant diseases is to introduce disease resistant genes. However, the pathogens can overcome rapidly the effectiveness of these genes when they are wildly used. Therefore, there is a constant need to find new resistance genes to replace the non-effective genes. The resistance gene pool in the cultivated wheat is depleted and there is a need to find new genes in the wild relative of wheat. Wild emmer (Triticum dicoccoides) the progenitor of the cultivated wheat can serve as valuable gene pool for breeding for disease resistance. Transferring of novel genes into elite cultivars is highly facilitated by the availability of information of their chromosomal location. Therefore, our goals in this study was to find stripe rust resistant and susceptible genotypes in Israeli T. dicoccoides population, genotype them using state of the art genotyping methods and to find association between genetic markers and stripe rust resistance. We have screened 129 accessions from our collection of wild emmer wheat for resistance to three isolates of stripe rust. About 30% of the accessions were resistant to one or more isolates, 50% susceptible, and the rest displayed intermediate response. The accessions were genotyped with Illumina'sInfinium assay which consists of 9K single nucleotide polymorphism (SNP) markers. About 13% (1179) of the SNPs were polymorphic in the wild emmer population. Cluster analysis based on SNP diversity has shown that there are two main groups in the wild population. A big cluster probably belongs to the Horanum ssp. and a small cluster of the Judaicum ssp. In order to avoid population structure bias, the Judaicum spp. was removed from the association analysis. In the remaining group of genotypes, linkage disequilibrium (LD) measured along the chromosomes decayed rapidly within one centimorgan. This is the first time when such analysis is conducted on a genome wide level in wild emmer. Such a rapid decay in LD level, quite unexpected for a selfer, was not observed in cultivated wheat collection. It indicates that wild emmer populations are highly suitable for association studies yielding a better resolution than association studies in cultivated wheat or genetic mapping in bi-parental populations. Significant association was found between an SNP marker located in the distal region of chromosome arm 1BL and resistance to one of the isolates. This region is not known in the literature to bear a stripe rust resistance gene. Therefore, there may be a new stripe rust resistance gene in this locus. With the current fast increase of wheat genome sequence data, genome wide association analysis becomes a feasible task and efficient strategy for searching novel genes in wild emmer wheat. In this study, we have shown that the wild emmer gene pool is a valuable source for new stripe rust resistance genes that can protect the cultivated wheat.
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Perl-Treves, Rafael, M. Kyle, and Esra Galun. Development and Application of a Molecular Genetic Map for Melon (Cucumis melo). United States Department of Agriculture, October 1993. http://dx.doi.org/10.32747/1993.7568094.bard.
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This project has generated a systematic survey of DNA polymorphism in Cucumis melo. An RFLP and RAPD survey of the major cultivar groups and botanical varieties of this species has been conducted, with the purpose of assessing the degree of molecular variation and phylogenetic relationships within the melon germplasm and, at the same time, develop sets of markets suitable for mapping the melon genome. Additional activities regarding variation in the melon germplasm in fruit traits and regeneration ability have been initiated as well. The necessary populations required for the development of a molecular map of the C. melo genome have been prepared. An F2 that segregated for 4 viral resistances, powdery mildew resitance and sex type has been derived from a PI 414723 x Topmark cross, and a RILs population has been prepared from it. We have confirmed the resistances in the population and have analyzed the genetic relationships between these resistances. Progress toward the construction of a molecular map of C. melo and the development of markers linked to those traits is described. We have so far screened the first few tens of markers in the F2 population, and many additional ones were screened in DNA bulks prepared from such population.
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Michelmore, Richard, Eviatar Nevo, Abraham Korol, and Tzion Fahima. Genetic Diversity at Resistance Gene Clusters in Wild Populations of Lactuca. United States Department of Agriculture, February 2000. http://dx.doi.org/10.32747/2000.7573075.bard.
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Genetic resistance is often the least expensive, most effective, and ecologically-sound method of disease control. It is becoming apparent that plant genomes contain large numbers of disease resistance genes. However, the numbers of different resistance specificities within a genepool and the genetic mechanisms generating diversity are poorly understood. Our objectives were to characterize diversity in clusters of resistance genes in wild progenitors of cultivated lettuce in Israel and California in comparison to diversity within cultivated lettuce, and to determine the extent of gene flow, recombination, and genetic instability in generating variation within clusters of resistance genes. Genetic diversity of resistance genes was analyzed in wild and cultivated germplasm using molecular markers derived from lettuce resistance gene sequences of the NBS-LRR type that mapped to the major cluster if resistance genes in lettuce (Sicard et al. 1999). Three molecular markers, one microsatellite marker and two SCAR markers that amplified LRR- encoding regions, were developed from sequences of resistance gene homologs at the Dm3 cluster (RGC2s) in lettuce. Variation for these markers was assessed in germplasm including 74 genotypes of cultivated lettuce, L. saliva and 71 accessions of the three wild Lactuca spp., L. serriola, L. saligna and L. virosa that represent the major species in the sexually accessible genepool for lettuce. Diversity was also studied within and between natural populations of L. serriola from Israel and California. Large numbers of haplotypes were detected indicating the presence of numerous resistance genes in wild species. We documented a variety of genetic events occurring at clusters of resistance genes for the second objective (Sicard et al., 1999; Woo el al., in prep; Kuang et al., in prepb). The diversity of resistance genes in haplotypes provided evidence for gene duplication and unequal crossing over during the evolution of this cluster of resistance genes. Comparison of nine resistance genes in cv. Diana identified 22 gene conversion and five intergenic recombinations. We cloned and sequenced a 700 bp region from the middle of RGC2 genes from six genotypes, two each from L. saliva, L. serriola, and L. saligna . We have identified over 60 unique RGC2 sequences. Phylogenetic analysis surprisingly demonstrated much greater similarity between than within genotypes. This led to the realization that resistance genes are evolving much slower than had previously been assumed and to a new model as to how resistance genes are evolving (Michelmore and Meyers, 1998). The genetic structure of L. serriola was studied using 319 AFLP markers (Kuang et al., in prepa). Forty-one populations from Turkey, Armenia, Israel, and California as well as seven European countries were examined. AFLP marker data showed that the Turkish and Armenian populations were the most polymorphic populations and the European populations were the least. The Davis, CA population, a recent post-Columbian colonization, showed medium genetic diversity and was genetically close to the Turkish populations. Our results suggest that Turkey - Armenia may be the center of origin and diversity of L. serriola and may therefore have the greatest diversity of resistance genes. Our characterization of the diversity of resistance genes and the genetic mechanisms generating it will allow informed exploration, in situ and ex situ conservation, and utilization of germplasm resources for disease control. The results of this project provide the basis for our future research work, which will lead to a detailed understanding of the evolution of resistance genes in plants.