1
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Muelbaier H, Arthen F, Collins G, Hickler T, Hohberg K, Lehmitz R, Pauchet Y, Pfenninger M, Potapov A, Romahn J, Schaefer I, Scheu S, Schneider C, Ebersberger I, Bálint M. Genomic evidence for the widespread presence of GH45 cellulases among soil invertebrates. Mol Ecol 2024:e17351. [PMID: 38712904 DOI: 10.1111/mec.17351] [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: 09/05/2023] [Revised: 12/06/2023] [Accepted: 02/26/2024] [Indexed: 05/08/2024]
Abstract
Lignocellulose is a major component of vascular plant biomass. Its decomposition is crucial for the terrestrial carbon cycle. Microorganisms are considered primary decomposers, but evidence increases that some invertebrates may also decompose lignocellulose. We investigated the taxonomic distribution and evolutionary origins of GH45 hydrolases, important enzymes for the decomposition of cellulose and hemicellulose, in a collection of soil invertebrate genomes. We found that these genes are common in springtails and oribatid mites. Phylogenetic analysis revealed that cellulase genes were acquired early in the evolutionary history of these groups. Domain architectures and predicted 3D enzyme structures indicate that these cellulases are functional. Patterns of presence and absence of these genes across different lineages prompt further investigation into their evolutionary and ecological benefits. The ubiquity of cellulase genes suggests that soil invertebrates may play a role in lignocellulose decomposition, independently or in synergy with microorganisms. Understanding the ecological and evolutionary implications might be crucial for understanding soil food webs and the carbon cycle.
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Affiliation(s)
- Hannah Muelbaier
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Freya Arthen
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Gemma Collins
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
| | - Thomas Hickler
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Department of Physical Geography, Goethe University, Frankfurt/Main, Germany
| | - Karin Hohberg
- Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Ricarda Lehmitz
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Yannick Pauchet
- Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Anton Potapov
- Senckenberg Museum for Natural History Görlitz, Görlitz, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- International Institute Zittau, TUD Dresden University of Technology, Zittau, Germany
| | - Juliane Romahn
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Institute of Insect Biotechnology, Justus-Liebig University, Giessen, Germany
| | - Ina Schaefer
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Animal Ecology, University of Goettingen, Goettingen, Germany
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology, University of Goettingen, Goettingen, Germany
| | - Clément Schneider
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Institute of Insect Biotechnology, Justus-Liebig University, Giessen, Germany
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Bulut B, Rigano L, Doria HB, Gemüth G, Pfenninger M. A multigenerational study can detect the evolutionary response to BaP exposure in the non-biting freshwater midge Chironomus riparius. Chemosphere 2024; 358:142242. [PMID: 38710409 DOI: 10.1016/j.chemosphere.2024.142242] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 03/18/2024] [Accepted: 05/02/2024] [Indexed: 05/08/2024]
Abstract
The release of polycyclic aromatic hydrocarbons (PAHs) into the environment is posing a threat to ecosystems and human health. Benzo(a)pyrene (BaP) is considered a biomarker of PAH exposure and is classified as a Group 1 carcinogen. However, it was not known whether BaP is mutagenic, i.e. induces inherited germline mutations. In this study, we used a recently established method, which combines short-term mutation accumulation lines (MAL) with whole genome sequencing (WGS) to assess mutagenicity in the non-biting midge Chironomus riparius. The mutagenicity analysis was supplemented by an evaluation of the development of population fitness in three successive generations in the case of chronic exposure to BaP at a high concentration (100 μg/L). In addition, the level of ROS-induced oxidative stress was examined in vivo. Exposure to the higher BaP concentration led to an increase in germline mutations relative to the control, while the lower concentration showed no mentionable effect. Against expectations, BaP exposure decreased ROS-level compared to the control and is thus probably not responsible for the increased mutation rate. Likewise, the higher BaP concentration decreased fitness measured as population growth rate per day (PGR) significantly over all generations, without signs of rapid evolutionary adaptations. Our results thus highlighted that high BaP exposure may influence the evolutionary trajectory of organisms.
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Affiliation(s)
- Burak Bulut
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany
| | - Lorenzo Rigano
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany; LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany.
| | - Halina Binde Doria
- LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany
| | - Gajana Gemüth
- LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany
| | - Markus Pfenninger
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany; LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany; Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becker-Weg 7, D-55128, Mainz, Germany
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3
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Collins G, Schneider C, Boštjančić LL, Burkhardt U, Christian A, Decker P, Ebersberger I, Hohberg K, Lecompte O, Merges D, Muelbaier H, Romahn J, Römbke J, Rutz C, Schmelz R, Schmidt A, Theissinger K, Veres R, Lehmitz R, Pfenninger M, Bálint M. The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution. Commun Biol 2023; 6:1241. [PMID: 38066075 PMCID: PMC10709333 DOI: 10.1038/s42003-023-05621-4] [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: 08/16/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Soil invertebrates are among the least understood metazoans on Earth. Thus far, the lack of taxonomically broad and dense genomic resources has made it hard to thoroughly investigate their evolution and ecology. With MetaInvert we provide draft genome assemblies for 232 soil invertebrate species, representing 14 common groups and 94 families. We show that this data substantially extends the taxonomic scope of DNA- or RNA-based taxonomic identification. Moreover, we confirm that theories of genome evolution cannot be generalised across evolutionarily distinct invertebrate groups. The soil invertebrate genomes presented here will support the management of soil biodiversity through molecular monitoring of community composition and function, and the discovery of evolutionary adaptations to the challenges of soil conditions.
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Affiliation(s)
- Gemma Collins
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Clément Schneider
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Ljudevit Luka Boštjančić
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg, France
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Landau, Germany
| | | | - Axel Christian
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Peter Decker
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Ingo Ebersberger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
| | - Karin Hohberg
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg, France
| | - Dominik Merges
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hannah Muelbaier
- Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
| | - Juliane Romahn
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Jörg Römbke
- ECT Oekotoxikologie GmbH, Flörsheim, Germany
| | - Christelle Rutz
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg, France
| | | | - Alexandra Schmidt
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Kathrin Theissinger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Landau, Germany
| | - Robert Veres
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Institute of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Ricarda Lehmitz
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Johannes Gutenberg University, Mainz, Germany
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany.
- Department of Insect Biotechnology, Justus-Liebig University, Gießen, Germany.
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4
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Riaz M, Warren D, Wittwer C, Cocchiararo B, Hundertmark I, Reiners TE, Klimpel S, Pfenninger M, Khaliq I, Nowak C. Using eDNA to understand predator-prey interactions influenced by invasive species. Oecologia 2023; 202:757-767. [PMID: 37594600 PMCID: PMC10474997 DOI: 10.1007/s00442-023-05434-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 03/16/2022] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
Invasive predatory species may alter population dynamic processes of their prey and impact biological communities and ecosystem processes. Revealing biotic interactions, however, including the relationship between predator and prey, is a difficult task, in particular for species that are hard to monitor. Here, we present a case study that documents the utility of environmental DNA analysis (eDNA) to assess predator-prey interactions between two invasive fishes (Lepomis gibbosus, Pseudorasbora parva) and two potential amphibian prey species, (Triturus cristatus, Pelobates fuscus). We used species-specific TaqMan assays for quantitative assessment of eDNA concentrations from water samples collected from 89 sites across 31 ponds during three consecutive months from a local amphibian hotspot in Germany. We found a negative relationship between eDNA concentrations of the predators (fishes) and prey (amphibians) using Monte-Carlo tests. Our study highlights the potential of eDNA application to reveal predator-prey interactions and confirms the hypothesis that the observed local declines of amphibian species may be at least partly caused by recently introduced invasive fishes. Our findings have important consequences for local conservation management and highlight the usefulness of eDNA approaches to assess ecological interactions and guide targeted conservation action.
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Affiliation(s)
- Maria Riaz
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany.
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany.
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Straße 9, 60438, Frankfurt Am Main, Germany.
| | - Dan Warren
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
| | - Claudia Wittwer
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Straße 9, 60438, Frankfurt Am Main, Germany
| | - Berardino Cocchiararo
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
| | - Inga Hundertmark
- Hessische Gesellschaft Für Ornithologie Und Naturschutz (HGON E. V.), Lindenstrasse 5, 61209, Echzell, Germany
| | - Tobias Erik Reiners
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany
- Hessische Gesellschaft Für Ornithologie Und Naturschutz (HGON E. V.), Lindenstrasse 5, 61209, Echzell, Germany
| | - Sven Klimpel
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Straße 9, 60438, Frankfurt Am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany
| | - Imran Khaliq
- Department of Education, Punjab, Pakistan
- Department of Aquatic Ecology Eawag (Swiss Federal Institute of Aquatic Science and Technology) Überlandstrasse 133, 8600, Dübendorf, Switzerland
- Snow and Landscape Research (WSL), Swiss Federal Institute for Forest, Flüelastr. 11, 7260, Davos Dorf, Switzerland
| | - Carsten Nowak
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
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5
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Nieto-Blázquez ME, Schreiber D, Mueller SA, Koch K, Nowak C, Pfenninger M. Correction: Human impact on the recent population history of the elusive European wildcat inferred from whole genome data. BMC Genomics 2023; 24:15. [PMID: 36631758 PMCID: PMC9835342 DOI: 10.1186/s12864-022-09047-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- María Esther Nieto-Blázquez
- grid.507705.0Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (SBiK-F), 60325 Frankfurt am Main, Germany
| | - Dennis Schreiber
- grid.507705.0Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (SBiK-F), 60325 Frankfurt am Main, Germany
| | - Sarah A. Mueller
- grid.5252.00000 0004 1936 973XDivision of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, Planegg-Martinsried, 82152 Munich, Germany ,grid.462628.c0000 0001 2184 5457Centre for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, 63571 Gelnhausen, Germany
| | - Katrin Koch
- European Wildcat Monitoring, Bund Für Umwelt Und Naturschutz, 55118 Rheinland-Pfalz, Mainz Germany
| | - Carsten Nowak
- grid.462628.c0000 0001 2184 5457Centre for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, 63571 Gelnhausen, Germany ,grid.511284.b0000 0004 8004 5574LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), 60325 Frankfurt am Main, Germany
| | - Markus Pfenninger
- grid.507705.0Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (SBiK-F), 60325 Frankfurt am Main, Germany ,grid.511284.b0000 0004 8004 5574LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), 60325 Frankfurt am Main, Germany ,grid.5802.f0000 0001 1941 7111Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, 55128 Mainz, Germany
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Pfenninger M, Foucault Q, Waldvogel AM, Feldmeyer B. Selective effects of a short transient environmental fluctuation on a natural population. Mol Ecol 2023; 32:335-349. [PMID: 36282585 DOI: 10.1111/mec.16748] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 09/21/2022] [Accepted: 10/21/2022] [Indexed: 01/11/2023]
Abstract
Natural populations experience continuous and often transient changes of environmental conditions. These in turn may result in fluctuating selection pressures leading to variable demographic and evolutionary population responses. Rapid adaptation as short-term response to a sudden environmental change has in several cases been attributed to polygenic traits, but the underlying genomic dynamics and architecture are poorly understood. In this study, we took advantage of a natural experiment in an insect population of the non-biting midge Chironomus riparius by monitoring genome-wide allele frequencies before and after a cold snap event. Whole genome pooled sequencing of time series samples revealed 10 selected haplotypes carrying ancient polymorphisms, partially with signatures of balancing selection. By constantly cold exposing genetically variable individuals in the laboratory, we could demonstrate with whole genome resequencing (i) that among the survivors, the same alleles rose in frequency as in the wild, and (ii) that the identified variants additively predicted fitness (survival time) of its bearers. Finally, by simultaneously sequencing the genome and the transcriptome of cold exposed individuals we could tentatively link some of the selected SNPs to the cis- and trans-regulation of genes and pathways known to be involved in cold response of insects, such as cytochrome P450 and fatty acid metabolism. Altogether, our results shed light on the strength and speed of selection in natural populations and the genomic architecture of its underlying polygenic trait. Population genomic time series data thus appear as promising tool for measuring the selective tracking of fluctuating selection in natural populations.
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Affiliation(s)
- Markus Pfenninger
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Quentin Foucault
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Ann-Marie Waldvogel
- Department of Ecological Genomics, Institute of Zoology, University of Cologne, Köln, Germany
| | - Barbara Feldmeyer
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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7
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Kramer IM, Pfenninger M, Feldmeyer B, Dhimal M, Gautam I, Shreshta P, Baral S, Phuyal P, Hartke J, Magdeburg A, Groneberg DA, Ahrens B, Müller R, Waldvogel AM. Genomic profiling of climate adaptation in Aedes aegypti along an altitudinal gradient in Nepal indicates nongradual expansion of the disease vector. Mol Ecol 2023; 32:350-368. [PMID: 36305220 DOI: 10.1111/mec.16752] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 01/11/2023]
Abstract
Driven by globalization, urbanization and climate change, the distribution range of invasive vector species has expanded to previously colder ecoregions. To reduce health-threatening impacts on humans, insect vectors are extensively studied. Population genomics can reveal the genomic basis of adaptation and help to identify emerging trends of vector expansion. By applying whole genome analyses and genotype-environment associations to populations of the main dengue vector Aedes aegypti, sampled along an altitudinal gradient in Nepal (200-1300 m), we identify putatively adaptive traits and describe the species' genomic footprint of climate adaptation to colder ecoregions. We found two differentiated clusters with significantly different allele frequencies in genes associated to climate adaptation between the highland population (1300 m) and all other lowland populations (≤800 m). We revealed nonsynonymous mutations in 13 of the candidate genes associated to either altitude, precipitation or cold tolerance and identified an isolation-by-environment differentiation pattern. Other than the expected gradual differentiation along the altitudinal gradient, our results reveal a distinct genomic differentiation of the highland population. Local high-altitude adaptation could be one explanation of the population's phenotypic cold tolerance. Carrying alleles relevant for survival under colder climate increases the likelihood of this highland population to a worldwide expansion into other colder ecoregions.
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Affiliation(s)
- Isabelle Marie Kramer
- Institute of Occupational, Social and Environmental Medicine, Goethe University, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | | | - Ishan Gautam
- Natural History Museum, Tribhuvan University, Kathmandu, Nepal
| | | | | | - Parbati Phuyal
- Institute of Occupational, Social and Environmental Medicine, Goethe University, Frankfurt am Main, Germany
| | - Juliane Hartke
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Axel Magdeburg
- Institute of Occupational, Social and Environmental Medicine, Goethe University, Frankfurt am Main, Germany
| | - David A Groneberg
- Institute of Occupational, Social and Environmental Medicine, Goethe University, Frankfurt am Main, Germany
| | - Bodo Ahrens
- Institute for Atmospheric and Environmental Sciences, Goethe University, Frankfurt am Main, Germany
| | - Ruth Müller
- Institute of Occupational, Social and Environmental Medicine, Goethe University, Frankfurt am Main, Germany.,Unit Entomology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Ann-Marie Waldvogel
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute of Zoology, University of Cologne, Cologne, Germany
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8
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Pfenninger M, Foucault Q. Population Genomic Time Series Data of a Natural Population Suggests Adaptive Tracking of Fluctuating Environmental Changes. Integr Comp Biol 2022; 62:1812-1826. [PMID: 35762661 DOI: 10.1093/icb/icac098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/07/2022] [Accepted: 06/16/2022] [Indexed: 01/05/2023] Open
Abstract
Natural populations are constantly exposed to fluctuating environmental changes that negatively affect their fitness in unpredictable ways. While theoretical models show the possibility of counteracting these environmental changes through rapid evolutionary adaptations, there have been few empirical studies demonstrating such adaptive tracking in natural populations. Here, we analyzed environmental data, fitness-related phenotyping and genomic time-series data sampled over 3 years from a natural Chironomus riparius (Diptera, Insecta) population to address this question. We show that the population's environment varied significantly on the time scale of the sampling in many selectively relevant dimensions, independently of each other. Similarly, phenotypic fitness components evolved significantly on the same temporal scale (mean 0.32 Haldanes), likewise independent from each other. The allele frequencies of 367,446 SNPs across the genome showed evidence of positive selection. Using temporal correlation of spatially coherent allele frequency changes revealed 35,574 haplotypes with more than one selected SNP. The mean selection coefficient for these haplotypes was 0.30 (s.d. = 0.68). The frequency changes of these haplotypes clustered in 46 different temporal patterns, indicating concerted, independent evolution of many polygenic traits. Nine of these patterns were strongly correlated with measured environmental variables. Enrichment analysis of affected genes suggested the implication of a wide variety of biological processes. Thus, our results suggest overall that the natural population of C. riparius tracks environmental change through rapid polygenic adaptation in many independent dimensions. This is further evidence that natural selection is pervasive at the genomic level and that evolutionary and ecological time scales may not differ at all, at least in some organisms.
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Affiliation(s)
- Markus Pfenninger
- Department Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.,Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128 Mainz, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Quentin Foucault
- Department Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.,Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128 Mainz, Germany
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9
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Khosrovyan A, Doria HB, Kahru A, Pfenninger M. Polyamide microplastic exposure elicits rapid, strong and genome-wide evolutionary response in the freshwater non-biting midge Chironomus riparius. Chemosphere 2022; 299:134452. [PMID: 35367228 DOI: 10.1016/j.chemosphere.2022.134452] [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] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/20/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Susceptibility to hazardous materials and contamination is largely determined by genetic make-up and evolutionary history of affected organisms. Yet evolutionary adaptation and microevolutionary processes triggered by contaminants are rarely considered in ecotoxicology. Using an evolve and resequencing approach, we investigated genome-wide responses of the midge C. riparius exposed to virgin polyamide microplastics (0-180 μm size range, at concentration 1 g kg-1) during seven consecutive generations. The results were integrated to a parallel life-cycle experiment ran under the same exposure conditions. Emergence, life-cycle trait, showed first a substantial reduction in larval survival, followed by a rapid recovery within three generations. On the genomic level, we observed substantial selectively driven allele frequency changes (mean 0.566 ± 0.0879) within seven generations, associated with a mean selection coefficient of 0.322, indicating very strong selection pressure. Putative selection targets were mainly connected to oxidative stress in the microplastics exposed C. riparius population. This is the first multigenerational study on chironomids to provide evidence that upon exposure to polyamide microplastic there are changes on the genomic level, providing basis to rapid adaptation of aquatic organisms to microplastics.
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Affiliation(s)
- Alla Khosrovyan
- National Institute of Chemical Physics and Biophysics, Laboratory of Environmental Toxicology, 23 Akadeemia Tee, 12618, Tallinn, Estonia.
| | - Halina Binde Doria
- Dept. Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany; LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
| | - Anne Kahru
- National Institute of Chemical Physics and Biophysics, Laboratory of Environmental Toxicology, 23 Akadeemia Tee, 12618, Tallinn, Estonia; Estonian Academy of Sciences, 6 Kohtu, 10130, Tallinn, Estonia
| | - Markus Pfenninger
- Dept. Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany; LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany; Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany
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10
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Doria HB, Hannappel P, Pfenninger M. Whole genome sequencing and RNA-seq evaluation allowed to detect Cd adaptation footprint in Chironomus riparius. Sci Total Environ 2022; 819:152843. [PMID: 35033566 DOI: 10.1016/j.scitotenv.2021.152843] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Evolutionary adaptation and phenotypic plasticity are important processes on how organisms respond to pollutant exposure. We dissected here the contribution of both processes to increased tolerance in Chironomus riparius to cadmium (Cd) exposure in a multi-generation experiment and inferred the underlying genomic basis. We simulated environmentally realistic conditions by continuously increasing contaminant concentration in six replicates initiated with 1000 larvae each, three pre-exposed to Cd and three not exposed to Cd (no-Cd) over eight generations. We measured life-cycle traits, transcriptomic responses and genome-wide allele frequency changes from this evolve and resequencing (E&R) experiment. Overall, life cycle tests revealed little phenotypic adaptation to Cd exposure, but a slightly increase in survival in the first larval stage was observed. Population genomic analyses showed a strong genome-wide selective response in all replicates, highlighting two main biological functions involved in development and growth of the chironomids. Emphasizing that laboratory conditions continually exert selective pressure. However, the integration of the transcriptomic to the genomic data allowed to distinguish pathways specifically selected by the Cd exposure related to microtubules and organelles and cellular movement. Those pathways could be functionally related to an excretion of metals. Thus, our results indicate that genetic adaptation to Cd in C. riparius can happen within few generations under an environmentally relevant exposure scenario, but substantial phenotypic tolerance might take more time to arise. With our approach, we introduce an experimental setup to fill the existing gap in evolutionary ecotoxicology to investigate these early signs of genetic adaptation.
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Affiliation(s)
- Halina Binde Doria
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany; Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany.
| | - Pauline Hannappel
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany; Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany; Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128 Mainz, Germany
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11
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Pfenninger M, Bálint M. On the use of population genomic time series for environmental monitoring. Am J Bot 2022; 109:497-499. [PMID: 35253207 DOI: 10.1002/ajb2.1836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Agricultural Sciences, Nutritional Sciences, and Environmental Management, Universität Giessen, Giessen, Germany
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12
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Pfenninger M, Doria HB, Nickel J, Thielsch A, Schwenk K, Cordellier M. Spontaneous rate of clonal single nucleotide mutations in Daphnia galeata. PLoS One 2022; 17:e0265632. [PMID: 35363773 PMCID: PMC8975155 DOI: 10.1371/journal.pone.0265632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/09/2021] [Accepted: 03/05/2022] [Indexed: 11/30/2022] Open
Abstract
Mutations are the ultimate source of heritable variation and therefore the fuel for evolution, but direct estimates of mutation rates exist only for few species. We estimated the spontaneous single nucleotide mutation rate among clonal generations in the waterflea Daphnia galeata with a short-term mutation accumulation approach. Individuals from eighteen mutation accumulation lines over five generations were deep sequenced to count de novo mutations that were not present in a pool of F1 individuals, representing the parental genotype. We identified 12 new nucleotide mutations in 90 clonal generational passages. This resulted in an estimated single nucleotide mutation rate of 0.745 x 10-9 (95% c.f. 0.39 x 10-9-1.26 x 10-9), which is slightly lower than recent estimates for other Daphnia species. We discuss the implications for the population genetics of Cladocerans.
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Affiliation(s)
- Markus Pfenninger
- Department Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Mainz, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Halina Binde Doria
- Department Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Jana Nickel
- Institut für Zoologie, Fakultät für Mathematik, Informatik und Naturwissenschaften, Universität Hamburg, Hamburg, Germany
| | - Anne Thielsch
- Institute for Environmental Sciences, Universität Koblenz-Landau, Landau, Germany
| | - Klaus Schwenk
- Institute for Environmental Sciences, Universität Koblenz-Landau, Landau, Germany
| | - Mathilde Cordellier
- Institut für Zoologie, Fakultät für Mathematik, Informatik und Naturwissenschaften, Universität Hamburg, Hamburg, Germany
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13
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Mishra B, Ulaszewski B, Meger J, Aury JM, Bodénès C, Lesur-Kupin I, Pfenninger M, Da Silva C, Gupta DK, Guichoux E, Heer K, Lalanne C, Labadie K, Opgenoorth L, Ploch S, Le Provost G, Salse J, Scotti I, Wötzel S, Plomion C, Burczyk J, Thines M. A Chromosome-Level Genome Assembly of the European Beech ( Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs. Front Genet 2022; 12:691058. [PMID: 35211148 PMCID: PMC8862710 DOI: 10.3389/fgene.2021.691058] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 12/14/2021] [Indexed: 01/14/2023] Open
Abstract
The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome-wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.
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Affiliation(s)
- Bagdevi Mishra
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.,Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Bartosz Ulaszewski
- Department of Genetics, ul. Chodkiewicza 30, Kazimierz Wielki University, Bydgoszcz, Poland
| | - Joanna Meger
- Department of Genetics, ul. Chodkiewicza 30, Kazimierz Wielki University, Bydgoszcz, Poland
| | - Jean-Marc Aury
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Isabelle Lesur-Kupin
- INRAE, Univ. Bordeaux, BIOGECO, Cestas, France.,HelixVenture, Mérignac, France.,Faculty of Biology, Plant Ecology and Geobotany, Philipps University Marburg, Marburg, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Corinne Da Silva
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Deepak K Gupta
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.,Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
| | | | - Katrin Heer
- Faculty of Biology, Plant Ecology and Geobotany, Philipps University Marburg, Marburg, Germany.,Forest Genetics, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | | | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Lars Opgenoorth
- Faculty of Biology, Plant Ecology and Geobotany, Philipps University Marburg, Marburg, Germany
| | - Sebastian Ploch
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | | | | | | | - Stefan Wötzel
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.,Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | | | - Jaroslaw Burczyk
- Department of Genetics, ul. Chodkiewicza 30, Kazimierz Wielki University, Bydgoszcz, Poland
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.,Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
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14
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Bolotov IN, Pasupuleti R, Subba Rao NV, Unnikrishnan SK, Chan N, Lunn Z, Win T, Gofarov MY, Kondakov AV, Konopleva ES, Lyubas AA, Tomilova AA, Vikhrev IV, Pfenninger M, Düwel SS, Feldmeyer B, Nesemann HF, Nagel KO. Oriental freshwater mussels arose in East Gondwana and arrived to Asia on the Indian Plate and Burma Terrane. Sci Rep 2022; 12:1518. [PMID: 35087130 PMCID: PMC8795121 DOI: 10.1038/s41598-022-05257-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 11/21/2021] [Accepted: 01/10/2022] [Indexed: 12/21/2022] Open
Abstract
Freshwater mussels cannot spread through oceanic barriers and represent a suitable model to test the continental drift patterns. Here, we reconstruct the diversification of Oriental freshwater mussels (Unionidae) and revise their taxonomy. We show that the Indian Subcontinent harbors a rather taxonomically poor fauna, containing 25 freshwater mussel species from one subfamily (Parreysiinae). This subfamily most likely originated in East Gondwana in the Jurassic and its representatives arrived to Asia on two Gondwanan fragments (Indian Plate and Burma Terrane). We propose that the Burma Terrane was connected with the Indian Plate through the Greater India up to the terminal Cretaceous. Later on, during the entire Paleogene epoch, these blocks have served as isolated evolutionary hotspots for freshwater mussels. The Burma Terrane collided with mainland Asia in the Late Eocene, leading to the origin of the Mekong’s Indochinellini radiation. Our findings indicate that the Burma Terrane had played a major role as a Gondwanan “biotic ferry” alongside with the Indian Plate.
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Affiliation(s)
- Ivan N Bolotov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia. .,Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russia. .,SSC/IUCN - Mollusc Specialist Group, Species Survival Commission, International Union for Conservation of Nature, Cambridge, CB2 3QZ, UK.
| | - Rajeev Pasupuleti
- Institute of Molecular Biotechnology (IMBT), Technical University of Graz, Petersgasse 14, 8010, Graz, Austria
| | | | - Suresh Kumar Unnikrishnan
- Regional Facility for DNA Fingerprinting (RFDF), Rajiv Gandhi Centre for Biotechnology (RGCB), Trivandrum, 695014, Kerala, India
| | - Nyein Chan
- Fauna & Flora International - Myanmar Programme, 34 D/9 San Yae Twin Street, Kaba Aye Pagoda Road, Bahan Township, 11201, Yangon, Myanmar
| | - Zau Lunn
- Fauna & Flora International - Myanmar Programme, 34 D/9 San Yae Twin Street, Kaba Aye Pagoda Road, Bahan Township, 11201, Yangon, Myanmar.,Biology Department, University of New Brunswick, 100 Tucker Park Road, PO Box 5050, Saint John, NB, E2L 4L5, Canada
| | - Than Win
- Department of Zoology, Dawei University, 14043, Dawei, Tanintharyi Region, Myanmar
| | - Mikhail Y Gofarov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia
| | - Alexander V Kondakov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia.,Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russia
| | - Ekaterina S Konopleva
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia.,Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russia
| | - Artyom A Lyubas
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia
| | - Alena A Tomilova
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia.,Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russia
| | - Ilya V Vikhrev
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia.,Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russia.,SSC/IUCN - Mollusc Specialist Group, Species Survival Commission, International Union for Conservation of Nature, Cambridge, CB2 3QZ, UK
| | - Markus Pfenninger
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Sophie S Düwel
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Barbara Feldmeyer
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | | | - Karl-Otto Nagel
- Malacological Section, Senckenberg Research Institute and Natural History Museum Frankfurt/M., Senckenberganlage 25, 60325, Frankfurt am Main, Germany
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15
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Pfenninger M, Schönnenbeck P, Schell T. ModEst: Accurate estimation of genome size from next generation sequencing data. Mol Ecol Resour 2021; 22:1454-1464. [PMID: 34882987 DOI: 10.1111/1755-0998.13570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 01/11/2023]
Abstract
Accurate estimates of genome sizes are important parameters for both theoretical and practical biodiversity genomics. Here we present a fast, easy-to-implement and accurate method to estimate genome size from the number of bases sequenced and the mean sequencing depth. To estimate the latter, we take advantage of the fact that an accurate estimation of the Poisson distribution parameter lambda is possible from truncated data, restricted to the part of the sequencing depth distribution representing the true underlying distribution. With simulations we show that reasonable genome size estimates can be gained even from low-coverage (10×), highly discontinuous genome drafts. Comparison of estimates from a wide range of taxa and sequencing strategies with flow cytometry estimates of the same individuals showed a very good fit and suggested that both methods yield comparable, interchangeable results.
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Affiliation(s)
- Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Philipp Schönnenbeck
- Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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16
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Doria HB, Caliendo C, Gerber S, Pfenninger M. Photoperiod is an important seasonal selection factor in Chironomus riparius (Diptera: Chironomidae). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Most organisms respond and can adapt to photoperiodic changes. This affects measurable end points like developmental time, survival and fertility. For ectotherms like Chironomus riparius, temperature is the most studied environmental cue regulating their life cycle, whereas photoperiodic influence is neglected. However, the developmental speed between summer and winter seasons of a field population could not be explained solely by temperature variations. Therefore, to have a comprehensive view on how photoperiods influence chironomid’s life cycle, we investigated if it plays a role in their development and if it acts as an important selective pressure on developmental time speed. To this end, first emerged C. riparius were artificially selected for seven generations. Pre-selected and unselected organisms could develop and breed independently under three light regimes: constant light (24:0 L:D), long days (16:8 L:D) and short days (8:16 L:D). Adult emergence, mean and median emergence time and fertility were integrated into the population growth rate to compare fitness. Our findings show that although developmental time is extended under short days, this same condition may exert a selective pressure towards a shorter development. Moreover, by also using photoperiodic clues to anticipate environmental changes, chironomids can potentially adapt to alterations in climate.
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Affiliation(s)
- Halina Binde Doria
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Straße, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany
| | - Cosima Caliendo
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University Mainz, Staudinger Weg, Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University Mainz, Staudinger Weg, Mainz, Germany
| | - Markus Pfenninger
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Straße, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg, Mainz, Germany
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17
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Nickel J, Schell T, Holtzem T, Thielsch A, Dennis SR, Schlick-Steiner BC, Steiner FM, Möst M, Pfenninger M, Schwenk K, Cordellier M. Hybridization Dynamics and Extensive Introgression in the Daphnia longispina Species Complex: New Insights from a High-Quality Daphnia galeata Reference Genome. Genome Biol Evol 2021; 13:6448229. [PMID: 34865004 PMCID: PMC8695838 DOI: 10.1093/gbe/evab267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2021] [Indexed: 01/02/2023] Open
Abstract
Hybridization and introgression are recognized as an important source of variation that influence adaptive processes; both phenomena are frequent in the genus Daphnia, a keystone zooplankton taxon in freshwater ecosystems that comprises several species complexes. To investigate genome-wide consequences of introgression between species, we provide here the first high-quality genome assembly for a member of the Daphnia longispina species complex, Daphnia galeata. We further resequenced 49 whole genomes of three species of the complex and their interspecific hybrids both from genotypes sampled in the water column and from single resting eggs extracted from sediment cores. Populations from habitats with diverse ecological conditions offered an opportunity to study the dynamics of hybridization linked to ecological changes and revealed a high prevalence of hybrids. Using phylogenetic and population genomic approaches, we provide first insights into the intra- and interspecific genome-wide variability in this species complex and identify regions of high divergence. Finally, we assess the length of ancestry tracts in hybrids to characterize introgression patterns across the genome. Our analyses uncover a complex history of hybridization and introgression reflecting multiple generations of hybridization and backcrossing in the Daphnia longispina species complex. Overall, this study and the new resources presented here pave the way for a better understanding of ancient and contemporary gene flow in the species complex and facilitate future studies on resting egg banks accumulating in lake sediment.
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Affiliation(s)
- Jana Nickel
- Institute of Zoology, Universität Hamburg, Germany
| | - Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Tania Holtzem
- Department of Ecology, University of Innsbruck, Austria
| | - Anne Thielsch
- Molecular Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | - Stuart R Dennis
- Department of Aquatic Ecology, EAWAG, Dübendorf, Switzerland
| | | | | | - Markus Möst
- Department of Ecology, University of Innsbruck, Austria
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany.,Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.,IoME, Gutenberg University, Mainz, Germany
| | - Klaus Schwenk
- Molecular Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
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18
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Abstract
Mutation is the source of genetic variation and the fundament of evolution. Temperature has long been suggested to have a direct impact on realized spontaneous mutation rates. If mutation rates vary in response to environmental conditions, such as the variation of the ambient temperature through space and time, they should no longer be described as species-specific constants. By combining mutation accumulation with whole-genome sequencing in a multicellular organism, we provide empirical support to reject the null hypothesis of a constant, temperature-independent mutation rate. Instead, mutation rates depended on temperature in a U-shaped manner with increasing rates toward both temperature extremes. This relation has important implications for mutation-dependent processes in molecular evolution, processes shaping the evolution of mutation rates, and even the evolution of biodiversity as such.
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Affiliation(s)
- Ann-Marie Waldvogel
- Senckenberg Biodiversity and Climate Research Centre, 60325 Frankfurt am Main, Germany
- Institute of Zoology, University of Cologne, 50674 Cologne, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, 60325 Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, 60325 Frankfurt am Main, Germany
- Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, 55128 Mainz, Germany
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19
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Chueca LJ, Schell T, Pfenninger M. De novo genome assembly of the land snail Candidula unifasciata (Mollusca: Gastropoda). G3 (Bethesda) 2021; 11:6287656. [PMID: 34849805 PMCID: PMC8496239 DOI: 10.1093/g3journal/jkab180] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/18/2021] [Indexed: 11/14/2022]
Abstract
Among all molluscs, land snails are a scientifically and economically interesting group comprising edible species, alien species and agricultural pests. Yet, despite their high diversity, the number of genome drafts publicly available is still scarce. Here, we present the draft genome assembly of the land snail Candidula unifasciata, a widely distributed species along central Europe, belonging to the Geomitridae family, a highly diversified taxon in the Western-Palearctic region. We performed whole genome sequencing, assembly and annotation of an adult specimen based on PacBio and Oxford Nanopore long read sequences as well as Illumina data. A genome draft of about 1.29 Gb was generated with a N50 length of 246 kb. More than 60% of the assembled genome was identified as repetitive elements. In total, 22,464 protein-coding genes were identified in the genome, of which 62.27% were functionally annotated. This is the first assembled and annotated genome for a geometrid snail and will serve as reference for further evolutionary, genomic and population genetic studies of this important and interesting group.
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Affiliation(s)
- Luis J Chueca
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main 60325, Germany.,Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV-EHU), Vitoria-Gasteiz 01006, Spain
| | - Tilman Schell
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main 60325, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main 60325, Germany.,Faculty of Biology, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, Mainz 55128, Germany
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20
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Pfenninger M, Reuss F, Kiebler A, Schönnenbeck P, Caliendo C, Gerber S, Cocchiararo B, Reuter S, Blüthgen N, Mody K, Mishra B, Bálint M, Thines M, Feldmeyer B. Genomic basis for drought resistance in European beech forests threatened by climate change. eLife 2021; 10:65532. [PMID: 34132196 PMCID: PMC8266386 DOI: 10.7554/elife.65532] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/07/2021] [Indexed: 12/30/2022] Open
Abstract
In the course of global climate change, Central Europe is experiencing more frequent and prolonged periods of drought. The drought years 2018 and 2019 affected European beeches (Fagus sylvatica L.) differently: even in the same stand, drought-damaged trees neighboured healthy trees, suggesting that the genotype rather than the environment was responsible for this conspicuous pattern. We used this natural experiment to study the genomic basis of drought resistance with Pool-GWAS. Contrasting the extreme phenotypes identified 106 significantly associated single-nucleotide polymorphisms (SNPs) throughout the genome. Most annotated genes with associated SNPs (>70%) were previously implicated in the drought reaction of plants. Non-synonymous substitutions led either to a functional amino acid exchange or premature termination. An SNP assay with 70 loci allowed predicting drought phenotype in 98.6% of a validation sample of 92 trees. Drought resistance in European beech is a moderately polygenic trait that should respond well to natural selection, selective management, and breeding. Climate change is having a serious impact on many ecosystems. In the summer of 2018 and 2019, around two thirds of European beech trees were damaged or killed by extreme drought. It is critical to keep these beech woods healthy, as they are central to the survival of over 6,000 other species of animals and plants. The level of damage caused by the drought varied between forests. However, not all the trees in each forest responded in the same way, with severely damaged trees often sitting next to fully healthy ones. This suggests that the genetic make-up of each tree determines how well it can adapt to drought rather than its local environment. To investigate this further, Pfenninger et al. studied the genome of over 400 European beech trees from the Hesse region in Germany. The samples came from pairs of neighbouring trees that had responded differently to the droughts. The analysis found more than 80 parts of the genome that differed between healthy and damaged trees. Pfenninger et al. then used this information to create a genetic test which can quickly and inexpensively predict how well an individual beech tree might survive in a drought. Applying this test to another 92 trees revealed that it can reliably detect which ones were healthy and which ones were damaged. Beech forests are typically managed by private owners, agencies or breeders that could use this genetic test to select and reproduce trees that are better adapted to drought. The goal now is to develop the test so that it can be used more widely to manage European beech trees and potentially other species.
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Affiliation(s)
- Markus Pfenninger
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Friederike Reuss
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Angelika Kiebler
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Philipp Schönnenbeck
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Cosima Caliendo
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Berardino Cocchiararo
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany.,Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
| | - Sabrina Reuter
- Ecological Networks lab, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Nico Blüthgen
- Ecological Networks lab, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Karsten Mody
- Ecological Networks lab, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany.,Department of Applied Ecology, Hochschule Geisenheim University, Geisenheim, Germany
| | - Bagdevi Mishra
- Biological Archives, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany.,Functional Environmental Genomics, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Agricultural Sciences, Nutritional Sciences, and Environmental Management, Universität Giessen, Giessen, Germany
| | - Marco Thines
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany.,Biological Archives, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Barbara Feldmeyer
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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21
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Chueca LJ, Schell T, Pfenninger M. Whole-genome re-sequencing data to infer historical demography and speciation processes in land snails: the study of two Candidula sister species. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200156. [PMID: 33813898 PMCID: PMC8059500 DOI: 10.1098/rstb.2020.0156] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Despite the global biodiversity of terrestrial gastropods and their ecological and economic importance, the genomic basis of ecological adaptation and speciation in land snail taxa is still largely unknown. Here, we combined whole-genome re-sequencing with population genomics to evaluate the historical demography and the speciation process of two closely related species of land snails from western Europe, Candidula unifasciata and C. rugosiuscula. Historical demographic analysis indicated fluctuations in the size of ancestral populations, probably driven by Pleistocene climatic fluctuations. Although the current population distributions of both species do not overlap, our approximate Bayesian computation model selection approach on several speciation scenarios suggested that gene flow has occurred throughout the divergence process until recently. Positively selected genes diverging early in the process were associated with intragenomic and cyto-nuclear incompatibilities, respectively, potentially fostering reproductive isolation as well as ecological divergence. Our results suggested that the speciation between species entails complex processes involving both gene flow and ecological speciation, and that further research based on whole-genome data can provide valuable understanding on species divergence. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Luis J. Chueca
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, 60325 Frankfurt am Main, Germany
- Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV-EHU), 01006 Vitoria-Gasteiz, Spain
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Tilman Schell
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, 60325 Frankfurt am Main, Germany
| | - Markus Pfenninger
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, 60325 Frankfurt am Main, Germany
- Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Institute of Organismic and Molecular Evolution (iOME), Faculty of Biology, Johannes Gutenberg University, 55128 Mainz, Germany
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22
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Chueca LJ, Kochmann J, Schell T, Greve C, Janke A, Pfenninger M, Klimpel S. De novo Genome Assembly of the Raccoon Dog ( Nyctereutes procyonoides). Front Genet 2021; 12:658256. [PMID: 33995489 PMCID: PMC8117329 DOI: 10.3389/fgene.2021.658256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022] Open
Affiliation(s)
- Luis J Chueca
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV-EHU), Vitoria-Gasteiz, Spain
| | - Judith Kochmann
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Tilman Schell
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany
| | - Carola Greve
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany
| | - Axel Janke
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Markus Pfenninger
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Mainz, Germany
| | - Sven Klimpel
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
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23
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Doria HB, Waldvogel AM, Pfenninger M. Measuring mutagenicity in ecotoxicology: A case study of Cd exposure in Chironomus riparius. Environ Pollut 2021; 272:116004. [PMID: 33187849 DOI: 10.1016/j.envpol.2020.116004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/14/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
Existing mutagenicity tests for metazoans lack the direct observation of enhanced germline mutation rates after exposure to anthropogenic substances, therefore being inefficient. Cadmium (Cd) is a metal described as a mutagen in mammalian cells and listed as a group 1 carcinogenic and mutagenic substance. But Cd mutagenesis mechanism is not yet clear. Therefore, in the present study, we propose a method coupling short-term mutation accumulation (MA) lines with subsequent whole genome sequencing (WGS) and a dedicated data analysis pipeline to investigate if chronic Cd exposure on Chironomus riparius can alter the rate at which de novo point mutations appear. Results show that Cd exposure did not affect the basal germline mutation rate nor the mutational spectrum in C. riparius, thereby arguing that exposed organisms might experience a range of other toxic effects before any mutagenic effect may occur. We show that it is possible to establish a practical and easily implemented pipeline to rapidly detect germ cell mutagens in a metazoan test organism. Furthermore, our data implicate that it is questionable to transfer mutagenicity assessments based on in vitro methods to complex metazoans.
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Affiliation(s)
- Halina Binde Doria
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany.
| | - Ann-Marie Waldvogel
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany; Department of Ecological Genomics, Institute of Zoology, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany; Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany; Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, D-55128, Mainz, Germany
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24
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Schreiber D, Pfenninger M. Genomic divergence landscape in recurrently hybridizing Chironomus sister taxa suggests stable steady state between mutual gene flow and isolation. Evol Lett 2021; 5:86-100. [PMID: 33552538 PMCID: PMC7857304 DOI: 10.1002/evl3.204] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/11/2020] [Accepted: 10/19/2020] [Indexed: 12/30/2022] Open
Abstract
Divergence is mostly viewed as a progressive process often initiated by selection targeting individual loci, ultimately resulting in ever increasing genomic isolation due to linkage. However, recent studies show that this process may stall at intermediate stable equilibrium states without achieving complete genomic isolation. We tested the extent of genomic isolation between two recurrently hybridizing nonbiting midge sister taxa, Chironomus riparius and Chironomus piger, by analyzing the divergence landscape. Using a principal component-based method, we estimated that only about 28.44% of the genomes were mutually isolated, whereas the rest was still exchanged. The divergence landscape was fragmented into isolated regions of on average 30 kb, distributed throughout the genome. Selection and divergence time strongly influenced lengths of isolated regions, whereas local recombination rate only had minor impact. Comparison of divergence time distributions obtained from several coalescence-simulated divergence scenarios with the observed divergence time estimates in an approximate Bayesian computation framework favored a short and concluded divergence event in the past. Most divergence happened during a short time span about 4.5 million generations ago, followed by a stable equilibrium between mutual gene flow through ongoing hybridization for the larger part of the genome and isolation in some regions due to rapid purifying selection of introgression, supported by high effective population sizes and recombination rates.
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Affiliation(s)
- Dennis Schreiber
- Department of Molecular EcologySenckenberg Biodiversity and Climate Research CentreFrankfurt am Main60325Germany
- Institute for Molecular and Organismic EvolutionJohannes Gutenberg UniversityMainz55128Germany
| | - Markus Pfenninger
- Department of Molecular EcologySenckenberg Biodiversity and Climate Research CentreFrankfurt am Main60325Germany
- Institute for Molecular and Organismic EvolutionJohannes Gutenberg UniversityMainz55128Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am Main60325Germany
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25
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Hartke J, Waldvogel A, Sprenger PP, Schmitt T, Menzel F, Pfenninger M, Feldmeyer B. Little parallelism in genomic signatures of local adaptation in two sympatric, cryptic sister species. J Evol Biol 2021; 34:937-952. [DOI: 10.1111/jeb.13742] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/03/2020] [Accepted: 11/03/2020] [Indexed: 01/06/2023]
Affiliation(s)
- Juliane Hartke
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
- Institute of Organismic and Molecular Evolution Johannes‐Gutenberg‐University Mainz Mainz Germany
| | - Ann‐Marie Waldvogel
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
- Institute for Zoology University of Cologne Cologne Germany
| | - Philipp P. Sprenger
- Institute of Organismic and Molecular Evolution Johannes‐Gutenberg‐University Mainz Mainz Germany
- Department of Animal Ecology and Tropical Biology, Biocentre, Am Hubland University of Würzburg Würzburg Germany
| | - Thomas Schmitt
- Department of Animal Ecology and Tropical Biology, Biocentre, Am Hubland University of Würzburg Würzburg Germany
| | - Florian Menzel
- Institute of Organismic and Molecular Evolution Johannes‐Gutenberg‐University Mainz Mainz Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
- Institute of Organismic and Molecular Evolution Johannes‐Gutenberg‐University Mainz Mainz Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG) Frankfurt am Main Germany
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
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26
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Weißbach S, Sys S, Hewel C, Todorov H, Schweiger S, Winter J, Pfenninger M, Torkamani A, Evans D, Burger J, Everschor-Sitte K, May-Simera HL, Gerber S. Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines. BMC Genomics 2021; 22:62. [PMID: 33468057 PMCID: PMC7814447 DOI: 10.1186/s12864-020-07362-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/30/2020] [Indexed: 12/14/2022] Open
Abstract
Background Next Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data from different experimental backgrounds can introduce strong biases. In order to methodically investigate the magnitude of systematic errors in single nucleotide variant calls, we performed a cross-sectional observational study on a genomic cohort of 99 subjects each sequenced via (i) Illumina HiSeq X, (ii) Illumina HiSeq, and (iii) Complete Genomics and processed with the respective bioinformatic pipeline. We also repeated variant calling for the Illumina cohorts with GATK, which allowed us to investigate the effect of the bioinformatics analysis strategy separately from the sequencing platform’s impact. Results The number of detected variants/variant classes per individual was highly dependent on the experimental setup. We observed a statistically significant overrepresentation of variants uniquely called by a single setup, indicating potential systematic biases. Insertion/deletion polymorphisms (indels) were associated with decreased concordance compared to single nucleotide polymorphisms (SNPs). The discrepancies in indel absolute numbers were particularly prominent in introns, Alu elements, simple repeats, and regions with medium GC content. Notably, reprocessing sequencing data following the best practice recommendations of GATK considerably improved concordance between the respective setups. Conclusion We provide empirical evidence of systematic heterogeneity in variant calls between alternative experimental and data analysis setups. Furthermore, our results demonstrate the benefit of reprocessing genomic data with harmonized pipelines when integrating data from different studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07362-8.
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Affiliation(s)
- Stephan Weißbach
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.,Institute of Developmental Biology and Neurobiology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Stanislav Sys
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Charlotte Hewel
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Hristo Todorov
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Susann Schweiger
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.,Leibniz Institute for Resilience Research, Mainz, Germany
| | - Jennifer Winter
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.,Leibniz Institute for Resilience Research, Mainz, Germany
| | - Markus Pfenninger
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Institute for Molecular and Organismic Evolution, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity, and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Ali Torkamani
- Department of Integrative Structural and Computational Biology, Scripps Research Translational Institute, California Campus, San Diego, USA
| | - Doug Evans
- Department of Integrative Structural and Computational Biology, Scripps Research Translational Institute, California Campus, San Diego, USA
| | - Joachim Burger
- Institute of Anthropology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | | | | | - Susanne Gerber
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.
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27
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Doria HB, Pfenninger M. A multigenerational approach can detect early Cd pollution in Chironomus riparius. Chemosphere 2021; 262:127815. [PMID: 32768752 DOI: 10.1016/j.chemosphere.2020.127815] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 06/11/2023]
Abstract
Cadmium (Cd) is a non-essential highly toxic metal and its presence in the environment has been a concern over the years. On the present study we adopt the spiked water exposure scenario to study early Cd contamination across five generations of the model organism Chironomus riparius. Animals were, at the beginning of each generation, submitted to 0, 1, 3.2, 10, 32 and 100 μg/L of Cd. Classical endpoints like total emergence, EmT50, fertility and the integrative fitness measure, population growth rate (PGR), were calculated at each generation. Results could demonstrate that exposure to brief and low Cd concentrations can affect all the measured endpoints and, therefore, initial Cd pollution in previously unpolluted sites can be detected after just five consecutive generations. Importantly, at 100 μg/L of Cd fertility was greatly impaired after three generations. Also, PGR calculation is a sensitive tool for monitoring early pollution of Cd. Yet, no adaptation to Cd over five generations could be observed on the present experimental setup.
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Affiliation(s)
- Halina Binde Doria
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt Am Main, Germany.
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt Am Main, Germany; Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt Am Main, Germany; Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany
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28
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Reuss F, Kreß A, Braun M, Magdeburg A, Pfenninger M, Müller R, Mehring M. Knowledge on exotic mosquitoes in Germany, and public acceptance and effectiveness of Bti and two self-prepared insecticides against Aedes japonicus japonicus. Sci Rep 2020; 10:18901. [PMID: 33144626 PMCID: PMC7641113 DOI: 10.1038/s41598-020-75780-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/08/2020] [Indexed: 12/05/2022] Open
Abstract
Mosquito-borne diseases are a continuous challenge to public health. To prevent transmission, Integrated Vector Management (IVM) applies preventive, control, and communicational strategies that should be feasible, environmentally benign, and sustainable. IVM shows higher efficiency when being supported by local communities. Accordingly, we applied a social-ecological approach to identify the public acceptance of control measures and effectiveness of Eurocent coins containing copper, clove essential oil (EO) and Bacillus thuringiensis israelensis (Bti). We performed field and laboratory experiments to demonstrate the toxicity of alternative substances against Aedes japonicus japonicus. In expert interviews, we asked for (1) knowledge on exotic mosquitoes in Germany, (2) potential chances of alternative substances in future mosquito control, and (3) their needs for further clarification before application. We assessed potential users' (4) awareness of exotic mosquitoes and (5) willingness to apply the substances. Self-prepared copper coins and EO were clearly preferred by potential users over Bti. However, 100% mortality of the sensitive first stage could not be reached with the number of ten 5-Eurocent coins showing limited toxicity. Clove EO was shown to work as oviposition deterrent and larvicide with a LC50 of 17 mg l-1 (95% CI: 15-19 mg l-1). This study shows the importance of potential users' perspectives in IVM and the need for authorised insecticides.
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Affiliation(s)
- Friederike Reuss
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Straße 14-16, 60325, Frankfurt am Main, Germany.
| | - Aljoscha Kreß
- Institute of Occupational Medicine, Social Medicine and Environmental Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Markus Braun
- Institute of Occupational Medicine, Social Medicine and Environmental Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Axel Magdeburg
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Straße 14-16, 60325, Frankfurt am Main, Germany
- Institute of Occupational Medicine, Social Medicine and Environmental Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Straße 14-16, 60325, Frankfurt am Main, Germany
- LOEWE TBG (Translational Biodiversity Genomics), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, Gresemundweg 2, 55128, Mainz, Germany
| | - Ruth Müller
- Institute of Occupational Medicine, Social Medicine and Environmental Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- Institute of Tropical Medicine, Nationalestraat 155, 2000, Antwerp, Belgium
| | - Marion Mehring
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Straße 14-16, 60325, Frankfurt am Main, Germany
- ISOE - Institute for Social-Ecological Research, Biodiversity and People, Hamburger Allee 45, 60486, Frankfurt am Main, Germany
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Hartke J, Schell T, Jongepier E, Schmidt H, Sprenger PP, Paule J, Bornberg-Bauer E, Schmitt T, Menzel F, Pfenninger M, Feldmeyer B. Hybrid Genome Assembly of a Neotropical Mutualistic Ant. Genome Biol Evol 2020; 11:2306-2311. [PMID: 31329228 PMCID: PMC6735702 DOI: 10.1093/gbe/evz159] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2019] [Indexed: 01/13/2023] Open
Abstract
The success of social insects is largely intertwined with their highly advanced chemical communication system that facilitates recognition and discrimination of species and nest-mates, recruitment, and division of labor. Hydrocarbons, which cover the cuticle of insects, not only serve as waterproofing agents but also constitute a major component of this communication system. Two cryptic Crematogaster species, which share their nest with Camponotus ants, show striking diversity in their cuticular hydrocarbon (CHC) profile. This mutualistic system therefore offers a great opportunity to study the genetic basis of CHC divergence between sister species. As a basis for further genome-wide studies high-quality genomes are needed. Here, we present the annotated draft genome for Crematogaster levior A. By combining the three most commonly used sequencing techniques—Illumina, PacBio, and Oxford Nanopore—we constructed a high-quality de novo ant genome. We show that even low coverage of long reads can add significantly to overall genome contiguity. Annotation of desaturase and elongase genes, which play a role in CHC biosynthesis revealed one of the largest repertoires in ants and a higher number of desaturases in general than in other Hymenoptera. This may provide a mechanistic explanation for the high diversity observed in C. levior CHC profiles.
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Affiliation(s)
- Juliane Hartke
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, Mainz, Germany
| | - Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Evelien Jongepier
- Molecular Evolution and Bioinformatics Group, Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität, Münster, Germany
| | - Hanno Schmidt
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis
| | - Philipp P Sprenger
- Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, Mainz, Germany.,Department of Animal Ecology and Tropical Biology, University of Würzburg, Biocentre - Am Hubland, Germany
| | - Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany
| | - Erich Bornberg-Bauer
- Molecular Evolution and Bioinformatics Group, Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität, Münster, Germany
| | - Thomas Schmitt
- Department of Animal Ecology and Tropical Biology, University of Würzburg, Biocentre - Am Hubland, Germany
| | - Florian Menzel
- Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, Mainz, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, Mainz, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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Zając KS, Hatteland BA, Feldmeyer B, Pfenninger M, Filipiak A, Noble LR, Lachowska-Cierlik D. A comprehensive phylogeographic study of Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Pulmonata: Arionidae) in Europe. ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-019-00417-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AbstractArion vulgaris Moquin-Tandon, 1855 is regarded as one of the 100 most invasive species in Europe. The native distribution range of this species is uncertain, but for many years, the Iberian Peninsula has been considered as the area of origin. However, recent studies indicate that A. vulgaris probably originated from France. We have investigated the genetic structure of 33 European populations (Poland, Norway, Germany, France, Denmark, Switzerland) of this slug, based on two molecular markers, mitochondrial cytochrome c oxidase subunit I (COI, mtDNA) and nuclear zinc finger (ZF, nDNA). Our investigation included published data from two previous studies, giving a total of 95 populations of A. vulgaris from 26 countries. This comprehensive dataset shows comparable haplotype diversity in Central, North and Western Europe, and significantly lower haplotype diversity in the East. All haplotypes observed in the East can be found in the other regions, and haplotype diversity is highest in the Central and Western region. Moreover, there is strong isolation by distance in Central and Western Europe, and only very little in the East. Furthermore, the number of unique haplotypes was highest in France. This pattern strongly suggests that A. vulgaris has originated from a region spanning from France to Western Germany; hence, the slug is probably alien/invasive in other parts of Europe, where it occurs. Our results indicate the necessity to cover as much of the distribution range of a species as possible before making conclusive assumptions about its origin and alien status.
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Riaz M, Kuemmerlen M, Wittwer C, Cocchiararo B, Khaliq I, Pfenninger M, Nowak C. Combining environmental DNA and species distribution modeling to evaluate reintroduction success of a freshwater fish. Ecol Appl 2020; 30:e02034. [PMID: 31680362 DOI: 10.1002/eap.2034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 07/18/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
Active species reintroduction is an important conservation tool when aiming for the restoration of biological communities and ecosystems. The effective monitoring of reintroduction success is a crucial factor in this process. Here, we used a combination of environmental DNA (eDNA) techniques and species distribution models (SDMs) to evaluate the success of recent reintroductions of the freshwater fish Alburnoides bipunctatus in central Germany. We built SDMs without and with eDNA presence data to locate further suitable reintroduction sites and potentially overlooked populations of the species. We successfully detected eDNA of A. bipunctatus at all reintroduction sites, as well as several adjacent sites mostly in downstream direction, which supports the success of reintroduction efforts. eDNA-based species detection considerably improved SDMs for A. bipunctatus, which allowed to identify species presence in previously unknown localities. Our results confirm the usefulness of eDNA techniques as standard tool to monitor reintroduced fish populations. We propose that combining eDNA with SDMs is a highly effective approach for long-term monitoring of reintroduction success in aquatic species.
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Affiliation(s)
- Maria Riaz
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, 63571, Gelnhausen, Germany
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Mathias Kuemmerlen
- Department of Systems Analysis, Integrated Assessment and Modelling, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Ueberlandstrasse 133, 8600, Duebendorf, Switzerland
| | - Claudia Wittwer
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, 63571, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, 63571, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Imran Khaliq
- Department of Zoology, Ghazi University, Dera Ghazi Khan, Pakistan
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, 63571, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
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Pfenninger M, Foucault Q. Genomic processes underlying rapid adaptation of a natural
Chironomus riparius
population to unintendedly applied experimental selection pressures. Mol Ecol 2020; 29:536-548. [DOI: 10.1111/mec.15347] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/13/2019] [Accepted: 12/24/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Markus Pfenninger
- Department of Molecular Ecology Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
- Institute for Molecular and Organismic Evolution Johannes Gutenberg University Mainz Germany
- LOEWE Centre for Translational Biodiversity Genomics Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
| | - Quentin Foucault
- Department of Molecular Ecology Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
- Institute for Molecular and Organismic Evolution Johannes Gutenberg University Mainz Germany
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Tiesmeyer A, Ramos L, Manuel Lucas J, Steyer K, Alves PC, Astaras C, Brix M, Cragnolini M, Domokos C, Hegyeli Z, Janssen R, Kitchener AC, Lambinet C, Mestdagh X, Migli D, Monterroso P, Mulder JL, Schockert V, Youlatos D, Pfenninger M, Nowak C. Range-wide patterns of human-mediated hybridisation in European wildcats. CONSERV GENET 2020. [DOI: 10.1007/s10592-019-01247-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
AbstractHybridisation between wild taxa and their domestic congeners is a significant conservation issue. Domestic species frequently outnumber their wild relatives in population size and distribution and may therefore genetically swamp the native species. The European wildcat (Felis silvestris) has been shown to hybridise with domestic cats (Felis catus). Previously suggested spatially divergent introgression levels have not been confirmed on a European scale due to significant differences in the applied methods to assess hybridisation of the European wildcat. We analysed 926 Felis spp. samples from 13 European countries, using a set of 86 selected ancestry-informative SNPs, 14 microsatellites, and ten mitochondrial and Y-chromosome markers to study regional hybridisation and introgression patterns and population differentiation. We detected 51 hybrids (four F1 and 47 F2 or backcrosses) and 521 pure wildcats throughout Europe. The abundance of hybrids varied considerably among studied populations. All samples from Scotland were identified as F2 hybrids or backcrosses, supporting previous findings that the genetic integrity of that wildcat population has been seriously compromised. In other European populations, low to moderate levels of hybridisation were found, with the lowest levels being in Central and Southeast Europe. The occurrence of distinct maternal and paternal markers between wildcat and domestic cat suggests that there were no severe hybridisation episodes in the past. The overall low (< 1%) prevalence of F1 hybrids suggests a low risk of hybridisation for the long-term genetic integrity of the wildcat in most of Europe. However, regionally elevated introgression rates confirm that hybridisation poses a potential threat. We propose regional in-depth monitoring of hybridisation rates to identify factors driving hybridisation so as to develop effective strategies for conservation.
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Waldvogel AM, Feldmeyer B, Rolshausen G, Exposito-Alonso M, Rellstab C, Kofler R, Mock T, Schmid K, Schmitt I, Bataillon T, Savolainen O, Bergland A, Flatt T, Guillaume F, Pfenninger M. Evolutionary genomics can improve prediction of species' responses to climate change. Evol Lett 2020; 4:4-18. [PMID: 32055407 PMCID: PMC7006467 DOI: 10.1002/evl3.154] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/31/2019] [Accepted: 11/26/2019] [Indexed: 01/08/2023] Open
Abstract
Global climate change (GCC) increasingly threatens biodiversity through the loss of species, and the transformation of entire ecosystems. Many species are challenged by the pace of GCC because they might not be able to respond fast enough to changing biotic and abiotic conditions. Species can respond either by shifting their range, or by persisting in their local habitat. If populations persist, they can tolerate climatic changes through phenotypic plasticity, or genetically adapt to changing conditions depending on their genetic variability and census population size to allow for de novo mutations. Otherwise, populations will experience demographic collapses and species may go extinct. Current approaches to predicting species responses to GCC begin to combine ecological and evolutionary information for species distribution modelling. Including an evolutionary dimension will substantially improve species distribution projections which have not accounted for key processes such as dispersal, adaptive genetic change, demography, or species interactions. However, eco‐evolutionary models require new data and methods for the estimation of a species' adaptive potential, which have so far only been available for a small number of model species. To represent global biodiversity, we need to devise large‐scale data collection strategies to define the ecology and evolutionary potential of a broad range of species, especially of keystone species of ecosystems. We also need standardized and replicable modelling approaches that integrate these new data to account for eco‐evolutionary processes when predicting the impact of GCC on species' survival. Here, we discuss different genomic approaches that can be used to investigate and predict species responses to GCC. This can serve as guidance for researchers looking for the appropriate experimental setup for their particular system. We furthermore highlight future directions for moving forward in the field and allocating available resources more effectively, to implement mitigation measures before species go extinct and ecosystems lose important functions.
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Affiliation(s)
- Ann-Marie Waldvogel
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
| | - Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
| | | | | | - Robert Kofler
- Institute of Population Genetics Vetmeduni Vienna Austria
| | - Thomas Mock
- School of Environmental Sciences University of East Anglia Norwich United Kingdom
| | - Karl Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics University of Hohenheim Stuttgart Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany.,Institute of Ecology, Evolution and Diversity Goethe-University Frankfurt am Main Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) Frankfurt am Main Germany
| | | | - Outi Savolainen
- Department of Ecology and Genetics University of Oulu Finland
| | - Alan Bergland
- Department of Biology University of Virginia Charlottesville Virginia
| | - Thomas Flatt
- Department of Biology University of Fribourg Fribourg Switzerland
| | - Frederic Guillaume
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zürich Switzerland
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) Frankfurt am Main Germany.,Institute for Organismic and Molecular Evolution Johannes Gutenberg University Mainz Germany
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Wieser A, Reuss F, Niamir A, Müller R, O'Hara RB, Pfenninger M. Modelling seasonal dynamics, population stability, and pest control in Aedes japonicus japonicus (Diptera: Culicidae). Parasit Vectors 2019; 12:142. [PMID: 30909930 PMCID: PMC6434845 DOI: 10.1186/s13071-019-3366-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/05/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The invasive temperate mosquito Aedes japonicus japonicus is a potential vector for various infectious diseases and therefore a target of vector control measures. Even though established in Germany, it is unclear whether the species has already reached its full distribution potential. The possible range of the species, its annual population dynamics, the success of vector control measures and future expansions due to climate change still remain poorly understood. While numerous studies on occurrence have been conducted, they used mainly presence data from relatively few locations. In contrast, we used experimental life history data to model the dynamics of a continuous stage-structured population to infer potential seasonal densities and ask whether stable populations are likely to establish over a period of more than one year. In addition, we used climate change models to infer future ranges. Finally, we evaluated the effectiveness of various stage-specific vector control measures. RESULTS Aedes j. japonicus has already established stable populations in the southwest and west of Germany. Our models predict a spread of Ae. j. japonicus beyond the currently observed range, but likely not much further eastwards under current climatic conditions. Climate change models, however, will expand this range substantially and higher annual densities can be expected. Applying vector control measures to oviposition, survival of eggs, larvae or adults showed that application of adulticides for 30 days between late spring and early autumn, while ambient temperatures are above 9 °C, can reduce population density by 75%. Continuous application of larvicide showed similar results in population reduction. Most importantly, we showed that with the consequent application of a mixed strategy, it should be possible to significantly reduce or even extinguish existing populations with reasonable effort. CONCLUSION Our study provides valuable insights into the mechanisms concerning the establishment of stable populations in invasive species. In order to minimise the hazard to public health, we recommend vector control measures to be applied in 'high risk areas' which are predicted to allow establishment of stable populations to establish.
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Affiliation(s)
- Andreas Wieser
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, Gresemundweg 2, 55128, Mainz, Germany. .,Centre for Biodiversity Dynamics, and Department of Mathematical Sciences, Norwegian University of Science and Technology NTNU, Sentralbygg 2, Gløshaugen, 7491, Trondheim, Norway.
| | - Friederike Reuss
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
| | - Aidin Niamir
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Ruth Müller
- Faculty of Medicine, Institute of Occupational Medicine, Social Medicine and Environmental Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.,Unit of Entomology, Institute of Tropical Medicine, Nationalenstraat 155, 2000, Antwerp, Belgium
| | - Robert B O'Hara
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Centre for Biodiversity Dynamics, and Department of Mathematical Sciences, Norwegian University of Science and Technology NTNU, Sentralbygg 2, Gløshaugen, 7491, Trondheim, Norway
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, Gresemundweg 2, 55128, Mainz, Germany
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Foucault Q, Wieser A, Heumann-Kiesler C, Diogo J, Cocchiararo B, Nowak C, Waldvogel AM, Pfenninger M. An experimental assessment of reproductive isolation and its consequences for seasonal hybridization dynamics. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Quentin Foucault
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg, Mainz, Germany
| | - Andreas Wieser
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg, Mainz, Germany
| | - Clara Heumann-Kiesler
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität, Frankfurt am Main, Germany
| | - Joao Diogo
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystraße, Gelnhausen, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystraße, Gelnhausen, Germany
| | - Ann-Marie Waldvogel
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany
| | - Markus Pfenninger
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg, Mainz, Germany
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Foucault Q, Wieser A, Waldvogel A, Feldmeyer B, Pfenninger M. Rapid adaptation to high temperatures in Chironomus riparius. Ecol Evol 2018; 8:12780-12789. [PMID: 30619582 PMCID: PMC6308882 DOI: 10.1002/ece3.4706] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/10/2018] [Accepted: 10/15/2018] [Indexed: 12/17/2022] Open
Abstract
Effects of seasonal or daily temperature variation on fitness and physiology of ectothermic organisms and their ways to cope with such variations have been widely studied. However, the way multivoltines organisms cope with temperature variations from one generation to the next is still not well understood. The aim of this study was to investigate whether the multivoltine midge Chironomus riparius Meigen (1803) responds mainly via acclimation as predicted by current theories or whether rapid genetic adaptation is involved. To investigate this issue, a common garden approach has been applied. A mix of larvae from five European populations was raised in the laboratory at three different pre-exposure temperatures (PET): 14, 20, and 26°C. After three and five generations, respectively, larvae were exposed to three treatment temperatures (TT): 14, 20, and 26°C. Mortality was monitored for the first 48 hr and after emergence. After three generations, significant mortality rate differences depended on an interaction of PET and TT. This finding supports the hypothesis that chironomids respond rapidly to climatic variation via adaptive mechanisms and to a lesser extent via phenotypic plasticity. The result of the experiment indicates that three generations were sufficient to adapt to warm temperature, decreasing the mortality rate, highlighting the potential for chironomids to rapidly respond to seasonally changing conditions.
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Affiliation(s)
- Quentin Foucault
- Molecular Ecology GroupSenckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- Institute for Organismic and Molecular EvolutionJohannes Gutenberg UniversitätMainzGermany
| | - Andreas Wieser
- Molecular Ecology GroupSenckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- Institute for Organismic and Molecular EvolutionJohannes Gutenberg UniversitätMainzGermany
| | - Ann‐Marie Waldvogel
- Molecular Ecology GroupSenckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Barbara Feldmeyer
- Molecular Ecology GroupSenckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Markus Pfenninger
- Molecular Ecology GroupSenckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- Institute for Organismic and Molecular EvolutionJohannes Gutenberg UniversitätMainzGermany
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Bálint M, Pfenninger M, Grossart HP, Taberlet P, Vellend M, Leibold MA, Englund G, Bowler D. Environmental DNA Time Series in Ecology. Trends Ecol Evol 2018; 33:945-957. [DOI: 10.1016/j.tree.2018.09.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/28/2018] [Accepted: 09/05/2018] [Indexed: 12/13/2022]
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Mishra B, Gupta DK, Pfenninger M, Hickler T, Langer E, Nam B, Paule J, Sharma R, Ulaszewski B, Warmbier J, Burczyk J, Thines M. A reference genome of the European beech (Fagus sylvatica L.). Gigascience 2018; 7:5017772. [PMID: 29893845 PMCID: PMC6014182 DOI: 10.1093/gigascience/giy063] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/19/2018] [Indexed: 01/09/2023] Open
Abstract
Background The European beech is arguably the most important climax broad-leaved tree species in Central Europe, widely planted for its valuable wood. Here, we report the 542 Mb draft genome sequence of an up to 300-year-old individual (Bhaga) from an undisturbed stand in the Kellerwald-Edersee National Park in central Germany. Findings Using a hybrid assembly approach, Illumina reads with short- and long-insert libraries, coupled with long Pacific Biosciences reads, we obtained an assembled genome size of 542 Mb, in line with flow cytometric genome size estimation. The largest scaffold was of 1.15 Mb, the N50 length was 145 kb, and the L50 count was 983. The assembly contained 0.12% of Ns. A Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis retrieved 94% complete BUSCO genes, well in the range of other high-quality draft genomes of trees. A total of 62,012 protein-coding genes were predicted, assisted by transcriptome sequencing. In addition, we are reporting an efficient method for extracting high-molecular-weight DNA from dormant buds, by which contamination by environmental bacteria and fungi was kept at a minimum. Conclusions The assembled genome will be a valuable resource and reference for future population genomics studies on the evolution and past climate change adaptation of beech and will be helpful for identifying genes, e.g., involved in drought tolerance, in order to select and breed individuals to adapt forestry to climate change in Europe. A continuously updated genome browser and download page can be accessed from beechgenome.net, which will include future genome versions of the reference individual Bhaga, as new sequencing approaches develop.
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Affiliation(s)
- Bagdevi Mishra
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University, Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Deepak K Gupta
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University, Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Johannes Gutenberg Universität, Fachbereich Biologie, Institut für Organismische und Molekulare Evolutionsbiologie (iOME), Gresemundweg 2, 55128 Mainz
| | - Thomas Hickler
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University, Department for Geology, Institute of Geography, Max-von-Laue-Str. 23, D-60438 Frankfurt am Main, Germany
| | - Ewald Langer
- University of Kassel, FB 10, Department of Ecology, Heinrich-Plett-Str. 40, D-34132 Kassel, Germany
| | - Bora Nam
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University, Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Juraj Paule
- Senckenberg Research Institute and Natural History Museum Frankfurt, Department of Botany and Molecular Evolution, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Rahul Sharma
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Bartosz Ulaszewski
- Kazimierz Wielki University, Department of Genetics, ul. Chodkiewicza 30, 85-064 Bydgoszcz, Poland
| | - Joanna Warmbier
- Kazimierz Wielki University, Department of Genetics, ul. Chodkiewicza 30, 85-064 Bydgoszcz, Poland
| | - Jaroslaw Burczyk
- Kazimierz Wielki University, Department of Genetics, ul. Chodkiewicza 30, 85-064 Bydgoszcz, Poland
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University, Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
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41
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Tills O, Truebano M, Feldmeyer B, Pfenninger M, Morgenroth H, Schell T, Rundle SD. Transcriptomic responses to predator kairomones in embryos of the aquatic snail Radix balthica. Ecol Evol 2018; 8:11071-11082. [PMID: 30519426 PMCID: PMC6262742 DOI: 10.1002/ece3.4574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/04/2018] [Accepted: 09/05/2018] [Indexed: 12/24/2022] Open
Abstract
The ability of organisms to respond to predation threat by exhibiting induced defenses is well documented, but studies on the potential mechanistic basis for such responses are scarce. Here, we examine the transcriptomic response to predator kairomones of two functionally distinct developmental stages in embryos of the aquatic snail Radix balthica: E8-the stage at which a range-finding trial indicated that kairomone-induced accelerated growth and development first occurred; and E9-the stage at which embryos switched from ciliary- to crawling-driven locomotion. We tested whether expression profiles were influenced by kairomones and whether this influence varied between stages. We also identified potential candidate genes for investigating mechanisms underpinning induced responses. There were 6,741 differentially expressed transcripts between developmental stages, compared to just five in response to predator kairomones. However, on examination of functional enrichment in the transcripts responding to predator kairomones and adopting a less stringent significance threshold, 206 transcripts were identified relating to muscle function, growth, and development, with this response being greater at the later E9 stage. Furthermore, these transcripts included putative annotations for genes identified as responding to predator kairomones in other taxa, including C1q, lectin, and actin domains. Globally, transcript expression appeared reduced in response to predator kairomones and we hypothesize that this might be a result of metabolic suppression, as has been reported in other taxa in response to predation threat.
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Affiliation(s)
- Oliver Tills
- Marine Biology and Ecology Research CentreUniversity of Plymouth, Drake CircusPlymouthUK
| | - Manuela Truebano
- Marine Biology and Ecology Research CentreUniversity of Plymouth, Drake CircusPlymouthUK
| | - Barbara Feldmeyer
- Molecular Ecology Group, Institute for Ecology, Evolution and DiversityGoethe‐UniversityFrankfurt am MainGermany
| | - Markus Pfenninger
- Molecular Ecology Group, Institute for Ecology, Evolution and DiversityGoethe‐UniversityFrankfurt am MainGermany
- Adaptation and ClimateSenckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Holly Morgenroth
- Marine Biology and Ecology Research CentreUniversity of Plymouth, Drake CircusPlymouthUK
| | - Tilman Schell
- Senckenberg Research Institute and Natural History Museum FrankfurtFrankfurtGermany
- LOWE‐TBG Centre for Translational Biodiversity GenomicsFrankfurtGermany
| | - Simon D. Rundle
- Marine Biology and Ecology Research CentreUniversity of Plymouth, Drake CircusPlymouthUK
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42
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Singh G, Grande FD, Schnitzler J, Pfenninger M, Schmitt I. Different diversification histories in tropical and temperate lineages in the ascomycete subfamily Protoparmelioideae (Parmeliaceae). MycoKeys 2018; 36:1-19. [PMID: 29997448 PMCID: PMC6037653 DOI: 10.3897/mycokeys.36.22548] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 06/19/2018] [Indexed: 11/12/2022] Open
Abstract
Background: Environment and geographic processes affect species' distributions as well as evolutionary processes, such as clade diversification. Estimating the time of origin and diversification of organisms helps us understand how climate fluctuations in the past might have influenced the diversification and present distribution of species. Complementing divergence dating with character evolution could indicate how key innovations have facilitated the diversification of species. Methods: We estimated the divergence times within the newly recognised subfamily Protoparmelioideae (Ascomycota) using a multilocus dataset to assess the temporal context of diversification events. We reconstructed ancestral habitats and substrate using a species tree generated in *Beast. Results: We found that the diversification in Protoparmelioideae occurred during the Miocene and that the diversification events in the tropical clade Maronina predate those of the extratropical Protoparmelia. Character reconstructions suggest that the ancestor of Protoparmelioideae was most probably a rock-dwelling lichen inhabiting temperate environments. Conclusions: Major diversification within the subtropical/tropical genus Maronina occurred between the Paleocene and Miocene whereas the diversifications within the montane, arctic/temperate genus Protoparmelia occurred much more recently, i.e. in the Miocene.
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Affiliation(s)
- Garima Singh
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Jan Schnitzler
- Department of Molecular Evolution and Plant Systematics, Institute of Biology, Leipzig University, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt am Main, Germany
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43
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Waldvogel AM, Wieser A, Schell T, Patel S, Schmidt H, Hankeln T, Feldmeyer B, Pfenninger M. The genomic footprint of climate adaptation in Chironomus riparius. Mol Ecol 2018; 27:1439-1456. [PMID: 29473242 DOI: 10.1111/mec.14543] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 02/09/2018] [Accepted: 02/09/2018] [Indexed: 12/31/2022]
Abstract
The gradual heterogeneity of climatic factors poses varying selection pressures across geographic distances that leave signatures of clinal variation in the genome. Separating signatures of clinal adaptation from signatures of other evolutionary forces, such as demographic processes, genetic drift and adaptation, to nonclinal conditions of the immediate local environment is a major challenge. Here, we examine climate adaptation in five natural populations of the harlequin fly Chironomus riparius sampled along a climatic gradient across Europe. Our study integrates experimental data, individual genome resequencing, Pool-Seq data and population genetic modelling. Common-garden experiments revealed significantly different population growth rates at test temperatures corresponding to the population origin along the climate gradient, suggesting thermal adaptation on the phenotypic level. Based on a population genomic analysis, we derived empirical estimates of historical demography and migration. We used an FST outlier approach to infer positive selection across the climate gradient, in combination with an environmental association analysis. In total, we identified 162 candidate genes as genomic basis of climate adaptation. Enriched functions among these candidate genes involved the apoptotic process and molecular response to heat, as well as functions identified in studies of climate adaptation in other insects. Our results show that local climate conditions impose strong selection pressures and lead to genomic adaptation despite strong gene flow. Moreover, these results imply that selection to different climatic conditions seems to converge on a functional level, at least between different insect species.
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Affiliation(s)
- Ann-Marie Waldvogel
- Molecular Ecology Group, Institute for Ecology, Evolution & Diversity, Goethe-University, Frankfurt am Main, Hesse, Germany.,Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
| | - Andreas Wieser
- Molecular Ecology Group, Institute for Ecology, Evolution & Diversity, Goethe-University, Frankfurt am Main, Hesse, Germany.,Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
| | - Tilman Schell
- Molecular Ecology Group, Institute for Ecology, Evolution & Diversity, Goethe-University, Frankfurt am Main, Hesse, Germany.,Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
| | - Simit Patel
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
| | - Hanno Schmidt
- Pathology, Microbiology & Immunology, University of California - Davis, Davis, CA, USA
| | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg-University, Mainz, Rhineland-Palatinate, Germany
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
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44
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Blank-Landeshammer B, Kollipara L, Biß K, Pfenninger M, Malchow S, Shuvaev K, Zahedi RP, Sickmann A. Combining De Novo Peptide Sequencing Algorithms, A Synergistic Approach to Boost Both Identifications and Confidence in Bottom-up Proteomics. J Proteome Res 2017; 16:3209-3218. [DOI: 10.1021/acs.jproteome.7b00198] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften − ISAS − e.V., 44139 Dortmund, Germany
| | - Karsten Biß
- Leibniz-Institut für Analytische Wissenschaften − ISAS − e.V., 44139 Dortmund, Germany
| | - Markus Pfenninger
- Biodiversity
and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany
- Faculty
of Biological Science, Institute for Ecology, Evolution and Diversity,
Department of Molecular Ecology, Goethe University, Max-von-Laue-Straße
9, 60438 Frankfurt
am Main, Germany
| | - Sebastian Malchow
- Leibniz-Institut für Analytische Wissenschaften − ISAS − e.V., 44139 Dortmund, Germany
| | - Konstantin Shuvaev
- Leibniz-Institut für Analytische Wissenschaften − ISAS − e.V., 44139 Dortmund, Germany
| | - René P. Zahedi
- Leibniz-Institut für Analytische Wissenschaften − ISAS − e.V., 44139 Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften − ISAS − e.V., 44139 Dortmund, Germany
- Medizinische
Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum, 44801 Bochum, Germany
- Department
of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen AB24 3FX, Scotland, United Kingdom
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45
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Oppold A, Pfenninger M. Direct estimation of the spontaneous mutation rate by short-term mutation accumulation lines in Chironomus riparius. Evol Lett 2017; 1:86-92. [PMID: 30283641 PMCID: PMC6121839 DOI: 10.1002/evl3.8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/10/2017] [Accepted: 04/03/2017] [Indexed: 12/15/2022] Open
Abstract
Mutations are the ultimate basis of evolution, yet their occurrence rate is known only for few species. We directly estimated the spontaneous mutation rate and the mutational spectrum in the nonbiting midge C. riparius with a new approach. Individuals from ten mutation accumulation lines over five generations were deep genome sequenced to count de novo mutations that were not present in a pool of F1 individuals, representing parental genotypes. We identified 51 new single site mutations of which 25 were insertions or deletions and 26 single nucleotide mutations. This shift in the mutational spectrum compared to other organisms was explained by the high A/T content of the species. We estimated a haploid mutation rate of 2.1 × 10-9 (95% confidence interval: 1.4 × 10-9 - 3.1 × 10-9) that is in the range of recent estimates for other insects and supports the drift barrier hypothesis. We show that accurate mutation rate estimation from a high number of observed mutations is feasible with moderate effort even for nonmodel species.
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Affiliation(s)
- Ann‐Marie Oppold
- Senckenberg Biodiversity and Climate Research CentreMolecular Ecology Group60325Frankfurt am MainGermany
- Faculty of Biological Science, Institute for Ecology, Evolution and DiversityGoethe University60438Frankfurt am MainGermany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research CentreMolecular Ecology Group60325Frankfurt am MainGermany
- Faculty of Biological Science, Institute for Ecology, Evolution and DiversityGoethe University60438Frankfurt am MainGermany
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46
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Hof C, Khaliq I, Prinzinger R, Böhning-Gaese K, Pfenninger M. Global patterns of thermal tolerances and vulnerability of endotherms to climate change remain robust irrespective of varying data suitability criteria. Proc Biol Sci 2017; 284:rspb.2017.0232. [PMID: 28539511 DOI: 10.1098/rspb.2017.0232] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/18/2017] [Indexed: 11/12/2022] Open
Affiliation(s)
- Christian Hof
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt, Germany
| | - Imran Khaliq
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt, Germany.,Department of Zoology, Ghazi University, Dera Ghazi Khan, Punjab, Pakistan
| | - Roland Prinzinger
- Metabolic Physiology, Department of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 13, Frankfurt 60438, Germany
| | - Katrin Böhning-Gaese
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt, Germany.,Department of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 13, Frankfurt 60438, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt, Germany
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47
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Kumar V, Lammers F, Bidon T, Pfenninger M, Kolter L, Nilsson MA, Janke A. The evolutionary history of bears is characterized by gene flow across species. Sci Rep 2017; 7:46487. [PMID: 28422140 PMCID: PMC5395953 DOI: 10.1038/srep46487] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [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: 11/23/2016] [Accepted: 03/17/2017] [Indexed: 01/03/2023] Open
Abstract
Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to large amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. Evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow.
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Affiliation(s)
- Vikas Kumar
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University Frankfurt, Institute for Ecology, Evolution &Diversity, Biologicum, Max-von-Laue-Str. 13, D-60439 Frankfurt am Main, Germany
| | - Fritjof Lammers
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University Frankfurt, Institute for Ecology, Evolution &Diversity, Biologicum, Max-von-Laue-Str. 13, D-60439 Frankfurt am Main, Germany
| | - Tobias Bidon
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University Frankfurt, Institute for Ecology, Evolution &Diversity, Biologicum, Max-von-Laue-Str. 13, D-60439 Frankfurt am Main, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University Frankfurt, Institute for Ecology, Evolution &Diversity, Biologicum, Max-von-Laue-Str. 13, D-60439 Frankfurt am Main, Germany
| | - Lydia Kolter
- AG Zoologischer Garten Cologne, Riehler Straße 173, 50735 Cologne, Germany
| | - Maria A Nilsson
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe University Frankfurt, Institute for Ecology, Evolution &Diversity, Biologicum, Max-von-Laue-Str. 13, D-60439 Frankfurt am Main, Germany
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48
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Oppold AM, Schmidt H, Rose M, Hellmann SL, Dolze F, Ripp F, Weich B, Schmidt-Ott U, Schmidt E, Kofler R, Hankeln T, Pfenninger M. Chironomus riparius
(Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence. Mol Ecol 2017; 26:3256-3275. [DOI: 10.1111/mec.14111] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 02/23/2017] [Accepted: 03/06/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Ann-Marie Oppold
- Molecular Ecology Group; Institute for Ecology, Evolution & Diversity; Goethe-University Frankfurt am Main; Max-von-Laue-Str. 9, 60438 Frankfurt am Main Hessen Germany
- Senckenberg Biodiversity and Climate Research Centre; Georg-Voigt-Str. 14-16 60325 Frankfurt am Main Hessen Germany
| | - Hanno Schmidt
- Senckenberg Biodiversity and Climate Research Centre; Georg-Voigt-Str. 14-16 60325 Frankfurt am Main Hessen Germany
| | - Marcel Rose
- Molecular Ecology Group; Institute for Ecology, Evolution & Diversity; Goethe-University Frankfurt am Main; Max-von-Laue-Str. 9, 60438 Frankfurt am Main Hessen Germany
| | - Sören Lukas Hellmann
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Florian Dolze
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Fabian Ripp
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Bettina Weich
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Urs Schmidt-Ott
- Department of Organismal Biology and Anatomy; University of Chicago; 920 E. 58th Street, 1061C Chicago IL 60637 USA
| | - Erwin Schmidt
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Robert Kofler
- Institut für Populationsgenetik; Vetmeduni Vienna 1210 Vienna Austria
| | - Thomas Hankeln
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Markus Pfenninger
- Molecular Ecology Group; Institute for Ecology, Evolution & Diversity; Goethe-University Frankfurt am Main; Max-von-Laue-Str. 9, 60438 Frankfurt am Main Hessen Germany
- Senckenberg Biodiversity and Climate Research Centre; Georg-Voigt-Str. 14-16 60325 Frankfurt am Main Hessen Germany
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49
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Dal Grande F, Sharma R, Meiser A, Rolshausen G, Büdel B, Mishra B, Thines M, Otte J, Pfenninger M, Schmitt I. Adaptive differentiation coincides with local bioclimatic conditions along an elevational cline in populations of a lichen-forming fungus. BMC Evol Biol 2017; 17:93. [PMID: 28359299 PMCID: PMC5374679 DOI: 10.1186/s12862-017-0929-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/01/2017] [Indexed: 12/12/2022] Open
Abstract
Background Many fungal species occur across a variety of habitats. Particularly lichens, fungi forming symbioses with photosynthetic partners, have evolved remarkable tolerances for environmental extremes. Despite their ecological importance and ubiquity, little is known about the genetic basis of adaption in lichen populations. Here we studied patterns of genome-wide differentiation in the lichen-forming fungus Lasallia pustulata along an altitudinal gradient in the Mediterranean region. We resequenced six populations as pools and identified highly differentiated genomic regions. We then detected gene-environment correlations while controlling for shared population history and pooled sequencing bias, and performed ecophysiological experiments to assess fitness differences of individuals from different environments. Results We detected two strongly differentiated genetic clusters linked to Mediterranean and temperate-oceanic climate, and an admixture zone, which coincided with the transition between the two bioclimates. High altitude individuals showed ecophysiological adaptations to wetter and more shaded conditions. Highly differentiated genome regions contained a number of genes associated with stress response, local environmental adaptation, and sexual reproduction. Conclusions Taken together our results provide evidence for a complex interplay between demographic history and spatially varying selection acting on a number of key biological processes, suggesting a scenario of ecological speciation. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0929-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
| | - Rahul Sharma
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Anjuli Meiser
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Burkhard Büdel
- Plant Ecology and Systematics, Biology Department, University of Kaiserslautern, 67653, Kaiserslautern, Germany
| | - Bagdevi Mishra
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
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Rieder V, Blank-Landeshammer B, Stuhr M, Schell T, Biß K, Kollipara L, Meyer A, Pfenninger M, Westphal H, Sickmann A, Rahnenführer J. DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs. BMC Bioinformatics 2017; 18:148. [PMID: 28253837 PMCID: PMC5335755 DOI: 10.1186/s12859-017-1514-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 01/31/2017] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The classification of samples on a molecular level has manifold applications, from patient classification regarding cancer treatment to phylogenetics for identifying evolutionary relationships between species. Modern methods employ the alignment of DNA or amino acid sequences, mostly not genome-wide but only on selected parts of the genome. Recently proteomics-based approaches have become popular. An established method for the identification of peptides and proteins is liquid chromatography-tandem mass spectrometry (LC-MS/MS). First, protein sequences from MS/MS spectra are identified by means of database searches, given samples with known genome-wide sequence information, then sequence based methods are applied. Alternatively, de novo peptide sequencing algorithms annotate MS/MS spectra and deduce peptide/protein information without a database. A newer approach independent of additional information is to directly compare unidentified tandem mass spectra. The challenge then is to compute the distance between pairwise MS/MS runs consisting of thousands of spectra. METHODS We present DISMS2, a new algorithm to calculate proteome-wide distances directly from MS/MS data, extending the algorithm compareMS2, an approach that also uses a spectral comparison pipeline. RESULTS Our new more flexible algorithm, DISMS2, allows for the choice of the spectrum distance measure and includes different spectra preprocessing and filtering steps that can be tailored to specific situations by parameter optimization. CONCLUSIONS DISMS2 performs well for samples from species with and without database annotation and thus has clear advantages over methods that are purely based on database search.
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Affiliation(s)
- Vera Rieder
- Department of Statistics, TU Dortmund University, Dortmund, Germany
| | | | - Marleen Stuhr
- Leibniz Center for Tropical Marine Ecology (ZMT), Bremen, Germany
| | - Tilman Schell
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany
| | - Karsten Biß
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
| | - Achim Meyer
- Leibniz Center for Tropical Marine Ecology (ZMT), Bremen, Germany
| | - Markus Pfenninger
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany
- Faculty of Biological Science, Institute for Ecology, Evolution and Diversity, Department of Molecular Ecology, Goethe University, Max-von-Laue-Straße 9, Frankfurt am Main, 60438 Germany
| | | | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
- Medizinische Fakultät, Medizinisches Proteom-Center (MPC), Ruhr-Universität Bochum, Universitätsstraße 150, Bochum, 44801 Germany
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