Genetic Contribution of Late Pleistocene Wild Boars in Guangxi to Domesticated Pigs
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摘要: 家猪是由居住在世界不同地区的人类对野猪的长期驯化而来，考古学研究表明近东和中国可能是家猪的驯养中心.为了寻找野猪对家猪驯化遗传贡献的分子证据，对采集于广西壮族自治区3个不同地点的30个晚更新世野猪化石样品开展了古DNA研究，从化石样品中获得了线粒体基因组的D-loop部分序列，结合现代家猪、野猪DNA同源序列信息，构建了Network网络结构图和系统发育树.结果表明广西古代野猪与欧洲猪科动物之间存在历史基因流，与亚洲家猪之间具有遗传的连续性，在家猪的驯化过程中有遗传贡献.研究结果从新的地域角度为家猪的多地区驯化起源提供了分子证据.Abstract: Pigs were domesticated from wild boars by humans living in different parts of the world. Archaeological studies show that the Near East and China may be the domestication centers of pigs. In order to find evidence for the genetic contribution of wild boars to pig domestication, ancient DNA study on 30 Late Pleistocene wild boar fossils collected from three caves in Guangxi, southern China was conducted. Through the use of the fragmented D-loop sequences and the homologous sequences of wild boars and domestic pigs across Asia and Europe, the network figure and phylogenetic trees of Suidae were reconstructed. The results show that the existence of historical gene flow between ancient Guangxi wild boars and European pigs, and there is a genetic continuity from ancient Guangxi wild boars to Asian domestic pigs, which suggests a genetic contribution of ancient wild boars to the pig domestication. Therefore, this study provides new molecular evidence of multiple and independent events for pig domestication in terms of geographic region.
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Key words:
- wild boar /
- Late Pleistocene /
- DNA /
- pig domestication /
- genetic contribution
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图 1 系统进化树所用家猪和野猪样品的地理位置分布示意图
Fig. 1. The geographical distribution of domestic pigs and wild boar samples used in phylogenetic tree
图 2 基于线粒体D-loop 167 bp序列构建的中介网络图
Fig. 2. Median-joining network based on 167 bp sequence of mitochondrial D-loop
图 3 基于260 bp D-loop序列构建的环形进化树
Fig. 3. A circular evolution tree based on 260 bp D-loop sequence
表 1 野猪化石样品信息
Table 1. Wild boar fossil sample information
样品编号 采集地点 年代 LSD-1~15 楼山洞，广西武鸣 1.3~2.4万a CMLST-0911-205-1~6 双坛洞，广西崇左 晚更新世 CMLST-0911-304-1 双坛洞，广西崇左 晚更新世 CMLST-0911-304-2 双坛洞，广西崇左 晚更新世 CMLST-0911-321 双坛洞，广西崇左 晚更新世 CMLST-0911-328 双坛洞，广西崇左 晚更新世 CMLST-0911-385-1 双坛洞，广西崇左 晚更新世 CMLST-0911-385-2 双坛洞，广西崇左 晚更新世 CSN-0811-15 弄巴山洞，广西崇左 3.0~5.0万a CSN-0811-137 弄巴山洞，广西崇左 3.0~5.0万a CSN-0811-201 弄巴山洞，广西崇左 3.0~5.0万a 注：在下文的数据分析中样品编号CMLST-0911-将简写为CMT-；CSN-0811-将简写为CSN-. 
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表 2 扩增D-loop序列的引物信息
Table 2. Primer information for amplification of D-loop sequences
引物编号 引物序列 引物扩增位置 扩增长度/去除引物后长度(bp) PDL-3* AATCGCCCACTCTTTCCC 456 131/93 PDL-4* CATGGCTGAGTCCAAGCATC 586 PDL-5* CGTGAAACCAGCAACCCG 333 146/104 PDL-6* TTAGGTGAGATGGTCCTGAAGTA 455 PDL-9 ACATGCGTATCACCACCATT 287 146/104 PDL-10 AGAACCAGATGCCTGTTAAAGT 432 PDL-13 CCAAAACAAGCATTCCATTCGTATG 4 112/62 PDL-14 GGGGTCGCATATTTGTATGTTTGTG 115 PDL-21 AGCATTCCATTCGTATGCAAACC 11 119/72 PDL-22 ATGGTTAAATTTTTGGGGTCGCAT 129 PDL-23 ACCCATAAAAATTGCGCACAAACAT 75 121/71 PDL-24 GCATGGGGACTAGCAGTTAATGCAC 195 PDL-27 TTATAGCCCTATGTACGTCGTGCAT 152 143/93 PDL-28 ACGCATGTTGACTGGAATTATTTGA 294 PDL-29 TCATTATTGATCGTACATAGCACAT 239 130/80 PDL-30 AGAGGGATCCCTGCCAAGCGGGTTG 368 PDL-31 GGCCCATAAATCGTGGGGGTTTCTA 379 132/82 PDL-32 TGATTAGTCATTAGTCCATCGAGAT 510 PDL-39 TAGCCCTATGTACGTCGTGCATTAA 155 139/89 PDL-40 CGCATGTTGACTGGAATTATTTGAC 293 注：标“*”的为阿德莱德大学重复性实验引物.
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表 3 获得D-loop序列结果统计
Table 3. Amplification result of D-loop fragments
引物样品 PDL-3, 4 PDL-5, 6 PDL-9, 10 PDL-13, 14 PDL-21, 22 PDL-23, 24 PDL-27, 28 PDL-29, 30 PDL-31, 32 PDL-39, 40 LSD-1 / / / / / / / ◆ ◆ / LSD-2 / / / / / / / ◆ ◆ / LSD-3 / / / / / / / ◆ / ◆ LSD-4 / / ◆ / / ◆ / / / / LSD-5 / / ◆ ◆ / ◆ / / / / LSD-6 / / / / / ◆ ◆ ◆ / ◆ LSD-7 / / / / / ◆ / / ◆ ◆ LSD-8 / / / / / ◆ / ◆ / ◆ LSD-9 / / / / / / / / / / LSD-10 / / ◆ / / ◆ / ◆ / ◆ LSD-11 / / / / / ◆ ◆ / ◆ ◆ LSD-12 / / / / / / ◆ / / / LSD-13 / / / / / ◆ ◆ / / ◆ LSD-14 / / / / / / ◆ ◆ ◆ ◆ LSD-15 / / / / / ◆ / ◆ / / CMT-205-1 ◆ / / / / ◆ / ◆ ◆ / CMT-205-2 ◆ / / / / ◆ ◆ ◆ / / CMT-205-3 ◆ / / / / ◆ / ◆ / / CMT-205-4 ◆ / ◆ / / ◆ / / ◆ / CMT-205-5 ◆ / / / ◆ ◆ / / / / CMT-205-6 / / / / / ◆ / / ◆ ◆ CMT-304-1 / ◆ ◆ / / ◆ / / / / CMT-304-2 ◆ / ◆ / / ◆ ◆ / / ◆ CMT-321 ◆ ◆ ◆ / / ◆ ◆ ◆ ◆ ◆ CMT-328 / / / / / / / / / / CMT-385-1 / / / / / ◆ / / / / CMT-385-2 / / / / / ◆ ◆ / / ◆ CSN-15 / / / / / ◆ ◆ ◆ ◆ ◆ CSN-137 ◆ ◆ ◆ / / ◆ / / / ◆ CSN-201 ◆ / / ◆ / ◆ / / / ◆ 注：“◆”表示获得序列；“/”表示未获得序列.
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表 4 单倍型序列变异位点(167 bp)
Table 4. Haplotype sequence variation sites (167 bp)
单倍型 变异位点 3 4 5 8 18 28 29 34 37 38 45 51 56 60 63 64 70 71 75 76 83 89 90 95 99 100 102 103 105 108 111 117 122 123 124 125 128 129 130 136 138 144 145 146 147 H1 A C T T G A T A T T A A G A T C T A G T C T C C T A C T C T A G A C C A A T T A G A A T T H2 - T - - - - - - - - - - - - - T - G - - - - - - - - - - - - - A - - - - - C - - - - - C - H3 - - - - - - - - - - - - - - - T - G - - - - - - - - - - - - - A - - - - - C - - - - - C - H4 - - - C - - - - - - - - - - - T - G - - - - - - - - T - - - - - - - - - - - - - - - - - - H5 - - - - - - - - - - - - - - - T - G - - - - - - - - - - - - - - - - - G - - - - - - - - - H6 - - - - - - - - - - - - - - - T - G - - - - - - - - - - - - - - - - - - - - - - - - - - - H7 - - - - - - - - - - - - - - - T - G - - T - - - - - - - - - - - - - - - - C - - - - - - - H8 - - - - - - - - - - - - - - - T - G - - - - - - - - T - - - - - - - - - - - - - - - - - - H9 - - - - - - - - - - - - - - - - - - - - - - - - - - T - - - - - - - - - - - - - - - - - - H10 - T - - - - - - - - - - - - - T - G - - - - - - - - T - - - - A - - - - - C - - - - - C - H11 - T - - - - - - - - - - - - - T - G - - - - - - - - T - - - - - - - T - - C - - - - - - - H12 - T - - - - - - C - - - - - - T - G - - - - - - - - T - - - - - - - T - - - - - - - - - - H13 - T - - - - - - - - - - - - - T - G - - - - - - C - T - - - - - - - - - - C - - - - - C - H14 - - - - - - - - - - - - - - - T - G - - - - - - - - - - - - - - - T - - - - - - - - - - - H15 - - - - - - - - - - - - - - - - - G - - - - - - - - T - - - - - - - - - - - - - - - - - - H16 - T - - - - - - - - - - - - - - - G - - - - - - - - T - - - - - - - - - - - - - - - - - - H17 - - - - - - - - - - - - - - - - - G - - - - - - - - - - - - - - - - - - - - - - - - - - - H18 - - - - - - - - - - - - - - - T - G - - - - - - - - - - - - - - - - T - - - - - - - - - - H19 - - - - - - - - - - - - - - - T - G - - - - - - C - T - - - G A - - - - - C - - - - - C - H20 - T - - - - - - - - - - - - - T - G - - - - - - - - - - - - - - - - - - - - - - - - - - - H21 - - - - - - - - - - - - - - - T - G - - - - - - - - T - - - G A - - - - - C - - - - - C - H22 - - - C - - - - - - - - - - - T - - - - - - - - - - - - - - - A - - - - - C - - - - - - - H23 - - C - - - - - C - - - - - - - - G - - - - - - - - - - - - - - - - T - - - - - - - - - - H24 - T - - - - - - C - - - - - - - - G - - - - - - - - - - - - - - - - - - - - - - - - - - - H25 - - C - - - - - - - - - - - - - - G - - - - - - - - - - - - - - - - - - - - - - - - - - - H26 - T - - - - - - - - - - - - - T - G - - - - - - - - - - - - - - - - - G - C - - - - - - C H27 - T - - - - - - - - - - - - - T - G - - - - - - - - T - - - - - - - - - - - - - - - G - C H28 - - - - - - - - - - - - - - - - - G - - - - - - - - - - - - - - - - - G - - - - - - G - - H29 - T - - - - - - - - - - - - - T - G - - - - - - - - - - T - - - - - - - - C - - - - - C - H30 - T - - - - - - - - - - - - - T - G - - - - T - - - - - T - - - - - - - - - - - - - - C - H31 - - C - - - - - C - - - - - - T - G - - - - - - - - - - - - - - - - - - - - - - - - - - - H32 - - - - - - - - - - - - - - - T - G - - - - T - - - - - - - - - - - - - - - - - - - - - - H33 - - - - - - - - - - - - - - - T - G - C - - - - - - - - - - - - - - - - - - - - - - - - - H34 - - - - - - - - - - - - - - - - - G - - - - - - - - T - - - - - - - - - - - - - A - - - - H35 - - - - - - - - - - - - - T - T - G - - - - - - - - - - - - - - - - - - - - - - - - - - - H36 - T - - - - - - - - - - - - - T - G - - - - - - - - T C - - - A - - - - - C - - - - - C - H37 - T - - - - - - - - - - - - - T - G - - T - - - - - - - - - - A - - - - - C - - - - - C - H38 - T - - - - - - - - - - - - - T - G - - - - - - - - - - - - G A - - - - - C - - - - - C - H39 - - - - - - - - - - - - - - - T - G - - - - - - - - T - - - - A - - - - - C - - - - - C - H40 - T - - - - - - C - - - - - - T - G - - - - - - - - - - - - - A - - - - - C - T - - - C - H41 - T - - - - - - - - - - - - - T - G - - - - - - - - - - - - - A - - - - - C - - - - - C - H42 - T - - - - - G - - - - - - - T - G - - - - - - - - - - - - - A - - - - - C - - - - - C - H43 - - - - A - - - - - - - - - - T - G - - - - - - - - T - - - - - - - - - - - - - - - - - - H44 - - - - - - - - - - - - - - - T - G - - - - - - - - - - - - - - - - - - - - - - - - - - - H45 G T - - - - - - - - - - - - - T - G - - - - - - - - - - T - - - - - - - - C - - - - - C - H46 - T - - - - - - - - - - - - - T - G - - - - - - - - T - - - - - - - - - - C - - - - G - C H47 - T - - - - - - - - - - - - - T - G - - - - - - - - T - - - - - - - - - - - - - - - - C - H48 - T - - - - - - C - - - - - - T - G - - - - - - - - - - - - - - - - - G - C - - - - - - - H49 - - - - - - - - - - - - - - - T - G - - - - - - - - - - - - G - - - - - - - - - - - - - - H50 - T - C - - - - C - - - - - C T - G - - - - - - - - T - - - - A - - - - - - - - - G - C - H51 - T - - - - - - - - G - - - - T - G - - - - - - - - - - - - - A - - - - - C - - - - - - - H52 - - - C - - - - - - - - - - - T - G - - - - - - - - T - - - - A - - - - - - - - - G - - - H53 - T - - - - - - C - - - - - - T - - - - - - - - - - - - - - - A - - - - - - - - - - - - - H54 - - - - - - - - - - - - A - - - - G A - - - - - - - T - - - - - - - - - - - - - - - - - - H55 - - - - - - - - - - - - - - - - - G - - - - - - C - - - - - - - - - - - - - - - - - - - - H56 - T - - - - - - - - - - - - - T - G - - - - - - - - - - - C - - - - - - - C - - - - - - C H57 - - - C - - - - C - - - - - - T - G - - - - - - - - T - - - - - - T - - - - - - - G - - - H58 - T - - - - - - - - G - - - - T - G - - - - - - - - T - - - - - - - - - - - - - - - - C - H59 - T C - - - - - C - - - - - - T - G - - - - - - - - - - - - - - - - - - - C - - - - - - - H60 - T - - - - - - - - - - - - - T - G - - - - - - - - T - - - G A - - - - - C - - - - - C - H61 - T - - - - - - C - - - - - - T A G - - - - - - - - - - T - - - - - - - - C - - - - - - - H62 - T - - - - - - C - - - - - - T - G - - - - - - - - - - T - - - - - - - - C C - - - - - - H63 - T - - - - - - - C - - - - - T - G - - - - - - - - - - T - - - - - - - - C - - - - - C - H64 - T - - - - C - C - - - - - - T - G - - - - - - - - - - T - - - - - - - - C - - - - - - - H65 - - - - - - - - - - - - - - - - - G - - - - - - - - - - - - - - - - - - - - - G - - - - - H66 - T - - - - - - - - - - - - - - - G - - - - - - C - T - - - - - - - - - - - - - - - - - - H67 - - - - - - - - - - - - - - - - - G - - - - - - - G T - - - - - - - - - - - - - - - - - - H68 - - - - - - - - - - - - - - - - - G - - - - - - - - - - - - - - - - T - - - - - - - - - - H69 - - - - - - - - - - - - - - - - - G - - - - - - - - - - - - - - - - - - - C - - - - - - - H70 - - - - - - - - - - - - - - - - - G - - - - - - - - - - T - - - - - - - - - - - - - - C - H71 - T - - - - - - C - - - - - - - - G - - - - - - - - T - - - - - - - - G - C - - - - - - - H72 - - - - - - - - - - - - - - - - - G - - T - - - - - - - - - - - - - - - - - - - - - - - - H73 - - - - - - - - C - - - - - - T - G - - T - - - - - - - - - - - - - - - - - - - - - - - - H74 - T - - - - - - C - - - - - - T - G - - - - T - - - - - - - - - - - - - - C - - - - - - C H75 - T - - - - - - C - - - - - C T - G - - - - - - - - - - - - - - - - - - - - - - - - - - - H76 - T - - - - - - - - - - - - - T - G - - - - - - - - T - - - - - - - - - - C - - - - G - - H77 - T - - - - - - C - - - - - C T - G - - - - - - - - T - - - - - - - - - - C - - - - - - - H78 - - - - - - - - - - - - - - - - - G - - T - - - - - - - T - - - - - - - - - - - - - - - - H79 - - C - - - - - - - - - - - - T - G - - - - - - - - T - - - - - - - - - - - - - - - - - - H80 - - C - - - - - - - - - - - - - - G - - - - - - - - T - - - - - - - - - - - - - - - - - - H81 - - C - - - - - - - - - - - - T - G - - - - - - - - - - - - - - - - T - - - - - - - - - - H82 - - - - - - - - - - - - - - - T - G - - - - - - - - T - - - G - - - - - - - - - - - - C - H83 - - - - - - - - - - - - - - - T - G - - - - - - - - T - - - - - - - - - G - - - - - - - - H84 - T C - - - - - C - - - - - - T - G - - - - - - - - T - - - - - - - - - - - - - - - - - - H85 - - C - A - - - C - - - - - - - - G - - - - - - - - - - - - - - - - - - - - - - - - - - - H86 - - - - - - - - C - - - - - - T - G - - - - - T C - - - - - - - - - - - - C - - - - - - - H87 - T - - - - - - - - - - - - - T - G - - - - T - - - - - T C - - - - - - - - - - - - - - - H88 - T - - - - - - - - - - - - - T - G - - - - T - - - - - - - - - - - - - - C - - - - - - - H89 - T - - - - - - - - - - - - - T - G - - - - T - - - - - T - - - - - - - - - - - - - - - C H90 - T - - - - - - - - - - - - - T - G - - - - - - - - - - - - - - - - - G - - - - - - - - - H91 - - - - - G - - - - - - - - - T - G - - - - - - - - - - - - - - - - - - - - - - - - - - - H92 - - C - - - - - C - - - - - - - - G - - - - - - C - - - - - - - - - - - - - - - - - - - - H93 - T - - - - - - - - - - - - - T - G - - - - T - - - - - T - - A - - T - - - - - - - - - C H94 - T - - - - - - - - - - - - - T - - - - - - T - - - - - T - - A - - - - - - - - - - - - - H95 - - - - - - - - - - - - - - - - - G - - - C - - - - - - - - - - - - - - - - - - - - - - - H96 - T - - - - - - - - - - - - - T - G - - T - T - - - T - T - - - - - - - - - - - - - - - - H97 - - - - - - - - - - - - - - - T - G - - - - - - - - T - - - - - - - T - - - - - - - - - - H98 - - - - - - - - - - - - - - - - - G - - - - - - - - T - - - - - G - - - - - - - - - - - - 注：“-”表示与单倍型H1具有相同的碱基.
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表 5 单倍型类型与物种组成
Table 5. Haplotype type and species composition
物种 单倍型类型 数量 单倍型名称 欧洲野猪 独立 5 H13, H38, H39, H40, H51 欧洲家猪 独立 8 H19, H21, H22, H36, H37, H41, H42, H60 亚洲野猪 独立 44 H4, H5, H7, H11, H12, H14, H27, H30, H32, H45, H46, H47, H49, H50, H52, H53, H54, H55, H56, H57, H58, H59, H61, H62, H63, H64, H70, H71, H72, H73, H74, H75, H76, H77, H78, H86, H87, H88, H89, H90, H93, H94, H95, H96 亚洲家猪 独立 22 H1, H9, H28, H33, H34, H35, H43, H44, H65, H66, H67, H68, H79, H80, H81, H82, H83, H84, H85, H91, H92, H97 大洋洲野猪 独立 1 H48 古代野猪 独立 1 H98 亚洲家猪，亚洲野猪 共享 4 H16, H18, H25, H31 亚洲家猪，欧洲家猪 共享 1 H23 亚洲野猪，欧洲家猪 共享 1 H29 亚洲家猪，古代野猪 共享 1 H69 亚洲野猪，欧洲野猪，欧洲家猪 共享 2 H3, H10 亚洲家猪，亚洲野猪，欧洲家猪 共享 2 H15, H24 亚洲家猪，亚洲野猪，古代野猪，欧洲家猪 共享 3 H6, H17, H20 亚洲家猪，亚洲野猪，欧洲野猪，大洋洲野猪 共享 1 H26 亚洲野猪，欧洲家猪，欧洲野猪，古代野猪 共享 1 H2 亚洲家猪，亚洲野猪，欧洲家猪，欧洲野猪，大洋洲野猪 共享 1 H8
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