Ancient DNA Analyses of the Spotted Hyena (Crocuta crocuta) from Lingxian Cave, Qinhuangdao, Hebei Province
-
摘要: 鬣狗科动物曾是一个数量十分可观的群体, 在5百万年前曾达到演化的鼎盛时期, 留下已鉴定化石种100余种.现生的鬣狗科动物仅有4种, 仅分布在亚洲和非洲部分地区.由于该科动物演化至今种类剧减、分布区退缩, 部分化石种与现生种的谱系演化关系尚不明确, 因此成为古生物学家和进化生物学家关注的生物类群之一.采用现代分子生物学方法, 提取扩增河北秦皇岛灵仙洞中鬣狗类化石的线粒体基因组古DNA片段, 通过与基因库中已有鬣狗科动物各属种同源序列的对比分析, 从分子水平确定该化石为斑鬣狗化石; 基于古DNA序列数据构建的系统进化树显示, 该地的斑鬣狗个体与我国东北地区及俄罗斯的化石斑鬣狗具有较近的亲缘关系, 而与西欧洞穴鬣狗及非洲现生斑鬣狗亲缘关系较远, 显示出斑鬣狗演化的分子地理谱系.Abstract: The extant hyena species are the remnants of a formerly diverse group of Hyaenidae, which reached its peak about 5 MYA and contained more than 100 fossil species. Hyenas have been the subject of a number of evolutionary and systematic studies during the last two centuries, due in large part to the dramatical loss of its diversity and geography. The phylogenetic studies incorporating both morphological and molecular analysis have yielded different conclusions regarding the evolutionary relationship between extant and extinct hyenas. In this study, partial ancient DNA sequence of cytochrome b gene in mitochondrial genome was successfully retrieved from Pleistocene hyena bones collected from Hebei Province in North China. The BLAST result shows that the cracked specimen is the teeth of a spotted hyena (Crocuta crocuta), which makes the classification of the specimen clear at the molecular level. Furthermore, both the obtained sequence and the homologous sequences extracted from GenBank were aligned and used as datasets for phylogenetic analyses. The phylogenetic tree shows that the two individuals from China and the one from Russia were joined together, appearing as a sister group of the branch combined by the west European fossils and the African extant hyenas, which suggests a phylogeographic pattern of the Pleistocene cave hyenas.
-
图 2 PCR产物琼脂糖凝胶电泳图
M: 100 bp DNA ladder; 1.正对照; 2.LXD-5;3.空白提取对照; 4.第一次PCR H2O对照; 5.第二次PCR H2O对照
Fig. 2. Gel electrophoresis image of PCR products
图 3 鬣狗科动物各属种79 bp同源序列碱基组成比对
Fig. 3. Aligned DNA sequence of the 79 bp fragment of Cyt b from Hyaenidae
图 4 基于Cyt b基因部分序列构建的鬣狗科UPGMA系统进化树(图中数字代表重复次数为1 000时的自展支持率)
Fig. 4. Distance matrix phylogenetic tree based on the partial sequences of Cyt b gene in Hyaenidae
图 5 本研究中用于系统发育分析的鬣狗科动物化石种和现生种地理分布
Fig. 5. Geographical distribution of the extinct and extant Hyaenidae which have been used in phylogenetic analyze in this study
表 1 本研究用到的核酸序列信息
Table 1. Data sets used in this paper
-
Cano, R. J., Poinar, H. N., Pieniazek, N. J., et al., 1993. Amplification and sequencing of DNA from a 120-135-million-year-old weevil. Nature, 363 (6429): 536-538. doi: 10.1038/363536a0 DeSalle, R., Gatesy, J., Wheeler, W., et al., 1992. DNA sequences from a fossil termite in Oligo-Miocene amber and their phylogenetic implications. Science, 257 (5078): 1933-1936. doi: 10.1126/science.1411508 Diedrich, C., 2008. The holotypes of the upper Pleistocene Crocutacr ocuta spelaea and Pantheraleo spelaea of the zoolithen cave hyena den and their palaeo-ecological interpretation. Zoological Journal of the Linnean Society, 154 (4): 822-831. doi: 10.1111/j.1096-3642.2008.00425.x Golenberg, E. M., Giannasi, D. E., Clegg, M. T., et al., 1990. Chloroplast DNA sequence from a Miocene Magnolia species. Nature, 334 (6267): 656-658. Huang, W. B., 1989. Taxonomy of the hyaenidae (hyaena and crocuta) of the pleistocene in China. Vertebrata Palasiatica, 27 (3): 197-204 (in Chinese with English abstract). Jenks, S. M., Werdelin, L., 1998. Taxonomy and systemetics of living hyaenas (Family Hyaenidae). In: Mills, M. G. L., Hofer, H., compilers. Hyaenas: Status survey and conservation action plan. IUCN/SSC Hyaena Specialist Group, I UCN Gland, Switzerland, 8-17. Koepfli, K. P., Jenks, S. M., Eizirik, E., et al., 2006. Molecular systematics of the hyaenidae: Relationships of a relictual lineage resolved by a molecular supermatrix. Molecular Phylogenetics and Evolution, 38 (3): 603-620. doi: 10.1016/j.ympev.2005.10.017 Kurtén, B., 1956. The status and affinities of Hyaena sinensis Owen and Hyaena ultima Matsumoto. Amer. Mus. Novit., 1764: 1-48. Kurtén, B., 1957. The bears and hyenas of the interglacials. Quaternaria, 4: 69-81. Markova, A. K., Smirnov, N. G., Kozharinov, A. V., et al., 1995. Late Pleistocene distribution and diversity of mammals in northern Eurasia. Paleontol. Evol., 28 (29): 5-134. Rohland, N., Malaspinas, A., Pollack, J. L., et al., 2007. Proboscidean mitogenomics: Chronology and mode of elephant evolution using mastodon as outgroup. Plos Biology, 5 (8): 1663-1671. Rohland, N., Pollack, J. L., Nagel, D., et al., 2005. The population history of extant and extinct hyenas. Molecular Biology and Evolution, 22 (12): 2435-2443. doi: 10.1093/molbev/msi244 Römpler, H., Krause, J., Dear, P. H., et al., 2006. Multiplex amplification of ancient DNA. Nature, 1 (2): 720-728. Sheng. G. L., Lai, X. L., Hou, X. D., 2009. Standard experimental system and new technologies on ancient DNA research. Chinese Journal of Biochemistry and Molecular Biology, 25 (2): 116-125 (in Chinese with English abstract). Sheng. G. L., Wu, L. J., Hou, X. D., et al., 2009. Short sequence effect of ancient DNA on mammoth phylogenetic analyses. Frontier of Earth Science in China, 3 (1): 100-106. doi: 10.1007/s11707-009-0010-z Tong, H. W., 2007. Occurrences of warm-adapted mammals in North China over the Quaternary period and their paleo-environmental significance. Science in China (Series D), 50 (9): 1327-1340. doi: 10.1007/s11430-007-0096-7 Tseng, Z. J., Jin, C. Z., Liu, J. Y., et al., 2008. Fossil Hyaenidae (mammalia: carnivora) from Huainan, Anhui Province, China. Vertebrata Palasiatica, 46 (2): 133-146. Turner, A., 1984. The interpretation of variation in fossil specimens of spotted hyena (Crocuta crocuta Erxleben, 1777) from Sterkfontein valley sites (mammalian: carnivora). Ann. Transvaal Mus., 33 (27): 399-418. Turner, A., Antón, M., Werdelin, L., 2008. Taxonomy and evolutionary patterns in the fossil Hyaenidae of Europe. Geobios, 41 (5): 677-687. doi: 10.1016/j.geobios.2008.01.001 Wayne, R. K., Leonard, J. A., Cooper, A., 1999. Full of sound and fury: History of ancient DNA. Annu. Rev. Ecol. Syst., 30: 457-477. doi: 10.1146/annurev.ecolsys.30.1.457 Watts, H. E., Holekamp, K. E., 2007. Hyena societies. Current Biology, 17 (16): 657-660. doi: 10.1016/j.cub.2007.06.002 Werdelin, L., 1999. Studies of fossil hyaenas: Affinities of Lycyaenops rhomboideae Kretzoi from Pestlörinc, Hungary. Zoological Journal of the Linnean Society, 126 (3): 307-317. Werdelin, L., Solounias, N., 1991. The hyaenidae: Taxonomy, systematics and evolution. The Fossils and Strata, 30: 1-104. Wozencraft, W. C., 1993. Carnivora. In: Wilson, D. E., Reeder, D. M., eds., Mammal species of the world: A taxonomic and geographic reference. Smithsonian Institution Press, Washington DC, 279-348. Wurster, D. H., Benirschke, K., 1968. Comparative cytogenetic studies in the order carnivora. Chromosoma, 24 (3): 336-382. doi: 10.1007/BF00336201 Yang, S. J., Lai, X. L., 2003. The first ancient DNA study of mammoth in China. Earth Science—Journal of China University of Geosciences, 28 (2): 136, 142 (in Chinese with English abstract). Yang, S. J., Lai, X. L., Shi, S. H., et al., 2006. New ancient DNA sequences suggest high genetic diversity for the Woolly Mammoth (Mammuthus primigenius). Progress in Nature Science, 16 (4): 380-386. Yang, Z. Q., Zhang, H. Q., Zhang, J., et al., 2006. Degradative factor analysis of ancient DNA preserved in human bones. J. Fourth Mil. Med. Univ., 27 (1): 90-92 (in Chinese with English abstract). 黄万波, 1989. 我国更新世两属鬣狗(Hyaena, Crocuta) 的关系与分类. 古脊椎动物学报, 27 (3): 197-204. https://www.cnki.com.cn/Article/CJFDTOTAL-GJZD198903006.htm 盛桂莲, 赖旭龙, 侯新东, 2009. 古DNA实验体系与技术. 中国生物化学与分子生物学报, 25 (2): 116-125. https://www.cnki.com.cn/Article/CJFDTOTAL-SWHZ200902005.htm 同号文, 2007. 第四纪以来中国北方出现过的喜暖动物及其古环境意义. 中国科学(D辑), 37 (7): 922-933. https://www.cnki.com.cn/Article/CJFDTOTAL-JDXK200707007.htm 杨淑娟, 赖旭龙, 2003. 中国首例猛犸象古DNA序列. 地球科学——中国地质大学学报, 28 (2): 136, 142. https://www.cnki.com.cn/Article/CJFDTOTAL-DQKX200302003.htm 杨周岐, 张虎勤, 张金, 等, 2006. 古人类骨骼DNA降解因素分析. 第四军医大学学报, 27 (1): 90-92. doi: 10.3321/j.issn:1000-2790.2006.01.027 -
下载:
点击查看大图
图(5) / 表(1)
计量
- 文章访问数: 3683
- HTML全文浏览量: 522
- PDF下载量: 100
- 被引次数: 0
