Lejla Kovačević

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

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.

Prediction of eye and skin color in diverse populations using seven SNPs.

An essential component in identifying human remains is the documentation of the decedents visible characteristics, such as eye, hair and skin color. However, if a decedent is decomposed or only skeletal remains are found, this critical, visibly identifying information is lost. It would be beneficial to use genetic information to reveal these visible characteristics. In this study, seven single nucleotide polymorphisms (SNPs), located in and nearby genes known for their important role in pigmentation, were validated on 554 samples, donated from non-related individuals of various populations. Six SNPs were used in predicting the eye color of an individual, and all seven were used to describe the skin coloration. The outcome revealed that these markers can be applied to all populations with very low error rates. However, the call-rate to determine the skin coloration varied between populations, demonstrating its complexity. Overall, these results prove the importance of these seven SNPs for potential forensic tests.

No Evidence from Genome-wide Data of a Khazar Origin for the Ashkenazi Jews

Abstract The origin and history of the Ashkenazi Jewish population have long been of great interest, and advances in high-throughput genetic analysis have recently provided a new approach for investigating these topics. We and others have argued on the basis of genome-wide data that the Ashkenazi Jewish population derives its ancestry from a combination of sources tracing to both Europe and the Middle East. It has been claimed, however, through a reanalysis of some of our data, that a large part of the ancestry of the Ashkenazi population originates with the Khazars, a Turkic-speaking group that lived to the north of the Caucasus region ∼1,000 years ago. Because the Khazar population has left no obvious modern descendants that could enable a clear test for a contribution to Ashkenazi Jewish ancestry, the Khazar hypothesis has been difficult to examine using genetics. Furthermore, because only limited genetic data have been available from the Caucasus region, and because these data have been concentrated in populations that are genetically close to populations from the Middle East, the attribution of any signal of Ashkenazi-Caucasus genetic similarity to Khazar ancestry rather than shared ancestral Middle Eastern ancestry has been problematic. Here, through integration of genotypes from newly collected samples with data from several of our past studies, we have assembled the largest data set available to date for assessment of Ashkenazi Jewish genetic origins. This data set contains genome-wide single-nucleotide polymorphisms in 1,774 samples from 106 Jewish and non-Jewish populations that span the possible regions of potential Ashkenazi ancestry: Europe, the Middle East, and the region historically associated with the Khazar Khaganate. The data set includes 261 samples from 15 populations from the Caucasus region and the region directly to its north, samples that have not previously been included alongside Ashkenazi Jewish samples in genomic studies. Employing a variety of standard techniques for the analysis of population-genetic structure, we found that Ashkenazi Jews share the greatest genetic ancestry with other Jewish populations and, among non-Jewish populations, with groups from Europe and the Middle East. No particular similarity of Ashkenazi Jews to populations from the Caucasus is evident, particularly populations that most closely represent the Khazar region. Thus, analysis of Ashkenazi Jews together with a large sample from the region of the Khazar Khaganate corroborates the earlier results that Ashkenazi Jews derive their ancestry primarily from populations of the Middle East and Europe, that they possess considerable shared ancestry with other Jewish populations, and that there is no indication of a significant genetic contribution either from within or from north of the Caucasus region.

Standing at the Gateway to Europe - The Genetic Structure of Western Balkan Populations Based on Autosomal and Haploid Markers

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.

Population study of fourteen X chromosomal short tandem repeat loci in a population from Bosnia and Herzegovina

6 0.1532 0.0045 6 7 0.0090 0.0090 7 8 0.1667 0.0090 8 9 0.0541 0.0450 0.2973 0.0450 0.0045 0.3964 0.0270 0.2117 9 10 0.3288 0.3784 0.0090 0.3018 0.3288 0.0405 0.1712 0.0045 0.0405 10 10.1 0.0045 10.1 11 0.3333 0.3153 0.0495 0.3604 0.2207 0.0090 0.2523 0.3333 0.1396 0.1892 11 11.1 0.0405 11.1 11.3 0.0135 11.3 12 0.2568 0.2027 0.0090 0.0946 0.0405 0.0856 0.0811 0.2297 0.0586 0.2973 0.1667 12 12.1 0.0090 12.1 12.3 0.1441 12.3 13 0.0270 0.0045 0.0901 0.0270 0.3153 0.1486 0.0270 0.3514 0.2838 0.0856 13 13.3 0.0450 0.1441 13.3 14 0.2297 0.0270 0.4054 0.0090 0.1171 0.0991 0.3243 14 14.3 0.1757 0.0135 14.3 15 0.2568 0.0676 0.0450 0.1486 0.0405 0.0090 0.3964 15 15.3 0.3964 15.3 16 0.2703 0.0135 0.0180 0.0045 0.1802 16 16.3 0.1712 16.3 17 0.1171 0.0225 0.0135 17 17.3 0.0135 17.3 18 0.0135 0.0631 18 19 0.0045 0.0135 0.0450 19 20 0.4144 0.0135 20 21 0.2477 0.0270 21 22 0.2342 0.0045 22 23 0.0180 0.0631 23 24 0.0045 0.2568 24 25 0.1577 25 26 0.1216 26 27 0.0586 27 28 0.1126 28 29 0.0045 29 30 0.0090 30 31 0.0045 31 H(exp) 0.7112 0.7125 0.7860 0.7070 0.7676 0.6890 0.8650 0.7826 0.7067 0.8179 0.6982 0.7524 0.7995 0.6977 H(exp) H(obs) 0.7353 0.7647 0.8088 0.5882 0.7206 0.6765 0.8676 0.7794 0.7647 0.8088 0.7206 0.7794 0.8235 0.7059 H(obs) PIC 0.6562 0.6620 0.7530 0.6574 0.7402 0.6253 0.8522 0.7507 0.6580 0.7929 0.6450 0.7147 0.7700 0.6432 PIC PDf 0.8616 0.8668 0.9212 0.8646 0.9186 0.8395 0.9690 0.9209 0.8653 0.9418 0.8557 0.9010 0.9303 0.8541 PDf PDm 0.7112 0.7125 0.7860 0.7070 0.7676 0.6890 0.8650 0.7826 0.7067 0.8179 0.6982 0.7524 0.7995 0.6977 PDm MECI 0.6562 0.6620 0.7530 0.6574 0.7402 0.6253 0.8522 0.7507 0.6580 0.7929 0.6450 0.7147 0.7700 0.6432 MECI MECII 0.5121 0.5191 0.6232 0.5135 0.6091 0.4786 0.7551 0.6204 0.5151 0.6732 0.5010 0.5788 0.6438 0.4983 MECII p (HWE) 0.7793 0.7268 0.0291 0.0248 0.2664 0.6202 0.4761 0.4936 0.4618 0.3779 0.9174 0.2490 0.1055 0.9458 p (HWE) Supplementary Table 1. Allele frequencies and Summary Statistics for 14 X chromosomal markers in a population from Bosnia and Herzegovina

Population Data at Two Short Tandem Repeat Loci D2S1338 and D19S433 in the Sample of Multinational Bosnia and Herzegovina Residents

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%]).