| 1. |
- Chen, Hwei-yen, 1983-, et al.
(författare)
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Germline mutation rate is elevated in young and old parents in Caenorhabditis remanei
- 2023
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Ingår i: Evolution Letters. - : Oxford University Press. - 2056-3744. ; 7:6, s. 478-489
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Tidskriftsartikel (refereegranskat)abstract
- The effect of parental age on germline mutation rate across generations is not fully understood. While some studies report a positive linear relationship of mutation rate with increasing age, others suggest that mutation rate varies with age but not in a linear fashion. We investigated the effect of parental age on germline mutations by generating replicated mutation accumulation lines in Caenorhabditis remanei at three parental ages ("Young T1" [Day 1], "Peak T2" [Day 2], and "Old T5" [Day 5] parents). We conducted whole-genome resequencing and variant calling to compare differences in mutation rates after three generations of mutation accumulation. We found that Peak T2 lines had an overall reduced mutation rate compared to Young T1 and Old T5 lines, but this pattern of the effect varied depending on the variant impact. Specifically, we found no high-impact variants in Peak T2 lines, and modifiers and up- and downstream gene variants were less frequent in these lines. These results suggest that animals at the peak of reproduction have better DNA maintenance and repair compared to young and old animals. We propose that C. remanei start to reproduce before they optimize their DNA maintenance and repair, trading the benefits of earlier onset of reproduction against offspring mutation load. The increase in offspring mutation load with age likely represents germline senescence. Germline mutations play a key role in evolution through the generation of novel genotypes. Estimating the mutation rate in species, populations, and individuals is one way to understand the relative timeframe of evolutionary processes, for the timing of historical events and for estimating heritability of traits and diseases. Individual age at reproduction is known to affect the number of mutations being transferred into the next generation and generally mutation rate is thought to increase with increasing parental age. However, preventing mutations in germ cells is potentially costly and it may pay off to optimize germline genome repair and maintenance during peak reproductive periods, and relax it during nonpeak periods. This idea has been put forward to explain for example the reduction of gonad size in seasonally reproducing animals during nonreproductive periods and supported by the finding that the mutation rate seems to be higher in teenage men compared to men during their peak reproductive ages. We further tested this idea of a nonlinear relationship between age and mutation rate by performing a mutation accumulation experiment in a short-lived nematode. We kept experimental lines and allowed adults to reproduce at different ages in different lines, with some lines reproducing before, some during, and some after their reproductive peak. We found that mutation rates are higher in nematode lines reproducing before or after the reproductive peak compared to those reproducing during the peak. Our results therefore support the idea that germline genome maintenance and repair is potentially costly and that the mutation rate does not just increase with age but is optimized during the peak reproductive age of an organism.
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| 2. |
- Chen, Hwei-yen, 1983-, et al.
(författare)
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Trade-off between somatic and germline repair in a vertebrate supports the expensive germ line hypothesis
- 2020
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 117:16, s. 8973-8979
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Tidskriftsartikel (refereegranskat)abstract
- The disposable soma theory is a central tenet of the biology of aging where germline immortality comes at the cost of an aging soma [T. B. L. Kirkwood, Nature 270, 301–304 (1977); T. B. L. Kirkwood, Proc. R. Soc. Lond. B Biol. Sci. 205, 531–546 (1979); T. B. L. Kirkwood, S. N. Austad, Nature 408, 233–238 (2000)]. Limited resources and a possible trade-off between the repair and maintenance of the germ cells and growth and maintenance of the soma may explain the deterioration of the soma over time. Here we show that germline removal allows accelerated somatic healing under stress. We tested “the expensive germ line” hypothesis by generating germline-free zebrafish Danio rerio and testing the effect of the presence and absence of the germ line on somatic repair under benign and stressful conditions. We exposed male fish to sublethal low-dose ionizing radiation, a genotoxic stress affecting the soma and the germ line, and tested how fast the soma recovered following partial fin ablation. We found that somatic recovery from ablation occurred substantially faster in irradiated germline-free fish than in the control germline-carrying fish where somatic recovery was stunned. The germ line did show signs of postirradiation recovery in germline-carrying fish in several traits related to offspring number and fitness. These results support the theoretical conjecture that germline maintenance is costly and directly trades off with somatic maintenance.
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| 3. |
- Fortes-Lima, Cesar A., PhD, 1985-, et al.
(författare)
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Population structure and admixture during the expansion of Bantu-speaking peoples across sub-Saharan Africa
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The migration of Bantu-speaking groups out of West Africa, thought to have started around 4 000 years ago, is known as the Bantu expansion. This movement of people changed the genetic landscape of sub-equatorial Africa. To investigate the demographic history and population structure in Bantu-speaking populations (BSP), we genotyped 1,740 individuals, including 1,487 Bantu speakers from 143 populations across 13 sub-Saharan African countries. We find patterns of fine-scale population structure that correlate with linguistics and geography. Bantu speakers received significant amounts of admixture through interaction with local groups from the regions that they expanded into. Spatial modeling indicated possible migration corridors during the Bantu-expansion. Inferences based on modern-day genomes, however, need to be supported by ancient DNA studies. We demonstrated the utility of our dataset as an exhaustive modern-day African comparative dataset for ancient DNA studies by comparing our data to published aDNA studies. By gathering the largest set of genome-wide data to date, enriched with new data from previously unsampled regions and people, we shed new light on the intricacies of the Bantu expansion.
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| 4. |
- Fortes-Lima, Cesar A., PhD, 1985-, et al.
(författare)
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The genetic legacy of the expansion of Bantu-speaking peoples in Africa
- 2024
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 625:7995, s. 540-547
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Tidskriftsartikel (refereegranskat)abstract
- The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent1-7. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000-4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals8. We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods9 and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies10 and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations.
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| 5. |
- Hammarén, Rickard, et al.
(författare)
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Ancestry contributions within geographically dispersed South African Coloured groups
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The South African Coloured people (SAC) are the most prominent admixed population in the country. They are descendants of local Khoe-San, and Bantu-speaking populations, European settlers, and enslaved people from the East and West Coast of Africa, South and East Asia, brought during the slave trade period. The term "Coloured" was an artificial category used by the South African apartheid government to group various groups with mixed ancestry. The term is still widely used today and is one of the ethnic categories in the South African government census. While the term is embraced by some people categorised as Coloured, it is rejected by others. This study aimed to investigate the remnant Khoekhoe and San genetic ancestry within various Coloured groups together with other ancestries introduced during colonial times. We generated novel genotyping, mtDNA, and Y-chromosome data for 65 individuals at two locations and, together with data from previously published studies, we assembled a dataset of 222 SAC individuals from 17 different geographic locations. This study has gathered the most extensive dataset of SAC individuals sampled from the largest number of sites to date. At 14 out of the 17 locations, Khoe-San was the majority ancestry. The Coloured populations display genetic ancestry from Khoe-San, West African, East African, East Asian, South Asian, and European groups at vastly varying amounts across the sampled locations, reflecting the history of South Africa, apartheid laws, and socio-cultural groupings. The ancestry proportions from different source populations differ by large fractions between the autosomes and uni-parental markers, which points to sex-biased admixture in the Coloured.This research highlights the importance of studying the South African Coloured population to comprehend the impact of complex migration patterns and historical systems of segregation in South Africa.
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| 6. |
- Meyer, Anja, et al.
(författare)
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A reassessment of archaeological human remains recovered from rock shelters in Cathkin Peak, South Africa
- 2021
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Ingår i: Azania. - : Routledge. - 0067-270X .- 1945-5534. ; 56:4, s. 508-538
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Tidskriftsartikel (refereegranskat)abstract
- Various skeletons from the uThukela region of the uKhahlamba-Drakensberg Mountains of South Africa were excavated from rock shelters there during the early part of the twentieth century, with limited accompanying data or analysis. This paper analyses and reports on nine such graves (eight of which contained human remains), excavated during 1931 near Cathkin Peak. The remains are currently housed in the Raymond A. Dart Archaeological Human Remains Collection, University of the Witwatersrand, Johannesburg. Most of the skeletons were radiocarbon-dated to between the fourteenth and mid-seventeenth centuries, but one is older and dates to between the seventh and ninth centuries AD. Remains recovered from the various shelters included those of both adults and children, males and females, indicating that these rock shelters were used for the burials of, and were possibly occupied by, a wide variety of individuals over a long period of time. Skeletal analyses revealed several signs of disease and trauma, attesting to some hardships living in this region of South Africa. Stable isotope analyses of carbon and nitrogen indicate a predominantly plant-based diet. Originally it was thought that these individuals’ remains represented those of the historic amaZizi people, however, radiocarbon dates indicate that they are contemporaneous with the Moor Park phase of the Blackburn branch, which predates the amaZizi by several decades. Of interest is the fact that one individual predates the Moor Park phase. This is significant and sheds some light on the movement of people from KwaZulu-Natal into the interior. Future ancient DNA analysis will provide more information on the origin and genetic relationship of these individuals.
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| 7. |
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| 8. |
- Steyn, Maryna, et al.
(författare)
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African Farmers, Not Stone Age Foragers : Reassessment of Human Remains from the Mumbwa Caves, Zambia
- 2023
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Ingår i: African Archaeological Review. - : Springer Nature. - 0263-0338 .- 1572-9842. ; 40:1, s. 53-72
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Tidskriftsartikel (refereegranskat)abstract
- In this article, we reassess the human remains from the Mumbwa Caves housed in the Raymond A. Dart Archaeological Human Remains Collection at the University of the Witwatersrand, South Africa. Based on new radiocarbon dates from human bone collagen and stable isotope analysis, our results revealed that the poorly preserved remains, comprising mostly crania and teeth, represent at least 16 individuals. Some of them have culturally modified anterior teeth. Enamel hypoplastic lesions were seen in a few individuals, which indicates disease and malnutrition during childhood. Radiocarbon dating revealed that all the individuals were buried at Mumbwa sometime between the late tenth and early twentieth century CE, with most dates clustering between the early sixteenth and the late nineteenth century. With the exception of a single individual who seems to have had a hunter-gatherer/forager diet, the carbon and nitrogen isotope values of others are consistent with what would be expected from a low-trophic farmer diet based on foodplants with C4 photosynthetic pathways. It is, therefore, our contention that, rather than being associated with the Stone Age as previously suggested, these individuals lived in more recent agricultural communities around the Mumbwa Caves.
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