Early Back-to-Africa Migration into the Horn of Africa

Hodgson, Jason A.; Mulligan, Connie J.; Al‐Meeri, Ali; Raaum, Ryan L.

doi:10.1371/journal.pgen.1004393

Cited by 94 publications

(128 citation statements)

References 109 publications

(185 reference statements)

Supporting

Mentioning

107

Contrasting

Order By: Relevance

“…Also of note is the modest variation in their PC1 scores. This is likely due to ancient admixture with Middle Eastern populations (Hodgson et al 2014). These results confirm that Ethiopians have a unique genetic structure among African populations.…”

Section: Structure Of Individuals Run On the Afr Arraysupporting

confidence: 71%

Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

et al. 2015

View full text Add to dashboard Cite

Using genome-wide genotypes, we characterized the genetic structure of 103,006 participants in the Kaiser Permanente Northern California multi-ethnic Genetic Epidemiology Research on Adult Health and Aging Cohort and analyzed the relationship to selfreported race/ethnicity. Participants endorsed any of 23 race/ethnicity/nationality categories, which were collapsed into seven major race/ ethnicity groups. By self-report the cohort is 80.8% white and 19.2% minority; 93.8% endorsed a single race/ethnicity group, while 6.2% endorsed two or more. Principal component (PC) and admixture analyses were generally consistent with prior studies. Approximately 17% of subjects had genetic ancestry from more than one continent, and 12% were genetically admixed, considering only nonadjacent geographical origins. Self-reported whites were spread on a continuum along the first two PCs, indicating extensive mixing among European nationalities. Self-identified East Asian nationalities correlated with genetic clustering, consistent with extensive endogamy. Individuals of mixed East AsianEuropean genetic ancestry were easily identified; we also observed a modest amount of European genetic ancestry in individuals selfidentified as Filipinos. Self-reported African Americans and Latinos showed extensive European and African genetic ancestry, and Native American genetic ancestry for the latter. Among 3741 genetically identified parent-child pairs, 93% were concordant for self-reported race/ ethnicity; among 2018 genetically identified full-sib pairs, 96% were concordant; the lower rate for parent-child pairs was largely due to intermarriage. The parent-child pairs revealed a trend toward increasing exogamy over time; the presence in the cohort of individuals endorsing multiple race/ethnicity categories creates interesting challenges and future opportunities for genetic epidemiologic studies.

show abstract

Section: Structure Of Individuals Run On the Afr Arraysupporting

confidence: 71%

Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

et al. 2015

View full text Add to dashboard Cite

show abstract

“…The signal of an ancient bottleneck in the Q1 (Bedouin) is not unexpected given previous analyses of genomic admixture that (Omberg et al 2012) and studies of worldwide population structure, which have inferred that the Q1 (Bedouin) genomes have the greatest proportion of Arab genetic ancestry, even when compared to Bedouins from outside Qatar and to Arabs in surrounding countries, including Yemen and Saudi Arabia (Hodgson et al 2014;Shriner et al 2014). To confirm a similarly minute amount of African admixture for the Q1 (Bedouin) in our sample, we applied three methodologies: (1) an ADMIXTURE (Alexander et al 2009) analysis of the genome-wide ancestry proportions in the 104 Qataris, the 1000 Genomes Project (The 1000 Genomes Project Consortium 2012), and Human Origins samples (Lazaridis et al 2014); (2) an ALDER (Loh et al 2013) analysis of the proportion and timing of African ancestry in these same populations; and (3) a SupportMix (Omberg et al 2012) analysis of the population assignments of local genomic segments of the 96 Q1 (Bedouin), Q2 (Persian-South Asian), or Q3 (African) Qatari genomes.…”

Section: Admixture Analysismentioning

confidence: 84%

“…Second, the combination of lower levels of Neanderthal admixture in the Q1 (Bedouin) than European/Asian populations and the outgroup position of the Q1 (Bedouin) compared to non-Africans in the pairwaise similarity clustering of high-density variants measured genome-wide, place the Q1 (Bedouin) as being the most distant relatives of other contemporary non-Africans. Given that the Q1 (Bedouin) have the greatest proportion of Arab genetic ancestry measured in contemporary populations (Hodgson et al 2014;Shriner et al 2014) and are among the best genetic representatives of the autochthonous population on the Arabian Peninsula, these two conclusions therefore point to the Bedouins being direct descendants of the earliest split after the out-of-Africa migration events that established a basal Eurasian population (Lazaridis et al 2014). This is also consistent with the majority of Q1 (Bedouin) being able to trace a significant portion of their autosomal ancestry through lineages that never left the peninsula after the out-of-Africa migration events since such deep ancestry would not be expected if the entire Arabian Peninsula population had been reestablished from Africa or a non-African population at a later point.…”

Section: Discussionmentioning

confidence: 99%

Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations

et al. 2016

View full text Add to dashboard Cite

An open question in the history of human migration is the identity of the earliest Eurasian populations that have left contemporary descendants. The Arabian Peninsula was the initial site of the out-of-Africa migrations that occurred between 125,000 and 60,000 yr ago, leading to the hypothesis that the first Eurasian populations were established on the Peninsula and that contemporary indigenous Arabs are direct descendants of these ancient peoples. To assess this hypothesis, we sequenced the entire genomes of 104 unrelated natives of the Arabian Peninsula at high coverage, including 56 of indigenous Arab ancestry. The indigenous Arab genomes defined a cluster distinct from other ancestral groups, and these genomes showed clear hallmarks of an ancient out-of-Africa bottleneck. Similar to other Middle Eastern populations, the indigenous Arabs had higher levels of Neanderthal admixture compared to Africans but had lower levels than Europeans and Asians. These levels of Neanderthal admixture are consistent with an early divergence of Arab ancestors after the out-of-Africa bottleneck but before the major Neanderthal admixture events in Europe and other regions of Eurasia. When compared to worldwide populations sampled in the 1000 Genomes Project, although the indigenous Arabs had a signal of admixture with Europeans, they clustered in a basal, outgroup position to all 1000 Genomes non-Africans when considering pairwise similarity across the entire genome. These results place indigenous Arabs as the most distant relatives of all other contemporary non-Africans and identify these people as direct descendants of the first Eurasian populations established by the out-of-Africa migrations.

show abstract

“…We chose starting effective population sizes (at the time of admixture) of 100, 200 and 500, and population growth parameters of 2, 5 and 10%, all of which are probably lower than those that reflect the true demographic history of Madagascar (hence, overestimating the amount of drift, and conservative with respect to our alternative hypothesis). [33]. Given 30 year generation times, these choices correspond to hypothetical admixture beginning at approximately 1000, 1300 and 2300 years ago, respectively.…”

Section: (C) Computer Simulations To Test Evolutionary Hypotheses Formentioning

confidence: 99%

Natural selection for the Duffy-null allele in the recently admixed people of Madagascar

et al. 2014

Self Cite

View full text Add to dashboard Cite

While gene flow between distantly related populations is increasingly recognized as a potentially important source of adaptive genetic variation for humans, fully characterized examples are rare. In addition, the role that natural selection for resistance to vivax malaria may have played in the extreme distribution of the protective Duffy-null allele, which is nearly completely fixed in mainland sub-Saharan Africa and absent elsewhere, is controversial. We address both these issues by investigating the evolution of the Duffy-null allele in the Malagasy, a recently admixed population with major ancestry components from both East Asia and mainland sub-Saharan Africa. We used genome-wide genetic data and extensive computer simulations to show that the high frequency of the Duffy-null allele in Madagascar can only be explained in the absence of positive natural selection under extreme demographic scenarios involving high genetic drift. However, the observed genomic single nucleotide polymorphism diversity in the Malagasy is incompatible with such extreme demographic scenarios, indicating that positive selection for the Duffy-null allele best explains the high frequency of the allele in Madagascar. We estimate the selection coefficient to be 0.066. Because vivax malaria is endemic to Madagascar, this result supports the hypothesis that malaria resistance drove fixation of the Duffy-null allele in mainland sub-Saharan Africa.

show abstract

Early Back-to-Africa Migration into the Horn of Africa

Cited by 94 publications

References 109 publications

Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations

Natural selection for the Duffy-null allele in the recently admixed people of Madagascar

Contact Info

Product

Resources

About