New uses for new haplotypes the human Y chromosome, disease and selection

Evolutionary profiles and complex admixture landscape in East Asia: New insights from modern and ancient Y chromosome variation perspectives

Human Y-chromosomes are characterized by nonrecombination and uniparental inheritance, carrying traces of human history evolution and admixture. Large-scale population-specific genomic sources based on advanced sequencing technologies have revolutionized our understanding of human Y chromosome diversity and its anthropological and forensic applications. Here, we reviewed and meta-analyzed the Y chromosome genetic diversity of modern and ancient people from China and summarized the patterns of founding lineages of spatiotemporally different populations associated with their origin, expansion, and admixture. We emphasized the strong association between our identified founding lineages and language-related human dispersal events correlated with the Sino-Tibetan, Altaic, and southern Chinese multiple-language families related to the Hmong-Mien, Tai-Kadai, Austronesian, and Austro-Asiatic languages. We subsequently summarize the recent advances in translational applications in forensic and anthropological science, including paternal biogeographical ancestry inference (PBGAI), surname investigation, and paternal history reconstruction. Whole-Y sequencing or high-resolution panels with high coverage of terminal Y chromosome lineages are essential for capturing the genomic diversity of ethnolinguistically diverse East Asians. Generally, we emphasized the importance of including more ethnolinguistically diverse, underrepresented modern and spatiotemporally different ancient East Asians in human genetic research for a comprehensive understanding of the paternal genetic landscape of East Asians with a detailed time series and for the reconstruction of a reference database in the PBGAI, even including new technology innovations of Telomere-to-Telomere (T2T) for new genetic variation discovery.

On the Forensic Use of Y-Chromosome Polymorphisms

Nowadays, the use of Y-chromosome polymorphisms forms an essential part of many forensic DNA investigations. However, this was not always the case. Only since 1992 have we seen that some forensic scientists started to have an interest in this chromosome. In this review, I will sketch a brief history focusing on the forensic use of Y-chromosome polymorphisms. Before describing the various applications of short-tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) on the Y-chromosome, I will discuss a few often ignored aspects influencing proper use and interpretation of Y-chromosome information: (i) genotyping Y-SNPs and Y-STRs, (ii) Y-STR haplotypes shared identical by state (IBS) or identical by descent (IBD), and (iii) Y-haplotype database frequencies.

Forensic features and phylogenetic analyses of the population of Nayagarh (Odisha), India using 23 Y-STRs

AIM

The present study was designed to explore the STR diversity and genomic history of the inhabitants of Nayagarh district of Odisha, India. We also tested the proficiency of the most recent, new generation PowerPlex^R Y23 multiplex system for forensic characterisation and to decipher the phylogenetic affinities.

SUBJECTS AND METHODS

The genetic diversity and polymorphism among 236 healthy unrelated male volunteers from Nayagarh district of Odisha, India was investigated. This investigation was carried out via 23 Y-chromosomal STRs using capillary electrophoresis.

RESULT

A total 223 unique haplotypes were reported. Discrimination capacity (DC), gene diversity (GD) and power of discrimination (PD) were observed as 0.945, 0.999999999998333, and 0.99999999999794, respectively. Polymorphic information content (PIC) and matching probability (PM) were reported as 0.999999999925535 and 2.06 × 10^-12, respectively. Simultaneously, the haplogroup analysis characterised with C2, E1b1a, E1b1b, G2a, H1, I2a, J2a, J2b, L, O, O1, O2, Q, R1a, R2, and T haplogroups, disclosing the possible geographical relatedness of the studied population to different areas of the world.

CONCLUSION

Phylogenetic analysis with previously reported Indian and Asian populations showed the genetic closeness of the studied population to different Indian populations and the Bangladeshi population of Dhaka, whereas the Bhotra population of Odisha and Han population of China showed much less genetic affinity.

Population data and genetic diversity analysis of 17 Y-STR loci in Saudi population

Background

The Y chromosome polymorphism has been widely studied for human migrations, population genetics, forensic applications, and paternity analysis. However, studies regarding genetic lineage and population genetic structure of the Y chromosome in different regions of Saudi Arabia are limited.

Aim

This study aimed to analyze the distribution of Y chromosome haplotypes in a sample of 125 native Saudi males from different geographic regions of Saudi Arabia and compare to previously published Y chromosome haplotype data from Saudi Arabia and some neighboring Arab populations.

Materials and methods

Buccal swabs were collected from 125 healthy unrelated native Saudi males from different geographic regions of Saudi Arabia. Genomic DNA was extracted by Chelex®100; 17 Y-STR loci were amplified using the AmpFℓlSTR Yfiler PCR amplification kit and detected on the 3130 Genetic AnalyzerTM. Allele frequency and gene diversity were calculated with online tool STRAF. The Saudi population data were compared with the neighboring populations using pairwise genetic distances and associated probability values were calculated using the Y Chromosome Haplotype Reference Database Website (YHRD) software.

Results and conclusion

One hundred six YSTR haplotypes and 102 YSTR alleles (excluding 4 null alleles) were identified having a discrimination capacity (DC) of 85.8%. The highest haplotype diversity (HD) and gene diversity (GD) were observed at the loci DYS 458 (0.817) and DYS385b (0.807), respectively. According to our results, the Iraqi and Qena (Egypt) populations appeared to have closer relatedness to the Saudi population as compared with Yemen. The UAE and Kuwait populations showed the same degree of relatedness to the Saudi population followed by Bahrain. On the contrary, the Adnanit and Qahtanit populations of Jordan demonstrated low genetic distance from the Saudi population. In short, studying a population sample of pure Saudi ethnicity enabled us to identify a unique set of haplotypes which may help in establishing genetic relatedness between Saudi and the neighboring Arab populations. The present paper, therefore, highlights the importance of ensuring ethnic originality of the study sample while conducting population genetics studies.

Predicted structural differences of four fertility-related Y-chromosome proteins in Macaca mulatta, M. fascicularis, and their Indochinese hybrids

Species in the genus Macaca typically live in multimale-multifemale social groups with male macaques exhibiting some of the largest testis: body weight ratios among primates. Males are believed to experience intense levels of sperm competition. Several spermatogenesis genes are located on the Y-chromosome and, interestingly, occasional hybridization between two species has led to the introgression of the rhesus macaque (Macaca mulatta) Y-chromosome deep into the range of the long-tailed macaque (M. fascicularis). These observations have led to the prediction that the successful introgression of the rhesus Y-haplotype is due to functional differences in spermatogenesis genes compared to those of the native long-tailed Y-haplotype. We examine here four Y-chromosomal loci-RBMY, XKRY, and two nearly identical copies of CDY-and their corresponding protein sequences. The genes were surveyed in representative animals from north of, south of, and within the rhesus x long-tailed introgression zone. Our results show a series of non-synonymous amino acid substitutions present between the two Y-haplotypes. Protein structure modeling via I-TASSER revealed different folding patterns between the two species' Y-proteins, and functional predictions via TreeSAAP further reveal physicochemical differences as a result of non-synonymous substitutions. These differences inform our understanding of the evolution of primate Y-proteins involved in spermatogenesis and, in turn, have biomedical implications for human male fertility.

A 16-plex Y-SNP typing system based on allele-specific PCR for the genotyping of Chinese Y-chromosomal haplogroups

Y-chromosomal SNP (Y-SNP), with its stable inheritance and low mutation, can provide Supplementary information in forensic investigation. While commonly used Y-chromosomal STR haplotypes show their limitations, typing of Y-SNP would become a powerful complement. In this study, a 16-plex Y-SNP typing system based on allele-specific PCR (AS-PCR) was developed to discriminate four dominant Y-chromosomal haplogroups (C-M130, D-CTS3946, N-M231, and O-M175) and 12 predominant sub-haplogroups of O-M175 (O1a-M119, O1a1a1a-CTS3265, O1b-M268, O1b1a2-Page59, O2-M122, O2a1-L127.1, O2a1b-F240, O2a1b1a1-CTS5820, O2a2-P201, O2a2b1a1-M177, O2a2b1a1a1a-Y17728, O2a2b1a2-F114). A series of experimental validation studies including sensitivity, species specificity, male-female mixture and inhibition were performed. The discrimination of the typing system was preliminarily proved with a haplogroup diversity of 0.9239. Altogether, the Y-SNP typing system based on AS-PCR should be capable of distinguishing China's dominant Y-chromosomal haplogroups in a rapid and reliable manner, thus can be employed as a useful complement in forensic casework.

A Fast and Specific Alignment Method for Minisatellite Maps

Background

Variable minisatellites count among the most polymorphic markers of eukaryotic and prokaryotic genomes. This variability can affect gene coding regions, like in the prion protein gene, or gene regulation regions, like for the cystatin B gene, and be associated or implicated in diseases: the Creutzfeld-Jakob disease and the myoclonus epilepsy type 1, for our examples. When it affects neutrally evolving regions, the polymorphism in length ( i.e., in number of copies) of minisatellites proved useful in population genetics.

Motivation

In these tandem repeat sequences, different mutational mechanisms let the number of copies, as well as the copies themselves, vary. Especially, the interspersion of events of tandem duplication/contraction and of punctual mutation makes the succession of variant repeats much more informative than the sole allele length. To exploit this information requires the ability to align minisatellite alleles by accounting for both punctual mutations and tandem duplications.

Results

We propose a minisatellite maps alignment program that improves on previous solutions. Our new program is faster, simpler, considers an extended evolutionary model, and is available to the community. We test it on the data set of 609 alleles of the MSY1 (DYF155S1) human minisatellite and confirm its ability to recover known evolutionary signals. Our experiments highlight that the informativeness of minisatellites resides in their length and composition polymorphisms. Exploiting both simultaneously is critical to unravel the implications of variable minisatellites in the control of gene expression and diseases.

Availability

Software is available at http://atgc.lirmm.fr/ms_align/

Etiologies underlying sex differences in Autism Spectrum Disorders

The male predominance of Autism Spectrum Disorders (ASD) is one of the best-known, and at the same time, one of the least understood characteristics of these disorders. In this paper we review genetic, epigenetic, hormonal, and environmental mechanisms underlying this male preponderance. Sex-specific effects of Y-linked genes (including SRY expression leading to testicular development), balanced and skewed X-inactivation, genes that escape X-inactivation, parent-of-origin allelic imprinting, and the hypothetical heterochromatin sink are reviewed. These mechanisms likely contribute to etiology, instead of being simply causative to ASD. Environments, both internal and external, also play important roles in ASD's etiology. Early exposure to androgenic hormones and early maternal immune activation comprise environmental factors affecting sex-specific susceptibility to ASD. The gene-environment interactions underlying ASD, suggested here, implicate early prenatal stress as being especially detrimental to boys with a vulnerable genotype.

Assignment of Y-chromosomal SNPs found in Japanese population to Y-chromosomal haplogroup tree

The relationship between Y-chromosome single-nucleotide polymorphisms (SNPs) registered in the Japanese SNP (JSNP) database (http://snp.ims.u-tokyo.ac.jp) and Y-binary haplogroup lineages was investigated to identify new Y-chromosomal binary haplogroup markers and further refine Y-chromosomal haplogroup classification in the Japanese population. We used SNPs for which it was possible to construct primers to make Y-specific PCR product sizes small enough to obtain amplification products even from degraded DNA, as this would allow their use not only in genetic but also in archeological and forensic studies. The genotype of 35 JSNP markers were determined, of which 14 were assigned to appropriate positions on the Y-chromosomal haplogroup tree, together with 5 additional new non-JSNP markers. These markers defined 14 new branches (C3/64562+13, C3/2613-27, D2a1b/006841*, D2a1b/119166-11A, D2a/022456*, D2a/119166-11A, D2a/119167rec/119167-40rec*, D2a/75888-GC, O3a3c/075888-9T/10T*, O3a3c/075888-9T/9T, O3a3/8425+6, O3a3/119166-13A*, O3a3/008002 and O3a4/037852) and 21 new internal markers on the 2008 Y-chromosome haplogroup tree. These results will provide useful information for Y-chromosomal polymorphic studies of East Asian populations, particularly those in and around Japan, in the fields of anthropology, genetics and forensics.

Admixture and population structure in Mexican-Mestizos based on paternal lineages

In the nonrecombining region of the Y-chromosome, there are single-nucleotide polymorphisms (Y-SNPs) that establish haplogroups with particular geographical origins (European, African, Native American, etc.). The complex process of admixture that gave rise to the majority of the current Mexican population (~93%), known as Mestizos, can be examined with Y-SNPs to establish their paternal ancestry and population structure. We analyzed 18 Y-SNPs in 659 individuals from 10 Mexican-Mestizo populations from different regions of the country. In the total population sample, paternal ancestry was predominately European (64.9%), followed by Native American (30.8%) and African (4.2%). However, the European ancestry was prevalent in the north and west (66.7-95%) and, conversely, Native American ancestry increased in the center and southeast (37-50%), whereas the African ancestry was low and relatively homogeneous (0-8.8%). Although this paternal landscape concurs with previous studies based on genome-wide SNPs and autosomal short tandem repeats (STRs), this pattern contrasts with the maternal ancestry, mainly of Native American origin, based on maternal lineages haplogroups. In agreement with historical records, these results confirm a strong gender-biased admixture history between European males and Native American females that gave rise to Mexican-Mestizos. Finally, pairwise comparisons and analysis of molecular variance tests demonstrated significant population structure (F(ST)=4.68%; P<0.00005), delimiting clusters that were geographically defined as the following: north-west, center-south and southeast.

Africa: the next frontier for human disease gene discovery?

The populations of Africa harbour the greatest human genetic diversity following an evolutionary history tracing its beginnings on the continent to time before the emergence of Homo sapiens. Signatures of selection are detectable as responses to ancient environments and cultural practices, modulated by more recent events including infectious epidemics, migrations, admixture and, of course, chance. The age of high-throughput biology is not passing Africa by. African-based cohort studies and networks with an African footprint are ideal springboards for disease-related genetic and genomic studies. Initiatives like HapMap, the 1000 Genomes Project, MalariaGEN, the INDEPTH network and Human Heredity and Health in Africa are catalysts to exploring African genetic diversity and its role in the spectrum from health to disease. The challenges are abundant in dissecting biological questions in the light of linguistic, cultural, geographic and political boundaries and their respective roles in shaping health-related profiles. Will studies based on African populations lead to a new wave of discovery of genetic contributors to disease?

Epigenetic profile of the euchromatic region of human Y chromosome

The genome of a multi-cellular organism acquires various functional capabilities in different cell types by means of distinct chromatin modifications and packaging states. Acquired during early development, the cell type-specific epigenotype is maintained by cellular memory mechanisms that involve epigenetic modifications. Here we present the epigenetic status of the euchromatic region of the human Y chromosome that has mostly been ignored in earlier whole genome epigenetic mapping studies. Using ChIP-on-chip approach, we mapped H3K9ac, H3K9me3, H3K27me3 modifications and CTCF binding sites while DNA methylation analysis of selected CpG islands was done using bisulfite sequencing. The global pattern of histone modifications observed on the Y chromosome reflects the functional state and evolutionary history of the sequences that constitute it. The combination of histone and DNA modifications, along with CTCF association in some cases, reveals the transcriptional potential of all protein coding genes including the sex-determining gene SRY and the oncogene TSPY. We also observe preferential association of histone marks with different tandem repeats, suggesting their importance in genome organization and gene regulation. Our results present the first large scale epigenetic analysis of the human Y chromosome and link a number of cis-elements to epigenetic regulatory mechanisms, enabling an understanding of such mechanisms in Y chromosome linked disorders.

Characterization of Y-chromosomal short tandem repeat markers in Pakistani populations

The Y chromosome microsatellite markers have been extensively used for population genetic studies and in individual identification and paternity testing in forensic medicine. In the present study, we report the data of five male-specific, polymorphic microsatellites in 740 unrelated male individuals from 12 different ethnic groups of Pakistan. The overall diversities of these individual loci in Pakistan ranged from 0.236 to 0.799. The total haplotypes identified were 152, and of these, 70 different haplotypes were present in only single individuals. Two haplotypes were found more frequently, 9_8_17_11_24 (13.5%) and 9_8_17_11_25 (8.6%), showing population-specific clustering in the Mohanna and the Brahui, respectively. An overall haplotype diversity of 0.965 in Pakistan suggested a high power of discrimination for these loci. Few populations, particularly the Mohanna and the Balti, showed lower haplotype diversity values for these loci (0.662 and 0.758, respectively). This set of microsatellite loci reported in the study can be used for population genetics and forensic medicine analysis. This study also demonstrates the importance of studying haplotype distribution pattern in population genetics.

Human genetic differentiation across the Strait of Gibraltar

BACKGROUND

The Strait of Gibraltar is a crucial area in the settlement history of modern humans because it represents a possible connection between Africa and Europe. So far, genetic data were inconclusive about the fact that this strait constitutes a barrier to gene flow, as previous results were highly variable depending on the genetic locus studied. The present study evaluates the impact of the Gibraltar region in reducing gene flow between populations from North-Western Africa and South-Western Europe, by comparing formally various genetic loci. First, we compute several statistics of population differentiation. Then, we use an original simulation approach in order to infer the most probable evolutionary scenario for the settlement of the area, taking into account the effects of both demography and natural selection at some loci.

RESULTS

We show that the genetic patterns observed today in the region of the Strait of Gibraltar may reflect an ancient population genetic structure which has not been completely erased by more recent events such as Neolithic migrations. Moreover, the differences observed among the loci (i.e. a strong genetic boundary revealed by the Y-chromosome polymorphism and, at the other extreme, no genetic differentiation revealed by HLA-DRB1 variation) across the strait suggest specific evolutionary histories like sex-mediated migration and natural selection. By considering a model of balancing selection for HLA-DRB1, we here estimate a coefficient of selection of 2.2% for this locus (although weaker in Europe than in Africa), which is in line with what was estimated from synonymous versus non-synonymous substitution rates. Selection at this marker thus appears strong enough to leave a signature not only at the DNA level, but also at the population level where drift and migration processes were certainly relevant.

CONCLUSIONS

Our multi-loci approach using both descriptive analyses and Bayesian inferences lead to better characterize the role of the Strait of Gibraltar in the evolution of modern humans. We show that gene flow across the Strait of Gibraltar occurred at relatively high rates since pre-Neolithic times and that natural selection and sex-bias migrations distorted the demographic signal at some specific loci of our genome.

Genetic origin of Kadai-speaking Gelong people on Hainan island viewed from Y chromosomes

The government of China defined 56 official ethnicities for the ethnic groups in China for political purposes; however, there are many more than 56 ethnic groups. Therefore, similar groups must be pooled for registry, and the so-called ethnicity identification is an important official mission in China. Here, we showed how genetics can help in the ethnicity identification for the Gelong people on Hainan Island. The Gelong speak a Kadai language whose other speakers (officially of the Gelao ethnicity) are all far in the southwest of China. Being registered as a Han ethnicity, the Gelong lost all the benefits assigned to the minorities. Y-chromosome typing was performed in a sample of 78 individuals. Twenty single nucleotide polymorphisms (SNPs) and seven short tandem repeats (STRs) were typed and eight haplogroups were detected, among which haplogroup O1a* was the most dominant. Compared with the Y haplogroups of the populations in south China, the Gelong were found to be closest to the Gelao and the Hlai using principal components (PCs) analysis, dendrogram clustering and STR networks. The genetic similarity between the Gelong and the Hlai may have resulted from the gene flow during thousands of years of neighboring history on Hainan Island, whereas the similarity between the Gelong and the Gelao may have resulted from their common ancestry because there is less possibility of gene flow over such a far distance. As both linguistic and genetic evidence support the similarity between the Gelong and the Gelao, we suggest that the Gelong register as Gelao for their official ethnicity. However, this identification is invalid until it is accepted by the Gelong people themselves and the Hainan government.

Genetic structure of Kuwaiti population revealed by Y-STR diversity

In this study, a sample of 126 Kuwaiti was analysed using 12 Y-chromosome short tandem repeat (STR) polymorphisms. A total of 101 different haplotypes were identified, among which 87 were individual specific. The high haplotype diversity (0.994) supports the usefulness of Y-STR markers in Kuwaiti population diversity investigation. Our results suggest a close genetic relationship between Kuwait and other populations of the Arabian Peninsula, and an even more pronounced similarity of Kuwaiti populations and Yemenis and Saudi Arabians.

Association of Y chromosome haplotypes with autism

There is significant male excess in autism. In this study, we investigated a possible Y chromosome effect by haplotype analysis. We investigated 12 single-nucleotide polymorphisms in Y-linked neuroligin 4, transducin beta-like 1, and eukaryotic translation initiation factor 1a genes in 146 autistic participants and 102 control participants of European American origin. The set of 12 single-nucleotide polymorphisms defined 9 Y chromosome haplotypes in autistic and control participants. Although the 2 most frequent haplotypes were equally distributed in the autistic and control participants, some haplotypes were overrepresented or underrepresented in autistic participants. The distribution of haplotypes between the autistic and control groups, as determined by Monte Carlo tests with Clump software, was significantly different (P = .0001 with 100,000 simulations). Our results are suggestive of a Y chromosome effect in autism.

Identification of mouse inbred strains through mitochondrial DNA single-nucleotide extension

Inbred mouse strains are used as model organisms for biomedical research in laboratories throughout the world. The most widely used of these strains had their genome sequenced recently, and phylogenetic studies have been performed, namely, based on mitochondrial DNA (mtDNA). This has allowed determining that few polymorphisms distinguish the mtDNAs of the common inbred strains, but a high number of differences are observed among the wild-derived strains. Taking advantage of these observations, we here present a single base extension typing strategy that, with only a pair of multiplex reactions, allows the distinction between common inbred and wild-derived mice strains, and provides the identification of ten different common inbred and six wild-derived mice mtDNA haplotypes. Given that all the animals inside a strain present the same mtDNA, this strategy allows a rapid identification of the strains without the need for probability calculations. We further test this approach in an island population of wild mice, which provides both an indication on its applicability in wild mice, and a comparison of evolutionary processes on inbred and wild mice that are restricted to a limited space. Rapid genotyping methods that allow the distinction of the different strains are important for both the distinction of materials such as tissue and cell collections and to identify the origin of new strains. Moreover, it may also prove valuable in forensic identification of materials collected in laboratory accidents, as well as in cases of scientific fraud.

Y-chromosome variation among Sudanese: restricted gene flow, concordance with language, geography, and history

We study the major levels of Y-chromosome haplogroup variation in 15 Sudanese populations by typing major Y-haplogroups in 445 unrelated males representing the three linguistic families in Sudan. Our analysis shows Sudanese populations fall into haplogroups A, B, E, F, I, J, K, and R in frequencies of 16.9, 7.9, 34.4, 3.1, 1.3, 22.5, 0.9, and 13% respectively. Haplogroups A, B, and E occur mainly in Nilo-Saharan speaking groups including Nilotics, Fur, Borgu, and Masalit; whereas haplogroups F, I, J, K, and R are more frequent among Afro-Asiatic speaking groups including Arabs, Beja, Copts, and Hausa, and Niger-Congo speakers from the Fulani ethnic group. Mantel tests reveal a strong correlation between genetic and linguistic structures (r = 0.31, P = 0.007), and a similar correlation between genetic and geographic distances (r = 0.29, P = 0.025) that appears after removing nomadic pastoralists of no known geographic locality from the analysis. The bulk of genetic diversity appears to be a consequence of recent migrations and demographic events mainly from Asia and Europe, evident in a higher migration rate for speakers of Afro-Asiatic as compared with the Nilo-Saharan family of languages, and a generally higher effective population size for the former. The data provide insights not only into the history of the Nile Valley, but also in part to the history of Africa and the area of the Sahel.

Machine-learning approaches for classifying haplogroup from Y chromosome STR data

Genetic variation on the non-recombining portion of the Y chromosome contains information about the ancestry of male lineages. Because of their low rate of mutation, single nucleotide polymorphisms (SNPs) are the markers of choice for unambiguously classifying Y chromosomes into related sets of lineages known as haplogroups, which tend to show geographic structure in many parts of the world. However, performing the large number of SNP genotyping tests needed to properly infer haplogroup status is expensive and time consuming. A novel alternative for assigning a sampled Y chromosome to a haplogroup is presented here. We show that by applying modern machine-learning algorithms we can infer with high accuracy the proper Y chromosome haplogroup of a sample by scoring a relatively small number of Y-linked short tandem repeats (STRs). Learning is based on a diverse ground-truth data set comprising pairs of SNP test results (haplogroup) and corresponding STR scores. We apply several independent machine-learning methods in tandem to learn formal classification functions. The result is an integrated high-throughput analysis system that automatically classifies large numbers of samples into haplogroups in a cost-effective and accurate manner.

Simultaneous detection and identification of trichothecene- and moniliformin-producing Fusarium species based on multiplex SNP analysis

AIM

To develop a multiplex identification method for trichothecene- and moniliformin-producing Fusarium species.

METHOD AND RESULTS

In this article, we present a single nucleotide polymorphism (SNP) assay to simultaneously detect and identify 16 trichothecene- and moniliformin-producing Fusarium species. A number of SNP primers are designed to detect clades of species with particular mycotoxigenic synthetic abilities. The assay is based on minisequencing using SNaPshot reactions and the SNP primers are designed based on motifs derived from phylogenetic analyses of translation elongation factor-1alpha sequences. The present version of the Fusarium SNP assay can distinguish major groups of trichothecene producers; the strict-type-A, the strict-type-B, the type-A and type-B trichothecene producers and the putative moniliformin producers. The SNP assay was validated against five naturally infected cereal samples that previously had been analysed morphologically, chemically and by a multiplex DNA array hybridization.

CONCLUSIONS

The Fusarium SNP assay reveals the advantages of using SNPs for multiplex species identification.

SIGNIFICANCE AND IMPACT OF THE STUDY

The current assay may qualify as a high-throughput screening method for small-grain cereals in the feed and food chain, and may facilitate detection of new or introduced Fusarium species.

Combining Autosomal and Y-Chromosomal Short Tandem Repeat Data in Paternity Testing with Male Child: Methods and Application

Paternity testing is being increasingly requested with the aim of challenging presumptive fatherhood. The ability to establish the biological father is usually based on the genotyping of autosomal short tandem repeat (STR) in alleged father, mother and child, but the use of Y-chromosomal STR has gained interest in the last few years. In this work, we propose a new probabilistic approach that combines autosomal and Y-chromosomal STR data in paternity testing with father/son pairs taking into account mutation events. We also suggest a new two-stage approach where we first type Y-STRs and possibly autosomal STR for the putative father and son, conditional on Y-STR results. We applied this approach to 22 cases. Our results show that Y-STRs can identify nonpaternity cases with high accuracy but need to be validated with autosomal STR to establish paternity. Moreover, the two-stage approach is less costly than the standard approach and is very useful in motherless cases.

Y-chromosomal binary haplogroups in the Japanese population and their relationship to 16 Y-STR polymorphisms

We investigated Y chromosomal binary and STR polymorphisms in 263 unrelated male individuals from the Japanese population and further examined the relationships between the two separate types of data. Using 47 biallelic markers we distinguished 20 haplogroups, four of which (D2b1/-022457, O3/-002611*, O3/-LINE1 del, and O3/-021354*) were newly defined in this study. Most haplogroups in the Japanese population are found in one of the three major clades, C, D, or O. Among these, two major lineages, D2b and O2b, account for 66% of Japanese Y chromosomes. Haplotype diversity of binary markers was calculated at 86.3%. The addition of 16 Y-STR markers increased the number of haplotypes to 225, yielding a haplotype diversity of 99.40%. A comparison of binary haplogroups and Y-STR type revealed a close association between certain binary haplogroups and Y-STR allelic or conformational differences, such as those at the DXYS156Y, DYS390m, DYS392, DYS437, DYS438 and DYS388 loci. Based on our data on the relationships between binary and STR polymorphisms, we estimated the binary haplogroups of individuals from STR haplotypes and frequencies of binary haplogroups in other Japanese, Korean and Taiwanese Han populations. The present data will enable researchers to connect data from binary haplogrouping in anthropological studies and Y-STR typing in forensic studies in East Asian populations, especially those in and around Japan.

Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

BACKGROUND

Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion.

RESULTS

The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes.

CONCLUSION

We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and giving a first description of the dog Y-chromosome phylogeny.

Lack of association between the incidence of testicular germ cell tumors and Y-chromosome haplogroups in the Japanese population

BACKGROUND

Despite being relatively uncommon, testicular germ cell tumors (TGCT) are the most common malignant disease in young men. Epidemiological studies concerning patients with testicular cancer indicate that the most of them have poor semen quality or testicular dysgenesis. However, many studies have shown that the Y chromosome harbors many candidate genes responsible for spermatogenesis process and development and maintenance of the germ cells. The Y chromosome is thought to have a relationship with the formation and progression of TGCT.

MATERIALS AND METHODS

To verify this relationship, we investigated if there is any correlation between the Y chromosome structural variations presented as different haplogroups and the occurrence of TGCT in the Japanese population. Using combined haplogroups based on typing of three Y chromosome polymorphic binary markers, we analyzed 68 TGCT derived from Japanese patients together with randomly selected 104 unrelated healthy Japanese matched male controls who were confirmed as residents of the same geographic area.

RESULTS

Our findings showed a lack of association between the incidence of TGCT and the different Y- chromosome haplogroups in Japanese population.

CONCLUSION

We concluded that there are no significant variations in males from different Y chromosome lineages regarding their susceptibility or resistance for developing TGCT. The previously hypothesized role of the Y chromosome in the development of TGCT is still uncertain and needs further verification.

Prostate cancer incidence varies among males from different Y-chromosome lineages

The incidence rate of prostate cancer in African-American males is two times higher than Caucasian men and ten times higher than Japanese men. The geographical specificity of Y haplogroups implies that males from different ethnic groups undoubtedly have various Y lineages with different Y-chromosomal characteristics that may affect their susceptibility or resistance to such a male-specific cancer. To confirm this hypothesis we studied the Y-chromosomal haplogroups of 92 Japanese prostate cancer patients comparing them with randomly selected 109 unrelated healthy Japanese male controls who were confirmed to be residents of the same geographical area. Males could be classified using three binary Y-chromosome markers (sex-determining region Y (SRY), YAP, 47z) into four haplogroups DE, O2b(*), O2b1, and untagged group. Our results confirmed that prostate cancer incidence varies among males from different Y-chromosome lineages. Males from DE and the untagged haplogroups are at a significantly higher risk to develop prostate cancer than O2b(*) and O2b1 haplogroups (P=0.01), odds ratio 2.17 and 95% confidence interval (1.16-4.07). Males from haplogroup DE are over-represented in the patient group showing a percentage of 41.3%. The underlying possible causes of susceptibility variations of different Y lineages for such a male-specific cancer tumorigenesis are discussed. These findings explain the lower incidence of prostate cancer in Japanese and other South East Asian males than other populations. To our knowledge, this is the first reliable study examining the association between prostate cancer and Y-chromosomal haplogroups, comparing prostate cancer patients with carefully selected matched controls.

High levels of nucleotide diversity in the European rabbit (Oryctolagus cuniculus) SRY gene

We have sequenced 2,388 bp of the European rabbit sex determining region Y (SRY) gene. These data provide a 10-fold increase in the coverage of the Y chromosome in this species, including the entire open reading frame of the SRY, the polyadenylation signal, and two repetitive sequences in the 5' -region. A survey of 2021 bp of this gene in eight domestic breeds and four wild individuals revealed a total of nine single nucleotide polymorphisms and one indel, defining two deeply divergent lineages. The resulting estimation of nucleotide diversity (pi=1.34 x10(-3)) is very high when compared with other species, but no variability was detected among the domestic breeds. This study represents a first step in the characterization of the European rabbit Y chromosome and its variability. These sequences can be used in additional phylogeographical analyses of the European rabbit and other Leporid species, as well as in evolutionary studies of sex determination and the Y chromosome in wild species.

Identification, characterization and forensic application of novel Y-STRs

Y-chromosomal polymorphic STRs are a powerful tool for forensic and evolutionary studies. Within the last decade, a series of Y-STR systems have been developed and demonstrated to be suitable for a variety of forensic applications including sexual assault cases and paternity testing. This review describes our recent studies on novel male-specific Y-STRs, involving identification, development of a multiplex-PCR system, population study and forensic application.

The origin of the isolated population of the Faroe Islands investigated using Y chromosomal markers

Historical, archaeological and linguistic sources suggest that the ancestors of the present day population in the Faroe Islands may have their origin in several different regions surrounding the North Atlantic Ocean. In this study we use binary and microsatellite markers of the Y chromosome to analyse genetic diversity in the Faroese population and to compare this with the distribution of genotypes in the putative ancestral populations. Using a combination of genetic distance measures, assignment and phylogenetic analyses, we find a high degree of similarity between the Faroese Y chromosomes and the Norwegian, Swedish and Icelandic Y chromosomes but also some similarity with the Scottish and Irish Y chromosomes. Diversity measures and estimates of effective population sizes also suggest that the original gene pool of the settlers have been influenced by random genetic drift, thus complicating direct comparisons with other populations. No extensive immigration from Iceland to the Faroe Islands can be documented in the historical record. We therefore hypothesise that the high degree of Y chromosome similarity between the two populations arose because they were colonised at approximately the same time by males originating from the same regions of Scandinavia and, to a lesser extent, from the British Isles.

Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing

The development of new methodologies for high-throughput SNP analysis is one of the most stimulating areas in genetic research. Here, we describe a rapid and robust assay to simultaneously genotype 17 mitochondrial DNA (mtDNA) coding region SNPs by minisequencing using SNaPshot. SNaPshot is a methodology based on a single base extension of an unlabeled oligonucleotide with labeled dideoxy terminators. The set of SNPs implemented in this multiplexed SNaPshot reaction allow us to allocate common mitochondrial West Eurasian haplotypes into their corresponding branch in the mtDNA skeleton, with special focus on those haplogroups lacking unambiguous diagnostic positions in the first and second hypervariable regions (HVS-I/II; by far, the most common segments analyzed by sequencing). Particularly interesting is the set of SNPs that subdivide haplogroup H; the most frequent haplogroup in Europe (40-50%) and one of the most poorly characterized phylogenetically in the HVS-I/II region. In addition, the polymorphic positions selected for this multiplex reaction increase considerably the discrimination power of current mitochondrial analysis in the forensic field and can also be used as a rapid screening tool prior to full sequencing analysis. The method has been validated in a sample of 266 individuals and shows high accuracy and robustness avoiding both the use of alternative time-consuming classical strategies (i.e. RFLP typing) and the need for high quantities of DNA template.

A Y chromosomal influence on prostate cancer risk: the multi-ethnic cohort study

BACKGROUND

A Y chromosomal role in prostate cancer has previously been suggested by both cytogenetic findings and patterns of Y chromosomal gene expression. We took advantage of the well established and stable phylogeny of the non-recombining segment of the Y chromosome to investigate the association between Y chromosomal DNA variation and prostate cancer risk.

METHODS

We examined the distribution of 116 Y lineages in 930 prostate cancer cases and 1208 controls from four ethnic groups from a cohort study in Hawaii and California.

RESULTS

One lineage, found only among the Japanese group in our study, was associated with a statistically significant predisposition to prostate cancer (odds ratio (OR) = 1.63; 95% confidence interval (CI) 1.07 to 2.47), and, in particular, to high severity disease in younger individuals (OR = 3.89; 95% CI 1.34 to 11.31).

CONCLUSIONS

This finding suggests that a Y chromosomal factor contributes significantly to the development of prostate cancer in Japanese men.

Y chromosome polymorphisms in medicine

Ninety-five percent of the length of the human Y chromosome is inherited as a single block in linkage from father to male offspring as a haploid entity. Thus, the Y chromosome represents an invaluable record of all mutations that have occurred along male lineages throughout evolution. For this reason, Y chromosomal DNA variation has been mainly used for investigations on human evolution and for forensic purposes or paternity analysis. Recently, Y chromosomal polymorphisms have been applied in molecular medicine from the perspective of male-specific (spermatogenic failure, testis and prostate cancer) and prevalently male-associated (hypertension, autism) diseases. The absence of recombination on the MSY (male-specific Y) region means that polymorphisms, located in this region, are in tight association with potential functional variations associated with Y-linked phenotypes. Thus, an indirect way to explore if Y chromosome genes are involved in the etiology of a specific disease is the definition of Y chromosome haplogroups in patients versus disease-free and/or the general population. Data on patients with reduced sperm count and prostate cancer indicate that the 'at risk Y haplogroup' may be different in different populations. The situation is rather contradictory for other male-specific or male-associated diseases and further multicenter--possibly multiethnic--studies are needed.

The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time

We estimate an effective mutation rate at an average Y chromosome short-tandem repeat locus as 6.9x10-4 per 25 years, with a standard deviation across loci of 5.7x10-4, using data on microsatellite variation within Y chromosome haplogroups defined by unique-event polymorphisms in populations with documented short-term histories, as well as comparative data on worldwide populations at both the Y chromosome and various autosomal loci. This value is used to estimate the times of the African Bantu expansion, the divergence of Polynesian populations (the Maoris, Cook Islanders, and Samoans), and the origin of Gypsy populations from Bulgaria.

Patterns of human genetic diversity: implications for human evolutionary history and disease

Since the completion of the human genome sequencing project, the discovery and characterization of human genetic variation is a principal focus for future research. Comparative studies across ethnically diverse human populations and across human and nonhuman primate species is important for reconstructing human evolutionary history and for understanding the genetic basis of human disease. In this review, we summarize data on patterns of human genetic diversity and the evolutionary forces (mutation, genetic drift, migration, and selection) that have shaped these patterns of variation across both human populations and the genome. African population samples typically have higher levels of genetic diversity, a complex population substructure, and low levels of linkage disequilibrium (LD) relative to non-African populations. We discuss these differences and their implications for mapping disease genes and for understanding how population and genomic diversity have been important in the evolution, differentiation, and adaptation of humans.

Insights into Iberian population origins through the construction of highly informative Y-chromosome haplotypes using biallelic markers, STRs, and the MSY1 minisatellite

To investigate the diversity of Y chromosomes in the Iberian Peninsula and the North African population of Maghreb, we constructed superhaplotypes on the basis of 10 biallelic markers, 7 microsatellites, and 1 minisatellite located in the nonrecombining portion of the human Y chromosome. The analysis of extremely high MSY1 variability was performed by reducing the MVR-codes to modular structures. Y-STRs and MSY1 data provide information about the relationship between closely related populations such as those of Iberia. Analysis of biallelic markers allowed us to identify 7 of 12 haplogroups defined by those polymorphisms. The haplogroup background showed clear differences between Iberian populations and the North African one. The use of differently mutating Y-chromosome markers allowed us to infer different population events at different time scales: the Paleolithic background of the Iberian Peninsula, the Neolithic fingerprint on Y-chromosome lineages, and the Iron Age influence in the populations of Iberia. Implications of our results for the highly debated origin of Basques are also discussed.

The human Y chromosome: an evolutionary marker comes of age

Until recently, the Y chromosome seemed to fulfil the role of juvenile delinquent among human chromosomes--rich in junk, poor in useful attributes, reluctant to socialize with its neighbours and with an inescapable tendency to degenerate. The availability of the near-complete chromosome sequence, plus many new polymorphisms, a highly resolved phylogeny and insights into its mutation processes, now provide new avenues for investigating human evolution. Y-chromosome research is growing up.

Male reproductive function and the human Y chromosome: is selection acting on the Y?

The human Y chromosome encodes genes that are essential for male sex determination, spermatogenesis and protection against Turner stigmata. In recent years mutations have been identified in Y-chromosome genes associated with these phenotypes and a series of microdeletions of the long arm of the Y have been defined that are specifically associated with male infertility. In parallel, the discovery of polymorphic markers on the Y, comprising of both slow-mutating binary markers and rapidly-mutating microsatellites, has enabled the high resolution definition of a large number of paternal lineages (haplogroups). These Y-chromosome haplogroups have been extensively used to trace population movements and understand human origins and histories, but recently a growing number of association studies have been performed aimed at assessing the relationship between the Y-chromosome background and Y-linked phenotypes such as infertility and male-specific cancers. These preliminary studies, comparing haplogroup distributions between case and control populations, are promising and suggest an association between different Y-chromosome lineages, sperm counts and prostate cancer. However, we highlight the need to extend these studies to other world populations. Increased sample numbers and a better haplogroup resolution using additional binary markers in association studies are necessary. By these approaches novel associations between Y-chromosome haplotypes and disease may be revealed and the degree to which selection is acting on the human Y chromosome may be determined.

Partial DAZ deletions in a family with five infertile brothers

OBJECTIVE

To study the genetic cause of infertility in a family with five infertile brothers.

DESIGN

Case report.

SETTINGS

Center for reproductive medicine at a university medical center.

PATIENT(S)

Five brothers presenting with primary infertility due to severely impaired spermatogenesis; also, their parents and two other paternally related family members.

INTERVENTION(S)

Fluorescence in situ hybridization and sequence family variant analysis was performed in leukocyte DNA to determine the number of deleted in azoospermia (DAZ) genes. Linkage analysis was performed for X chromosome inheritance, and mitochondrial DNA (mtDNA) was screened for mutations.

MAIN OUTCOME MEASURE(S)

DAZ gene copy number, X chromosome linkage, and mtDNA sequence.

RESULT(S)

With conventional polymerase chain reaction (PCR) analysis, no deletions of the AZFc region were found, but with fluorescence in situ hybridization and sequence family variant analysis, only two DAZ genes instead of four were detected in all individuals tested. The five brothers did not share an identical X chromosomal locus, and no mutations were found in the mtDNA of the index patient.

CONCLUSION(S)

A reduced copy number of the DAZ genes is found in five infertile brothers with severely impaired spermatogenesis, as well as in their normospermic father and in two other fertile paternally related family members. This illustrates that the phenotype associated with a reduced copy number of the DAZ genes can be extremely variable.

Y is there a risk to being male?

Being male or female can make a vital difference to many important biological functions and can lead to disparities in health. The Y chromosome carries the sex-determining sex reversal Y (SRY) gene and recent studies show that it might also harbor genes that have important biological functions other than sex determination. One such example is the emerging evidence from animal models and humans that supports the presence of cardiovascular genes on the Y chromosome. A significant amount of work remains to identify these genes; however, we report here observations linking the Y chromosome to hypertension, which could explain the higher incidence of cardiovascular disease in males compared with females.

High level of male-biased Scandinavian admixture in Greenlandic Inuit shown by Y-chromosomal analysis

We have used binary markers and microsatellites on the Y chromosome to analyse diversity in a sample of Greenlandic Inuit males. This sample contains Y chromosomes typical of those found in European populations. Because the Y chromosome has a unique and robust phylogeny of a time depth that precedes the split between European and Native American populations, it is possible to assign chromosomes in an admixed population to either continental source. On this basis, 58+/-6% of these Y chromosomes have been assigned to a European origin. The high proportion of European Y chromosomes contrasts with a complete absence of European mitochondrial DNA and indicates strongly male-biased European admixture into Inuit. Comparison of the European component of Inuit Y chromosomes with European population data suggests that they have their origins in Scandinavia. There are two potential source populations: Norse settlers from Iceland, who may have been assimilated 500 years ago, and the Danish-Norwegian colonists of the eighteenth century. Insufficient differentiation between modern Icelandic and Danish Y chromosomes means that a choice between these cannot be made on the basis of diversity analysis. However, the extreme sex bias in the admixture makes the later event more likely as the source.

The genetic legacy of the Mongols

We have identified a Y-chromosomal lineage with several unusual features. It was found in 16 populations throughout a large region of Asia, stretching from the Pacific to the Caspian Sea, and was present at high frequency: approximately 8% of the men in this region carry it, and it thus makes up approximately 0.5% of the world total. The pattern of variation within the lineage suggested that it originated in Mongolia approximately 1,000 years ago. Such a rapid spread cannot have occurred by chance; it must have been a result of selection. The lineage is carried by likely male-line descendants of Genghis Khan, and we therefore propose that it has spread by a novel form of social selection resulting from their behavior.

Comparative analysis of short tandem repeats and single nucleotide polymorphisms on the Y-chromosome in Germans, Chinese and Thais

We have typed genomic DNA samples from 95 individuals from Western Germany, 78 individuals from Bangkok/Thailand and 56 individuals from Chengdu/China for 11 Y-chromosomal diallelic polymorphisms and eight short tandem repeat (STR) systems. For single nucleotide polymorphism (SNP) analysis, a rapid method was applied using the single base extension technology (minisequencing) in combination with capillary electrophoresis. PCR products for SRY-8299, Tat, SRY2627, 92R7, SRY1532, M9, M13, M17/M19 and M20 were pooled and used as templates for the commercially available SNaPshot kit. In addition to these ten SNPs we also tested the Y-chromosomal diallelic Alu repeat insertion DYS287 (YAP) by agarose gel electrophoresis as well as the Y-chromosomal STR systems DYS19, DYS389I+II, DYS390, DYS391, DYS392, DYS393 and DYS385 by fluorescent multiplex fragment analysis. Among the 11 diallelic SNP/Alu systems, only six were found to be polymorphic in the three population samples. From these a total number of seven different haplogroups could be identified in the three populations. Of these, five haplogroups were present in Germans, five in Thais, and only two in Chinese. These haplogroup trees clearly represent population-specific structures. Haplogroup 26 is represented at a high frequency in the Thai and Chinese populations whereas it is absent in Germans. The Y-STR data confirm a haplogroup-specific distribution of Y-STR haplotypes. Only a few cases of identical STR haplotypes in the same SNP haplogroups were detected in each of the three populations studied.

Relationship between Y-chromosomal DNA haplotype and sperm count in Italy

Forty Italian individuals with sperm counts in the range 20-130x10(6)/ml were typed with eleven Y-specific binary markers. Five Y haplogroups (1, 2, 3, 9 and 21) were present in the sample. In Italy, in contrast to Denmark, sperm counts were similar in the different haplogroups.