Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History

Schlebusch, Carina M.; Skoglund, Pontus; Sjödin, Per; Gattepaille, Lucie M.; Hernandez, Dena G.; Jay, Flora; Li, Sen; Jongh, Michael De; Singleton, Andrew B.; Blum, Michaël G. B.; Soodyall, Himla; Jakobsson, Mattias

doi:10.1126/science.1227721

Cited by 386 publications

(596 citation statements)

References 137 publications

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“…Indeed, previous inferences based on human genetic data have estimated these events to have happened 60 kya for the out-of-Africa (Eriksson et al 2012), 20 kya for the arrival into the Americas (Eriksson et al 2012), and 110 kya for San divergence (Hammer et al 2011;Veeramah et al 2011;Schlebusch et al 2012). On the other hand, the time inferred from the H. pylori dataset for the San split under the most likely model, which includes migration, is older than 500,000 generations.…”

Section: Adaptation In Helicobacter Pylori Whole Genome 953mentioning

confidence: 93%

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

et al. 2015

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Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of particular significance for both clinical and evolutionary studies. Here we present the first such whole genome analysis of 60 globally distributed strains, from which we inferred worldwide population structure and demographic history and shed light on interesting global and local events of positive selection, with particular emphasis on the evolution of San-associated lineages. Our results indicate a more ancient origin for the association of humans and H. pylori than previously thought. We identify several important perspectives for future clinical research on candidate selected regions that include both previously characterized genes (e.g., transcription elongation factor NusA and tumor necrosis factor alpha-inducing protein Tipa) and hitherto unknown functional genes.KEYWORDS adaptation; neutral evolution; human pathogens H ELICOBACTER pylori is a Gram-negative bacterium that infects the mucosa of the human stomach. It was first described in the 1980s, when it was initially identified in association with chronic gastritis and later causally linked to serious gastric pathologies such as gastric cancer and ulcers (Marshall and Warren 1984;Suerbaum and Michetti 2002). It infects .80% of humans in developing countries and, although its prevalence is lower in developed countries, nearly 50% of the worldwide human population is infected (Ghose et al. 2005;Salih 2009;Salama et al. 2013).Due to its clinical and evolutionary importance, there has been considerable research on mechanisms of H. pylori transmission, as well as on the population genetics and phylogenetic relationships among global isolates. Thus far, population genetic analyses have mainly focused on seven housekeeping genes (usually referred to as multilocus sequence typing or MLST), with the primary conclusions being that H. pylori strains appear highly structured, and their phylogeographic patterns correlate consistently with that of their human hosts. Given that the H. pylori-humans association is at least 100,000 years old (Moodley et al. 2012), the current population structure of H. pylori may be regarded as mirroring past human expansions and migrations Linz et al. 2007;Breurec et al. 2011) and thus help us shed light on yet unknown dynamics of local demographic processes in human evolution. However, despite the knowledge gained thus far, the long-term global demographic history of H. pylori has never been directly inferred. The long, intimate association of H. pylori with humans suggests a history of bacterial adaptation. Considerable attention has focused on specific genes involved in modulating adaptive immunity of the host (for a review see Yamaoka 2010 andSalama et al. 2013) and on genomic changes occurring during acute and chronic H. pylori infection (Kennemann et al. 2011;Linz et a...

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Section: Adaptation In Helicobacter Pylori Whole Genome 953mentioning

confidence: 93%

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

et al. 2015

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“…Even prior to the arrival of the Europeans, admixture occurred among the indigenous groups, specifically among the Khoikhoi and San (commonly pooled and referred to as Khoe-San), and Bantu-speakers [16,17]. Nine of the 11 South African national languages are recognized as Bantu languages, a sub-group of the Niger-Congo languages.…”

Section: Introductionmentioning

confidence: 99%

Ancestry estimation in South Africa using craniometrics and geometric morphometrics

Stull

Kenyhercz

L'Abbé

2014

Forensic Science International

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Population history and positive assortative mating directs gene flow in such a way that biological differences are recognized among groups. In turn, forensic anthropologists quantify biological differences to estimate ancestry. Some anthropologists argue that highly admixed population groups, such as South African coloureds, cannot achieve acceptable accuracies because within group variance is too large. Whereas ancestry estimation in South Africa has been limited to craniometric data from South African 2 blacks and whites, the current study integrates craniometric and geometric morphometric data from the three largest South African groups.Crania from 377 South African individuals (black = 158, white =112, and coloured = 107) comprised the sample. Standard measurements were collected and the coordinate data were subjected to Generalized Procrustes Analysis (GPA), which resulted in size-free shape variables (ProCoords). A principal component analysis was used to combine the shape variation captured in the ProCoords (ProCoords PC). Linear discriminant analysis (LDA), using equal priors, stepwise variable selection and leaveone-out cross-validation, was conducted on the ProCoords, the ProCoords PCs, and the traditional craniometric data.The LDA using 18 stepwise selected ProCoords resulted in the highest crossvalidated accuracy (89%). Utilization of geometric morphometric data emphasized that the relative location of cranial landmarks was more discriminating than simple linear distances. Regardless of high levels of genetic admixture, South African coloureds are a homogeneous group and morphologically distinct from other contemporaneous South African populations. Furthermore, the present study demonstrated a correspondence between peer-reported race and morphological differences in the crania of black, white, and coloured South Africans.

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“…The Western Cape Province of South Africa has a rich genetic history, arising from many parts of the world including the local ancient Khoisan population [8][9][10][11] , the greater Bantu groups from the Niger-Congo phylum 12,[14][15][16] , European settlers 17,18 and slaves from the East 18,19 . Marriages amongst the different population groups were once common 17,20 , and produced a heterogeneous new and genetically unique population in the Western Cape, until apartheid was introduced and resulted in a drastic decrease in cross-population gene flow 6,20,25 .…”

Section: Discussionmentioning

confidence: 99%

“…These two historical groups are collectively referred to as the Khoisan or the Khoe-San, and speak a distinctive click language. 11 Although the Khoisan maintained an isolated ancient lifestyle for centuries and remained genetically distinct with unique physical characteristics from Europeans, Asian and other Africans 8 , the genetic profiles of some tribes (such as the Khwe groups) show high proportions of Bantuspeaking admixture 10,11 .…”

Section: Population Demographic Originmentioning

confidence: 99%

Composition of the Kirsten Skeletal Collection at Stellenbosch University

Alblas¹,

Greyling²,

Geldenhuys³

2018

S. Afr. J. Sci.

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The Kirsten Skeletal Collection is curated in the Division of Anatomy and Histology, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa. It comprises the largest documented cadaver-derived South African coloured skeletal collection in the world. Our aim in this paper is to present an inventory and characterise the identified skeletons in the Kirsten Skeletal Collection as well as provide a descriptive indication of what researchers can expect to encounter at the anthropology unit at Stellenbosch University. The skeletal material was derived mainly from the cadaver donation programme of the Division of Anatomy and Histology over a 58-year period (1957–2015). All pertinent information for each individual skeleton is entered into a database and a full skeletal inventory is established. The skeletal database registry was analysed to demonstrate the distribution of age, sex and population affinity of individuals in the collection. Currently, this collection consists of 1161 skeletons with known records. Despite differences in the age and sex composition, the skeletal profile in general reflects mainly the profile of the Western Cape population. Most individuals were born between 1920 and 1950, placing the Kirsten Skeletal Collection in the early to mid-20th century. The age at death for the greatest proportion (41.8%) of individuals was between 40 and 60 years. Current biological profile techniques in age, ancestry and sex estimation can be improved and, among others, new regional and ancestral specific standards for the biologically unique and diverse South African coloured population can be developed.

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Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History

Cited by 386 publications

References 137 publications

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

Ancestry estimation in South Africa using craniometrics and geometric morphometrics

Composition of the Kirsten Skeletal Collection at Stellenbosch University

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