HUMAN PALAEOGENOMICS EVA CHOCHOLOVÁ LABORATORY OF BIOLOGICAL AND MOLECULAR ANTHROPOLOGY DEPARTMENT OF EXPERIMENTAL BIOLOGY QUIZ 1. Why is HTS better for aDNA, considering fragment length? Most fragments ~ 30-70 bp, cannot be targeted by PCR based methods. 2. What is the endogenous aDNA proportion in extracted samples? Varies greatly!! Authors usually describe about 5 %. 3. What is important when choosing a marker for metabarcoding? + length! 4. What is the difference between single- and double-stranded library prep? QUIZ 5. What is enrichment and when to use it? 6. What is the PCR amplification bias and why does it matter? Is there a way to prevent it? HUMAN PALAEOGENOMICS ?Group 1 Reasons for including scientists from studied populations/regions Group 2 Reasons against including scientists from studied populations/regions (or challenges) ARCHAEOLOGICAL SOURCES as discussed in Gokhman et al., 2017 EpigenomicsGenomicsArtefacts Gokhman et al., 2017; DOI: 10.1093/molbev/msx211 Preservation Interpretation Current populations Differences Change over long time Environmentally responsive, plastic = + many more that were not discussed in detail, such as anthropology, proteomics, isotope analysis, palaeozoology, palaeobotany…Mitchell and Rawlence., 2021; DOI: 10.1016/j.tree.2020.10.005 Gokhman et al., 2017; DOI: 10.1093/molbev/msx211 ANCIENT HUMAN GENOMES Settlements and environmentArtefactsHuman tissues ANCIENT HUMAN GENOMES Human tissues ANCIENT HUMAN GENOMES Artefacts ANCIENT HUMAN GENOMES Settlements and environment https://www.nobelprize.org/prizes/medicine/2022/summary/ ANCIENT HUMAN GENOMES https://www.nobelprize.org/prizes/medicine/2022/summary/ ANCIENT HUMAN GENOMES • Two copies • Long • Recombining • Inherited from both parents • Great amount of information • More copies per cell • Shorter, circular • Generally without recombination • Maternal • Limited insight https://evolution.berkeley.edu/evo-news/making-sense-of-ancient-hominin-dna/ Mallick et al., 2024; DOI: 10.1038/s41597-024-03031-7 HUMAN EVOLUTION 430,000 years ago Pollen et al., 2023; DOI: 10.1038/s41576-022-00568-4 HUMAN EVOLUTION NEANDERTHAL AND DENISOVAN DNA https://www.nobelprize.org/prizes/medicine/2022/summary/ https://www.nobelprize.org/prizes/medicine/2022/summary/ NEANDERTHAL AND DENISOVAN DNA Reilly et al., 2022; DOI: 10.1016/j.cub.2022.08.027 Reilly et al., 2022; DOI: 10.1016/j.cub.2022.08.027 Reilly et al., 2022; DOI: 10.1016/j.cub.2022.08.027 NEANDERTHAL AND DENISOVAN DNA Eastern Neanderthal group spread west about 120,000 years ago Slon et al., 2018; DOI: 10.1038/s41586-018-0455-x Reilly et al., 2022; DOI: 10.1016/j.cub.2022.08.027 • Introgression deserts – regions depleted of certain ancestry (Neanderthal in this case) compared to expected patterns without natural selection NEANDERTHAL AND DENISOVAN DNA  FOXP2 – speech and language  Genes expressed in brain and testes  More gene regulation compared to protein structure  Skin and pigmentation (BNC2, POU2F2, HYAL2, OCA2, KRT71, KRT80)  Metabolism (SLC16A11, TSHR, TBC1D1) – lipids and energy regulation!  Immunity (OAS, TLR1/6/10)  EPAS1 from Denisovans – high altitude adaptation in Tibetans Reilly et al., 2022; DOI: 10.1016/j.cub.2022.08.027 MIGRATION AND CONTACT • Mitochondrial Eve https://biologos.org/series/evolution-basics/articles/mitochondrial-eve-and-y-chromosome-adam MIGRATION AND CONTACT • Y-chromosome Adam https://biologos.org/series/evolution-basics/articles/mitochondrial-eve-and-y-chromosome-adam MIGRATION AND CONTACT • Autosomes https://biologos.org/series/evolution-basics/articles/mitochondrial-eve-and-y-chromosome-adam MIGRATION AND CONTACT • Kinship Vai et al., 2020; DOI: 10.3389/fevo.2020.00083 MIGRATION AND CONTACT IBD • Kinship IBD = identical by decent (inherited from the same ancestor) IBS = identical by state MIGRATION AND CONTACT Wallacea - Island originally between Sunda Shelf and Pleistocene Sahul Carlhoff et al., 2021; DOI: 10.1038/s41586-021-03823-6 Carlhoff et al., 2021; DOI: 10.1038/s41586-021-03823-6 MIGRATION AND CONTACT Skoglund et al., 2016; DOI: 10.1038/nature19844 Skoglund et al., 2016; DOI: 10.1038/nature19844 MIGRATION AND CONTACT Gallego Llorente et al., 2015; DOI: 10.1126/science.aad2879 DISEASE-RELATED CHANGES Kerner et al., 2023; DOI: 10.1038/s41591-023-02244-4 HISTORICAL FIGURES • G. J. Mendel • L. van Beethoven • Tatanka Iyotake HISTORICAL FIGURES HISTORICAL FIGURES ! • Introgression deserts • Birch Pitch • Universal Bias • Tissues connected to archaeological sources • Cultural adaptations • When to use sedaDNA