SciCombinator

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Concept: Indian subcontinent

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In recent times, several new species of amphibians have been described from India. Many of these discoveries are from biodiversity hotspots or from within protected areas. We undertook amphibian surveys in human dominated landscapes outside of protected areas in south western region of India between years 2013-2015. We encountered a new species of Microhyla which is described here as Microhyla laterite sp. nov. It was delimited using molecular, morphometric and bioacoustics comparisons. Microhyla laterite sp. nov. appears to be restricted to areas of the West coast of India dominated by laterite rock formations. The laterite rock formations date as far back as the Cretaceous-Tertiary boundary and are considered to be wastelands in-spite of their intriguing geological history. We identify knowledge gaps in our understanding of the genus Microhyla from the Indian subcontinent and suggest ways to bridge them.

Concepts: Species, Geology, Indian subcontinent, Tetrapod, Amphibian, Frog, Toad, Salamander

50

Australia was one of the earliest regions outside Africa to be colonized by fully modern humans, with archaeological evidence for human presence by 47,000 years ago (47 kya) widely accepted [1, 2]. However, the extent of subsequent human entry before the European colonial age is less clear. The dingo reached Australia about 4 kya, indirectly implying human contact, which some have linked to changes in language and stone tool technology to suggest substantial cultural changes at the same time [3]. Genetic data of two kinds have been proposed to support gene flow from the Indian subcontinent to Australia at this time, as well: first, signs of South Asian admixture in Aboriginal Australian genomes have been reported on the basis of genome-wide SNP data [4]; and second, a Y chromosome lineage designated haplogroup C(∗), present in both India and Australia, was estimated to have a most recent common ancestor around 5 kya and to have entered Australia from India [5]. Here, we sequence 13 Aboriginal Australian Y chromosomes to re-investigate their divergence times from Y chromosomes in other continents, including a comparison of Aboriginal Australian and South Asian haplogroup C chromosomes. We find divergence times dating back to ∼50 kya, thus excluding the Y chromosome as providing evidence for recent gene flow from India into Australia.

Concepts: DNA, Gene, Cell, Human, Chromosome, Indian subcontinent, Indian Ocean, XY sex-determination system

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India’s unique and highly diverse biota combined with its unique geodynamical history has generated significant interest in the patterns and processes that have shaped the current distribution of India’s flora and fauna and their biogeographical relationships. Fifty four million year old Cambay amber from northwestern India provides the opportunity to address questions relating to endemism and biogeographic history by studying fossil insects. Within the present study seven extant and three fossil genera of biting midges are recorded from Cambay amber and five new species are described: Eohelea indica Stebner & Szadziewski n. sp., Gedanohelea gerdesorum Stebner & Szadziewski n. sp., Meunierohelea cambayana Stebner & Szadziewski n. sp., Meunierohelea borkenti Stebner & Szadziewski n. sp., and Meunierohelea orientalis Stebner & Szadziewski n. sp. Fossils of species in the genera Leptoconops Skuse, 1889, Forcipomyia Meigen, 1818, Brachypogon Kieffer, 1899, Stilobezzia Kieffer, 1911, Serromyia Meigen, 1818, and Mantohelea Szadziewski, 1988 are recorded without formal description. Furthermore, one fossil belonging to the genus Camptopterohelea Wirth & Hubert, 1960 is included in the present study. Our study reveals faunal links among Ceratopogonidae from Cambay amber and contemporaneous amber from Fushun, China, Eocene Baltic amber from Europe, as well as the modern Australasian and the Oriental regions. These findings imply that faunal exchange between Europe, Asia and India took place before the formation of Cambay amber in the early Eocene.

Concepts: Present, Nematocera, Biology, Species, Indian subcontinent, Genus, Fossil

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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.

Concepts: Gene, Genetics, India, Indian subcontinent, Indian Ocean, Asia, South Asia, Central Asia

30

The South Asian Monson (SAM) is one of the most intense climatic elements yet its initiation and variations are not well established. Dating the deposits of SAM wind-driven currents in IODP cores from the Maldives yields an age of 12. 9 Ma indicating an abrupt SAM onset, over a short period of 300 kyrs. This coincided with the Indian Ocean Oxygen Minimum Zone expansion as revealed by geochemical tracers and the onset of upwelling reflected by the sediment’s content of particulate organic matter. A weaker ‘proto-monsoon’ existed between 12.9 and 25 Ma, as mirrored by the sedimentary signature of dust influx. Abrupt SAM initiation favors a strong influence of climate in addition to the tectonic control, and we propose that the post Miocene Climate Optimum cooling, together with increased continentalization and establishment of the bipolar ocean circulation, i.e. the beginning of the modern world, shifted the monsoon over a threshold towards the modern system.

Concepts: Climate, Weather, India, Indian subcontinent, Indian Ocean, Sri Lanka, Ocean, Monsoon

28

Located only a short distance off the southernmost shore of the Greater Indian subcontinent, the island of Sri Lanka has long been inhabited by various ethnic populations. Mainly comprising the Vedda, Sinhalese (Up- and Low-country) and Tamil (Sri Lankan and Indian); their history of settlements on the island and the biological relationships among them have remained obscure. It has been hypothesized that the Vedda was probably the earliest inhabitants of the area, followed by Sinhalese and Tamil from the Indian mainland. This study, in which 271 individuals, representing the Sri Lankan ethnic populations mentioned, were typed for their mitochondrial DNA (mtDNA) hypervariable segment 1 (HVS-1) and part of hypervariable segment 2 (HVS-2), provides implications for their settlement history on the island. From the phylogenetic, principal coordinate and analysis of molecular variance results, the Vedda occupied a position separated from all other ethnic people of the island, who formed relatively close affiliations among themselves, suggesting a separate origin of the former. The haplotypes and analysis of molecular variance revealed that Vedda people’s mitochondrial sequences are more related to the Sinhalese and Sri Lankan Tamils' than the Indian Tamils' sequences. MtDNA haplogroup analysis revealed that several West Eurasian haplogroups as well as Indian-specific mtDNA clades were found amongst the Sri Lankan populations. Through a comparison with the mtDNA HVS-1 and part of HVS-2 of Indian database, both Tamils and Sinhalese clusters were affiliated with Indian subcontinent populations than Vedda people who are believed to be the native population of the island of Sri Lanka.Journal of Human Genetics advance online publication, 7 November 2013; doi:10.1038/jhg.2013.112.

Concepts: DNA, Indian subcontinent, Sri Lanka, Maldives, Tamil language, Tamil people, Jaffna, Sinhalese people

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Despite repeated outbreaks of poxvirus infections unique to the Indian subcontinent region and veterinary research work in this field, much less diagnostic awareness with resultant treatment protocols have been formulated in the human medical field.

Concepts: Medicine, Disease, Geography, Indian subcontinent, Continents, Indian Ocean, Outbreak, Atypical depression

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Visceral leishmaniasis (VL) is a disease caused by two known vector-borne parasite species (Leishmania donovani, L. infantum), transmitted to man by phlebotomine sand flies (species: Phlebotomus and Lutzomyia), resulting in ≈50,000 human fatalities annually, ≈67% occurring on the Indian subcontinent. Indoor residual spraying is the current method of sand fly control in India, but alternative means of vector control, such as the treatment of livestock with systemic insecticide-based drugs, are being evaluated. We describe an individual-based, stochastic, life-stage-structured model that represents a sand fly vector population within a village in India and simulates the effects of vector control via fipronil-based drugs orally administered to cattle, which target both blood-feeding adults and larvae that feed on host feces.

Concepts: India, Indian subcontinent, Leishmaniasis, Leishmania, Flies, Phlebotominae, Phlebotomus, Lutzomyia

26

Food is medicine and vice versa. In Hindu and Ayurvedic medicine, and among human cultures of the Indian subcontinent in general, the perception of the food-medicine continuum is especially well established. The preparation of the exhilarating, gold-coloured Soma, Amrita or Ambrosia, the elixir and food of the ‘immortals’ - the Hindu pantheon -, by the ancient Indo-Aryans, is described in the Rigveda in poetic hymns. Different theories regarding the botanical identity of Soma circulate, but no pharmacologically and historically convincing theory exists to date.

Concepts: Indian subcontinent, Soma, Hinduism, Immortality, Vedas, Indra, Sanskrit words and phrases, Hindu mythology

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The global distribution of J2-M172 sub-haplogroups has been associated with Neolithic demic diffusion. Two branches of J2-M172, J2a-M410 and J2b-M102 make a considerable part of Y chromosome gene pool of the Indian subcontinent. We investigated the Neolithic contribution of demic dispersal from West to Indian paternal lineages, which majorly consists of haplogroups of Late Pleistocene ancestry. To accomplish this, we have analysed 3023 Y-chromosomes from different ethnic populations, of which 355 belonged to J2-M172. Comparison of our data with worldwide data, including Y-STRs of 1157 individuals and haplogroup frequencies of 6966 individuals, suggested a complex scenario that cannot be explained by a single wave of agricultural expansion from Near East to South Asia. Contrary to the widely accepted elite dominance model, we found a substantial presence of J2a-M410 and J2b-M102 haplogroups in both caste and tribal populations of India. Unlike demic spread in Eurasia, our results advocate a unique, complex and ancient arrival of J2a-M410 and J2b-M102 haplogroups into Indian subcontinent.

Concepts: Chromosome, Genetic genealogy, India, Indian subcontinent, Asia, Y chromosome, South Asia, Eurasia