1
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Johnson OL, Tobler R, Schmidt JM, Huber CD. Population genetic simulation: Benchmarking frameworks for non-standard models of natural selection. Mol Ecol Resour 2024; 24:e13930. [PMID: 38247258 DOI: 10.1111/1755-0998.13930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024]
Abstract
Population genetic simulation has emerged as a common tool for investigating increasingly complex evolutionary and demographic models. Software capable of handling high-level model complexity has recently been developed, and the advancement of tree sequence recording now allows simulations to merge the efficiency and genealogical insight of coalescent simulations with the flexibility of forward simulations. However, frameworks utilizing these features have not yet been compared and benchmarked. Here, we evaluate various simulation workflows using the coalescent simulator msprime and the forward simulator SLiM, to assess resource efficiency and determine an optimal simulation framework. Three aspects were evaluated: (1) the burn-in, to establish an equilibrium level of neutral diversity in the population; (2) the forward simulation, in which temporally fluctuating selection is acting; and (3) the final computation of summary statistics. We provide typical memory and computation time requirements for each step. We find that the fastest framework, a combination of coalescent and forward simulation with tree sequence recording, increases simulation speed by over twenty times compared to classical forward simulations without tree sequence recording, although it does require six times more memory. Overall, using efficient simulation workflows can lead to a substantial improvement when modelling complex evolutionary scenarios-although the optimal framework ultimately depends on the available computational resources.
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Affiliation(s)
- Olivia L Johnson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Raymond Tobler
- Evolution of Cultural Diversity Initiative, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Joshua M Schmidt
- Department of Ophthalmology, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | - Christian D Huber
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
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2
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Davidson R, Williams MP, Roca-Rada X, Kassadjikova K, Tobler R, Fehren-Schmitz L, Llamas B. Allelic bias when performing in-solution enrichment of ancient human DNA. Mol Ecol Resour 2023; 23:1823-1840. [PMID: 37712846 DOI: 10.1111/1755-0998.13869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023]
Abstract
In-solution hybridisation enrichment of genetic variation is a valuable methodology in human paleogenomics. It allows enrichment of endogenous DNA by targeting genetic markers that are comparable between sequencing libraries. Many studies have used the 1240k reagent-which enriches 1,237,207 genome-wide SNPs-since 2015, though access was restricted. In 2021, Twist Biosciences and Daicel Arbor Biosciences independently released commercial kits that enabled all researchers to perform enrichments for the same 1240 k SNPs. We used the Daicel Arbor Biosciences Prime Plus kit to enrich 132 ancient samples from three continents. We identified a systematic assay bias that increases genetic similarity between enriched samples and that cannot be explained by batch effects. We present the impact of the bias on population genetics inferences (e.g. Principal Components Analysis, ƒ-statistics) and genetic relatedness (READ). We compare the Prime Plus bias to that previously reported of the legacy 1240k enrichment assay. In ƒ-statistics, we find that all Prime-Plus-generated data exhibit artefactual excess shared drift, such that within-continent relationships cannot be correctly determined. The bias is more subtle in READ, though interpretation of the results can still be misleading in specific contexts. We expect the bias may affect analyses we have not yet tested. Our observations support previously reported concerns for the integration of different data types in paleogenomics. We also caution that technological solutions to generate 1240k data necessitate a thorough validation process before their adoption in the paleogenomic community.
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Affiliation(s)
- Roberta Davidson
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Matthew P Williams
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Biology Department, The Pennsylvania State University, Pennsylvania, USA
| | - Xavier Roca-Rada
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kalina Kassadjikova
- UCSC Paleogenomics, Department of Anthropology, University of California, California, USA
| | - Raymond Tobler
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, Department of Anthropology, University of California, California, USA
- UCSC Genomics Institute, University of California, California, USA
| | - Bastien Llamas
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia
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3
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Tobler R, Souilmi Y, Huber CD, Bean N, Turney CSM, Grey ST, Cooper A. The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa. Proc Natl Acad Sci U S A 2023; 120:e2213061120. [PMID: 37220274 PMCID: PMC10235988 DOI: 10.1073/pnas.2213061120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 03/14/2023] [Indexed: 05/25/2023] Open
Abstract
The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.
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Affiliation(s)
- Raymond Tobler
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
- Environment Institute, The University of Adelaide, Adelaide, SA5005, Australia
| | - Christian D. Huber
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
| | - Nigel Bean
- Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, SA5005, Australia
- School of Mathematical Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | - Chris S. M. Turney
- Division of Research, University of Technology Sydney, Ultimo, NSW2007, Australia
| | - Shane T. Grey
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW2052, Australia
- Transplantation Immunology Group, Translation Science Pillar, Garvan Institute of Medical Research, Darlinghurst, NSW2010, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
- Blue Sky Genetics, Ashton, SA5137, Australia
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4
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Taufik L, Teixeira JC, Llamas B, Sudoyo H, Tobler R, Purnomo GA. Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects. Genes (Basel) 2022; 13:genes13122373. [PMID: 36553640 PMCID: PMC9778601 DOI: 10.3390/genes13122373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Genomic sequence data from worldwide human populations have provided a range of novel insights into our shared ancestry and the historical migrations that have shaped our global genetic diversity. However, a comprehensive understanding of these fundamental questions has been impeded by the lack of inclusion of many Indigenous populations in genomic surveys, including those from the Wallacean archipelago (which comprises islands of present-day Indonesia located east and west of Wallace's and Lydekker's Lines, respectively) and the former continent of Sahul (which once combined New Guinea and Australia during lower sea levels in the Pleistocene). Notably, these regions have been important areas of human evolution throughout the Late Pleistocene, as documented by diverse fossil and archaeological records which attest to the regional presence of multiple hominin species prior to the arrival of anatomically modern human (AMH) migrants. In this review, we collate and discuss key findings from the past decade of population genetic and phylogeographic literature focussed on the hominin history in Wallacea and Sahul. Specifically, we examine the evidence for the timing and direction of the ancient AMH migratory movements and subsequent hominin mixing events, emphasising several novel but consistent results that have important implications for addressing these questions. Finally, we suggest potentially lucrative directions for future genetic research in this key region of human evolution.
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Affiliation(s)
- Leonard Taufik
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia
- Correspondence: (L.T.); (G.A.P.)
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, ACT 2601, Australia
- Centre for Interdisciplinary Studies, University of Coimbra, 3004-531 Coimbra, Portugal
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2601, Australia
- Indigenous Genomics Research Group, Telethon Kids Institute, Adelaide, SA 5001, Australia
| | - Herawati Sudoyo
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia
| | - Raymond Tobler
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, ACT 2601, Australia
| | - Gludhug A. Purnomo
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Correspondence: (L.T.); (G.A.P.)
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5
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Souilmi Y, Tobler R, Johar A, Williams M, Grey ST, Schmidt J, Teixeira JC, Rohrlach A, Tuke J, Johnson O, Gower G, Turney C, Cox M, Cooper A, Huber CD. Admixture has obscured signals of historical hard sweeps in humans. Nat Ecol Evol 2022; 6:2003-2015. [PMID: 36316412 PMCID: PMC9715430 DOI: 10.1038/s41559-022-01914-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 09/16/2022] [Indexed: 11/06/2022]
Abstract
The role of natural selection in shaping biological diversity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied on genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between diverged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species. Through analyses of ancient and modern human genomes, we show that previously reported Holocene-era admixture has masked more than 50 historic hard sweeps in modern European genomes. Our results imply that this canonical mode of selection has probably been underappreciated in the evolutionary history of humans and suggest that our current understanding of the tempo and mode of selection in natural populations may be inaccurate.
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Affiliation(s)
- Yassine Souilmi
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
| | - Raymond Tobler
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, Australian Capital Territory, Australia.
| | - Angad Johar
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA.
| | - Matthew Williams
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Shane T Grey
- Transplantation Immunology Group, Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, New South Wales, Australia
| | - Joshua Schmidt
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - João C Teixeira
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Adam Rohrlach
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, South Australia, Australia
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Jonathan Tuke
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, South Australia, Australia
- School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Olivia Johnson
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Graham Gower
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Chris Turney
- Chronos 14Carbon-Cycle Facility and Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Murray Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia.
- BlueSky Genetics, Ashton, South Australia, Australia.
| | - Christian D Huber
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
- Department of Biology, Penn State University, University Park, PA, USA.
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6
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Oliva A, Tobler R, Llamas B, Souilmi Y. Additional evaluations show that specific BWA-aln settings still outperform BWA-mem for ancient DNA data alignment. Ecol Evol 2022; 11:18743-18748. [PMID: 35003706 PMCID: PMC8717315 DOI: 10.1002/ece3.8297] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/07/2021] [Accepted: 10/15/2021] [Indexed: 11/07/2022] Open
Abstract
Xu et al. (2021) recently recommended a new parameterization of BWA-mem as a superior alternative to the widely-used BWA-aln algorithm to map ancient DNA sequencing data. Here, we compare the BWA-mem parameterization recommended by Xu et al. with the best-performing alignment methods determined in the recent benchmarks of Oliva and colleagues (2021), demonstrating that BWA-aln is still the gold-standard for ancient DNA read alignment .
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Affiliation(s)
- Adrien Oliva
- Australian Centre for Ancient DNASchool of Biological SciencesFaculty of SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Raymond Tobler
- Australian Centre for Ancient DNASchool of Biological SciencesFaculty of SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
- The Environment InstituteFaculty of SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Bastien Llamas
- Australian Centre for Ancient DNASchool of Biological SciencesFaculty of SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
- The Environment InstituteFaculty of SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
- National Centre for Indigenous GenomicsAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Yassine Souilmi
- Australian Centre for Ancient DNASchool of Biological SciencesFaculty of SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
- The Environment InstituteFaculty of SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
- National Centre for Indigenous GenomicsAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
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7
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Cooper A, Turney CSM, Palmer J, Hogg A, McGlone M, Wilmshurst J, Lorrey AM, Heaton TJ, Russell JM, McCracken K, Anet JG, Rozanov E, Friedel M, Suter I, Peter T, Muscheler R, Adolphi F, Dosseto A, Faith JT, Fenwick P, Fogwill CJ, Hughen K, Lipson M, Liu J, Nowaczyk N, Rainsley E, Bronk Ramsey C, Sebastianelli P, Souilmi Y, Stevenson J, Thomas Z, Tobler R, Zech R. Response to Comment on "A global environmental crisis 42,000 years ago". Science 2021; 374:eabi9756. [PMID: 34793203 DOI: 10.1126/science.abi9756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Alan Cooper
- South Australian Museum, Adelaide, SA 5000, Australia, and BlueSky Genetics, P.O. Box 287, Adelaide, SA 5137, Australia
| | - Chris S M Turney
- Chronos 14Carbon-Cycle Facility and Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jonathan Palmer
- Chronos Carbon-Cycle Facility and Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Alan Hogg
- Radiocarbon Dating Laboratory, University of Waikato, Hamilton, New Zealand
| | - Matt McGlone
- Ecosystems and Conservation, Landcare Research, P.O. Box 69040, Lincoln, New Zealand
| | - Janet Wilmshurst
- Ecosystems and Conservation, Landcare Research, P.O. Box 69040, Lincoln, New Zealand.,School of Environment, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Andrew M Lorrey
- National Institute of Water and Atmospheric Research Ltd., Auckland, New Zealand
| | - Timothy J Heaton
- School of Mathematics and Statistics, University of Sheffield, Sheffield S3 7RH, UK
| | - James M Russell
- Department of Geological Sciences, Brown University, Providence, RI 02912, USA
| | | | - Julien G Anet
- Zurich University of Applied Sciences, Centre for Aviation, Winterthur, Switzerland
| | - Eugene Rozanov
- Institute for Atmospheric and Climatic Science, ETH Zurich, Zurich, Switzerland.,Physikalisch-Meteorologisches Observatorium Davos and World Radiation Center, Davos, Switzerland.,Department of Physics of Earth, Faculty of Physics, St. Petersburg State University, St. Petersburg, Russia
| | - Marina Friedel
- Institute for Atmospheric and Climatic Science, ETH Zurich, Zurich, Switzerland
| | - Ivo Suter
- Swiss Federal Laboratories for Materials Science and Technology (Empa), Dübendorf, Switzerland
| | - Thomas Peter
- Institute for Atmospheric and Climatic Science, ETH Zurich, Zurich, Switzerland
| | - Raimund Muscheler
- Department of Geology, Quaternary Sciences, Lund University, Lund, Sweden
| | - Florian Adolphi
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Anthony Dosseto
- Wollongong Isotope Geochronology Laboratory, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
| | - J Tyler Faith
- Natural History Museum of Utah and Department of Anthropology, University of Utah, Salt Lake City, UT 84108, USA
| | - Pavla Fenwick
- Gondwana Tree-Ring Laboratory, P.O. Box 14, Little River, Canterbury 7546, New Zealand
| | - Christopher J Fogwill
- School of Geography, Geology and the Environment, University of Keele, Keele, Staffordshire, UK
| | - Konrad Hughen
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Matthew Lipson
- Centre for Excellence in Climate System Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jiabo Liu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Norbert Nowaczyk
- Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, Section 4.3, Potsdam, Germany
| | - Eleanor Rainsley
- School of Geography, Geology and the Environment, University of Keele, Keele, Staffordshire, UK
| | - Christopher Bronk Ramsey
- Research Laboratory for Archaeology and the History of Art, School of Archaeology, University of Oxford, Oxford OX1 3TG, UK
| | - Paolo Sebastianelli
- Faculty of Mathematics, Astronomy and Physics (FAMAF), National University of Córdoba, Córdoba, Argentina, and School of Chemistry, University of New South Wales, Kensington, NSW 2052, Australia
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, SA 5000, Australia
| | - Janelle Stevenson
- Archaeology and Natural History, School of Culture History and Language, ANU College of Asia and the Pacific, Canberra, ACT 2601, Australia
| | - Zoe Thomas
- Chronos Carbon-Cycle Facility and Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Raymond Tobler
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, SA 5000, Australia
| | - Roland Zech
- Institute of Geography, Friedrich-Schiller-University Jena, Jena, Germany
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8
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Cooper A, Turney CSM, Palmer J, Hogg A, McGlone M, Wilmshurst J, Lorrey AM, Heaton TJ, Russell JM, McCracken K, Anet JG, Rozanov E, Friedel M, Suter I, Peter T, Muscheler R, Adolphi F, Dosseto A, Faith JT, Fenwick P, Fogwill CJ, Hughen K, Lipson M, Liu J, Nowaczyk N, Rainsley E, Ramsey CB, Sebastianelli P, Souilmi Y, Stevenson J, Thomas Z, Tobler R, Zech R. Response to Comment on "A global environmental crisis 42,000 years ago". Science 2021; 374:eabh3655. [PMID: 34793228 DOI: 10.1126/science.abh3655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Our paper about the impacts of the Laschamps Geomagnetic Excursion 42,000 years ago has provoked considerable scientific and public interest, particularly in the so-called Adams Event associated with the initial transition of the magnetic poles. Although we welcome the opportunity to discuss our new ideas, Hawks' assertions of misrepresentation are especially disappointing given his limited examination of the material.
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Affiliation(s)
- Alan Cooper
- South Australian Museum, Adelaide, SA 5000, Australia, and BlueSky Genetics, P.O. Box 287, Adelaide, SA 5137, Australia
| | - Chris S M Turney
- Chronos 14Carbon-Cycle Facility and Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jonathan Palmer
- Chronos Carbon-Cycle Facility and Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Alan Hogg
- Radiocarbon Dating Laboratory, University of Waikato, Hamilton, New Zealand
| | - Matt McGlone
- Ecosystems and Conservation, Landcare Research, P.O. Box 69040, Lincoln, New Zealand
| | - Janet Wilmshurst
- Ecosystems and Conservation, Landcare Research, P.O. Box 69040, Lincoln, New Zealand.,School of Environment, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Andrew M Lorrey
- National Institute of Water and Atmospheric Research Ltd., Auckland, New Zealand
| | - Timothy J Heaton
- School of Mathematics and Statistics, University of Sheffield, Sheffield S3 7RH, UK
| | - James M Russell
- Department of Geological Sciences, Brown University, Providence, RI 02912, USA
| | | | - Julien G Anet
- Zurich University of Applied Sciences, Centre for Aviation, Winterthur, Switzerland
| | - Eugene Rozanov
- Institute for Atmospheric and Climatic Science, ETH Zurich, Zurich, Switzerland.,Physikalisch-Meteorologisches Observatorium Davos and World Radiation Center, Davos, Switzerland.,Department of Physics of Earth, Faculty of Physics, St. Petersburg State University, St. Petersburg, Russia
| | - Marina Friedel
- Institute for Atmospheric and Climatic Science, ETH Zurich, Zurich, Switzerland
| | - Ivo Suter
- Swiss Federal Laboratories for Materials Science and Technology (Empa), Dübendorf, Switzerland
| | - Thomas Peter
- Institute for Atmospheric and Climatic Science, ETH Zurich, Zurich, Switzerland
| | - Raimund Muscheler
- Department of Geology, Quaternary Sciences, Lund University, Lund, Sweden
| | - Florian Adolphi
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Anthony Dosseto
- Wollongong Isotope Geochronology Laboratory, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
| | - J Tyler Faith
- Natural History Museum of Utah and Department of Anthropology, University of Utah, Salt Lake City, UT 84108, USA
| | - Pavla Fenwick
- Gondwana Tree-Ring Laboratory, P.O. Box 14, Little River, Canterbury 7546, New Zealand
| | - Christopher J Fogwill
- School of Geography, Geology and the Environment, University of Keele, Keele, Staffordshire, UK
| | - Konrad Hughen
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Matthew Lipson
- Centre for Excellence in Climate System Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jiabo Liu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Norbert Nowaczyk
- Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, Section 4.3, Potsdam, Germany
| | - Eleanor Rainsley
- School of Geography, Geology and the Environment, University of Keele, Keele, Staffordshire, UK
| | - Christopher Bronk Ramsey
- Research Laboratory for Archaeology and the History of Art, School of Archaeology, University of Oxford, Oxford OX1 3TG, UK
| | - Paolo Sebastianelli
- Faculty of Mathematics, Astronomy and Physics (FAMAF), National University of Córdoba, Córdoba, Argentina, and School of Chemistry, University of New South Wales, Kensington, NSW 2052, Australia
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, SA 5000, Australia
| | - Janelle Stevenson
- Archaeology and Natural History, School of Culture History and Language, ANU College of Asia and the Pacific, Canberra, ACT 2601, Australia
| | - Zoe Thomas
- Chronos Carbon-Cycle Facility and Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Raymond Tobler
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, SA 5000, Australia
| | - Roland Zech
- Institute of Geography, Friedrich-Schiller-University Jena, Jena, Germany
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9
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Affiliation(s)
- Salvador Herrando‐Pérez
- Australian Centre for Ancient DNA School of Biological Sciences The University of Adelaide Adelaide SA Australia
- Department of Biogeography and Global Change Museo Nacional de Ciencias NaturalesSpanish National Research Council (CSIC) Madrid Spain
| | - Raymond Tobler
- Australian Centre for Ancient DNA School of Biological Sciences The University of Adelaide Adelaide SA Australia
- Evolution of Cultural Diversity Initiative Australian National University Canberra ACT Australia
| | - Christian D. Huber
- Australian Centre for Ancient DNA School of Biological Sciences The University of Adelaide Adelaide SA Australia
- Department of Biology The Pennsylvania State University University Park PA USA
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10
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Oliva A, Tobler R, Cooper A, Llamas B, Souilmi Y. Systematic benchmark of ancient DNA read mapping. Brief Bioinform 2021; 22:6217726. [PMID: 33834210 DOI: 10.1093/bib/bbab076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 01/05/2021] [Accepted: 02/16/2021] [Indexed: 11/12/2022] Open
Abstract
The current standard practice for assembling individual genomes involves mapping millions of short DNA sequences (also known as DNA 'reads') against a pre-constructed reference genome. Mapping vast amounts of short reads in a timely manner is a computationally challenging task that inevitably produces artefacts, including biases against alleles not found in the reference genome. This reference bias and other mapping artefacts are expected to be exacerbated in ancient DNA (aDNA) studies, which rely on the analysis of low quantities of damaged and very short DNA fragments (~30-80 bp). Nevertheless, the current gold-standard mapping strategies for aDNA studies have effectively remained unchanged for nearly a decade, during which time new software has emerged. In this study, we used simulated aDNA reads from three different human populations to benchmark the performance of 30 distinct mapping strategies implemented across four different read mapping software-BWA-aln, BWA-mem, NovoAlign and Bowtie2-and quantified the impact of reference bias in downstream population genetic analyses. We show that specific NovoAlign, BWA-aln and BWA-mem parameterizations achieve high mapping precision with low levels of reference bias, particularly after filtering out reads with low mapping qualities. However, unbiased NovoAlign results required the use of an IUPAC reference genome. While relevant only to aDNA projects where reference population data are available, the benefit of using an IUPAC reference demonstrates the value of incorporating population genetic information into the aDNA mapping process, echoing recent results based on graph genome representations.
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Affiliation(s)
- Adrien Oliva
- Australian Centre for Ancient DNA at the University of Adelaide, Australia
| | - Raymond Tobler
- Australian Centre for Ancient DNA at the University of Adelaide, Australia
| | - Alan Cooper
- Australian Research Council Laureate Fellow specializing in ancient DNA, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA at the University of Adelaide, Australia
| | - Yassine Souilmi
- Australian Centre for Ancient DNA at the University of Adelaide, Australia
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11
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Cooper A, Turney CSM, Palmer J, Hogg A, McGlone M, Wilmshurst J, Lorrey AM, Heaton TJ, Russell JM, McCracken K, Anet JG, Rozanov E, Friedel M, Suter I, Peter T, Muscheler R, Adolphi F, Dosseto A, Faith JT, Fenwick P, Fogwill CJ, Hughen K, Lipson M, Liu J, Nowaczyk N, Rainsley E, Bronk Ramsey C, Sebastianelli P, Souilmi Y, Stevenson J, Thomas Z, Tobler R, Zech R. A global environmental crisis 42,000 years ago. Science 2021; 371:811-818. [PMID: 33602851 DOI: 10.1126/science.abb8677] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022]
Abstract
Geological archives record multiple reversals of Earth's magnetic poles, but the global impacts of these events, if any, remain unclear. Uncertain radiocarbon calibration has limited investigation of the potential effects of the last major magnetic inversion, known as the Laschamps Excursion [41 to 42 thousand years ago (ka)]. We use ancient New Zealand kauri trees (Agathis australis) to develop a detailed record of atmospheric radiocarbon levels across the Laschamps Excursion. We precisely characterize the geomagnetic reversal and perform global chemistry-climate modeling and detailed radiocarbon dating of paleoenvironmental records to investigate impacts. We find that geomagnetic field minima ~42 ka, in combination with Grand Solar Minima, caused substantial changes in atmospheric ozone concentration and circulation, driving synchronous global climate shifts that caused major environmental changes, extinction events, and transformations in the archaeological record.
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Affiliation(s)
- Alan Cooper
- South Australian Museum, Adelaide, SA 5000, Australia. .,BlueSky Genetics, PO Box 287, Adelaide, SA 5137, Australia
| | - Chris S M Turney
- Chronos Carbon-Cycle Facility, and Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Jonathan Palmer
- Chronos Carbon-Cycle Facility, and Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Alan Hogg
- Radiocarbon Dating Laboratory, University of Waikato, Hamilton 3240, New Zealand
| | - Matt McGlone
- Landcare Research, PO Box 69040, Lincoln, New Zealand
| | - Janet Wilmshurst
- Landcare Research, PO Box 69040, Lincoln, New Zealand.,School of Environment, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Andrew M Lorrey
- National Institute of Water and Atmospheric Research Ltd, Auckland 1010, New Zealand
| | - Timothy J Heaton
- School of Mathematics and Statistics, University of Sheffield, Sheffield S3 7RH, UK
| | - James M Russell
- Department of Geological Sciences, Brown University, Providence, RI 02912, USA
| | - Ken McCracken
- University of New South Wales, Sydney, NSW 2052, Australia
| | - Julien G Anet
- Zurich University of Applied Sciences, Centre for Aviation, 8401 Winterthur, Switzerland
| | - Eugene Rozanov
- Institute for Atmospheric and Climatic Science, ETH Zurich, 8006 Zurich, Switzerland.,Physikalisch-Meteorologisches Observatorium Davos and World Radiation Center, 7260 Davos, Switzerland.,Department of Physics of Earth, Faculty of Physics, St. Petersburg State University, St. Petersburg 198504, Russia
| | - Marina Friedel
- Institute for Atmospheric and Climatic Science, ETH Zurich, 8006 Zurich, Switzerland
| | - Ivo Suter
- Swiss Federal Laboratories for Materials Science and Technology (Empa), 8600 Dübendorf, Switzerland
| | - Thomas Peter
- Institute for Atmospheric and Climatic Science, ETH Zurich, 8006 Zurich, Switzerland
| | - Raimund Muscheler
- Department of Geology, Quaternary Sciences, Lund University, 22362 Lund, Sweden
| | - Florian Adolphi
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Anthony Dosseto
- Wollongong Isotope Geochronology Laboratory, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
| | - J Tyler Faith
- Natural History Museum of Utah and Department of Anthropology, University of Utah, Salt Lake City, UT 84108, USA
| | - Pavla Fenwick
- Gondwana Tree-Ring Laboratory, PO Box 14, Little River, Canterbury 7546, New Zealand
| | - Christopher J Fogwill
- School of Geography, Geology and the Environment, University of Keele, Keele, Staffordshire ST5 5BG, UK
| | - Konrad Hughen
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Mathew Lipson
- Centre of Excellence for Climate System Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jiabo Liu
- Southern University of Science and Technology, Department of Ocean Science and Engineering, Shenzhen 518055, China
| | - Norbert Nowaczyk
- Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, Section 4.3, 14473 Potsdam, Germany
| | - Eleanor Rainsley
- School of Geography, Geology and the Environment, University of Keele, Keele, Staffordshire ST5 5BG, UK
| | - Christopher Bronk Ramsey
- Research Laboratory for Archaeology and the History of Art, School of Archaeology, University of Oxford, OX1 3TG, UK
| | - Paolo Sebastianelli
- Faculty of Mathematics, Astronomy and Physics (FAMAF), National University of Cordoba, X5000HUA, Argentina
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, SA 5000, Australia
| | - Janelle Stevenson
- Archaeology and Natural History, School of Culture History and Language, ANU College of Asia and the Pacific, Canberra, ACT 2601, Australia.,Australia ARC Centre of Excellence for Australian Biodiversity and Heritage, Australian National University, ACT 2601, Australia
| | - Zoë Thomas
- Chronos Carbon-Cycle Facility, and Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Raymond Tobler
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, SA 5000, Australia
| | - Roland Zech
- Institute of Geography, Friedrich-Schiller-University Jena, 07743 Jena, Germany
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12
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Lan D, Tobler R, Souilmi Y, Llamas B. genozip: a fast and efficient compression tool for VCF files. Bioinformatics 2020; 36:4091-4092. [PMID: 32407471 PMCID: PMC7332572 DOI: 10.1093/bioinformatics/btaa290] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/01/2020] [Accepted: 04/27/2020] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION genozip is a new lossless compression tool for Variant Call Format (VCF) files. By applying field-specific algorithms and fully utilizing the available computational hardware, genozip achieves the highest compression ratios amongst existing lossless compression tools known to the authors, at speeds comparable with the fastest multi-threaded compressors. AVAILABILITY AND IMPLEMENTATION genozip is freely available to non-commercial users. It can be installed via conda-forge, Docker Hub, or downloaded from github.com/divonlan/genozip. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Divon Lan
- School of Biological Sciences, The Environment Institute, Faculty of Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Raymond Tobler
- School of Biological Sciences, The Environment Institute, Faculty of Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Yassine Souilmi
- School of Biological Sciences, The Environment Institute, Faculty of Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Bastien Llamas
- School of Biological Sciences, The Environment Institute, Faculty of Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
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13
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Barghi N, Tobler R, Nolte V, Jakšić AM, Mallard F, Otte KA, Dolezal M, Taus T, Kofler R, Schlötterer C. Genetic redundancy fuels polygenic adaptation in Drosophila. PLoS Biol 2019; 17:e3000128. [PMID: 30716062 PMCID: PMC6375663 DOI: 10.1371/journal.pbio.3000128] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 02/14/2019] [Accepted: 01/14/2019] [Indexed: 12/31/2022] Open
Abstract
The genetic architecture of adaptive traits is of key importance to predict evolutionary responses. Most adaptive traits are polygenic-i.e., result from selection on a large number of genetic loci-but most molecularly characterized traits have a simple genetic basis. This discrepancy is best explained by the difficulty in detecting small allele frequency changes (AFCs) across many contributing loci. To resolve this, we use laboratory natural selection to detect signatures for selective sweeps and polygenic adaptation. We exposed 10 replicates of a Drosophila simulans population to a new temperature regime and uncovered a polygenic architecture of an adaptive trait with high genetic redundancy among beneficial alleles. We observed convergent responses for several phenotypes-e.g., fitness, metabolic rate, and fat content-and a strong polygenic response (99 selected alleles; mean s = 0.059). However, each of these selected alleles increased in frequency only in a subset of the evolving replicates. We discerned different evolutionary paradigms based on the heterogeneous genomic patterns among replicates. Redundancy and quantitative trait (QT) paradigms fitted the experimental data better than simulations assuming independent selective sweeps. Our results show that natural D. simulans populations harbor a vast reservoir of adaptive variation facilitating rapid evolutionary responses using multiple alternative genetic pathways converging at a new phenotypic optimum. This key property of beneficial alleles requires the modification of testing strategies in natural populations beyond the search for convergence on the molecular level.
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Affiliation(s)
- Neda Barghi
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Raymond Tobler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Ana Marija Jakšić
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - François Mallard
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | | | - Marlies Dolezal
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Plattform Bioinformatik und Biostatistik, Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Thomas Taus
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
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14
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Schlötterer C, Kofler R, Versace E, Tobler R, Franssen SU. Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation. Heredity (Edinb) 2015; 114:431-40. [PMID: 25269380 PMCID: PMC4815507 DOI: 10.1038/hdy.2014.86] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/01/2014] [Accepted: 07/14/2014] [Indexed: 12/20/2022] Open
Abstract
Evolve and resequence (E&R) is a new approach to investigate the genomic responses to selection during experimental evolution. By using whole genome sequencing of pools of individuals (Pool-Seq), this method can identify selected variants in controlled and replicable experimental settings. Reviewing the current state of the field, we show that E&R can be powerful enough to identify causative genes and possibly even single-nucleotide polymorphisms. We also discuss how the experimental design and the complexity of the trait could result in a large number of false positive candidates. We suggest experimental and analytical strategies to maximize the power of E&R to uncover the genotype-phenotype link and serve as an important research tool for a broad range of evolutionary questions.
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Affiliation(s)
- C Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - R Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - E Versace
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Center for Mind/Brain Sciences, University of Trento, Rovereto, Italy
| | - R Tobler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - S U Franssen
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
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15
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Bastide H, Betancourt A, Nolte V, Tobler R, Stöbe P, Futschik A, Schlötterer C. A genome-wide, fine-scale map of natural pigmentation variation in Drosophila melanogaster. PLoS Genet 2013; 9:e1003534. [PMID: 23754958 PMCID: PMC3674992 DOI: 10.1371/journal.pgen.1003534] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 04/11/2013] [Indexed: 11/25/2022] Open
Abstract
Various approaches can be applied to uncover the genetic basis of natural phenotypic variation, each with their specific strengths and limitations. Here, we use a replicated genome-wide association approach (Pool-GWAS) to fine-scale map genomic regions contributing to natural variation in female abdominal pigmentation in Drosophila melanogaster, a trait that is highly variable in natural populations and highly heritable in the laboratory. We examined abdominal pigmentation phenotypes in approximately 8000 female European D. melanogaster, isolating 1000 individuals with extreme phenotypes. We then used whole-genome Illumina sequencing to identify single nucleotide polymorphisms (SNPs) segregating in our sample, and tested these for associations with pigmentation by contrasting allele frequencies between replicate pools of light and dark individuals. We identify two small regions near the pigmentation genes tan and bric-à-brac 1, both corresponding to known cis-regulatory regions, which contain SNPs showing significant associations with pigmentation variation. While the Pool-GWAS approach suffers some limitations, its cost advantage facilitates replication and it can be applied to any non-model system with an available reference genome. Phenotypic variation is abundant in natural populations, but its genetic basis is not always well-understood. Here, we examine the genetic basis of body pigmentation in Drosophila, a trait with a long history of study in Drosophila genetics and evolution. We conducted the first genome-wide scan for polymorphism associated with pigmentation variation in a large natural sample of D. melanogaster, and found SNPs near two genes, tan and bric-à-brac 1, affecting the trait. The SNPs associated with pigmentation variation in these genes appear to act by affecting the regulation of the pigmentation genes, rather than their protein coding sequence.
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Affiliation(s)
- Héloïse Bastide
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
| | | | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
| | - Raymond Tobler
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
| | - Petra Stöbe
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
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17
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18
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Tobler R. [Experiences with aid to Romania. The difficulty of helping effectively]. Krankenpfl Soins Infirm 1995; 88:20-3. [PMID: 7853835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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20
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Gast MJ, Tobler R, Strickler RC, Odem R, Pineda J. Laser vaporization of endometriosis in an infertile population: the role of complicating infertility factors. Fertil Steril 1988; 49:32-6. [PMID: 3335272 DOI: 10.1016/s0015-0282(16)59643-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
One hundred twenty-two infertility patients with endometriosis were evaluated and treated using laparoscopy and laser vaporization to provide immediate elimination of all intraperitoneal disease. Ninety-five couples (77.8%) had one or more infertility factors (other than endometriosis) contributing to their infertility. Cervical factors, male factors, and luteal defects were associated with significantly decreased pregnancy rates, despite the use of laser vaporization. The number of contributing factors seemed to be unrelated to the likelihood of success in achieving pregnancy. The authors emphasize the need for total evaluation of other infertility factors in these patients. Such factors should be corrected prior to the use of laser laparoscopy, if possible, and dealt with on a continuing basis following use of this technique.
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Affiliation(s)
- M J Gast
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, Missouri 63110
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21
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Abstract
Two children with monosomy 10p13 are reported. In the first case the monosomy was the result of a maternal balanced translocation t(3;10) (p27;p13) while the second case was a de novo mutation. We reviewed clinical details of cases reported so far and found that certain symptoms are typical of the deletion of a comparatively large segment of chromosome 10 short arms. These symptoms include mental and growth retardation, skull abnormalities, antimongoloid slant of the eyes, ear abnormalities, anteverted nostrils, abnormalities of the hands and feet, cryptorchidism in boys, and, primarily, hypoplasia or aplasia of the olfactory bulbs and olfactory tracts as well as narrow palpebral fissures or eyelid ptosis.
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22
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Tobler R. [Insurance coverage of the newborn (in Switzerland) (author's transl)]. Schweiz Rundsch Med Prax 1975; 64:1591-3. [PMID: 1208353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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23
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Köng E, Tobler R, Biró Z. [Recognition of cerebral movement disorders in premature infants]. Praxis 1968; 57:1530-1533. [PMID: 5757104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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24
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Jeannet M, Metaxas-Bühler M, Tobler R. Anomalie héréditaire de la membrane érythrocytaire avec
test de Coombs direct positif et modification de l'antigène
de groupe N. Vox Sang 1964. [DOI: 10.1159/000464947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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25
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Taillard W, Prader A, Tobler R. LE RACHITISME HÉRÉDITAIRE RÉSISTANT À LA VITAMINE D (DIABSPACETE PHOSPHORÉ). Hum Hered 1957. [DOI: 10.1159/000150948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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