An ultra-high discrimination Y chromosome short tandem repeat multiplex DNA typing system

Genetic Diversity Based on the Analysis of 27 Y- Short Tandem Repetition (STR) Loci in Two Populations in the Apuseni Mountains, Romania

BACKGROUND

Y chromosome analysis is used in various fields of forensic genetics, genetic genealogy, and evolutionary research, due to its unique characteristics. Short tandem repetitions (STR) are particularly relevant in population genetic studies. The aim of this study is to analyze the genetic profile of two populations in the Apuseni Mountains area, Băița and Roșia Montană, Romania.

METHODS

27 STR loci of the Y chromosome were analyzed to investigate the genetic profile of two populations from the Apuseni Mountains area. Investigating genetic diversity by analyzing allele frequency, haplotype frequency, calculating forensic parameters, and presenting the main haplogroups identified based on Y-STR markers.

RESULTS

Gene diversity in the batch from Băița varies from 0.515 for the DYS393 locus to 0.947 for the DYS385 locus. In the Roșia Montană population, gene diversity ranges from 0.432 for DYS393 to 0.931 for DYS385. The haplotype diversity in Roșia Montană was 0.991, and the haplotype diversity was 1.000 in the population from Băița. A total of nine haplogroups was identified in the batch from Băița, while only seven haplogroups were observed in the batch from Roșia Montană. Both groups are based on the same five major haplogroups (E, G, I, J, and R) and the most common haplogroup is R1b in both populations.

CONCLUSION

In this study, the genetic diversity of two distinct populations was assessed using genetic analyses based on different markers. Analysis of Y-STR profiles revealed significant genetic diversity in both studied groups. All haplogroups identified were similar to those present in other Romanian populations.

Development and validation of a new multiplex for upgrading Y-STRs population databases from 12 to 23 markers and its forensic casework application

Y chromosomal short tandem repeats (Y-STRs) are used in forensic investigations as a useful complementary tool to autosomal markers. The ongoing development of new kits with an increasing number of markers makes it necessary to update populations typed in the Y-STR Haplotype Reference Database to reach at least 23 Y-STRs. A novel Y-STR multiplex panel was developed to offer a cost-efficient alternative to update Y-STR haplotypes from 12 to 23 loci. This panel includes the eleven markers, DYS448, DYS456, DYS458, DYS635, Y-GATA H4, DYS576, DYS481, DYS549, DYS533, DYS570 and DYS643, as well as DYS385a/b for traceability purpose. Developmental validation of this panel was conducted following the recommendations of the Scientific Working Group on DNA Analysis Methods (SWGDAM), showing high sensitivity, tolerance to common inhibitors as well as high species specificity. It was efficient for degraded DNA samples and for detection of male mixtures. When applying it for extending the current data of the Ibiza population, both the discrimination capacity and the haplotype diversity increased from 0.5952 to 0.9048 and from 0.9808 to 0.9977, respectively. Together, the study demonstrates the suitability of this panel in forensic casework.

Population and Mutational Assessment of Novel Repeats in 13RM Y-STRs in Unrelated Males Born in Gilgit, Pakistan

Because they are totally transferred to the future generations until mutations occur, Y chromosome genetic markers are commonly utilised in forensics for the classification of male lineages for criminal justice purposes. The mutation rate of Rapidly Mutating Y-STRs (RM Y-STRs) markers is high. That is not seen in other Y-STRs markers, and they appear to be effective in distinguishing paternally related men. This study aimed to estimate the population and mutational parameters of 13 RM Y-STRs in 13 unrelated males born in Gilgit, Pakistan. Repeat there was no population substructure and strong discriminating capacity in the counts. In this population, there were higher mutation rates with the unusual structure of repeats. More research is needed to better characterize these loci in diverse Pakistani groups.

A novel multiplex of 12 multicopy Y-STRs for forensic application

Y chromosomal short tandem repeats (Y-STRs) have been applied overwhelmingly in forensic areas for solving paternity identification and sexual assault cases. Yet the widely used Y-STR kits contain mostly single-copy markers, which may restrict the discrimination power. Here, a novel Y-STR multiplex was developed and validated in order to complement the currently available Y-STR kits, especially on differentiating male relatives. The assay includes twelve multicopy Y-STR loci (DYF371, DYF383S1, DYS385, DYF387S1, DYS389I/II, DYF399S1, DYF404S1, DYF409S1, DYF411S1, DYS464, DYS526, DYS527; four of them are rapidly mutating ones), 1 single-copy Y-STR (DYS391), and Amelogenin, and was optimized to amplify at annealing temperature of 59°C and 28 cycles. Validation studies show that full profiles are obtained with 0.125 ng of male DNA. The system is capable of overcoming high concentrations of inhibitors such as hematin, EDTA, and humic acid. Besides, the results demonstrate good sizing precision and the ability to detect male-specific profiles in male/female DNA mixtures at a ratio of 1:800. Excellent species specificity was also observed in microorganisms and non-primates, while detectable peaks were found in some primates. Based on published genetic data, gene diversity values were above 0.7 for most of the loci in our multiplex, inferring a high capacity in discriminating unrelated and related male individuals. The kit is of great potential for forensic application.

Comprehensive genetic structure analysis of Han population from Dalian City revealed by 20 Y-STRs

BACKGROUND

Dalian is a city formed in the 1880s in Liaoning province, Northeastern China with a population of 6.69 million now. Han is the largest ethnic group not only across Mainland China (92%) and Taiwan (97%) but also considered to be the largest ethnic group of the world contributing to above 18% of world's population.

METHODS

In the current study, we genotyped Goldeneye® 20Y System loci in 879 unrelated male individuals from the Han ethnic group in Dalian city and calculated the forensic parameters of the 20 Y-STR loci.

RESULTS

In total, we observed 855 haplotypes, among which 835 (94.99%) were unique. The discrimination capacity (DC) of overall Goldeneye® 20Y System is 97.27% and it slightly reduces to 96.93% when only Y-filer® set of 17 Y-STRs were used, which mitigates using the extended set of markers in this population. We found DYS388 showed the lowest gene diversity (0.5151), whereas DYS389II showed the highest gene diversity (0.7621) in single copy Y-STR, and DYS385 showed the highest gene diversity (0.9683) among all.

CONCLUSION

Multidimensional scaling (MDS) analysis based upon pairwise Rst genetic distance showed difference among Han population from the east to the west and from the north to the south. We also predicted haplogroups using Y-STR haplotypes, which showed the dominance of Haplogroup O (65.2%) followed by Haplogroup C (14.5%) in Dalian Han population. Moreover, we found 10 individuals showed a null allele at the DYS448 in our samples. We also performed linear discriminatory analysis (LDA) between Han and other prominent Chinese minority ethnic groups. We presented Y-STRs data in the Y-Chromosome Haplotype Reference Database (YHRD) for the future forensic and other usage.

Historical human remains identification through maternal and paternal genetic signatures in a founder population with extensive genealogical record

OBJECTIVES

We describe a method to identify human remains excavated from unmarked graves in historical Québec cemeteries by combining parental-lineage genetic markers with the whole-population genealogy of Québec contained in the BALSAC database.

MATERIALS AND METHODS

The remains of six men were exhumed from four historical cemeteries in the province of Québec, Canada. DNA was extracted from the remains and genotyped to reveal their mitochondrial and Y-chromosome haplotypes, which were compared to a collection of haplotypes of genealogically-anchored modern volunteers. Maternal and paternal genealogies were searched in the BALSAC genealogical record for parental couples matching the mitochondrial and the Y-chromosome haplotypic signatures, to identify candidate sons from whom the remains could have originated.

RESULTS

Analysis of the matching genealogies identified the parents of one man inhumed in the cemetery of the investigated parish during its operating time. The candidate individual died in 1833 at the age of 58, a plausible age at death in light of osteological analysis of the remains.

DISCUSSION

This study demonstrates the promising potential of coupling genetic information from living individuals to genealogical data in BALSAC to identify historical human remains. If genetic coverage is increased, the genealogical information in BALSAC could enable the identification of 87% of the men (n = 178,435) married in Québec before 1850, with high discriminatory power in most cases since >75% of the parental couples have unique biparental signatures in most regions. Genotyping and identifying Québec's historical human remains are a key to reconstructing the genomes of the founders of Québec and reinhuming archeological remains with a marked grave.

Population genetics of 19 Y-STR loci in Yanbian Korean samples from China

BACKGROUND

China harbors 56 ethnic groups, including Korean, with a population size of approximately 1.92 million at the 2010 census. Most of the Koreans live in Northeastern parts of China, including Jilin (59.64%), Heilongjiang (20.21%), and Liaoning (12.55%) provinces, and the rest are spread to other parts of China. Koreans across China share a common culture, which is similar to Korea.

METHODS

We have explored the genetic characteristics of 20 Y-chromosomal short tandem repeat (Y-STR) loci in 252 unrelated Chinese Korean male individuals from Jilin Province, using a Goldeneye 20Y amplification kit. Moreover, phylogenetic analysis was performed between the Korean population and other relevant populations based on the Y-STR haplotypes.

RESULTS

We have found 237 different haplotypes among 252 unrelated individuals. The haplotype frequencies ranged from 0.0238 to 0.0040, while gene diversity ranged from 0.9666 (DYS385a/b) to 0.2260 (DYS391). The random match probability was 0.0048, the haplotype diversity was 0.9992 ± 0.0006 and discrimination capacity was 0.9405. Population comparison revealed that Korean populations are lining up together with other Korean populations from East Asia.

CONCLUSION

Our results showed that the 20 Y-STR loci in the Yanbian Korean population are valuable for forensic application and human genetics. The Yanbian Koreans have lined up with other Korean population from China and Korea while showing significant differences from other East Asian populations.

Discriminating power of rapidly mutating Y-STRs in deep rooted endogamous pedigrees from Sindhi population of Pakistan

Rapidly mutating Y-STRs (RM Y-STRs) have been paid much attention in recent years. The 13 RM Y-STRs (DYF387S1, DYF399S1, DYF403S1a/b, DYF404S1, DYS449, DYS518, DYS526I/II, DYS547, DYS570, DYS576, DYS612, DYS626, and DYS627) have been proved to have substantially higher haplotype diversity and discrimination capacity than conventionally used Y-STRs indicating the considerable power in paternal lineage differentiation in endogamous populations, separation of which is usually impossible with standard Y-STRs. In current study, we analyzed the RM Y-STRs and PowerPlex® Y23 System in 216 male relatives from 18 deep rooted endogamous Sindhi families from Pakistan. Mutations were frequently observed at DYF399S1, DYS449, DYS518DYS547 and DYF403S1b2 loci, which are known to mutate more rapidly than other RM Y-STRs. Overall differentiation rate with RM Y-STRs was as high as 32.88%, while those with PowerPlex® Y23 System and AmpFℓSTR® Yfiler™ kit were 6.85% and 3.65% respectively. The differentiation rate of RM Y-STRs was 29.22% and 26.03% higher than those of AmpFlSTR® Yfiler™ kit and PowerPlex® Y23 System, respectively.

Forensic use of Y-chromosome DNA: a general overview

The male-specific part of the human Y chromosome is widely used in forensic DNA analysis, particularly in cases where standard autosomal DNA profiling is not informative. A Y-chromosomal gene fragment is applied for inferring the biological sex of a crime scene trace donor. Haplotypes composed of Y-chromosomal short tandem repeat polymorphisms (Y-STRs) are used to characterise paternal lineages of unknown male trace donors, especially suitable when males and females have contributed to the same trace, such as in sexual assault cases. Y-STR haplotyping applied in crime scene investigation can (i) exclude male suspects from involvement in crime, (ii) identify the paternal lineage of male perpetrators, (iii) highlight multiple male contributors to a trace, and (iv) provide investigative leads for finding unknown male perpetrators. Y-STR haplotype analysis is employed in paternity disputes of male offspring and other types of paternal kinship testing, including historical cases, as well as in special cases of missing person and disaster victim identification involving men. Y-chromosome polymorphisms are applied for inferring the paternal bio-geographic ancestry of unknown trace donors or missing persons, in cases where autosomal DNA profiling is uninformative. In this overview, all different forensic applications of Y-chromosome DNA are described. To illustrate the necessity of forensic Y-chromosome analysis, the investigation of a prominent murder case is described, which initiated two changes in national forensic DNA legislation both covering Y-chromosome use, and was finally solved via an innovative Y-STR dragnet involving thousands of volunteers after 14 years. Finally, expectations for the future of forensic Y-chromosome DNA analysis are discussed.

Enhanced DNA Profiling of the Semen Donor in Late Reported Sexual Assaults: Use of Y-Chromosome-Targeted Pre-amplification and Next Generation Y-STR Amplification Systems

In some cases of sexual assault the victim may not report the assault for several days after the incident due to various factors. The ability to obtain an autosomal STR profile of the semen donor from a living victim rapidly diminishes as the post-coital interval is extended due to the presence of only a small amount of male DNA amidst an overwhelming amount of female DNA. Previously, we have utilized various technological tools to overcome the limitations of male DNA profiling in extended interval post-coital samples including the use of Y-chromosome STR profiling, cervical sample, and post-PCR purification permitting the recovery of Y-STR profiles of the male DNA from samples collected 5-6 days after intercourse. Despite this success, the reproductive biology literature reports the presence of spermatozoa in the human cervix up to 7-10 days post-coitus. Therefore, novel and improved methods for recovery of male profiles in extended interval post-coital samples were required. Here, we describe enhanced strategies, including Y-chromosome-targeted pre-amplification and next generation Y-STR amplification kits, that have resulted in the ability to obtain probative male profiles from samples collected 6-9 days after intercourse.

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.

A Y-short tandem repeat specific DNA enhancement strategy to aid the analysis of late reported (≥ 6 days) sexual assault cases

The ability to obtain an autosomal short tandem repeat (STR) profile of the semen donor from the reproductive tract of a living victim rapidly diminishes as the post-coital interval increases. This is of concern where victims of sexual assault provide vaginal samples several days after the incident. In order to overcome the technological impediments inherent in autosomal DNA typing with extended interval samples, we previously employed the use of Y chromosome STR profiling which, by targeting only male DNA, can eliminate masking of the male profile (by the victim's alleles) or critical polymerase chain reaction reagent titration (due to excessive female DNA). Thus employing Y-STR profiling and additional enhancement strategies, we reported the ability to recover Y-STR profiles from samples collected 5 to 6 days after intercourse. However, the reproductive biology literature indicates that spermatozoa are found in the human cervix up to 7 to 10 days post coitus. Thus, even with improved extraction and profiling techniques, we failed to routinely recover profiles from samples collected ≥ 6 days after intercourse. The aim of the present work was to develop additional strategies to permit the recovery of male donor DNA profiles from ≥ 6 post-coital samples. Using nested polymerase chain reaction and DNA concentration procedures that together maximize the recovery and targeting of male DNA, we demonstrate the ability to obtain semen donor Y-STR profiles in extended interval post-coital samples collected 6 to 9 days after intercourse. This approaches the recognized time limits of sperm residence in the cervico-vaginal canal as described in the clinical literature.

Disclosing the genetic structure of Brazil through analysis of male lineages with highly discriminating haplotypes

In a large variety of genetic studies, probabilistic inferences are made based on information available in population databases. The accuracy of the estimates based on population samples are highly dependent on the number of chromosomes being analyzed as well as the correct representation of the reference population. For frequency calculations the size of a database is especially critical for haploid markers, and for countries with complex admixture histories it is important to assess possible substructure effects that can influence the coverage of the database. Aiming to establish a representative Brazilian population database for haplotypes based on 23 Y chromosome STRs, more than 2,500 Y chromosomes belonging to Brazilian, European and African populations were analyzed. No matter the differences in the colonization history of the five geopolitical regions that currently exist in Brazil, for the Y chromosome haplotypes of the 23 studied Y-STRs, a lack of genetic heterogeneity was found, together with a predominance of European male lineages in all regions of the country. Therefore, if we do not consider the diverse Native American or Afro-descendent isolates, which are spread through the country, a single Y chromosome haplotype frequency database will adequately represent the urban populations in Brazil. In comparison to the most commonly studied group of 17 Y-STRs, the 23 markers included in this work allowed a high discrimination capacity between haplotypes from non-related individuals within a population and also increased the capacity to discriminate between paternal relatives. Nevertheless, the expected haplotype mutation rate is still not enough to distinguish the Y chromosome profiles of paternally related individuals. Indeed, even for rapidly mutating Y-STRs, a very large number of markers will be necessary to differentiate male lineages from paternal relatives.

Performance evaluation and optimization of multiplex PCRs for the highly discriminating OSU 10-locus set Y-STRs

In a previous study, a new set of Y-chromosome short tandem repeats, the OSU 10-locus set (MPM1 and MPM2), was shown to have a higher discrimination power when evaluated against the 10 SWGDAM loci on a common population panel. Here, we describe the optimization of the multiplex reactions using dye-labeled primers followed by performance evaluations. The loci exhibited high precision, human male specificity, reliability in different body fluids, high sensitivity, stability, and the ability to amplify nonprobative casework and mixture samples. Stutter for the all of the loci, with the exception of the highly polymorphic locus DYS688, was similar to that observed for autosomal loci. The results of the performance evaluations reinforced the utility of these loci.

Design and validation of a highly discriminatory 10-locus Y-chromosome STR multiplex system

The Y-chromosome STRs (short tandem repeat) markers are routinely utilized in the resolution of forensic casework related to sexual assault. For this, the forensic community has adopted a set of eleven (core) Y-STR that is incorporated in all commercial diagnostic systems. Our previous studies of Y-STR polymorphisms in the South African population identified low levels of diversity and discrimination capacity for many commercial marker sets, determining a limited applicability of these systems to the local population groups. To overcome this shortcoming, we designed a Y-STR 10-plex system that shows higher discriminatory capacity (DC) than available commercial systems. The markers were selected from a population group of 283 individuals with African, European and Asian ancestry genotyped at 45 Y-STRs, applying an optimization based selection procedure to achieve the highest possible DC with the minimal number of markers. The 10-plex was satisfactorily subjected to developmental validation tests following the SWGDAM guidelines and shows potential for its application to genealogical and evolutionary studies.

Y-STR diversity in the Himalayas

Linguistic and ethnic diversity throughout the Himalayas suggests that this mountain range played an important role in shaping the genetic landscapes of the region. Previous Y-chromosome work revealed that the Himalayas acted as a biased bidirectional barrier to gene flow across the cordillera. In the present study, 17 Y-chromosomal short tandem repeat (Y-STR) loci included in the AmpFlSTR® Yfiler kit were analyzed in 344 unrelated males from three Nepalese populations (Tamang, Newar, and Kathmandu) and a general collection from Tibet. The latter displays the highest haplotype diversity (0.9990) followed by Kathmandu (0.9977), Newar (0.9570), and Tamang (0.9545). The overall haplotype diversity for the Himalayan populations at 17 Y-STR loci was 0.9973, and the corresponding values for the extended (11 loci) and minimal (nine loci) haplotypes were 0.9955 and 0.9942, respectively. No Y-STR profiles are shared across the four Himalayan collections at the 17-, 11-, and nine-locus resolutions considered, indicating a lack of recent gene flow among them. Phylogenetic analyses support our previous findings that Kathmandu, and to some extent Newar, received significant genetic influence from India while Tamang and Tibet exhibit limited or no gene flow from the subcontinent. A median-joining network of haplogroup O3a3c-M134 based on 15 Y-STR loci from our four Himalayan populations suggests either a male founder effect in Tamang, possibly from Tibet, or a recent bottleneck following their arrival south of the Himalayas from Tibet leading to their highly reduced Y single-nucleotide polymorphism and Y-STR diversity. The genetic uniqueness of the four Himalayan populations examined in this study merits the creation of separate databases for individual identification, parentage analysis, and population genetic studies.

[Genetic polymorphism of 17 Y-STR loci in four minority populations in Guangxi of China]

To investigate the genetic polymorphism of Y-chromosomal short tandem repeats (STR) loci in Jing, Yi, Yao, and Zhuang minority populations from Guangxi Province, China. 17 Y-STR loci were co-amplified using AmpFlSTR(R) Yfiler PCR Amplification Kit System, and the PCR products were analyzed by genetic analyzer. Cluster and phylogenic tree analyses were conducted to show the genetic distance among the populations. There were 61 different haplotypes in 100 unrelated Yao males, 67 in 105 unrelated Yi males, 79 in 103 unrelated Jing males, and 91 in 107 unrelated Zhuang males. The haplotype diversities of Jing, Yi, Yao and Zhuang were determined as 0.9784, 0.9866, 0.9911, and 0.9956, respectively. Among these 4 minority populations, the genetic distance between Jing and Zhuang was the smallest (0.0391), while the genetic distance between Yi and Yao was the largest (0.3376). The 17 Y-STR loci in the 4 minority populations from Guangxi Province revealed a highly polymorphic genetic distribution, which show a high potential for population genetics and forensic practice.

Kinship and Y-chromosome analysis of 7th century human remains: novel DNA extraction and typing procedure for ancient material

AIM

To develop novel DNA extraction and typing procedure for DNA identification of the 7th century human remains, determine the familiar relationship between the individuals, estimate the Y-chromosome haplogroup, and compare the Y-chromosome haplotype with the contemporary populations.

METHODS

DNA from preserved femur samples was extracted using the modified silica-based extraction technique. Polymerase chain reaction amplification was performed using human identification kits MiniFiler, Identifiler, and Y-filer and also laboratory-developed and validated Y-chromosome short tandem repeat (STR) pentaplexes with short amplicons.

RESULTS

For 244A, 244B, 244C samples, full autosomal DNA profiles (15 STR markers and Amelogenin) and for 244D, 244E, 244F samples, MiniFiler profiles were produced. Y-chromosome haplotypes consisting of up to 24 STR markers were determined and used to predict the Y-chromosome haplogroups and compare the resulting haplotypes with the current population. Samples 244A, 244B, 244C, and 244D belong to Y-chromosome haplogroup R1b and the samples 244E and 244F to haplogroup G2a. Comparison of ancient haplotypes with the current population yielded numerous close matches with genetic distance below 2.

CONCLUSION

Application of forensic genetics in archaeology enables retrieving new types of information and helps in data interpretation. The number of successfully typed autosomal and Y-STR loci from ancient specimens in this study is one of the largest published so far for aged samples.

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 approximately 4.8 x 10(-4) for 31 ssY-STRs with no mutations observed to 1.3 x 10(-2) and 1.5 x 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.