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.
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MANK, JUDITH E., and JOHN C. AVISE. "Individual organisms as units of analysis: Bayesian-clustering alternatives in population genetics." Genetical Research 84, no. 3 (December 2004): 135–43. http://dx.doi.org/10.1017/s0016672304007190.
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Population genetic analyses traditionally focus on the frequencies of alleles or genotypes in ‘populations’ that are delimited a priori. However, there are potential drawbacks of amalgamating genetic data into such composite attributes of assemblages of specimens: genetic information on individual specimens is lost or submerged as an inherent part of the analysis. A potential also exists for circular reasoning when a population's initial identification and subsequent genetic characterization are coupled. In principle, these problems are circumvented by some newer methods of population identification and individual assignment based on statistical clustering of specimen genotypes. Here we evaluate a recent method in this genre – Bayesian clustering – using four genotypic data sets involving different types of molecular markers in non-model organisms from nature. As expected, measures of population genetic structure (FST and ΦST) tended to be significantly greater in Bayesian a posteriori data treatments than in analyses where populations were delimited a priori. In the four biological contexts examined, which involved both geographic population structures and hybrid zones, Bayesian clustering was able to recover differentiated populations, and Bayesian assignments were able to identify likely population sources of specific individuals.
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JARNE, P., and A. THÉRON. "Genetic structure in natural populations of flukes and snails: a practical approach and review." Parasitology 123, no. 7 (November 2001): 27–40. http://dx.doi.org/10.1017/s0031182001007715.
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Several aspects of the coevolutionary dynamics in host-parasite systems may be better quantified based on analyses of population structure using neutral genetic markers. This includes, for example, the migration rates of hosts and parasites. In this respect, the current situation, especially in fluke-snail systems is unsatisfactory, since basic population genetics data are lacking and the appropriate methodology has rarely been used. After reviewing the forces acting on population structure (e.g. genetic drift or the mating system) and how they can be analysed in models of structured populations, we propose a simplified, indicative framework for conducting analyses of population structure in hosts and parasites. This includes consideration of markers, sampling, data analysis, comparison of structure in hosts and parasites and use of external data (e.g. from population dynamics). We then focus on flukes and snails, highlighting important biological traits with regard to population structure. The few available studies indicate that asexual amplification of flukes within snails strongly influences adult flukes populations. They also show that the genetic structure among populations in strongly affected by traits in other than snails (e.g. definitive host dispersal behaviour), as snails populations have limited migration. Finally more studies would allow us to deepen our current understanding of selective interference between flukes and snails (e.g. manipulation of host mating system by parasites), and evaluate how this affect population structure at neutral markers.
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Lin, Hui-Wen, and Yi-Hau Chen. "Association Analysis under Population Stratification: A Two-Stage Procedure Utilizing Population- and Family-Based Analyses." Human Heredity 69, no. 3 (2010): 160–70. http://dx.doi.org/10.1159/000267996.
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Polley, Spencer D., Watcharee Chokejindachai, and David J. Conway. "Allele Frequency-Based Analyses Robustly Map Sequence Sites Under Balancing Selection in a Malaria Vaccine Candidate Antigen." Genetics 165, no. 2 (October 1, 2003): 555–61. http://dx.doi.org/10.1093/genetics/165.2.555.
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Abstract The Plasmodium falciparum apical membrane antigen 1 (AMA1) is a leading candidate for a malaria vaccine. Here, within-population analyses of alleles from 50 Thai P. falciparum isolates yield significant evidence for balancing selection on polymorphisms within the disulfide-bonded domains I and III of the surface accessible ectodomain of AMA1, a result very similar to that seen previously in a Nigerian population. Studying the frequency of nucleotide polymorphisms in both populations shows that the between-population component of variance (FST) is significantly lower in domains I and III compared to the intervening domain II and compared to 11 unlinked microsatellite loci. A nucleotide site-by-site analysis shows that sites with exceptionally high or low FST values cluster significantly into serial runs, with four runs of low values in domain I and one in domain III. These runs may map the sequences that are consistently under the strongest balancing selection from naturally acquired immune responses.
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Roberts, Mark A., Tonia S. Schwartz, and Stephen A. Karl. "Global Population Genetic Structure and Male-Mediated Gene Flow in the Green Sea Turtle (Chelonia mydas): Analysis of Microsatellite Loci." Genetics 166, no. 4 (April 1, 2004): 1857–70. http://dx.doi.org/10.1093/genetics/166.4.1857.
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Abstract We assessed the degree of population subdivision among global populations of green sea turtles, Chelonia mydas, using four microsatellite loci. Previously, a single-copy nuclear DNA study indicated significant male-mediated gene flow among populations alternately fixed for different mitochondrial DNA haplotypes and that genetic divergence between populations in the Atlantic and Pacific Oceans was more common than subdivisions among populations within ocean basins. Even so, overall levels of variation at single-copy loci were low and inferences were limited. Here, the markedly more variable microsatellite loci confirm the presence of male-mediated gene flow among populations within ocean basins. This analysis generally confirms the genetic divergence between the Atlantic and Pacific. As with the previous study, phylogenetic analyses of genetic distances based on the microsatellite loci indicate a close genetic relationship among eastern Atlantic and Indian Ocean populations. Unlike the single-copy study, however, the results here cannot be attributed to an artifact of general low variability and likely represent recent or ongoing migration between ocean basins. Sequence analyses of regions flanking the microsatellite repeat reveal considerable amounts of cryptic variation and homoplasy and significantly aid in our understanding of population connectivity. Assessment of the allele frequency distributions indicates that at least some of the loci may not be evolving by the stepwise mutation model.
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Davy, Christina M., and Robert W. Murphy. "Conservation genetics of the endangered Spotted Turtle (Clemmys guttata) illustrate the risks of “bottleneck tests”." Canadian Journal of Zoology 92, no. 2 (February 2014): 149–62. http://dx.doi.org/10.1139/cjz-2013-0188.
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Studies of population genetics in turtles have suggested that turtles do not experience genetic impacts of bottlenecks as strongly as expected. However, recent studies cast doubt on two commonly used tests implemented in the program BOTTLENECK, suggesting that these findings should be re-evaluated. The Spotted Turtle (Clemmys guttata (Schneider, 1792)) is endangered both globally and within Canada, but genetic data required to develop effective recovery strategies are unavailable. Here, we conducted the first study of population genetic structure in C. guttata. We then used multiple small populations of C. guttata as replicates to test whether the commonly used program BOTTLENECK could detect the genetic signature of bottlenecks in our study populations, which are all thought to have experienced significant declines in the past 2–3 generations (75 years). Turtles (n = 256) were genotyped at 11 microsatellite loci. A suite of Bayesian population genetics analyses and a principal coordinates analysis identified a minimum of 6 distinct genetic populations and a maximum of 10 differentiated subpopulations across the sampled Canadian range of C. guttata, which corresponded to demographically independent units. BOTTLENECK failed to detect population declines. A literature review found that bottleneck tests in 17 of 18 previous genetic studies of tortoises and freshwater turtles were based on suboptimal sampling, potentially confounding their results. High retention of genetic diversity (allelic richness and heterozygosity) in isolated populations of C. guttata and other turtle species is encouraging for species recovery, but conclusions about the prevalence of genetic bottlenecks in such populations should be re-examined.
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Bonnin, Isabelle, Jean-Marie Prosperi, and Isabelle Olivieri. "Genetic Markers and Quantitative Genetic Variation in Medicago truncatula (Leguminosae): A Comparative Analysis of Population Structure." Genetics 143, no. 4 (August 1, 1996): 1795–805. http://dx.doi.org/10.1093/genetics/143.4.1795.
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Abstract Two populations of the selfing annual Medicago truncatula Gaertn. (Leguminoseae), each subdivided into three subpopulations, were studied for both metric traits (quantitative characters) and genetic markers (random amplified polymorphic DNA and one morphological, single-locus marker). Hierarchical analyses of variance components show that (1) populations are more differentiated for quantitative characters than for marker loci, (2) the contribution of both within and among subpopulations components of variance to overall genetic variance of these characters is reduced as compared to markers, and (3) at the population level, within population structure is slightly but not significantly larger for markers than for quantitative traits. Under the hypothesis that most markers are neutral, such comparisons may be used to make hypotheses about the strength and heterogeneity of natural selection in the face of genetic drift and gene flow. We thus suggest that in these populations, quantitative characters are under strong divergent selection among populations, and that gene flow is restricted among populations and subpopulations.
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Joly, HI, M. Zeh-Nlo, P. Danthu, and C. Aygalent. "Population Genetics of an African Acacia, Acacia albida. I. Genetic Diversity of Populations From West Africa." Australian Journal of Botany 40, no. 1 (1992): 59. http://dx.doi.org/10.1071/bt9920059.
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Acacia albida (Faidherbia albida) is an important species for agroforestry and widely distributed in Africa. This paper proposes a genetic control for 14 enzymatic systems. The eight more reliable ones, involving 10 loci, have been used to study the genetic diversity of 22 populations, mostly from west Africa. A. albida exhibits a high level of genetic diversity (H = 0.45) compared with that found in Australian acacias studied so far. Most populations exhibited a deficit in heterozygotes (FIS = 0.21). All analyses showed large differences between western and eastern populations.
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Testroet, Philip, Dietmar Quandt, Arnoldo Santos Guerra, Kai Müller, and Wolfram Lobin. "Population genetics and conservation of Sideroxylon canariense (Sapotaceae) on the Canary Islands." Vieraea Folia scientiarum biologicarum canariensium 41, Vieraea 41 (2013): 319–32. http://dx.doi.org/10.31939/vieraea.2013.41.21.
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Genetic diversity patterns of different populations were studied in Sideroxylon canariense, a Canary Island endemic of conservation concern. The species range is composed of a number of very small and isolated populations. Genetic variation of these populations was analyzed using: (1) inter simple sequence repeats (ISSR), a common fingerprinting method in plant population genetics, and (2) nucleotide sequence analyses of the nuclear ITS region. While no intraspecific variation was detected among the ITS sequences, the ISSR data showed a very low degree of intraspecific genetic diversity among S. canariense populations on the Canaries, with very few genotypes. We believe that many of the populations consist of a single individual that propagates asexually. Action is urgently required to protect and propagate the highly endangered populations.
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Bilska, Katarzyna, and Monika Szczecińska. "Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics ofPulsatilla patenspopulations." PeerJ 4 (November 2, 2016): e2504. http://dx.doi.org/10.7717/peerj.2504.
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BackgroundResearch into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation inPulsatilla patenspopulations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction).MethodsThe experiment was conducted on 14 Polish populations ofP. patensand threeP. patenspopulations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific toP. patensand three ISJ primers.ResultsSSR markers revealed a higher level of genetic variation than ISJ markers (He= 0.609,He= 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parametersFSTand ΦPTfor SSR (20%) and ΦPTfor ISJ (21%) markers was similar. Analysis conducted in theStructureprogram divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations ofP. patensfor ISJ markers, but not for SSR markers.ConclusionsThe results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.
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François, Olivier, and Clément Gain. "A spectral theory for Wright’s inbreeding coefficients and related quantities." PLOS Genetics 17, no. 7 (July 19, 2021): e1009665. http://dx.doi.org/10.1371/journal.pgen.1009665.
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Wright’s inbreeding coefficient, FST, is a fundamental measure in population genetics. Assuming a predefined population subdivision, this statistic is classically used to evaluate population structure at a given genomic locus. With large numbers of loci, unsupervised approaches such as principal component analysis (PCA) have, however, become prominent in recent analyses of population structure. In this study, we describe the relationships between Wright’s inbreeding coefficients and PCA for a model of K discrete populations. Our theory provides an equivalent definition of FST based on the decomposition of the genotype matrix into between and within-population matrices. The average value of Wright’s FST over all loci included in the genotype matrix can be obtained from the PCA of the between-population matrix. Assuming that a separation condition is fulfilled and for reasonably large data sets, this value of FST approximates the proportion of genetic variation explained by the first (K − 1) principal components accurately. The new definition of FST is useful for computing inbreeding coefficients from surrogate genotypes, for example, obtained after correction of experimental artifacts or after removing adaptive genetic variation associated with environmental variables. The relationships between inbreeding coefficients and the spectrum of the genotype matrix not only allow interpretations of PCA results in terms of population genetic concepts but extend those concepts to population genetic analyses accounting for temporal, geographical and environmental contexts.
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Tsehay, Sewalem, Rodomiro Ortiz, Eva Johansson, Endashaw Bekele, Kassahun Tesfaye, Cecilia Hammenhag, and Mulatu Geleta. "New Transcriptome-Based SNP Markers for Noug (Guizotia abyssinica) and Their Conversion to KASP Markers for Population Genetics Analyses." Genes 11, no. 11 (November 20, 2020): 1373. http://dx.doi.org/10.3390/genes11111373.
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The development and use of genomic resources are essential for understanding the population genetics of crops for their efficient conservation and enhancement. Noug (Guizotia abyssinica) is an economically important oilseed crop in Ethiopia and India. The present study sought to develop new DNA markers for this crop. Transcriptome sequencing was conducted on two genotypes and 628 transcript sequences containing 959 single nucleotide polymorphisms (SNPs) were developed. A competitive allele-specific PCR (KASP) assay was developed for the SNPs and used for genotyping of 24 accessions. A total of 554 loci were successfully genotyped across the accessions, and 202 polymorphic loci were used for population genetics analyses. Polymorphism information content (PIC) of the loci varied from 0.01 to 0.37 with a mean of 0.24, and about 49% of the loci showed significant deviation from the Hardy-Weinberg equilibrium. The mean expected heterozygosity was 0.27 suggesting moderately high genetic variation within accessions. Low but significant differentiation existed among accessions (FST = 0.045, p < 0.0001). Landrace populations from isolated areas may have useful mutations and should be conserved and used in breeding this crop. The genomic resources developed in this study were shown to be useful for population genetics research and can also be used in, e.g., association genetics.
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Song, W., L. J. Cao, Y. Z. Wang, B. Y. Li, and S. J. Wei. "Novel microsatellite markers for the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae) and effects of null alleles on population genetics analyses." Bulletin of Entomological Research 107, no. 3 (November 7, 2016): 349–58. http://dx.doi.org/10.1017/s0007485316000936.
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AbstractThe oriental fruit moth (OFM) Grapholita molesta (Lepidoptera: Tortricidae) is an important economic pest of stone and pome fruits worldwide. We sequenced the OFM genome using next-generation sequencing and characterized the microsatellite distribution. In total, 56,674 microsatellites were identified, with 11,584 loci suitable for primer design. Twenty-seven polymorphic microsatellites, including 24 loci with trinucleotide repeat and three with pentanucleotide repeat, were validated in 95 individuals from four natural populations. The allele numbers ranged from 4 to 40, with an average value of 13.7 per locus. A high frequency of null alleles was observed in most loci developed for the OFM. Three marker panels, all of the loci, nine loci with the lowest null allele frequencies, and nine loci with the highest null allele frequencies, were established for population genetics analyses. The null allele influenced estimations of genetic diversity parameters but not the OFM's genetic structure. Both a STRUCTURE analysis and a discriminant analysis of principal components, using the three marker panels, divided the four natural populations into three groups. However, more individuals were incorrectly assigned by the STRUCTURE analysis when the marker panel with the highest null allele frequency was used compared with the other two panels. Our study provides empirical research on the effects of null alleles on population genetics analyses. The microsatellites developed will be valuable markers for genetic studies of the OFM.
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Turner, Thomas F., Joel C. Trexler, John L. Harris, and Jody L. Haynes. "Nested Cladistic Analysis Indicates Population Fragmentation Shapes Genetic Diversity in a Freshwater Mussel." Genetics 154, no. 2 (February 1, 2000): 777–85. http://dx.doi.org/10.1093/genetics/154.2.777.
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Abstract Recently developed phylogeographic analyses that incorporate genealogical relationships of alleles offer the exciting prospect of disentangling historical from contemporary events. However, the relative advantages and shortfalls of this approach remain to be studied. We compared the nested cladistic method to the more traditional analysis of variance approach in a study of intraspecific genetic variation in the freshwater mussel, Lampsilis hydiana. We surveyed 257 specimens for nucleotide sequence level variation in a fragment of the mitochondrial 16S rRNA gene. When compared side by side, nested cladistic analysis and analysis of molecular variance (AMOVA) identified fragmentation of Arkansas river populations from remaining populations to the southwest. Nested cladistic analysis identified a second, more recent separation of Ouachita and Upper Saline river populations that was not detected by AMOVA. Differences among analytical methods probably arise from treatment of spatial hierarchical information: hierarchical groups emerge via a parsimony criterion in nested cladistic analysis but must be specified a priori in AMOVA. Both methods identified significant genetic structure among localities within hierarchical groups. Results from AMOVA suggested little gene flow among local populations with an island model. However, inferences about process that gave rise to patterns at this level were not possible in nested cladistic analysis, because an ancestral (interior) haplotype was not observed for a key one-step clade in the parsimony network. Our results suggest that, under some circumstances, nested cladistic analysis has lower power than more traditional analysis of variance to infer processes at the local population level.
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Piorski, NM, A. Sanches, LF Carvalho-Costa, T. Hatanaka, M. Carrillo-Avila, PD Freitas, and PM Galetti Jr. "Contribution of conservation genetics in assessing neotropical freshwater fish biodiversity." Brazilian Journal of Biology 68, no. 4 suppl (November 2008): 1039–50. http://dx.doi.org/10.1590/s1519-69842008000500011.
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Human activities have a considerable impact on hydrographic systems and fish fauna. The present review on conservation genetics of neotropical freshwater fish reveals that DNA analyses have been promoting increased knowledge on the genetic structure of fish species and their response to environmental changes. This knowledge is fundamental to the management of wild fish populations and the establishment of Evolutionary Significant Units capable of conserving genetic integrity. While population structuring can occur even in long-distance migratory fish, isolated populations can show reduced genetic variation and be at greater risk of extinction. Phylogeography and phylogeny have been powerful tools in understanding the evolution of fish populations, species and communities in distinct neotropic environments. Captive fish can be used to introduce new individuals and genes into the wild and their benefits and disadvantages can be monitored through genetic analysis. Understanding how fish biodiversity in neotropical freshwaters is generated and maintained is highly important, as these habitats are transformed by human development and fish communities are increasingly exploited as food sources to sustain a growing human population.
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Ovenden, Jennifer R., Bree J. Tillett, Michael Macbeth, Damien Broderick, Fiona Filardo, Raewyn Street, Sean R. Tracey, and Jayson Semmens. "Stirred but not shaken: population and recruitment genetics of the scallop (Pecten fumatus) in Bass Strait, Australia." ICES Journal of Marine Science 73, no. 9 (May 8, 2016): 2333–41. http://dx.doi.org/10.1093/icesjms/fsw068.
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Abstract We report population genetic structure and fine-scale recruitment processes for the scallop beds (Pecten fumatus) in Bass Strait and the eastern coastline of Tasmania in southern Australia. Conventional population pairwise FST analyses are compared with novel discriminant analysis of principal components (DAPC) to assess population genetic structure using allelic variation in 11 microsatellite loci. Fine-scale population connectivity was compared with oceanic features of the sampled area. Disjunct scallop beds were genetically distinct, but there was little population genetic structure between beds connected by tides and oceanic currents. To identify recruitment patterns among and within beds, pedigree analyses determined the distribution of parent–offspring and sibling relationships in the sampled populations. Beds in northeastern Bass Strait were genetically distinct to adjacent beds (FST 0.003–0.005) and may not contribute to wider recruitment based on biophysical models of larval movement. Unfortunately, pedigree analyses lacked power to further dissect fine-scale recruitment processes including self-recruitment. Our results support the management of disjunct populations as separate stocks and the protection of source populations among open water beds. The application of DAPC and parentage analyses in the current study provided valuable insight into their potential power to determine population connectivity in marine species with larval dispersal.
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Karl, S. A., B. W. Bowen, and J. C. Avise. "Global population genetic structure and male-mediated gene flow in the green turtle (Chelonia mydas): RFLP analyses of anonymous nuclear loci." Genetics 131, no. 1 (May 1, 1992): 163–73. http://dx.doi.org/10.1093/genetics/131.1.163.
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Abstract We introduce an approach for the analysis of Mendelian polymorphisms in nuclear DNA (nDNA), using restriction fragment patterns from anonymous single-copy regions amplified by the polymerase chain reaction, and apply this method to the elucidation of population structure and gene flow in the endangered green turtle, Chelonia mydas. Seven anonymous clones isolated from a total cell DNA library were sequenced to generate primers for the amplification of nDNA fragments. Nine individuals were screened for restriction site polymorphisms at these seven loci, using 40 endonucleases. Two loci were monomorphic, while the remainder exhibited a total of nine polymorphic restriction sites and three size variants (reflecting 600-base pair (bp) and 20-bp deletions and a 20-bp insertion). A total of 256 turtle specimens from 15 nesting populations worldwide were then scored for these polymorphisms. Genotypic proportions within populations were in accord with Hardy-Weinberg expectations. Strong linkage disequilibrium observed among polymorphic sites within loci enabled multisite haplotype assignments. Estimates of the standardized variance in haplotype frequency among global collections (FST = 0.17), within the Atlantic-Mediterranean (FST = 0.13), and within the Indian-Pacific (FST = 0.13), revealed a moderate degree of population substructure. Although a previous study concluded that nesting populations appear to be highly structured with respect to female (mitochondrial DNA) lineages, estimates of Nm based on nDNA data from this study indicate moderate rates of male-mediated gene flow. A positive relationship between genetic similarity and geographic proximity suggests historical connections and/or contemporary gene flow between particular rookery populations, likely via matings on overlapping feeding grounds, migration corridors or nonnatal rookeries.
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Benfer, David, Andrew M. Baker, Tina Ball, Ian Gynther, Heather Janetzki, and Susan Fuller. "Conservation genetics of the water mouse, Xeromys myoides Thomas, 1889." Australian Journal of Zoology 62, no. 5 (2014): 382. http://dx.doi.org/10.1071/zo14019.
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The water mouse, Xeromys myoides, is currently recognised as a vulnerable species in Australia, inhabiting a small number of distinct and isolated coastal regions of Queensland and the Northern Territory. An examination of the evolutionary history and contemporary influences shaping the genetic structure of this species is required to make informed conservation management decisions. Here, we report the first analysis undertaken on the phylogeography and population genetics of the water mouse across its mainland Australian distribution. Genetic diversity was assessed at two mitochondrial DNA (Cytochrome b, 1000 bp; D-loop, 400 bp) and eight microsatellite DNA loci. Very low genetic diversity was found, indicating that water mice underwent a recent expansion throughout their Australian range and constitute a single evolutionarily significant unit. Microsatellite analyses revealed that the highest genetic diversity was found in the Mackay region of central Queensland; population substructure was also identified, suggesting that local populations may be isolated in this region. Conversely, genetic diversity in the Coomera region of south-east Queensland was very low and the population in this region has experienced a significant genetic bottleneck. These results have significant implications for future management, particularly in terms of augmenting populations through translocations or reintroducing water mice in areas where they have gone extinct.
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Aesomnuk, Wanchana, Siriphat Ruengphayak, Vinitchan Ruanjaichon, Tanee Sreewongchai, Chanate Malumpong, Apichart Vanavichit, Theerayut Toojinda, Samart Wanchana, and Siwaret Arikit. "Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers." Agronomy 11, no. 5 (May 17, 2021): 995. http://dx.doi.org/10.3390/agronomy11050995.
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Rice is a staple food for more than half of the world’s population. Modern rice varieties have been developed for high yield and quality; however, there has been a substantial loss of diversity. A greater number of genetically dynamic landraces could offer valuable and useful genetic resources for rice improvement. In this study, the genetic diversity and population structure of 365 accessions of lowland and upland landraces from four populations from different geographical regions of Thailand were investigated using 75 SNP markers. Clustering analyses using maximum likelihood, Principal Coordinate Analysis (PCoA), and Discriminant Analysis of Principal Components (DAPC) clustered these landraces into two main groups, corresponding to indica and japonica groups. The indica group was further clustered into two subgroups according to the DAPC and STRUCTURE analyses (K = 3). The analysis of molecular variance (AMOVA) analysis results revealed that 91% of the variation was distributed among individuals, suggesting a high degree of genetic differentiation among rice accessions within the populations. Pairwise FST showed the greatest genetic differentiation between the northeastern and southern populations and the smallest genetic differentiation between the northern and northeastern populations. Isolation-by-distance analysis based on a Mantel test indicated a significant relationship between the genetic distance and geographic distance among the Thai rice landraces. The results from this study provide insight into the genetic diversity of Thai rice germplasm, which will enhance the germplasm characterization, conservation, and utilization in rice genetics and breeding.
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Fu, Yun-xin. "New Statistical Tests of Neutrality for DNA Samples From a Population." Genetics 143, no. 1 (May 1, 1996): 557–70. http://dx.doi.org/10.1093/genetics/143.1.557.
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Abstract The purpose of this paper is to develop statistical tests of the neutral model of evolution against a class of alternative models with the common characteristic of having an excess of mutations that occurred a long time ago or a reduction of recent mutations compared to the neutral model. This class of population genetics models include models for structured populations, models with decreasing effective population size and models of selection and mutation balance. Four statistical tests were proposed in this paper for DNA samples from a population. Two of these tests, one new and another a modification of an existing test, are based on EWENS' sampling formula, and the other two new tests make use of the frequencies of mutations of various classes. Using simulated samples and regression analyses, the critical values of these tests can be computed from regression equations. This approach for computing the critical values of a test was found to be appropriate and quite effective. We examined the powers of these four tests using simulated samples from structured populations, populations with linearly decreasing sizes and models of selection and mutation balance and found that they are more powerful than existing statistical tests of the neutral model of evolution.
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Pakstis, Andrew J., Neeru Gandotra, William C. Speed, Michael Murtha, Curt Scharfe, and Kenneth K. Kidd. "The population genetics characteristics of a 90 locus panel of microhaplotypes." Human Genetics 140, no. 12 (October 13, 2021): 1753–73. http://dx.doi.org/10.1007/s00439-021-02382-0.
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AbstractSingle-nucleotide polymorphisms (SNPs) and small genomic regions with multiple SNPs (microhaplotypes, MHs) are rapidly emerging as novel forensic investigative tools to assist in individual identification, kinship analyses, ancestry inference, and deconvolution of DNA mixtures. Here, we analyzed information for 90 microhaplotype loci in 4009 individuals from 79 world populations in 6 major biogeographic regions. The study included multiplex microhaplotype sequencing (mMHseq) data analyzed for 524 individuals from 16 populations and genotype data for 3485 individuals from 63 populations curated from public repositories. Analyses of the 79 populations revealed excellent characteristics for this 90-plex MH panel for various forensic applications achieving an overall average effective number of allele values (Ae) of 4.55 (range 1.04–19.27) for individualization and mixture deconvolution. Population-specific random match probabilities ranged from a low of 10–115 to a maximum of 10–66. Mean informativeness (In) for ancestry inference was 0.355 (range 0.117–0.883). 65 novel SNPs were detected in 39 of the MHs using mMHseq. Of the 3018 different microhaplotype alleles identified, 1337 occurred at frequencies > 5% in at least one of the populations studied. The 90-plex MH panel enables effective differentiation of population groupings for major biogeographic regions as well as delineation of distinct subgroupings within regions. Open-source, web-based software is available to support validation of this technology for forensic case work analysis and to tailor MH analysis for specific geographical regions.
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Huang, Kang, Derek W. Dunn, Kermit Ritland, and Baoguo Li. "polygene : Population genetics analyses for autopolyploids based on allelic phenotypes." Methods in Ecology and Evolution 11, no. 3 (December 29, 2019): 448–56. http://dx.doi.org/10.1111/2041-210x.13338.
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Romero-Soler, Katya J., Ivón M. Ramírez-Morillo, Eduardo Ruiz-Sanchez, Claudia T. Hornung-Leoni, and Germán Carnevali. "Historical biogeography and comparative phylogeography of the Mexican genus Bakerantha (Bromeliaceae): insights into evolution and diversification." Botanical Journal of the Linnean Society 199, no. 1 (December 13, 2021): 109–27. http://dx.doi.org/10.1093/botlinnean/boab084.
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Abstract We studied the rupicolous and dioecious species of Bakerantha (Bromeliaceae) that grow as narrow endemics in central-eastern Mexico. We aimed to describe the spatio-temporal framework in which Bakerantha and its species originated using a phylogeographic and population genetics approach. We carried out population genetics analyses on 29 populations of the five Bakerantha spp., using plastid and nuclear DNA sequences. The data were used to analyse their diversity, genetic structure and demography, to carry out molecular dating and to reconstruction their ancestral area. Our analyses revealed that speciation in Bakerantha began in the Late Pliocene, associated with vicariance resulting from the rise of the Trans-Mexican Volcanic Belt, a barrier that isolated the Bakerantha spp. to its north and south, and subsequent dispersal events in the Sierra Madre Oriental. Genetic data suggest that the species have achieved a high degree of genetic differentiation and variation, but most of them lack intraspecific structure, even though species have remained stable over the time due their life history traits.
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Siegenthaler, Timothy B., Kurt Lamour, and Zachariah R. Hansen. "Population structure of Phytophthora capsici in the state of Tennessee." Mycological Progress 21, no. 1 (January 2022): 159–66. http://dx.doi.org/10.1007/s11557-021-01769-7.
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AbstractThe plant pathogen Phytophthora capsici can be found all throughout the USA, and the population genetics of this organism have been studied within many of these states. Until now, no work has been done in the state of Tennessee to investigate the population structure and genetics of P. capsici found there. The population structure of P. capsici was explored using 296 isolates collected from five counties in Tennessee in 2004, 2007, 2018, and 2019. Samples were genotyped using 39 single nucleotide polymorphism (SNP) genetic markers. Multiple analyses indicate that the population structure of P. capsici in Tennessee exists in isolated clusters structured by geography. Geographically separate populations were genetically distinct, suggesting there is limited or no outcrossing among populations, but there is significant sexual reproduction occurring within populations. These findings corroborate previous studies of P. capsici throughout the midwestern and northeastern USA, where populations are generally sexually reproducing and structured by geography. This study provides the first characterization of P. capsici population structure in Tennessee.
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Rahimi, Sedigheh, Masoud Sheidai, Ahmad Mehrabian, and Fahimeh Koohdar. "Population genetic study in Epilobium minutiflorum (Onagraceae) in Iran." Genetika 54, no. 2 (2022): 677–88. http://dx.doi.org/10.2298/gensr2202677r.
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The genus Epilobium has about 200 species in which taxonomic subdivisions are difficult but possible. Species E. minutiflorum due to its fluffy white inflorescence and small miniature flowers and beaked seeds, it is one of the most prominent species of the genus Epilobium in the region. We have no data on the population genetic structure of this species in the Iran. Therefore a population genetic and morphological investigation was performed through light on genetic and morphological variability in this taxa. We used SCoT molecular markers for population genetic investigation. Genetic diversity analyses revealed a moderate genetic variability between E. minutiflorum populations, while PCoA showed some degree of genetic admixture among populations. AMOVA produced significant genetic difference among populations. Morphometric analysis showed that high degree of overlap among the studied populations. However, the results showed that SCoT marker has a good discrimination power and can differentiate the studied populations. This marker can be used to evaluate genetic diversity and identify genotypes of E. minutiflorum populations.
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Hoffmann, Harald, and Andreas Roggenkamp. "Population Genetics of the Nomenspecies Enterobacter cloacae." Applied and Environmental Microbiology 69, no. 9 (September 2003): 5306–18. http://dx.doi.org/10.1128/aem.69.9.5306-5318.2003.
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ABSTRACT The genetic heterogeneity of the nomenspecies Enterobacter cloacae is well known. Enterobacter asburiae, Enterobacter cancerogenus, Enterobacter dissolvens, Enterobacter hormaechei, Enterobacter kobei, and Enterobacter nimipressuralis are closely related to it and are subsumed in the so-called E. cloacae complex. DNA-DNA hybridization studies performed previously identified at least five DNA-relatedness groups of this complex. In order to analyze the genetic structure and the phylogenetic relationships between the clusters of the nomenspecies E. cloacae, 206 strains collected from 22 hospitals, a veterinarian, and an agricultural center in 11 countries plus all 13 type strains of the genus and reference strain CDC 1347-71R were examined with a combination of sequence and PCR-restriction fragment length polymorphism (PCR-RFLP) analyses of the three housekeeping genes hsp60, rpoB, and hemB as well as ampC, the gene of a class C β-lactamase. Based on the neighbor-joining tree of the hsp60 sequences, 12 genetic clusters (I to XII) and an unstable sequence crowd (xiii) were identified. The robustness of the genetic clusters was confirmed by analyses of rpoB and hemB sequences and ampC PCR-RFLPs. Sequence crowd xiii split into two groups after rpoB analysis. Only three strains formed a cluster with the type strain of E. cloacae, indicating that the minority of isolates identified as E. cloacae truly belong to the species; 13% of strains grouped with other type strains of the genus, suggesting that the phenotypes of these species seem to be more heterogeneous than so far believed. Three clusters represented 70% of strains, but none of them included a type or reference strain. The genetic clustering presented in this study might serve as a framework for future studies dealing with taxonomic, evolutionary, epidemiological, or pathogenetic characteristics of bacteria belonging to the E. cloacae complex.
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Kartavtsev, Yuri P., Nadezda I. Zaslavskaya, Olga V. Svinyna, and Akihiro Kijima. "Allozyme and morphometric variability in the dogwhelk, Nucella heyseana (Gastropoda:Muricidae) from Russian and Japanese waters: evidence for a single species under different names." Invertebrate Systematics 20, no. 6 (2006): 771. http://dx.doi.org/10.1071/is05051.
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A complicated issue of very variable shell morphology in dogwhelks has led to a detailed discussion and set of complex analyses based on the methods of biochemical genetics, molecular genetics, and morphometrics. In this investigation, 29 allozyme loci and five morphometric shell characters were analysed for six samples of Nucella heyseana (Dunker, 1882) from Sakhalin Island, Primorye (Russia) and Onagawa Bay (Japan). An unweighted pair group method with arithmetic mean dendrogram was constructed using genetic distances for the six populations of N. heyseana sampled, and when combined with an earlier study of N. freycinetti Deshayes, 1841, indicated that two separate species are present. However, the population genetic analysis in combination with multivariate analysis of variance, discriminant and factor analyses for morphometric traits lead us to conclude that all six samples taken from Russian and Japanese waters belong to a single species. The taxon, known in Japanese and Korean literature as N. freycinetti, is actually N. heyseana and N. freycinetti is the appropriate name for another species discovered earlier. For N. heyseana Nei’s minimal unbiased genetic distances were examined at three hierarchical levels: (1) within Onagawa Bay (Pacific coast of Honshu), Dm = 0.0059 ± 0.0056; (2) within the group of populations in Peter the Great Bay (Japan Sea, Russia), Dm = 0.0083 ± 0.0067 (Kartavtsev et al., 2000), and (3) within the whole area investigated in the north-western Pacific, Dm = 0.1550 ± 0.0209. Allele frequency heterogeneity and hierarchical variability showed that each bay contains a genetically distinct population of this species.
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Pfeiler, Edward, Carlos A. Flores-López, Jesús Gerardo Mada-Vélez, Juan Escalante-Verdugo, and Therese A. Markow. "Genetic Diversity and Population Genetics of Mosquitoes (Diptera: Culicidae:Culexspp.) from the Sonoran Desert of North America." Scientific World Journal 2013 (2013): 1–11. http://dx.doi.org/10.1155/2013/724609.
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The population genetics and phylogenetic relationships ofCulexmosquitoes inhabiting the Sonoran Desert region of North America were studied using mitochondrial DNA and microsatellite molecular markers. Phylogenetic analyses of mitochondrial cytochromecoxidase subunit I (COI) from mosquitoes collected over a wide geographic area, including the Baja California peninsula, and mainland localities in southern Arizona, USA and Sonora, Mexico, showed several well-supported partitions corresponding toCx. quinquefasciatus, Cx. tarsalis,and two unidentified species,Culexsp. 1 and sp. 2.Culex quinquefasciatuswas found at all localities and was the most abundant species collected.Culex tarsaliswas collected only at Tucson, Arizona and Guaymas, Sonora. The two unidentified species ofCulexwere most abundant at Navojoa in southern Sonora. Haplotype and nucleotide diversities in the COI gene segment were substantially lower inCx. quinquefasciatuscompared with the other three species. Analysis of molecular variance revealed little structure among seven populations ofCx. quinquefasciatus, whereas significant structure was found between the two populations ofCx. tarsalis. Evidence for an historical population expansion beginning in the Pleistocene was found forCx. tarsalis. Possible explanations for the large differences in genetic diversity betweenCx. quinquefasciatusand the other species ofCulexare presented.
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Templeton, A. R., E. Routman, and C. A. Phillips. "Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum." Genetics 140, no. 2 (June 1, 1995): 767–82. http://dx.doi.org/10.1093/genetics/140.2.767.
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Abstract Nonrandom associations of alleles or haplotypes with geographical location can arise from restricted gene flow, historical events (fragmentation, range expansion, colonization), or any mixture of these factors. In this paper, we show how a nested cladistic analysis of geographical distances can be used to test the null hypothesis of no geographical association of haplotypes, test the hypothesis that significant associations are due to restricted gene flow, and identify patterns of significant association that are due to historical events. In this last case, criteria are given to discriminate among contiguous range expansion, long-distance colonization, and population fragmentation. The ability to make these discriminations depends critically upon an adequate geographical sampling design. These points are illustrated with a worked example: mitochondrial DNA haplotypes in the salamander Ambystoma tigrinum. For this example, prior information exists about restricted gene flow and likely historical events, and the nested cladistic analyses were completely concordant with this prior information. This concordance establishes the plausibility of this nested cladistic approach, but much future work will be necessary to demonstrate robustness and to explore the power and accuracy of this procedure.
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Ogbonna, Alex C., Luciano Rogerio Braatz de Andrade, Lukas A. Mueller, Eder Jorge de Oliveira, and Guillaume J. Bauchet. "Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication." Theoretical and Applied Genetics 134, no. 5 (February 11, 2021): 1343–62. http://dx.doi.org/10.1007/s00122-021-03775-5.
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Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.
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Barker, J. S. F., P. D. East, and B. S. Weir. "TEMPORAL AND MICROGEOGRAPHIC VARIATION IN ALLOZYME FREQUENCIES IN A NATURAL POPULATION OF DROSOPHILA BUZZATII." Genetics 112, no. 3 (March 1, 1986): 577–611. http://dx.doi.org/10.1093/genetics/112.3.577.
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ABSTRACT Temporal variation in allozyme frequencies at six loci was studied by making monthly collections over 4 yr in one population of the cactophilic species Drosophila buzzatii. Ten sites were defined within the study locality, and for all temporal samples, separate collections were made at each of these sites. Population structure over microgeographic space and changes in population structure over time were analyzed using F-statistic estimators, and multivariate analyses of allele and genotype frequencies with environmental variables were carried out.—Allele frequencies showed significant variation over time, although there were no clear cyclical or seasonal patterns. A biplot analysis of allele frequencies over seasons within years and over years showed clear discrimination among years by alleles at four loci. During the 4 yr, three alleles showed directional changes which were associated with directional changes in environmental variables. Significant associations with one or more environmental variables were found for allele frequencies at every locus and for both expected and observed heterozygosities (except those for Est-1 and Est-2). Thus, variation in allele frequencies over time cannot be attributed solely to drift. Significant linkage disequilibria were detected among three loci (Est-2, Hex and Aldox), but there was no evidence for spatial or temporal patterns.—The F-statistic analyses showed significant differentiation among months within years for all loci, but the statistic used (coancestry) was heterogeneous among loci. Estimates of F (inbreeding) for all loci were significantly different from zero, with the loci in four groups, Adh-1 (negative), Pgm (small positive), Est-2 and Hex (intermediate) and Est-1 and Aldox (high positive). The correlation of genes within individuals within populations (f) for each locus in each month by site sample differed among loci, as did the patterns of change in f over time (seasons). Heterogeneity in the F-statistic estimates indicates that natural selection is directly or indirectly affecting allele and genotype frequencies at some loci. However, the F-statistic analyses showed essentially no microgeographic structure (i.e., among sites), although there was significant heterogeneity in allele frequencies among flies emerging from individual rots.—Thus, microspatial heterogeneity probably is most important at the level of individual rots, and coupled with habitat selection, it could be a major factor promoting diversifying selection and the maintenance of polymorphism. Resolution of the nature of this selection and of the apparent inbreeding detected at all loci except Adh-1 will require detailed study of the breeding structure of the population at the microhabitat level (individual rots) and of gene flow within the population.
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Urnikyte, Alina, Alma Molyte, and Vaidutis Kučinskas. "Genome-Wide Landscape of North-Eastern European Populations: A View from Lithuania." Genes 12, no. 11 (October 28, 2021): 1730. http://dx.doi.org/10.3390/genes12111730.
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There are still several unanswered questions regarding about ancient events in the Lithuanian population. The Lithuanians, as the subject of this study, are of great interest as they represent a partially isolated population maintaining an ancient genetic composition and show genetic uniqueness in European comparisons. To elucidate the genetic relationships between the Lithuania and North-Eastern European and West Siberian populations, we analyzed the population structure, effective population size, and recent positive selection from genome-wide single nucleotide polymorphism (SNP) data. We identified the close genetic proximity of Lithuanians to neighboring populations (Latvians, Estonians, Belarusians) and in part with West and South Slavs (Poles, Slovaks, and Slovenians), however, with particular genetic distinctiveness. The estimated long-term Ne values ranged from ~5900 in the Estonian population to ~2400 in the South Russian population. The divergence times between the Lithuanian and study populations ranged from 240 to 12,871 YBP. We also found evidence of selection in 24 regions, 21 of which have not been discovered in previous analyses of selection. Undoubtedly, the genetic diversity analysis of geographically specific regions may provide new insights into microevolutionary processes affecting local human populations.
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Estoup, A., L. Garnery, M. Solignac, and J. M. Cornuet. "Microsatellite variation in honey bee (Apis mellifera L.) populations: hierarchical genetic structure and test of the infinite allele and stepwise mutation models." Genetics 140, no. 2 (June 1, 1995): 679–95. http://dx.doi.org/10.1093/genetics/140.2.679.
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Abstract Samples from nine populations belonging to three African (intermissa, scutellata and capensis) and four European (mellifera, ligustica, carnica and cecropia) Apis mellifera subspecies were scored for seven microsatellite loci. A large amount of genetic variation (between seven and 30 alleles per locus) was detected. Average heterozygosity and average number of alleles were significantly higher in African than in European subspecies, in agreement with larger effective population sizes in Africa. Microsatellite analyses confirmed that A. mellifera evolved in three distinct and deeply differentiated lineages previously detected by morphological and mitochondrial DNA studies. Dendrogram analysis of workers from a given population indicated that super-sisters cluster together when using a sufficient number of microsatellite data whereas half-sisters do not. An index of classification was derived to summarize the clustering of different taxonomic levels in large phylogenetic trees based on individual genotypes. Finally, individual population x loci data were used to test the adequacy of the two alternative mutation models, the infinite allele model (IAM) and the stepwise mutation models. The better fit overall of the IAM probably results from the majority of the microsatellites used including repeats of two or three different length motifs (compound microsatellites).
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Podolsky, R. H., and T. P. Holtsford. "Population structure of morphological traits in Clarkia dudleyana. I. Comparison of FST between allozymes and morphological traits." Genetics 140, no. 2 (June 1, 1995): 733–44. http://dx.doi.org/10.1093/genetics/140.2.733.
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Abstract Studies of genetic variation at allozyme loci, assumed to be selectively neutral, have provided valuable insights into the genetic structure of numerous populations. The degree to which population structure of allozyme variation reflects that of quantitative traits, however, is not well resolved. Here, we compare estimates of population differentiation (FST) of 11 populations for allozymes with those for nine discrete and nine continuous morphological traits. Overall, the allozymes have the lowest FST estimates, indicating relatively little population differentiation. Excepting two traits, petal width and long internode length, the continuous morphological traits have estimates similar to those from allozymes. The discrete morphological traits tend to have the highest estimates. On a single trait basis, estimates of FST for four discrete and two continuous traits are higher than those for allozymes. A more detailed (narrow-sense quantitative) genetic study of two populations suggests that these estimates of FST may underestimate the true value because of dominance. Clustering analyses show that the pattern of differentiation for the discrete morphological traits strongly reflects the geographical distribution of the populations, whereas the patterns for the continuous traits and allozymes do not. These results suggest that selection has been occurring on the discrete morphological traits, selecting toward a common optimum within each geographic group, and optima differing among geographic groups.
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Cheng, Yu-Heng, Meng-Tao Sun, Ning Wang, Chang-Zhe Gao, Han-Qi Peng, Jie-Ying Zhang, Man-Man Gu, and Da-Bing Lu. "Population Genetics of Oncomelania hupensis Snails from New-Emerging Snail Habitats in a Currently Schistosoma japonicum Non-Endemic Area." Tropical Medicine and Infectious Disease 8, no. 1 (January 5, 2023): 42. http://dx.doi.org/10.3390/tropicalmed8010042.
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Schistosomiasis is still one of the most significant neglected tropical diseases worldwide, and China is endemic for Schistosoma japonicum. With its great achievement in schistosomiasis control, the government of China has set the goal to eliminate the parasitic disease at the country level by 2030. However, one major challenge is the remaining huge areas of habitats for the intermediate host Oncomelania hupensis. This is further exacerbated by an increasing number of new emerging snail habitats reported each year. Therefore, population genetics on snails in such areas will be useful in evaluation of snail control effect and/or dispersal. We then sampled snails from new emerging habitats in Taicang of Jiangsu, China, a currently S. japonicum non-endemic area from 2014 to 2017, and performed population genetic analyses based on nine microsatellites. Results showed that all snail populations had low genetic diversity, and most genetic variations originated from within snail populations. The estimated effective population size for the 2015 population was infinitive. All snails could be separated into two clusters, and further DIYABC analysis revealed that both the 2016 and the 2017 populations may derive from the 2015, indicating that the 2017 population must have been missed in the field survey performed in 2016. These findings may have implications in development of more practical guidelines for snail monitoring and control.
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Han, Xuekai, Ruyi Xu, Yuyu Zheng, Meirong Gao, and Liying Sui. "Development of EST-SSR markers and genetic diversity analysis among three Artemia species from different geographic populations." Crustaceana 92, no. 7 (July 26, 2019): 841–51. http://dx.doi.org/10.1163/15685403-00003916.
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Abstract Artemia is one of the most important live food items used in larviculture. In order to study the genetic diversity of Artemia in China, 170 novel simple sequence repeats (SSR) markers were identified from expressed sequence tags (ESTs) of the transcriptome library of Artemia parthenogenetica. Of these, 8 microsatellite loci were developed to characterize three geographical populations of Artemia. The results showed the expected and observed heterozygosity varied from 0.43 to 0.50 and from 0.59 to 0.64, respectively. The PIC (polymorphic information content) ranged from 0.37 to 0.45. These observations indicated that the Yuncheng population has the highest genetic diversity, whereas the Shuanghu population has the lowest. The Fst value (genetic differentiation coefficient) indicated that the three populations are highly differentiated. Genetic identity analyses revealed that the Yuncheng and Shuanghu populations have the closest relationship. The SSR markers described here will serve as a valuable tool for further studies in population and conservation genetics on Artemia.
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Parker, Katherine, A. Mesut Erzurumluoglu, and Santiago Rodriguez. "The Y Chromosome: A Complex Locus for Genetic Analyses of Complex Human Traits." Genes 11, no. 11 (October 29, 2020): 1273. http://dx.doi.org/10.3390/genes11111273.
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The Human Y chromosome (ChrY) has been demonstrated to be a powerful tool for phylogenetics, population genetics, genetic genealogy and forensics. However, the importance of ChrY genetic variation in relation to human complex traits is less clear. In this review, we summarise existing evidence about the inherent complexities of ChrY variation and their use in association studies of human complex traits. We present and discuss the specific particularities of ChrY genetic variation, including Y chromosomal haplogroups, that need to be considered in the design and interpretation of genetic epidemiological studies involving ChrY.
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Bijlsma, R., R. W. Allard, and A. L. Kahler. "NONRANDOM MATING IN AN OPEN-POLLINATED MAIZE POPULATION." Genetics 112, no. 3 (March 1, 1986): 669–80. http://dx.doi.org/10.1093/genetics/112.3.669.
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ABSTRACT Randomness of fertilization was studied in an open-pollinated population of maize (Zea mays L.) through allozyme assays of seedlings from open-pollinated seeds produced on both tasseled and detasseled plants. Mixed-mating-model estimates of the amount of outcrossing (t) were not significantly different from t = 1.00 for four enzyme loci (Adh1, Idh2, Got1 and Acp1), indicating that fertilizations were at random in the population. However, for loci Prx1 and Est4, estimates of t were significantly smaller than unity-0.80 and 0.70 for tasseled plants and 0.81 and 0.80 for detasseled plants. The excesses of homogametic fertilizations detected on the detasseled plants could not have been due to selffertilization, s = 1 - t, because the detasseled plants shed no pollen. Analyses of allelic frequencies in the pollen that produced seed on the detasseled plants established that different maternal plants sampled genetically different populations of pollen from the outcross pollen pool. It was suggested that the causes of the differential sampling were temporal variation in the pollen pool, and/or gametophytic selection, correlated with marker-locus genotype. Two-, three- and four-locus interactions among the marker loci were often statistically significant, indicating that the factors responsible for the nonrandom gametic unions observed in the maize population studied were complexly interactive.
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Luo, Z. W., R. Thompson, and J. A. Woolliams. "A Population Genetics Model of Marker-Assisted Selection." Genetics 146, no. 3 (July 1, 1997): 1173–83. http://dx.doi.org/10.1093/genetics/146.3.1173.
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A deterministic two-loci model was developed to predict genetic response to marker-assisted selection (MAS) in one generation and in multiple generations. Formulas were derived to relate linkage disequilibrium in a population to the proportion of additive genetic variance used by MAS, and in turn to an extra improvement in genetic response over phenotypic selection. Predictions of the response were compared to those predicted by using an infinite-loci model and the factors affecting efficiency of MAS were examined. Theoretical analyses of the present study revealed the nonlinearity between the selection intensity and genetic response in MAS. In addition to the heritability of the trait and the proportion of the marker-associated genetic variance, the frequencies of the selectively favorable alleles at the two loci, one marker and one quantitative trait locus, were found to play an important role in determining both the short- and long-term efficiencies of MAS. The evolution of linkage disequilibrium and thus the genetic response over several generations were predicted theoretically and examined by simulation. MAS dissipated the disequilibrium more quickly than drift alone. In some cases studied, the rate of dissipation was as large as that to be expected in the circumstance where the true recombination fraction was increased by three times and selection was absent.
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Schellin-Becker, Claudia Marina, Verónica Calonga-Solís, Marcelo Malaghini, Luiza Rauen Sabbag, Maria Luiza Petzl-Erler, Danillo G. Augusto, and Danielle Malheiros. "Population structure and forensic genetic analyses in Guarani and Kaingang Amerindian populations from Brazil." Forensic Science International: Genetics 58 (May 2022): 102678. http://dx.doi.org/10.1016/j.fsigen.2022.102678.
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