Найден в донных отложениях небольшой речки в Коченёвском районе Новосибирской области. После того, как фрагмент черепа (это лобная кость с верхней частью глазниц) высох, стало понятно, что по сохранности это, скорее всего, плейстоцен. Пока что отдал фрагмент антропологам, они снимут с него всю возможную информацию. Предварительные результаты такие: это, конечно, сапиенс, но с рядом архаичных признаков, предположительно женщина около 20-25 лет.

Upd.1: Данную находку отсеквенировали в Лейпциге, в институте Макса Планка. Скорее всего она голоценовая. Гаплотип, к которому принадлежит этот человек, появился только в голоценовое время. Поэтому не стали делать прямую дату.

Upd.2: В конце мая приезжал Бенц Виола, непосредственно принимавший участие в ее изучении,но, к сожалению, никакой новой информации он не привёз, кроме того что череп этот по гаплотипу – голоценовый. Должен выслать позже распечатку результатов исследования этой черепной крышки.

Upd.3: Генетики не сдаются - последние их исследования поставили более конкретную дату. Да, это голоцен. И более конкретно - раннее средневековье. Приблизительно 6 век н.э.

Upd.4: Только сейчас удалось немного прояснить ситуацию в отношении фрагмента черепа с Чика. Из него в институте Макса Планка в Лейпциге была выделена митохондриальная ДНК. Она показала, что находка, несомненно, голоценовая. Данный гаплотип появился только в голоцене. Прямую дату по кости пока не делали.Находку будут исследовать и в дальнейшем (поскольку их интересует, по-видимому, не только плейстоценовый человек, но и голоценовый, тем более с территории Сибири), но на настоящий момент она не является приоритетной – поняли что голоцен, и отложили пока что в сторонку.

Итак, сам отчет об изучении черепной крышки:

Ancient DNA and radiocarbon dating of a hominin skull from the Chik River (Russia)
Dpt. of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
Viviane Slon, July 2017

1. Materials and methods
1.1. Materials
We analyzed a hominin skull cap (SP4659 in our database) discovered in the Chik riverbed, the Ob basin (Kochenevo Region, Novosibirsk Province, Russia), 300m downstream from the railway bridge and 15-20m downstream from the footbridge. Prior to sampling, the skull fragment was µCT-scanned by the Human Evolution Dept. at MPI-EVA.

1.2. DNA extraction and library preparation
Following the removal of surface material, a sample of 41.6mg was removed from the specimen using a sterile dentistry drill. DNA was extracted using a silica-based method targeted at the retrieval of short DNA molecules (Dabney et al., 2013). An aliquot of the extract (E4661) was converted into a single-stranded DNA library (D6922) (Gansauge et al., 2017), and barcoded with a pair of unique indexes (Kircher et al., 2012).

1.3. Mitochondrial capture
The indexed DNA library (D6970) was enriched for mitochondrial DNA (mtDNA) sequences with probes covering the full human mitochondrial genome (Maricic et al., 2010; Fu et al., 2013).

1.4. Sequencing and raw sequence processing
The captured library (D4397) was pooled with other libraries originating from other projects and sequenced on a MiSeq platform (Illumina). Furthermore, an aliquot of the DNA library, which had not been captured for mitochondrial sequences, underwent shotgun sequencing.

1.5 Mapping to a reference genome
Sequences were aligned to the human reference genome using parameters adapted to ancient DNA (Meyer et al., 2012). For nuclear sequences, sequences shorter than 35 bases and with a mapping quality lower than 30 were discarded to avoid spurious alignments to the reference genome. Mitochondrial sequences were retained for further analyses only if they were longer than 30 bases.

1.6 Sampling for radiocarbon dating and isotope analysis
Following the removal of surface material from a different area of the skull, a sample of 506.9mg was removed from the specimen and sent to the Oxford Radiocarbon Accelerator Unit (ORAU) for radiocarbon dating and isotope analysis.

2. Results
2.1. DNA library from the Chik River specimen
The number of DNA molecules recovered from the Chik River specimen was 6.83x109, which was higher than extraction and library preparation negative controls, indicating a successful preparation of the sample for sequencing.
For the shotgun data, 41.4 million reads were generated, out of which 0.27% could be mapped to the human nuclear genome. After enrichment for mitochondrial sequences, 47,161 unique mtDNA sequences were generated. Molecules were seen multiple times (average duplication rate of 5.6), indicating an adequate sequencing depth.

2.2. Ancient DNA authenticity
The ends of ancient DNA molecules tend to carry uracils (U), which arise over time through deamination of cytosines (C) (Briggs et al., 2007) and are read by DNA polymerases as thymines (T). Thus, the presence of ancient DNA in a sample can be evaluated based on the frequency of C to T substitutions at the 5’ and 3’ ends of the sequences (Krause et al., 2010). 19.2% and 10.7% of Cs at the end of the mtDNA fragments (5’ and 3’ end, respectively) appeared as Ts. This suggests that the DNA library contains molecules of ancient origin.

2.3 Phylogenetic analysis
We aimed to determine whether the endogenous mtDNA of the Chik River specimen is most closely related to modern human, Neandertal or Denisovan mitochondrial genomes. In order to mitigate the influence of putative contamination by present-day human DNA, we restricted the analysis to sequences carrying an apparent C to T substitution at one of their ends (Meyer et al., 2014). Using 3,455 such sequences, the mitochondrial sequence of the Chik River specimen was partially reconstructed. The average mtDNA coverage was 9.6-fold, and 2,637 positions could not be confidently called.
This partial mtDNA sequence was aligned to the mtDNAs of ten present-day humans, ten ancient modern humans, ten Neandertals, four Denisovans, a hominin from Sima de los Huesos (Spain) and a chimpanzee (Pan troglodytes). The Chik River mitochondrial genome falls within the variation of modern humans (Fig. 1).

Fig.1

Figure 1. Neighbor-joining tree relating the partial mtDNA sequence of the Chik River specimen (in red) to other ancient and present-day mtDNAs. This analysis shows that the Chik River mtDNA sequence falls within modern human variation. Ancient specimens are noted in italics. Support for each branch is based on 500 bootstrap replications. The phylogenetic tree was produced in MEGA6 (Tamura et al., 2013), using a chimpanzee mtDNA as an outgroup.

2.4 Sex determination
We determined the sex of the Chik River specimen by comparing the number of putatively deaminated sequences mapping to the X chromosome to the average number of such sequences mapping to the autosomes. The coverage of the X chromosome is half the coverage of the autosomes (ratio of 0.5), indicating that the Chik River specimen was a male.

2.5 Radiocarbon dating and isotope analysis
Radiocarbon dating and isotope analysis were carried out at the Oxford Radiocarbon Accelerator Unit (ORAU). The Chik River specimen (OxA-35789) was dated to 1524±24 uncal. BP. The sample displayed d15N = +14.1 ‰ which suggests a possible aquatic dietary component and associated radiocarbon reservoir effects.

3. Conclusions
The extraction and sequencing of DNA from the Chik River specimen were technically successful. In concurrence with the radiocarbon dating, we find that this individual carried a mitochondrial genome of the modern human type.
4. References
Briggs, A.W., Stenzel, U., Johnson, P.L.F., Green, R.E., Kelso, J., Prüfer, K., Meyer, M., Krause, J., Ronan, M.T., Lachmann, M., Pääbo, S., 2007. Patterns of damage in genomic DNA sequences from a Neandertal. Proceedings of the National Academy of Sciences of the United States of America 104(37), 14616-14621.
Dabney, J., Knapp, M., Glocke, I., Gansauge, M.-T., Weihmann, A., Nickel, B., Valdiosera, C., García, N., Pääbo, S., Arsuaga, J.-L., Meyer, M., 2013. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proceedings of the National Academy of Sciences of the United States of America 110(39), 15758-15763.
Fu, Q., Meyer, M., Gao, X., Stenzel, U., Burbano, H.A., Kelso, J., Pääbo, S., 2013. DNA analysis of an early modern human from Tianyuan Cave, China. Proceedings of the National Academy of Sciences of the United States of America 110(6), 2223-2227.
Gansauge, M.T., Gerber, T., Glocke, I., Korlevic, P., Lippik, L., Nagel, S., Riehl, L.M., Schmidt, A., Meyer, M., 2017. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Research 45(10):e79.
Kircher, M., Sawyer, S., Meyer, M., 2012. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Research 40(1), e3.
Krause, J., Briggs, A.W., Kircher, M., Maricic, T., Zwyns, N., Derevianko, A., Pääbo, S., 2010. A complete mtDNA genome of an early modern human from Kostenki, Russia. Current Biology 20(3), 231-236.
Maricic, T., Whitten, M., Pääbo, S., 2010. Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products. PLoS ONE 5(11), e14004.
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J.G., Jay, F., Prüfer, K., de Filippo, C., Sudmant, P.H., Alkan, C., Fu, Q., Do, R., Rohland, N., Tandon, A., Siebauer, M., Green, R.E., Bryc, K., Briggs, A.W., Stenzel, U., Dabney, J., Shendure, J., Kitzman, J., Hammer, M.F., Shunkov, M.V., Derevianko, A.P., Patterson, N., Andrés, A.M., Eichler, E.E., Slatkin, M., Reich, D., Kelso, J., Pääbo, S., 2012., A high-coverage genome sequence from an archaic Denisovan individual. Science 338(6104), 222-6.
Meyer, M., Fu, Q., Aximu-Petri, A., Glocke, I., Nickel, B., Arsuaga, J.-L., Martínez, I., Gracia, A., Bermúdez de Castro, J.M., Carbonell, E., Pääbo, S., 2014. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505(7483), 403-406.
Tamura, K., Stecher, G., Peterson, D., Filipski, A., Kumar, S., 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution 30, 2725-2729.


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Ключевые слова (тэги): Homo, голоцен, sapiens