Geographical and linguistic structure in the people of Kenya demonstrated using 21 autosomal STRs

The software package ML-RELATE [Kalinowski S.T. Wagner A.P. Taper M.L. ML-Relate: a computer program for maximum likelihood estimation of relatedness and relationship.], in conjunction with Yfiler Plus profiling (data not shown) and ancestry information, was used to screen for any undeclared brothers within the dataset. STRAF 1.0.5 [STRAF—a convenient online tool for STR data evaluation in forensic genetics.] was used to calculate allele frequencies, Random Match Probability (PM), Power of Discrimination (PD), Power of Exclusion (PE), Typical Paternity Index (TPI), Genetic Diversity (GD, also equivalent to expected heterozygosity) and observed heterozygosity. Arlequin v 3.5.2.2 [Excoffier L. Lischer H.E. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.] was used to test Hardy-Weinberg equilibrium, to calculate expected heterozygosity, and to perform AMOVA on genotypes and RST genetic distance matrices to investigate genetic diversity within and between the eight provinces and five language groups. Genetic distances were visualised using Principal Coordinates Analysis (PCoA) within the GenAlEx suite [GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and researc.] for language groups, provinces and counties within Kenya using the full GlobalFiler profiles. Distances were calculated from the Pairwise Population Matrix of Mean Population Codominant Genotypic Genetic Distances and the scaling on the axes corresponds to the resultant Eigenvalues. Pairwise FST values calculated with POPTREE2 [Takezaki N. Nei M. Tamura K. POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface.] were based upon allele frequencies at the 15 STR loci targeted by the AmpFlSTR Identifiler kit (CSF1PO, D13S317, D16S539, D18S51, D19S433, D21S11, D2S1338, D3S1358, D5S818, D7S820, D8S1179, FGA, THO1, TPOX and vWA) that were shared with other African population studies. The FST values were also used to generate multidimensional scaling (MDS) plots with the (MASS) package [Venables W.N. Ripley B.D. ] in the R library. The data generated here were compared with data from other populations as follows: African Americans in USA N = 543 [Moretti T.R. Baumstark A.L. Defenbaugh D.A. Keys K.M. Smerick J.B. Budowle B. Validation of short tandem repeats (STRs) for forensic usage: performance testing of fluorescent multiplex STR systems and analysis of authentic and simulated forensic samples.], amaXhosa and amaZulu in South Africa N = 120 and N = 100 respectively [Ristow P.G. Cloete K.W. D’Amato M.E. GlobalFiler((R)) express DNA amplification kit in South Africa: extracting the past from the present.]; Angolans in Cabinda N = 152 [Guerreiro S. Ribeiro T. Porto M.J. Carneiro de Sousa M.J. Dario P. Characterization of GlobalFiler loci in Angolan and Guinean populations inhabiting Southern Portugal.]; Botswana N = 990 [Tau T. Wally A. Fanie T.P. Ngono G.L. Mpoloka S.W. Davison S. D’Amato M.E. Genetic variation and population structure of Botswana populations as identified with AmpFLSTR Identifiler short tandem repeat (STR) loci.]; Equatorial Guineans in Madrid N = 134 [Alves C. Gusmao L. Lopez-Parra A.M. Soledad Mesa M. Amorim A. Arroyo-Pardo E. STR allelic frequencies for an African population sample (Equatorial Guinea) using AmpFlSTR Identifiler and Powerplex 16 kits.]; Guinea Bissauans in Portugal N = 70 [Guerreiro S. Ribeiro T. Porto M.J. Carneiro de Sousa M.J. Dario P. Characterization of GlobalFiler loci in Angolan and Guinean populations inhabiting Southern Portugal.]; Kenya N = 150 [MSc Thesis: Kenya Population Forensic Data on a Sixteen Loci Microsatellite DNA System.]; Mozambique N = 42 [Alves C. Gusmao L. Damasceno A. Soares B. Amorim A. Contribution for an African autosomic STR database (AmpF/STR Identifiler and Powerplex 16 System) and a report on genotypic variations.]; Namibian Ovambo (Bantu) N = 195 [Muro T. Fujihara J. Imamura S. Nakamura H. Yasuda T. Takeshita H. Allele frequencies for 15 STR loci in Ovambo population using AmpFlSTR Identifiler Kit.]; Rwandan Tutsi (Bantu) N = 124 [Regueiro M. Carril J.C. Pontes M.L. Pinheiro M.F. Luis J.R. Caeiro B. Allele distribution of 15 PCR-based loci in the Rwanda Tutsi population by multiplex amplification and capillary electrophoresis.]; Saudi Arabians N = 523 [Khubrani Y.M. Wetton J.H. Jobling M.A. Analysis of 21 autosomal STRs in Saudi Arabia reveals population structure and the influence of consanguinity.]; Somalians resident in Denmark N = 404 [Tomas C. Mogensen H.S. Friis S.L. Hallenberg C. Stene M.C. Morling N. Concordance study and population frequencies for 16 autosomal STRs analyzed with PowerPlex(R) ESI 17 and AmpFlSTR(R) NGM SElect in Somalis, Danes and Greenlanders.]; Sudan – N = 498 [Babiker H.M. Schlebusch C.M. Hassan H.Y. Jakobsson M. Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR) loci.]; Meru (Bantu) from Northern Tanzania N = 172 [

W. Charoenchote, AmpFℓSTR® Identifiler™ STR Allele Frequencies and PowerPlex® Y-STR Haplotype Frequencies of the Meru Population of Northern Tanzania, California State University, Sacramento, 2008.

]; Ugandan Karamoja N = 218 [Gomes V. Sanchez-Diz P. Alves C. Gomes I. Amorim A. Carracedo A. Gusmao L. Population data defined by 15 autosomal STR loci in Karamoja population (Uganda) using AmpF/STR Identifiler kit.].

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