Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations

BackgroundPopulation demography and gene flow among African groups, as well as the putative archaic introgression of ancient hominins, have been poorly explored at the genome level.ResultsHere, we examine 15 African populations covering all major continental linguistic groups, ecosystems, and lifestyles within Africa through analysis of whole-genome sequence data of 21 individuals sequenced at deep coverage. We observe a remarkable correlation among genetic diversity and geographic distance, with the hunter-gatherer groups being more genetically differentiated and having larger effective population sizes throughout most modern-human history. Admixture signals are found between neighbor populations from both hunter-gatherer and agriculturalists groups, whereas North African individuals are closely related to Eurasian populations. Regarding archaic gene flow, we test six complex demographic models that consider recent admixture as well as archaic introgression. We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (similar to 4.0% in Khoisan, similar to 4.3% in Mbuti Pygmies, and similar to 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage.ConclusionThe present study represents an in-depth genomic analysis of a Pan African set of individuals, which emphasizes their complex relationships and demographic history at population level.Peer reviewe

SISALv2: A comprehensive speleothem isotope database with multiple age-depth models

Characterizing the temporal uncertainty in palaeoclimate records is crucial for analysing past climate change, correlating climate events between records, assessing climate periodicities, identifying potential triggers and evaluating climate model simulations. The first global compilation of speleothem isotope records by the SISAL (Speleothem Isotope Synthesis and Analysis) working group showed that age model uncertainties are not systematically reported in the published literature, and these are only available for a limited number of records (ca. 15 %, n = 107=691). To improve the usefulness of the SISAL database, we have (i) improved the database's spatiooral coverage and (ii) created new chronologies using seven different approaches for age depth modelling. We have applied these alternative chronologies to the records from the first version of the SISAL database (SISALv1) and to new records compiled since the release of SISALv1. This paper documents the necessary changes in the structure of the SISAL database to accommodate the inclusion of the new age models and their uncertainties as well as the expansion of the database to include new records and the qualitycontrol measures applied. This paper also documents the age depth model approaches used to calculate the new chronologies. The updated version of the SISAL database (SISALv2) contains isotopic data from 691 speleothem records from 294 cave sites and new age depth models, including age depth temporal uncertainties for 512 speleothems. SISALv2 is available at https://doi.org/10.17864/1947.256 (Comas-Bru et al., 2020a). © 2020 Author(s)

The Iso2k Database: A global compilation of paleo-δ18O and δ2H records to aid understanding of Common Era climate

Reconstructions of global hydroclimate during the Common Era (CE; the past ~ 2000 years) are important for providing context for current and future global environmental change. Stable isotope ratios in water are quantitative indicators of hydroclimate on regional to global scales, and these signals are encoded in a wide range of natural geologic archives. Here we present the Iso2k database, a global compilation of previously published datasets from a variety of natural archives that record the stable oxygen (δ18O) or hydrogen (δ2H) isotopic composition of environmental waters, which reflect hydroclimate changes over the CE. The Iso2k database contains 756 isotope records from the terrestrial and marine realms, including: glacier and ground ice (205); speleothems (68); corals, sclerosponges, and mollusks (145); wood (81); lake sediments and other terrestrial sediments (e.g., loess) (158); and marine sediments (99). Individual datasets have temporal resolutions ranging from sub-annual to centennial, and include chronological data where available. A fundamental feature of the database is its comprehensive metadata, which will assist both experts and non-experts in the interpretation of each record and in data synthesis. Key metadata fields have standardized vocabularies to facilitate comparisons across diverse archives and with climate model simulated fields. This is the first global-scale collection of water isotope proxy records from multiple types of geological and biological archives. It is suitable for evaluating hydroclimate processes through time and space using large-scale synthesis, model-data intercomparison and (paleo)data assimilation. The Iso2k database is available for download at: https://doi.org/10.6084/m9.figshare.11553162 (McKay and Konecky, 2020)

The time scale of recombination rate evolution in great apes

We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history. Nature 499:471-475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths. We show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time scale of complete hotspot turnover. Further, using species-specific PRDM9 sequences to predict potential binding sites (PBS), we show higher predicted PRDM9 binding in recombination hotspots as compared to matched cold spot regions in multiple great ape species, including at least one chimpanzee subspecies. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10-15Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, on the basis of multiple linear regression analysis, we found that various correlates of recombination rate persist throughout the African great apes including repeats, diversity, and divergence. Our study is the first to analyze within- And between-species genome-wide recombination rate variation in several close relatives

The Iso2k database: a global compilation of paleo-δ18O and δ2H records to aid understanding of common era climate

Reconstructions of global hydroclimate during the Common Era (CE; the past ~2,000 years) are important for providing context for current and future global environmental change. Stable isotope ratios in water are quantitative indicators of hydroclimate on regional to global scales, and these signals are encoded in a wide range of natural geologic archives. Here we present the Iso2k database, a global compilation of previously published datasets from a variety of natural archives that record the stable oxygen (δ18O) or hydrogen (δ²H) isotopic composition of environmental waters, which reflect hydroclimate changes over the CE. The Iso2k database contains 756 isotope records from the terrestrial and marine realms, including: glacier and ground ice (205); speleothems (68); corals, sclerosponges, and mollusks (145); wood (81); lake sediments and other terrestrial sediments (e.g., loess) (158); and marine sediments (99). Individual datasets have temporal resolutions ranging from sub-annual to centennial, and include chronological data where available. A fundamental feature of the database is its comprehensive metadata, which will assist both experts and non-experts in the interpretation of each record and in data synthesis. Key metadata fields have standardized vocabularies to facilitate comparisons across diverse archives and with climate model simulated fields. This is the first global-scale collection of water isotope proxy records from multiple types of geological and biological archives. It is suitable for evaluating hydroclimate processes through time and space using large-scale synthesis, model-data intercomparison and (paleo)data assimilation. The Iso2k database is available for download at: https://doi.org/10.25921/57j8-vs18 (Konecky and McKay, 2020) and is also accessible via through the NOAA/WDS Paleo Data landing page: https://www.ncdc.noaa.gov/paleo/study/29593