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Journal Article Archive 2016-10-14T01:03:42+00:00

Journal Article Archive

Y-chromosome short tandem repeat intermediate variant alleles DYS3922, DYS4492, and DYS3852 delineate new phylogenetic substructure in human Y-chromosome haplogroup tree

Journal: Croatian medical journal | Year: 2009

Abstract:

AIM:
To determine the human Y-chromosome haplogroup backgrounds of intermediate-sized variant alleles displayed by short tandem repeat (STR) loci DYS392, DYS449, and DYS385, and to evaluate the potential of each intermediate variant to elucidate new phylogenetic substructure within the human Y-chromosome haplogroup tree.
METHODS:
Molecular characterization of lineages was achieved using a combination of Y-chromosome haplogroup defining binary polymorphisms and up to 37 short tandem repeat loci. DNA sequencing and median-joining network analyses were used to evaluate Y-chromosome lineages displaying intermediate variant alleles.
RESULTS:
We show that DYS392.2 occurs on a single haplogroup background, specifically I1*-M253, and likely represents a new phylogenetic subdivision in this European haplogroup. Intermediate variants DYS449.2 and DYS385.2 both occur on multiple haplogroup backgrounds, and when evaluated within specific haplogroup contexts, delineate new phylogenetic substructure, with DYS449.2 being informative within haplogroup A-P97 and DYS385.2 in haplogroups D-M145, E1b1a-M2, and R1b*-M343. Sequence analysis of variant alleles observed within the various haplogroup backgrounds showed that the nature of the intermediate variant differed, confirming the mutations arose independently.
CONCLUSIONS:
Y-chromosome short tandem repeat intermediate variant alleles, while relatively rare, typically occur on multiple haplogroup backgrounds. This distribution indicates that such mutations arise at a rate generally intermediate to those of binary markers and STR loci. As a result, intermediate-sized Y-STR variants can reveal phylogenetic substructure within the Y-chromosome phylogeny not currently detected by either binary or Y-STR markers alone, but only when such variants are evaluated within a haplogroup context.

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

Y-chromosome STRs in an Antioquian (Colombia) population sample

Journal: Forensic Science International | Year: 2006

Abstract:

Haplotype data were obtained from a sample of 777 unrelated male individuals from Antioquia Department (Colombia), for eight Y-chromosome STRs (DYS19, DYS385, DYS389 I, DYS389 II, DYS390, DYS391, DYS392 and DYS393). A total of 442 different haplotypes were identified of which 334 were represented only once in the database and the most frequent haplotype was found in 32 individuals. A high haplotype diversity was found (99.45%). Genetic distances were calculated using previously published haplotype data and the lowest values were found for the comparisons with samples of lberian origin.

Peoples: - | Places: Antioquia Department and Colombia | Topics: - | DNA Type: Y-STR

Y-Chromosome Variability in Four Native American Populations from Panama

Journal: Human Biology | Year: 2008

Abstract:

The allele and haplotype frequencies for 13 Y-chromosome short tandem repeats (STRs) [nine STR loci of the minimal Y-chromosome haplotype (DYS19 -DYS385a -DYS385b -DYS389I -DYS389II -DYS390 -DYS391 – DYS392 -DYS393) plus four additional loci (DYS388, DYS426, DYS439, DXYS156)] were determined in 99 males from 4 Panamanian native American populations, including the Chibcha-speaking Ngöbé and Kuna and the Chocóspeaking Emberá and Wounan. Fifty haplotypes were identified, of which 48 (96%) were specific to a single population and 29 (63%) were found in only a single individual. Gene diversity per locus per population ranged from 0 to 0.814, with the highest gene diversity present at the DYS389II locus in the Emberá. The haplotypic discrimination capacity was low, ranging from 42.3% in the Kuna to 63.1% in theWounan. The four tribes showed a high degree of differentiation both at the Y chromosome and in the mitochondrial genome, highlighting the importance of genetic structure even in geographically proximate and linguistically related populations.

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

Y-chromosome variation and Irish origins

Journal: Nature | Year: 2000

Abstract:

Ireland's position on the western edge of Europe suggests that the genetics of its population should have been relatively undisturbed by the demographic movements that have shaped variation on the mainland. We have typed 221 Y chromosomes from Irish males for seven (slowly evolving) biallelic and six (quickly evolving) simple tandem-repeat markers. When these samples are partitioned by surname, we find significant differences in genetic frequency between those of Irish Gaelic and of foreign origin, and also between those of eastern and western Irish origin. Connaught, the westernmost Irish province, lies at the geographical and genetic extreme of a Europe-wide cline.

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

Y-SNP haplogroups in the Antalya population in Turkish Republic

Journal: Romanian Journal of Legal Medicine | Year: 2009

Abstract:

SNPs are known to be the most abundant source of sequence variation in the human genome. The SNPs in the NRY (non-recombining Y-chromosome) region which passes from father to son as unchanged haplotype-blocks escaping recombination, provides important advantages in the investigations of sexual assault crimes, in the cases of parentage testing especially if the mother or alleged father is unavailable for testing and in the evolutionary studies. The aim of this study, was to determine the frequencies of Y SNP markers and the haplogroups, in order to define the Y-chromosome SNP markers which are polymorphic, have high discrimination power and can be used in forensic investigations in the Antalya population. For each of 75 unrelated males from Antalya, 35 different Y-SNP markers were amplified in a single reaction using multiplex minisequencing method. In the study, 18 markers of them were found to be polymorphic. The most frequent YSNP markers with mutations were M139 (100%), SRY10831/SRY1532 (92%), M89 (85.3%), M213 (85.3%), M9 (44%), 92R7 (30.6%), 12F2 (30.6%), M45 (29.3%), M172 (26.6%) and M173 (22.6%). The Y-chromosome haplogroups of Antalya population were defined by these 18 Y-SNP polymorphic loci and the frequencies and the distribution of haplogroups were determined. J2*(xJ2F2) (26.6%), K*(xN3,O,P) (13.3%), E3b (9.3%), F*(xH,I,J,K) (8%), R1a1*(xR1a1b) (8%), R1b*(xR1b1, R1b6, R1b8) (8%), P*(xQ3a,R1) (8%) haplogroups were identified as the most abundant in Antalya population. These haplogroups are reported as widespread also in European and neighboring Near Eastern populations.

Peoples: | Places: | Topics: | DNA Type:

Y-SNPs analysis using two different approaches in a Northern Portugal male population sample

Journal: Forensic Science International: Genetics Supplement Series | Year: 2008

Abstract:

The non-recombining portion of the human Y (NRY) chromosome has various types of variation, including single nucleotide polymorphism (SNP). In spite of their low discrimination power, they provide a powerful and simple exclusion tool for forensic purposes. A special advantage of SNPs is that it can potentially detect smaller DNA fragments (analysis of degraded DNA). The aim of this work consisted in the analysis of a group of SNP polymorphisms (M2, M9, M35, M89, M45, M170, M172, M173, M207 and P25) in a Northern Portugal male population sample, which allows the determination of the most common European haplogroups, including the Northern Portugal ones. The method used for typing these polymorphisms was the real-time PCR with TaqMan probes on the ABI 7000 platform (Applied Biosystems). We had some difficulties in typing some of the markers using this approach. However, the preliminary results obtained for the defined haplogroups are in accordance with those described in close European populations. To confirm the typing and solve the doubts that emerged from the real-time approach, the samples were also typed using SNapShot.

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

Y-STR analysis in Brazilian and South Amerindian populations

Journal: American Journal of Human Biology | Year: 2008

Abstract:

A sample of 203 Brazilian males from Rio Grande do Sul (RS), the Brazilian southernmost state, was typed for 11 Y-STR markers (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, and DYS439). We also typed 42 individuals from two South Amerindian tribes (Kaingang and Guarani) to use the data as parental Amerindian contribution to our analyses. Gene and haplotypic diversities were estimated, with the South Amerindian samples showing smaller values for these parameters than Brazilians. To obtain a more comprehensive picture of the genetic structure of the Brazilian population as a whole, the Y-STR data from the RS sample was compared with those already published. No genetic substructuring was observed in the comparisons performed. Multidimensional scaling confirmed the proposed European source of most Y-chromosome Brazilian patrilineages. Am. J. Hum. Biol., 2008. copyright 2007 Wiley-Liss, Inc.

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

Y-STR diversity and sex-biased gene flow among Caribbean populations

Journal: Gene | Year: 2013

Abstract:

In the present study, we report, for the first time, the allele and haplotype frequencies of 17 Y-STR (Y-filer) loci in the populations of Haiti, Jamaica and the Bahamas (Abaco, Eleuthera, Exuma, Grand Bahama, Long Island and New Providence). This investigation was undertaken to assess the paternal genetic structure of the abovementioned Caribbean islands. A total of 607 different haplotypes were identified among the 691 males examined, of which 537 (88.5%) were unique. Haplotype diversities (HD) ranged from 0.989 in Long Island to 1.000 in Grand Bahama, with limited haplotype sharing observed among these Caribbean collections. Discriminatory capacity (DC) values were also high, ranging from 79.1% to 100% in Long Island and Grand Bahama, respectively, illustrating the capacity of this set of markers to differentiate between patrilineal related individuals within each population. Phylogenetic comparison of the Bahamian, Haitian and Jamaican groups with available African, European, East Asian and Native American populations reveals strong genetic ties with the continental African collections, a finding that corroborates our earlier work using autosomal STR and Y-chromosome binary markers. In addition, various degrees of sex-biased gene flow exhibiting disproportionately higher European paternal (as compared to autosomal) influences were detected in all Caribbean islands genotyped except for Abaco and Eleuthera. We attribute the presence or absence of asymmetric gene flow to unique, island specific demographic events and family structures.

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

Y-STR genetic diversity in autochthonous Andalusians from Huelva and Granada provinces (Spain)

Journal: Forensic Science International: Genetics | Year: 2012

Abstract:

Seventeen Y-chromosomal short tandem repeats (STRs) were analyzed in 347 healthy, unrelated, autochthonous males from the Andalusian provinces of Huelva (N = 167) and Granada (N = 180). AmpFlSTR Y-filer PCR Amplification kit (Applied Biosystems) was used to type the Y-STR markers. A total of 156 and 166 different haplotypes for the 17 Y-STR set were detected in Huelva, and Granada, respectively. The same haplotype diversity was found for both samples (0.998 ± 0.001), and the overall discrimination capacity was 0.904. The most common minimal haplotype (DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393) in both subpopulations was 14-13-16-24-11-13-13, which is also the most frequent haplotype among Atlantic European populations. Comparison analysis using pairwise RST values and Analysis of Molecular Variance (AMOVA) revealed a significant genetic distance between our Andalusian samples and other ones from the northern Iberian fringe (including Basque and Pyrenean populations). However, results from the multi-dimensional scaling analysis (MDS) yielded a well-defined group of Iberian populations separated from the other Mediterranean clusters observed.

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

Y-STR genetic diversity of Croatian (Bayash) Roma

Journal: Forensic Science International: Genetics | Year: 2008

Abstract:

Seventeen Y-chromosomal short tandem repeats (STRs) (DYS19, DYS385, DYS389I, DYS398II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATA H4.1) were typed in DNA samples from 146 unrelated adult Romani Bayash men from eastern and northwestern Croatia. Analysed Croatian Bayash Romani population represents an example of genetically homogenous population characterised by low levels of haplotype diversity and unique haplotype ratio as well as sharing of the same most frequent (founding) haplotype and its close derivatives by more than one third of the analyzed men. Despite almost exclusive sharing of the same minimal haplotype and its closely related derivates on the background of the Indian Y SNP haplogroup H1, we observed considerable level of genetic differentiation of Romani populations across Europe that should not be neglected in forensic statistics.

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

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