| 21. |
- Breton, Gwenna, et al.
(author)
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Lactase Persistence Alleles Reveal Partial East African Ancestry of Southern African Khoe Pastoralists
- 2014
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In: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 24:8, s. 852-858
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Journal article (peer-reviewed)abstract
- The ability to digest milk into adulthood, lactase persistence (LP), as well as specific genetic variants associated with LP, is heterogeneously distributed in global populations [1-4]. These variants were most likely targets of selection when some populations converted from hunter-gatherer to pastoralist or farming lifestyles [5-7]. Specific LP polymorphisms are associated with particular geographic regions and populations [1-4, 8-10]; however, they have not been extensively studied in southern Africa. We investigate the LP-regulatory region in 267 individuals from 13 southern African populations (including descendants of hunter-gatherers, pastoralists, and agropastoralists), providing the first comprehensive study of the LP-regulatory region in a large group of southern Africans. The "East African" LP single-nucleotide polymorphism (SNP) (14010G>C) was found at high frequency (>20%) in a strict pastoralist Khoe population, the Nama of Namibia, suggesting a connection to East Africa, whereas the "European" LP SNP (13910C>T) was found in populations of mixed ancestry. Using genome-wide data from various African populations, we identify admixture (13%) in the Nama, from an Afro-Asiatic group dating to >1,300 years ago, with the remaining fraction of their genomes being from San hunter-gatherers. We also find evidence of selection around the LCT gene among Khoe-speaking groups, and the substantial frequency of the 14010C variant among the Nama is best explained by adaptation to digesting milk. These genome-local and genome-wide results support a model in which an East African group brought pastoralist practices to southern Africa and admixed with local hunter-gatherers to form the ancestors of Khoe people.
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| 22. |
- Breton, Gwenna, et al.
(author)
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The “BaTwa” populations from remote areas in Zambia retain ancestry of past forager groups
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Other publication (other academic/artistic)abstract
- Sub-equatorial Africa is inhabited today predominantly by Bantu-speaking farmers of west African descent. However, before the arrival of agriculture and pastoralism ~2,000 years ago, the region was inhabited by hunter-gatherers. The incoming farmer populations replaced, displaced or admixed with local hunter-gatherer groups. In some regions such as southern and central Africa, current-day farming populations have absorbed a large local hunter-gatherer genetic component. In other regions, such as Malawi, and Mozambique current-day populations have absorbed little to none of the local component. In this study, we generated genome-wide SNP data from two populations from Zambia thought to represent former hunter-gatherers, known locally as “BaTwa”, but for which no direct evidence exists of a hunter-gatherer past, either in language or lifestyle. We compared the BaTwa data to three Bantu-speaker agropastoralist populations from Zambia, and to other African and non-African populations. We show that the two BaTwa populations harbor a hunter-gatherer-like genetic component, representing respectively ~20% and ~30% of their genetic ancestry, while the rest is similar to Bantu-speaker agropastoralists. Although the component is closest related to current-day Khoe-San populations from southern Africa, results still suggest a unique local hunter-gatherer component. These results accord with Middle and Late Holocene skeletal evidence from Zambia and Malawi for a regionally separate hunter-gatherer population, which is now only detectable among the BaTwa. A two-way admixture scenario between a Bantu-speaker agropastoralist-like source and a hunter-gatherer-like source is supported for the two populations, occurring ~40 and ~16 generations ago respectively. These estimates are consistent with archaeological records for the arrival of agropastoralists in northern and central Zambia respectively. The study demonstrate the value of studying underrepresented minority groups to better understand the complexity of regional population histories.
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| 23. |
- Bridel, Claire, et al.
(author)
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Diagnostic Value of Cerebrospinal Fluid Neurofilament Light Protein in Neurology : A Systematic Review and Meta-analysis
- 2019
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In: JAMA Neurology. - : American Medical Association (AMA). - 2168-6149 .- 2168-6157. ; 76:9, s. 1035-1048
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Research review (peer-reviewed)abstract
- Importance Neurofilament light protein (NfL) is elevated in cerebrospinal fluid (CSF) of a number of neurological conditions compared with healthy controls (HC) and is a candidate biomarker for neuroaxonal damage. The influence of age and sex is largely unknown, and levels across neurological disorders have not been compared systematically to date.Objectives To assess the associations of age, sex, and diagnosis with NfL in CSF (cNfL) and to evaluate its potential in discriminating clinically similar conditions.Data Sources PubMed was searched for studies published between January 1, 2006, and January 1, 2016, reporting cNfL levels (using the search terms neurofilament light and cerebrospinal fluid) in neurological or psychiatric conditions and/or in HC.Study Selection Studies reporting NfL levels measured in lumbar CSF using a commercially available immunoassay, as well as age and sex.Data Extraction and Synthesis Individual-level data were requested from study authors. Generalized linear mixed-effects models were used to estimate the fixed effects of age, sex, and diagnosis on log-transformed NfL levels, with cohort of origin modeled as a random intercept.Main Outcome and Measure The cNfL levels adjusted for age and sex across diagnoses.Results Data were collected for 10 059 individuals (mean [SD] age, 59.7 [18.8] years; 54.1% female). Thirty-five diagnoses were identified, including inflammatory diseases of the central nervous system (n = 2795), dementias and predementia stages (n = 4284), parkinsonian disorders (n = 984), and HC (n = 1332). The cNfL was elevated compared with HC in a majority of neurological conditions studied. Highest levels were observed in cognitively impaired HIV-positive individuals (iHIV), amyotrophic lateral sclerosis, frontotemporal dementia (FTD), and Huntington disease. In 33.3% of diagnoses, including HC, multiple sclerosis, Alzheimer disease (AD), and Parkinson disease (PD), cNfL was higher in men than women. The cNfL increased with age in HC and a majority of neurological conditions, although the association was strongest in HC. The cNfL overlapped in most clinically similar diagnoses except for FTD and iHIV, which segregated from other dementias, and PD, which segregated from atypical parkinsonian syndromes.Conclusions and Relevance These data support the use of cNfL as a biomarker of neuroaxonal damage and indicate that age-specific and sex-specific (and in some cases disease-specific) reference values may be needed. The cNfL has potential to assist the differentiation of FTD from AD and PD from atypical parkinsonian syndromes.
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| 24. |
- Choin, Jeremy, et al.
(author)
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Genomic insights into population history and biological adaptation in Oceania
- 2021
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In: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 592:7855, s. 583-589
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Journal article (peer-reviewed)abstract
- The Pacific region is of major importance for addressing questions regarding human dispersals, interactions with archaic hominins and natural selection processes(1). However, the demographic and adaptive history of Oceanian populations remains largely uncharacterized. Here we report high-coverage genomes of 317 individuals from 20 populations from the Pacific region. We find that the ancestors of Papuan-related ('Near Oceanian') groups underwent a strong bottleneck before the settlement of the region, and separated around 20,000-40,000 years ago. We infer that the East Asian ancestors of Pacific populations may have diverged from Taiwanese Indigenous peoples before the Neolithic expansion, which is thought to have started from Taiwan around 5,000 years ago(2-4). Additionally, this dispersal was not followed by an immediate, single admixture event with Near Oceanian populations, but involved recurrent episodes of genetic interactions. Our analyses reveal marked differences in the proportion and nature of Denisovan heritage among Pacific groups, suggesting that independent interbreeding with highly structured archaic populations occurred. Furthermore, whereas introgression of Neanderthal genetic information facilitated the adaptation of modern humans related to multiple phenotypes (for example, metabolism, pigmentation and neuronal development), Denisovan introgression was primarily beneficial for immune-related functions. Finally, we report evidence of selective sweeps and polygenic adaptation associated with pathogen exposure and lipid metabolism in the Pacific region, increasing our understanding of the mechanisms of biological adaptation to island environments.
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| 25. |
- Chylenski, Maciej, et al.
(author)
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Late Danubian mitochondrial genomes shed light into the Neolithisation of Central Europe in the 5th millennium BC
- 2017
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In: BMC Evolutionary Biology. - : BIOMED CENTRAL LTD. - 1471-2148. ; 17
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Journal article (peer-reviewed)abstract
- Background: Recent aDNA studies are progressively focusing on various Neolithic and Hunter-Gatherer (HG) populations, providing arguments in favor of major migrations accompanying European Neolithisation. The major focus was so far on the Linear Pottery Culture (LBK), which introduced the Neolithic way of life in Central Europe in the second half of 6th millennium BC. It is widely agreed that people of this culture were genetically different from local HGs and no genetic exchange is seen between the two groups. From the other hand some degree of resurgence of HGs genetic component is seen in late Neolithic groups belonging to the complex of the Funnel Beaker Cultures (TRB). Less attention is brought to various middle Neolithic cultures belonging to Late Danubian sequence which chronologically fall in between those two abovementioned groups. We suspected that genetic influx from HG to farming communities might have happened in Late Danubian cultures since archaeologists see extensive contacts between those two communities. Results: Here we address this issue by presenting 5 complete mitochondrial genomes of various late Danubian individuals from modern-day Poland and combining it with available published data. Our data show that Late Danubian cultures are maternally closely related to Funnel Beaker groups instead of culturally similar LBK. Conclusions: We assume that it is an effect of the presence of individuals belonging to U5 haplogroup both in Late Danubians and the TRB. The U5 haplogroup is thought to be a typical for HGs of Europe and therefore we argue that it is an additional evidence of genetic exchange between farming and HG groups taking place at least as far back as in middle Neolithic, in the Late Danubian communities.
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| 26. |
- Chylenski, Maciej, et al.
(author)
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Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age
- 2023
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 14
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Journal article (peer-reviewed)abstract
- The demographic history of East-Central Europe after the Neolithic period remains poorly explored, despite this region being on the confluence of various ecological zones and cultural entities. Here, the descendants of societies associated with steppe pastoralists form Early Bronze Age were followed by Middle Bronze Age populations displaying unique characteristics. Particularly, the predominance of collective burials, the scale of which, was previously seen only in the Neolithic. The extent to which this re-emergence of older traditions is a result of genetic shift or social changes in the MBA is a subject of debate. Here by analysing 91 newly generated genomes from Bronze Age individuals from present Poland and Ukraine, we discovered that Middle Bronze Age populations were formed by an additional admixture event involving a population with relatively high proportions of genetic component associated with European hunter-gatherers and that their social structure was based on, primarily patrilocal, multigenerational kin-groups. By analysing 91 Bronze Age genomes from East-Central Europe, the authors discovered that Middle Bronze Age populations were formed by an admixture event involving hunter-gatherers and that the social structure of resulting population was primarily patrilocal.
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| 27. |
- Cotgreave, Ian, et al.
(author)
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Pyriproxifen and microcephaly: an investigation of potential ties to the ongoing "Zika epidemic"
- 2016
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Reports (other academic/artistic)abstract
- As part of the Swetox mission to react to emerging concerns in chemical health and environmental safety, a preliminary litterature investigation was undertaken to gather all readily available scientific information on PPF with respect to safety assessment, in order to better understand potential links between chemical exposure and the devopment of microcephaly in affected areas. Therefore the contents of the report do not constitute an attempt at either questioning the use of existing regulatory data in the manner prescribed by international regulatory proceedures, or as a new risk assessment, based on the scientific information and concepts discussed. Here we report our findings, with particular emphasis on exisiting regulatory information, potential for lack of translation of results from regulatory animal testing to humans, lack of human exposure data and suggestions on plausible mode(s) of action of PPF in human neurodevelopmental adversities such as microcephaly.
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| 28. |
- Coutinho, Alexandra, et al.
(author)
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Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups
- 2021
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In: American Journal of Physical Anthropology. - : John Wiley & Sons. - 0002-9483 .- 1096-8644. ; 174:4, s. 701-713
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Journal article (peer-reviewed)abstract
- Previous studies show that the indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting ~400 years ago and their descendants are today mixed with Europeans and Asians. To gain insight on the occupants of the Vaalkrans Shelter located at the southernmost tip of Africa, we investigated the genetic make-up of an individual who lived there about 200 years ago. We further contextualize the genetic ancestry of this individual among prehistoric and current groups. From a hair sample excavated at the shelter, which was indirectly dated to about 200 years old, we sequenced the genome (1.01 times coverage) of a Later Stone Age individual. We analyzed the Vaalkrans genome together with genetic data from 10 ancient (pre-colonial) individuals from southern Africa spanning the last 2000 years. We show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter–gatherers and ~20% to a mixed East African-Eurasian source. This genetic make-up is similar to modern-day Khoekhoe individuals from the Northern Cape Province (South Africa) and Namibia, but in the southern Cape, the Vaalkrans man's descendants have likely been assimilated into mixed-ancestry “Coloured” groups. The Vaalkrans man's genome reveals that Khoekhoe pastoralist groups/individuals lived in the southern Cape as late as 200 years ago, without mixing with non-African colonists or Bantu-speaking farmers. Our findings are also consistent with the model of a Holocene pastoralist migration, originating in Eastern Africa, shaping the genomic landscape of historic and current southern African populations.
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| 29. |
- Coutinho, Alexandra, et al.
(author)
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The Evolution of Adaptive traits in Indigenous human populations in Sub-Saharan Africa
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Other publication (other academic/artistic)abstract
- Several well-known genetic variants that confer disease resistance or other adaptive advantages have been investigated in modern-day populations across the globe. In particular, sub-Saharan African populations display variation for many of these loci. In this study, we investigate allele frequencies underlying functional variants of interest in sub-Saharan African populations. By also investigating sequence data from ancient human remains from excavated sites in sub-Saharan Africa, we can start to get an indication of the allele frequency trajectories of adaptive variants, how they have diffused through the African genetic landscape, and how much migration and admixture played a role in the distribution of these variants in modern-day African populations. Our results show that as well as selection, migration has had a large influence on changing allele frequency through time in variants associated with disease resistance, salt sensitivity and metabolism. Yet in other variants, such as some associated with skin pigmentation, allele frequencies have changed little over time. Lastly, this study emphasizes the need for continued study of African populations, as due to the sheer genetic diversity present in Africa, different functional variants may confer similar means of adaptation than those we know for out-of-Africa populations. This study is the first to comprehensively investigate adaptive variants in both ancient and modern Africans, and further research will continue to reveal how the genetic landscape of modern humans has changed, and continues to change through time.
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| 30. |
- Coutinho, Alexandra, et al.
(author)
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The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders
- 2020
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In: American Journal of Physical Anthropology. - : Wiley. - 0002-9483 .- 1096-8644. ; 172:4, s. 638-649
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Journal article (peer-reviewed)abstract
- ObjectivesIn order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub‐Neolithic hunter‐gatherer Pitted Ware culture. By investigating the genetic make‐up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture‐influenced burials), we could determine the impact of migration and the impact of cultural influences.MethodsWe sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene‐pools.ResultsThe genomic data show that all individuals belonged to one genetic population—a population associated with the Pitted Ware culture—irrespective of the burial style.ConclusionWe conclude that the Pitted Ware culture communities were not impacted by gene‐flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange.
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