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A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.

Purps J, Siegert S, Willuweit S, Nagy M, Alves C, Salazar R, Angustia SM, Santos LH, Anslinger K, Bayer B, Ayub Q, Wei W, Xue Y, Tyler-Smith C, Bafalluy MB, Martínez-Jarreta B, Egyed B, Balitzki B, Tschumi S, Ballard D, Court DS, Barrantes X, Bäßler G, Wiest T, Berger B, Niederstätter H, Parson W, Davis C, Budowle B, Burri H, Borer U, Koller C, Carvalho EF, Domingues PM, Chamoun WT, Coble MD, Hill CR, Corach D, Caputo M, D'Amato ME, Davison S, Decorte R, Larmuseau MH, Ottoni C, Rickards O, Lu D, Jiang C, Dobosz T, Jonkisz A, Frank WE, Furac I, Gehrig C, Castella V, Grskovic B, Haas C, Wobst J, Hadzic G, Drobnic K, Honda K, Hou Y, Zhou D, Li Y, Hu S, Chen S, Immel UD, Lessig R, Jakovski Z, Ilievska T, Klann AE, García CC, de Knijff P, Kraaijenbrink T, Kondili A, Miniati P, Vouropoulou M, Kovacevic L, Marjanovic D, Lindner I, Mansour I, Al-Azem M, Andari AE, Marino M, Furfuro S, Locarno L, Martín P, Luque GM, Alonso A, Miranda LS, Moreira H, Mizuno N, Iwashima Y, Neto RS, Nogueira TL, Silva R, Nastainczyk-Wulf M, Edelmann J, Kohl M, Nie S, Wang X, Cheng B, Núñez C, Pancorbo MM, Olofsson JK, Morling N, Onofri V, Tagliabracci A, Pamjav H, Volgyi A, Barany G, Pawlowski R, Maciejewska A, Pelotti S, Pepinski W, Abreu-Glowacka M, Phillips C, Cárdenas J, Rey-Gonzalez D, Salas A, Brisighelli F, Capelli C, Toscanini U, Piccinini A, Piglionica M, Baldassarra SL, Ploski R, Konarzewska M, Jastrzebska E, Robino C, Sajantila A, Palo JU, Guevara E, Salvador J, Ungria MC, Rodriguez JJ, Schmidt U, Schlauderer N, Saukko P, Schneider PM, Sirker M, Shin KJ, Oh YN, Skitsa I, Ampati A, Smith TG, Calvit LS, Stenzl V, Capal T, Tillmar A, Nilsson H, Turrina S, De Leo D, Verzeletti A, Cortellini V, Wetton JH, Gwynne GM, Jobling MA, Whittle MR, Sumita DR, Wolańska-Nowak P, Yong RY, Krawczak M, Nothnagel M, Roewer L - Forensic Sci Int Genet (2014)

Bottom Line: Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework.A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study.Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.

View Article: PubMed Central - PubMed

Affiliation: Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany.

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Population structure revealed by PPY23. Interpolated maps depict the first MDS components of pairwise RST values for PPY23. (a) Two-dimensional MDS analysis for the whole data set (129 populations); (b) four-dimensional MDS analysis for populations of European residency and ancestry alone (68 populations). Sample locations are marked in white. Color coding is on an arbitrary rainbow scale that assigns yellow and magenta to the opposite ends of the scale.
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fig0030: Population structure revealed by PPY23. Interpolated maps depict the first MDS components of pairwise RST values for PPY23. (a) Two-dimensional MDS analysis for the whole data set (129 populations); (b) four-dimensional MDS analysis for populations of European residency and ancestry alone (68 populations). Sample locations are marked in white. Color coding is on an arbitrary rainbow scale that assigns yellow and magenta to the opposite ends of the scale.

Mentions: Multidimensional scaling (MDS) analysis was performed based upon linearized RST, separately for the five marker sets, considering either all 129 populations or the 68 populations of European residency and ancestry alone. When assessed for the PPY23 marker panel, Kruskal's stress value showed a clear ‘elbow’ with increasing dimensionality in both population sets, pinpointing an optimal trade-off between explained variation and dimensionality. For the worldwide analysis, two MDS components were optimal with PPY23 whereas four components were deemed optimal for the Europeans-only analysis. Both solutions explained the haplotypic variation well, with R2 = 95.1% in the worldwide analysis and R2 = 99.2% in the Europeans-only analysis. For comparability, MDS analyses for other marker panels were carried out with two or four dimensions, respectively. Haplotypic variation among populations within continental groups was lower than between continental groups (Fig. S3). For all five marker sets, the first MDS component clearly separated the African populations from the non-African populations (Fig. 6a, Fig. S4). Moreover, MDS also confirmed the previously reported East–West separation in the Y-STR haplotype variation [32] in the European analysis (Fig. 6b, Fig. S5). Higher MDS components were strongly dependent upon the respective marker set (Figs. S4–S6) and lacked comparably clear population patterns.


A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.

Purps J, Siegert S, Willuweit S, Nagy M, Alves C, Salazar R, Angustia SM, Santos LH, Anslinger K, Bayer B, Ayub Q, Wei W, Xue Y, Tyler-Smith C, Bafalluy MB, Martínez-Jarreta B, Egyed B, Balitzki B, Tschumi S, Ballard D, Court DS, Barrantes X, Bäßler G, Wiest T, Berger B, Niederstätter H, Parson W, Davis C, Budowle B, Burri H, Borer U, Koller C, Carvalho EF, Domingues PM, Chamoun WT, Coble MD, Hill CR, Corach D, Caputo M, D'Amato ME, Davison S, Decorte R, Larmuseau MH, Ottoni C, Rickards O, Lu D, Jiang C, Dobosz T, Jonkisz A, Frank WE, Furac I, Gehrig C, Castella V, Grskovic B, Haas C, Wobst J, Hadzic G, Drobnic K, Honda K, Hou Y, Zhou D, Li Y, Hu S, Chen S, Immel UD, Lessig R, Jakovski Z, Ilievska T, Klann AE, García CC, de Knijff P, Kraaijenbrink T, Kondili A, Miniati P, Vouropoulou M, Kovacevic L, Marjanovic D, Lindner I, Mansour I, Al-Azem M, Andari AE, Marino M, Furfuro S, Locarno L, Martín P, Luque GM, Alonso A, Miranda LS, Moreira H, Mizuno N, Iwashima Y, Neto RS, Nogueira TL, Silva R, Nastainczyk-Wulf M, Edelmann J, Kohl M, Nie S, Wang X, Cheng B, Núñez C, Pancorbo MM, Olofsson JK, Morling N, Onofri V, Tagliabracci A, Pamjav H, Volgyi A, Barany G, Pawlowski R, Maciejewska A, Pelotti S, Pepinski W, Abreu-Glowacka M, Phillips C, Cárdenas J, Rey-Gonzalez D, Salas A, Brisighelli F, Capelli C, Toscanini U, Piccinini A, Piglionica M, Baldassarra SL, Ploski R, Konarzewska M, Jastrzebska E, Robino C, Sajantila A, Palo JU, Guevara E, Salvador J, Ungria MC, Rodriguez JJ, Schmidt U, Schlauderer N, Saukko P, Schneider PM, Sirker M, Shin KJ, Oh YN, Skitsa I, Ampati A, Smith TG, Calvit LS, Stenzl V, Capal T, Tillmar A, Nilsson H, Turrina S, De Leo D, Verzeletti A, Cortellini V, Wetton JH, Gwynne GM, Jobling MA, Whittle MR, Sumita DR, Wolańska-Nowak P, Yong RY, Krawczak M, Nothnagel M, Roewer L - Forensic Sci Int Genet (2014)

Population structure revealed by PPY23. Interpolated maps depict the first MDS components of pairwise RST values for PPY23. (a) Two-dimensional MDS analysis for the whole data set (129 populations); (b) four-dimensional MDS analysis for populations of European residency and ancestry alone (68 populations). Sample locations are marked in white. Color coding is on an arbitrary rainbow scale that assigns yellow and magenta to the opposite ends of the scale.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4127773&req=5

fig0030: Population structure revealed by PPY23. Interpolated maps depict the first MDS components of pairwise RST values for PPY23. (a) Two-dimensional MDS analysis for the whole data set (129 populations); (b) four-dimensional MDS analysis for populations of European residency and ancestry alone (68 populations). Sample locations are marked in white. Color coding is on an arbitrary rainbow scale that assigns yellow and magenta to the opposite ends of the scale.
Mentions: Multidimensional scaling (MDS) analysis was performed based upon linearized RST, separately for the five marker sets, considering either all 129 populations or the 68 populations of European residency and ancestry alone. When assessed for the PPY23 marker panel, Kruskal's stress value showed a clear ‘elbow’ with increasing dimensionality in both population sets, pinpointing an optimal trade-off between explained variation and dimensionality. For the worldwide analysis, two MDS components were optimal with PPY23 whereas four components were deemed optimal for the Europeans-only analysis. Both solutions explained the haplotypic variation well, with R2 = 95.1% in the worldwide analysis and R2 = 99.2% in the Europeans-only analysis. For comparability, MDS analyses for other marker panels were carried out with two or four dimensions, respectively. Haplotypic variation among populations within continental groups was lower than between continental groups (Fig. S3). For all five marker sets, the first MDS component clearly separated the African populations from the non-African populations (Fig. 6a, Fig. S4). Moreover, MDS also confirmed the previously reported East–West separation in the Y-STR haplotype variation [32] in the European analysis (Fig. 6b, Fig. S5). Higher MDS components were strongly dependent upon the respective marker set (Figs. S4–S6) and lacked comparably clear population patterns.

Bottom Line: Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework.A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study.Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.

View Article: PubMed Central - PubMed

Affiliation: Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany.

Show MeSH
Related in: MedlinePlus