Principal-components analysis of prehistoric South Asian crania

Principal-components analysis is used as an investigative procedure for establishing temporal, spatial and evolutionary-developmental changes in Homo sapiens skeletal specimens from prehistoric sites in South Asia. It is concluded that cranial variables which cluster hunter-gatherers within the sample are related to facial architecture with respect to robusticity and size. Older models presumably reflecting genetic affinities and racial classifications of prehistoric South Asians which were based upon univariate-bivariate statistical analyses are not supported by the results of this principal-components analysis.     

Admixture and diversity in West African cattle populations

We present a population genetic analysis of microsatellite variation in 16 West African cattle populations. West Africa represents a unique juxtaposition of different climatic and ecological zones in a relatively small geographical area. While more humid coastal regions are inhabited by the tsetse fly, a vector which spreads trypanosomiasis among cattle, the disease is not transmitted in the drier areas outside this zone. This is the most thorough study of genetic diversity in cattle within this area, which contains genetically important trypanotolerant Bos taurus breeds. Genetic relationships among the many breeds are examined and levels of diversity are assessed. Admixture levels were determined using a variety of methods. Ancestry informative or population-associated alleles (PAAs) were selected using populations from India, the Near East and Europe. Multivariate analysis, the admix program and model-based Bayesian admixture analysis approaches were also employed. These analyses reveal the direct impact of ecological factors and the profound effect of admixture on the cattle of this region. They also highlight the importance of efforts to prevent further dilution of African taurine breeds by B. indicus cattle.     

The South Asian Genome

The genetic sequence variation of people from the Indian subcontinent who comprise one-quarter of the world''s population, is not well described. We carried out whole genome sequencing of 168 South Asians, along with whole-exome sequencing of 147 South Asians to provide deeper characterisation of coding regions. We identify 12,962,155 autosomal sequence variants, including 2,946,861 new SNPs and 312,738 novel indels. This catalogue of SNPs and indels amongst South Asians provides the first comprehensive map of genetic variation in this major human population, and reveals evidence for selective pressures on genes involved in skin biology, metabolism, infection and immunity. Our results will accelerate the search for the genetic variants underlying susceptibility to disorders such as type-2 diabetes and cardiovascular disease which are highly prevalent amongst South Asians.     

Genome-wide genetic diversity,population structure and admixture analysis in African and Asian cattle breeds

Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69 903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.     

Inter- and intra-population genetic divergence of East Asian cattle populations: focusing on Korean cattle

In order to facilitate the on-going cattle conservation and improvement programs in Korea, we examined genetic relationships among East Asian cattle, focusing on Korean native cattle, using complete mitochondrial DNA control region sequences. In total, 67 haplotypes were discriminated by 97 variable sites in East Asian cattle. Of the variable sites, 35 represented singleton variable sites and 62 were parsimony informative sites. For Korean cattle, 30 haplotypes were discriminated by 40 variable sites. The variable sites identified in this study correspond to transition or transversion point mutations. Inter-populations genetic distance varied from 0.004 to 0.052 for East Asian cattle populations. The genetic divergence observed between Korean Brown and Jeju Black (0.004) was among the lowest. The Mongolian cattle were slightly divergent from other East Asian cattle populations studied. The network analysis uncovered that Jeju Black and Yunbian samples represented the possible ancestral Haplotype within T3 Bos taurus main lineage. Thus, we hypothesized that the Jeju and Yunbian cattle may represent one of the original native North East Asian cattle in the region.     

A comparative whole genome analysis of Helicobacter pylori from a human dense South Asian setting

Helicobacter pylori, a Gram-negative bacterium, is associated with a wide range of gastric diseases such as gastritis, duodenal ulcer, and gastric cancer. The prevalence of H pylori and risk of disease vary in different parts of the world based on the prevailing bacterial lineage. Here, we present a contextual and comparative genomics analysis of 20 clinical isolates of H pylori from patients in Bangladesh. Despite a uniform host ethnicity (Bengali), isolates were classified as being part of the HpAsia2 (50%) or HpEurope (50%) population. Out of twenty isolates, eighteen isolates were cagA positive, with two HpEurope isolates being cagA negative, three EPIYA motif patterns (AB, AB-C, and ABC-C) were observed among the cagA-positive isolates. Three vacA genotypes were observed with the s1m1i1dic1 genotype observed in 75% of isolates; the s1m2i1d1c2 and s2m2i2d2c2 genotypes were found to be 15% and 10% of isolates, respectively. The non-virulent genotypes s2m2i2d2c2 was only observed in HpEurope population isolates. Genotypic analysis of oipA gene, present in all isolates, revealed five different patterns of the CT repeat; all HpAsia2 isolates were in “ON” while 20% of HpEurope isolates were genotypically “OFF.” The three blood group antigen binding adhesins encoded genes (bab genes) examined and we observed that the most common genotype was (babA/babB/-) found in eight isolates, notably six were HpAsia2 isolates. The babA gene was found in all HpAsia2 isolates but present in only half of the HpEurope isolates. In silico antibiotic susceptibility analysis revealed that 40% of the strains were multi-drug resistant. Mutations associated with resistance to metronidazole, fluoroquinolone, and clarithromycin were detected 90%, 45%, and 5%, respectively, in H pylori strain. In conclusion, it is evident that two populations of H pylori with similar antibiotic profiles are predominant in Bangladesh, and it appears that genotypically the HpAisa2 isolates are potentially more virulent than the HpEurope isolates.     

Genetic diversity of north-east Asian cattle based on microsatellite data

In order to assess the genetic variability and population structure of north-east Asian cattle, 13 microsatellite loci were analysed for a total of 200 individuals including Korean, Chinese, Japanese Black and European Holstein cattle. Observed and expected heterozygosity, two estimators (F(ST) and G(ST)) of gene differentiation, and Nei's DA distance were evaluated. Based on expected mean heterozygosity, the lowest genetic diversity was exhibited in Japanese Black cattle (H(E)=0.471), and the highest in Chinese cattle (H(E)=0.744). Korean cattle revealed a relatively high degree of genetic diversity (H(E)=0.728). Average proportion of genetic variation because of interpopulation subdivision among north-east Asian cattle varied between 10.9 and 9.9%, depending on the estimator used. N-J tree based on Nei's DA genetic distance showed that Korean and Chinese cattle are closely related, whereas Japanese Black cattle are clearly distinct from the other two populations, forming a north-east Asian outgroup.     

Phylogenetic relationships of Northeast Asian cattle to other cattle populations determined using mitochondrial DNA D-loop sequence polymorphism

Phylogenetic relationships of Northeast Asian cattle to various other cattle breeds including Bos taurus, Bos indicus, and Bison bison were assessed using mtDNA D-loop sequences. A neighbor-joining tree was constructed using sequences determined for 4 Cheju Black, 4 Cheju Yellow, 4 Korean Yellow cattle (Bos taurus), and 2 American Brahman cattle (Bos indicus), and also published sequences for 31 Japanese Black cattle, 45 European breed cattle, 6 African zebus, 2 African taurines, and 6 Indian zebus. Five American bisons (Bison bison) were used as an outgroup. The neighbor-joining tree showed that American bisons and Indian zebus are clearly separate from other cattle breeds, respectively, and African cattle clustered together, although with a low bootstrap probability (<50%). Results indicate that cattle in Northeast Asia, Europe, and Africa are closely related to each other–suggesting their recent divergence, but are separate from Indian zebus.     

Religion and economic activity in the South Asian population

Anthropological and sociological literature points to the importance of religion as a basis for understanding the diverse nature of Britain's South Asian population. Using a rare quantitative source, the 1994 National Survey of Ethnic Minorities, and against a backdrop of relative neglect by quantitative social scientists, this article considers the religious dimension to observed differences in economic activity among South Asians. The analysis reports substantial differences between religious sub-groups (by age and sex) across a range of key measures, including: differences in the proportion who are economically active; differences in the proportion of the economically active who successfully gain employment; among the employed, differences in the type of jobs held and in reported income. The analysis suggests a more complex picture than the Muslim/non-Muslim dichotomy often inferred from analysis using conventional ethnic group classifications, with notable differences between Indian Sikhs and Hindus, and between Indian Muslims and Pakistani and Bangladeshi Muslims.     

Symbol and Sustenance: Cattle in South Asian Culture

Domesticated Indian zebu cattle were present on the western margins of the South Asian subcontinent as early as 6000 B.C. Cattle were important in the agricultural economy of the Harappan civilization of the Indus Valley, but archaeological evidence suggests the bull was also assuming a symbolic or religious role in this culture during the third millennium B.C. There is, however, little to suggest that the cow was viewed as sacred. Following the decline of the Harappan civilization, northwestern India was settled by Aryan-speaking peoples who laid the foundations of modern Indian society. The Aryans were pastoral by nature and the economic importance of cattle to this society is mirrored in the role of cattle in ritual, in the pastoral symbolism of the Vedic literature (the ancient religious literature of Hinduism), and also in the association of the cow with various Vedic deities. Yet, again there is nothing to suggest the cow was viewed as sacred at this time. It is not until the appearance of the ahimsa philosophy at the end of the Vedic period, and the acceptance of this belief in the major religious philosophies of the region (Jainism, Buddhism, and later Hinduism), that the concept of the sanctity and inviolability of the cow began to crystallize. The “sacred-cow concept” appears as established doctrine in Hindu literature by the end of the medieval period (ca. fourth century A.D.), although popular practice appears to be at variance with this doctrine. A variety of historical, political, religious and social factors appear to have contributed to the general acceptance of the sacred cow doctrine by the Hindu population at large. During the 1960s, the “sacred cow” was at the center of a controversy in the social sciences concerning whether the concept was essentially religious in nature or reflected the ecological realities of the cattle economy of the Indian subcontinent. This debate notwithstanding, cattle remain central to the Indian economy, but also play a significant role in the religion and rituals of modern Hinduism, particularly those related to the worship of Krishna. Cattle have also assumed a political role in contemporary India, with anti-cow-slaughter legislation and the protection of the cow being identified with the emerging Hindutva movement. No understanding of South Asian culture can be complete without an awareness of the economic, historical, political and religious dimensions of cattle in the Indian subcontinent.     

The paleobiology of Amphipithecidae, South Asian late Eocene primates

Analysis of the teeth, orbital, and gnathic regions of the skull, and fragmentary postcranial bones provides evidence for reconstructing a behavioral profile of Amphipithecidae: Pondaungia, Amphipithecus, Myanmarpithecus (late middle Eocene, Myanmar) and Siamopithecus (late Eocene, Thailand). At 5-8 kg, Pondaungia, Amphipithecus, and Siamopithecus are perhaps the largest known Eocene primates. The dental and mandibular anatomy suggest that large-bodied amphipithecids were hard-object feeders. The shape of the mandibular corpus and stiffened symphysis suggest an ability to resist large internal loads during chewing and to recruit significant amounts of muscle forces from both the chewing and non-chewing sides of the jaw so as to increase bite force during mastication. The large spatulate upper central incisor of Pondaungia and projecting robust canines of all the larger amphipithecids suggest that incisal food preparation was important. The molars of Siamopithecus, Amphipithecus, and Pondaungia have weak shearing crests. This, and the thick molar enamel found in Pondaungia, suggests a diet of seeds and other hard objects low in fiber. In contrast, Myanmarpithecus was smaller, about 1-2 kg; its cheek teeth suggest a frugivorous diet and do not imply seed eating. Postcranial bones (humerus, ulna, and calcaneus) of a single large amphipithecid individual from Myanmar suggest an arboreal quadrupedal locomotor style like that of howler monkeys or lorises. The humeral head is rounded, proximally oriented, and the tuberosities are low indicating an extremely mobile glenohumeral joint. The great thickness of the midshaft cortical bone of the humerus implies enhanced ability to resist bending and torsion, as seen among slow moving primate quadrupeds. The elbow joint exhibits articular features for enhanced stability in habitually flexed positions, features also commonly found in slow moving arboreal quadrupeds. The short distal load arm of the calcaneus is consistent with, but not exclusive to, slow, arboreal quadrupedalism, and suggests no reliance on habitual leaping.