Population data for 12 Y-chromosome STR loci in a sample from El Salvador

Haplotype, allele frequencies and population data of 12 Y-chromosome STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 were determined from a sample of 150 unrelated male individuals from El Salvador, Central America. A total of 131 haplotypes were identified by the 12 Y-STR loci of which 118 were unique. The haplotype diversity (99.08%) and the proportion of different haplotypes (87.33%) were estimated. R_ST genetic distances were calculated between El Salvador and other populations from Southern and Central America, Europe and Africa. The highest R_ST genetic distances were found when comparing El Salvador with African populations (0.334 ? R_ST ? 0.395). The lowest non-significant distance was found in the comparison with Honduras. The observed genetic distances between El Salvador and Southern and Central Native groups presented a wide range of values (from 0.024 to 0.210) that can be explained by the differences in the proportion of European versus Amerindian contributions in these population groups. The Multi Dimensional Scaling (MDS) plot analysis, based on pairwise R_ST values, showed that the general population of El Salvador is closer to the European cluster (composed by European and South American general population samples from Brazil, Argentina, Colombia and Venezuela) than to the Southern/Central American cluster of Native and Mestizo populations.     

The effects of Asian population substructure on Y STR forensic analyses

A total of 3046 males of Chinese, Malay, Thai, Japanese, and Indian population affinity were previously typed for the Y STR loci DYS19, DYS385 (counted as two loci), DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS456, DYS458, DYS635, DYS448, and Y GATA H4 using the AmpFlSTR® Yfiler™ kit. These samples were assessed for population genetic parameters that impact forensic statistical calculations. All population samples were highly polymorphic for the 16 Y STR markers with the marker DYS385 being the most polymorphic, because it is comprised of two loci. Most (2677 out of a total of 2806 distinct haplotypes) of the 16 marker haplotypes observed in the sample populations were represented only once in the data set. Haplotype diversities were greater than 99.57% for the Chinese, Malay, Thai, Japanese, and Indian sample populations. For the Y STR markers, population substructure correction was considered when calculating the rarity of a Y STR profile. An F_ST value, rather than a R_ST value, is more appropriate under a forensic model. Because the F_ST values are very small within the Asian populations, the estimate of the rarity of a haplotype comprised of 10–16 markers does not need substructure correction. However haplotypes with fewer markers may require F_ST corrections when calculating the rarity of the profile.     

Haplotype analysis of the polymorphic 40 Y-STR markers in Chinese populations

Forty Y-STR loci were analyzed in 1128 males from the following six Chinese ethnic populations: Han (n = 300), Hui (n = 244), Korean (n = 100), Mongolian (n = 100), Uighur (n = 284) and Tibetan (n = 100), utilizing two new generation multiplex Y-STR systems, AGCU Y24 STR and GFS Y24 STR genotyping kits, which allow for the genotyping of 24 loci from a single amplification reaction in each system. The lowest estimates of genetic diversity (below 0.5) correspond to markers DYS391 (0.441658) and DYS437 (0.496977), and the greatest diversity corresponds to markers DYS385a/b (0.969919) and DYS527a/b (0.94676). A considerable number of duplicate and off-ladder alleles were also revealed. Additionally, there were 1111 different haplotypes identified from the total 1128 samples, of which 1095 were unique. Notably, no shared haplotypes between populations were observed. The estimated overall haplotype diversity (HD) was 0.999085, and its discrimination capacity (DC) was 0.970745. An MDS plot based on the genetic distances between populations showed the genetic similarity of the southern Han population to the Northern populations of Hui, Korean, Mongolian and Uighur and a clear genetic departure of the Tibetan population from other populations. For the Y STR markers, population substructure correction was considered when calculating the rarity of the Y STR profile. However, because the haplotype based Fst values are extremely small within the present data (0.000153 with 40 Y-STRs), no substructure correction is required to estimate the rarity of a haplotype comprising 40 markers. In summary, the results of our study indicate that the 40 Y-STRs have a high level of polymorphism in Chinese ethnic groups and could therefore be a powerful tool for forensic applications and population genetic studies.     

Population data for 12 Y-chromosome STR loci in a sample from Honduras

Haplotype, allele frequencies and population data of 12 Y-chromosome STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 were determined from a sample of 128 unrelated male individuals from Honduras, Central America. A total of 112 haplotypes were identified by the 12 Y-STR loci of which 98 were unique. The haplotype diversity (98.99%) and the proportion of different haplotypes (87.50%) were estimated. Genetic distances were calculated between Honduras and other populations from Southern and Central America, Europe and Africa. The analysis of a Multi Dimensional Scaling (MDS) plot, based on pairwise R_ST genetic distances, allowed to conclude that Honduras is highly differentiated from the African samples (0.343  R_ST  0.620; P = 0.000) and from a Native American sample from Argentina, Tobas (R_ST = 0.210, P = 0.000). Honduras showed a lower genetic distance to the European cluster (composed by European and South American general population samples from Brazil, Argentina, Colombia and Venezuela) than to the Central American cluster (Mexico and El Salvador).     

Genetic population study of Y-chromosome markers in Benin and Ivory Coast ethnic groups

Ninety-six single nucleotide polymorphisms (SNPs) and seventeen short tandem repeat (STRs) were investigated on the Y-chromosome of 288 unrelated healthy individuals from populations in Benin (Bariba, Yoruba, and Fon) and the Ivory Coast (Ahizi and Yacouba). We performed a multidimensional scaling analysis based on F_ST and R_ST genetic distances using a large extensive database of sub-Saharan African populations. There is more genetic homogeneity in Ivory Coast populations compared with populations from Benin. Notably, the Beninese Yoruba are significantly differentiated from neighbouring groups, but also from the Yoruba from Nigeria (F_ST > 0.05; P < 0.01). The Y-chromosome dataset presented here provides new valuable data to understand the complex genetic diversity and human male demographic events in West Africa.     

Population and forensic data for three sets of forensic genetic markers in four ethnic groups from Iran: Persians,Lurs, Kurds and Azeris

A total of 255 individuals (Persians, Lurs, Kurds and Azeris) from Iran were typed for three sets of forensic genetic markers with the NGM SElect™, DIPplex^® and Argus X-12 kits. Statistically significant deviations (P ≤ 0.002) from Hardy–Weinberg expectations were observed for the insertion-deletion markers HLD97 and HLD93 after Holm–Šidák correction. Statistically significant (P < 0.05) levels of linkage disequilibrium were observed between markers within two of the four studied X-chromosomal linkage groups. AMOVA analyses of the three sets of markers did not show population structure when the individuals were grouped according to their ethnic group. The Iranian population grouped closely to populations living geographically near to Iran based on pairwise F_ST distances. The matching probabilities ranged from 1 in 3.2 × 10⁷ males by using haplotype frequencies of four X-chromosomal haplogroups to 1 in 3.4 × 10²¹ individuals for the 16 autosomal STRs.     

Results for five sets of forensic genetic markers studied in a Greek population sample

A population sample of 223 Greek individuals was typed for five sets of forensic genetic markers with the kits NGM SElect™, SNPforID 49plex, DIPplex^®, Argus X-12 and PowerPlex^® Y23. No significant deviation from Hardy–Weinberg expectations was observed for any of the studied markers after Holm–Šidák correction. Statistically significant (P < 0.05) levels of linkage disequilibrium were observed between markers within two of the studied X-chromosome linkage groups. AMOVA analyses of the five sets of markers did not show population structure when the individuals were grouped according to their geographic origin. The Greek population grouped closely to the other European populations measured by F_ST^* distances. The match probability ranged from a value of 1 in 2 × 10⁷ males by using haplotype frequencies of four X-chromosome haplogroups in males to 1 in 1.73 × 10²¹ individuals for 16 autosomal STRs.     

Y chromosome microsatellite genetic variation in two Native American populations from Argentina: Population stratification and mutation data

Two Native American populations from North and northwest regions of Argentina (Toba and Colla) were analyzed for 17 Y chromosome short tandem repeat loci (Y-STRs), namely, DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1. Over 357 allele transfers, two one-step mutations could be detected at DYS456 and GATA H4.1 loci. A new 16.1 ‘micro-variant’ allele was observed for DYS385, characterized by an insertion at the fifth GAAA repeat. We also observed two alleles at the DYS448 locus in three samples (two from Toba and one from Colla). A total of 34 and 16 different haplotypes were detected for Toba and Colla, respectively, the former with a haplotype diversity value of 0.9769 ± 0.01, whereas 0.9497 ± 0.02 for the latter. Significant population differences were observed between Colla and Toba, at least in part, due to a more prevalent European input in the Colla. In agreement with this observation is the fact that the genetic distances between Colla and Iberian populations are lower than those observed between Iberian and any other Native American population. The results of multiscaling dimensional analysis and genetic distances (Rst) among Native American population samples also reflect this fact. The data show the existence of clear population stratification in the Argentina, a fact that should be taken into account in forensic casework.     

Investigation of extended Y chromosome STR haplotypes in Sardinia

Y-chromosomal variation of selected single nucleotide polymorphisms (SNPs) and 32 short tandem repeat (STR) loci was evaluated in Sardinia in three open population groups (Northern Sardinia, n = 40; Central Sardinia, n = 56; Southern Sardinia, n = 91) and three isolates (Desulo, n = 34; Benetutti, n = 45, Carloforte, n = 42). The tested Y-STRs consisted of Yfiler^® Plus markers and the seven rapidly mutating (RM) loci not included in the YFiler^® Plus kit (DYF399S1, DYF403S1ab, DYF404S1, DYS526ab, DYS547, DYS612, and DYS626).As expected, inclusion of additional Y-STR loci increased haplotype diversity (h), though complete differentiation of male lineages was impossible even by means of RM Y-STRs (h = 0.99997).Analysis of molecular variance indicated that the three open populations were fairly homogeneous, whereas signs of genetic heterogeneity could be detected when the three isolates were also included in the analysis.Multidimensional scaling analysis showed that, even for extended haplotypes including RM Y-STR markers, Sardinians were clearly differentiated from populations of the Italian peninsula and Sicily. The only exception was represented by the Carloforte sample that, in accordance with its peculiar population history, clustered with Northern/Central Italian populations.The introduction of extended forensic Y-STR panels, including highly variable RM Y-STR markers, is expected to reduce the impact of population structure on haplotype frequency estimations. However, our results show that the availability of geographically detailed reference databases is still important for the assessment of the evidential value of a Y-haplotype match.     

Allele frequencies and haplotypes for 28 Y-STRs in Ovambo population

Y-chromosomal 28 short tandem repeat (STR) loci were investigated in unrelated healthy individuals of the Ovambo population from Namibia (n = 54). Sixteen Y-chromosome short tandem repeat (Y-STR) polymorphic loci (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385, DYS393, DYS391, DYS439, DYS635, DYS392, GATAH4, DYS437, DYS438, and DYS448) were analyzed using AmpFISTR Yfiler Polymerase Chain Reaction (PCR) Amplification Kit. DYS441–445 and DYS446, DYS447, DYS449, DYS450, DYS459a/b, DYS463 and DYS464a/b/c/d were investigated using a multiplex PCR system. Fifty-one haplotypes were identified in 54 Ovambos. The STR diversity values for Y-STRs loci ranged from 0.036 (DYS392) to 0.900 (DYS 385).     

Concordance study and population frequencies for 16 autosomal STRs analyzed with PowerPlex® ESI 17 and AmpFℓSTR® NGM SElect™ in Somalis,Danes and Greenlanders

A concordance study of the results of PowerPlex^® ESI 17 and AmpFℓSTR^® NGM SElect™ kits obtained from 591 individuals from Somalia (N = 198), Denmark (N = 199) and Greenland (N = 194) was performed. Among 9456 STR types, seven discordant results were found with the two kits: one observed in the D19S433 system in an individual from Denmark and six in the SE33 system in six individuals from Somalia. Sequencing of SE33 in the six samples with discordant results showed G > A transition 15 bp downstream of the repeat unit in three of the individuals, and G > A transition 68 bp downstream of the repeat unit in the other three individuals. Population data for 16 autosomal STR systems analyzed in 989 individuals from Somalia, Denmark and Greenland are also presented. The highest mean heterozygosity was observed in Danes (82.5%). With the exception of D8S1179 in Danes, no significant deviations from Hardy–Weinberg expectations were observed. Only one pair of systems (D12S391 and D18S51) showed significant allelic association in Greenlanders (after Holm-Šidák correction). A MDS plot drawn from pairwise F_ST values calculated between 21 populations showed a clear displacement of the Greenlandic population versus the other ones included in the analyses. The highest combined chance of exclusion and power of discrimination was observed for Danes reaching values of 99.9999987% and 1 in 1.8 × 10²¹, respectively.     

Haplotype and mutation analysis for newly suggested Y-STRs in Korean father–son pairs

In this study, 363 Korean father–son haplotype transfers in 351 families were analyzed using an in-house multiplex PCR system for 14 Y-STRs (DYS385a/b, DYF387S1, DYS391, DYS449, DYS460, DYS481, DYS518, DYS533, DYS549, DYS570, DYS576, DYS627 and DYS643), that included 11 loci newly added to the PowerPlex Y23 system or the Yfiler Plus system. The Y-STRs showed gene diversity values ranging from 0.2499 to 0.9612; the multicopy Y-STR loci DYS385 and DYF387S1 had high gene diversity of 0.9612 and 0.9457, respectively. In addition, DYF387S1, which has two copies, showed three alleles in seven individuals, and micro-variant alleles were observed in 14 individuals at four loci (DYS448, DYS518, DYS570 and DYS627). Among 351 haplotypes for the 11 newly added Y-STRs, 350 different haplotypes were observed, with an overall haplotype diversity of 0.9999 and discrimination capacity of 99.72%. In 363 haplotype transfers from 351 pedigrees, 29 single-step mutations were observed at 11 Y-STRs. Locus-specific mutation rate estimates varied from 0.0 to 1.93 × 10⁻², with an average estimated mutation rate of 6.66 × 10⁻³. Two father–son pairs had mutations at two different loci in 11 Y-STRs. The number of pairs with mutations at multiple loci increased to five when the mutation event was investigated for haplotype transfer at 28 Y-STRs including 17 Yfiler loci and 11 Y-STRs examined in this study: four father–son pairs had mutations at two loci, and one pair had mutations at three loci. Overall, mutations were frequently observed at DYS449, DYS576 and DYS627 loci, which are known to be rapidly mutating Y-STRs. Mutation rate estimates at most loci were not significantly different from rates in other populations, but estimates for DYF387S1, DYS518 and DYS570 were considerably lower in the Korean population than in other populations.     

Effects of obstacle height on obstacle crossing in mild Parkinson's disease

The aim of this study was to compare the locomotor behavior of people with Parkinson's disease (PD) and healthy older adults during obstacle negotiation, both in the approaching and crossing phases. Twelve people with idiopathic PD, with mild to moderate disease, and 12 healthy individuals (CG) walked across an 8 m pathway for three obstacle conditions: no obstacle, low obstacle and high obstacle. Each performed five trials for each obstacle condition. Performance was more disturbed for the high obstacle than the low obstacle. During the approach phase, people with PD demonstrated shorter stride length (F_1,22 = 8.55, P = 0.008) and greater stride duration (F_1,22 = 7.371, P = 0.013) than controls. Those with PD also increased their stance phase durations (F_1,22 = 7.426, P = 0.012) for both obstacle conditions, while the CG maintained comparable step durations for all conditions. For the crossing phase, people with PD demonstrated shorter step length (F_1,22 = 9.699, P = 0.005) over the obstacle. Leading limbs were closer to the obstacle, before and after crossing. Thus PD hypokinesia compromises the approach and crossing phases of obstacle negotiation.     

Population genetics of 17 Y-STR markers in West Libya (Tripoli region)

Seventeen Y-chromosomal Short Tandem Repeats (Y-STR) included in the AmpFlSTR Y-filer PCR Amplification kit (Applied Biosystems) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4) were genotyped in a population sample of 176 unrelated males from western Libya (Tripoli region). A total of 142 different haplotypes were found, 124 being unique. Haplotype diversity was 0.9950. Both R_ST pairwise analyses and multidimensional scaling plot show a close genetic relationship between Tripoli and North African populations.     

Haplotype frequencies of the PowerPlex® Y system in a Mexican-Mestizo population sample from Mexico City

The PowerPlex^® Y system including 11 Y-STRs (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438 and DYS439) was analyzed by capillary electrophoresis in 357 males from Mexico City. Haplotype frequency for this system was reported. The haplotype diversity was 99.56 ± 0.04%, and gene diversity ranged from 51.4% for DYS393 to 92.5% for DYS385. AMOVA tests including previous reports from Mexico (Chihuahua and Jalisco States), demonstrated significant genetic heterogeneity between north and western populations regarding Mexico City, justifying the establishment of local databases in this country for male-identification purposes.     

Improving global and regional resolution of male lineage differentiation by simple single-copy Y-chromosomal short tandem repeat polymorphisms

We analyzed 67 short tandem repeat polymorphisms from the non-recombining part of the Y-chromosome (Y-STRs), including 49 rarely studied simple single-copy (ss)Y-STRs and 18 widely used Y-STRs, in 590 males from 51 populations belonging to 8 worldwide regions (HGDP-CEPH panel). Although autosomal DNA profiling provided no evidence for close relationship, we found 18 Y-STR haplotypes (defined by 67 Y-STRs) that were shared by two to five men in 13 worldwide populations, revealing high and widespread levels of cryptic male relatedness. Maximal (95.9%) haplotype resolution was achieved with the best 25 out of 67 Y-STRs in the global dataset, and with the best 3–16 markers in regional datasets (89.6–100% resolution). From the 49 rarely studied ssY-STRs, the 25 most informative markers were sufficient to reach the highest possible male lineage differentiation in the global (92.2% resolution), and 3–15 markers in the regional datasets (85.4–100%). Considerably lower haplotype resolutions were obtained with the three commonly used Y-STR sets (Minimal Haplotype, PowerPlex Y^®, and AmpFlSTR^® Yfiler^®). Six ssY-STRs (DYS481, DYS533, DYS549, DYS570, DYS576 and DYS643) were most informative to supplement the existing Y-STR kits for increasing haplotype resolution, or – together with additional ssY-STRs – as a new set for maximizing male lineage differentiation. Mutation rates of the 49 ssY-STRs were estimated from 403 meiotic transfers in deep-rooted pedigrees, and ranged from ∼4.8 × 10⁻⁴ for 31 ssY-STRs with no mutations observed to 1.3 × 10⁻² and 1.5 × 10⁻² for DYS570 and DYS576, respectively, the latter representing the highest mutation rates reported for human Y-STRs so far. Our findings thus demonstrate that ssY-STRs are useful for maximizing global and regional resolution of male lineages, either as a new set, or when added to commonly used Y-STR sets, and support their application to forensic, genealogical and anthropological studies.     

Fibular taping does not influence ankle dorsiflexion range of motion or balance measures in individuals with chronic ankle instability

ObjectivesTo determine the effects of fibular taping on ankle dorsiflexion range of motion (ROM) and dynamic balance in individuals with chronic ankle instability (CAI).DesignSingle-blind, randomized crossover.MethodsTwenty-three individuals (age = 23.4 ± 2.5 years, height = 171.6 ± 12.4 cm, mass = 71.5 ± 13.1 kg) with CAI were allocated to either a fibular taping intervention or sham taping intervention (tape applied without tension) over the course of two visits. Weight-bearing ankle dorsiflexion ROM and components of the Star Excursion Balance Test (SEBT) were measured before and after intervention.ResultsThere was not a significant change in ankle dorsiflexion ROM when comparing the taping interventions (F_1,43 = 1.03, P = .32), but both interventions resulted in a small increase (F_1,43 = 8.07, P = .007) in dorsiflexion ROM (pre = 36.7° ± 6.9°, post = 37.7° ± 6.2°). This increase in ROM did not exceed the established minimal detectable change for dorsiflexion ROM. Fibular taping with tension produced an increase (F_1,41 = 5.84, P = .02) (pre = 69.0 ± 9.1%, post = 70.6 ± 8.6%) in posterolateral reach distance when compared to taping without tension (pre = 72.7 ± 11.0%, post = 71.4 ± 9.6%), but this increase did not exceed the established minimal detectable change. There was not a significant change in dynamic balance between groups for the anterior (F_1,41 = 2.33, P = .14) and posteromedial (F_1,41 = .41, P = .53) reach directions.ConclusionsAlthough small changes in ankle dorsiflexion ROM and posterolateral reach distances were observed, these changes did not exceed established minimal detectable change values for these measures. These results suggest that the benefits of fibular taping are not related to an increase in ankle dorsiflexion ROM or dynamic balance.     

Genetic characterization of Guinea-Bissau using a 12 X-chromosomal STR system: Inferences from a multiethnic population

A male West African sample from Guinea-Bissau (West-African coast) was genetically analyzed using 12 X chromosomal short tandem repeats that are grouped into four haplotype groups. Linkage disequilibrium was tested (p ≤ 0.0008) and association was detected for the majority of markers in three out of the four studied haplotype clusters. The sample of 332 unrelated individuals analyzed in this study belonged to several recognized ethnic groups (n = 18) which were used to evaluate the genetic variation of Guinea-Bissau’s population. Pairwise genetic distances (F_ST) did not reveal significant differences among the majority of groups. An additional 110 samples from other countries also belonging to West Africa were as well compared with the sample of Guinea-Bissau. No significant differences were found between these two groups of West African individuals, supporting the genetic homogeneity of this region on the X chromosome level. The generation of over 100 DNA West African sequences provided new insights into the repeat sequence structure of some of the present X-STRs. Parameters for forensic evaluation were also calculated for each X-STR, supporting the potential application of these markers in typical kinship scenarios. Also, the high power of discrimination values for samples of female and male origin observed in this study, confirms the usefulness of the present X-STRs in identification analysis.     

Highly discriminatory capacity of the PowerPlex® Y23 System for the study of isolated populations

In order to evaluate the forensic utility of the new PowerPlex^® Y23 System, two Northern Spanish populations, the autochthonous Basque Country (N = 105) and Cantabria (N = 98), were typed. Two of the new markers incorporated in the panel, the rapid mutating loci DYS576 and DYS570, were among the most discriminative markers in both population datasets. In terms of the analysis of 23 Y-STRs, the two populations showed high haplotype diversities, with values slightly superior in the population of Cantabria (1 ± 0.0015) than in the Basque Country (0.9987 ± 0.0016). The comparison of the discrimination capacity obtained with the analysis of 23 Y-STRs and other available markers sets of 12 Y-STRs (PowerPlex^® Y System) or 17 Y-STRs (YFiler™), clearly demonstrated an improvement in the population of the Basque Country. Nevertheless, in Cantabria this augment was only seen when the number of markers was increased from 12 to 23, since the study of 17 Y-STRs was enough to differentiate all haplotypes. Therefore, this study shows that the improvement in forensic parameters by increasing the number of Y-STR markers analyzed is much more pronounced in the case of isolated populations such as the autochthonous population of the Basque Country, as it facilitates the differentiation among similar haplotypes. Moreover, by the use of the PowerPlex^® Y23 identification of population specific haplotypes increased in both populations. Ultimately, the analysis of 23 Y-STRs differentiated among the two geographically close populations of Basque Country and Cantabria. Indeed it showed significant differences between the Basque Country population and all European populations included, meanwhile Cantabria did exhibit significant proximity with the Iberian and the majority of European populations considered.