North African Jewish and non-Jewish populations form distinctive, orthogonal clusters

Campbell, Christopher L. et al.North African Jews constitute the second largest Jewish Diaspora group. However, their relatedness to each other; to European, Middle Eastern, and other Jewish Diaspora groups; and to their former North African non-Jewish neighbors has not been well defined. Here, genome-wide analysis of five North African Jewish groups (Moroccan, Algerian, Tunisian, Djerban, and Libyan) and comparison with other Jewish and non-Jewish groups demonstrated distinctive North African Jewish population clusters with proximity to other Jewish populations and variable degrees of Middle Eastern, European, and North African admixture. Two major subgroups were identified by principal component, neighbor joining tree, and identity-by-descent analysis - Moroccan/ Algerian and Djerban/Libyan - that varied in their degree of European admixture. These populations showed a high degree of endogamy and were part of a larger Ashkenazi and Sephardic Jewish group. By principal component analysis, these North African groups were orthogonal to contemporary populations from North and South Morocco, Western Sahara, Tunisia, Libya, and Egypt. Thus, this study is compatible with the history of North African Jews - founding during Classical Antiquity with proselytism of local populations, followed by genetic isolation with the rise of Christianity and then Islam, and admixture following the emigration of Sephardic Jews during the Inquisition.This work was supported in part by the Lewis and Rachel Rudin Foundation, the Iranian-American Jewish Federation of New York, the US–Israel Binational Science Foundation, National Institutes of Health Grant 5 U54 CA121852, and Ruth and Sidney Lapidus. L.R.B. and D.C. were supported by Ministerio de Ciencia e Innovación Grant CGL2010-14944/BOS.Peer Reviewe

High-depth African genomes inform human migration and health

The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed1. Here we performed whole-genome sequencing analyses of 426 individuals— comprising 50 ethnolinguistic groups, including previously unsampled populations— to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that population from Zambia were a likely intermediate site along the routes of expansion of Bantuspeaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon—but in other genes, variants denoted as ‘likely pathogenic’ in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health

Genomic Ancestry of North Africans Supports Back-to-Africa Migrations

North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from “back-to-Africa” gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa

High-depth African genomes inform human migration and health.

The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed1. Here we performed whole-genome sequencing analyses of 426 individuals-comprising 50 ethnolinguistic groups, including previously unsampled populations-to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that Zambia was a likely intermediate site along the routes of expansion of Bantu-speaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon-but in other genes, variants denoted as 'likely pathogenic' in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health

High-depth African genomes inform human migration and health

The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed1. Here we performed whole-genome sequencing analyses of 426 individuals—comprising 50 ethnolinguistic groups, including previously unsampled populations—to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that Zambia was a likely intermediate site along the routes of expansion of Bantu-speaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon—but in other genes, variants denoted as ‘likely pathogenic’ in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health

High-depth African genomes inform human migration and health

The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed1. Here we performed whole-genome sequencing analyses of 426 individuals—comprising 50 ethnolinguistic groups, including previously unsampled populations—to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that Zambia was a likely intermediate site along the routes of expansion of Bantu-speaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon—but in other genes, variants denoted as ‘likely pathogenic’ in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health

Whole genome sequencing from 3,000 year-old wheat reveals dispersal and domestication history

Trabajo presentado al Third Jack R. Harlan International Symposium, celebrado en Montpellier (Francia) del 3 al 7 de junio de 2019

Gene flow from North Africa contributes to differential human genetic diversity in southern Europe

Botigué, Laura R. et al.Human genetic diversity in southern Europe is higher than in other regions of the continent. This difference has been attributed to postglacial expansions, the demic diffusion of agriculture from the Near East, and gene flow from Africa. Using SNP data from 2,099 individuals in 43 populations, we show that estimates of recent shared ancestry between Europe and Africa are substantially increased when gene flow from North Africans, rather than Sub-Saharan Africans, is considered. The gradient of North African ancestry accounts for previous observations of low levels of sharing with Sub-Saharan Africa and is independent of recent gene flow from the Near East. The source of genetic diversity in southern Europe has important biomedical implications; we find that most disease risk alleles from genome-wide association studies follow expected patterns of divergence between Europe and North Africa, with the principal exception of multiple sclerosis.M.H. and C.D.B. were supported by National Institutes of Health Grant 3R01HG003229. L.R.B. and D.C. were supported by Ministerio de Ciencia e Innovación Grant GL2010-14944/BOS and Generalitat de Catalunya Grant 2009SGR1101. C.F. was supported by Instituto de Salud Carlos III Grant PI11/00623. The Spanish National Institute for Bioinformatics supported this project.Peer Reviewe

Local adaptation in humans and other primates

Resumen del trabajo presentado al Seminario del CRAG, celebrado el 6 de marzo de 2020.Peer reviewe

Crop archaeogenomics: A powerful resource in need of a well-defined regulation framework

[Societal Impact Statement]: Crop archaeogenomics has rapidly flourished in recent years, leading to a new way of understanding the past and bringing answers to important questions about human history in relation to plant management and food production. Furthermore, the knowledge derived from the analysis of ancient crops can contribute to the development of a more sustainable future. However, the extant legal framework presents a number of challenges when applied to this research field, particularly in the current scenario of disparities in scientific outcomes between countries. We expose the uncertainties of the legal framework and the factors that maintain or exacerbate these inequalities, as well as possible solutions.[Summary]: Crop archaeogenomics is a flourishing field that has greatly benefited from next-generation sequencing technologies. Ancient and historical plant remains are currently considered genetic resources and as such are subject to legal frameworks like those implemented by the Nagoya Protocol. In addition to the challenges in complying with genetic resource regulations that crop archaeogenomics share with other basic plant research disciplines, there are additional difficulties specific to this interdisciplinary field that includes science and humanities, namely, the need to comply with two different legislations before accessing the samples (one for genetic resources and one for cultural heritage), along with a high risk of not obtaining DNA. As a result, most studies to date have been done on samples for which the laws regulating genetic resources did not apply, sometimes avoiding the need of reaching Access and Benefit Sharing agreements with the country that originally provided the samples. This phenomenon is likely to worsen in the future, as the archaeological record is a limited resource and competition between laboratories will only widen the gap between developed and developing economies. Because crop archaeogenomics is a new and promising scientific field, it is desirable to begin a dialogue with other basic biological research fields to facilitate the implementation of these agreements so that basic sciences can easily utilize these biological samples while ensuring the rights of all parties involved.A.I. is a FPI fellow (PRE2018-083529). L. B is a Ramón y Cajal Fellow. (RYC2018-024770-I) both fellowships funded by the Ministerio de Ciencia e Innovación—Agencia Estatal de Investigación/Fondo Social Europeo. We acknowledge financial support from the Spanish Ministry of Science and Innovation-State Research Agency (AEI), through the “Severo Ochoa Programme for Centres of Excellence in R&D” SEV-2015-0533 and CEX2019-000902-S. This work was also supported by the CERCA programme by the Generalitat de Catalunya.Peer reviewe