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    广西地区晚更新世野猪对家猪的遗传贡献

    侯新东 盛桂莲 袁俊霞 王元 金昌柱 赖旭龙

    侯新东, 盛桂莲, 袁俊霞, 王元, 金昌柱, 赖旭龙, 2018. 广西地区晚更新世野猪对家猪的遗传贡献. 地球科学, 43(11): 3976-3988. doi: 10.3799/dqkx.2018.333
    引用本文: 侯新东, 盛桂莲, 袁俊霞, 王元, 金昌柱, 赖旭龙, 2018. 广西地区晚更新世野猪对家猪的遗传贡献. 地球科学, 43(11): 3976-3988. doi: 10.3799/dqkx.2018.333
    Hou Xindong, Sheng Guilian, Yuan Junxia, Wang Yuan, Jin Changzhu, Lai Xulong, 2018. Genetic Contribution of Late Pleistocene Wild Boars in Guangxi to Domesticated Pigs. Earth Science, 43(11): 3976-3988. doi: 10.3799/dqkx.2018.333
    Citation: Hou Xindong, Sheng Guilian, Yuan Junxia, Wang Yuan, Jin Changzhu, Lai Xulong, 2018. Genetic Contribution of Late Pleistocene Wild Boars in Guangxi to Domesticated Pigs. Earth Science, 43(11): 3976-3988. doi: 10.3799/dqkx.2018.333

    广西地区晚更新世野猪对家猪的遗传贡献

    doi: 10.3799/dqkx.2018.333
    基金项目: 

    国家自然科学基金项目 41672017

    中国科学院重点部署项目 KZZD-EW-03

    国家自然科学基金项目 41202013

    国家自然科学基金项目 41472014

    详细信息
      作者简介:

      侯新东(1977-), 男, 副教授, 主要从事分子古生物学与分子生态学研究

      通讯作者:

      盛桂莲

    • 中图分类号: Q911

    Genetic Contribution of Late Pleistocene Wild Boars in Guangxi to Domesticated Pigs

    • 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.

       

    • 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-.
      下载: 导出CSV

      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.
      下载: 导出CSV

      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.
      下载: 导出CSV

      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.
      下载: 导出CSV

      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
      下载: 导出CSV
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