Citation: | Sheng Guilian, Tao Hualin, Song Shiwen, Yuan Junxia, Lai Xulong, 2025. Applications of Ancient DNA Research in the Field of Geobiology. Earth Science, 50(3): 1105-1121. doi: 10.3799/dqkx.2024.155 |
Ahmed, E., Parducci, L., Unneberg, P., et al., 2018. Archaeal Community Changes in Lateglacial Lake Sediments: Evidence from Ancient DNA. Quaternary Science Reviews, 181: 19-29. https://doi.org/10.1016/j.quascirev.2017.11.037
|
Allentoft, M. E., Sikora, M., Sjögren, K. G., et al., 2015. Population Genomics of Bronze Age Eurasia. Nature, 522: 167-172. https://doi.org/10.1038/nature14507
|
Baca, M., Popović, D., Stefaniak, K., et al., 2016. Retreat and Extinction of the Late Pleistocene Cave Bear (Ursus Spelaeus Sensu Lato). The Science of Nature, 103(11): 92. https://doi.org/10.1007/s00114-016-1414-8
|
Barlow, A., Cahill, J. A., Hartmann, S., et al., 2018. Partial Genomic Survival of Cave Bears in Living Brown Bears. Nature Ecology & Evolution, 2: 1563-1570. https://doi.org/10.1038/s41559-018-0654-8
|
Barnes, I., Matheus, P., Shapiro, B., et al., 2002. Dynamics of Pleistocene Population Extinctions in Beringian Brown Bears. Science, 295(5563): 2267-2270. https://doi.org/10.1126/science.1067814
|
Barnett, R., Shapiro, B., Barnes, I., et al., 2009. Phylogeography of Lions (Panthera Leo ssp.) Reveals Three Distinct Taxa and a Late Pleistocene Reduction in Genetic Diversity. Mol Ecol, 18(8): 1668-1677. https://doi.org/10.1111/j.1365-294x.2009.04134.x
|
Barnosky, A. D., Koch, P. L., Feranec, R. S., et al., 2004. Assessing the Causes of Late Pleistocene Extinctions on the Continents. Science, 306(5693): 70-75. https://doi.org/10.1126/science.1101476
|
Bergström, A., Stanton, D. W. G., Taron, U. H., et al., 2022. Grey Wolf Genomic History Reveals a Dual Ancestry of Dogs. Nature, 607: 313-320. https://doi.org/10.1038/s41586-022-04824-9
|
Boessenkool, S., McGlynn, G., Epp, L. S., et al., 2014. Use of Ancient Sedimentary DNA as a Novel Conservation Tool for High-Altitude Tropical Biodiversity. Conservation Biology, 28(2): 446-455. https://doi.org/10.1111/cobi.12195
|
Bos, K. I., Schuenemann, V. J., Golding, G. B., et al., 2011. A Draft Genome of Yersinia Pestis from Victims of the Black Death. Nature, 478: 506-510. https://doi.org/10.1038/nature10549
|
Brown, T. A., Jones, M. K., Powell, W., et al., 2009. The Complex Origins of Domesticated Crops in the Fertile Crescent. Trends in Ecology & Evolution, 24(2): 103-109. https://doi.org/10.1016/j.tree.2008.09.008
|
Cai, D. W., Zhu, S. Q., Gong, M., et al., 2022. Radiocarbon and Genomic Evidence for the Survival of Equus Sussemionus until the Late Holocene. eLife, 11: e73346. https://doi.org/10.7554/elife.73346
|
Capo, E., Giguet-Covex, C., Rouillard, A., et al., 2021. Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. Quaternary, 4(1): 6. https://doi.org/10.3390/quat4010006
|
Coolen, M. J. L., Overmann, J., 1998. Analysis of Subfossil Molecular Remains of Purple Sulfur Bacteria in a Lake Sediment. Applied and Environmental Microbiology, 64(11): 4513-4521. https://doi.org/10.1128/aem.64.11.4513-4521.1998
|
Cruzan, M. B., Templeton, A. R., 2000. Paleoecology and Coalescence: Phylogeographic Analysis of Hypotheses from the Fossil Record. Trends in Ecology & Evolution, 15(12): 491-496. https://doi.org/10.1016/s0169-5347(00)01998-4
|
Da Fonseca, R. R., Smith, B. D., Wales, N., et al., 2015. The Origin and Evolution of Maize in the Southwestern United States. Nature Plants, 1: 14003. https://doi.org/10.1038/nplants.2014.3
|
Dalén, L., Heintzman, P. D., Kapp, J. D., et al., 2023. Deep-Time Paleogenomics and the Limits of DNA Survival. Science, 382(6666): 48-53. https://doi.org/10.1126/science.adh7943
|
Dalton, D. L., Prost, S., 2021. Rhinoceros Genomes Uncover Family Secrets. Nature, 599: 209-210. https://doi.org/10.1038/d41586-021-02777-z
|
Dannemann, M., Kelso, J., 2017. The Contribution of Neanderthals to Phenotypic Variation in Modern Humans. The American Journal of Human Genetics, 101(4): 578-589. https://doi.org/10.1016/j.ajhg.2017.09.010
|
Davison, J., Ho, S. Y. W., Bray, S. C., et al., 2011. Late-Quaternary Biogeographic Scenarios for the Brown Bear (Ursus Arctos), a Wild Mammal Model Species. Quaternary Science Reviews, 30(3-4): 418-430. https://doi.org/10.1016/j.quascirev.2010.11.023
|
Debruyne, R., Barriel, V., Tassy, P., 2003. Mitochondrial Cytochrome B of the Lyakhov Mammoth (Proboscidea, Mammalia): New Data and Phylogenetic Analyses of Elephantidae. Molecular Phylogenetics and Evolution, 26(3): 421-434. https://doi.org/10.1016/S1055-7903(02)00292-0
|
Deng, T., Xue, X. X., 1997. The First Appearance of the True Horse (Genus Equus) as a Marker for the Lower Boundary of the Quaternary. Journal of Stratigraphy, 21(2): 109-116 (in Chinese with English abstract).
|
Díez-del-Molino, D., Dehasque, M., Chacón-Duque, J. C., et al., 2023. Genomics of Adaptive Evolution in the Woolly Mammoth. Current Biology, 33(9): 1753-1764. https://doi.org/10.1016/j.cub.2023.03.084
|
Du, Z. C., Sheng, G. L., Hu, J. M., et al., 2024. Mitochondrial Genetic Diversity and Evolutionary History of Late Pleistocene Woolly Mammoths in Northeast China. Chinese Science Bulletin, 70(1): 121-133 (in Chinese).
|
Eisenmann, V., Sergej, V., 2011. Unexpected Finding of a New Equus Species (Mammalia, Perissodactyla) Belonging to a Supposedly Extinct Subgenus in Late Pleistocene Deposits of Khakassia (Southwestern Siberia). Geodiversitas, 33(3): 519-530. https://doi.org/10.5252/g2011n3a5
|
Enk, J., Devault, A., Widga, C., et al., 2016. Mammuthus Population Dynamics in Late Pleistocene North America: Divergence, Phylogeography, and Introgression. Frontiers in Ecology and Evolution, 4: 42. https://doi.org/10.3389/fevo.2016.00042
|
Fages, A., Hanghøj, K., Khan, N., et al., 2019. Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series. Cell, 177(6): 1419-1435. https://doi.org/10.1016/j.cell.2019.03.049
|
Frantz, L. A. F., Haile, J., Lin, A. T., et al., 2019. Ancient Pigs Reveal a Near-Complete Genomic Turnover Following Their Introduction to Europe. Proceedings of the National Academy of Sciences, 116(35): 17231-17238. https://doi.org/10.1073/pnas.1901169116
|
Frei, D., De-Kayne, R., Selz, O. M., et al., 2022. Genomic Variation from an Extinct Species Is Retained in the Extant Radiation Following Speciation Reversal. Nature Ecology & Evolution, 6: 461-468. https://doi.org/10.1038/s41559-022-01665-7
|
Freitas, F. O., Bendel, G., Allaby, R. G., et al., 2003. DNA from Primitive Maize Landraces and Archaeological Remains: Implications for the Domestication of Maize and Its Expansion into South America. Journal of Archaeological Science, 30(7): 901-908. https://doi.org/10.1016/S0305-4403(02)00269-8
|
Froese, D., Stiller, M., Heintzman, P. D., et al., 2017. Fossil and Genomic Evidence Constrains the Timing of Bison Arrival in North America. Proceedings of the National Academy of Sciences, 114: 3457-3462. https://doi.org/10.1073/pnas.1620754114
|
Fu, Q. M., Meyer, M., Gao, X., et al., 2013. DNA Analysis of an Early Modern Human from Tianyuan Cave, China. Proceedings of the National Academy of Sciences, 110(6): 2223-2227. https://doi.org/10.1073/pnas.1221359110
|
Green, R. E., Krause, J., Briggs, A. W., et al., 2010. A Draft Sequence of the Neandertal Genome. Science, 328: 710-722. https://doi.org/10.1126/science.1188021
|
Green, R. E., Krause, J., Ptak, S. E., et al., 2006. Analysis of One Million Base Pairs of Neanderthal DNA. Nature, 444: 330-336. https://doi.org/10.1038/nature05336
|
Green, R. E., Malaspinas, A. S., Krause, J., et al., 2008. A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing. Cell, 134(3): 416-426. https://doi.org/10.1016/j.cell.2008.06.021
|
Hajdinjak, M., Mafessoni, F., Skov, L., et al., 2021. Initial Upper Palaeolithic Humans in Europe Had Recent Neanderthal Ancestry. Nature, 592: 253-257. https://doi.org/10.1038/s41586-021-03335-3
|
Heintzman, P. D., Zazula, G. D., MacPhee, R. D., et al., 2017. A New Genus of Horse from Pleistocene North America. eLife, 6: e29944. https://doi.org/10.7554/elife.29944
|
Higuchi, R., Bowman, B., Freiberger, M., et al., 1984. DNA Sequences from the Quagga, an Extinct Member of the Horse Family. Nature, 312: 282-284. https://doi.org/10.1038/312282a0
|
Hoshino, T., Doi, H., Uramoto, G. I., et al., 2020. Global Diversity of Microbial Communities in Marine Sediment. Proceedings of the National Academy of Sciences, 117(44): 27587-27597. https://doi.org/10.1073/pnas.1919139117
|
Hou, X. D., Zhao, J., Zhang, H. C., et al., 2022. Paleogenomes Reveal a Complex Evolutionary History of Late Pleistocene Bison in Northeastern China. Genes (Basel), 13(10): 1684. https://doi.org/10.3390/genes13101684
|
Hu, J. M., Westbury, M. V., Yuan, J. X., et al., 2022. An Extinct and Deeply Divergent Tiger Lineage from Northeastern China Recognized through Palaeogenomics. Proceedings of the Royal Society B: Biological Sciences, 289(1979): 20220617. https://doi.org/10.1098/rspb.2022.0617
|
Hu, J., Westbury, M. V., Yuan, J. X., et al., 2021. Ancient Mitochondrial Genomes from Chinese Cave Hyenas Provide Insights into the Evolutionary History of the Genus Crocuta. Crocuta. Proceedings of the Royal Society B, 288(1943): 20202934. https://doi.org/10.1098/rspb.2020.2934
|
Hublin, J. J., Sirakov, N., Aldeias, V., et al., 2020. Initial Upper Palaeolithic Homo Sapiens from Bacho Kiro Cave, Bulgaria. Nature, 581: 299-302. https://doi.org/10.1038/s41586-020-2259-z
|
Jaenicke-Després, V., Buckler, E. S., Smith, B. D., et al., 2003. Early Allelic Selection in Maize as Revealed by Ancient DNA. Science, 302(5648): 1206-1208. https://doi.org/10.1126/science.1089056
|
Kato, S., Arakaki, S., Nagano, A. J., et al., 2024. Genomic Landscape of Introgression from the Ghost Lineage in a Gobiid Fish Uncovers the Generality of Forces Shaping Hybrid Genomes. Molecular Ecology, 33(20): e17216. https://doi.org/10.1111/mec.17216
|
Kirillova, I. V., Chernova, O. F., van der Made, J., et al., 2017. Discovery of the Skull of Stephanorhinus Kirchbergensis (Jäger, 1839) Above the Arctic Circle. Quaternary Research, 88: 537-550. https://doi.org/10.1017/qua.2017.53
|
Kjær, K. H., Winther Pedersen, M., De Sanctis, B., et al., 2022. A 2-Million-Year-Old Ecosystem in Greenland Uncovered by Environmental DNA. Nature, 612: 283-291. https://doi.org/10.1038/s41586-022-05453-y
|
Ko, A. M., Zhang, Y. Q., Yang, M. A., et al., 2018. Mitochondrial Genome of a 22 000-Year-Old Giant Panda from Southern China Reveals a New Panda Lineage. Current Biology, 28(12): R693-R694. https://doi.org/10.1016/j.cub.2018.05.008
|
Koch, P. L., Barnosky, A. D., 2006. Late Quaternary Extinctions: State of the Debate. Annual Review of Ecology, Evolution, and Systematics, 37: 215-250. https://doi.org/10.1146/annurev.ecolsys.34.011802.132415
|
Kosintsev, P., Mitchell, K. J., Devièse, T., et al., 2019. Evolution and Extinction of the Giant Rhinoceros Elasmotherium Sibiricum Sheds Light on Late Quaternary Megafaunal Extinctions. Nature Ecology & Evolution, 3: 31-38. https://doi.org/10.1038/s41559-018-0722-0
|
Krings, M., Stone, A., Schmitz, R. W., et al., 1997. Neandertal DNA Sequences and the Origin of Modern Humans. Cell, 90(1): 19-30. https://doi.org/10.1016/S0092-8674(00)80310-4
|
Kuhlwilm, M., de Manuel, M., Nater, A., et al., 2016. Evolution and Demography of the Great Apes. Current Opinion in Genetics & Development, 41: 124-129. https://doi.org/10.1016/j.gde.2016.09.005
|
Kumar, V., Lammers, F., Bidon, T., et al., 2017. The Evolutionary History of Bears Is Characterized by Gene Flow across Species. Scientific Reports, 7: 46487. https://doi.org/10.1038/srep46487
|
Larson, G., Cucchi, T., Fujita, M., et al., 2007. Phylogeny and Ancient DNA of Sus Provides Insights into Neolithic Expansion in Island Southeast Asia and Oceania. Proceedings of the National Academy of Sciences, 104: 4834-4839. https://doi.org/10.1073/pnas.0607753104
|
Larson, G., Dobney, K., Albarella, U., et al., 2005. Worldwide Phylogeography of Wild Boar Reveals Multiple Centers of Pig Domestication. Science, 307(5715): 1618-1621. https://doi.org/10.1126/science.1106927
|
Li, T., Lai, X. L., Wang, W., et al., 2004. Taxonomy and Evolution of Giant Panda. Bulletin of Geological Science and Technology, 23(3): 40-46 (in Chinese with English abstract). doi: 10.3969/j.issn.1000-7849.2004.03.008
|
Librado, P., Gamba, C., Gaunitz, C., et al., 2017. Ancient Genomic Changes Associated with Domestication of the Horse. Science, 356(6336): 442-445. https://doi.org/10.1126/science.aam5298
|
Lin, H. F., Hu, J. M., Baleka, S., et al., 2023. A Genetic Glimpse of the Chinese Straight-Tusked Elephants. Biology Letters, 19(7): 20230078. https://doi.org/10.1098/rsbl.2023.0078
|
Lippold, S., Knapp, M., Kuznetsova, T., et al., 2011. Discovery of Lost Diversity of Paternal Horse Lineages Using Ancient DNA. Nature Communications, 2: 450. https://doi.org/10.1038/ncomms1447
|
Liu, S. L., Westbury, M. V., Dussex, N., et al., 2021a. Ancient and Modern Genomes Unravel the Evolutionary History of the Rhinoceros Family. Cell, 184(19): 4874-4885. https://doi.org/10.1016/j.cell.2021.07.032
|
Liu, S. S., Kruse, S., Scherler, D., et al., 2021b. Sedimentary Ancient DNA Reveals a Threat of Warming-Induced Alpine Habitat Loss to Tibetan Plateau Plant Diversity. Nature Communications, 12: 2995. https://doi.org/10.1038/s41467-021-22986-4
|
Lord, E., Dussex, N., Kierczak, M., et al., 2020. Pre-Extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros. Current Biology, 30(19): 3871-3879. https://doi.org/10.1016/j.cub.2020.07.046
|
Lorenzen, E. D., Nogués-Bravo, D., Orlando, L., et al., 2011. Species-Specific Responses of Late Quaternary Megafauna to Climate and Humans. Nature, 479: 359-364. https://doi.org/10.1038/nature10574
|
Lucena-Perez, M., Paijmans, J. L. A., Nocete, F., et al., 2024. Recent Increase in Species-Wide Diversity after Interspecies Introgression in the Highly Endangered Iberian Lynx. Nature Ecology & Evolution, 8: 282-292. https://doi.org/10.1038/s41559-023-02267-7
|
Mascher, M., Schuenemann, V. J., Davidovich, U., et al., 2016. Genomic Analysis of 6 000-Year-Old Cultivated Grain Illuminates the Domestication History of Barley. Nature Genetics, 48(9): 1089-1093. https://doi.org/10.1038/ng.3611
|
McManus, K. F., Kelley, J. L., Song, S., et al., 2015. Inference of Gorilla Demographic and Selective History from Whole-Genome Sequence Data. Molecular Biology and Evolution, 32(3): 600-612. https://doi.org/10.1093/molbev/msu394
|
Meyer, M., Arsuaga, J. L., de Filippo, C., et al., 2016. Nuclear DNA Sequences from the Middle Pleistocene Sima de Los Huesos Hominins. Nature, 531: 504-507. https://doi.org/10.1038/nature17405
|
Meyer, M., Kircher, M., Gansauge, M. T., et al., 2012. A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science, 338(6104): 222-226. https://doi.org/10.1126/science.1224344
|
Meyer, M., Palkopoulou, E., Baleka, S., et al., 2017. Palaeogenomes of Eurasian Straight-Tusked Elephants Challenge the Current View of Elephant Evolution. eLife, 6: e25413. https://doi.org/10.7554/elife.25413
|
Miller, W., Drautz, D. I., Ratan, A., et al., 2008. Sequencing the Nuclear Genome of the Extinct Woolly Mammoth. Nature, 456: 387-390. https://doi.org/10.1038/nature07446
|
Miller, W., Schuster, S. C., Welch, A. J., et al., 2012. Polar and Brown Bear Genomes Reveal Ancient Admixture and Demographic Footprints of Past Climate Change. Proceedings of the National Academy of Sciences, 109(36): E2382-E2390. https://doi.org/10.1073/pnas.1210506109
|
Murchie, T. J., Monteath, A. J., Mahony, M. E., et al., 2021. Collapse of the Mammoth-Steppe in Central Yukon as Revealed by Ancient Environmental DNA. Nature Communications, 12: 7120. https://doi.org/10.1038/s41467-021-27439-6
|
Noonan, J. P., Coop, G., Kudaravalli, S., et al., 2006. Sequencing and Analysis of Neanderthal Genomic DNA. Science, 314(5802): 1113-1118. https://doi.org/10.1126/science.1131412
|
Noro, M., Masuda, R., Dubrovo, I. A., et al., 1998. Molecular Phylogenetic Inference of the Woolly Mammoth Mammuthus Primigenius, Based on Complete Sequences of Mitochondrial Cytochrome B and 12S Ribosomal RNA Genes. Journal of Molecular Evolution, 46(3): 314-326. https://doi.org/10.1007/pl00006308
|
O'Brien, S. J., Pan, W., Lu, Z., 1994. Pandas, People and Policy. Nature, 369: 179-180. https://doi.org/10.1038/369179a0
|
Orlando, L., 2020. Ancient Genomes Reveal Unexpected Horse Domestication and Management Dynamics. BioEssays, 42(1): e1900164. https://doi.org/10.1002/bies.201900164
|
Orlando, L., Ginolhac, A., Zhang, G. J., et al., 2013. Recalibrating Equus Evolution Using the Genome Sequence of an Early Middle Pleistocene Horse. Nature, 499(7456): 74-78. https://doi.org/10.1038/nature12323
|
Orlando, L., Leonard, J. A., Thenot, A., et al., 2003. Ancient DNA Analysis Reveals Woolly Rhino Evolutionary Relationships. Molecular Phylogenetics and Evolution, 28(3): 485-499. https://doi.org/10.1016/S1055-7903(03)00023-X
|
Orlando, L., Metcalf, J. L., Alberdi, M. T., et al., 2009. Revising the Recent Evolutionary History of Equids Using Ancient DNA. Proceedings of the National Academy of Sciences, 106(51): 21754-21759. https://doi.org/10.1073/pnas.0903672106
|
Ozawa, T., Hayashi, S., Mikhelson, V. M., 1997. Phylogenetic Position of Mammoth and Steller's Sea Cow within Tethytheria Demonstrated by Mitochondrial DNA Sequences. Journal of Molecular Evolution, 44(4): 406-413. https://doi.org/10.1007/pl00006160
|
Parducci, L., Jørgensen, T., Tollefsrud, M. M., et al., 2012. Glacial Survival of Boreal Trees in Northern Scandinavia. Science, 335(6072): 1083-1086. https://doi.org/10.1126/science.1216043
|
Pawar, H., Rymbekova, A., Cuadros-Espinoza, S., et al., 2023. Ghost Admixture in Eastern Gorillas. Nature Ecology & Evolution, 7(9): 1503-1514. https://doi.org/10.1038/s41559-023-02145-2
|
Poinar, H. N., Schwarz, C., Qi, J., et al., 2006. Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA. Science, 311(5759): 392-394. https://doi.org/10.1126/science.1123360
|
Price, M., Hongo, H., 2020. The Archaeology of Pig Domestication in Eurasia. Journal of Archaeological Research, 28(4): 557-615. https://doi.org/10.1007/s10814-019-09142-9
|
Prüfer, K., Racimo, F., Patterson, N., et al., 2014. The Complete Genome Sequence of a Neanderthal from the Altai Mountains. Nature, 505(7481): 43-49. https://doi.org/10.1038/nature12886
|
Racimo, F., Sankararaman, S., Nielsen, R., et al., 2015. Evidence for Archaic Adaptive Introgression in Humans. Nature Reviews Genetics, 16(6): 359-371. https://doi.org/10.1038/nrg3936
|
Reich, D., Green, R. E., Kircher, M., et al., 2010. Genetic History of an Archaic Hominin Group from Denisova Cave in Siberia. Nature, 468(7327): 1053-1060. https://doi.org/10.1038/nature09710
|
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. https://doi.org/10.1093/molbev/msi244
|
Salis, A. T., Bray, S. C. E., Lee, M. S. Y., et al., 2022. Lions and Brown Bears Colonized North America in Multiple Synchronous Waves of Dispersal across the Bering Land Bridge. Molecular Ecology, 31(24): 6407-6421. https://doi.org/10.1111/mec.16267
|
Sandoval-Velasco, M., Dudchenko, O., Rodríguez, J. A., et al., 2024. Three-Dimensional Genome Architecture Persists in a 52 000-Year-Old Woolly Mammoth Skin Sample. Cell, 187: 3541-3562. https://doi.org/10.1101/2023.06.30.547175
|
Sheng, G. L., Barlow, A., Cooper, A., et al., 2018. Ancient DNA from Giant Panda (Ailuropoda Melanoleuca) of South-Western China Reveals Genetic Diversity Loss during the Holocene. Genes, 9(4): 198. https://doi.org/10.3390/genes9040198
|
Sheng, G. L., Basler, N., Ji, X. P., et al., 2019. Paleogenome Reveals Genetic Contribution of Extinct Giant Panda to Extant Populations. Current Biology, 29(10): 1695-1700. https://doi.org/10.1016/j.cub.2019.04.021
|
Sheng, G. L., Soubrier, J., Liu, J. Y., et al., 2014. Pleistocene Chinese Cave Hyenas and the Recent Eurasian History of the Spotted Hyena, Crocuta Crocuta. Molecular Ecology, 23: 522-533. https://doi.org/10.1111/mec.12576
|
Sheng, G. L., Yuan, J. X., Yi, J., et al., 2009. Ancient DNA Analyses of the Spotted Hyena (Crocuta Crocuta) from Lingxian Cave, Qinhuangdao, Hebei Province. Earth Science, 34(6): 877-883 (in Chinese with English abstract). doi: 10.3321/j.issn:1000-2383.2009.06.001
|
Simonti, C. N., Vernot, B., Bastarache, L., et al., 2016. The Phenotypic Legacy of Admixture between Modern Humans and Neandertals. Science, 351(6274): 737-741. https://doi.org/10.1126/science.aad2149
|
Sjögren, P., Edwards, M. E., Gielly, L., et al., 2017. Lake Sedimentary DNA Accurately Records 20th Century Introductions of Exotic Conifers in Scotland. The New Phytologist, 213(2): 929-941. https://doi.org/10.1111/nph.14199
|
Skoglund, P., Mathieson, I., 2018. Ancient Genomics of Modern Humans: The First Decade. Annual Review of Genomics and Human Genetics, 19: 381-404. https://doi.org/10.1146/annurev-genom-083117-021749
|
Slon, V., Hopfe, C., Weiß, C. L., et al., 2017. Neandertal and Denisovan DNA from Pleistocene Sediments. Science, 356(6338): 605-608. https://doi.org/10.1126/science.aam9695
|
Slon, V., Mafessoni, F., Vernot, B., et al., 2018. The Genome of the Offspring of a Neanderthal Mother and a Denisovan Father. Nature, 561(7721): 113-116. https://doi.org/10.1038/s41586-018-0455-x
|
Sommer, R. S., Benecke, N., Lõugas, L., et al., 2011. Holocene Survival of the Wild Horse in Europe: A Matter of Open Landscape? Journal of Quaternary Science, 26(8): 805-812. https://doi.org/10.1002/jqs.1509
|
Stuart, A. J., 2015. Late Quaternary Megafaunal Extinctions on the Continents: A Short Review. Geological Journal, 50(3): 338-363. https://doi.org/10.1002/gj.2633
|
Sun, X., Liu, Y. C., Tiunov, M. P., et al., 2023. Ancient DNA Reveals Genetic Admixture in China during Tiger Evolution. Nature Ecology & Evolution, 7(11): 1914-1929. https://doi.org/10.1038/s41559-023-02185-8
|
van der Valk, T., Pečnerová, P., Díez-Del-Molino, D., et al., 2021. Million-Year-Old DNA Sheds Light on the Genomic History of Mammoths. Nature, 591(7849): 265-269. https://doi.org/10.1038/s41586-021-03224-9
|
Vernot, B., Zavala, E. I., Gómez-Olivencia, A., et al., 2021. Unearthing Neanderthal Population History Using Nuclear and Mitochondrial DNA from Cave Sediments. Science, 372(6542): eabf1667. https://doi.org/10.1126/science.abf1667
|
Wang, J., Xia, H., Yao, J. T., et al., 2020. Subsistence Strategies of Prehistoric Hunter-Gatherers on the Tibetan Plateau during the Last Deglaciation. Science China Earth Sciences, 50(3): 380-390 (in Chinese with English abstract). http://d.wanfangdata.com.cn/periodical/zgkx-ed202003005
|
Wang, Y. C., Pedersen, M. W., Alsos, I. G., et al., 2021. Late Quaternary Dynamics of Arctic Biota from Ancient Environmental Genomics. Nature, 600(7887): 86-92. https://doi.org/10.1038/s41586-021-04016-x
|
Wei, F., 2022. Population History of the Giant Panda. Springer, New York.
|
Weinstock, J., Willerslev, E., Sher, A., et al., 2005. Evolution, Systematics, and Phylogeography of Pleistocene Horses in the New World: A Molecular Perspective. PLoS Biology, 3(8): e241. https://doi.org/10.1371/journal.pbio.0030241
|
Westbury, M. V., Hartmann, S., Barlow, A., et al., 2020. Hyena Paleogenomes Reveal a Complex Evolutionary History of Cross-Continental Gene Flow between Spotted and Cave Hyena. Science Advances, 6(11): eaay0456. https://doi.org/10.1126/sciadv.aay0456
|
Willerslev, E., Davison, J., Moora, M., et al., 2014. Fifty Thousand Years of Arctic Vegetation and Megafaunal Diet. Nature, 506(7486): 47-51. https://doi.org/10.1038/nature12921
|
Willerslev, E., Gilbert, M. T. P., Binladen, J., et al., 2009. Analysis of Complete Mitochondrial Genomes from Extinct and Extant Rhinoceroses Reveals Lack of Phylogenetic Resolution. BMC Evolutionary Biology, 9: 95. https://doi.org/10.1186/1471-2148-9-95
|
Willerslev, E., Hansen, A. J., Binladen, J., et al., 2003. Diverse Plant and Animal Genetic Records from Holocene and Pleistocene Sediments. Science, 300(5620): 791-795. https://doi.org/10.1126/science.1084114
|
Xiao, B., Wang, T. J., Lister, A. M., et al., 2023. Ancient and Modern Mitogenomes of Red Deer Reveal Its Evolutionary History in Northern China. Quaternary Science Reviews, 301: 107924. https://doi.org/10.1016/j.quascirev.2022.107924
|
Xie, S. C., 2023. Geobiology. Higher Education Press, Beijing (in Chinese).
|
Yang, H., Golenberg, E. M., Shoshani, J., 1996. Phylogenetic Resolution within the Elephantidae Using Fossil DNA Sequence from the American Mastodon (Mammut Americanum) as an Outgroup. Proceedings of the National Academy of Sciences, 93(3): 1190-1194. https://doi.org/10.1073/pnas.93.3.1190
|
Yang, M. A., Gao, X., Theunert, C., et al., 2017. 40, 000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia. Current Biology, 27(20): 3202-3208. https://doi.org/10.1016/j.cub.2017.09.030
|
Yin, H. F., Xie, S. C., Tong, J. N., et al., 2009. On the Significance of Geobiology. Acta Palaeontologica Sinica, 48(3): 293-301 (in Chinese). http://en.cnki.com.cn/Article_en/CJFDTOTAL-GSWX200903001.htm
|
Yuan, J. X., Hou, X. D., Barlow, A., et al., 2019. Molecular Identification of Late and Terminal Pleistocene Equus Ovodovi from Northeastern China. PLoS One, 14(5): e0216883. https://doi.org/10.1371/journal.pone.0216883
|
Yuan, J. X., Hu, J. M., Liu, W. H., et al., 2024. Camelus Knoblochi Genome Reveals the Complex Evolutionary History of Old World Camels. Current Biology, 34(11): 2502-2508. https://doi.org/10.1016/j.cub.2024.04.050
|
Yuan, J. X., Sheng, G. L., Preick, M., et al., 2020. Mitochondrial Genomes of Late Pleistocene Caballine Horses from China Belong to a Separate Clade. Quaternary Science Reviews, 250: 106691. https://doi.org/10.1016/j.quascirev.2020.106691
|
Yuan, J. X., Sun, G. J., Xiao, B., et al., 2023. Ancient Mitogenomes Reveal a High Maternal Genetic Diversity of Pleistocene Woolly Rhinoceros in Northern China. BMC Ecology and Evolution, 23(1): 56. https://doi.org/10.1186/s12862-023-02168-0
|
Zavala, E. I., Jacobs, Z., Vernot, B., et al., 2021. Pleistocene Sediment DNA Reveals Hominin and Faunal Turnovers at Denisova Cave. Nature, 595(7867): 399-403. https://doi.org/10.1038/s41586-021-03675-0
|
Zhang, D. J., Xia, H. A., Chen F. H., et al., 2020. Denisovan DNA in Late Pleistocene Sediments from Baishiya Karst Cave on the Tibetan Plateau. Science, 370: 584-587. https://doi.org/10.1126/science.abb6320
|
Zhang, M., Liu, Y. C., Li, Z. P., et al., 2022. Ancient DNA Reveals the Maternal Genetic History of East Asian Domestic Pigs. Journal of Genetics and Genomics, 49(6): 537-546. https://doi.org/10.1016/j.jgg.2021.11.014
|
Zhang, N. F., Shao, X. Y., Guo, Y. Q., et al., 2023. Ancient Mitochondrial Genomes Provide New Clues to the Origin of Domestic Cattle in China. Genes, 14(7): 1313. https://doi.org/10.3390/genes14071313
|
邓涛, 薛祥煦, 1997. 重论真马(Equus属)首次出现可作为第四纪下限的标志. 地层学杂志, 21(2): 109-116.
|
杜至诚, 盛桂莲, 胡家铭, 等, 2025. 中国东北晚更新世真猛犸象的线粒体遗传多样性及其演化历史. 科学通报, 70(1): 121-133.
|
李涛, 赖旭龙, 王頠, 等, 2004. 大熊猫的分类与演化综述. 地质科技情报, 23(3): 40-46.
|
盛桂莲, 袁俊霞, 伊剑, 等, 2009. 河北秦皇岛灵仙洞斑鬣狗化石的古DNA初步分析. 地球科学, 34(6): 877-883. http://www.earth-science.net/article/id/1902
|
王建, 夏欢, 姚娟婷, 等, 2020. 青藏高原末次冰消期狩猎采集人群的生存策略研究. 中国科学: 地球科学, 50(3): 380-390.
|
谢树成, 2023. 地球生物学. 北京: 高等教育出版社.
|
殷鸿福, 谢树成, 童金南, 等, 2009. 谈地球生物学的重要意义. 古生物学报, 48(3): 293-301.
|