{"entity": "researcher", "timestamp": "2026-07-12T08:54:05.859Z", "family": "Breton", "given": "Gwenna", "initials": "G", "orcid": "0000-0002-4100-9963", "affiliations": ["Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv\u00e4gen 18C, 752 36, Uppsala, Sweden. gwenna.breton@ebc.uu.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/757353d5314b4c20ac2ef4833dd207d9.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/757353d5314b4c20ac2ef4833dd207d9"}}, "publications": [{"entity": "publication", "iuid": "e25c443cc2a84c89b1642a768afa88b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e25c443cc2a84c89b1642a768afa88b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e25c443cc2a84c89b1642a768afa88b0"}}, "title": "BaTwa populations from Zambia retain ancestry of past hunter-gatherer groups.", "authors": [{"family": "Breton", "given": "Gwenna", "initials": "G", "orcid": "0000-0002-4100-9963", "researcher": {"href": "https://publications.scilifelab.se/researcher/757353d5314b4c20ac2ef4833dd207d9.json"}}, {"family": "Barham", "given": "Lawrence", "initials": "L"}, {"family": "Mudenda", "given": "George", "initials": "G"}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2024-08-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "7307", "issn-l": "2041-1723"}, "abstract": "Sub-equatorial Africa is today inhabited predominantly by Bantu-speaking groups of Western African descent who brought agriculture to the Luangwa valley in eastern Zambia ~2000 years ago. Before their arrival the area was inhabited by hunter-gatherers, who in many cases were subsequently replaced, displaced or assimilated. In Zambia, we know little about the genetic affinities of these hunter-gatherers. We examine ancestry of two isolated communities in Zambia, known as BaTwa and possible descendants of recent hunter-gatherers. We genotype over two million genome-wide SNPs from two BaTwa populations (total of 80 individuals) and from three comparative farming populations to: (i) determine if the BaTwa carry genetic links to past hunter-gatherer-groups, and (ii) characterise the genetic affinities of past Zambian hunter-gatherer-groups. The BaTwa populations do harbour a hunter-gatherer-like genetic ancestry and Western African ancestry. The hunter-gatherer component is a unique local signature, intermediate between current-day Khoe-San ancestry from southern Africa and central African rainforest hunter-gatherer ancestry.", "doi": "10.1038/s41467-024-50733-y", "pmid": "39181874", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Gothenburg": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11344834"}, {"db": "pii", "key": "10.1038/s41467-024-50733-y"}], "notes": [], "created": "2024-10-21T11:15:04.878Z", "modified": "2024-11-25T10:17:25.391Z"}, {"entity": "publication", "iuid": "b25e3b7b87f74800833f5282c1e78098", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b25e3b7b87f74800833f5282c1e78098.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b25e3b7b87f74800833f5282c1e78098"}}, "title": "Experimental Evaluation of a Direct Fitness Effect of the De Novo Evolved Mouse Gene Pldi.", "authors": [{"family": "Linnenbrink", "given": "Miriam", "initials": "M", "orcid": "0000-0003-0163-3056", "researcher": {"href": "https://publications.scilifelab.se/researcher/bea3667ac83f4d72a7603ec75362c157.json"}}, {"family": "Breton", "given": "Gwenna", "initials": "G", "orcid": "0000-0002-4100-9963", "researcher": {"href": "https://publications.scilifelab.se/researcher/757353d5314b4c20ac2ef4833dd207d9.json"}}, {"family": "Misra", "given": "Pallavi", "initials": "P", "orcid": "0000-0001-8547-793X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd215131b4e2465085afb3659f1967f0.json"}}, {"family": "Pfeifle", "given": "Christine", "initials": "C", "orcid": "0009-0003-4762-0602", "researcher": {"href": "https://publications.scilifelab.se/researcher/a49e120682a2434da8da8c984fa53e62.json"}}, {"family": "Dutheil", "given": "Julien Y", "initials": "JY", "orcid": "0000-0001-7753-4121", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e10ad188dac4206949942827ec0dea6.json"}}, {"family": "Tautz", "given": "Diethard", "initials": "D", "orcid": "0000-0002-0460-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/dec0e6229b6a461c841ebe304cac80c5.json"}}], "type": "journal article", "published": "2024-05-02", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "5", "issn-l": "1759-6653"}, "abstract": "De novo evolved genes emerge from random parts of noncoding sequences and have, therefore, no homologs from which a function could be inferred. While expression analysis and knockout experiments can provide insights into the function, they do not directly test whether the gene is beneficial for its carrier. Here, we have used a seminatural environment experiment to test the fitness of the previously identified de novo evolved mouse gene Pldi, which has been implicated to have a role in sperm differentiation. We used a knockout mouse strain for this gene and competed it against its parental wildtype strain for several generations of free reproduction. We found that the knockout (ko) allele frequency decreased consistently across three replicates of the experiment. Using an approximate Bayesian computation framework that simulated the data under a demographic scenario mimicking the experiment's demography, we could estimate a selection coefficient ranging between 0.21 and 0.61 for the wildtype allele compared to the ko allele in males, under various models. This implies a relatively strong selective advantage, which would fix the new gene in less than hundred generations after its emergence.", "doi": "10.1093/gbe/evae084", "pmid": "38742287", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11091481"}, {"db": "pii", "key": "7668359"}], "notes": [], "created": "2024-11-01T08:24:59.306Z", "modified": "2024-11-01T08:24:59.606Z"}, {"entity": "publication", "iuid": "82e6a97de5654b9c834fc163bc54498a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/82e6a97de5654b9c834fc163bc54498a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/82e6a97de5654b9c834fc163bc54498a"}}, "title": "Comparison of sequencing data processing pipelines and application to underrepresented African human populations.", "authors": [{"family": "Breton", "given": "Gwenna", "initials": "G", "orcid": "0000-0002-4100-9963", "researcher": {"href": "https://publications.scilifelab.se/researcher/757353d5314b4c20ac2ef4833dd207d9.json"}}, {"family": "Johansson", "given": "Anna C V", "initials": "ACV"}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}], "type": "journal article", "published": "2021-10-09", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "volume": "22", "issue": "1", "pages": "488", "issn-l": "1471-2105"}, "abstract": "Population genetic studies of humans make increasing use of high-throughput sequencing in order to capture diversity in an unbiased way. There is an abundance of sequencing technologies, bioinformatic tools and the available genomes are increasing in number. Studies have evaluated and compared some of these technologies and tools, such as the Genome Analysis Toolkit (GATK) and its \"Best Practices\" bioinformatic pipelines. However, studies often focus on a few genomes of Eurasian origin in order to detect technical issues. We instead surveyed the use of the GATK tools and established a pipeline for processing high coverage full genomes from a diverse set of populations, including Sub-Saharan African groups, in order to reveal challenges from human diversity and stratification.\n\nWe surveyed 29 studies using high-throughput sequencing data, and compared their strategies for data pre-processing and variant calling. We found that processing of data is very variable across studies and that the GATK \"Best Practices\" are seldom followed strictly. We then compared three versions of a GATK pipeline, differing in the inclusion of an indel realignment step and with a modification of the base quality score recalibration step. We applied the pipelines on a diverse set of 28 individuals. We compared the pipelines in terms of count of called variants and overlap of the callsets. We found that the pipelines resulted in similar callsets, in particular after callset filtering. We also ran one of the pipelines on a larger dataset of 179 individuals. We noted that including more individuals at the joint genotyping step resulted in different counts of variants. At the individual level, we observed that the average genome coverage was correlated to the number of variants called.\n\nWe conclude that applying the GATK \"Best Practices\" pipeline, including their recommended reference datasets, to underrepresented populations does not lead to a decrease in the number of called variants compared to alternative pipelines. We recommend to aim for coverage of > 30X if identifying most variants is important, and to work with large sample sizes at the variant calling stage, also for underrepresented individuals and populations.", "doi": "10.1186/s12859-021-04407-x", "pmid": "34627144", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12859-021-04407-x"}, {"db": "pmc", "key": "PMC8502359"}], "notes": [], "created": "2021-10-29T13:57:36.217Z", "modified": "2024-01-16T13:48:38.276Z"}, {"entity": "publication", "iuid": "26891b7047fe4d50971760420593e083", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26891b7047fe4d50971760420593e083.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26891b7047fe4d50971760420593e083"}}, "title": "Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens.", "authors": [{"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Breton", "given": "Gwenna", "initials": "G", "orcid": "0000-0002-4100-9963", "researcher": {"href": "https://publications.scilifelab.se/researcher/757353d5314b4c20ac2ef4833dd207d9.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Naidoo", "given": "Thijessen", "initials": "T"}, {"family": "Hollfelder", "given": "Nina", "initials": "N"}, {"family": "Sj\u00f6strand", "given": "Agnes E", "initials": "AE"}, {"family": "Xu", "given": "Jingzi", "initials": "J"}, {"family": "Gattepaille", "given": "Lucie M", "initials": "LM"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG", "orcid": "0000-0001-5235-6461", "researcher": {"href": "https://publications.scilifelab.se/researcher/62a8063a48a446a7947d55f9900894a6.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "de Jongh", "given": "Michael", "initials": "M"}, {"family": "Lombard", "given": "Marlize", "initials": "M", "orcid": "0000-0002-0675-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04e97bbc9914f358864988174b9b58d.json"}}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2020-10-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "37", "issue": "10", "pages": "2944-2954"}, "abstract": "The southern African indigenous Khoe-San populations harbor the most divergent lineages of all living peoples. Exploring their genomes is key to understanding deep human history. We sequenced 25 full genomes from five Khoe-San populations, revealing many novel variants, that 25% of variants are unique to the Khoe-San, and that the Khoe-San group harbors the greatest level of diversity across the globe. In line with previous studies, we found several gene regions with extreme values in genome-wide scans for selection, potentially caused by natural selection in the lineage leading to Homo sapiens and more recent in time. These gene regions included immunity-, sperm-, brain-, diet-, and muscle-related genes. When accounting for recent admixture, all Khoe-San groups display genetic diversity approaching the levels in other African groups and a reduction in effective population size starting around 100,000 years ago. Hence, all human groups show a reduction in effective population size commencing around the time of the Out-of-Africa migrations, which coincides with changes in the paleoclimate records, changes that potentially impacted all humans at the time.", "doi": "10.1093/molbev/msaa140", "pmid": "32697301", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5874945"}, {"db": "pmc", "key": "PMC7530619"}], "notes": [], "created": "2020-12-08T23:26:14.491Z", "modified": "2024-01-16T13:48:41.609Z"}]}