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SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations

Alexis Dereeper, Felix Homa, Gwendoline Andres, Guilhem Sempere, Gautier Sarah, Yann Hueber, Jean-François Dufayard, Manuel Ruiz
2015 Nucleic Acids Research  
proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density.  ...  SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels.  ...  ACKNOWLEDGEMENTS We thank Bertrand Pitollat who maintains the computing facilities (web servers and HPC). We are grateful to people that interact regularly for the improvements of the system.  ... 
doi:10.1093/nar/gkv351 pmid:26040700 pmcid:PMC4489301 fatcat:bwzcwxw53jgjbfqykr7rvgsf7m

Understanding the origin of species with genome-scale data: modelling gene flow

Vitor Sousa, Jody Hey
2013 Nature reviews genetics  
Acknowledgements This work was supported by grants from the US National Science Foundation and the US National Institutes of Health to J.H.  ...  For instance, 60,000 SNPs from 82 dog breeds and wild canids (obtained with SNP arrays) supported a population tree with admixture events (as in FIG. 1c) rather than a pure isolation model 66 (as  ...  Low-coverage (8×) Illumina sequencing of 5 individuals from each species yielded a total of 12.74 million SNPs, and an AFS analysis led to an estimated speciation time of 400,000 years with a low level  ... 
doi:10.1038/nrg3446 pmid:23657479 pmcid:PMC5568773 fatcat:6py54e5jwva3dmbdgscj5fzt5e

SHIPS: Spectral Hierarchical Clustering for the Inference of Population Structure in Genetic Studies

Matthieu Bouaziz, Caroline Paccard, Mickael Guedj, Christophe Ambroise, Thomas Mailund
2012 PLoS ONE  
SHIPS was applied to a set of simulated discrete and admixed datasets and to real SNP datasets, that are data from the HapMap and Pan-Asian SNP consortium.  ...  This method takes genetic data as input to cluster individuals into homogeneous sub-populations and with the use of the gap statistic estimates the optimal number of such sub-populations.  ...  Acknowledgments We thank Marine Jeanmougin for helpful discussions and thank Fabrice Glibert, Gilles Grasseau, Maurice Baudry and Ilya Chumakov for their support.  ... 
doi:10.1371/journal.pone.0045685 pmid:23077494 pmcid:PMC3470591 fatcat:z26x4xta3bbj3l6s3t5jmst3ye

An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes

Yann X C Bourgeois, Ben H Warren
2021 Molecular Ecology  
Characterizing the population history of a species and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy.  ...  Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history.  ...  We also thank Gabriel Renaud and Peter Ralph for suggesting additional methods. AUTH O R CO NTR I B UTI O N YB wrote the first draft of the manuscript and maintained the website.  ... 
doi:10.1111/mec.15989 pmid:34009688 fatcat:q5ctfy5uvzbu7j24s26ai764me

Genetic diversity and effective population sizes of thirteen Indian cattle breeds

Eva M. Strucken, Netsanet Z. Gebrehiwot, Marimuthu Swaminathan, Sachin Joshi, Mohammad Al Kalaldeh, John P. Gibson
2021 Genetics Selection Evolution  
Effective population sizes (Ne) increased during a period post-domestication, notably for Ongole cattle, and then declined during the last 100 generations.  ...  Conclusions The changes in the estimates of effective population size are consistent with domestication from a large native population followed by consolidation into breeds with a more limited population  ...  Dhanikachalam and P. Deshpande to collect and process the samples are gratefully acknowledged.  ... 
doi:10.1186/s12711-021-00640-3 pmid:34074236 fatcat:hmufozzbibbobc67lj5rvzcz3q

Trans-Atlantic exchanges have shaped the population structure of the Lyme disease agent Borrelia burgdorferi sensu stricto

S. Castillo-Ramírez, V. Fingerle, S. Jungnick, R. K. Straubinger, S. Krebs, H. Blum, D. M. Meinel, H. Hofmann, P. Guertler, A. Sing, G. Margos
2016 Scientific Reports  
For example, NGS data has been used to study pathogen evolution within a single patient 1 , transmission chains within a single hospital 2,3 and clonal diversification over time and space 4,5 .  ...  Furthermore, the advent of next-generation sequencing (NGS) has allowed scientists to handle large population samples and to address a variety of biological questions concerning the evolution and ecology  ...  Acknowledgements The study was supported by the Bavarian Ministry for Health and Care and by the German Federal Ministry of Health via the Robert Koch-Institute and its National Reference Laboratories  ... 
doi:10.1038/srep22794 pmid:26955886 pmcid:PMC4783777 fatcat:ipaoyew7qfeqvglj22aiwjouvi

'Mutiny on the Bounty': the genetic history of Norfolk Island reveals extreme gender-biased admixture

Miles C. Benton, Shani Stuart, Claire Bellis, Donia Macartney-Coxson, David Eccles, Joanne E. Curran, Geoff Chambers, John Blangero, Rod A. Lea, Lyn R. Griffiths
2015 Investigative Genetics  
These results comprehensively characterise the unique genderbiased admixture of this genetic isolate and further support the historical records relating to Norfolk Island.  ...  Conclusions: Our results significantly refine previous population genetic studies investigating Polynesian versus Caucasian diversity in the Norfolk Island population and add information that is beneficial  ...  The resultant SNP data were imported to R with haplotype and phylogenetic analysis performed using APE. SNP labelling was performed in accordance with the minimal skeleton Y tree [12] .  ... 
doi:10.1186/s13323-015-0028-9 pmid:26339467 pmcid:PMC4558825 fatcat:b3mqujc3yjfevgi25w2f5xqdxu

A genome wide pattern of population structure and admixture in peninsular Malaysia Malays

Wan Isa Hatin, Ab Rajab Nur-Shafawati, Ali Etemad, Wenfei Jin, Pengfei Qin, Shuhua Xu, Li Jin, Soon-Guan Tan, Pornprot Limprasert, Merican Amir Feisal, Mohammed Rizman-Idid, Bin Alwi Zilfalil
2014 The HUGO Journal  
We also have included in the analysis 12 other study populations from Thailand, Indonesia, China, India, Africa and Orang Asli sub-groups in Malay Peninsula, obtained from the Pan Asian SNP Initiative  ...  More than 98% of these northern Malays haplotypes could be found in either Indians or Chinese populations, indicating a highly admixture pattern among populations.  ...  Also, CAS-MPG Partner Institute Computational Biology, Fudan University, Shanghai, China for helping us with the data analysis; and PASNPI Consortium for allowing us to use their genotype data.  ... 
doi:10.1186/s11568-014-0005-z pmid:27090253 fatcat:nncwl6l52zhvbanw5d3xzy4e3i

Genetic Diversity and Signatures of Selection in 15 Chinese Indigenous Dog Breeds Revealed by Genome-Wide SNPs

Qianyong Yang, Hao Chen, Junhua Ye, Chenlong Liu, Rongxing Wei, Congying Chen, Lusheng Huang
2019 Frontiers in Genetics  
The genotyping data of 170K SNP chips in Western dogs were downloaded from the LUPA (a European initiative of canine genome project) database.  ...  Chinese indigenous and Western dog breeds were clearly differentiated into two separate clades revealed by the PCA and NJ-tree.  ...  We used the data set with 128,034 SNPs to estimate genetic differentiation and admixture among 46 populations under 0-5 migration events via TreeMix (v1.13).  ... 
doi:10.3389/fgene.2019.01174 pmid:31803243 pmcid:PMC6872681 fatcat:zdybnfuwwvgklotzyuw6kvk354

Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium

P.-R. Loh, M. Lipson, N. Patterson, P. Moorjani, J. K. Pickrell, D. Reich, B. Berger
2013 Genetics  
We de ne an LDbased three-population test for admixture and identify scenarios in which it can detect admixture events that previous formal tests cannot.  ...  We implement all of these advances in a software package, ALDER, which we validate in simulations and apply to test for admixture among all populations from the Human Genome Diversity Project (HGDP), highlighting  ...  ., J.P. and D.R. are grateful for support from NSF HOMINID grant 1032255 and NIH grant GM100233.  ... 
doi:10.1534/genetics.112.147330 pmid:23410830 pmcid:PMC3606100 fatcat:2ufx2gzhj5cbxdsf7vpj4lo6s4

PPARGC1A Variation Associated With DNA Damage, Diabetes, and Cardiovascular Diseases: The Boston Puerto Rican Health Study

C.-Q. Lai, K. L. Tucker, L. D. Parnell, X. Adiconis, B. Garcia-Bailo, J. Griffith, M. Meydani, J. M. Ordovas
2007 Diabetes  
RESULTS-With respect to urinary 8-OHdG, PPARGC1A variants showed significant association, and PPARGC1A haplotypes exhibited significant association after correction for multiple testing.  ...  CONCLUSIONS-It is plausible that low physical activity combined with risk haplotyes contribute to the high prevalence of type 2 diabetes in this population.  ...  Department of Agriculture Research Service Contracts 53-K06-5-10 and 58-1950-9-001. We thank three anonymous reviewers for corrections and suggestions to improve the manuscript.  ... 
doi:10.2337/db07-1238 pmid:18162502 pmcid:PMC2519884 fatcat:zdxsovw6abg5zhobuevb2peezm

pcadapt: an R package to perform genome scans for selection based on principal component analysis [article]

Keurcien Luu, Eric Bazin, Michael G.B. Blum
2016 bioRxiv   pre-print
Because population structure is ascertained with principal component analysis, the package is fast and works with large-scale data. It can handle missing data and pooled sequencing data.  ...  Because pcadapt handles next-generation sequencing data, it is a valuable tool for data analysis in molecular ecology.  ...  Understanding why BayeScan is severely impacted by admixture is 353 Because 353 NGS data become more and more massive, careful numerical implementation 354 is crucial.  ... 
doi:10.1101/056135 fatcat:zejnwj4xgrhphkxy7isa5zcosi

Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis

Wei Xia, Tingting Luo, Wei Zhang, Annaliese S. Mason, Dongyi Huang, Xiaolong Huang, Wenqi Tang, Yajing Dou, Chunyu Zhang, Yong Xiao
2019 Frontiers in Plant Science  
for genome-wide association analysis.  ...  High-density single nucleotide polymorphisms (SNPs) are used as highly favored makers to analyze genetic diversity and population structure, to construct high-density genetic maps and provide genotypes  ...  Genetic diversity, population structure, and LD were estimated by 1,261,501 newly developed genome-wide SNPs.  ... 
doi:10.3389/fpls.2019.00130 pmid:30809240 pmcid:PMC6380268 fatcat:giq3a5o3unh7ncmsgczhs63lre

Species delimitation in the grey zone: introgression obfuscates phylogenetic inference and species boundaries in a cryptic frog complex (Ranidae: Pulchrana picturata) [article]

Kin Onn Chan, Carl Hutter, Perry Lee Wood, Lee Grismer, Rafe Brown
2019 bioRxiv   pre-print
However, a comprehensive species delimitation framework that considers spatial and genetic population structure, introgression, and the use of species delimitation methods based on parameter estimation  ...  boundaries between populations and species are less clear.  ...  We used default settings for the ABGD analysis and estimated a maximum 230 likelihood phylogeny with IQ-TREE based on the 16S marker, to use as input for the mPTP 231 analysis.  ... 
doi:10.1101/832683 fatcat:eupjkydu6jfrrparlaj2xsuine

The Evolutionary History of New Zealand Deschampsia Is Marked by Long-Distance Dispersal, Endemism, and Hybridization

Zhiqing Xue, Josef Greimler, Ovidiu Paun, Kerry Ford, Michael H. J. Barfuss, Jorge O. Chiapella
2021 Biology  
Both data provided strong evidence for hybridization between D. cespitosa and D. chapmanii.  ...  We used RADseq to test species delimitations, infer a dated species tree, and investigate gene flow patterns between the New Zealand endemics and the D. cespitosa populations of New Zealand, Australia  ...  Acknowledgments: The authors thank Hui Shang (Shanghai, China) and Chang-Gee Jang (Kongju, South-Korea) for help in sampling and Tod F.  ... 
doi:10.3390/biology10101001 pmid:34681100 fatcat:zfwupz23kbej7keo4lwafgsvqi
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