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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | a154fb2 | Lily Heald | 2026-03-26 | wflow_publish("analysis/introduction.Rmd") |
| html | 9264fbc | Lily Heald | 2026-03-26 | Build site. |
| Rmd | 1d15761 | Lily Heald | 2026-03-26 | wflow_publish("analysis/introduction.Rmd") |
| html | ce1571b | Lily Heald | 2026-03-26 | Build site. |
| html | a008c4f | Lily Heald | 2026-03-26 | Build site. |
| Rmd | 05c4750 | Lily Heald | 2026-03-26 | stack snp distribution |
| html | 05c4750 | Lily Heald | 2026-03-26 | stack snp distribution |
| Rmd | a476f32 | Lily Heald | 2026-02-10 | Update introduction |
| html | a476f32 | Lily Heald | 2026-02-10 | Update introduction |
| html | 189b205 | Lily Heald | 2026-02-10 | Update introduction |
| Rmd | 6165154 | Lily Heald | 2026-02-10 | Update introduction |
| Rmd | c555bc3 | Lily Heald | 2026-02-10 | Clean bar chart |
| html | c555bc3 | Lily Heald | 2026-02-10 | Clean bar chart |
| html | 5cd4031 | Lily Heald | 2026-02-09 | Update introduction |
| Rmd | 4ea9339 | Lily Heald | 2026-02-09 | Update introduction |
| Rmd | 441e6fe | Lily Heald | 2026-02-09 | echo false for clean workflowr |
| html | 441e6fe | Lily Heald | 2026-02-09 | echo false for clean workflowr |
| Rmd | 790813f | Lily Heald | 2026-02-09 | add distribution of simons genomes |
| html | 790813f | Lily Heald | 2026-02-09 | add distribution of simons genomes |
| Rmd | 4a52a41 | Lily Heald | 2026-02-04 | Add distribution bar chart |
| html | 4a52a41 | Lily Heald | 2026-02-04 | Add distribution bar chart |
| Rmd | 289d9ed | Lily Heald | 2026-01-30 | add den3 |
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| Rmd | fe99e78 | Lily Heald | 2026-01-14 | add Denisova 25 |
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| Rmd | 7bb18d4 | Lily Heald | 2025-11-20 | update sample names |
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| Rmd | 9209569 | Lily Heald | 2025-11-20 | add altai neanderthal |
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| Rmd | 50940c0 | Lily Heald | 2025-11-07 | Update introduction.Rmd |
| Rmd | f1b70cb | Lily Heald | 2025-11-07 | add Hstadel depth |
| Rmd | 7beeddd | Lily Heald | 2025-11-07 | add depth figure |
| Rmd | 967f438 | Lily Heald | 2025-11-07 | update callout |
| html | 967f438 | Lily Heald | 2025-11-07 | update callout |
| html | cc7d134 | Lily Heald | 2025-11-06 | updated figures |
| Rmd | b2f5585 | Lily Heald | 2025-11-06 | Update introduction.Rmd |
| html | 13755f1 | Lily Heald | 2025-11-06 | workflowr |
| Rmd | 46a0913 | Lily Heald | 2025-11-06 | start workflowr |
Ancient genome availability
DNA can persist for up to hundreds of thousands of years in skeletal remains, and can even be extracted from sediments. However, extracting such DNA poses a challenge. Ancient DNA is typically present in very small amounts, is highly fragmented, and contaminated with other endogenous organic molecules which inhibit enzymatic DNA manipulations which must be performed prior to sequencing, or exogenous DNA. There are high-quality genomic sequences available for two Denisovans and three Neanderthals. There are also low coverage sequences available from 14 Neanderthals, spanning spatially from Gibraltar to Siberia and temporally from 39 to 120ka. A total of eleven archaic genomic samples will be analysed in this study, including all five high coverage genomes.
Modern reference genomes
Modern human genomes were obtained from the Simons Genome Diversity Project (SGDP). A panel of 15 individuals representing broad global diversity (Africa, Europe, East Asia, Central Asia, and Oceania) to provide a stable reference frame for principal component analysis (PCA). Variant call files (VCFs) were downloaded as whole-genome SNP datasets aligned to the GRCh37/hg19 reference genome.
Distribution of pigmentation SNPs
In order to allow for comparison of genome-wide ancestry patterns with structure driven by a targeted functional SNP set. For pigmentation-specific analyses, a panel consisting of 395 SNPs previously associated with pigmentation phenotypes published on the NHGRI-EBI Catalog of human genome-wide association studies was used. The by-chromosome distribution of these SNPs is shown below.
sessionInfo()R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS 26.3.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Detroit
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
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[4] sysfonts_0.8.9 reshape2_1.4.5 lubridate_1.9.4
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[10] purrr_1.2.1 readr_2.1.6 tidyr_1.3.2
[13] tibble_3.3.1 tidyverse_2.0.0 ggrepel_0.9.6
[16] viridis_0.6.5 viridisLite_0.4.2 ggspatial_1.1.10
[19] raster_3.6-32 sp_2.2-0 sf_1.0-24
[22] rnaturalearthdata_1.0.0 rnaturalearth_1.2.0 ggplot2_4.0.2
[25] workflowr_1.7.2
loaded via a namespace (and not attached):
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[29] cli_3.6.5 rmarkdown_2.30 generics_0.1.4 otel_0.2.0
[33] rstudioapi_0.18.0 httr_1.4.7 tzdb_0.5.0 DBI_1.2.3
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[53] R6_2.6.1 rprojroot_2.1.1 evaluate_1.0.5 lattice_0.22-7
[57] httpuv_1.6.16 bslib_0.10.0 class_7.3-23 Rcpp_1.1.1
[61] gridExtra_2.3 whisker_0.4.1 xfun_0.56 fs_1.6.6
[65] getPass_0.2-4 pkgconfig_2.0.3