| 1. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics
- 2016
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 572, s. 697-712
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Tidskriftsartikel (refereegranskat)abstract
- Sewage treatment plants (STPs) have repeatedly been suggested as “hotspots” for the emergence and dissemination of antibiotic-resistant bacteria. A critical question still unanswered is if selection pressures within STPs, caused by residual antibiotics or other co-selective agents, are sufficient to specifically promote resistance. To address this, we employed shotgun metagenomic sequencing of samples from different steps of the treatment process in three Swedish STPs. In parallel, concentrations of selected antibiotics, biocides and metals were analyzed. We found that concentrations of tetracycline and ciprofloxacin in the influent were above predicted concentrations for resistance selection, however, there was no consistent enrichment of resistance genes to any particular class of antibiotics in the STPs, neither for biocide and metal resistance genes. The most substantial change of the bacterial communities compared to human feces occurred already in the sewage pipes, manifested by a strong shift from obligate to facultative anaerobes. Through the treatment process, resistance genes against antibiotics, biocides and metals were not reduced to the same extent as fecal bacteria. The OXA-48 gene was consistently enriched in surplus and digested sludge. We find this worrying as OXA-48, still rare in Swedish clinical isolates, provides resistance to carbapenems, one of our most critically important classes of antibiotics. Taken together, metagenomics analyses did not provide clear support for specific antibiotic resistance selection. However, stronger selective forces affecting gross taxonomic composition, and with that resistance gene abundances, limit interpretability. Comprehensive analyses of resistant/non-resistant strains within relevant species are therefore warranted.
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| 2. |
- 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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| 3. |
- 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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| 4. |
- 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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| 5. |
- Hammarén, Rickard, 1989-, et al.
(författare)
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Eurasian back-migration into Northeast Africa was a complex and multifaceted process
- 2023
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 18:11
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies have identified Northeast Africa as an important area for human movements during the Holocene. Eurasian populations have moved back into Northeastern Africa and contributed to the genetic composition of its people. By gathering the largest reference dataset to date of Northeast, North, and East African as well as Middle Eastern populations, we give new depth to our knowledge of Northeast African demographic history. By employing local ancestry methods, we isolated the Non-African parts of modern-day Northeast African genomes and identified the best putative source populations. Egyptians and Sudanese Copts bore most similarities to Levantine populations whilst other populations in the region generally had predominantly genetic contributions from the Arabian peninsula rather than Levantine populations for their Non-African genetic component. We also date admixture events and investigated which factors influenced the date of admixture and find that major linguistic families were associated with the date of Eurasian admixture. Taken as a whole we detect complex patterns of admixture and diverse origins of Eurasian admixture in Northeast African populations of today.
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| 6. |
- Hammarén, Rickard, 1989-, et al.
(författare)
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Eurasian back-migrations into Northeast Africa was a complex and multifaceted process
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Recent studies have identified Northeast Africa as an important area for human movements during the Holocene. Eurasian populations have moved back into Northeastern Africa and contributed to the genetic composition of its people. By gathering the largest reference dataset to date of Northeast, North, and East African as well as Middle Eastern populations, we give new depth to our knowledge of Northeast African demographic history. By employing local ancestry methods, we isolated the Non-African parts of modern-day Northeast African genomes and identified the best putative source populations. Egyptians and Sudanese Copts bore most similarities to Levantine populations whilst other populations in the region generally had predominantly genetic contributions from Arabian peninsula rather than Levantine populations for their Non-African genetic component. We also date admixture events and investigated which factors influenced the date of admixture and find that major linguistic families were associated with the date of Eurasian admixture. Taken as a whole we detect complex patterns of admixture and diverse origins of Eurasian admixture in Northeast African populations of today.
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| 7. |
- Hammarén, Rickard, et al.
(författare)
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FARAO: the flexible all-round annotation organizer
- 2016
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 32:23, s. 3664-3666
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Tidskriftsartikel (refereegranskat)abstract
- Summary: With decreasing costs of generating DNA sequence data, genome and metagenome projects have become accessible to a wider scientific community. However, to extract meaningful information and visualize the data remain challenging. We here introduce FARAO, a highly scalable software for organization, visualization and integration of annotation and read coverage data that can also combine output data from several bioinformatics tools. The capabilities of FARAO can greatly aid analyses of genomic and metagenomic datasets. Availability and Implementation: FARAO is implemented in Perl and is supported under Unix-like operative systems, including Linux and macOS. The Perl source code is freely available for download under the MIT License from http://microbiology.se/software/farao/.
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| 8. |
- Hammarén, Rickard, 1989-
(författare)
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From the migrations of herders and farmers to the colonial era and the modern-day : Genetic inferences on African demographic history
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Africa is the birthplace of the human species and home to great linguistic, cultural, and genetic diversity. Despite this, the genetics of the peoples of the continent remains understudied. In this thesis, I apply population genetic approaches, to contribute to the knowledge of human demographic history in Africa. Specifically, I investigated three events that have had major impacts on human population genetics in Africa. Paper I, investigated Eurasian back migrations into Northeast Africa and what genetic patterns this has left in the current-day populations of the area. I identified complex demography and linguistic stratification of Eurasian admixture in the region. These genetic patterns coincide in time with historical events such as the spread of Islam, the fall of the Kingdom of Aksum, and trade routes across the Red Sea. Paper II focused on the Bantu expansion, the different migratory routes of Bantu-speakers out of West Africa, and how they shaped the genetic makeup of the peoples of sub-equatorial Africa. We compiled the most comprehensive geographically distributed genetic dataset of Bantu-speaking individuals to date. I investigated the spatial patterns of migrations and the decline of genetic diversity from their homeland. I find evidence for serial founder events and migrations across Zambia and the Congo basin to the rest of sub-equatorial Africa. Paper III and IV involved South Africa and the effects that European colonialism and 20:th century policies have had on the country's genetic landscape. Paper III focuses on the Afrikaner population of South Africa, descendants of the first European settlers of the Cape colony, I describe the extent of African and Asian admixture in this population and investigate evidence of selection and adaptive admixture. Paper IV focuses on the Coloured population of South Africa, an emergent cultural identity. The Coloured population traces their origin primarily to Khoe-San women, manumitted slaves, and European men from the Cape colony. The term Coloured was also used for admixed individuals under the Apartheid racial classification system. The Coloured has one of the most complex admixture histories in the world, with genetic ancestry from Europe, East and South Asia, West and East Africa, as well as southern African Khoe-San. In our paper, we describe these complex patterns, the differences in sex-biased admixture, and determine the admixture dates across an extensive collection of Coloured, across South Africa. My work thus highlights complex genetic patterns within African human demographic history and shows how profoundly it has been shaped by the movement of people in the last 5 000 years.
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| 9. |
- Hollfelder, Nina, et al.
(författare)
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Patterns of African and Asian admixture in the Afrikaner population of South Africa
- 2020
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Ingår i: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 18:1
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Tidskriftsartikel (refereegranskat)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 current-day European populations.
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| 10. |
- Jemt, Anders, 1985-, et al.
(författare)
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Evaluation of methods for whole genome and transcriptome sequencing from nanograms of FFPE samples
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The most widely used method for the preservation of clinical tissue specimens is formalin fixation and paraffin embedding (FFPE). Simultaneous analysis of RNA and DNA from samples preserved using this method have long proved problematic, primarily due to lack of material. Here, we describe an attempt to build a complete analysis package for RNA and DNA extracted from single tissue sections. The workflow includes quality control of the extracted material, library preparation and data analysis. We extract DNA with varying integrity from FFPE sections and subject them to whole genome sequencing using two library preparation methods, Illumina TruSeq Nano using the Illumina NeoPrep and Rubicon Genomics ThruPlex. We are able to obtain some usable data, albeit with high duplication rates, demonstrating both the possibilities and challenges of sequencing damaged DNA. Two different approaches to transcriptome sequencing are assessed, the TruSeq RNA Access library preparation kit from Illumina and the SMARTer Stranded Total RNA-Seq Kit - Pico Input from Clonetech. The sequence capture approach of the TruSeq kit is shown to be more robust to low integrity RNA compared to the SMARTer kit. However, the SMARTer kit needs much less starting material and is able to yield data about all transcripts, not just protein coding mRNA.
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