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A parallel adaptive GA for linkage disequilibrium in genomics

L. Vermeulen-Jourdan, C. Dhaenens, E.-G. Talbi
18th International Parallel and Distributed Processing Symposium, 2004. Proceedings.  
In this paper, we treat the linkage disequilibrium, used to discover haplotypes, candidate to explain multi-factorial diseases such as diabetes or obesity, as an optimization problem where a given objective  ...  Results of this study show that exact algorithms are not adapted to this specific problem and lead us to the development of a parallel dedicated adaptive multipopulation genetic algorithm that is able  ...  Therefore, in a linkage disequilibrium study, two SNPs of an haplotype must verify the two following conditions: their 2 by 2 disequilibrium must be less than a thresh- old Ë ½ . the difference between  ... 
doi:10.1109/ipdps.2004.1303165 dblp:conf/ipps/Vermeulen-JourdanDT04 fatcat:j4riyx26onhphmm6iso2wadguu


2005 International Journal of Foundations of Computer Science  
In this article, we model a linkage disequilibrium study (genomic study) as an optimization problem where a given objective function has to be optimized.  ...  Results of this study show that exact algorithms are not adapted to this specific problem and lead us to the development of a parallel dedicated adaptive multipopulation genetic algorithm that is able  ...  This is scheme Linkage disequilibrium study with a parallel adaptive GA 17 Fig. 10 . An example of evolution of mutation rates. 6 of the table.  ... 
doi:10.1142/s0129054105002978 fatcat:56cq3722crbavpahiou5ndqqbe

Short Communication Characterization of 12 microsatellite loci for the Pacific lamprey, Entosphenus tridentatus (Petromyzontidae), and cross-amplification in five other lamprey species

E.K. Spice, T.A. Whitesel, C.T. McFarlane, M.F. Docker
2011 Genetics and Molecular Research  
We optimized 12 polymorphic microsatellite loci for the Pacific lamprey. Three to 13 alleles per locus were observed in a sample of 51 fish collected from the West Fork Illinois River, Oregon.  ...  The Pacific lamprey (Entosphenus tridentatus) is an anadromous fish that is of conservation concern in North America and Asia.  ...  The findings and conclusions in this manuscript are those of the authors and do not necessarily represent the views of the USFWS.  ... 
doi:10.4238/2011.december.22.2 pmid:22194188 fatcat:4z33qulusvfnhnw34ixk7hsdua

Parallel evolution? Microsatellite variation of recently isolated marine and freshwater three-spined stickleback

G. Á. Ólafsdóttir, S. S. Snorrason, M. G. Ritchie
2007 Journal of Fish Biology  
There are indications of strong selection on loci linked to dorsal spine length, providing another potential example of parallel divergence at the genomic level in three-spined stickleback.  ...  test for selection on marine and freshwater three-spined stickleback morphs in Iceland.  ...  Kristja´nsson for help with fieldwork and useful discussions on the Hraunsfjordur system and T. Kristja´nsson for help with fieldwork.  ... 
doi:10.1111/j.1095-8649.2007.01398.x fatcat:wpcevtfzfjc5rotnkx6wo26zme

Natural selection and parallel clinal and seasonal changes in Drosophila melanogaster [article]

Murillo F. Rodrigues, Maria D. Vibranovski, Rodrigo Cogni
2020 bioRxiv   pre-print
Identifying the role of selection in driving latitudinal and seasonal change is not trivial, but one promising approach is to look for parallel clinal and seasonal variation.  ...  We show that there is a genome-wide pattern of clinal variation mirroring seasonal variation, which cannot be explained by linked selection alone.  ...  To test the effect of 223 linkage disequilibrium (LD) in our outlier analyses, we plotted P-values against distance to a 224 top SNP.  ... 
doi:10.1101/2020.03.19.999011 fatcat:jpnzd45jyrhhrmdeimhyl6dxaa

Microsatellite Marker Development and Characterization in the Spotted Babylon, Babylonia areolata (Link, 1807): Detection of Duplicated Loci at High Frequency

Wang Yan
2012 International Journal of Aquaculture  
in the genome.  ...  Four polymorphic microsatellite markers were developed for the spotted babylon, Babylonia areolata, from a microsatellite enriched library.  ...  No linkage disequilibrium was detected among all the loci at p>0.05 (after Bonferroni correction).  ... 
doi:10.5376/ija.2012.02.0002 fatcat:suodd7l5anfi7bcmvoqgzotumi

Eight polymorphic microsatellite markers for the spotted babylon, Babylonia areolata (Buccinidae)

Y. Wang, H. Lu, J. Zheng, K. Long, Y.H. Shi, Z.F. Gu, A.M. Wang
2011 Genetics and Molecular Research  
Eight polymorphic microsatellite markers were developed for this species, from a microsatellite-enriched library.  ...  These microsatellite loci should be useful for future population genetic studies and marker-assisted breeding in this species.  ...  No linkage disequilibrium was detected among all the loci at P > 0.05 (after Bonferroni's correction).  ... 
doi:10.4238/2011.december.21.5 pmid:22194180 fatcat:s3qd6ff6wvbprdphsgfgbfekni

Non-allelic gene conversion enables rapid evolutionary change at multiple regulatory sites encoded by transposable elements

Christopher E Ellison, Doris Bachtrog
2015 eLife  
to a newly formed X chromosome in Drosophila.  ...  These results describe a novel route by which fully functional regulatory elements can arise rapidly from TEs and implicate non-allelic gene conversion as having an important role in accelerating the evolutionary  ...  In 384 contrast, the majority of ISY elements harbor the GA haplotype, but these two alleles are not in perfect linkage 385 disequilibrium among ISY elements.  ... 
doi:10.7554/elife.05899 pmid:25688566 pmcid:PMC4384637 fatcat:w7xp2afygjdltovnaou7dbkpwi

Parallels, nonparallels, and plasticity in population differentiation of threespine stickleback within a lake

2009 Biological Journal of the Linnean Society  
In the present study, we examine parallel morphological, neutral, and potentially adaptive genetic divergence of threespine stickleback inhabiting different habitats within a lake.  ...  The frequent occurrence of parallel phenotypic divergence in similar habitats is often evoked when emphasizing the role of ecology in adaptive radiation and speciation.  ...  ACKNOWLEDGEMENTS We thank Gelen Rodriguez Delgado, Herdís Unnur Valsdóttur, and Daniel Gutierrez Hernandez for assistance in the field and laboratory, and Bjarni Kr.  ... 
doi:10.1111/j.1095-8312.2009.01318.x fatcat:ka4m4cwtmvfk5m3g4yjolo2qki

A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae)

Ryo Kakioka, Tomoyuki Kokita, Hiroki Kumada, Katsutoshi Watanabe, Noboru Okuda
2013 BMC Genomics  
Linkage maps are also useful for comparative genomics in non-model organisms.  ...  The construction of linkage maps is a first step in exploring the genetic basis for adaptive phenotypic divergence in closely related species by quantitative trait locus (QTL) analysis.  ...  This study was partly supported by Grants-in-Aid from the Ministry of Education, Culture, Sports, Science and Technology of Japan (No. 20370009 and No. 23657019) and "Formation of a Strategic Base for  ... 
doi:10.1186/1471-2164-14-32 pmid:23324215 pmcid:PMC3583795 fatcat:idm44dlwd5bg5kl3dahthvxdnq

Transition from environmental to partial genetic sex determination in Daphnia through the evolution of a female-determining incipient W-chromosome [article]

Celine M. O. Reisser, Dominique Fasel, Evelin Hurlimann, Marinela Dukic, Cathy Haag-Liautard, Virginie Thuillier, Yan Galimov, Christoph R Haag
2016 bioRxiv   pre-print
Despite low levels of recombination, the associated region contains signs of historical recombination, suggesting a role for selection acting on several genes thereby maintaining linkage disequilibrium  ...  We now show that the sex-determining genomic region maps to the same low-recombining peri-centromeric region of linkage group 3 (LG3) in three highly divergent populations of D. magna, and spans 3.6 Mb  ...  Skuratov for sampling permits, and David Frey for help with culture maintenance indoors. We thank the Department of Biosystem Science and Engineering of the ETH Zurich, in particular C. Beisel and I.  ... 
doi:10.1101/064311 fatcat:6iqbxz6x7rcltkdtywrlrwc4ri

Specific association of a CLEC16A/KIAA0350 polymorphism with NOD2/CARD15− Crohn's disease patients

Ana Márquez, Jezabel Varadé, Gema Robledo, Alfonso Martínez, Juan Luis Mendoza, Carlos Taxonera, Miguel Fernández-Arquero, Manuel Díaz-Rubio, María Gómez-García, Miguel Angel López-Nevot, Emilio G de la Concha, Javier Martín (+1 others)
2009 European Journal of Human Genetics  
Jezabel Varade´is a fellow and Elena Urcelay works for the Fundación para la Investigación Biome´dica-Hospital Clínico San Carlos.  ...  Acknowledgements Alfonso Martínez holds a research contract of the Spanish Health Ministry (04/00175).  ...  Therefore, either this CLEC16A polymorphism or some other in strong linkage disequilibrium with it would be responsible for the observed effect on NOD2 À CD patients.  ... 
doi:10.1038/ejhg.2009.50 pmid:19337309 pmcid:PMC2986636 fatcat:n67fr3xcvvgv3d5vcnsewjo3xa

Isolation and characterization of 12 microsatellite loci forRhamnus alaternus(Rhamnaceae)

2009 Molecular Ecology Resources  
We detected 69 alleles in 49 individuals genotyped (mean number of alleles per locus was 4.79) in two different populations.  ...  Twelve polymorphic microsatellite loci were developed for Rhamnus alaternus using an enriched-library approach.  ...  Byrne M, Parrish TL, Moran GF (1998) References Acknowledgements We kindly thank the staff of the 'Los Alcornocales' Natural Park for permissions and logistical support in the area.  ... 
doi:10.1111/j.1755-0998.2009.02657.x pmid:21564881 fatcat:tvbh5nj55zhmlg7s5q7wjifvdm

Climate adaptation shaped by subtle to moderate allele frequency shifts in loblolly pine [article]

Amanda R De La Torre, David B Neale
2019 bioRxiv   pre-print
Keywords: GEA, loblolly pine, local adaptation, high-density linkage map  ...  In this study, we test for associations between 87k SNPs, obtained from whole-genome re-sequencing of loblolly pine individuals, and 270 environmental variables and combinations of them.  ...  consensus 830 genetic map for Pinus taeda and Pinus elliottii and extent of linkage disequilibrium in two 831 genotype-phenotype discovery populations of Pinus taeda.  ... 
doi:10.1101/635862 fatcat:3yzrkmadargmlhhrdqydmucra4

Genome-Wide Association Mapping of Anthracnose ( ) Resistance in the U.S. Sorghum Association Panel

Hugo E. Cuevas, Louis K. Prom, Elizabeth A. Cooper, Joseph E. Knoll, Xinzhi Ni
2018 The Plant Genome  
A limited number of resistant accessions are present in the temperateadapted germplasm; other exotic sources of resistance are not currently available for breeding programs. Among 335  ...  linkage disequilibrium with SNP Chr.1: 66786128 (r 2 > 0.70).  ...  of linkage disequilibrium among races (Morris et al., 2013a) , other mutations within Caudatum germplasm that are in linkage disequilibrium with this SNP, and complex resistance-related molecular mechanisms  ... 
doi:10.3835/plantgenome2017.11.0099 pmid:30025025 fatcat:6mio2ui4affr7hs3ywib77lhrq
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