Identification of Ajnala skeletal remains using multiple forensic anthropological methods and techniques: a bioarchaeological report.

Fragmented and badly damaged commingled human remains present a tough challenge for their identification pursuits in forensic anthropology. Thousands of unknown human remains along with items of contextual identity, reportedly belonging to 282 Indian sepoys killed in 1857, were exhumed non-scientifically from a disused ancient well at Ajnala (Amritsar, India). In this manuscript, the non-scientific excavation of unknown human remains from the abandoned well, their forensic anthropological strategies for identification purposes, challenges being faced and future possibilities of their biological profiling have been discussed. Multiple methods and techniques like anthropological examinations, odontological profiling, radiological analyses, stable isotope and mitochondrial DNA (mtDNA) analyses were applied to few bones and teeth collected from the Ajnala skeletal assemblage. Though majority of studied bones and teeth were found belonging to adult males, very few of them had morphological, osteological and molecular features questioning the authenticity and validity of the written records. Due to certain ambiguous findings or gaps observed between the anthropological analyses of the Ajnala skeletal remains and the reported versions about their affiliations; certain advanced radiological, chemical and molecular techniques were applied to estimate their probable age, sex and populational affinity. The obtained radiological, isotopic and molecular signatures of the remains were compared with the available databases to estimate their affinity with the individuals of geographic area to whom the remains reportedly belonged to. The maternally inherited mtDNA haplogroup assignments, and stable isotope analysis of carbon and oxygen suggested that the studied human remains belonged to the individuals from West Bengal, Bihar, Odisha, Awadh (presently in Uttar Pradesh) and parts of Meghalaya and Manipur as potential regions of their geographic identity and thus, attributing the victims to be non-local to the site. However, merely on the basis of forensic anthropological examinations of very few bones and teeth (collected out of a huge collection of thousands of bones and teeth); it would be just an unqualified and sweeping conclusion to claim their identity as adult or non-adult, male or female, local or non-local, victims of 1857 mass killings or to the victims of ceremonial sacrifices or criminal activities committed in the past. A sufficient number of bones and teeth along with items of personal identity needs to be examined with multiple scientific techniques to arrive at some valid conclusions about their biological identity

Complete mitochondrial genome sequence of Asiatic lion (Panthera leo persica)

The complete mitochondrial genome sequence 17,059 bp of Asiatic lion (Panthera leo persica) has been sequenced with the use of next generation sequencing technology using Ion TorrentPGM platform. The complete mitochondrial genome sequence of Asiatic lion consists of 13 protein-coding, 22 tRNA and two rRNA genes and 1 Control Region (CR). The mitochondrial genome is relatively similar to other felid mitochondrial genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases to be typical of those reported for other mammals. The nucleotide composition of Asiatic lion mitogenome shows that there is more A-T% than G-C% on the positive strand as revealed by positive AT and CG skews. The overall base composition is 31.9% of A, 27.2% of C, 14.5% of G and 26.2% of T. Most of the genes have ATA start codons, except ND1, COX2, ATP8, ATP6, ND4 and ND5 have ATG start codons

Genetic affinities of the Jewish populations of India

Due to the lack of written records or inscription, the origin and affiliation of Indian Jewish populations with other world populations remain contentious. Previous genetic studies have found evidence for a minor shared ancestry of Indian Jewish with Middle Eastern (Jewish) populations. However, these studies (relied on limited individuals), haven’t explored the detailed temporal and spatial admixture process of Indian Jewish populations with the local Indian populations. Here, using large sample size with combination of high resolution biparental (autosomal) and uniparental markers (Y chromosome and mitochondrial DNA), we reconstructed genetic history of Indian Jewish by investigating the patterns of genetic diversity. Consistent with the previous observations, we detected minor Middle Eastern specific ancestry component among Indian Jewish communities, but virtually negligible in their local neighbouring Indian populations. The temporal test of admixture suggested that the first admixture of migrant Jewish populations from Middle East to South India (Cochin) occurred during fifth century. Overall, we concluded that the Jewish migration and admixture in India left a record in their genomes, which can link them to the ‘Jewish Diaspora’

The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent.

Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of SLC24A5 in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 22-28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India

Ancient mtDNA from the extinct Indian cheetah supports unexpectedly deep divergence from African cheetahs

Abstract: The Indian cheetah was hunted to extinction by the mid-20th century. While analysis of 139 bp of mitochondrial DNA (mtDNA) has confirmed that the Indian cheetah was part of the Asiatic subspecies (Acinonyx jubatus venaticus), the detailed relationships between cheetah populations remains unclear due to limited genetic data. We clarify these relationships by studying larger fragments of cheetah mtDNA, both from an Indian cheetah museum specimen and two African cheetah, one modern and one historic, imported into India at different times. Our results suggest that the most recent common ancestor of cheetah mtDNA is approximately twice as ancient as currently recognised. The Indian and Southeast African (Acinonyx jubatus jubatus) cheetah mtDNA diverged approximately 72 kya, while the Southeast and Northeast African (Acinonyx jubatus soemmeringii) cheetah mtDNA diverged around 139 kya. Additionally, the historic African cheetah sampled from India proved to have an A. j. jubatus haplotype, suggesting a hitherto unrecognised South African route of cheetah importation into India in the 19th century. Together, our results provide a deeper understanding of the relationships between cheetah subspecies, and have important implications for the conservation of A. j. venaticus and potential reintroduction of cheetahs into India

Ancient mtDNA from the extinct Indian cheetah supports unexpectedly deep divergence from African cheetahs

Abstract: The Indian cheetah was hunted to extinction by the mid-20th century. While analysis of 139 bp of mitochondrial DNA (mtDNA) has confirmed that the Indian cheetah was part of the Asiatic subspecies (Acinonyx jubatus venaticus), the detailed relationships between cheetah populations remains unclear due to limited genetic data. We clarify these relationships by studying larger fragments of cheetah mtDNA, both from an Indian cheetah museum specimen and two African cheetah, one modern and one historic, imported into India at different times. Our results suggest that the most recent common ancestor of cheetah mtDNA is approximately twice as ancient as currently recognised. The Indian and Southeast African (Acinonyx jubatus jubatus) cheetah mtDNA diverged approximately 72 kya, while the Southeast and Northeast African (Acinonyx jubatus soemmeringii) cheetah mtDNA diverged around 139 kya. Additionally, the historic African cheetah sampled from India proved to have an A. j. jubatus haplotype, suggesting a hitherto unrecognised South African route of cheetah importation into India in the 19th century. Together, our results provide a deeper understanding of the relationships between cheetah subspecies, and have important implications for the conservation of A. j. venaticus and potential reintroduction of cheetahs into India

"Like sugar in milk": reconstructing the genetic history of the Parsi population.

BACKGROUND: The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations using high-resolution genetic variation data on autosomal and uniparental loci (Y-chromosomal and mitochondrial DNA). Additionally, we also assayed mitochondrial DNA polymorphisms among ancient Parsi DNA samples excavated from Sanjan, in present day Gujarat, the place of their original settlement in India. RESULTS: Among present-day populations, the Parsis are genetically closest to Iranian and the Caucasus populations rather than their South Asian neighbors. They also share the highest number of haplotypes with present-day Iranians and we estimate that the admixture of the Parsis with Indian populations occurred ~1,200 years ago. Enriched homozygosity in the Parsi reflects their recent isolation and inbreeding. We also observed 48% South-Asian-specific mitochondrial lineages among the ancient samples, which might have resulted from the assimilation of local females during the initial settlement. Finally, we show that Parsis are genetically closer to Neolithic Iranians than to modern Iranians, who have witnessed a more recent wave of admixture from the Near East. CONCLUSIONS: Our results are consistent with the historically-recorded migration of the Parsi populations to South Asia in the 7th century and in agreement with their assimilation into the Indian sub-continent's population and cultural milieu "like sugar in milk". Moreover, in a wider context our results support a major demographic transition in West Asia due to the Islamic conquest

Low carbon warehouse management under cap-and-trade policy

© 2016 Elsevier Ltd Green warehouse management plays a significant part in developing a carbon efficient supply chain. This research examines the behaviour change in warehouse management decisions under the cap-and-trade emission policy and explores the role of green technology investment in managing the trade-offs between the economic and environment performances of warehousing operations. This study analyses the optimal decisions in warehouse management and technology investment under the cap-and-trade emissions policy to assist the practitioners in making efficient decisions. Moreover, this study also investigates the effect of initial carbon emission allowance and transaction costs of the unit carbon emission trading with the outside market, on the economic and environment performances of warehousing operations. The findings of this study provide useful insights in greening the warehousing operations and reducing the carbon emissions