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Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa.

ABSTRACT: How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African-related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African-related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.

SUBMITTER: Prendergast ME

PROVIDER: S-EPMC6827346 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa.

Prendergast Mary E ME Lipson Mark M Sawchuk Elizabeth A EA Olalde Iñigo I Ogola Christine A CA Rohland Nadin N Sirak Kendra A KA Adamski Nicole N Bernardos Rebecca R Broomandkhoshbacht Nasreen N Callan Kimberly K Culleton Brendan J BJ Eccles Laurie L Harper Thomas K TK Lawson Ann Marie AM Mah Matthew M Oppenheimer Jonas J Stewardson Kristin K Zalzala Fatma F Ambrose Stanley H SH Ayodo George G Gates Henry Louis HL Gidna Agness O AO Katongo Maggie M Kwekason Amandus A Mabulla Audax Z P AZP Mudenda George S GS Ndiema Emmanuel K EK Nelson Charles C Robertshaw Peter P Kennett Douglas J DJ Manthi Fredrick K FK Reich David D

Science (New York, N.Y.) 20190530 6448

How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African-related peoples and eastern African foragers formed ...[more]

PMID: 31147405

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Project description:Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome were significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population. Please note that the data from the comparable cohort of patients in the USUS data was published as supplemental material of PMID: 22760045 but not submitted to GEO The 'patient_info.txt' contains 12 clinical, 7 immunological and 3 microbiological variables for each patient.

Dataset Information

Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa.

Publications

Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa.

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