Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Handbook of enzyme electrophoresis in human genetics

The establishment of agricultural economies based upon domestic animals began independently in many parts of the world and led to both increases in human population size and the migration of people carrying domestic plants and animals. The precise circumstances of the earliest phases of these events remain mysterious given their antiquity and the fact that subsequent waves of migrants have often replaced the first. Through the use of more than 1,500 modern (including 151 previously uncharacterized specimens) and 18 ancient (representing six East Asian archeological sites) pig (Sus scrofa) DNA sequences sampled across East Asia, we provide evidence for the long-term genetic continuity between modern and ancient Chinese domestic pigs. Although the Chinese case for independent pig domestication is supported by both genetic and archaeological evidence, we discuss five additional (and possibly) independent domestications of indigenous wild boar populations: one in India, three in peninsular Southeast Asia, and one off the coast of Taiwan. Collectively, we refer to these instances as “cryptic domestication,” given the current lack of corroborating archaeological evidence. In addition, we demonstrate the existence of numerous populations of genetically distinct and widespread wild boar populations that have not contributed maternal genetic material to modern domestic stocks. The overall findings provide the most complete picture yet of pig evolution and domestication in East Asia, and generate testable hypotheses regarding the development and spread of early farmers in the Far East.

/pdf/patterns-of-east-asian-pig-domestication-migration-and-5a88vyu95w.pdf

Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA

Les plantes cultivees, les mauvaises herbes, les bovins et les animaux commensaux ont tous ete transportes par l’action de l’homme a travers l’ocean Indien depuis les temps prehistoriques. Dans cet article, nous examinons les preuves, principalement issues de l’archeobotanique et de l’archeozoologie, mais aussi de la genetique, de ces echanges. Ces derniers peuvent etre divises en deux grandes sous-regions d’interactions : l’une plus ancienne et dans le Nord, et l’autre plus tardive et au milieu de l’ocean Indien. Le premier et le plus ancien ensemble d’echanges a eu lieu dans tout le nord-ouest de l’ocean Indien, pres de l’Arabie il y a environ 2 000 ans av. J.-C. Cette periode a vu le transfert de plusieurs plantes cultivees, d’Afrique a l’Inde, notamment Sorghum bicolor, Pennisetum glaucum, Eleusine coracana, Lablab purpureus, et Vigna unguiculata. Les donnees actuelles favorisent l’hypothese d’un transfert direct par mer plutot que par la peninsule Arabique. Les transferts de l’Asie a l’Afrique incluent notamment le mil Panicum miliaceum, le zebu, meme si tous deux ont du voyager jusqu’a l’Afrique via la peninsule Arabique. La seconde epoque d’echanges a eu lieu probablement apres 1 000 av. J.-C., mais la date est sujette a caution. Ces echanges ont porte principalement sur les transferts de l’Asie a la cote et aux iles de l’Afrique de l’Est, bien que quelques especes aient ete transferees a des parties de l’Asie a ce moment ou plus tard. Les contributions importantes d’Asie tropicale a l’agriculture tropicale africaine ont ete Musa sapientum, Colocasia esculenta et Dioscorea alata, meme si les preuves archeologiques sont limitees a la banane. En outre, des mauvaises herbes, telles que Trainthema spp. et Spermacoce spp., et des animaux commensaux, Rattus rattus, Mus musculus, et Suncus murinus, ont ete involontairement transportes de l’Asie a l’Afrique comme cela a ete demontre par la biogeographie et la genetique. D’autres mauvaises herbes qui probablement comprennent Striga asiatica et Spermaococe ocymoides ont ete deplacees de l’Afrique a l’Asie. Ces nombreux transferts prehistoriques d’organismes suggerent que les petites societes de peche cotiere et maritime de la cote d’Afrique et d’Asie ont ete des agents actifs d’echange et d’interaction, meme si leurs vestiges sont moins visibles et moins etudies par les archeologues que ceux des societes plus tardives de peche et d’echanges maritimes sur les marges de l’Ocean Indien.

https://journals.openedition.org/oceanindien/pdf/698

Crops, cattle and commensals across the Indian Ocean. Current and Potential Archaeobiological Evidence

Crops, cattle and commensals across the Indian Ocean

The musk shrew (Suncus murinus) is a small mammalian species belonging to Insectivora. It is widely distributed in Asia. To identify the genetic relationship among wild musk shrew populations and examine its migration route, we investigated the populations of Cambodia and Bhutan by using mitochondrial DNA restriction fragment length polymorphism analysis and compared them with other Asian populations previously described. Four haplotypes were detected in Cambodia and eight in Bhutan. A total of 53 haplotypes were detected in Asia and were classified largely into two groups, the Continental and Island types, based on a minimum spanning network. From the distribution of mtDNA types in wild musk shrews, three major population groups are identified in Asia: South Asia, Southeast Asia, and Malay. It is suggested that the Malay population group was a mix of South and Southeast Asian population groups and that this was a contact area of the two groups. In addition, other contact areas between the South and Southeast Asian groups exist in Myanmar, but unlike the Malay, the Myanmar area was the border of these groups.

Population structure of wild musk shrews (Suncus murinus) in Asia based on mitochondrial DNA variation, with research in Cambodia and Bhutan.

The musk shrew (Suncus murinus) is an insectivore species that inhabits tropical and subtropical Asia widely. To clarify the genetic relationship among wild musk shrew populations, we examined the electrophoretic variants of biparentally inherited genetic markers at 10 loci coding for eight blood proteins/enzymes in a total of 639 animals and compared the results obtained from the mitochondrial DNA data. The principal-component analysis performed using the allele frequency data revealed that the 17 populations could be divided into two major groups, a South Asian group and a Southeast Asian group that includes several island populations bound by Myanmar. The degrees of genetic divergence among populations were higher within the Southeast Asian group than within the South Asian group. This finding was incongruent with the mtDNA diversity. Analysis conducted at the individual level showed that a shrew from the central region in Myanmar that carries a South Asian type of mtDNA showed the electrophoretic variants specific to the Southeast Asian group, suggesting that this region is a contact zone between the two major groups.

https://link.springer.com/content/pdf/10.1007%2Fs10528-007-9096-8.pdf

Phylogeography of Wild Musk Shrew ( Suncus Murinus ) Populations in Asia Based on Blood Protein/Enzyme Variation

In this study, we analyzed DNA sequence of mitochondrial DNA (mtDNA) control regions on the 130 native domestic pigs and eight wild boars in the mainland South and South-east Asian countries including Bhutan, Cambodia, Laos, Myanmar, and Vietnam. Forty-four haplotypes were found in the 138 individuals, 41 were in the domestic and four were in wild boars. Only one haplotype was shared by domestic and wild population in Bhutan. In other cases, mtDNA of wild boars did not show close affinity to that of the domestic pigs in the same location, indicating that the native domestic pigs in these countries did not originate in the present habitat. Phylogenetic analyzes of mtDNA haplotypes recapitulated several major clusters identified in other studies, but 11 haplotypes were grouped in a new cluster we named MTSEA. In most cases, more than one lineage group were present in a sampling station, indicating that the present indigenous domestic pigs may have multiple origins. The MTSEA haplotypes were present in relatively high frequencies in domestic pigs in the mountainous area of mainland South-east Asia (Cambodia and Laos), with a few found in Myanmar and Bhutan. The distributions of MTSEA haplotypes are in great conformity with the distribution of present-day Mon-Khmer language and indicated the existence of yet another independent domestication. The D2 haplotypes that distribute high frequency (almost 100%) throughout the Chinese breeds were dominant in Bhutan, Myanmar, and Vietnam. These results suggest an existence of human-mediated dispersal of domestic pigs from north to the south during the historical expansion of Sino-Tibetan and Tai peoples. The D3 haplotypes previously reported in north India were found in sympatric domestic and wild pigs in Bhutan. The D3 haplotype is an important proof of independent domestication event and/or great gene flow between wild and domestic pigs in the foot of Himalaya.

Mitochondrial diversity of native pigs in the mainland South and South‐east Asian countries and its relationships between local wild boars

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Population structure of wild musk shrews (Suncus murinus) in Asia based on mitochondrial DNA variation, with research in Cambodia and Bhutan.

Phylogeography of Wild Musk Shrew ( Suncus Murinus ) Populations in Asia Based on Blood Protein/Enzyme Variation

Mitochondrial diversity of native pigs in the mainland South and South‐east Asian countries and its relationships between local wild boars