Search

Your search keyword '"Skaro, V."' showing total 20 results
Start Over Author "Skaro, V."
20 results on '"Skaro, V."'

1. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Author

Karmin M., Saag L., Vicente M., Wilson Sayres M., Järve M., Talas U., Rootsi S., Ilumäe A., Mägi R., Mitt M., Pagani L., Puurand T., Faltyskova Z., Clemente F., Cardona A., Metspalu E., Sahakyan H., Yunusbayev B., Hudjashov G., DeGiorgio M., Loogväli E., Eichstaedt C., Eelmets M., Chaubey G., Tambets K., Litvinov S., Mormina M., Xue Y., Ayub Q., Zoraqi G., Korneliussen T., Akhatova F., Lachance J., Tishkoff S., Momynaliev K., Ricaut F., Kusuma P., Razafindrazaka H., Pierron D., Cox M., Sultana G., Willerslev R., Muller C., Westaway M., Lambert D., Skaro V., Kovačević L., Turdikulova S., Dalimova D., Khusainova R., Trofimova N., Akhmetova V., Khidiyatova I., Lichman D., Isakova J., Pocheshkhova E., Sabitov Z., Barashkov N., Nymadawa P., Mihailov E., Seng J., Evseeva I., Migliano A., Abdullah S., Andriadze G., Primorac D., Atramentova L., Utevska O., Yepiskoposyan L., Marjanović D., Kushniarevich A., and Behar D.

Abstract

© 2015 Karmin et al. It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

Published
2015

2. Towards complete male individualization with rapidly mutating Y-chromosomal STRs

Author

Ballantyne, KN, Ralf, A, Aboukhalid, R, Achakzai, NM, Anjos, MJ, Ayub, Q, Balažic, J, Ballantyne, J, Ballard, DJ, Berger, B, Bobillo, C, Bouabdellah, M, Burri, H, Butler, J, Capal, T, Caratti, S, Carracedo, A, Cartault, F, Carvalho, EF, Cheng, B, Coble, MD, Comas, D, Corach, D, D'Amato, ME, Davison, S, de Carvalho, EF, de Knijff, Peter, de Ungria, M, Decorte, Ronny, Dobosz, T, Dupuy, BM, Elmrghni, S, Gliwinski, M, Gomes, SC, Grol, L, Haas, C, Hanson, E, Henke, J, Hill, CR, Holmlund, G, Honda, K, Immel, U, Inoue, S, Jobling, MA, Kaddura, M, Kim, JS, Kim, SH, Kim, W, King, TE, Klausriegler, E, Kling, D, Kovacevic, LL, Kovatsi, L, Krajewski, P, Kravchenko, S, Larmuseau, Maarten, Lee, EY, Lee, SH, Lessig, R, Livshits, LA, Marjanovic, D, Minarik, M, Mizuno, N, Moreira, H, Morling, N, Mukherjee, M, Nagaraju, J, Neuhuber, F, Nie, S, Nilasitsataporn, P, Nishi, T, Oh, HH, Olofsson, J, Onofri, V, Palo, JU, Pamjav, H, Parson, W, Payet, C, Petlach, M, Phillips, C, Ploski, R, Prasad, SPR, Primorac, D, Purnnomo, GA, Purps, J, Rangel, H, Rebala, K, Rerkamnuaychoke, B, Rey, D, Robino, C, Rodríguez, F, Roewer, L, Rosa, A, Sajantila, A, Sala, A, Salvador, J, Sanz, P, Schmitt, C, Sharma, AK, Silva, DA, Shin, KJ, Sijen, T, Sirker, M, Siváková, D, Skaro, V, Solano-Matamoros, C, Souto, L, Stenzl, V, Sudoyo, H, Syndercombe-Court, D, Tagliabracci, A, Taylor, D, Tillmar, A, Tsybovsky, IS, Tyler-Smith, C, van der Gaag, K, Vanek, D, Völgyi, A, Ward, D, Willemse, P, Winkler, C, Yap, EPH, Yong, RYY, Zupanic Pajnic, I, and Kayser, M

Subjects
haplotypes, paternal lineage, RM YSTRs, Y-STRs, forensic, Y-chromosome
Abstract

Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836–0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father–son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RMY-STRs in identifying and separating unrelated and related males and provides a reference database. ispartof: Human Mutation vol:35 issue:8 pages:1021-1032 status: published

Published
2014

3. Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats

Author

Ballantyne, K.N., Ralf, A., Aboukhalid, R., Achakzai, N.M., Anjos, M.J., Ayub, Q., Balazic, J., Ballantyne, J., Ballard, D.J., Berger, B., Bobillo, C., Bouabdellah, M., Burri, H., Capal, T., Caratti, S., Cardenas, J., Cartault, F., Carvalho, E.F., Carvalho, M., Cheng, B.W., Coble, M.D., Comas, D., Corach, D., D'Amato, M.E., Davison, S., Knijff, P. de, Ungria, M.C.A. de, Decorte, R., Dobosz, T., Dupuy, B.M., Elmrghni, S., Gliwinski, M., Gomes, S.C., Grol, L., Haas, C., Hanson, E., Henke, J., Henke, L., Herrera-Rodriguez, F., Hill, C.R., Holmlund, G., Honda, K., Immel, U.D., Inokuchi, S., Jobling, M.A., Kaddura, M., Kim, J.S., Kim, S.H., Kim, W., King, T.E., Klausriegler, E., Kling, D., Kovacevic, L., Kovatsi, L., Krajewski, P., Kravchenko, S., Larmuseau, M.H.D., Lee, E.Y., Lessig, R., Livshits, L.A., Marjanovic, D., Minarik, M., Mizuno, N., Moreira, H., Morling, N., Mukherjee, M., Munier, P., Nagaraju, J., Neuhuber, F., Nie, S.J., Nilasitsataporn, P., Nishi, T., Oh, H.H., Olofsson, J., Onofri, V., Palo, J.U., Pamjav, H., Parson, W., Petlach, M., Phillips, C., Ploski, R., Prasad, S.P.R., Primorac, D., Purnomo, G.A., Purps, J., Rangel-Villalobos, H., Rebala, K., Rerkamnuaychoke, B., Gonzalez, D.R., Robino, C., Roewer, L., Rosa, A., Sajantila, A., Sala, A., Salvador, J.M., Sanz, P., Schmitt, C., Sharma, A.K., Silva, D.A., Shin, K.J., Sijen, T., Sirker, M., Sivakova, D., Skaro, V., Solano-Matamoros, C., Souto, L., Stenzl, V., Sudoyo, H., Syndercombe-Court, D., Tagliabracci, A., Taylor, D., Tillmar, A., Tsybovsky, I.S., Tyler-Smith, C., Gaag, K.J. van der, Vanek, D., Volgyi, A., Ward, D., Willemse, P., Yap, E.P.H., Yong, R.Y.Y., Pajnic, I.Z., Kayser, M., Hjelt Institute (-2014), Forensic Medicine, PaleOmics Laboratory, and Genetic Identification

Subjects
Male, Rural Population, haplotypes, Y-chromosome, Y-STRs, RM Y-STRs, paternal lineage, forensic, Asia, Forensic Science, Urban Population, Cell- och molekylärbiologi, education, Paternity, Gene Frequency, Humans, Alleles, Chromosomes, Human, Y, 1184 Genetics, developmental biology, physiology, Genetic Variation, DNA Fingerprinting, RM Y-STRs, Y-STRs, Y-chromosome, forensic, haplotypes, paternal lineage, Pedigree, Europe, Genetics, Population, Africa, 3111 Biomedicine, Americas, Cell and Molecular Biology, Microsatellite Repeats, Rättsmedicin
Abstract

Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father-son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RMY-STRs in identifying and separating unrelated and related males and provides a reference database. Published 2014 Wiley Periodicals, Inc.**

Published
2014

4. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Author

Karmin, M., Saag, L., Vicente, M., Wilson Sayres, M.A., Jarve, M., Talas, U.G., Rootsi, S., Ilumae, A.M., Magi, R., Mitt, M., Pagani, L., Puurand, T., Faltyskova, Z., Clemente, F., Cardona, A., Metspalu, E., Sahakyan, H., Yunusbayev, B., Hudjashov, G., DeGiorgio, M., Loogvali, E.L., Eichstaedt, C., Eelmets, M., Chaubey, G., Tambets, K., Litvinov, S., Mormina, M., Xue, Y., Ayub, Q., Zoraqi, G., Korneliussen, T.S., Akhatova, F., Lachance, J., Tishkoff, S., Momynaliev, K., Ricaut, F.X., Kusuma, P., Razafindrazaka, H., Pierron, D., Cox, M.P., Sultana, G.N., Willerslev, R., Muller, C., Westaway, M., Lambert, D., Skaro, V., Kovacevic, L., Turdikulova, S., Dalimova, D., Khusainova, R., Trofimova, N., Akhmetova, V., Khidiyatova, I., Lichman, D.V., Isakova, J., Pocheshkhova, E., Sabitov, Z., Barashkov, N.A., Nymadawa, P., Mihailov, E., Seng, J.W., Evseeva, I., Migliano, A.B., Abdullah, S., Andriadze, G., Primorac, D., Atramentova, L., Utevska, O., Yepiskoposyan, L., Marjanovic, D., Kushniarevich, A., Behar, D.M., Gilissen, C., Vissers, L., Veltman, J.A., Balanovska, E., Derenko, M., Malyarchuk, B., Metspalu, A., Fedorova, S., Eriksson, A., Manica, A., Mendez, F.L., Karafet, T.M., Veeramah, K.R., Bradman, N., Hammer, M.F., Osipova, L.P., Balanovsky, O., Khusnutdinova, E.K., Johnsen, K., Remm, M., Thomas, M.G., Tyler-Smith, C., Underhill, P.A., Willerslev, E., Nielsen, R., Metspalu, M., Villems, R., Kivisild, T., Karmin, M., Saag, L., Vicente, M., Wilson Sayres, M.A., Jarve, M., Talas, U.G., Rootsi, S., Ilumae, A.M., Magi, R., Mitt, M., Pagani, L., Puurand, T., Faltyskova, Z., Clemente, F., Cardona, A., Metspalu, E., Sahakyan, H., Yunusbayev, B., Hudjashov, G., DeGiorgio, M., Loogvali, E.L., Eichstaedt, C., Eelmets, M., Chaubey, G., Tambets, K., Litvinov, S., Mormina, M., Xue, Y., Ayub, Q., Zoraqi, G., Korneliussen, T.S., Akhatova, F., Lachance, J., Tishkoff, S., Momynaliev, K., Ricaut, F.X., Kusuma, P., Razafindrazaka, H., Pierron, D., Cox, M.P., Sultana, G.N., Willerslev, R., Muller, C., Westaway, M., Lambert, D., Skaro, V., Kovacevic, L., Turdikulova, S., Dalimova, D., Khusainova, R., Trofimova, N., Akhmetova, V., Khidiyatova, I., Lichman, D.V., Isakova, J., Pocheshkhova, E., Sabitov, Z., Barashkov, N.A., Nymadawa, P., Mihailov, E., Seng, J.W., Evseeva, I., Migliano, A.B., Abdullah, S., Andriadze, G., Primorac, D., Atramentova, L., Utevska, O., Yepiskoposyan, L., Marjanovic, D., Kushniarevich, A., Behar, D.M., Gilissen, C., Vissers, L., Veltman, J.A., Balanovska, E., Derenko, M., Malyarchuk, B., Metspalu, A., Fedorova, S., Eriksson, A., Manica, A., Mendez, F.L., Karafet, T.M., Veeramah, K.R., Bradman, N., Hammer, M.F., Osipova, L.P., Balanovsky, O., Khusnutdinova, E.K., Johnsen, K., Remm, M., Thomas, M.G., Tyler-Smith, C., Underhill, P.A., Willerslev, E., Nielsen, R., Metspalu, M., Villems, R., and Kivisild, T.

Abstract

Contains fulltext : 153022.pdf (publisher's version ) (Open Access), It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

Published
2015

7. Twelve-year experience in identification of skeletal remains from mass graves

Author

Andelinovic, S., Sutlovic, D., Ivkosic, Ie, Skaro, V., Ivkosic, A., Frane Paic, Rezic, B., Definis-Gojanovic, M., and Primorac, D.

Subjects
oligonucleotide probe analysis, PCR-based loci, allele frequencies, Croatian population, DNA analysis, war victims, bone, amplification, Herzegovina, extraction
Abstract

Aim was to present twelve-year (1993-2005) experience in identification of human remains found in mass graves in Croatia and Bosnia and Herzegovina (BH), as well as remains that presumably belonged to Croatian citizens given by Serbia and Montenegro. The unique experience of identification of more than a thousand of skeletal samples is valuable for better organization of post-mortem identifications. Standard forensic methods and methods based on DNA analysis were used for identification of human remains from mass graves. DNA was isolated using standard phenol/chloroform/isoamyl alcohol extraction. In some cases, decalcification and repurification were used prior to the extraction to overcome inhibition of amplification process. Different DNA systems were used for DNA quantitation and amplification (AluQuant, short tandem repeats (STR) commercial systems, Y chromosome STRs, and mitochondrial DNA [mtDNA]). Typing of PCR products was performed on AmpliType (R) PM and AmpliType (R) DQA1 DNA probe strips, ABI PRISM (R) 310 Genetic Analyzer and immobilized sequence-specific oligonucleotide (SSO) probes. Up-to-date analysis of 1, 155 skeletal samples resulted in 703 positively identified bodies: 577 using standard forensic methods, 109 by DNA typing, and 17 by combination of these two methods. The majority of identifications from 1993 to 1999 was, as usual, achieved by standard forensic methods. Later on, these methods were not sufficient and DNA analysis was requested. It was performed in 42% of all cases in 12 years. The crucial step in DNA analysis is extraction of genomic DNA. Standard phenol/chloroform/isoamyl alcohol extraction, complemented with other methods and modifications, proved as the most successful method for this step. In certain cases, the quality and/or quantity of nDNA was not satisfying and the analysis of the mtDNA was performed. Our experience demonstrated that the advent of forensic DNA analysis methods greatly increased our ability to positively identify previously unknown skeletal remains by a comparative genetic analysis with presumptive relatives.

8. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Author

Karmin M., Saag L., Vicente M., Wilson Sayres M., Järve M., Talas U., Rootsi S., Ilumäe A., Mägi R., Mitt M., Pagani L., Puurand T., Faltyskova Z., Clemente F., Cardona A., Metspalu E., Sahakyan H., Yunusbayev B., Hudjashov G., DeGiorgio M., Loogväli E., Eichstaedt C., Eelmets M., Chaubey G., Tambets K., Litvinov S., Mormina M., Xue Y., Ayub Q., Zoraqi G., Korneliussen T., Akhatova F., Lachance J., Tishkoff S., Momynaliev K., Ricaut F., Kusuma P., Razafindrazaka H., Pierron D., Cox M., Sultana G., Willerslev R., Muller C., Westaway M., Lambert D., Skaro V., Kovačević L., Turdikulova S., Dalimova D., Khusainova R., Trofimova N., Akhmetova V., Khidiyatova I., Lichman D., Isakova J., Pocheshkhova E., Sabitov Z., Barashkov N., Nymadawa P., Mihailov E., Seng J., Evseeva I., Migliano A., Abdullah S., Andriadze G., Primorac D., Atramentova L., Utevska O., Yepiskoposyan L., Marjanović D., Kushniarevich A., Behar D., Karmin M., Saag L., Vicente M., Wilson Sayres M., Järve M., Talas U., Rootsi S., Ilumäe A., Mägi R., Mitt M., Pagani L., Puurand T., Faltyskova Z., Clemente F., Cardona A., Metspalu E., Sahakyan H., Yunusbayev B., Hudjashov G., DeGiorgio M., Loogväli E., Eichstaedt C., Eelmets M., Chaubey G., Tambets K., Litvinov S., Mormina M., Xue Y., Ayub Q., Zoraqi G., Korneliussen T., Akhatova F., Lachance J., Tishkoff S., Momynaliev K., Ricaut F., Kusuma P., Razafindrazaka H., Pierron D., Cox M., Sultana G., Willerslev R., Muller C., Westaway M., Lambert D., Skaro V., Kovačević L., Turdikulova S., Dalimova D., Khusainova R., Trofimova N., Akhmetova V., Khidiyatova I., Lichman D., Isakova J., Pocheshkhova E., Sabitov Z., Barashkov N., Nymadawa P., Mihailov E., Seng J., Evseeva I., Migliano A., Abdullah S., Andriadze G., Primorac D., Atramentova L., Utevska O., Yepiskoposyan L., Marjanović D., Kushniarevich A., and Behar D.

Abstract

© 2015 Karmin et al. It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

9. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Author

Karmin M., Saag L., Vicente M., Wilson Sayres M., Järve M., Talas U., Rootsi S., Ilumäe A., Mägi R., Mitt M., Pagani L., Puurand T., Faltyskova Z., Clemente F., Cardona A., Metspalu E., Sahakyan H., Yunusbayev B., Hudjashov G., DeGiorgio M., Loogväli E., Eichstaedt C., Eelmets M., Chaubey G., Tambets K., Litvinov S., Mormina M., Xue Y., Ayub Q., Zoraqi G., Korneliussen T., Akhatova F., Lachance J., Tishkoff S., Momynaliev K., Ricaut F., Kusuma P., Razafindrazaka H., Pierron D., Cox M., Sultana G., Willerslev R., Muller C., Westaway M., Lambert D., Skaro V., Kovačević L., Turdikulova S., Dalimova D., Khusainova R., Trofimova N., Akhmetova V., Khidiyatova I., Lichman D., Isakova J., Pocheshkhova E., Sabitov Z., Barashkov N., Nymadawa P., Mihailov E., Seng J., Evseeva I., Migliano A., Abdullah S., Andriadze G., Primorac D., Atramentova L., Utevska O., Yepiskoposyan L., Marjanović D., Kushniarevich A., Behar D., Karmin M., Saag L., Vicente M., Wilson Sayres M., Järve M., Talas U., Rootsi S., Ilumäe A., Mägi R., Mitt M., Pagani L., Puurand T., Faltyskova Z., Clemente F., Cardona A., Metspalu E., Sahakyan H., Yunusbayev B., Hudjashov G., DeGiorgio M., Loogväli E., Eichstaedt C., Eelmets M., Chaubey G., Tambets K., Litvinov S., Mormina M., Xue Y., Ayub Q., Zoraqi G., Korneliussen T., Akhatova F., Lachance J., Tishkoff S., Momynaliev K., Ricaut F., Kusuma P., Razafindrazaka H., Pierron D., Cox M., Sultana G., Willerslev R., Muller C., Westaway M., Lambert D., Skaro V., Kovačević L., Turdikulova S., Dalimova D., Khusainova R., Trofimova N., Akhmetova V., Khidiyatova I., Lichman D., Isakova J., Pocheshkhova E., Sabitov Z., Barashkov N., Nymadawa P., Mihailov E., Seng J., Evseeva I., Migliano A., Abdullah S., Andriadze G., Primorac D., Atramentova L., Utevska O., Yepiskoposyan L., Marjanović D., Kushniarevich A., and Behar D.

Abstract

© 2015 Karmin et al. It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

10. Genomic analyses inform on migration events during the peopling of Eurasia.

Author

Pagani L, Lawson DJ, Jagoda E, Mörseburg A, Eriksson A, Mitt M, Clemente F, Hudjashov G, DeGiorgio M, Saag L, Wall JD, Cardona A, Mägi R, Wilson Sayres MA, Kaewert S, Inchley C, Scheib CL, Järve M, Karmin M, Jacobs GS, Antao T, Iliescu FM, Kushniarevich A, Ayub Q, Tyler-Smith C, Xue Y, Yunusbayev B, Tambets K, Mallick CB, Saag L, Pocheshkhova E, Andriadze G, Muller C, Westaway MC, Lambert DM, Zoraqi G, Turdikulova S, Dalimova D, Sabitov Z, Sultana GNN, Lachance J, Tishkoff S, Momynaliev K, Isakova J, Damba LD, Gubina M, Nymadawa P, Evseeva I, Atramentova L, Utevska O, Ricaut FX, Brucato N, Sudoyo H, Letellier T, Cox MP, Barashkov NA, Skaro V, Mulahasanovic L, Primorac D, Sahakyan H, Mormina M, Eichstaedt CA, Lichman DV, Abdullah S, Chaubey G, Wee JTS, Mihailov E, Karunas A, Litvinov S, Khusainova R, Ekomasova N, Akhmetova V, Khidiyatova I, Marjanović D, Yepiskoposyan L, Behar DM, Balanovska E, Metspalu A, Derenko M, Malyarchuk B, Voevoda M, Fedorova SA, Osipova LP, Lahr MM, Gerbault P, Leavesley M, Migliano AB, Petraglia M, Balanovsky O, Khusnutdinova EK, Metspalu E, Thomas MG, Manica A, Nielsen R, Villems R, Willerslev E, Kivisild T, and Metspalu M

Subjects
Animals, Humans, Africa ethnology, Asia, Datasets as Topic, Estonia, Europe, Fossils, Gene Flow, Genetics, Population, Heterozygote, History, Ancient, Neanderthals genetics, New Guinea, Population Dynamics, Genome, Human genetics, Genomics, Human Migration history, Racial Groups genetics
Abstract

High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago., Competing Interests: The authors declare no competing financial interests.

Published
2016
Full Text
View/download PDF

11. A recent bottleneck of Y chromosome diversity coincides with a global change in culture.

Author

Karmin M, Saag L, Vicente M, Wilson Sayres MA, Järve M, Talas UG, Rootsi S, Ilumäe AM, Mägi R, Mitt M, Pagani L, Puurand T, Faltyskova Z, Clemente F, Cardona A, Metspalu E, Sahakyan H, Yunusbayev B, Hudjashov G, DeGiorgio M, Loogväli EL, Eichstaedt C, Eelmets M, Chaubey G, Tambets K, Litvinov S, Mormina M, Xue Y, Ayub Q, Zoraqi G, Korneliussen TS, Akhatova F, Lachance J, Tishkoff S, Momynaliev K, Ricaut FX, Kusuma P, Razafindrazaka H, Pierron D, Cox MP, Sultana GN, Willerslev R, Muller C, Westaway M, Lambert D, Skaro V, Kovačevic L, Turdikulova S, Dalimova D, Khusainova R, Trofimova N, Akhmetova V, Khidiyatova I, Lichman DV, Isakova J, Pocheshkhova E, Sabitov Z, Barashkov NA, Nymadawa P, Mihailov E, Seng JW, Evseeva I, Migliano AB, Abdullah S, Andriadze G, Primorac D, Atramentova L, Utevska O, Yepiskoposyan L, Marjanovic D, Kushniarevich A, Behar DM, Gilissen C, Vissers L, Veltman JA, Balanovska E, Derenko M, Malyarchuk B, Metspalu A, Fedorova S, Eriksson A, Manica A, Mendez FL, Karafet TM, Veeramah KR, Bradman N, Hammer MF, Osipova LP, Balanovsky O, Khusnutdinova EK, Johnsen K, Remm M, Thomas MG, Tyler-Smith C, Underhill PA, Willerslev E, Nielsen R, Metspalu M, Villems R, and Kivisild T

Subjects
Base Sequence, DNA, Mitochondrial genetics, Genetic Variation genetics, Genetics, Population, Haplotypes genetics, Humans, Male, Models, Genetic, Phylogeny, Sequence Analysis, DNA, Chromosomes, Human, Y genetics, Evolution, Molecular, Racial Groups genetics
Abstract

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males., (© 2015 Karmin et al.; Published by Cold Spring Harbor Laboratory Press.)

Published
2015
Full Text
View/download PDF

12. Standing at the gateway to Europe--the genetic structure of Western balkan populations based on autosomal and haploid markers.

Author

Kovacevic L, Tambets K, Ilumäe AM, Kushniarevich A, Yunusbayev B, Solnik A, Bego T, Primorac D, Skaro V, Leskovac A, Jakovski Z, Drobnic K, Tolk HV, Kovacevic S, Rudan P, Metspalu E, and Marjanovic D

Subjects
Balkan Peninsula, Chromosomes, Human, Y, Cluster Analysis, DNA, Mitochondrial, Evolution, Molecular, Genetic Variation, Geography, Humans, Polymorphism, Single Nucleotide, Chromosomes, Human, Ethnicity genetics, Genetic Markers, Genetics, Population, Haplotypes
Abstract

Contemporary inhabitants of the Balkan Peninsula belong to several ethnic groups of diverse cultural background. In this study, three ethnic groups from Bosnia and Herzegovina - Bosniacs, Bosnian Croats and Bosnian Serbs - as well as the populations of Serbians, Croatians, Macedonians from the former Yugoslav Republic of Macedonia, Montenegrins and Kosovars have been characterized for the genetic variation of 660 000 genome-wide autosomal single nucleotide polymorphisms and for haploid markers. New autosomal data of the 70 individuals together with previously published data of 20 individuals from the populations of the Western Balkan region in a context of 695 samples of global range have been analysed. Comparison of the variation data of autosomal and haploid lineages of the studied Western Balkan populations reveals a concordance of the data in both sets and the genetic uniformity of the studied populations, especially of Western South-Slavic speakers. The genetic variation of Western Balkan populations reveals the continuity between the Middle East and Europe via the Balkan region and supports the scenario that one of the major routes of ancient gene flows and admixture went through the Balkan Peninsula.

Published
2014
Full Text
View/download PDF

13. Toward male individualization with rapidly mutating y-chromosomal short tandem repeats.

Author

Ballantyne KN, Ralf A, Aboukhalid R, Achakzai NM, Anjos MJ, Ayub Q, Balažic J, Ballantyne J, Ballard DJ, Berger B, Bobillo C, Bouabdellah M, Burri H, Capal T, Caratti S, Cárdenas J, Cartault F, Carvalho EF, Carvalho M, Cheng B, Coble MD, Comas D, Corach D, D'Amato ME, Davison S, de Knijff P, De Ungria MC, Decorte R, Dobosz T, Dupuy BM, Elmrghni S, Gliwiński M, Gomes SC, Grol L, Haas C, Hanson E, Henke J, Henke L, Herrera-Rodríguez F, Hill CR, Holmlund G, Honda K, Immel UD, Inokuchi S, Jobling MA, Kaddura M, Kim JS, Kim SH, Kim W, King TE, Klausriegler E, Kling D, Kovačević L, Kovatsi L, Krajewski P, Kravchenko S, Larmuseau MH, Lee EY, Lessig R, Livshits LA, Marjanović D, Minarik M, Mizuno N, Moreira H, Morling N, Mukherjee M, Munier P, Nagaraju J, Neuhuber F, Nie S, Nilasitsataporn P, Nishi T, Oh HH, Olofsson J, Onofri V, Palo JU, Pamjav H, Parson W, Petlach M, Phillips C, Ploski R, Prasad SP, Primorac D, Purnomo GA, Purps J, Rangel-Villalobos H, Rębała K, Rerkamnuaychoke B, Gonzalez DR, Robino C, Roewer L, Rosa A, Sajantila A, Sala A, Salvador JM, Sanz P, Schmitt C, Sharma AK, Silva DA, Shin KJ, Sijen T, Sirker M, Siváková D, Skaro V, Solano-Matamoros C, Souto L, Stenzl V, Sudoyo H, Syndercombe-Court D, Tagliabracci A, Taylor D, Tillmar A, Tsybovsky IS, Tyler-Smith C, van der Gaag KJ, Vanek D, Völgyi A, Ward D, Willemse P, Yap EP, Yong RY, Pajnič IZ, and Kayser M

Subjects
Africa, Alleles, Americas, Asia, DNA Fingerprinting statistics & numerical data, Europe, Gene Frequency, Genetic Variation, Humans, Male, Paternity, Pedigree, Rural Population, Urban Population, Chromosomes, Human, Y chemistry, DNA Fingerprinting methods, Genetics, Population, Haplotypes, Microsatellite Repeats
Abstract

Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father-son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database., (© 2014 The Authors. **Human Mutation published by Wiley Periodicals, Inc.)

Published
2014
Full Text
View/download PDF

14. Genetic polymorphisms of 15 STR loci in the population of the island of Cres (Croatia).

Author

Novokmet N, Marjanović D, Skaro V, Projić P, Lauc G, Grahovac B, Ostojić S, Kapović M, and Rudan P

Subjects
Alleles, Croatia, Gene Frequency, Genetic Variation, Geography, Humans, Polymerase Chain Reaction, Microsatellite Repeats, Polymorphism, Genetic
Abstract

Background: The population of the island of Cres presents one of the few persisting Eastern Adriatic isolates and is thereby suitable for human population differentiation analyses., Aim: The aim of this study was to analyse the genetic structure of the island of Cres with respect to its eight sub-populations and to compare the genetic variation of the island of Cres with other Eastern Adriatic islands and the Croatian mainland., Subjects and Methods: Fifteen AmpFlSTR identifiler loci were analysed in a sample group of 122 unrelated autochthonous individuals from the island of Cres, Croatia., Results: Analysis of STR polymorphisms revealed genetic homogeneity among sub-populations of the island of Cres and small but significant levels of genetic heterogeneity among geographically distant Eastern Adriatic islands., Conclusion: Despite a considerable degree of genetic homogeneity among the studied Eastern Adriatic islands, small but significant differentiation between distant islands indicates geographic sub-structuring which follows the isolation by distance model. This study is supportive of the notion that STR markers are useful for genetic differentiation between larger and geographically more distant regions.

Published
2011
Full Text
View/download PDF

15. Forensic efficiency parameters for the 15 STR loci in the population of the island of Cres (Croatia).

Author

Novokmet N, Marjanović D, Skaro V, Projić P, Lauc G, Grahovac B, Mohar B, Kapović M, and Rudan P

Subjects
Adult, Croatia, Gene Frequency, Genetic Markers, Humans, Polymorphism, Genetic, DNA Fingerprinting, Microsatellite Repeats
Abstract

Forensic parameters based on 15 AmpFISTR Identifiler short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818 and FGA) were evaluated in the sample of 122 unrelated, autochthonous, adult individuals from the Island of Cres (Croatia). PCR amplification was performed with the AmpFISTR Identifiler PCR Amplification Kit and the amplified products were separated and detected using the ABI 3130 DNA genetic analyzer. The agreement with Hardy Weinberg Equilibrium (HWE) was confirmed for all loci (p > 0.05). The combined power of discrimination (PD) and the combined power of exclusion (PE) for the 15 tested STR loci were 0.99999999999999997988728679 and 0.999997397, respectively. According to the presented data, D18S51 proved to be the most informative marker followed by markers D2S1338 and D21S11. Interpopulation comparisons in allele frequencies with other East Adriatic Islands revealed significant differences for all analyzed population pairs ranging from 4 loci (Cres vs. Hvar) to 1 locus (Cres vs. Krk). Furthermore, allele frequencies comparisons of Cres and Croatian mainland revealed the lack of statistically significant differences at all studied loci. The results of the current study indicate that the examined fifteen STR loci are useful genetic markers for individual identification and paternity testing in Croatian population from the Island of Cres.

Published
2009

16. Identification of skeletal remains of Communist Armed Forces victims during and after World War II: combined Y-chromosome (STR) and MiniSTR approach.

Author

Marjanović D, Durmić-Pasić A, Kovacević L, Avdić J, Dzehverović M, Haverić S, Ramić J, Kalamujić B, Lukić Bilela L, Skaro V, Projić P, Bajrović K, Drobnic K, Davoren J, and Primorac D

Subjects
Humans, Male, Slovenia, Bone and Bones, Chromosomes, Human, Y, Crime Victims, Forensic Anthropology methods, Microsatellite Repeats genetics, Military Personnel, World War II
Abstract

Aim: To report on the use of STR, Y-STRs, and miniSTRs typing methods in the identification of victims of revolutionary violence and crimes against humanity committed by the Communist Armed Forces during and after World War II in which bodies were exhumed from mass and individual graves in Slovenia., Methods: Bone fragments and teeth were removed from human remains found in several small and closely located hidden mass graves in the Skofja Loka area (Lovrenska Grapa and Zolsce) and 2 individual graves in the Ljubljana area (Podlipoglav), Slovenia. DNA was isolated using the Qiagen DNA extraction procedure optimized for bone and teeth. Some DNA extracts required additional purification, such as N-buthanol treatment. The QuantifilerTM Human DNA Quantification Kit was used for DNA quantification. Initially, PowerPlex 16 kit was used to simultaneously analyze 15 short tandem repeat (STR) loci. The PowerPlex S5 miniSTR kit and AmpF/STR MiniFiler PCR Amplification Kit was used for additional analysis if preliminary analysis yielded weak partial or no profiles at all. In 2 cases, when the PowerPlex 16 profiles indicated possible relatedness of the remains with reference samples, but there were insufficient probabilities to call the match to possible male paternal relatives, we resorted to an additional analysis of Y-STR markers. PowerPlex Y System was used to simultaneously amplify 12 Y-STR loci. Fragment analysis was performed on an ABI PRISM 310 genetic analyzer. Matching probabilities were estimated using the DNA-View software., Results: Following the Y-STR analysis, 1 of the "weak matches" previously obtained based on autosomal loci, was confirmed while the other 1 was not. Combined standard STR and miniSTR approach applied to bone samples from 2 individual graves resulted in positive identifications. Finally, using the same approach on 11 bone samples from hidden mass grave Zolosce, we were able to obtain 6 useful DNA profiles., Conclusion: The results of this study, in combination with previously obtained results, demonstrate that Y-chromosome testing and mini-STR methodology can contribute to the identification of human remains of victims of revolutionary violence from World War II.

Published
2009
Full Text
View/download PDF

17. DNA identification of skeletal remains from the World War II mass graves uncovered in Slovenia.

Author

Marjanović D, Durmić-Pasić A, Bakal N, Haverić S, Kalamujić B, Kovacević L, Ramić J, Pojskić N, Skaro V, Projić P, Bajrović K, Hadziselimović R, Drobnic K, Huffine E, Davoren J, and Primorac D

Subjects
Humans, Slovenia, DNA Fingerprinting, Forensic Anthropology, World War II
Abstract

Aim: To present the joint effort of three institutions in the identification of human remains from the World War II found in two mass graves in the area of Skofja Loka, Slovenia., Methods: The remains of 27 individuals were found in two small and closely located mass graves. The DNA was isolated from bone and teeth samples using either standard phenol/chloroform alcohol extraction or optimized Qiagen DNA extraction procedure. Some recovered samples required the employment of additional DNA purification methods, such as N-buthanol treatment. Quantifiler Human DNA Quantification Kit was used for DNA quantification. PowerPlex 16 kit was used to simultaneously amplify 15 short tandem repeat (STR) loci. Matching probabilities were estimated using the DNA View program., Results: Out of all processed samples, 15 remains were fully profiled at all 15 STR loci. The other 12 profiles were partial. The least successful profile included 13 loci. Also, 69 referent samples (buccal swabs) from potential living relatives were collected and profiled. Comparison of victims' profile against referent samples database resulted in 4 strong matches. In addition, 5 other profiles were matched to certain referent samples with lower probability., Conclusion: Our results show that more than 6 decades after the end of the World War II, DNA analysis may significantly contribute to the identification of the remains from that period. Additional analysis of Y-STRs and mitochondrial DNA (mtDNA) markers will be performed in the second phase of the identification project.

Published
2007

18. Allele frequencies for 15 short tandem repeat loci in representative sample of Croatian population.

Author

Projić P, Skaro V, Samija I, Pojskić N, Durmić-Pasić A, Kovacević L, Bakal N, Primorac D, and Marjanović D

Subjects
Croatia, Humans, Gene Frequency, Genetics, Population, Microsatellite Repeats
Abstract

Aim: To study the distribution of allele frequencies of 15 short tandem repeat (STR) loci in a representative sample of Croatian population., Methods: A total of 195 unrelated Caucasian individuals born in Croatia, from 14 counties and the City of Zagreb, were sampled for the analysis. All the tested individuals were voluntary donors. Buccal swab was used as the DNA source. AmpFlSTR Identifiler was applied to simultaneously amplify 15 STR loci. Total reaction volume was 12.5 microL. The PCR amplification was carried out in PE Gene Amp PCR System Thermal Cycler. Electrophoresis of the amplification products was preformed on an ABI PRISM 3130 Genetic Analyzer. After PCR amplification and separation by electrophoresis, raw data were compiled, analyzed, and numerical allele designations of the profiles were obtained. Deviation from Hardy-Weinberg equilibrium, observed and expected heterozygosity, power of discrimination, and power of exclusion were calculated. Bonferroni's correction was used before each comparative analysis., Results: We compared Croatian data with those obtained from geographically neighboring European populations. The significant difference (at P<0.01) in allele frequencies was recorded only between Croatian and Slovenian populations for vWA locus. There was no significant deviation from Hardy-Weinberg equilibrium for all the observed loci., Conclusion: Obtained population data concurred with the expected "STR data frame" for this part of Europe.

Published
2007

19. Population data at two short tandem repeat loci D2S1338 and D19S433 in the sample of multinational Bosnia and Herzegovina residents.

Author

Marjanovic D, Pojskic N, Davoren J, Kovacevic L, Durmic A, Bakal N, Drobnic K, Primorac D, Skaro V, Bajrovic K, and Hadziselimovic R

Subjects
Bosnia and Herzegovina, DNA Fingerprinting, Humans, Polymerase Chain Reaction, Gene Frequency, Genetics, Population, Tandem Repeat Sequences
Abstract

Population: We have analyzed the distribution of allele frequencies at two short tandem repeats loci (D2S1338 and D19S433) in a multinational sample of Bosnia and Herzegovina (B&H) residents. A total of 110 unrelated male and female individuals (Caucasians) from different regions of B&H were sampled for the analysis. We ensured that the sample reflected approximate proportional participation of the three main ethnic groups in the population of B&H (Bosniacs-Muslim [45%], Serbs [34%], Croats [21%]).

Published
2006
Full Text
View/download PDF

20. Twelve-year experience in identification of skeletal remains from mass graves.

Author

Andelinović S, Sutlović D, Erceg Ivkosić I, Skaro V, Ivkosić A, Paić F, Rezić B, Definis-Gojanović M, and Primorac D

Subjects
Croatia, DNA analysis, Decalcification Technique, Genetics, Medical, Humans, Bone and Bones, Forensic Anthropology methods, Forensic Medicine methods
Abstract

Aim: To present twelve-year (1993-2005) experience in identification of human remains found in mass graves in Croatia and Bosnia and Herzegovina (BH), as well as remains that presumably belonged to Croatian citizens given by Serbia and Montenegro. The unique experience of identification of more than a thousand of skeletal samples is valuable for better organization of post-mortem identifications., Methods: Standard forensic methods and methods based on DNA analysis were used for identification of human remains from mass graves. DNA was isolated using standard phenol/chloroform/isoamyl alcohol extraction. In some cases, decalcification and repurification were used prior to the extraction to overcome inhibition of amplification process. Different DNA systems were used for DNA quantitation and amplification (AluQuant, short tandem repeats (STR) commercial systems, Y chromosome STRs, and mitochondrial DNA [mtDNA]). Typing of PCR products was performed on AmpliType PM and AmpliType DQA1 DNA probe strips, ABI PRISM(R) 310 Genetic Analyzer and immobilized sequence-specific oligonucleotide (SSO) probes., Results: Up-to-date analysis of 1,155 skeletal samples resulted in 703 positively identified bodies: 577 using standard forensic methods, 109 by DNA typing, and 17 by combination of these two methods. The majority of identifications from 1993 to 1999 was, as usual, achieved by standard forensic methods. Later on, these methods were not sufficient and DNA analysis was requested. It was performed in 42% of all cases in 12 years. The crucial step in DNA analysis is extraction of genomic DNA. Standard phenol/chloroform/isoamyl alcohol extraction, complemented with other methods and modifications, proved as the most successful method for this step. In certain cases, the quality and/or quantity of nDNA was not satisfying and the analysis of the mtDNA was performed., Conclusion: Our experience demonstrated that the advent of forensic DNA analysis methods greatly increased our ability to positively identify previously unknown skeletal remains by a comparative genetic analysis with presumptive relatives.

Published
2005

Catalog

Books, media, physical & digital resources
See catalog results