Higuchi, R. et al. DNA sequences from the quagga, an extinct member of the horse family. Nature 312, 282–284 (1984).
Google Scholar
Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl. Acad. Sci. U. S. A. 110, 15758–15763 (2013).
Google Scholar
Hansen, H. B. et al. Comparing ancient DNA preservation in petrous bone and tooth cementum. PLoS ONE 12, e0170940 (2017).
Google Scholar
Hagan, R. W. et al. Comparison of extraction methods for recovering ancient microbial DNA from paleofeces. Am. J. Phys. Anthropol. 171, 275–284 (2020).
Google Scholar
Epp, L. S., Zimmermann, H. H. & Stoof-Leichsenring, K. R. Sampling and extraction of ancient DNA from sediments. In Ancient DNA. Methods in Molecular Biology (eds Shapiro, B. et al.) 31–44 (Humana Press, 2019).
Modi, A. et al. Combined methodologies for gaining much information from ancient dental calculus: testing experimental strategies for simultaneously analysing DNA and food residues. Archaeol. Anthropol. Sci. 12, 10 (2020).
Google Scholar
Campos, P. F. & Gilbert, M. T. P. DNA extraction from keratin and chitin. In Ancient DNA. Methods in Molecular Biology (eds Shapiro, B. et al.) 57–63 (Humana Press, 2019).
Adler, C. J. et al. Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the neolithic and industrial revolutions. Nat. Genet. 45, 450-455e1 (2013).
Google Scholar
Warinner, C. et al. Pathogens and host immunity in the ancient human oral cavity. Nat. Genet. 46, 336–344 (2014).
Google Scholar
Weyrich, L. S. et al. Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus. Nature 544, 357–361 (2017).
Google Scholar
Slon, V. et al. Neandertal and Denisovan DNA from Pleistocene sediments. Science 356, 605–608 (2017).
Google Scholar
Teasdale, M. D. et al. The York Gospels: a 1000-year biological palimpsest. R. Soc. Open. Sci. 4, 170988 (2017).
Google Scholar
Boast, A. et al. Coprolites reveal ecological interactions lost with the extinction of New Zealand birds. Proc. Natl. Acad. Sci. U. S. A. 115, 1546–1551 (2018).
Google Scholar
Zarrillo, S. et al. The use and domestication of Theobroma cacao during the mid-Holocene in the upper Amazon. Nat. Ecol. Evol. 2, 1879–1888 (2018).
Google Scholar
Cano, R. J. et al. Amplification and sequencing of DNA from a 120–135 million-year-old weevil. Nature 363, 536–538 (1993).
Google Scholar
DeSalle, R. et al. DNA sequences from a fossil termite in Oligo-Miocene amber and their phylogenetic implications. Science 257, 1933–1936 (1992).
Google Scholar
Sherratt, E. et al. Amber fossils demonstrate deep-time stability of Caribbean lizard communities. Proc. Natl. Acad. Sci. U. S. A. 112, 9961–9966 (2015).
Google Scholar
Sadowski, E. M. et al. Carnivorous leaves from Baltic amber. Proc. Natl. Acad. Sci. U. S. A. 112, 190–195 (2015).
Google Scholar
Xing, L. et al. A feathered dinosaur tail with primitive plumage trapped in mid-Cretaceous amber. Curr. Biol. 26, 3352–3360 (2016).
Google Scholar
Rikkinen, J., Grimaldi, D. A. & Schmidt, A. R. Morphological stasis in the first myxomycete from the Mesozoic, and the likely role of cryptobiosis. Sci. Rep. 9, 19730 (2019).
Google Scholar
Peñalver, E. et al. Thrips pollination of Mesozoic gymnosperms. Proc. Natl. Acad. Sci. U. S. A. 109, 8623–8628 (2012).
Google Scholar
Cai, C. et al. Beetle pollination of cycads in the mesozoic. Curr. Biol. 28, 2806-2812.e1 (2018).
Google Scholar
Bao, T., Wang, B., Li, J. & Dilcher, D. Pollination of Cretaceous flowers. Proc. Natl. Acad. Sci. U. S. A. 116, 24707–24711 (2019).
Google Scholar
Labandeira, C. Amber. Paleont. Soc. Pap. 20, 163–215 (2014).
Google Scholar
Solórzano-Kraemer, M. M. et al. A revised definition for copal and its significance for palaeontological and Anthropocene biodiversity-loss studies. Sci. Rep. 10, 19904 (2020).
Google Scholar
Clifford, D. J. & Hatcher, P. G. Structural transformations of polylabdanoid resinites during maturation. Org. Geochem. 23, 407–418 (1995).
Google Scholar
Lambert, J. B., Santiago-Blay, J. A., Wu, Y. & Levy, A. J. Examination of amber and 490 related materials by NMR spectroscopy. Magn. Reson. Chem. 53, 2–8 (2015).
Google Scholar
Stankiewicz, B. A. et al. Chemical preservation of plants and insects in natural resins. Proc. Biol. Sci. 265, 641–647 (1998).
Google Scholar
McCoy, V. E. et al. Ancient amino acids from fossil feathers in amber. Sci. Rep. 9, 6420 (2019).
Google Scholar
Bada, J. L. et al. Amino acid racemization in amber-entombed insects: implications for DNA preservation. Geochim. Cosmochim. Acta. 58, 3131–3135 (1994).
Google Scholar
Collins, M. J. et al. Is amino acid racemization a useful tool for screening for ancient DNA in bone?. Proc. R. Soc. B 276, 2971–2977 (2009).
Google Scholar
Allentoft, M. E. et al. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc. R. Soc. B 279, 4724–4733 (2012).
Google Scholar
Kistler, L. et al. A new model for ancient DNA decay based on paleogenomic meta-analysis. Nucleic Acids Res. 45, 6310–6320 (2017).
Google Scholar
DeSalle, R., Barcia, M. & Wray, C. PCR jumping in clones of 30-million-year-old DNA fragments from amber preserved termites (Mastotermes electrodominicus). Experientia 49, 906–909 (1993).
Google Scholar
Poinar, G. O., Poinar, H. N. & Cano, R. J. DNA from amber inclusions. In Ancient DNA (eds Herrmann, B. & Hummel, S.) 92–103 (Springer, 1994).
Austin, J. J. et al. Problems of reproducibility: does geologically ancient DNA survive in amber-preserved insects?. Proc. Roy. Soc. Lond. Ser. B 264, 467–474 (1997).
Google Scholar
Penney, D. et al. Absence of ancient DNA in sub-fossil insect inclusions preserved in ‘Anthropocene’ Colombian copal. PLoS ONE 8, e73150 (2013).
Google Scholar
Peris, D. et al. DNA from resin-embedded organisms: past, present and future. PLoS ONE 15, e0239521 (2020).
Google Scholar
Reich, D. et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468, 1053–1060 (2010).
Google Scholar
Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012).
Google Scholar
Prüfer, K. et al. The complete genome sequence of a Neandertal from the Altai Mountains. Nature 505, 43–49 (2014).
Google Scholar
Prüfer, K. et al. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 358, 655–658 (2017).
Google Scholar
Meyer, M. et al. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature 531, 504–507 (2016).
Google Scholar
Gilbert, M. T., Bandelt, H. J., Hofreiter, M. & Barnes, I. Assessing ancient DNA studies. Trends Ecol. Evol. 20, 541–544 (2005).
Google Scholar
Willerslev, E. & Cooper, A. Ancient DNA. Proc. Biol. Sci. 272, 3–16 (2005).
Google Scholar
Penney, D., Wadsworth, C. & Green, D. I. Extraction of inclusions from (sub)fossil resins, with description of a new species of stingless bee (Hymenoptera: Apidae: Meliponini), in quaternary Colombian copal. Paleontol. Contrib. 2013, 7:1–6 (2013).
Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 6, pdb.prot5448 (2010).
Google Scholar
Modi, A. et al. Complete mitochondrial sequences from Mesolithic Sardinia. Sci. Rep. 7, 42869 (2017).
Google Scholar
Peltzer, A. et al. EAGER: efficient ancient genome reconstruction. Genome Biol. 17, 60 (2016).
Google Scholar
Andrews, S. FastQC: a quality control tool for high throughput sequence data (2010). Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Google Scholar
Schubert, M. et al. Improving ancient DNA read mapping against modern reference genomes. BMC Genomics 13, 178 (2012).
Google Scholar
Li, H. et al. The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Google Scholar
Altschul, S. et al. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).
Google Scholar
Jackman, S. D. et al. ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter. Genome Res. 27, 768–777 (2017).
Google Scholar
Huson, D. H. et al. MEGAN community edition: interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput. Biol. 12, e1004957 (2016).
Google Scholar
Hofreiter, M., Jaenicke, V., Serre, D., Haeseler, A. & Pääbo, S. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res. 9, 4793–4799 (2011).
Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl. Acad. Sci. U. S. A. 104, 14616–14621 (2007).
Google Scholar
Sawyer, S., Krause, J., Guschanski, K., Savolainen, V. & Pääbo, S. Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLoS ONE 7, e34131 (2012).
Google Scholar
Jonsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. & Orlando, L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).
Google Scholar
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).
Google Scholar
Kumar, S. et al. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).
Google Scholar
Noonan, J. P. et al. Genomic sequencing of pleistocene cave bears. Science 309, 597–599 (2005).
Google Scholar
Green, R. E. et al. Analysis of one million base pairs of Neanderthal DNA. Nature 444, 330–336 (2006).
Google Scholar
Garcia-Garcera, M. et al. Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics. PLoS ONE 6, e24161 (2011).
Google Scholar
Llamas, B. et al. From the field to the laboratory: Controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era. STAR 3, 1–14 (2017).
Google Scholar
Wintertona, S. L., Brian, M. W. & Evert, I. S. Phylogeny and Bayesian divergence time estimations of small-headed Xies (Diptera: Acroceridae) using multiple molecular markers. Mol. Phylogenet. Evol. 43, 808–832 (2007).
Google Scholar
Gillung, J. P. & Wintertona, S. L. Evolution of fossil and living spider flies based onmorphological and molecular data (Diptera, Acroceridae). Syst. Entomol. 44, 820–841 (2019).
Google Scholar
Klasson, L. et al. The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans. Proc. Natl. Acad. Sci. U. S. A. 106, 5725–5730 (2009).
Google Scholar
Daley, T. & Smith, A. D. Predicting the molecular complexity of sequencing libraries. Nat. Methods 10, 325–327 (2013).
Google Scholar
Source: Ecology - nature.com
