Genetic Structure and Biodiversity of Pigs (Sus scrofa) in South Asia and Papua New Guinea

Biodiversity of livestock resources is critically important for achieving food security and alleviating poverty for the rapidly growing human population. Indigenous pigs (Sus scrofa) are an important part of these resources and have significant socio-economic and cultural importance to the livelihood of several hundreds of ethnic rural communities in South Asia and Papua New Guinea (PNG). However, very little attention has been given to research and development, and conservation of indigenous pigs, which are becoming increasingly marginalised by the introduction of exotic breeds. The objectives of this research project were to investigate the genetic biodiversity of indigenous pigs, and to document their physical characteristics, population trends, farming practices, and their socio-cultural and economic importance to the livelihood of rural communities living in South Asia and PNG. Findings from the field surveys have indicated that pig improvement programmes in South Asia and PNG have mainly focused on introduction of exotic germplasm, whose influence is increasing. Indigenous pigs, which are hardy, resistant to many diseases, and adaptable to harsh rural environments with low inputs, are increasingly marginalised by introduction of commercial pigs of European origin. From the population trend, it was estimated that Bhutanese indigenous pigs will become extinct within the next decade, while Nepal, Sri Lanka and PNG will face dire shortage of their native genetic resources in the future unless appropriate measures are taken to prevent this genetic erosion. Once lost, these important resources are largely irreplaceable. Therefore, to protect and conserve indigenous pigs for breeding and sustainable utilization, it is imperative to understand their genetic structure and diversity. These were determined using microsatellite markers and mitochondrial DNA (mtDNA) sequences. The microsatellites were used for their abundance, even distribution in the genome, and high polymorphism while haploidy and uniparental inheritance properties have made mtDNA a powerful tool to examine relatedness of the populations and track the matrilineal component of historic genetic diversity and migration routes.Using 21 microsatellite markers that were recommended by the Food and Agriculture Organization (FAO) of the United Nations and the International Society for Animal Genetics (ISAG), we have investigated the genetic structure and diversity of 313 domestic and wild boar from South Asia. Our analyses revealed four domestic and one wild boar populations in Bhutan, two domestic pig populations in Nepal, and clearly segregated populations of village pigs and wild boar in Sri Lanka. All populations showed equal or higher expected heterozygosities than Australian commercial pigs of composite breed. There was negligible genetic differentiation between one Bhutanese and one Nepalese population. When compared to Sri Lanka populations, the Himalayan pig populations from Bhutan and Nepal were closely related, not unexpected given their close geographical distribution. Surprisingly, the Sri Lankan village pigs clustered with Australian commercial pigs implying substantial genetic contamination by European pigs. In addition to the microsatellite analyses, mtDNA control region sequences (652bp) were generated from 242 animals, both domestic pigs and wild boar, from South Asia. This included 11 wild boar museum specimens and even one ancient domestic pig sample. The sequences of seventy-three haplotypes detected in South Asia were combined with Genbank sequences representing almost 1800 wild boar and domestic pigs from all over the world. Our analyses, which are currently the most comprehensive porcine mtDNA sequence analyses ever performed, revealed very complex clustering patterns of porcine haplotypes but with clear phylogeographic signals. The segregation of European and Asian pigs was consistent with independent domestication of pigs in Europe and Asia. We observed three major mitochondrial porcine clades, which are unique to the Indian sub-continent. The shared haplotypes between domestic pigs of Bhutan, Northeast India, and Nepal with wild boar, possibly belonging to Sus scrofa cristatus from Northern India (Kashmir, West Bengal, and Chattishgarh) within Mixed Clade 1 (MC1) provides support for an independent centre of “cryptic domestication” in the foothills of the Himalayas and the Indian sub-continent. However, in the absence of corroborating archaeological or fossil evidence, this could also have resulted from an introgression of maternal genes from MC1 wild boar to domestic pigs. We also confirm the presence of two additional novel wild boar clades, the Northern South Asia (NSA) and Southern South Asia (SSA), which could possibly belong to two different wild boar subspecies (S. s. davidi and S. s. affinis) in Northern South Asia and Sri Lanka respectively. Both NSA and SSA have not been detected in any domestic pigs. In addition to these, the W17 and W12 haplotypes detected in Bhutanese wild boar have not been detected in domestic pigs both in current and previous studies. The South Asian domestic pigs have also been influenced by widely distributed east Asian and European pigs. The shared haplotypes within and between domestic pigs of South Asia indicate some ancestral genetic signatures or movement of domestic pigs between countries, presumably mediated by humans. Similarly, genotype data from sixty seven individual pigs were used to determine the genetic structure and diversity of indigenous domestic pigs of PNG. Despite using a relatively small number of individuals for population genetic analysis, we observed five inferred populations within indigenous domestic pigs. These inferred populations, which had low to moderate genetic differentiation, correlated well with sampling localities in PNG. They showed higher expected heterozygosities than Australian commercial pigs. To complement this, mtDNA analyses on 24 haplotypes (1044bp) from 70 domestic pigs and 3 haplotypes from 5 Australian commercial pigs were combined with 186 major porcine haplotypes retrieved from Genbank. We observed that the mitochondria of indigenous domestic pigs of PNG have been mainly influenced by Pacific clade (D6) or Oceania haplotypes followed by General Asian (D2) and European (D1). The shared haplotypes between wild and indigenous domestic pigs within D6 suggested that the latter have been derived from wild or feral pigs in the region and within PNG. The D2 haplotypes were also quite common within PNG domestic pigs. It is possible that pigs with D2 haplotypes may have been introduced along with pigs with D6 haplotypes during the expansion of the Lapita and Polynesian culture in Oceania. It is also likely that D2 haplotypes have been the result of introduction of European pigs carrying D2 haplotypes, which are reasonably common within Australian commercial pigs of European origin. Our extensive analyses of both domestic and wild boar haplotypes suggest the presence of a genuine wild boar mtDNA signature (D5) of Southeast Asian origin, within some Australian feral pigs and one domestic pig of PNG. This thesis concludes that both South Asian and PNG pigs retain reasonably high levels of genetic structure and biodiversity and can thus continue to provide valuable information and resources for future agriculture that may no longer be retained in the vast majority of intensively selected commercial pigs. Our findings, which meet the requirements of FAO’s Global Plan of Action for Animal Genetic Resources, provides useful baseline scientific information on which any policy or holistic conservation decision related to pigs in the regions should be based

The Impacts of Mining on Livelihood and Development in Nyoenpaling Chiwog under Phuntshopelri Gewog, Samtse

<p><i><strong>Abstract</strong></i><strong>—</strong> <i>Mining plays a key role in facelifting the economic status of the people of its catchment area and nation particularly for developing countries, and Bhutan is no exception. In Bhutan mining provides employment and livelihood to a good number of people. Nyoenpaling Chiwog under Phuntshopelri Gewog, Samtse has been an important mining site for limestone, and dolomite since a few decades ago and will be hereafter too. However, the contribution of mining activity to livelihood and development is unclear today. So, there is a need for a thorough study on the impact of mining in Nyoenpaling Chiwog. The objective of this paper is to document the impact of mining in mining catchment areas. The data were collected from mining site localities through a mixed-method research approach. The study reveals that local people are not very positive about having mining sites in their area. There is an indication that local people are not benefiting as expected. The responses of residents suggest that adequate infrastructure development like a paved transport network, safe drinking water, bridge, and river embankment could ease their living in the area. Therefore, the study aims to explore the possibility of addressing these issues by concerned stakeholders. Addressing these issues can have a greater positive impact on the livelihood of people living here.</i></p&gt

New Herpetofaunal Records from the Kingdom of Bhutan Obtained through Citizen Science

Social media has, in the past decade, emerged unexpectedly as a powerful tool in citizen science (Liberatore et al. 2018). Whether unintended or formally integrated, it offers, among other benefits, mass participation in activities such as data collection in inventories, monitoring, or natural history observations (Tulloch 2013). It can be argued that such activities often do not consume taxpayers’ contributions, as formal research projects tend to do, and can provide a cost-effective means of data collection (Goldstien et al. 2014). The vast number of (and rapidly rising) online resources and virtual specialists available to identify samples serve as references and reviewers of such data, increasing the speed over traditional forms of data collection (e.g., scientific publishing) and providing the capacity to absorb multiple opinions. Nonetheless, challenges that remain in citizen science programs are directing the data towards priority scientific objectives and needs, and achieving high standards in data quality (Ambrose-Oji et al. 2014)