The genetic variation of lactase persistence alleles in northeast Africa

Lactase persistence (LP) is a well-studied example of a Mendelian trait under selection in some human groups due to gene-culture co-evolution. We investigated the frequencies of genetic variants linked to LP in Sudanese and South Sudanese populations. These populations have diverse subsistence patterns, and some are dependent on milk to various extents, not only from cows, but also from other livestock such as camels and goats. We sequenced a 316bp region involved in regulating the expression of the LCT gene on chromosome 2, which encompasses five polymorphisms that have been associated with LP. Pastoralist populations showed a higher frequency of LP-associated alleles compared to non-pastoralist groups, hinting at positive selection also in northeast African pastoralists. There was no incidence of the East African LP allele (−14010:C) in the Sudanese groups, and only one heterozygote individual for the European LP allele (−13910:T), suggesting limited recent admixture from these geographic regions. Among the LP variants, the −14009:G variant occurs at the highest frequency among the investigated populations, followed by the −13915:G variant, which is likely of Middle Eastern origin, consistent with Middle Eastern gene-flow to the Sudanese populations. The Beja population of the Beni Amer show three different LP-variants at substantial and similar levels, resulting in one of the greatest frequencies of LP-variants among all populations across the world.Competing Interest StatementThe authors have declared no competing interest.Introduction Results and Discussion - Allele frequencies - Haplotype Structure - Selection Scan Conclusion Materials and Methods - Phasing and imputation to analyze haplotype structure - Locus specific branch length (LSBL

Outcomes of births attended by private midwives in the Gauteng Province of South Africa : a retrospective cohort study

Midwives are important role players in providing women-centred care for low-risk pregnant women. South African women use either public or private health care services during pregnancy and birth. As the public sector is overburdened, women do not receive a high level of continuity of care there. The private sector is mainly obstetrician-led and intervention-driven. Private midwife-led care is available in South Africa, but is limited to the major cities. No evidence could be found about the outcomes of private midwife-led care in South Africa. The objective reported in this paper was to compare the outcomes of and interventions during births attended by private midwives in Gauteng with the latest Cochrane review on midwife-led care. A retrospective cohort design was used to audit the birth registers of private midwives in Gauteng, focusing on outcomes and interventions as in the most recent Cochrane review on midwife-led care. The maternal and neonatal outcomes of Gauteng midwives' patients were reassuring. Compared to women in the Cochrane review, significantly more Gauteng women had an intact perineum (53.4% vs 29%), fewer had interventions such as induction of labour (9.6% vs 19.3%), but more had caesarean sections (19.3% vs 13.3%). Overall foetal loss (0.3% vs 2.7%) and NICU admissions (4.3% vs 7.1%) occurred significantly less frequently in the Gauteng sample. The study's findings indicated that private midwife-led care in Gauteng compared well with that in the rest of the world in terms of outcomes and intervention rates.https://www.elsevier.com/locate/ijanshj2024Nursing ScienceSDG-03:Good heatlh and well-bein

Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations

<p>Abstract</p> <p>Background</p> <p>The ability of the Y chromosome to retain a record of its evolution has seen it become an essential tool of molecular anthropology. In the last few years, however, it has also found use in forensic genetics, providing information on the geographic origin of individuals. This has been aided by the development of efficient screening methods and an increased knowledge of geographic distribution. In this study, we describe the development of single base extension assays used to resolve 61 Y chromosome haplogroups, mainly within haplogroups A, B and E, found in Africa.</p> <p>Results</p> <p>Seven multiplex assays, which incorporated 60 Y chromosome markers, were developed. These resolved Y chromosomes to 61 terminal branches of the major African haplogroups A, B and E, while also including a few Eurasian haplogroups found occasionally in African males. Following its validation, the assays were used to screen 683 individuals from Southern Africa, including south eastern Bantu speakers (BAN), Khoe-San (KS) and South African Whites (SAW). Of the 61 haplogroups that the assays collectively resolved, 26 were found in the 683 samples. While haplogroup sharing was common between the BAN and KS, the frequencies of these haplogroups varied appreciably. Both groups showed low levels of assimilation of Eurasian haplogroups and only two individuals in the SAW clearly had Y chromosomes of African ancestry.</p> <p>Conclusions</p> <p>The use of these single base extension assays in screening increased haplogroup resolution and sampling throughput, while saving time and DNA. Their use, together with the screening of short tandem repeat markers would considerably improve resolution, thus refining the geographic ancestry of individuals.</p

Memoria del 2001: Instituto de Recursos Naturales y Agrobiología de Sevilla.

145 páginas.Durante el primer año del siglo XXI el Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS) ha seguido realizando su labor investigadora y formativa así como la de asistencia técnica tanto externa como interna y de divulgación tanto de los resultados obtenidos como de su capacidad de I+D. La actividad investigadora del IRNAS se ha mantenido en la línea del año anterior, siendo financiada fundamentalmente mediante proyectos concedidos por la UE, la CICYT-FEDER, Junta de Andalucía, otros Ministerios y la empresa privada, siendo este último sector el que menos contribuye a esta financiación. Parece obvio que tenemos que hacer entre todos un esfuerzo por captar mayores recursos de este sector productivo. Como consecuencia de la actividad investigadora realizada se han publicado 50 artículos en revistas internacionales, recogidas en SCI, 6 en revistas nacionales, 45 trabajos en libros o publicaciones colectivas, 4 Tesis doctorales, 2 de licenciatura, 5 trabajos Fin de Carrera, 5 Fin de Curso, así como 6 patentes registradas. El personal del IRNAS ha participado en congresos internacionales con 66 comunicaciones y en nacionales con 20. En el aspecto formativo se ha contribuido a la formación de 47 personas de diversa cualificación académica mediante los contratos asignados al IRNAS tras el convenio INEM-CSIC. Así mismo, se sigue participando en diversos programas de Doctorado, Master y Cursos tanto en la Universidad Hispalense como en la Pablo de Olavide, de Sevilla, habiéndose defendido las Tesis Doctorales, de Licenciatura y proyectos Fin de Carrera mencionados anteriormente. En el ámbito internacional el IRNAS sigue implicado en su tradicional política de intercambio y colaboración con paises europeos, latinoamericanos y del Magreb, como indican las Acciones Integradas del MCYT, Convenios y Acciones Especiales del CSIC, etc. que recogen esta Memoria. En la Finca experimental “La Hampa” se han seguido realizando las experiencias de campo que necesitan llevar a cabo diversos grupos del IRNAS, en el contexto de proyectos financiados con fondos gubernamentales nacionales, autonómicos, europeos y de empresas privadas.Peer reviewe

Human origins in Southern African palaeo-wetlands? Strong claims from weak evidence

Attempts to identify a ‘homeland’ for our species from genetic data are widespread in the academic literature. However, even when putting aside the question of whether a ‘homeland’ is a useful concept, there are a number of inferential pitfalls in attempting to identify the geographic origin of a species from contemporary patterns of genetic variation. These include making strong claims from weakly informative data, treating genetic lineages as representative of populations, assuming a high degree of regional population continuity over hundreds of thousands of years, and using circumstantial observations as corroborating evidence without considering alternative hypotheses on an equal footing, or formally evaluating any hypothesis. In this commentary we review the recent publication that claims to pinpoint the origins of ‘modern humans’ to a very specific region in Africa (Chan et al., 2019), demonstrate how it fell into these inferential pitfalls, and discuss how this can be avoided

Patterns of African and Asian admixture in the Afrikaner population of South Africa

Abstract: Background: The Afrikaner population of South Africa is the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the Coloured populations of South Africa. Differences in ancestry, social class, culture, sex ratio and geographic structure led to distinct and characteristic admixture patterns in the Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records previously estimated the contribution of non-Europeans into the Afrikaners to be between 5.5 and 7.2%. Results: To investigate the genetic ancestry of the Afrikaner population today (11–13 generations after initial colonization), we genotyped approximately five million genome-wide markers in 77 Afrikaner individuals and compared their genotypes to populations across the world to determine parental source populations and admixture proportions. We found that the majority of Afrikaner ancestry (average 95.3%) came from European populations (specifically northwestern European populations), but that almost all Afrikaners had admixture from non-Europeans. The non-European admixture originated mostly from people who were brought to South Africa as slaves and, to a lesser extent, from local Khoe-San groups. Furthermore, despite a potentially small founding population, there is no sign of a recent bottleneck in the Afrikaner compared to other European populations. Admixture amongst diverse groups from Europe and elsewhere during early colonial times might have counterbalanced the effects of a small founding population. Conclusions: While Afrikaners have an ancestry predominantly from northwestern Europe, non-European admixture signals are ubiquitous in the Afrikaner population. Interesting patterns and similarities could be observed between genealogical predictions and our genetic inferences. Afrikaners today have comparable inbreeding levels to currentday European populations

Possible Positive Selection for an Arsenic-Protective Haplotype in Humans

BACKGROUND: Arsenic in drinking water causes severe health effects. Indigenous people in the South American Andes have likely lived with arsenic-contaminated drinking water for thousands of years. Inhabitants of San Antonio de los Cobres (SAC) in the Argentinean highlands generally carry an AS3MT (the major arsenic-metabolizing gene) haplotype associated with reduced health risks due to rapid arsenic excretion and lower urinary fraction of the monomethylated metabolite. OBJECTIVES: We hypothesized an adaptation to high-arsenic living conditions via a possible positive selection for protective AS3MT variants and compared AS3MT haplotype frequencies among different indigenous groups. METHODS: Indigenous groups we evaluated were a) inhabitants of SAC and villages near Salta in northern Argentina (n = 346), b) three Native American populations from the Human Genome Diversity Project (HGDP; n = 25), and c) five Peruvian populations (n = 97). The last two groups have presumably lower historical exposure to arsenic. RESULTS: We found a significantly higher frequency of the protective AS3MT haplotype in the SAC population (68.7%) compared with the HGDP (14.3%, p < 0.001, Fisher exact test) and Peruvian (50.5%, p < 0.001) populations. Genome-wide micro-satellite (n = 671) analysis showed no detectable level of population structure between SAC and Peruvian populations (measure of population differentiation F-ST = 0.006) and low levels of structure between SAC and HGDP populations (F-ST < 0.055 for all pairs of populations compared). CONCLUSIONS: Because population stratification seems unlikely to explain the differences in AS3MT haplotype frequencies, our data raise the possibility that, during a few thousand years, natural selection for tolerance to the environmental stressor arsenic may have increased the frequency of protective variants of AS3MT. Further studies are needed to investigate this hypothesis

Cancer prevalence in 129 breast-ovarian cancer families tested for BRCA1 and BRCA2 mutations

Background. Women who carry germline mutations in the breast-ovarian cancer susceptibility genes, BRCA1 and BRCA2, are at very high risk of developing breast and/or ovarian cancer. Both genes are tumour suppressor genes that protect all cells from deregulation, and there are reports of their involvement in other cancers that vary and seem to depend on the population investigated. It is therefore important to investigate the other associated cancers in different populations to assist with risk assessments. Objectives. To assess the cancer risk profile in BRCA-mutation-positive and negative South African breast-ovarian cancer families, mainly of Caucasian origin. Design. Descriptive study in which the prevalence of all cancers in the pedigrees of BRCA1- and BRCA2-mutation-positive groups and a group of families without mutations in either gene were compared with the general population. Results. As expected, female breast and ovarian cancer was significantly increased in all three groups. Furthermore, male breast cancer was significantly elevated in the BRCA2-positive and BRCA-negative groups. Stomach cancer prevalence was significantly elevated in the BRCA2-positive families compared with the general population. Conclusions. These results can be applied in estimation of cancer risks and may contribute to more comprehensive counselling of mutation-positive Caucasian breast and/or ovarian cancer families

Recent acquisition of Helicobacter pylori by Baka Pygmies

Both anatomically modern humans and the gastric pathogen Helicobacter pylori originated in Africa, and both species have been associated for at least 100,000 years. Seven geographically distinct H. pylori populations exist, three of which are indigenous to Africa: hpAfrica1, hpAfrica2, and hpNEAfrica. The oldest and most divergent population, hpAfrica2, evolved within San hunter-gatherers, who represent one of the deepest branches of the human population tree. Anticipating the presence of ancient H. pylori lineages within all hunter-gatherer populations, we investigated the prevalence and population structure of H. pylori within Baka Pygmies in Cameroon. Gastric biopsies were obtained by esophagogastroduodenoscopy from 77 Baka from two geographically separated populations, and from 101 non-Baka individuals from neighboring agriculturalist populations, and subsequently cultured for H. pylori. Unexpectedly, Baka Pygmies showed a significantly lower H. pylori infection rate (20.8%) than non-Baka (80.2%). We generated multilocus haplotypes for each H. pylori isolate by DNA sequencing, but were not able to identify Baka-specific lineages, and most isolates in our sample were assigned to hpNEAfrica or hpAfrica1. The population hpNEAfrica, a marker for the expansion of the Nilo-Saharan language family, was divided into East African and Central West African subpopulations. Similarly, a new hpAfrica1 subpopulation, identified mainly among Cameroonians, supports eastern and western expansions of Bantu languages. An age-structured transmission model shows that the low H. pylori prevalence among Baka Pygmies is achievable within the timeframe of a few hundred years and suggests that demographic factors such as small population size and unusually low life expectancy can lead to the eradication of H. pylori from individual human populations. The Baka were thus either H. pylori-free or lost their ancient lineages during past demographic fluctuations. Using coalescent simulations and phylogenetic inference, we show that Baka almost certainly acquired their extant H. pylori through secondary contact with their agriculturalist neighbors