In parallel with WCAG 2.1, the Accessibility Guidelines Working Group is developing another major version of accessibility guidelines. The result of this work is expected to be a more substantial restructuring of web accessibility guidance than would be realistic for dot-releases of WCAG 2. The work follows a research-focused, user-centered design methodology to produce the most effective and flexible outcome, including the roles of content authoring, user agent support, and authoring tool support. This is a multi-year effort, so WCAG 2.1 is needed as an interim measure to provide updated web accessibility guidance to reflect changes on the web since the publication of WCAG 2.0. The Working Group might also develop additional interim versions, continuing with WCAG 2.2, on a similar short timeline to provide additional support while the major version is completed.
On the nuclear level we merged the SNP data of our three ancient individuals with 2,367 modern individuals34,35 and 294 ancient genomes36 and performed PCA on the joined data set. We found the ancient Egyptian samples falling distinct from modern Egyptians, and closer towards Near Eastern and European samples (Fig. 4a, Supplementary Fig. 3, Supplementary Table 5). In contrast, modern Egyptians are shifted towards sub-Saharan African populations. Model-based clustering using ADMIXTURE37 (Fig. 4b, Supplementary Fig. 4) further supports these results and reveals that the three ancient Egyptians differ from modern Egyptians by a relatively larger Near Eastern genetic component, in particular a component found in Neolithic Levantine ancient individuals36 (Fig. 4b). In contrast, a substantially larger sub-Saharan African component, found primarily in West-African Yoruba, is seen in modern Egyptians compared to the ancient samples. In both PCA and ADMIXTURE analyses, we did not find significant differences between the three ancient samples, despite two of them having nuclear contamination estimates over 5%, which indicates no larger impact of modern DNA contamination. We used outgroup f3-statistics38 (Fig. 5a,b) for the ancient and modern Egyptians to measure shared genetic drift with other ancient and modern populations, using Mbuti as outgroup. We find that ancient Egyptians are most closely related to Neolithic and Bronze Age samples in the Levant, as well as to Neolithic Anatolian and European populations (Fig. 5a,b). When comparing this pattern with modern Egyptians, we find that the ancient Egyptians are more closely related to all modern and ancient European populations that we tested (Fig. 5b), likely due to the additional African component in the modern population observed above. By computing f3-statistics38, we determined whether modern Egyptians could be modelled as a mixture of ancient Egyptian and other populations. Our results point towards sub-Saharan African populations as the missing component (Fig. 5c), confirming the results of the ADMIXTURE analysis. We replicated the results based on f3-statistics using only the least contaminated sample (with
(a) Principal Component Analysis-based genome-wide SNP data of three ancient Egyptians, 2,367 modern individuals and 294 previously published ancient genomes, (b) subset of the full ADMIXTURE analysis (Supplementary Fig. 4).
The resulting FastQ files have been processed using EAGER v1.92 (ref. 57). To achieve improved coverages at both ends of the mitochondrial reference, we used the CircularMapper option in EAGER. All reads with a mapping quality of at least 30 were kept for the subsequent analysis. Duplicate reads have been removed using DeDup v0.9.10, included in the EAGER pipeline. The coverage and statistics calculation has been performed inside the EAGER pipeline and indels have been realigned using RealignerTargetCreator and IndelRealigner from the GATK58. Mitochondrial haplogroups have been determined using HaploGrep 2 (ref. 59). Further details of the analysis parameters can be found in Supplementary Note 3. As can be seen in Supplementary Data 1, we achieved coverages ranging from 11-fold up to 4284-fold on the mitochondrial genome, with an average of 408-fold.
We used the ADMIXTURE software on the merged data set to cluster ancestry proportions using different numbers of clusters37. The lowest cross-validation error was obtained using K=16 and we show the results of that run in Supplementary Fig. 4. A subset is shown in Fig. 4b.
The genetic distances were calculated in Arlequin v18.104.22.168 using the Tamura and Nei substitution model and a gamma shape value of 0.26, determined to be the best setting for the data using jModelTest v2.1.10. We selected the best parameters suggested by the Akaike and Bayesian information criterion (AIC and BIC).
The replication crisis is an ongoing methodological crisis that affects parts of the social and life sciences. In subsequent investigations, the results of many scientific studies are proven to be unrepeatable. The crisis has long-standing roots; the phrase was coined in the early 2010s as part of a growing awareness of the problem. The replication crisis represents an important body of research in metascience, which aims to improve the quality of all scientific research while reducing waste. 2b1af7f3a8