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

Prendergast, Mary E.; Lipson, Mark; Sawchuk, Elizabeth A.; Olalde, Ïñigo; Ogola, Christine; Rohland, Nadin; Sirak, Kendra; Adamski, Nicole; Bernardos, Rebecca; Broomandkhoshbacht, Nasreen; Callan, Kimberly; Culleton, Brendan J.; Eccles, Laurie; Harper, Thomas K.; Lawson, Ann Marie; Mah, Matthew; Oppenheimer, Jonas; Stewardson, Kristin; Zalzala, Fatma; Ambrose, Stanley H.; Ayodo, George; Gates, Henry Louis; Gidna, Agness; Katongo, Maggie; Kwekason, Amandus; Mabulla, Audax; Mudenda, George; Ndiema, Emmanuel; Nelson, Charles M.; Robertshaw, Peter; Kennett, Douglas J.; Manthi, Fredrick K.; Reich, David

doi:10.1126/science.aaw6275

Cited by 120 publications

(156 citation statements)

References 110 publications

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“…However, we also report on seven alternative sampling locations on four other skeletal elements, all of which performed equally well in our evaluation, that show promise as suitable alternatives to the petrous pyramid. Though our sample set is limited both temporally and geographically, our results are likely informative for other climatic regions, time periods and perhaps even in anatomically comparable species as has already been demonstrated for the petrous portions itself [76][77][78][79] . It should also be noted that, as this study has focused on identifying the most efficient sampling locations from which host (in this case human) DNA can be recovered, the sampling strategies and suggestions put forth here may not be applicable in studies seeking to retrieve DNA from pathogens, the microbiome, or other co-cohabitating organisms within the host.…”

Section: Discussionmentioning

confidence: 75%

A systematic investigation of human DNA preservation in medieval skeletons

Parker

Rohrlach

Friederich

et al. 2020

Preprint

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Ancient DNA (aDNA) analyses necessitate the destructive sampling of archaeological material.Currently the dense inner portion of the petrous pyramid, the location of the skull that houses the inner ear, is the most sought after skeletal element for molecular analyses of ancient humans as it has been shown to yield high amounts of endogenous DNA. Destructive sampling of the petrous pyramid, assuming its recovery, is often not recommended for highly valued specimens. To investigate alternatives, we present a survey of human aDNA preservation for each of ten skeletal elements in a skeletal collection from Medieval Germany. Through comparison of human DNA content and quality we confirm best performance of the petrous pyramid and identify seven additional sampling locations across four skeletal elements that yield adequate aDNA for most applications in human palaeogenetics. Our study provides a better perspective on DNA preservation across the human skeleton and takes a further step toward the more responsible use of ancient materials in human aDNA studies. 2 26 27 28 29 30 31 32 33 34 35 36 37 38Recent advances in minimally invasive sampling techniques 26 have led to a better balance between preservation of the anthropological record and the need for the production of reliable genetic data 27,28 ; however, the threat of damage to internal microstructures that form an important basis of morphological assessments 29-31 can still introduce hesitancy on the part of curators and physical anthropologists in making the petrous pyramid available for aDNA applications. These factors, in conjunction with the chance of incomplete recovery of crania at excavation 32 or restricted sampling of highly valued specimens, make the identification of alternative sampling locations based on quantitative evaluations of DNA preservation across the skeleton of clear benefit. Teeth have been widely used for the study of aDNA 33,34 , though the 30-fold covered genome of an archaic hominin from Denisova Cave from a distal phalanx demonstrates molecular preservation in elements that are not typically considered for paleogenetics work 4 . Despite these successes, a systematic and extensive study of differential DNA preservation across multiple human skeletal elements, such as those done in the context of modern forensics 35,36 , has yet to be attempted on archaeological remains. Our limited understanding of DNA preservation across the human skeleton is a significant hurdle for the efficient, practical, and ethical study of aDNA, which has particular relevance to the field of ancient population genetics where large sample sizes are needed for robust analytical resolution.DNA preservation can be influenced by many factors including burial practises and treatment of the deceased, geology, as well as environmental and climatic conditions 37 , where the chronological age of a sample is thought to play only a secondary role 38,39 . To serve as a baseline for future investigations seeking to incorporate and extrapolate the effects of these sources of v...

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Section: Discussionmentioning

confidence: 75%

A systematic investigation of human DNA preservation in medieval skeletons

Parker

Rohrlach

Friederich

et al. 2020

Preprint

View full text Add to dashboard Cite

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“…Specific alleles for lactase persistence, a trait that indicates human co-evolution with cattle, sheep and goat and milk consumption in adulthood, developed and were positively selected in Eastern Africa [19], including the major allele C-14010, dated to around 6-7000 years [19], the time of introduction of domesticated animals. Recent research on ancient DNA suggests a clear admixture of early pastoralistic groups with Eastern Africans by at least 4000 years [39]. Nevertheless, Eastern Africa also display a long history of contact with Arabia/Near East [40,41] that could have promote multiple transmission events of domesticates and pathogen further increasing the diversity of the M. bovis in Eastern Africa.…”

Section: Plos Neglected Tropical Diseasesmentioning

confidence: 99%

Evolutionary analysis of Mycobacterium bovis genotypes across Africa suggests co-evolution with livestock and humans

et al. 2020

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Mycobacterium bovis is the pathogenic agent responsible for bovine tuberculosis (bTB), a zoonotic disease affecting mostly cattle, but also transmittable to humans and wildlife. Genetic studies on M. bovis allow to detect possible routes of bTB transmission and the identification of genetic reservoirs that may provide an essential framework for public health action. We used a database with 1235 M. bovis genotypes collected from different regions in Africa with 45 new Mozambican samples. Our analyses, based on phylogeographic and population genetics' approaches, allowed to identify two clear trends. First, the genetic diversity of M. bovis is geographically clustered across the continent, with the only incidences of long-distance sharing of genotypes, between South Africa and Algeria, likely due to recent European introductions. Second, there is a broad gradient of diversity from Northern to Southern Africa with a diversity focus on the proximity to the Near East, where M. bovis likely emerged with animal domestication in the last 10,000 years. Diversity indices are higher in Eastern Africa, followed successively by Northern, Central, Southern and Western Africa, roughly correlating with the regional archaeological records of introduction of animal domesticates. Given this scenario M. bovis in Africa was probably established millennia ago following a concomitant spread with cattle, sheep and goat. Such scenario could translate into long-term locally adapted lineages across Africa. This work describes a novel scenario for the spread of M. bovis in Africa using the available genetic data, opening the field to further studies using higher resolution genomic data.

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“…3) [90,130]. However, in recent years human paleogenomics studies have been successfully conducted using samples from arid, subtropical and even tropical zones [131][132][133][134][135][136][137][138][139][140][141][142].…”

Section: Technology Advances: Deep Sequencing + Dense Bones = Paleogementioning

confidence: 99%

Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics

2019

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Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.

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

Cited by 120 publications

References 110 publications

A systematic investigation of human DNA preservation in medieval skeletons

A systematic investigation of human DNA preservation in medieval skeletons

Evolutionary analysis of Mycobacterium bovis genotypes across Africa suggests co-evolution with livestock and humans

Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics

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