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Human settlement and migrations along sides of Bay-of-Bengal have played a vital role in shaping the genetic landscape of Bangladesh, Eastern India and Southeast Asia. Bangladesh and Northeast India form the vital land bridge between the South and Southeast Asia. To reconstruct the population history of this region and to see whether this diverse region geographically acted as a corridor or barrier for human interaction between South Asia and Southeast Asia, we, for the first time analyzed high resolution uniparental (mtDNA and Y chromosome) and biparental autosomal genetic markers among aboriginal Bangladesh tribes currently speaking Tibeto-Burman language. All the three studied populations; Chakma, Marma and Tripura from Bangladesh showed strikingly high homogeneity among themselves and strong affinities to Northeast Indian Tibeto-Burman groups. However, they show substantially higher molecular diversity than Northeast Indian populations. Unlike Austroasiatic (Munda) speakers of India, we observed equal role of both males and females in shaping the Tibeto-Burman expansion in Southern Asia. Moreover, it is noteworthy that in admixture proportion, TB populations of Bangladesh carry substantially higher mainland Indian ancestry component than Northeast Indian Tibeto-Burmans. Largely similar expansion ages of two major paternal haplogroups (O2a and O3a3c), suggested that they arose before the differentiation of any language group and approximately at the same time. Contrary to the scenario proposed for colonization of Northeast India as male founder effect that occurred within the past 4,000 years, we suggest a significantly deep colonization of this region. Overall, our extensive analysis revealed that the population history of South Asian Tibeto-Burman speakers is more complex than it was suggested before.

Background: The central Indian state Madhya Pradesh is often called as 'heart of India' and has always been an important region functioning as a trinexus belt for three major language families (Indo-European, Dravidian and Austroasiatic). There are less detailed genetic studies on the populations inhabited in this region. Therefore, this study is an attempt for extensive characterization of genetic ancestries of three tribal populations, namely; Bharia, Bhil and Sahariya, inhabiting this region using haploid and diploid DNA markers. Methodology/Principal Findings: Mitochondrial DNA analysis showed high diversity, including some of the older sublineages of M haplogroup and prominent R lineages in all the three tribes. Y-chromosomal biallelic markers revealed high frequency of Austroasiatic-specific M95-O2a haplogroup in Bharia and Sahariya, M82-H1a in Bhil and M17-R1a in Bhil and Sahariya. The results obtained by haploid as well as diploid genetic markers revealed strong genetic affinity of Bharia (a Dravidian speaking tribe) with the Austroasiatic (Munda) group. The gene flow from Austroasiatic group is further confirmed by their Y-STRs haplotype sharing analysis, where we determined their founder haplotype from the North Munda speaking tribe, while, autosomal analysis was largely in concordant with the haploid DNA results. Conclusions/Significance: Bhil exhibited largely Indo-European specific ancestry, while Sahariya and Bharia showed admixed genetic package of Indo-European and Austroasiatic populations. Hence, in a landscape like India, linguistic label doesn't unequivocally follow the genetic footprints. © 2012 Sharma et al.

Life tables of birth intervals and median birth intervals in two Indian states, Uttar Pradesh and Kerala, were computed for several subgroups of the study population. Multivariate hazards modelling technique was used to examine the net effect of each of the variables studied. The results show a substantial effect of socioeconomic variables in child-spacing after controlling for the major intermediate variables.Child spacing patterns have been found to be reflected in the interaction between a variety of biological and social factors in India. Birth intervals differ from Western patterns: long lengths of postpartum amenorrhea and prolonged breast feeding. Cox proportional hazards models and descriptive statistics are used to examine birth intervals among 3514 households in the Varanasi district of Uttar Pradesh state in 1978, and among 3000 households from 3 districts in Kerala state in 1980. Women using contraception or who were sterilized were excluded from the analysis. Birth spacing among Urrar Pradesh women was 44 months from marriage to first birth and 32 months between subsequent births. In Kerala, the first birth interval was 20 months and subsequent intervals were up to 30 months. In Uttar Pradesh, the median birth interval declined as age at marriage increased; in the sample populations, age-at-marriage groups differed widely in their birth intervals. Birth intervals also varied with household economic status. Based on the social status index and educational status of husband and wife in Uttar Pradesh, differences in median birth intervals were minimal but large for the extent of childbearing. 28% of higher class women had a 5th child compared to 2% among low status groups. When controlling for marriage age and other variables, the proportional hazards model showed that all groups, other than the high status group, had a statistically significant higher risk of a birth. When using education as the status measure in Kerala, the findings on birth interval were similar, but the proportion having a 2nd birth was higher among lower status groups. Husband's education did not have much effect on birth interval. Religion did not strongly affect the risk of birth other than for first births in Uttar Pradesh. In Kerala, there were shorter birth intervals among Muslims and a higher probability of parity progression to the next birth. Muslims and Christians versus Hindus had a significantly higher adjusted risk of birth. Infant mortality shortened birth intervals for women in Uttar Pradesh by 9 months, and the adjusted risk of a next birth was 2 times higher. Kerala results were similar, but replacement was less likely with higher order births. Both states had slightly longer birth intervals after a male child.

Background - The availability of multiple whole genome sequences has facilitated in silico identification of fixed and polymorphic transposable elements (TE). Whereas polymorphic loci serve as makers for phylogenetic and forensic analysis, fixed species-specific transposon insertions, when compared to orthologous loci in other closely related species, may give insights into their evolutionary significance. Besides, TE insertions are not isolated events and are frequently associated with subtle sequence changes concurrent with insertion or post insertion. These include duplication of target site, 3' and 5' flank transduction, deletion of the target locus, 5' truncation or partial deletion and inversion of the transposon, and post insertion changes like inter or intra element recombination, disruption etc. Although such changes have been studied independently, no automated platform to identify differential transposon insertions and the associated array of sequence changes in genomes of the same or closely related species is available till date. To this end, we have designed RISCI - 'Repeat Induced Sequence Changes Identifier' - a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify differential transposon insertions and associated sequence changes using specific alignment signatures, which may then be examined for their downstream effects. Results - We showcase the utility of RISCI by comparing full length and truncated L1HS and AluYa5 retrotransposons in the reference human genome with the chimpanzee genome and the alternate human assemblies (Celera and HuRef). Comparison of the reference human genome with alternate human assemblies using RISCI predicts 14 novel polymorphisms in full length L1HS, 24 in truncated L1HS and 140 novel polymorphisms in AluYa5 insertions, besides several insertion and post insertion changes. We present comparison with two previous studies to show that RISCI predictions are broadly in agreement with earlier reports. We also demonstrate its versatility by comparing various strains of Mycobacterium tuberculosis for IS 6100 insertion polymorphism. Conclusions - RISCI combines comparative genomics with subtractive hybridization, inferring changes only when exclusive to one of the two genomes being compared. The pipeline is generic and may be applied to most transposons and to any two or more genomes sharing high sequence similarity. Such comparisons, when performed on a larger scale, may pull out a few critical events, which may have seeded the divergence between the two species under comparison.