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Journal articles on the topic 'Genetic admixture model'

Author: Grafiati

Published: 5 June 2025

Last updated: 2 August 2025

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1

Wu, Yufeng. "Inference of population admixture network from local gene genealogies: a coalescent-based maximum likelihood approach." Bioinformatics 36, Supplement_1 (2020): i326—i334. http://dx.doi.org/10.1093/bioinformatics/btaa465.

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Abstract Motivation Population admixture is an important subject in population genetics. Inferring population demographic history with admixture under the so-called admixture network model from population genetic data is an established problem in genetics. Existing admixture network inference approaches work with single genetic polymorphisms. While these methods are usually very fast, they do not fully utilize the information [e.g. linkage disequilibrium (LD)] contained in population genetic data. Results In this article, we develop a new admixture network inference method called GTmix. Differ

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Deng, Hong-Wen. "Population Admixture May Appear to Mask, Change or Reverse Genetic Effects of Genes Underlying Complex Traits." Genetics 159, no. 3 (2001): 1319–23. http://dx.doi.org/10.1093/genetics/159.3.1319.

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Abstract Association studies using random population samples are increasingly being applied in the identification and inference of genetic effects of genes underlying complex traits. It is well recognized that population admixture may yield false-positive identification of genetic effects for complex traits. However, it is less well appreciated that population admixture can appear to mask, change, or reverse true genetic effects for genes underlying complex traits. By employing a simple population genetics model, we explore the effects and the conditions of population admixture in masking, cha

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Madbouly, Abeer, Tao Wang, Mark Albrecht, et al. "Investigating Effect of Genetic Admixture and Donor/Recipient Genetic Disparity on Transplant Outcomes." Blood 126, no. 23 (2015): 3229. http://dx.doi.org/10.1182/blood.v126.23.3229.3229.

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Abstract Aim Survival after hematopoietic cell transplantation (HCT) is dependent on donor/recipient (D/R) HLA matching. However disparities in survival were reported for some ethnicities despite comparable HLA matching. Individual ethnicities/races, as reported through self-identification, can change over time. Most studies have shown that African-American recipients (AAFA race) experience worse survival. Another way to investigate ancestry is to use Ancestry Informative Marker SNPs (AIMs), providing ancestral admixture. We hypothesized that information on donor and recipient genetic admixtur

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Mimno, David, David M. Blei, and Barbara E. Engelhardt. "Posterior predictive checks to quantify lack-of-fit in admixture models of latent population structure." Proceedings of the National Academy of Sciences 112, no. 26 (2015): E3441—E3450. http://dx.doi.org/10.1073/pnas.1412301112.

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Admixture models are a ubiquitous approach to capture latent population structure in genetic samples. Despite the widespread application of admixture models, little thought has been devoted to the quality of the model fit or the accuracy of the estimates of parameters of interest for a particular study. Here we develop methods for validating admixture models based on posterior predictive checks (PPCs), a Bayesian method for assessing the quality of fit of a statistical model to a specific dataset. We develop PPCs for five population-level statistics of interest: within-population genetic varia

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Shchur, Vladimir, Jesper Svedberg, Paloma Medina, Russell Corbett-Detig, and Rasmus Nielsen. "On the Distribution of Tract Lengths During Adaptive Introgression." G3: Genes|Genomes|Genetics 10, no. 10 (2020): 3663–73. http://dx.doi.org/10.1534/g3.120.401616.

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Admixture is increasingly being recognized as an important factor in evolutionary genetics. The distribution of genomic admixture tracts, and the resulting effects on admixture linkage disequilibrium, can be used to date the timing of admixture between species or populations. However, the theory used for such prediction assumes selective neutrality despite the fact that many famous examples of admixture involve natural selection acting for or against admixture. In this paper, we investigate the effects of positive selection on the distribution of tract lengths. We develop a theoretical framewo

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Karacaören, Burak. "Empirical comparison of association and admixture mapping for body weight using F<sub>2</sub> mice data set." Archives Animal Breeding 57, no. 1 (2014): 1–6. http://dx.doi.org/10.7482/0003-9438-57-005.

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Abstract. Recent advances in molecular genetics have provided hundreds of thousands of single nucleotide polymorphisms (SNPs) to detect mutations in genes related with complex traits. Undetected shared ancestry within samples of individuals could lead to the detection of false genomic signals in association mapping. Pedigree-based relationship matrices or genomic relationship matrices could be used in a mixed model to predict and correct for genetic stratifications. Genotypic information of founder populations could also be used to explore patterns of inheritance for complex traits by admixtur

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Grote, Mark N. "A Covariance Structure Model for the Admixture of Binary Genetic Variation." Genetics 176, no. 4 (2007): 2405–20. http://dx.doi.org/10.1534/genetics.107.071779.

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Prendergast, Mary E., Mark Lipson, Elizabeth A. Sawchuk, et al. "Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa." Science 365, no. 6448 (2019): eaaw6275. http://dx.doi.org/10.1126/science.aaw6275.

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How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African–related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture w

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Bhattacharjee, Ranjana, Paterne Agre, Guillaume Bauchet, et al. "Genotyping-by-Sequencing to Unlock Genetic Diversity and Population Structure in White Yam (Dioscorea rotundata Poir.)." Agronomy 10, no. 9 (2020): 1437. http://dx.doi.org/10.3390/agronomy10091437.

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White yam (Dioscorearotundata Poir.) is one of the most important tuber crops in West Africa, where it is indigenous and represents the largest repository of biodiversity through several years of domestication, production, consumption, and trade. In this study, the genotyping-by-sequencing (GBS) approach was used to sequence 814 genotypes consisting of genebank landraces, breeding lines, and market varieties to understand the level of genetic diversity and pattern of the population structure among them. The genetic diversity among different genotypes was assessed using three complementary clus

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Chikhi, Lounès, Michael W. Bruford, and Mark A. Beaumont. "Estimation of Admixture Proportions: A Likelihood-Based Approach Using Markov Chain Monte Carlo." Genetics 158, no. 3 (2001): 1347–62. http://dx.doi.org/10.1093/genetics/158.3.1347.

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Abstract When populations are separated for long periods and then brought into contact for a brief episode in part of their range, this can result in genetic admixture. To analyze this type of event we considered a simple model under which two parental populations (P1 and P2) mix and create a hybrid population (H). After that event, the three populations evolve under pure drift without exchange during T generations. We developed a new method, which allows the simultaneous estimation of the time since the admixture event (scaled by the population size ti = T/Ni, where Ni is the effective popula

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LUO, Ting, Rui WANG, and Chuan-Chao WANG. "Inferring the population structure and admixture history of three Hmong-Mien-speaking Miao tribes from southwest China based on genome-wide SNP genotyping." Annals of Human Biology 48, no. 5 (2021): 418–29. https://doi.org/10.1080/03014460.2021.2005825.

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<strong>Background: </strong> Hmong-Mien speaking Miao, also called Hmong, is the sixth largest ethnic group in mainland China. However, the fine-scale genetic profiles and population history of Miao populations in southwest China, especially in Guizhou province, remain uncharacterised due to a scarcity of samples of genome-wide data from different tribes. <strong>Aim: </strong> To further investigate the population substructure and admixture history of the Guizhou Miao minority. <strong>Subjects and methods: </strong> We collected 29 samples from three Miao tribes of Guizhou province in south

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Li, Yao, Xingwang Zhang, Lu Wang, Victoria L. Sork, Lingfeng Mao, and Yanming Fang. "Influence of Pliocene and Pleistocene climates on hybridization patterns between two closely related oak species in China." Annals of Botany 129, no. 2 (2021): 231–45. http://dx.doi.org/10.1093/aob/mcab140.

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Abstract Background and Aims Contemporary patterns of genetic admixture reflect imprints of both ancient and recent gene flow, which can provide us with valuable information on hybridization history in response to palaeoclimate change. Here, we examine the relationships between present admixture patterns and past climatic niche suitability of two East Asian Cerris oaks (Quercus acutissima and Q. chenii) to test the hypothesis that the mid-Pliocene warm climate promoted while the Pleistocene cool climate limited hybridization among local closely related taxa. Methods We analyse genetic variatio

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HE, Guanglin, Yunhe ZHANG, Lan-Hai WEI, et al. "The genomic formation of Tanka people, an isolated "gypsies in water" in the coastal region of Southeast China." American Journal of Biological Anthropology 178, no. 1 (2022): 154–70. https://doi.org/10.1002/ajpa.24495.

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<strong>Objectives </strong>Three different hypotheses proposed via the controversial evidence from cultural, anthropological, and uniparental genetic analyses, respectively, stated that Tanka people probably originated from Han Chinese, ancient Baiyue tribe, or the admixture of them. Therefore, the genetic origin and admixture history of the Tanka people, an isolated “Gypsies in water” in the coastal region of Southeast China, are needed to be genetically clarified using genome-wide SNP data. <strong>Materials and methods </strong>To elucidate the genetic origin of the S

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Wattanadilokcahtkun, Pish, Piangjai Chalermwong, Worapong Singchat, et al. "Genetic admixture and diversity in Thai domestic chickens revealed through analysis of Lao Pa Koi fighting cocks." PLOS ONE 18, no. 10 (2023): e0289983. http://dx.doi.org/10.1371/journal.pone.0289983.

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Lao Pa Koi (LPK) chicken is a popular fighting breed in Thailand, prized for (its unique characteristics acquired by selective breeding), and a valuable model for exploring the genetic diversity and admixture of red junglefowls and domestic chickens. In this study, genetic structure and diversity of LPK chicken were assessed using 28 microsatellite markers and mitochondrial DNA (mtDNA) D-loop sequences, and the findings were compared to a gene pool library from “The Siam Chicken Bioresource Project”. High genetic variability was observed in LPK chickens using mtDNA D-loop haplotype analysis, a

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Szmatoła, Tomasz, Katarzyna Ropka-Molik, Mirosław Tyra, et al. "The Genetic Structure of Five Pig Breeds Maintained in Poland." Annals of Animal Science 16, no. 4 (2016): 1019–27. http://dx.doi.org/10.1515/aoas-2016-0006.

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Abstract The aim of this study was to evaluate genetic variability of five pig populations maintained in Poland with the usage of model based clustering method (MCMC approach) on microsatellite data. A high degree of genetic diversity with the values corrected for sample sizes was observed for four breeds: 0.740 for Polish Landrace, 0.697 for Pietrain, 0.692 for Polish Large White and 0.688 for Puławska. Duroc breed, however, was characterized by the lowest genetic diversity (0.589), allelic richness and number of effective alleles. As for Structure software results, each breed was represented

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Vaishnaw, Vivek, Naseer Mohammad, Syed Arif Wali, et al. "AFLP markers for analysis of genetic diversity and structure of teak (Tectona grandis) in India." Canadian Journal of Forest Research 45, no. 3 (2015): 297–306. http://dx.doi.org/10.1139/cjfr-2014-0279.

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Five amplified fragment length polymorphism (AFLP) primer combinations (E-AAC × M-CAT, E-AAC × M-CTG, E-ACA × M-CTC, E-ACA × M-CTA, and E-ACC × M-CTA) were employed for analysis of genetic diversity, differentiation, and structure of 96 genotypes of teak (Tectona grandis L. f.) from 10 natural locations in India. The analysis of the AFLP marker data by both versions, i.e., GST and θ, of F statistics showed a similar trend due to the outcrossing nature of teak. The primer combination E-AAC × M-CAT detected maximum polymorphism in the teak genome. The analysis of molecular variance assigned a la

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Lehocká, Kristína, Barbora Olšanská, Radovan Kasarda, Ondrej Kadlečík, Anna Trakovická, and Nina Moravčíková. "The Genetic Structure of Slovak Spotted Cattle Based on Genome-wide Analysis." Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis 68, no. 1 (2020): 57–61. http://dx.doi.org/10.11118/actaun202068010057.

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The objective of the study was to determine the membership probability and level of admixture among Slovak Spotted cattle and historically related breeds (Ayshire, Holstein, Swiss Simmental and Slovak Pinzgau). The analysis was based on the panel of 35 934 SNPs that were used for genotyping of 423 individuals. The optimal number of clusters was estimated in two ways; by analysis of Bayesian information criterion and Bayesian clustering algorithm. The optimal number of clusters ranged from 3 to 5, depending on the applied approach. Subsequently, the population structure was tested by discrimina

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Estoup, Arnaud, Ian J. Wilson, Claire Sullivan, Jean-Marie Cornuet, and Craig Moritz. "Inferring Population History From Microsatellite and Enzyme Data in Serially Introduced Cane Toads,Bufo marinus." Genetics 159, no. 4 (2001): 1671–87. http://dx.doi.org/10.1093/genetics/159.4.1671.

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AbstractMuch progress has been made on inferring population history from molecular data. However, complex demographic scenarios have been considered rarely or have proved intractable. The serial introduction of the South-Central American cane toad Bufo marinus in various Caribbean and Pacific islands involves four major phases: a possible genetic admixture during the first introduction, a bottleneck associated with founding, a transitory population boom, and finally, a demographic stabilization. A large amount of historical and demographic information is available for those introductions and c

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Forhan, Gerald, Jean-Louis Martiel, and Michael G. B. Blum. "A deterministic model of admixture and genetic introgression: The case of Neanderthal and Cro-Magnon." Mathematical Biosciences 216, no. 1 (2008): 71–76. http://dx.doi.org/10.1016/j.mbs.2008.08.004.

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Jiménez, Rosa Alicia, and Juan Francisco Ornelas. "Historical and current introgression in a Mesoamerican hummingbird species complex: a biogeographic perspective." PeerJ 4 (January 12, 2015): e1556. http://dx.doi.org/10.7717/peerj.1556.

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The influence of geologic and Pleistocene glacial cycles might result in morphological and genetic complex scenarios in the biota of the Mesoamerican region. We tested whether berylline, blue-tailed and steely-blue hummingbirds,Amazilia beryllina,Amazilia cyanuraandAmazilia saucerottei, show evidence of historical or current introgression as their plumage colour variation might suggest. We also analysed the role of past and present climatic events in promoting genetic introgression and species diversification. We collected mitochondrial DNA (mtDNA) sequence data and microsatellite loci scores

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DELORME, RICHARD, JEAN-LOUIS GOLMARD, NADIA CHABANE, et al. "Admixture analysis of age at onset in obsessive–compulsive disorder." Psychological Medicine 35, no. 2 (2005): 237–43. http://dx.doi.org/10.1017/s0033291704003253.

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Background. Age at onset (AAO) has been useful to explore the clinical, neurobiological and genetic heterogeneity of obsessive–compulsive disorder (OCD). However, none of the various thresholds of AAO used in previous studies have been validated, and it remains an unproven notion that AAO is a marker for different subtypes of OCD. If AAO is a clinical indicator of different biological subtypes, then subgroups based on distinct AAOs should have separate normal distributions as well as different clinical characteristics.Method. Admixture analysis was used to determine the best-fitting model for

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Malani, Shubham, Waltram Ravelombola, Aurora Manley, and Hanh Pham. "Genetic Diversity and Population Structure Analysis in Guar." Plants 13, no. 22 (2024): 3183. http://dx.doi.org/10.3390/plants13223183.

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Guar [Cyamopsis tetragonoloba (L.) Taub] was domesticated in India and Pakistan. It is mainly self-pollinated, bushy, and deeply tap-rooted. Guar seed endosperm contains galactomannan gum, which is used in many food products, pharmaceuticals, cosmetics, explosives, meat products, and pet foods, and in the textile industry, yet its genetic diversity remains largely underexplored. Using 7000 high-quality single nucleotide polymorphism (SNP) markers acquired from genotyping by sequencing (GBS), we analyzed the genetic diversity and population structure in 225 guar accessions from India, Pakistan,

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Buswell, Victoria, Jonathan Ellis, J. Huml, et al. "When One’s Not Enough: Colony Pool-Seq Outperforms Individual-Based Methods for Assessing Introgression in Apis mellifera mellifera." Insects 14, no. 5 (2023): 421. http://dx.doi.org/10.3390/insects14050421.

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The human management of honey bees (Apis mellifera) has resulted in the widespread introduction of subspecies outside of their native ranges. One well known example of this is Apis mellifera mellifera, native to Northern Europe, which has now been significantly introgressed by the introduction of C lineage honey bees. Introgression has consequences for species in terms of future adaptive potential and long-term viability. However, estimating introgression in colony-living haplodiploid species is challenging. Previous studies have estimated introgression using individual workers, individual dro

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de Oliveira, Danyllo Amaral, Paulo Henrique Muller da Silva, Evandro Novaes, and Dario Grattapaglia. "Genome-wide analysis highlights genetic admixture in exotic germplasm resources of Eucalyptus and unexpected ancestral genomic composition of interspecific hybrids." PLOS ONE 18, no. 8 (2023): e0289536. http://dx.doi.org/10.1371/journal.pone.0289536.

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Eucalyptus is an economically important genus comprising more than 890 species in different subgenera and sections. Approximately twenty species of subgenus Symphyomyrtus account for 95% of the world’s planted eucalypts. Discrimination of closely related eucalypt taxa is challenging, consistent with their recent phylogenetic divergence and occasional hybridization in nature. Admixture, misclassification or mislabeling of Eucalyptus germplasm resources maintained as exotics have been suggested, although no reports are available. Moreover, hybrids with increased productivity and traits complemen

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Ellis, David, Oswaldo Chavez, Joseph Coombs, et al. "Genetic identity in genebanks: application of the SolCAP 12K SNP array in fingerprinting and diversity analysis in the global in trust potato collection." Genome 61, no. 7 (2018): 523–37. http://dx.doi.org/10.1139/gen-2017-0201.

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Breeders rely on genetic integrity of material from genebanks; however, admixture, mislabeling, and errors in original data can occur and be detrimental. Two hundred and fifty accessions, representing paired samples consisting of original mother plants and their in vitro counterparts from the cultivated potato collection at the International Potato Center (CIP) were fingerprinted using the Infinium 12K V2 Potato Array to confirm genetic identity of the accessions and evaluate genetic diversity of the potato collection. Diploid, triploid, and tetraploid accessions were included, representing se

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Dadousis, Christos, Francesca Cecchi, Michela Ablondi, Maria Chiara Fabbri, Alessandra Stella, and Riccardo Bozzi. "Keep Garfagnina alive. An integrated study on patterns of homozygosity, genomic inbreeding, admixture and breed traceability of the Italian Garfagnina goat breed." PLOS ONE 16, no. 1 (2021): e0232436. http://dx.doi.org/10.1371/journal.pone.0232436.

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The objective of this study was to investigate the genetic diversity of the Garfagnina (GRF) goat, a breed that currently risks extinction. For this purpose, 48 goats were genotyped with the Illumina CaprineSNP50 BeadChip and analyzed together with 214 goats belonging to 9 other Italian breeds (~25 goats/breed), whose genotypes were available from the AdaptMap project [Argentata (ARG), Bionda dell’Adamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT), Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and Valpassiria (VSS)]. Comparative analyses were conducted on i) runs of ho

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Ayala, Nicolas M., Maximilian Genetti, and Russell Corbett-Detig. "Inferring multi-locus selection in admixed populations." PLOS Genetics 19, no. 11 (2023): e1011062. http://dx.doi.org/10.1371/journal.pgen.1011062.

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Admixture, the exchange of genetic information between distinct source populations, is thought to be a major source of adaptive genetic variation. Unlike mutation events, which periodically generate single alleles, admixture can introduce many selected alleles simultaneously. As such, the effects of linkage between selected alleles may be especially pronounced in admixed populations. However, existing tools for identifying selected mutations within admixed populations only account for selection at a single site, overlooking phenomena such as linkage among proximal selected alleles. Here, we de

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Labouisse, Jean-Pierre, Philippe Cubry, Frédéric Austerlitz, Ronan Rivallan, and Hong Anh Nguyen. "New insights on spatial genetic structure and diversity of Coffea canephora (Rubiaceae) in Upper Guinea based on old herbaria." Plant Ecology and Evolution 153, no. 1 (2020): 82–100. http://dx.doi.org/10.5091/plecevo.2020.1584.

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Backgrounds and aims – Previous studies showed that robusta coffee (Coffea canephora Pierre ex A.Froehner), one of the two cultivated coffee species worldwide, can be classified in two genetic groups: the Guinean group originating in Upper Guinea and the Congolese group in Lower Guinea and Congolia. Although C. canephora of the Guinean group is an important resource for genetic improvement of robusta coffee, its germplasm is under-represented in ex situ gene banks and its genetic diversity and population structure have not yet been investigated. Methods – To overcome the limitations of living

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Rogers, Jeffrey, Muthuswamy Raveendran, R. Alan Harris, et al. "The comparative genomics and complex population history ofPapiobaboons." Science Advances 5, no. 1 (2019): eaau6947. http://dx.doi.org/10.1126/sciadv.aau6947.

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Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genusPapio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture

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Tahami, Mohadeseh Sadat, Vlad Dincă, Kyung Min Lee, et al. "Genomics Reveal Admixture and Unexpected Patterns of Diversity in a Parapatric Pair of Butterflies." Genes 12, no. 12 (2021): 2009. http://dx.doi.org/10.3390/genes12122009.

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We studied the evolutionary relationship of two widely distributed parapatric butterfly species, Melitaea athalia and Melitaea celadussa, using the ddRAD sequencing approach, as well as genital morphology and mtDNA data. M. athalia was retrieved as paraphyletic with respect to M. celadussa. Several cases of mito-nuclear discordance and morpho-genetic mismatch were found in the contact zone. A strongly diverged and marginally sympatric clade of M. athalia from the Balkans was revealed. An in-depth analysis of genomic structure detected high levels of admixture between M. athalia and M. celaduss

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Labouisse, Jean-Pierre, Philippe Cubry, Frédéric Austerlitz, Ronan Rivallan, and Hong Nguyen. "New insights on spatial genetic structure and diversity of Coffea canephora (Rubiaceae) in Upper Guinea based on old herbaria." Plant Ecology and Evolution 153, no. (1) (2020): 82–100. https://doi.org/10.5091/plecevo.2020.1584.

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<b>Backgrounds and aims</b> – Previous studies showed that robusta coffee (<em>Coffea canephora</em> Pierre ex A.Froehner), one of the two cultivated coffee species worldwide, can be classified in two genetic groups: the Guinean group originating in Upper Guinea and the Congolese group in Lower Guinea and Congolia. Although <em>C. canephora</em> of the Guinean group is an important resource for genetic improvement of robusta coffee, its germplasm is under-represented in <em>ex situ</em> gene banks and its genetic diversity and population structure have not yet been investigated. <b>Methods</b>

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Dean, Laura L., Isabel S. Magalhaes, Andrew Foote, Daniele D’Agostino, Suzanne McGowan, and Andrew D. C. MacColl. "Admixture between Ancient Lineages, Selection, and the Formation of Sympatric Stickleback Species-Pairs." Molecular Biology and Evolution 36, no. 11 (2019): 2481–97. http://dx.doi.org/10.1093/molbev/msz161.

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Abstract Ecological speciation has become a popular model for the development and maintenance of reproductive isolation in closely related sympatric pairs of species or ecotypes. An implicit assumption has been that such pairs originate (possibly with gene flow) from a recent, genetically homogeneous ancestor. However, recent genomic data have revealed that currently sympatric taxa are often a result of secondary contact between ancestrally allopatric lineages. This has sparked an interest in the importance of initial hybridization upon secondary contact, with genomic reanalysis of classic exa

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Bertl, Johanna, Harald Ringbauer, and Michael G. B. Blum. "Can secondary contact following range expansion be distinguished from barriers to gene flow?" PeerJ 6 (October 1, 2018): e5325. http://dx.doi.org/10.7717/peerj.5325.

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Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough informa

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André, Thiago, Chodon Sass, Roxana Yockteng, Tânia Wendt, Clarisse Palma-Silva, and Chelsea D. Specht. "Deep genetic structure of a ground-herb along contrasting environments of seasonally dry understories in Amazonia and Cerrado as revealed from targeted genomic sequencing." Botanical Journal of the Linnean Society 199, no. 1 (2021): 196–209. http://dx.doi.org/10.1093/botlinnean/boab072.

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Abstract Central South America primarily comprises seasonally dry tropical domains, where a sharp rainy season defines phenological and yearly growth patterns. Here we examine if the genetic structure of the understorey ground-herb Chamaecostus subsessilis species complex, from South American seasonally dry forests, is defined by intrinsic contrasting environments of the Cerrado and southern Amazonia. We analysed a dataset of c. 20 kb of sequence data from targeted capture high-throughput sequencing using PCR-generated probes. We used an admixture model and population pairwise FST comparisons

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Zampakas, Konstantinos, Maria V. Alvanou, Anastasia Kalapouti, et al. "Genetic Profile of Greek Indigenous Honey Bee Populations, Local Extinctions, Geographical Distinction, and Patterns, by Using mtDNA COI and Nuclear CSD Gene Analysis Markers." Journal of Zoological Systematics and Evolutionary Research 2024 (May 9, 2024): 1–13. http://dx.doi.org/10.1155/2024/5466016.

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Evaluation and conservation of local genetic resources of the domestic honey bee populations is important, especially in regions with high diversity levels as well as high honey bee colony density. Greece is rich in honey bee biodiversity, hosting several subspecies, with the status of them being, though, doubtful. The purpose of the present study was to investigate the genetic relationships of both stationary and movable honey bee populations, originating from many location throughout Greece. Two molecular markers were utilized, namely, the conserved mitochondrial COI gene and the highly vari

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Basler, Ryan. "Diversity ofFusariumspecies isolated from UK forage maize and the population structure ofF. graminearumfrom maize and wheat." PeerJ 4 (June 21, 2016): e2143. http://dx.doi.org/10.7717/peerj.2143.

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Pre-harvest contamination of forage maize by mycotoxin producingFusariumspecies was investigated in the UK in 2011 and 2012. A total of 15Fusariumspecies were identified from a collection of 1,761Fusariumisolates recovered from maize stalks and kernels. This study characterized the diversity ofFusariumspecies present in forage maize in the UK. The predominant species detected wereF. graminearum(32.9%) andF. culmorum(34.1%). Along with those species;F. avenacem, F. cerealis, F. equiseti, F. langsethiae, F. napiforme, F. oxysporum, F. poae, F. proliferatum, F. scripi, F. solani, F. subglutinans,

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Xia, Qijing, and Yongcheng Ji. "Study on Frost Resistance of Recycled Rubber Straw Concrete Using Particle Swarm Optimization Enhanced Artificial Neural Networks." Polymers 16, no. 22 (2024): 3191. http://dx.doi.org/10.3390/polym16223191.

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Rubber particles and straw powder were used to prepare recycled rubber straw concrete, and the freeze–thaw test was conducted on the recycled rubber straw concrete using the quick-freezing method. The frost resistance of the recycled rubber straw concrete was evaluated by determining the relative dynamic modulus of elasticity, the rate of mass loss, and the flexural strength of the recycled rubber straw concrete in the process of freezing and thawing. SEM was used to observe the microstructure of the recycled rubber straw concrete after the freezing and thawing process. SEM observed the micros

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Putz, Austin M., Patrick Charagu, and Abe Huisman. "99 Breed authentication of five lines comparing Structure, Admixture, and an allele frequency method." Journal of Animal Science 98, Supplement_3 (2020): 25. http://dx.doi.org/10.1093/jas/skaa054.044.

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Abstract Two commonly used population structure software packages are freely available for breed authentication, Structure and Admixture. Structure uses a Bayesian approach to model population structure, while Admixture uses a frequentist approach. More recently, an allele frequency method has been updated to use quadratic programming to constrain the multiple linear regression coefficients of the regression of genotype count (divided by two) on the matrix of allele frequencies for each known breed or line. This constraint forced coefficients to sum to one and be greater than or equal to 0 and

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Diaz-Lacava, A. N., M. Walier, D. Holler, et al. "Genetic Geostatistical Framework for Spatial Analysis of Fine-Scale Genetic Heterogeneity in Modern Populations: Results from the KORA Study." International Journal of Genomics 2015 (2015): 1–15. http://dx.doi.org/10.1155/2015/693193.

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Aiming to investigate fine-scale patterns of genetic heterogeneity in modern humans from a geographic perspective, a genetic geostatistical approach framed within a geographic information system is presented. A sample collected for prospective studies in a small area of southern Germany was analyzed. None indication of genetic heterogeneity was detected in previous analysis. Socio-demographic and genotypic data of German citizens were analyzed (212 SNPs;n=728). Genetic heterogeneity was evaluated with observed heterozygosity (HO). Best-fitting spatial autoregressive models were identified, usi

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Zhang, Xinjun, Bernard Kim, Kirk E. Lohmueller, and Emilia Huerta-Sánchez. "The Impact of Recessive Deleterious Variation on Signals of Adaptive Introgression in Human Populations." Genetics 215, no. 3 (2020): 799–812. http://dx.doi.org/10.1534/genetics.120.303081.

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Admixture with archaic hominins has altered the landscape of genomic variation in modern human populations. Several gene regions have been identified previously as candidates of adaptive introgression (AI) that facilitated human adaptation to specific environments. However, simulation-based studies have suggested that population genetic processes other than adaptive mutations, such as heterosis from recessive deleterious variants private to populations before admixture, can also lead to patterns in genomic data that resemble AI. The extent to which the presence of deleterious variants affect t

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Yang, Xiong, Kai Yuan, Xumin Ni, Ying Zhou, Wei Guo, and Shuhua Xu. "AdmixSim: A Forward-Time Simulator for Various Complex Scenarios of Population Admixture." Frontiers in Genetics 11 (December 3, 2020). http://dx.doi.org/10.3389/fgene.2020.601439.

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Background: Population admixture is a common phenomenon in humans, animals, and plants, and it plays a very important role in shaping individual genetic architecture and population genetic diversity. Inference of population admixture, however, is very challenging and typically relies on in silico simulation. We are aware of the lack of a computerized tool for such a purpose. A simulator capable of generating data under various complex admixture scenarios would facilitate the study of recombination, linkage disequilibrium, ancestry tracing, and admixture dynamics in admixed populations. We desc

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Rogers, Alan R. "Legofit: estimating population history from genetic data." BMC Bioinformatics 20, no. 1 (2019). http://dx.doi.org/10.1186/s12859-019-3154-1.

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Abstract Background Our current understanding of archaic admixture in humans relies on statistical methods with large biases, whose magnitudes depend on the sizes and separation times of ancestral populations. To avoid these biases, it is necessary to estimate these parameters simultaneously with those describing admixture. Genetic estimates of population histories also confront problems of statistical identifiability: different models or different combinations of parameter values may fit the data equally well. To deal with this problem, we need methods of model selection and model averaging,

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Agranat-Tamir, Lily, Jazlyn A. Mooney, and Noah A. Rosenberg. "Counting the genetic ancestors from source populations in members of an admixed population." GENETICS, January 30, 2024. http://dx.doi.org/10.1093/genetics/iyae011.

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Abstract In a genetically admixed population, admixed individuals possess genealogical and genetic ancestry from multiple source groups. Under a mechanistic model of admixture, we study the number of distinct ancestors from the source populations that the admixture represents. Combining a mechanistic admixture model with a recombination model that describes the probability that a genealogical ancestor is a genetic ancestor, for a member of a genetically admixed population, we count genetic ancestors from the source populations—those genealogical ancestors from the source populations who contri

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Wang, Yonghui, Zicheng Zhao, Xinyao Miao, et al. "eSMC: a statistical model to infer admixture events from individual genomics data." BMC Genomics 23, S4 (2022). http://dx.doi.org/10.1186/s12864-022-09033-2.

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Abstract Background Inferring historical population admixture events yield essential insights in understanding a species demographic history. Methods are available to infer admixture events in demographic history with extant genetic data from multiple sources. Due to the deficiency in ancient population genetic data, there lacks a method for admixture inference from a single source. Pairwise Sequentially Markovian Coalescent (PSMC) estimates the historical effective population size from lineage genomes of a single individual, based on the distribution of the most recent common ancestor between

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Wiens, Ben J., and Jocelyn P. Colella. "That's Not a Hybrid: How to Distinguish Patterns of Admixture and Isolation By Distance." Molecular Ecology Resources, October 28, 2024. http://dx.doi.org/10.1111/1755-0998.14039.

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ABSTRACTDescribing naturally occurring genetic variation is a fundamental goal of molecular phylogeography and population genetics. Popular methods for this task include STRUCTURE, a model‐based algorithm that assigns individuals to genetic clusters, and principal component analysis (PCA), a parameter‐free method. The ability of STRUCTURE to infer mixed ancestry makes it popular for documenting natural hybridisation, which is of considerable interest to evolutionary biologists, given that such systems provide a window into the speciation process. Yet, STRUCTURE can produce misleading results w

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Brugger, Steven W., and Mary F. Davis. "Influence of Admixture on Phenotypes." Current Protocols 3, no. 12 (2023). http://dx.doi.org/10.1002/cpz1.953.

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AbstractIndividuals of European descent have historically been the focus of genetic studies and possess relatively homogenous genomes. As a result, analytical methods have been developed and optimized with such genomes in mind. African‐descent and Latino individuals generally possess genomes of greater architectural complexity due to mosaic genomic ancestry, which can extensively and intricately impact phenotypic expression. As such, genetic analyses of admixed individuals require that genetic admixture be quantified to accurately model the impact of genetic variation on phenotypic expression.

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Flegontova, Olga, Ulaş Işıldak, Eren Yüncü, et al. "Performance of qpAdm-based screens for genetic admixture on admixture-graph-shaped histories and stepping-stone landscapes." GENETICS, April 2, 2025. https://doi.org/10.1093/genetics/iyaf047.

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Abstract qpAdm is a statistical tool that is often used for testing large sets of alternative admixture models for a target population. Despite its popularity, qpAdm remains untested on two-dimensional stepping-stone landscapes and in situations with low pre-study odds (low ratio of true to false models). We tested high-throughput qpAdm protocols with typical properties such as number of source combinations per target, model complexity, model feasibility criteria, etc. Those protocols were applied to admixture-graph-shaped and stepping-stone simulated histories sampled randomly or systematical

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Mooney, Jazlyn A., Lily Agranat-Tamir, Jonathan K. Pritchard, and Noah A. Rosenberg. "On the number of genealogical ancestors tracing to the source groups of an admixed population." GENETICS 224, no. 3 (2023). http://dx.doi.org/10.1093/genetics/iyad079.

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Abstract Members of genetically admixed populations possess ancestry from multiple source groups, and studies of human genetic admixture frequently estimate ancestry components corresponding to fractions of individual genomes that trace to specific ancestral populations. However, the same numerical ancestry fraction can represent a wide array of admixture scenarios within an individual’s genealogy. Using a mechanistic model of admixture, we consider admixture genealogically: how many ancestors from the source populations does the admixture represent? We consider African-Americans, for whom con

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Gebrehiwot, N. Z., E. M. Strucken, H. Aliloo, K. Marshall, and J. P. Gibson. "The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data." BMC Genomics 21, no. 1 (2020). http://dx.doi.org/10.1186/s12864-020-07270-x.

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Abstract Background Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds. Methods Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred catt

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Chuan-Chao, Wang. "Fine-scale population admixture landscape of Tai-Kadai-speaking Maonan in Southwest China inferred from genome-wide SNP data." November 15, 2021. https://doi.org/10.5281/zenodo.5701604.

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Guizhou province harbored extensive ethnolinguistic and cultural diversity and was occupied by Sino-Tibetan-, Hmong-Mien- and Tai-Kadai-speaking populations. However, previous genetic analyses mainly focused on the genetic admixture history of the former two linguistic groups, the admixture history of Tai-Kadai-speaking populations in Guizhou needed to be further characterized. Thus, we genotyped genome-wide SNP data from 41 Tai-Kadai-speaking Maonan people and make a comprehensive population genetic analysis to explore their genetic origin and admixture history based on the sharing alleles an

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