2022
North Asian population relationships in a global context
Kidd KK, Evsanaa B, Togtokh A, Brissenden JE, Roscoe JM, Dogan M, Neophytou PI, Gurkan C, Bulbul O, Cherni L, Speed WC, Murtha M, Kidd JR, Pakstis AJ. North Asian population relationships in a global context. Scientific Reports 2022, 12: 7214. PMID: 35508562, PMCID: PMC9068624, DOI: 10.1038/s41598-022-10706-x.Peer-Reviewed Original ResearchConceptsPopulation genetic studiesPhylogenetic tree analysisAutosomal variationSex chromosomesGenetic variationMost populationsGenetic studiesExtensive variationPopulation relationshipsGenome ConsortiumK projectNorth AsiaRefinement of analysisAsian ethnic groupsGlobal contextAutosomesTree analysisChromosomesAsia populationEthnic groupsMitochondriaPopulationMicrohaplotypesSmall subsetNative Americans
2012
Reconstructing Native American population history
Reich D, Patterson N, Campbell D, Tandon A, Mazieres S, Ray N, Parra MV, Rojas W, Duque C, Mesa N, García LF, Triana O, Blair S, Maestre A, Dib JC, Bravi CM, Bailliet G, Corach D, Hünemeier T, Bortolini MC, Salzano FM, Petzl-Erler ML, Acuña-Alonzo V, Aguilar-Salinas C, Canizales-Quinteros S, Tusié-Luna T, Riba L, Rodríguez-Cruz M, Lopez-Alarcón M, Coral-Vazquez R, Canto-Cetina T, Silva-Zolezzi I, Fernandez-Lopez JC, Contreras AV, Jimenez-Sanchez G, Gómez-Vázquez MJ, Molina J, Carracedo Á, Salas A, Gallo C, Poletti G, Witonsky DB, Alkorta-Aranburu G, Sukernik RI, Osipova L, Fedorova SA, Vasquez R, Villena M, Moreau C, Barrantes R, Pauls D, Excoffier L, Bedoya G, Rothhammer F, Dugoujon JM, Larrouy G, Klitz W, Labuda D, Kidd J, Kidd K, Di Rienzo A, Freimer NB, Price AL, Ruiz-Linares A. Reconstructing Native American population history. Nature 2012, 488: 370-374. PMID: 22801491, PMCID: PMC3615710, DOI: 10.1038/nature11258.Peer-Reviewed Original ResearchStructural diversity and African origin of the 17q21.31 inversion polymorphism
Steinberg KM, Antonacci F, Sudmant PH, Kidd JM, Campbell CD, Vives L, Malig M, Scheinfeldt L, Beggs W, Ibrahim M, Lema G, Nyambo TB, Omar SA, Bodo JM, Froment A, Donnelly MP, Kidd KK, Tishkoff SA, Eichler EE. Structural diversity and African origin of the 17q21.31 inversion polymorphism. Nature Genetics 2012, 44: 872-880. PMID: 22751100, PMCID: PMC3408829, DOI: 10.1038/ng.2335.Peer-Reviewed Original ResearchCrohn's Disease Risk Alleles on the NOD2 Locus Have Been Maintained by Natural Selection on Standing Variation
Nakagome S, Mano S, Kozlowski L, Bujnicki JM, Shibata H, Fukumaki Y, Kidd JR, Kidd KK, Kawamura S, Oota H. Crohn's Disease Risk Alleles on the NOD2 Locus Have Been Maintained by Natural Selection on Standing Variation. Molecular Biology And Evolution 2012, 29: 1569-1585. PMID: 22319155, PMCID: PMC3697811, DOI: 10.1093/molbev/mss006.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SubstitutionCrohn DiseaseGene FrequencyGenetic Predisposition to DiseaseGenotyping TechniquesHaplotypesHumansModels, GeneticModels, MolecularNod2 Signaling Adaptor ProteinPhylogenyPolymorphism, Single NucleotideProtein Structure, SecondaryProtein Structure, TertiaryRisk FactorsSelection, GeneticSequence Analysis, DNAConceptsDisease risk allelesNatural selectionCD risk allelesGenome-wide association studiesClassical linkage analysisMost recent common ancestorPhylogenetic network analysisRecent common ancestorNOD2 proteinProtein structural predictionRecent genome-wide association studiesHigh-frequency haplotypesSerious conformational changesEuropean populationsAmino acid substitutionsRisk allelesStanding variationDeleterious haplotypesEvolutionary studiesCoalescent simulationsCommon ancestorGenomic regionsNon-European populationsEntire genomeDiploid individuals
2011
Single nucleotide polymorphisms and haplotypes in Native American populations
Kidd JR, Friedlaender F, Pakstis AJ, Furtado M, Fang R, Wang X, Nievergelt CM, Kidd KK. Single nucleotide polymorphisms and haplotypes in Native American populations. American Journal Of Biological Anthropology 2011, 146: 495-502. PMID: 21913176, PMCID: PMC3658315, DOI: 10.1002/ajpa.21560.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsNative American populationsAutosomal markersModern Native American populationsNucleotide polymorphismsOld World populationsEvolutionary relationshipsAmerican populationDifferent small setsDNA polymorphismsEurasian originAncestry inferenceMultiple populationsPolymorphismLarge comprehensive datasetAscertainment biasesNew WorldSmall independent setsMarkersComprehensive datasetClose relationshipPopulationHaplotypesNew informationThe Molecular Origin and Consequences of Escape from miRNA Regulation by HLA-C Alleles
O'hUigin C, Kulkarni S, Xu Y, Deng Z, Kidd J, Kidd K, Gao X, Carrington M. The Molecular Origin and Consequences of Escape from miRNA Regulation by HLA-C Alleles. American Journal Of Human Genetics 2011, 89: 424-431. PMID: 21907013, PMCID: PMC3169826, DOI: 10.1016/j.ajhg.2011.07.024.Peer-Reviewed Original Research
2010
The Distribution and Most Recent Common Ancestor of the 17q21 Inversion in Humans
Donnelly MP, Paschou P, Grigorenko E, Gurwitz D, Mehdi SQ, Kajuna SL, Barta C, Kungulilo S, Karoma NJ, Lu RB, Zhukova OV, Kim JJ, Comas D, Siniscalco M, New M, Li P, Li H, Manolopoulos VG, Speed WC, Rajeevan H, Pakstis AJ, Kidd JR, Kidd KK. The Distribution and Most Recent Common Ancestor of the 17q21 Inversion in Humans. American Journal Of Human Genetics 2010, 86: 161-171. PMID: 20116045, PMCID: PMC2820164, DOI: 10.1016/j.ajhg.2010.01.007.Peer-Reviewed Original Research
2001
Modern African Ape Populations as Genetic and Demographic Models of the Last Common Ancestor of Humans, Chimpanzees, and Gorillas
Jensen-Seaman M, Deinard A, Kidd K. Modern African Ape Populations as Genetic and Demographic Models of the Last Common Ancestor of Humans, Chimpanzees, and Gorillas. Journal Of Heredity 2001, 92: 475-480. PMID: 11948214, DOI: 10.1093/jhered/92.6.475.Peer-Reviewed Original ResearchConceptsLast common ancestorEffective population sizeNucleotide diversityCommon ancestorStrong female philopatryStrong geographic structuringPopulation sizeHuman evolutionary historyNuclear lociGeographic structuringModern humansFemale philopatryEvolutionary historyAncestral populationsGorilla lineageMolecular dataNuclear DNAClose relativesDemographic modelsAfrican ape speciesApe populationsApe speciesNatal groupSpeciesDispersal systemMitochondrial DNA variation and biogeography of eastern gorillas
Jensen‐Seaman M, Kidd K. Mitochondrial DNA variation and biogeography of eastern gorillas. Molecular Ecology 2001, 10: 2241-2247. PMID: 11555266, DOI: 10.1046/j.0962-1083.2001.01365.x.Peer-Reviewed Original ResearchMeSH KeywordsAfricaAnimalsDNA, MitochondrialGenetic VariationGorilla gorillaHaplotypesHumansPhylogenyConceptsMitochondrial DNA variationDNA variationEastern gorillasD-loop haplotypesFirst hypervariable segmentPopulation bottlenecksDistinct cladesGenetic diversityControl regionD-loopHypervariable segmentCladeLast Glacial MaximumGorillasForest reductionHaplotypesGlacial MaximumBiogeographyEast AfricaGlobal coolingDiversityMutationsLow levelsVariationFragmentation
2000
Worldwide Genetic Analysis of the CFTR Region
Mateu E, Calafell F, Lao O, Bonné-Tamir B, Kidd J, Pakstis A, Kidd K, Bertranpetit J. Worldwide Genetic Analysis of the CFTR Region. American Journal Of Human Genetics 2000, 68: 103-117. PMID: 11104661, PMCID: PMC1234903, DOI: 10.1086/316940.Peer-Reviewed Original ResearchConceptsCystic fibrosis transmembrane conductance regulator (CFTR) geneShort tandem repeat polymorphismsSingle nucleotide polymorphismsLinkage disequilibriumHaplotype backgroundTransmembrane conductance regulator geneWorldwide population samplesModern human populationsHaplotype variationHigh heterozygosityCFTR regionOut of AfricaRegulator geneSevere genetic disorderGenetic analysisMutation rateDifferent haplotypesAncestral haplotypeAllele sizeOutcome of differencesSNP haplotypesLD analysisNon-AfricansHaplotypesLD measuresSequence variability and candidate gene analysis in complex disease: association of µ opioid receptor gene variation with substance dependence
Hoehe M, Köpke K, Wendel B, Rohde K, Flachmeier C, Kidd K, Berrettini W, Church G. Sequence variability and candidate gene analysis in complex disease: association of µ opioid receptor gene variation with substance dependence. Human Molecular Genetics 2000, 9: 2895-2908. PMID: 11092766, DOI: 10.1093/hmg/9.19.2895.Peer-Reviewed Original ResearchConceptsComplex genotype-phenotype relationshipsGenotype-phenotype relationshipsCandidate genesSequence variabilitySequence variantsGene sequence informationDNA sequence variationCandidate gene analysisSpecific sequence variantsPrime candidate geneCombination of variantsSequence comparisonSequence variationSequence informationHuman mu-opioid receptor geneDifferent haplotypesGene analysisGenesComplex diseasesReceptor geneOpioid receptor geneHaplotypesGene variationMultiple individualsModel systemShort Tandem-Repeat Polymorphism/Alu Haplotype Variation at the PLAT Locus: Implications for Modern Human Origins
Tishkoff S, Pakstis A, Stoneking M, Kidd J, Destro-Bisol G, Sanjantila A, Lu R, Deinard A, Sirugo G, Jenkins T, Kidd K, Clark A. Short Tandem-Repeat Polymorphism/Alu Haplotype Variation at the PLAT Locus: Implications for Modern Human Origins. American Journal Of Human Genetics 2000, 67: 901-925. PMID: 10986042, PMCID: PMC1287905, DOI: 10.1086/303068.Peer-Reviewed Original ResearchMeSH KeywordsAfrica South of the SaharaAllelesAlu ElementsAnimalsChromosomes, Human, Pair 8Dinucleotide RepeatsEvolution, MolecularGene FrequencyGenetic VariationHaplotypesHominidaeHumansLinkage DisequilibriumMicronesiaPapua New GuineaPhylogenyPolymorphism, GeneticSequence DeletionTandem Repeat SequencesConceptsNon-African populationsHaplotype variationGene flowLinkage disequilibriumShort tandem repeat polymorphismsHaplotype diversityPLAT locusLarge effective population sizesAncient gene flowEffective population sizeDinucleotide short tandem repeat polymorphismsRecent common ancestryAlu insertion/deletion polymorphismHuman evolutionary historyDiverse human populationsModern human originsEvolutionary historyCommon ancestryAfrican populationsPopulation substructureAlu elementsPolymorphic Alu elementsPopulation sizeRare haplotypesDinucleotide repeatsHaplotypes and Linkage Disequilibrium at the Phenylalanine Hydroxylase Locus, PAH, in a Global Representation of Populations
Kidd J, Pakstis A, Zhao H, Lu R, Okonofua F, Odunsi A, Grigorenko E, Tamir B, Friedlaender J, Schulz L, Parnas J, Kidd K. Haplotypes and Linkage Disequilibrium at the Phenylalanine Hydroxylase Locus, PAH, in a Global Representation of Populations. American Journal Of Human Genetics 2000, 66: 1882-1899. PMID: 10788337, PMCID: PMC1378054, DOI: 10.1086/302952.Peer-Reviewed Original Research
1999
Evolution of the HOXB6 intergenic region: Motif conservation at the lateral plate mesoderm (LPM) enhancer element
Deinard A, Dorit R, Castiglione C, Jiang Z, Becker D, Ruddle F, Schugart K, Kidd K. Evolution of the HOXB6 intergenic region: Motif conservation at the lateral plate mesoderm (LPM) enhancer element. Journal Of Experimental Zoology 1999, 285: 170-176. PMID: 10440728, DOI: 10.1002/(sici)1097-010x(19990815)285:2<170::aid-jez9>3.0.co;2-j.Peer-Reviewed Original ResearchEvolution of a HOXB6 intergenic region within the great apes and humans
Deinard A, Kidd K. Evolution of a HOXB6 intergenic region within the great apes and humans. Journal Of Human Evolution 1999, 36: 687-703. PMID: 10330333, DOI: 10.1006/jhev.1999.0298.Peer-Reviewed Original ResearchConceptsCommon ancestorGenetic variationGenetic dataIntraspecific genetic variationHomo-Pan cladeGreat apesNuclear lociGreat ape speciesMolecular evolutionIntraspecific dataPhylogenetic reconstructionIntergenic regionIntraspecific variationDNA sequencesNucleotide substitutionsGenetic polymorphismsHomo-PanPygmy chimpanzeesApe speciesCommon chimpanzeesCladeHomo sapiens sapiensAncestorGorillasLoci
1998
Hominoid phylogeny: inferences from a sub-terminal minisatellite analyzed by repeat expansion detection (RED)
Deinard A, Sirugo G, Kidd K. Hominoid phylogeny: inferences from a sub-terminal minisatellite analyzed by repeat expansion detection (RED). Journal Of Human Evolution 1998, 35: 313-7. PMID: 9749409.Peer-Reviewed Original Research
1992
DNA sequence polymorphism within hominoid species exceeds the number of phylogenetically informative characters for a HOX2 locus.
Ruano G, Rogers J, Ferguson-Smith A, Kidd K. DNA sequence polymorphism within hominoid species exceeds the number of phylogenetically informative characters for a HOX2 locus. Molecular Biology And Evolution 1992, 9: 575-586. PMID: 1352841, DOI: 10.1093/oxfordjournals.molbev.a040743.Peer-Reviewed Original ResearchConceptsSeparate speciation eventsDNA sequence polymorphismsMaximum parsimony methodsBase pair differencesDenaturing gradient gelGene treesSpeciation eventsSpecies clustersBase pair substitutionsPhylogenetic treeInformative charactersComplete sequenceSequence polymorphismsHominoid speciesSpecies variabilityDifferent allelesG. gorillaSpeciesP. troglodytesAllelesGradient gelsGorillasSequenceTreesGenus
1991
Study of an additional 58 DNA markers in five human populations from four continents.
Bowcock A, Hebert J, Mountain J, Kidd J, Rogers J, Kidd K, Cavalli-Sforza L. Study of an additional 58 DNA markers in five human populations from four continents. Gene Geography 1991, 5: 151-73. PMID: 1841601.Peer-Reviewed Original Research