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古DNA:罗马尼亚新石器时代猪,安纳托利亚起源

同时有一定欧洲野猪的混血。

abbr_c4ad41accb7c38bce5e3c82bcd1c28f9.pdf (458.22 KB)

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新石器时代欧洲的中东起源家猪占据优势,而后本土起源家猪将它们排挤出去,跟人一样。
O3a3c* (M134+, M117-)
摘要:Current evidence suggests that pigs were first domesticated in Eastern Anatolia during the ninth millennium cal BC(注:Giuffra- Andersson团队2000年发表在《Genetics》上的"The origin of the domestic pig: independent domestication and subsequent introgression".称中国是独立起源于9kya) before dispersing into Europe with Early Neolithic farmers from the beginning of the seventh millennium.
Recent ancient DNA (aDNA) research also indicates the incorporation of Euro-pean wild boar into domestic stock during the Neolithization process. In order to establish the timing of the arrival of domestic pigs into Europe, and to test hypotheses regarding the role European wild boar played in the domestication process, we combined a geometric morphometric analysis (allowing us to combine tooth size and shape) of 449 Romanian ancient teeth with aDNA analysis.
Our results firstly substantiate claims that the first domestic pigs in Romania possessed the same mtDNA signatures found in Neolithic pigs in west and central Anatolia. Second, we identified a significant proportion of individuals with large molars whose tooth shape matched that of archaeological (likely) domestic pigs.
These large ‘domestic shape’ specimens were present from the outset of the Romanian Neolithic (6100–5500 cal BC) through to later prehistory, suggesting a long history of admixture between introduced dom-estic pigs and local wild boar. Finally, we confirmed a turnover in mitochondrial lineages found in domestic pigs, possibly coincident with human migration into Anatolia and the Levant that occurred in later prehistory.
物格而后知至,知至而后意诚,意诚而后心正,心正而后身修,身修而后家齐,家齐而后国治,国治而后天下平...
本帖最后由 imvivi001 于 2017-6-18 20:52 编辑

参阅:Giuffra- Andersson团队2000年发表在《Genetics》上的:
The origin of the domestic pig: independent domestication and subsequent introgression.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1461048/
E. Giuffra,1 J. M. H. Kijas,1 V. Amarger, O¨ . Carlborg, J.-T. Jeon and L. Andersson
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala Biomedical Centre,
S-751 24 Uppsala, Sweden
Manuscript received June 18, 1999
Accepted for publication November 29, 1999

ABSTRACT
The domestic pig originates from the Eurasian wild boar (Sus scrofa). We have sequenced mitochondrial DNA and nuclear genes from wild and domestic pigs from Asia and Europe. Clear evidence was obtained for domestication to have occurred independently from wild boar subspecies in Europe and Asia. The time since divergence of the ancestral forms was estimated at ~500,000 years, well before domestication ~9,000 years ago.
       Historical records indicate that Asian pigs were introduced into Europe during the 18th and early 19th centuries. We found molecular evidence for this introgression and the data indicated a hybrid origin of some major “European” pig breeds. The study is an advance in pig genetics and has
important implications for the maintenance and utilization of genetic diversity in this livestock species.

(注:1、文章说的‘亚洲猪’参照物是中国‘梅山猪’;2、数据显示,当年达尔文关于亚洲家猪起源于一个完全不同于西亚野猪祖先的猜测是错误的;3、印度家猪起源于中国;)
物格而后知至,知至而后意诚,意诚而后心正,心正而后身修,身修而后家齐,家齐而后国治,国治而后天下平...
参阅:Giuffra- Andersson团队2000年发表在《Genetics》上的:
The origin of the domestic pig: independent domestication and subsequent introgression.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC146104 ...
imvivi001 发表于 2017-6-18 19:20
根据这个研究,现代欧洲猪其实就是‘古中国猪’与‘古西亚猪’的混血种,这个倒是与现代欧洲人的血统的形成过程差不多,呵呵
物格而后知至,知至而后意诚,意诚而后心正,心正而后身修,身修而后家齐,家齐而后国治,国治而后天下平...
这个是中国研究者发表在《nature》上的研究成果
Heredity - Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication  https://www.nature.com/hdy/journal/v105/n3/full/hdy2009191a.html
J Li1,2, H Yang2, J-r Li3, H-p Li3, T Ning1,2, X-R Pan1, P Shi2 and Y-P Zhang1,2

1Laboratory for Conservation and Utilization of Bio-resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
2State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
3Department of Computational Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
Correspondence: Professor Y-P Zhang, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochangdong ST, Yunnan, Kunming 650223, China. E-mail: zhangyp@mail.kiz.ac.cn; Professor P Shi, E-mail: ship@mail.kiz.ac.cn


Introduction
Domestication promotes abundant morphological polymorphisms in domesticated animals relative to their wild ancestors (Andersson, 2001; Diamond, 2002). An obvious example is coat colour variation. For wild animals, colouration has a very important role in their ecological and behavioural adaptation and offers at least three broad categories of function: concealment, communication and regulation of physiological processes (Stoner et al., 2003). In contrast, coat colours of domestic animals mainly represent human needs or cultural preferences and result from strong artificial selection and domestication bottlenecks (Innan and Kim, 2004). Domestication is reflected at the molecular level as a ‘footprint of artificial selection and demography’ at domestication target loci. Therefore, analyses and comparisons of DNA sequence diversity between wild ancestors and their domestic counterparts provide insight into the genetic basis of morphological variation.

The Chinese domestic pig provides an ideal model for studying the molecular mechanism of phenotypic variation because of several special features. Unlike most other domestic animals, the wild ancestors of domesticated pigs and a number of outgroup species are still present in the world, which is convenient for examining ancestral and derived mutations as well as inferring the processes of artificial selection (Chen et al., 2007). Moreover, the origin and history of Chinese domestic pigs have been deciphered. As one of the first domesticated animals in China, the presence of domesticated pigs can be traced back to ~8000 years (Yuan and Rowan, 2002). Our previous research on mitochondrial DNA showed that Chinese domestic pigs were separately domesticated from wild boars in the Mekong region and in the middle and downstream regions of the Yangtze River (Wu et al., 2007). Since the initial domestication, more than 48 indigenous breeds have been domesticated so far (Zhang, 1986). It is interesting that the black colour is found to be predominant in most of the Chinese indigenous pig breeds and can be used to clearly distinguish it from its wild progenitors (Geng and Liu, 2003; Shi et al., 2004, 2006; Fang et al., 2009).

The coat colour differences between Chinese domestic pigs and their wild progenitors led to the hypothesis that the allele dominating the black coat colour was possibly under artificial selection during the domestication of Chinese domestic pigs. This hypothesis can be tested by examining the selective pressure on coat colour gene(s) in Chinese domestic pigs and wild boars. The melanocortin receptor 1 (MC1R) has already been identified as a major determinant of pigment phenotype (Lin and Fisher, 2007). MC1R has a vital role in melanogenesis, as melanocytes produce black/brown eumelanin with active MC1R and red/yellow pheomelanin without MC1R signalling (Robbins et al., 1993). Polymorphisms in MC1R have also been documented and associated with coat colour variance in many domestic species, such as dogs, chickens, cats and cattle (Klungland et al., 1995; Eizirik et al., 2003; Kerje et al., 2003; Anderson et al., 2009). In pigs, six MC1R alleles associated with different colour phenotypes have been reported (Giuffra et al., 2000; Kijas et al., 1998, 2001). This evidence strongly suggested that MC1R might be an ideal marker to test our hypothesis.

In recent research, Fang et al. (2009) compared the non-synonymous/synonymous substitution rate ratio (dN/dS) between Asian and European domestic pigs and suggested that positive selection acted on the MC1R locus in domestic pigs. However, evidence of artificial selection on Chinese domestic pigs remains incomplete. On the one hand, the alleles were described from a limited sample size of Chinese domestic pigs (n=23) and wild boars (n=3); therefore, the results should be interpreted with caution. A larger population genetic data set is still to be developed to detect the effects of demographic events during pig domestication, because domestication bottlenecks can lead to patterns similar to those of selective sweep. On the other hand, it is widely known that pig domestication occurred independently in Europe and China (Giuffra et al., 2000; Larson et al., 2005). The large dN/dS ratio (23.5) between European and Chinese domestic pigs could be due to selection operating on European domestic pigs, in which a total of six non-synonymous sites were found, twice that of Chinese domestic pigs. Indeed, the dN/dS ratio (0.25) of Chinese domestic pigs was significantly less than one, which cannot be taken as an evidence for positive selection. Therefore, to provide direct evidence of selection during domestication, it is necessary to focus on the comparison between Chinese domestic pigs and their wild ancestors in addition to a comparison between the two lineages that underwent independent domestication (that is, European domestic pigs and Chinese domestic pigs).

To get a comprehensive understanding of the selection pressure acting on coat colour during the domestication of pigs in China, we extended previous research to detect the genetic variations and degree of artificial selection in newly acquired 1552 bp sequences of MC1R. Our research included the entire MC1R-coding region and partial 5′ and 3′ flanking regions from 157 samples of Chinese domestic pigs and 40 samples of Chinese wild boars. Moreover, to detect a potential bottleneck effect, we sequenced a 707-bp glucose phosphate isomerase pseudogene (GPIP) from a subset of the MC1R samples. Our analysis of amino-acid change patterns, haplotype structure and nucleotide diversity, together with our bottleneck and hitchhiking model simulations and selection tests, provide clear evidence that strong artificial selection forces operated on the MC1R locus in Chinese domestic pigs. This artificial selection correlates with the black colour preference in ancient China during animal sacrifice and reflects the impact of culture on domestication.
物格而后知至,知至而后意诚,意诚而后心正,心正而后身修,身修而后家齐,家齐而后国治,国治而后天下平...
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