The past two years have seen the increased study of Y-chromosome polymorphisms and their relationship to human evolution and variation. Low Y-chromosome sequence diversity indicates that the common ancestor of all extant Y chromosomes lived relatively recently and the consensus of estimates of time to the most recent common ancestor concur with estimates of the mitochondrial DNA ancestor; but we do not know where this ‘Adam’ lived. Though the reason for low nucleotide diversity on the Y-chromosome remains unresolved, some of the mutations are proving highly informative in tracing human prehistoric migrations and are generating new hypotheses on human colonizations and migrations. The recent discovery of highly polymorphic microsatellites on the Y offers new possibilities for the investigation of more recent human evolutionary events, including the identification of male founders. Show
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Genetic Y chromosome markers characterize paternal inheritance, since they are fully transmitted to next generations unless mutations occur [1–3]. Y short tandem repeats markers (Y-STRs) are widely applied in forensic genetics because of their high capacity of discriminate lineages. Show abstractNavigate Down Y chromosome genetic markers are used for characterization of male lineages, since they are fully transmitted to next generations unless mutations occur. RM-YSTRs markers display high mutation rates, which is unusually observed in other Y-STRs markers, and seem to be efficient in discriminating paternally related males. The aim of this study was to estimate population and mutational parameters of 13 RM-YSTRs in 258 males born in Rio de Janeiro, Brazil. Population analysis showed high discrimination capacity and no population substructure. Elevated mutation rates were found in this population. For a better characterization of these loci in different Brazilian populations more studies are needed. 2012, Gene Citation Excerpt : Considering the low levels of J1, J2 and G, it is interesting that 5 centuries of occupation by the Ottoman empire did not impacted substantially the patrilineage component of Serbia. Furthermore, although only present at nominal frequencies, Serbian J chromosomes display a very high haplotype diversity likely reflecting the different Middle Eastern migrations that have been associated with this haplogroup (Mitchell and Hammer, 1996; Semino et al., 1996). In addition, this high diversity within J2 lineages from Serbia, as well as other Balkan populations relative to other European groups is consistent with the diffusion of these lineages into Europe from the southern Balkans (Di Giacomo et al., 2004; Semino et al., 2004). Show abstractNavigate Down Whether present-day European genetic variation and its distribution patterns can be attributed primarily to the initial peopling of Europe by anatomically modern humans during the Paleolithic, or to latter Near Eastern Neolithic input is still the subject of debate. Southeastern Europe has been a crossroads for several cultures since Paleolithic times and the Balkans, specifically, would have been part of the route used by Neolithic farmers to enter Europe. Given its geographic location in the heart of the Balkan Peninsula at the intersection of Central and Southeastern Europe, Serbia represents a key geographical location that may provide insight to elucidate the interactions between indigenous Paleolithic people and agricultural colonists from the Fertile Crescent. In this study, we examine, for the first time, the Y-chromosome constitution of the general Serbian population. A total of 103 individuals were sampled and their DNA analyzed for 104 Y-chromosome bi-allelic markers and 17 associated STR loci. Our results indicate that approximately 58% of Serbian Y-chromosomes (I1-M253, I2a-P37.2 and R1a1a-M198) belong to lineages believed to be pre-Neolithic. On the other hand, the signature of putative Near Eastern Neolithic lineages, including E1b1b1a1-M78, G2a-P15, J1-M267, J2-M172 and R1b1a2-M269 accounts for 39% of the Y-chromosome. Haplogroup frequency distributions in Western and Eastern Europe reveal a spotted landscape of paleolithic Y chromosomes, undermining continental-wide generalizations. Furthermore, an examination of the distribution of Y-chromosome filiations in Europe indicates extreme levels of Paleolithic lineages in a region encompassing Serbia, Bosnia-Herzegovina and Croatia, possibly the result of Neolithic migrations encroaching on Paleolithic populations against the Adriatic Sea. 2007, Forensic Science International Citation Excerpt : Short tandem repeat markers (STR) from the MSY (male specific region Y) on the Y chromosome are useful for studying the male specific lineage evolution [1–4] and forensic applications [5–10]. Show abstractNavigate Down Haplotype frequencies for 11 Y-STR markers (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438 and DYS439) in a Romani population (n = 63) from Slovakia, Jats of Haryana (n = 84) and Jat Sikhs (n = 80) from India were determined. The Slovakian Romani, the Haryana and Sikh populations were endogamous based on their unique haplotype ratio and haplotype diversity values, although the Sikh population appeared to be more diverse. AMOVA revealed non-significant differences between the Romanies and significant differences with non-Romani populations. The Macedonian Romani population differed from all Romani populations examined. Frequent haplotypes observed in Romani populations were sporadic in northwest Indian populations. Thirteen out of 316 populations worldwide were found to share the six most frequent haplotypes of the Slovakian Romanies when the screening conditions were narrowed based on the population size to be over 40, the occurrence of the haplotypes was more than one and the sum frequencies of the most frequent haplotypes was at least 0.02. The most common haplotypes were also observed in other Romani groups. When searching with two Indian (Malbar and Malaysian Indian) most frequent haplotypes under the same conditions matches could be detected in all Romani populations except for the Macedonian Romanies. The search with the Jat Sikhs and Jats of Haryana most frequent haplotypes resulted no matches in Romani populations. 2004, Legal Medicine Show abstractNavigate Down This study reports the first data on Y-chromosome-specific short tandem repeat (STR) haplotype frequencies, in the population of the island of Sicily (Italy), based on the combination of alleles at the following 10 Y-chromosome loci DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, and DYS439. In a total of 117 males, 108 unique haplotypes were observed, with 99 of them being singletons. The 10 locus haplotypes generated a diversity value of 0.9987 and discriminatory power (DP) of 92.30%. The data on the seven of the 10 polymorphisms (DYS19; DYS389I; DYS389II; DYS390; DYS391; DYS392 and DYS393) that have been most studied in worldwide populations were compared with similar data from neighboring Mediterranean populations in order to address the question of shared ancestry, gene flow and population affinities. Overall, results indicate Sicily is closest genetically to the mainland Italian population but also with evidence of a significant African component in the male gene pool. These findings are consistent with those obtained from other genetic markers (autosomal and mitochondrial DNA as well as the classical blood groups) and also with the recorded settlement history (either peaceful or due to invasion) of the island. 2004, Forensic Science International Show abstractNavigate Down In this study, we analyzed allelic sequences of 10 novel Y-specific STR loci, DYS454, DYS510, DYS513, DYS520, DYS542, DYS544, DYS552, DYS561, DYS587 and DYS593, surveyed the distribution of haplotypes in a Chinese Han population. Extracted DNA was amplified with PCR, followed by a horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system. Purified alleles were sequenced on DNA sequencer (ABI Model 377) to verify the number of motif repeats. The number of alleles observed at each locus ranged from 3 to 8, yielding 102 haplotypes in 103 unrelated males samples. The allele diversity values for each locus ranged from 0.2099 (DYS544) to 0.7523 (DYS552). The haplotype diversity using all these loci was 0.9998. Our study revealed that they were valuable Y-specific markers for forensic applications. Y-chromosome and mtDNA polymorphisms in Iraq, a crossroad of the early human dispersal and of post-Neolithic migrations2003, Molecular Phylogenetics and Evolution Show abstractNavigate Down Analyses of mtDNA and Y-chromosome variation were performed in a sample of Iraqis, a scarcely investigated population of the “Fertile Crescent.” A total of 216 mtDNAs were screened for the diagnostic RFLP markers of the main Eurasian and African haplogroups. A subset of these samples, whose HVS-I sequences were previously obtained, was also examined by high-resolution restriction analysis. The Y-chromosome variation was investigated in 139 subjects by using 17 biallelic markers and the 49a,f/Taq I system. For both uniparental systems, the large majority of the haplogroups observed in the Iraqi population are those (H, J, T, and U for the mtDNA, and J(xM172) and J-M172 for the Y chromosome) considered to have originated in the Middle East and to have later spread all over Western Eurasia. However, about 9% of the mtDNAs and 30% of the Y-chromosomes most likely represent arrivals from distant geographic regions. The different proportion of long-range genetic input observed for the mtDNA and the Y chromosome appears to indicate that events of gene flow to this area might have involved mainly males rather than females. Research article Forensic Science International: Genetics, Volume 7, Issue 6, 2013, pp. 568-572 Show abstractNavigate Down We have compared phylogenies and time estimates for Y-chromosomal lineages based on resequencing ∼9 Mb of DNA and applying the program GENETREE to similar analyses based on the more standard approach of genotyping 26 Y-SNPs plus 21 Y-STRs and applying the programs NETWORK and BATWING. We find that deep phylogenetic structure is not adequately reconstructed after Y-SNP plus Y-STR genotyping, and that times estimated using observed Y-STR mutation rates are several-fold too recent. In contrast, an evolutionary mutation rate gives times that are more similar to the resequencing data. In principle, systematic comparisons of this kind can in future studies be used to identify the combinations of Y-SNP and Y-STR markers, and time estimation methodologies, that correspond best to resequencing data. Research article The American Journal of Human Genetics, Volume 98, Issue 4, 2016, pp. 728-734 Show abstractNavigate Down Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447–806 kya). This is ∼2.1 (95% CI: 1.7–2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups. Research article The evolutionary history of Southern AfricaCurrent Opinion in Genetics & Development, Volume 53, 2018, pp. 157-164 Show abstractNavigate Down The genomic variability of Southern African groups is characterized by an exceptional degree of diversity, which is the result of long-term local evolutionary history, migrations and gene-flow. Over the last few years several investigations have identified and described signatures related to these processes, revealing how ancient and more recent events have shaped the structure and ancestry composition of local populations. Here we discuss recent insights into the genetic history of the Southernmost part of the African continent provided by the analysis of modern and ancient genomes. Future work is expected to clarify the population dynamics associated with the emergence of Homo sapiens across Africa and the details of the process of dispersion and admixture associated with the arrival of Bantu-speaking groups in the region. Research article The efficiency of Y-chromosome markers in forensic trace analysis and their inclusion in the Austrian National DNA DatabaseForensic Science International: Genetics Supplement Series, Volume 4, Issue 1, 2013, pp. e172-e173 Show abstractNavigate Down Y-STR markers are a valuable tool in the analysis of biological traces in which a mixture of male and female trace material is to be expected. It is possible to generate a Y-chromosome DNA profile, even if all the prior sperm tests are negative and no sign of any male component is found in amelogenin. In 38 of a total of 239 sexual offences a perpetrator trace was identified solely using Y-STR analysis. Based on these findings, the Austrian National DNA Database was expanded to include Y-STRs in 2012 with the primary objective to identify serial sexual offences. Research article Selection in utero and population health: Theory and typology of researchSSM - Population Health, Volume 5, 2018, pp. 101-113 Show abstractNavigate Down Public health researchers may assume, based on the fetal origins literature, that “scarring” of birth cohorts describes the population response to modern-day stressors. We contend, based on extensive literature concerned with selection in utero, that this assumption remains questionable. At least a third and likely many more of human conceptions fail to yield a live birth. Those that survive to birth, moreover, do not represent their conception cohort. Increasing data availability has led to an improved understanding of selection in utero and its implications for population health. The literature describing selection in utero, however, receives relatively little attention from social scientists. We aim to draw attention to the rich theoretical and empirical literature on selection in utero by offering a typology that organizes this diverse work along dimensions we think important, if not familiar, to those studying population health. We further use the typology to identify important gaps in the literature. This work should interest social scientists for two reasons. First, phenomena of broad scholarly interest (i.e., social connectivity, bereavement) affect the extent and timing of selection in utero. Second, the life-course health of a cohort depends in part on the strength of such selection. We conclude by identifying new research directions and with a reconciliation of the apparent contradiction between the “fetal origins” literature and that describing selection in utero. Research article Late Middle Pleistocene hominin teeth from Panxian Dadong, South ChinaJournal of Human Evolution, Volume 64, Issue 5, 2013, pp. 337-355 Show abstractNavigate Down The hominin teeth and evidence of hominin activities recovered from 1991 to 2005 at the Panxian Dadong site in South China are dated to the late Middle Pleistocene (MIS 8–6 or ca. 130–300 ka), a period for which very little is known about the morphology of Asian populations. The present study provides the first detailed morphometric description and comparisons of four hominin teeth (I1, C1, P3 and P3) from this site. Our study shows that the Panxian Dadong teeth combine archaic and derived features that align them with Middle and Upper Pleistocene fossils from East and West Asia and Europe. These teeth do not display any typical Neanderthal features and they are generally more derived than other contemporaneous populations from Asia and Africa. However, the derived traits are not diagnostic enough to specifically link the Panxian Dadong teeth to Homo sapiens, a common problem when analyzing the Middle Pleistocene dental record from Africa and Asia. These findings are contextualized in the discussion of the evolutionary course of Asian Middle Pleistocene hominins, and they highlight the necessity of incorporating the Asian fossil record in the still open debate about the origin of H. sapiens. Why is the Y chromosome ideal for tracking ancestry?It turns out that because the Y chromosome, unlike the other human chromosomes, does not have a nearly identical partner, Y-DNA can be traced far back into the past. In fact, every living male can trace their Y-DNA back to a single man, Y-Adam (as he is known).
Why is Y chromosome DNA important in Archaeology?Y- chromosomal DNA evidence suggests a date for the arrival of humans in the Americas anywhere between 10-20,000 years ago. This suggests human occupation of the Americas prior to the rise of the Clovis lithic culture, but makes the earliest proposed dates of human arrivals some 25,000 years ago.
What is the significance of the Y chromosome?The Y chromosome contains a "male-determining gene," the SRY gene, that causes testes to form in the embryo and results in development of external and internal male genitalia. If there is a mutation in the SRY gene, the embryo will develop female genitalia despite having XY chromosomes.
Is the Y chromosome evolution?The human Y chromosome is intriguing not only because it harbours the master-switch gene that determines gender but also because of its unusual evolutionary history. The Y chromosome evolved from an autosome, and its evolution has been characterized by massive gene decay.
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