Post by djoser-xyyman on Apr 6, 2019 14:23:52 GMT -5
Gene flow from North Africa contributes to differential human genetic diversity in southern Europe
Laura R. Botigué
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Quotes:
“Multiple models have been proposed to explain clinal gradients of human genetic diversity in Europe including directional migration, climate, natural selection, and isolation by distance (1–4). A particular pattern of interest is the higher level of genetic diversity in southern European populations compared with those in northern latitudes. Three main hypotheses have been proposed to explain this phenomenon. Under the first hypothesis, populations retreated to glacial refugia in southern Europe about 20,000 y ago (ya), but when these populations later recolonized the continent, only a subset of the genetic diversity was carried into northern regions (5). The second hypothesis is that gene flow from the Near East, associated with the demic diffusion of agriculture, differentially affected geographic regions and in particular introduced additional genetic diversity to southeastern Europe (6, 7). The third hypothesis suggests that increased genetic diversity is the result of migrations from the African continent into southern Europe (8, 9). These hypotheses are not mutually exclusive; however, we focus on testing a hypothesis of gene flow from Africa to Europe, which has ***received the LEAST AMOUNT OF ATTENTION ***and may be the easiest to detect due to the recent time frame of the proposed demographic event.
However, strong similarities in pottery production are also found between southern Iberia and Northwest Africa 7,500 ya. The existence of “maritime pioneers” in the Mediterranean Sea during this period has been hypothesized (21).”
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oH! The quotes aren’t mine. HA! HA! HA! hA! Lol! I guess Laura found it to be hilarious also. I wasn’t the only one.
Continuing
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Lastly, three recent studies highlight the possibility of genetic exchange between Europe and Africa. Moorjani et al. (9) estimated that about 1–3% of recent Sub-Saharan African ancestry is present in multiple southern European populations; Cerezo et al. (23) find evidence of older (11,000 ya) Sub-Saharan gene flow toward Europe based on mtDNA genomes; and Auton et al. (8) found that short haplotypes were shared between the Yoruban Nigerians and southwestern Europeans. However, given the geographic barrier imposed by the Sahara Desert between North Africa and Sub-Saharan Africa, and the proximity of North Africa to Europe, it is plausible that gene flow from Africa to Europe actually originated in North Africa. North Africans are significantly genetically diverged from Sub-Saharan populations (24, 25), and hence previous studies may not have accurately estimated the proportion or range of admixture in Europe by using a Sub-Saharan sample as a source population.
We aim to quantify the extent and pattern of recent gene flow between European and African populations. We use allele frequencies to estimate North African ancestry proportions in European populations. To quantify the variance in ancestry in European populations and obtain bounds on the time since admixture, we use a quantitative model for the decrease in ancestry variance with the time since admixture (30). We additionally detect gene flow between populations by analyzing long haplotypes shared identically by descent (IBD) with high-density SNP genotyping data (31, 32). We investigate regional patterns of haplotype sharing between North Africa, Sub-Saharan Africa, the Near East, and Europe in detail, and observe a*** significant latitudinal gradient**** of North African ancestry within Europe characterized by a dramatic difference between the Iberian Peninsula and the neighboring regions.
To estimate allele-based sharing between Africans and Europeans, we applied an unsupervised clustering algorithm, ADMIXTURE (33), to data from all populations (SI Appendix, Table S1). We explored k = 2–10 ancestral populations and performed 10 iterations for each k(SI Appendix, Figs. S1 and S2). Our analysis does not assume that source populations are unadmixed; that is, since the analysis is run unsupervised, Sub-Saharan African ancestry, for example, can be detected in both North Africans and Europeans. Furthermore, estimates of admixture based on hundreds of thousands of markers (as we use here) show little bias using an unsupervised approach when the ancestral populations are significantly diverged (34). As the number of k ancestral clusters increased, we observed several well-supported population-specific ancestry clusters. We conservatively present k = 3 through 6 (Fig. 1) but additional results are presented in the SI Appendix.
At k = 4, the ancestry assignment differentiated between non-Jewish European populations (from now on referred to as “European”), European Jews, Sub-Saharan Africans, and a group formed by Near Eastern and North African populations. At k = 5,6 components mainly assigned to North African populations and Tunisian Berbers, respectively, clearly appear. European populations sharing this North African ancestral component are almost exclusively in southern Europe (Fig. 1 and SI Appendix, Fig. S3). Southern European populations have a high proportion (5–35%) of joint Near Eastern | North African ancestry assigned at k = 4. However, identification of distinct Near Eastern and North African ancestries in k ≥ 5 differentiates southeastern from southwestern Europe. Southwestern European populations average between 4% and 20% of their genomes assigned to a North African ancestral cluster (SI Appendix, Fig. S3), whereas this value does not exceed 2% in southeastern European populations
Additionally, IBD sharing between North Africa and Europe is nearly an order of magnitude higher than that between Sub-Saharan Africa and Europe, of which a total of 30% of its IBD segments are also shared between North Africa and Europe.
This sharing is highest in the Iberian Peninsula for both North Africa and Sub-Saharan African IBD segments.
Overall, these results support the hypothesis that Sub-Saharan gene flow detected in Europe entered with North African gene flow.
To pinpoint which specific North African regions exchanged migrants with Europe, we calculated WEA between a given European population and each of the seven North African and Near Eastern populations (Fig. 3 and SI Appendix, Table S3). Southwestern European populations, and in particular the Canary Islands, show the highest levels of IBD sharing with northwestern African populations (i.e., the Maghreb: Morocco, Western Sahara, Algeria, and Tunisia), whereas southeastern European populations share more IBD segments with Egypt and the Near East (SI Appendix, Fig. S7). Whereas inferred IBD sharing does not indicate directionality, the North African samples that have highest IBD sharing with Iberian populations also tend to have the lowest proportion of the European cluster in ADMIXTURE (Fig. 1), e.g., Saharawi, Tunisian Berbers, and South Moroccans. For example, the Andalucians share many IBD segments with the Tunisians (Fig. 3), who present extremely minimal levels of European ancestry. This suggests that ***GENE FLOW OCCURRED FROM AFRICA TO EUROPE RATHER THAN THE OTHER WAY AROUND.***
These results also rule out a model where observed sharing between Europe and North Africa is the result of recent gene flow from the Near East into both regions.
These results also rule out a model where observed sharing between Europe and North Africa is the result of recent gene flow from the Near East into both regions. We compared IBD between Qatari (the best Near Eastern representatives genotyped with the Affymetrix platform currently available, SI Appendix, Fig. S8), Europe, and North Africa. As shown in Fig. 3 and SI Appendix, Fig. S7), southwestern Europe has more IBD segments shared with the Maghreb than Qatar, whereas eastern Mediterranean populations share more segments IBD with the Near East than with western North Africa. On the other hand, northern European populations show only limited IBD sharing with both North Africa and the Near East (Figs. 2C and and33 and
The southwest-to-northeast gradient of North African IBD sharing (Fig. 2B) and the distinct peak in sharing between Iberia and the Maghreb (Fig. 3) indicate that sharing in southwestern Europe is independent of gene flow from the Near East. It is possible that this sharp peak of North African IBD sharing in Iberia contributes to the apparent isolation of Iberian populations from other Europeans (43).
Laura R. Botigué
-------------
Quotes:
“Multiple models have been proposed to explain clinal gradients of human genetic diversity in Europe including directional migration, climate, natural selection, and isolation by distance (1–4). A particular pattern of interest is the higher level of genetic diversity in southern European populations compared with those in northern latitudes. Three main hypotheses have been proposed to explain this phenomenon. Under the first hypothesis, populations retreated to glacial refugia in southern Europe about 20,000 y ago (ya), but when these populations later recolonized the continent, only a subset of the genetic diversity was carried into northern regions (5). The second hypothesis is that gene flow from the Near East, associated with the demic diffusion of agriculture, differentially affected geographic regions and in particular introduced additional genetic diversity to southeastern Europe (6, 7). The third hypothesis suggests that increased genetic diversity is the result of migrations from the African continent into southern Europe (8, 9). These hypotheses are not mutually exclusive; however, we focus on testing a hypothesis of gene flow from Africa to Europe, which has ***received the LEAST AMOUNT OF ATTENTION ***and may be the easiest to detect due to the recent time frame of the proposed demographic event.
However, strong similarities in pottery production are also found between southern Iberia and Northwest Africa 7,500 ya. The existence of “maritime pioneers” in the Mediterranean Sea during this period has been hypothesized (21).”
--------------
oH! The quotes aren’t mine. HA! HA! HA! hA! Lol! I guess Laura found it to be hilarious also. I wasn’t the only one.
Continuing
-----------
Lastly, three recent studies highlight the possibility of genetic exchange between Europe and Africa. Moorjani et al. (9) estimated that about 1–3% of recent Sub-Saharan African ancestry is present in multiple southern European populations; Cerezo et al. (23) find evidence of older (11,000 ya) Sub-Saharan gene flow toward Europe based on mtDNA genomes; and Auton et al. (8) found that short haplotypes were shared between the Yoruban Nigerians and southwestern Europeans. However, given the geographic barrier imposed by the Sahara Desert between North Africa and Sub-Saharan Africa, and the proximity of North Africa to Europe, it is plausible that gene flow from Africa to Europe actually originated in North Africa. North Africans are significantly genetically diverged from Sub-Saharan populations (24, 25), and hence previous studies may not have accurately estimated the proportion or range of admixture in Europe by using a Sub-Saharan sample as a source population.
We aim to quantify the extent and pattern of recent gene flow between European and African populations. We use allele frequencies to estimate North African ancestry proportions in European populations. To quantify the variance in ancestry in European populations and obtain bounds on the time since admixture, we use a quantitative model for the decrease in ancestry variance with the time since admixture (30). We additionally detect gene flow between populations by analyzing long haplotypes shared identically by descent (IBD) with high-density SNP genotyping data (31, 32). We investigate regional patterns of haplotype sharing between North Africa, Sub-Saharan Africa, the Near East, and Europe in detail, and observe a*** significant latitudinal gradient**** of North African ancestry within Europe characterized by a dramatic difference between the Iberian Peninsula and the neighboring regions.
To estimate allele-based sharing between Africans and Europeans, we applied an unsupervised clustering algorithm, ADMIXTURE (33), to data from all populations (SI Appendix, Table S1). We explored k = 2–10 ancestral populations and performed 10 iterations for each k(SI Appendix, Figs. S1 and S2). Our analysis does not assume that source populations are unadmixed; that is, since the analysis is run unsupervised, Sub-Saharan African ancestry, for example, can be detected in both North Africans and Europeans. Furthermore, estimates of admixture based on hundreds of thousands of markers (as we use here) show little bias using an unsupervised approach when the ancestral populations are significantly diverged (34). As the number of k ancestral clusters increased, we observed several well-supported population-specific ancestry clusters. We conservatively present k = 3 through 6 (Fig. 1) but additional results are presented in the SI Appendix.
At k = 4, the ancestry assignment differentiated between non-Jewish European populations (from now on referred to as “European”), European Jews, Sub-Saharan Africans, and a group formed by Near Eastern and North African populations. At k = 5,6 components mainly assigned to North African populations and Tunisian Berbers, respectively, clearly appear. European populations sharing this North African ancestral component are almost exclusively in southern Europe (Fig. 1 and SI Appendix, Fig. S3). Southern European populations have a high proportion (5–35%) of joint Near Eastern | North African ancestry assigned at k = 4. However, identification of distinct Near Eastern and North African ancestries in k ≥ 5 differentiates southeastern from southwestern Europe. Southwestern European populations average between 4% and 20% of their genomes assigned to a North African ancestral cluster (SI Appendix, Fig. S3), whereas this value does not exceed 2% in southeastern European populations
Additionally, IBD sharing between North Africa and Europe is nearly an order of magnitude higher than that between Sub-Saharan Africa and Europe, of which a total of 30% of its IBD segments are also shared between North Africa and Europe.
This sharing is highest in the Iberian Peninsula for both North Africa and Sub-Saharan African IBD segments.
Overall, these results support the hypothesis that Sub-Saharan gene flow detected in Europe entered with North African gene flow.
To pinpoint which specific North African regions exchanged migrants with Europe, we calculated WEA between a given European population and each of the seven North African and Near Eastern populations (Fig. 3 and SI Appendix, Table S3). Southwestern European populations, and in particular the Canary Islands, show the highest levels of IBD sharing with northwestern African populations (i.e., the Maghreb: Morocco, Western Sahara, Algeria, and Tunisia), whereas southeastern European populations share more IBD segments with Egypt and the Near East (SI Appendix, Fig. S7). Whereas inferred IBD sharing does not indicate directionality, the North African samples that have highest IBD sharing with Iberian populations also tend to have the lowest proportion of the European cluster in ADMIXTURE (Fig. 1), e.g., Saharawi, Tunisian Berbers, and South Moroccans. For example, the Andalucians share many IBD segments with the Tunisians (Fig. 3), who present extremely minimal levels of European ancestry. This suggests that ***GENE FLOW OCCURRED FROM AFRICA TO EUROPE RATHER THAN THE OTHER WAY AROUND.***
These results also rule out a model where observed sharing between Europe and North Africa is the result of recent gene flow from the Near East into both regions.
These results also rule out a model where observed sharing between Europe and North Africa is the result of recent gene flow from the Near East into both regions. We compared IBD between Qatari (the best Near Eastern representatives genotyped with the Affymetrix platform currently available, SI Appendix, Fig. S8), Europe, and North Africa. As shown in Fig. 3 and SI Appendix, Fig. S7), southwestern Europe has more IBD segments shared with the Maghreb than Qatar, whereas eastern Mediterranean populations share more segments IBD with the Near East than with western North Africa. On the other hand, northern European populations show only limited IBD sharing with both North Africa and the Near East (Figs. 2C and and33 and
The southwest-to-northeast gradient of North African IBD sharing (Fig. 2B) and the distinct peak in sharing between Iberia and the Maghreb (Fig. 3) indicate that sharing in southwestern Europe is independent of gene flow from the Near East. It is possible that this sharp peak of North African IBD sharing in Iberia contributes to the apparent isolation of Iberian populations from other Europeans (43).