A comprehensive portrait of Y-STR diversity of Indian populations and comparison with 129 worldwide populations

Singh, Mugdha; Sarkar, Anujit; Nandineni, Madhusudan R.

doi:10.1038/s41598-018-33714-2

Cited by 26 publications

(17 citation statements)

References 42 publications

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“…YHRD tools were used to perform AMOVA based on R ST and MDS was performed to infer the genetic relationship among the various populations 19 . For comparison of patrilineal affinities with Indian populations, Y-STR data from our laboratory was included 15 , whereas for comparison with populations from neighboring countries, published data was incorporated 18 (Supplementary Table S1). Male individuals from both the populations were assigned haplogroups based on the Y-STRs employing Whit Athey's haplogroup predictor tool 44 .…”

Section: Pcr Amplification Genotyping and Sequencing Autosomal And mentioning

confidence: 99%

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The genetic affinities of Gujjar and Ladakhi populations of India

Singh

Sarkar

Kumar

et al. 2020

Sci Rep

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The Union Territories of Jammu and Kashmir (J&K) and Ladakh in North India owing to their unique geographic location offer a wide variety of landscape from plains to high altitudes and is a congruence of many languages and cultural practices. Here, we present the genetic diversity studies of Gujjars from Jammu region of J&K and Ladakhi population based on a battery of autosomal single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs), Y-chromosomal STRs and the control region of the mitochondrial genome. These two populations were observed to be genetically distant to each other as well as to other populations from India. Interestingly, Y-STR analyses showed a closer affinity of Gujjars to other nomadic populations of Pashtuns from Baghlans and Kunduz provinces of Afghanistan and Pashtuns and Sindhis of Pakistan. Gujjars exhibited lesser genetic diversity as compared to Ladakhi population. M30f and M9 were the most abundant mitochondrial haplogroups observed among Gujjars and Ladakhis, respectively. A lower matrilineal to patrilineal diversity was observed for both these populations. The current study presents the first comprehensive analysis of Gujjars and Ladakhis and reveals their unique genetic affiliations with other populations of the world. The Indian subcontinent, which represents about one-sixth of the world population, is a unique conglomerate of multiple cultures, languages and genetic diversity. Together with sub-Himalayan countries and the present day Pakistan, Bangladesh and Sri Lanka, the Indian subcontinent is one of the oldest geographical regions inhabited by modern humans and is a witness to ancient human migratory histories 1. The two northernmost Union Territories of India viz., Jammu and Kashmir (J&K) and Ladakh, owing to their geographical location, are believed to have served as a corridor for ancient human migrations between main land of Indian subcontinent and NorthEast Asia, Eurasia or Africa 2,3. The populations of J&K and Ladakh offer a unique platform for looking into the past anthropological and demographic events which may have shaped the extant human population diversity. However, there is scant information about these populations in phylogenetic studies reported in the literature 4-6. In this study we have attempted to understand the genetic relationship of Gujjars (GJ) from Jammu region of J&K and Ladakhis (LL) with other populations of Indian subcontinent. Gujjars inhabit the northwestern region of the Indian subcontinent spanning across the regions of J&K, Himachal Pradesh (HP), Rajasthan (RJ), Haryana and Gujarat in India, and in the neighboring countries of Pakistan and Afghanistan. In the Union Territory of J&K, Gujjars constitute the third-largest population group and follow a nomadic/semi-nomadic lifestyle and are dependent on rearing of cattle, goats and sheep 7. Few research groups had previously reported on the genetic diversity studies among Gujjars 8-11 , however, considering the unique geographical distribution of Gujjars and their under-representation...

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Section: Pcr Amplification Genotyping and Sequencing Autosomal And mentioning

confidence: 99%

“…Our previous studies based on analysis of autosomal STRs 14 and Y-chromosomal STRs 15 that included populations from J&K (JK) (other than GJ and LL populations), suggested that JK individuals were not genetically isolated from other populations of India. This observation was in concordance with a previous report 16 .…”

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The genetic affinities of Gujjar and Ladakhi populations of India

Singh

Sarkar

Kumar

et al. 2020

Sci Rep

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“…As expected, such similarities reduce the accuracy of STR-based prediction tools. This conclusion is supported in separate studies [37], [38], [40], which suggest SNP analysis as a second validation step if accurate predictions are required. Thus, the most recent studies use a combination of STR and SNP as genetic markers [41], [42] for haplogroup predictions.…”

Section: Introductionmentioning

confidence: 58%

A Novel Deep Neural Networks Model Based on Prime Numbers for Y DNA Haplogroup Prediction

2020

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Most of the Y chromosome (Ychr) region (approximately 95%) passes unchanged from father to son, except by the gradual accumulation of single-nucleotide polymorphism (SNP) mutations. This results in mutations being inherited together, where all males in the direct family will have an identical pattern of variations. These mutation patterns serve as markers and can be mapped into clusters known as Y DNA haplogroups. Besides lineage tracing, haplogroups have been associated with male infertility, semen parameters, and, more recently, disease progression in several populations. Thus, haplogroup prediction research is gaining importance because of the increasing interest in personalized medicine. Of note, there are two approaches to predicting haplogroups, where the difference lies in the genetic markers: short tandem repeats (STRs) or SNPs are inputs to the haplogroup prediction tools. STRs are not without limitations, as similar STR haplotypes exist between haplogroups, and this reduces the effectiveness of STR-based haplogroup prediction tools. By contrast, current SNP-based haplogroup prediction tools are computationally expensive. There have been no studies to date that leverage traditional machine learning and deep learning algorithms to identify mutation patterns using SNPs only, and this paper proposes a novel SNP-based deep neural networks (DNNs) model. However, DNNs suffer the curse of dimensionality and become computationally expensive with large datasets. Thus, this paper overcomes the limitation of the network by proposing a novel feature extraction method based on prime numbers that computes features in either the forward or reverse direction of the SNPs data. Our experimental results show that the model achieves a categorical cross-entropy loss value as low as 0.001 on the training dataset and as low as 0.039 on the test dataset.

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“…From the intercontinental perspective, a MDS was performed between Maoming Han and 21 worldwide populations (Kim et al, 2001;Miranda et al, 2001;Roewer et al, 2005;Mizuno et al, 2008;Alam et al, 2010;Laouina et al, 2011;Wolfgramm Ede et al, 2011;Ramos-Luis et al, 2014;Xu et al, 2015;Han et al, 2016;Rapone et al, 2016;Wang et al, 2017;Alonso Morales et al, 2018;Fan et al, 2018c;Singh et al, 2018;Henry et al, 2019;Lang et al, 2019;Li et al, 2019;Salvador et al, 2019;Reid and Heathfield, 2020). As shown in Supplementary Figure 1, (Yang et al, 2014;Shu et al, 2015;Han et al, 2016;Wang et al, 2016Wang et al, , 2017Xu et al, 2016;Yao et al, 2016;Jiang et al, 2017;Chen et al, 2018;Fan et al, 2018c;Lang et al, 2019;Yin et al, 2020) are listed in Supplementary 2B).…”

Section: Genetic Differences Between Maoming Han and Han Chinese Populations From Southern And Northern Mainland Chinamentioning

confidence: 99%

Insights Into Forensic Features and Genetic Structures of Guangdong Maoming Han Based on 27 Y-STRs

Fan

Xie

et al. 2021

Front. Genet.

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Maoming is located in the southwest region of Guangdong Province and is the cradle of Gaoliang culture, which is the representative branch of Lingnan cultures. Historical records showed that the amalgamations between Gaoliang aborigines and distinct ethnic minorities had some influences on the shaping of Gaoliang culture, especially for the local Tai-kadai language-speaking Baiyue and Han Chinese from Central China. However, there is still no exact genetic evidence for the influences on the genetic pool of Maoming Han, and the genetic relationships between Maoming Han and other Chinese populations are still unclear. Hence, in order to get a better understanding of the paternal genetic structures and characterize the forensic features of 27 Y-chromosomal short tandem repeats (Y-STRs) in Han Chinese from Guangdong Maoming, we firstly applied the AmpFLSTR® Yfiler® Plus PCR Amplification Kit (Thermo Fisher Scientific, Waltham, MA, United States) to genotype the haplotypes in 431 Han males residing in Maoming. A total of 263 different alleles were determined across all 27 Y-STRs with the corresponding allelic frequencies from 0.0004 to 0.7401, and the range of genetic diversity (GD) was 0.4027 (DYS391) to 0.9596 (DYS385a/b). In the first batch of 27 Yfiler data in Maoming Han, 417 distinct haplotypes were discovered, and nine off-ladder alleles were identified at six Y-STRs; in addition, no copy number variant or null allele was detected. The overall haplotype diversity (HD) and discrimination capacity (DC) of 27 Yfiler were 0.9997 and 0.9675, respectively, which demonstrated that the 6-dye and 27-plex system has sufficient system effectiveness for forensic applications in Maoming Han. What is more, the phylogenetic analyses indicated that Maoming Han, which is a Southern Han Chinese population, has a close relationship with Meizhou Kejia, which uncovered that the role of the gene flows from surrounding Han populations in shaping the genetic pool of Maoming Han cannot be ignored. From the perspectives of genetics, linguistics, and geographies, the genetic structures of Han populations correspond to the patterns of the geographical-scale spatial distributions and the relationships of language families. Nevertheless, no exact genetic evidence supports the intimate relationships between Maoming Han and Tai-Kadai language-speaking populations and Han populations of Central Plains in the present study.

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A comprehensive portrait of Y-STR diversity of Indian populations and comparison with 129 worldwide populations

Cited by 26 publications

References 42 publications

The genetic affinities of Gujjar and Ladakhi populations of India

The genetic affinities of Gujjar and Ladakhi populations of India

A Novel Deep Neural Networks Model Based on Prime Numbers for Y DNA Haplogroup Prediction

Insights Into Forensic Features and Genetic Structures of Guangdong Maoming Han Based on 27 Y-STRs

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