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  • 1
    Online Resource
    Online Resource
    "Pilotierung einer transienten Datenbank für genetische Varianten ungeklärter Signifikanz (VarWatch)" : Abschlussbericht zum BMBF-geförderten Vorhaben : Laufzeit: Juli 2015-Juli 2017 (kostenneutral verlängert bis März 2018) (2018)
    [Kiel] : [Christian-Albrechts-Universität zu Kiel]
    Details Availability
    Keywords: Forschungsbericht ; Biobank
    Type of Medium: Online Resource
    Pages: 1 Online-Ressource (13 Seiten, 288,05 KB) , Diagramme
    URL: https://doi.org/10.2314/GBV:1049124243
    DOI: 10.2314/GBV:1049124243
    Language: German
    Note: Förderkennzeichen BMBF 01EK1506 , Unterschiede zwischen dem gedruckten Dokument und der elektronischen Ressource können nicht ausgeschlossen werden
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  • 2
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    Genomic data of marine three-spined sticklebacks (2019)
    PANGAEA
    In:  Supplement to: Heckwolf, Melanie; Meyer, Britta S; Häsler, Robert; Höppner, Marc P; Eizaguirre, Christophe; Reusch, Thorsten B H (2020): Two different epigenetic information channels in wild three-spined sticklebacks are involved in salinity adaptation. Science Advances, 6(12), eaaz1138, https://doi.org/10.1126/sciadv.aaz1138
    Details
    Publication Date: 2023-01-13
    Description: While environmentally inducible epigenetic marks are discussed as one mechanism of transgenerational plasticity, environmentally stable epigenetic marks emerge randomly. When resulting in variable phenotypes, stable marks can be targets of natural selection analogous to DNA sequence-based adaptation processes. We studied both postulated pathways in natural populations of three-spined sticklebacks (Gasterosteus aculeatus) and sequenced their methylomes and genomes across a salinity cline. Consistent with local adaptation, populations showed differential methylation (pop-DMS) at genes enriched for osmoregulatory processes. In a two-generation experiment, 62% of these pop-DMS were insensitive to salinity manipulation, suggesting that they could be stable targets for natural selection. Two-thirds of the remaining inducible pop-DMS became more similar to patterns detected in wild populations from the corresponding salinity, and this pattern accentuated over consecutive generations, indicating a mechanism of adaptive transgenerational plasticity. Natural DNA methylation patterns can thus be attributed to two epigenetic pathways underlying the rapid emergence of adaptive phenotypes in the face of environmental change.
    Keywords: Baltic Sea; Local adaptation; population genomics; three-spined stickleback; Whole genome sequencing
    Type: Dataset
    Format: application/zip, 4 datasets
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    DATA PANGAEA
  • 3
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    High quality G-to-A SNPs from the genomes of 96 wild caught three-spine sticklebacks (2019)
    PANGAEA
    Details
    Publication Date: 2023-01-13
    Description: To improve the methylation estimates in our study, we corrected for SNPs, which could have led to a wrong methylation call. The excluded positions were derived with custom written perl scripts from C-to-T and G-to-A-SNPs with genotype quality of 20 and a minimum allele frequency of 0.005 from the 96 wild caught three-spined sticklebacks with a combination of custom written Perl and R-scripts using packages from methylkit and GenomicRanges. This BED-file contains the G-to-A-SNPs, in which the first field is the name of the chromosome; the second describes the start position and the third the end position of the feature in standard chromosomal coordinates.
    Keywords: Baltic Sea; BED; Local adaptation; methylation call; population genomics; SNP; three-spined stickleback; Whole genome sequencing
    Type: Dataset
    Format: application/zip, 5.8 MBytes
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    DATA PANGAEA
  • 4
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    High quality C-to-T SNPs from the genomes of 96 wild caught three-spine sticklebacks (2019)
    PANGAEA
    Details
    Publication Date: 2023-01-13
    Description: To improve the methylation estimates in our study, we corrected for SNPs, which could have led to a wrong methylation call. The excluded positions were derived with custom written perl scripts from C-to-T and G-to-A-SNPs with genotype quality of 20 and a minimum allele frequency of 0.005 from the 96 wild caught three-spined sticklebacks with a combination of custom written Perl and R-scripts using packages from methylkit and GenomicRanges. This BED-file contains the C-to-T SNPs, in which the first field is the name of the chromosome; the second describes the start position and the third the end position of the feature in standard chromosomal coordinates.
    Keywords: Baltic Sea; BED; Local adaptation; methylation call; population genomics; SNP; three-spined stickleback; Whole genome sequencing
    Type: Dataset
    Format: application/zip, 5.8 MBytes
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 5
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    Genomic data of three-spined sticklebacks from Kiel (KIE), Germany and Nynäshamn (NYN), Sweden around inducible differentially methylated sites in decreasing salinity (2019)
    PANGAEA
    Details
    Publication Date: 2023-01-13
    Description: This vcf file is generated from genomic data of three-spined sticklebacks from Kiel (KIE), Germany and Nynäshamn (NYN), Sweden. The individuals from Kiel are S3, S4, S19, S20, S33, S34, S47, S48, S49, S50, S63, S64, S77, S78, S89, S90. The individuals from NYN are S5, S6, S21, S22, S35, S36, S37, S38, S51, S52, S65, S66, S79, S80, S85, S86. It contains high quality biallelic positions (GQ=20) and is filtered for minor allele frequencies of maf = 0.05, allows 40 % of missing data (13 individuals) and a read depth of 〉=5. Further this vcf file is subset to the inducible differentially methylated sites (DMS) (198sites) in decreasing PSU (_6PSU) with 5 kilobases (kb) before and after DMS. With this file further calculations were performed to estimate the genetic differentiation (i.e. Fst) between the different populations (see manuscript indicated below).
    Keywords: Baltic Sea; Local adaptation; population genomics; three-spined stickleback; VCF; Whole genome sequencing
    Type: Dataset
    Format: application/zip, 1.6 MBytes
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    DATA PANGAEA
  • 6
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    Genomic data of three-spined sticklebacks from Kiel (KIE) and Sylt (SYL), Germany around inducible differentially methylated sites in increasing salinity (2019)
    PANGAEA
    Details
    Publication Date: 2023-01-13
    Description: This vcf file is generated from genomic data of three-spined sticklebacks from Kiel (KIE) and Sylt (SYL), Germany. The individuals from Kiel are S3, S4, S19, S20, S33, S34, S47, S48, S49, S50, S63, S64, S77, S78, S89, S90. The individuals from SYL are S9, S10, S17, S18, S31, S32, S45, S46, S59, S60, S61, S62, S73, S74, S87, S88. It contains high quality biallelic positions (GQ=20) and is filtered for minor allele frequencies of maf = 0.05, allows 40 % of missing data (13 individuals) and a read depth of 〉=5. Further this vcf file is subset to the inducible differentially methylated sites (DMS) (148sites) in increasing PSU (_33PSU) with 5 kilobases (kb) before and after DMS. With this file further calculations were performed to estimate the genetic differentiation (i.e. Fst) between the different populations (see manuscript indicated below).
    Keywords: Baltic Sea; Local adaptation; population genomics; three-spined stickleback; VCF; Whole genome sequencing
    Type: Dataset
    Format: application/zip, 1.2 MBytes
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    DATA PANGAEA
  • 7
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    Differential expression of immune receptors in two marine sponges upon exposure to microbial-associated molecular patterns (2018)
    Nature Research
    In:  Scientific Reports, 8 (1). Art.Nr. 16081.
    Details
    Publication Date: 2021-03-19
    Description: The innate immune system helps animals to navigate the microbial world. The response to microbes relies on the specific recognition of microbial-associated molecular patterns (MAMPs) by immune receptors. Sponges (phylum Porifera), as early-diverging animals, provide insights into conserved mechanisms for animal-microbe crosstalk. However, experimental data is limited. We adopted an experimental approach followed by RNA-Seq and differential gene expression analysis in order to characterise the sponge immune response. Two Mediterranean species, Aplysina aerophoba and Dysidea avara, were exposed to a “cocktail” of MAMPs (lipopolysaccharide and peptidoglycan) or to sterile artificial seawater (control) and sampled 1 h, 3 h, and 5 h post-treatment for RNA-Seq. The response involved, first and foremost, a higher number of differentially-expressed genes in A. aerophoba than D. avara. Secondly, while both species constitutively express a diverse repertoire of immune receptors, they differed in their expression profiles upon MAMP challenge. The response in D. avara was mediated by increased expression of two NLR genes, whereas the response in A. aerophoba involved SRCR and GPCR genes. From the set of annotated genes we infer that both species activated apoptosis in response to MAMPs while in A. aerophoba phagocytosis was additionally stimulated. Our study assessed for the first time the transcriptomic responses of sponges to MAMPs and revealed conserved and species-specific features of poriferan immunity as well as genes potentially relevant to animal-microbe interactions.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1038/s41598-018-34330-w
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 8
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    The evolution of microendemism in a reef fish (Hypoplectrus maya) (2019)
    Wiley
    In:  Molecular Ecology, 28 (11). pp. 2872-2885.
    Details
    Publication Date: 2022-01-31
    Description: Marine species tend to have extensive distributions, which are commonly attributed to the dispersal potential provided by planktonic larvae and the rarity of absolute barriers to dispersal in the ocean. Under this paradigm, the occurrence of marine microendemism without geographic isolation in species with planktonic larvae poses a dilemma. The recently described Maya hamlet (Hypoplectrus maya, Serranidae) is exactly such a case, being endemic to a 50-km segment of the Mesoamerican Barrier Reef System (MBRS). We use whole-genome analysis to infer the demographic history of the Maya hamlet and contrast it with the sympatric and pan-Caribbean black (H. nigricans), barred (H. puella) and butter (H. unicolor) hamlets, as well as the allopatric but phenotypically similar blue hamlet (H. gemma). We show that H. maya is indeed a distinct evolutionary lineage, with genomic signatures of inbreeding and a unique demographic history of continuous decrease in effective population size since it diverged from congeners just ~3,000 generations ago. We suggest that this case of microendemism may be driven by the combination of a narrow ecological niche and restrictive oceanographic conditions in the southern MBRS, which is consistent with the occurrence of an unusually high number of marine microendemics in this region. The restricted distribution of the Maya hamlet, its decline in both census and effective population sizes, and the degradation of its habitat place it at risk of extinction. We conclude that the evolution of marine microendemism can be a fast and dynamic process, with extinction possibly occurring before speciation is complete.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1111/mec.15110
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 9
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    Inter-chromosomal coupling between vision and pigmentation genes during genomic divergence (2019)
    Nature Research
    In:  Nature Ecology & Evolution, 3 (4). pp. 657-667.
    Details
    Publication Date: 2022-01-31
    Description: Recombination between loci underlying mate choice and ecological traits is a major evolutionary force acting against speciation with gene flow. The evolution of linkage disequilibrium between such loci is therefore a fundamental step in the origin of species. Here, we show that this process can take place in the absence of physical linkage in hamlets—a group of closely related reef fishes from the wider Caribbean that differ essentially in colour pattern and are reproductively isolated through strong visually-based assortative mating. Using full-genome analysis, we identify four narrow genomic intervals that are consistently differentiated among sympatric species in a backdrop of extremely low genomic divergence. These four intervals include genes involved in pigmentation (sox10), axial patterning (hoxc13a), photoreceptor development (casz1) and visual sensitivity (SWS and LWS opsins) that develop islands of long-distance and inter-chromosomal linkage disequilibrium as species diverge. The relatively simple genomic architecture of species differences facilitates the evolution of linkage disequilibrium in the presence of gene flow.
    Type: Article , PeerReviewed
    Format: text
    Format: text
    DOI: 10.1038/s41559-019-0814-5
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 10
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    Two different epigenetic information channels in wild three-spined sticklebacks are involved in salinity adaptation (2020)
    AAAS (American Association for the Advancement of Science)
    Details
    Publication Date: 2023-03-09
    Description: Epigenetic inheritance has been proposed to contribute to adaptation and acclimation via two information channels: (i) inducible epigenetic marks that enable transgenerational plasticity and (ii) noninducible epigenetic marks resulting from random epimutations shaped by selection. We studied both postulated channels by sequencing methylomes and genomes of Baltic three-spined sticklebacks ( Gasterosteus aculeatus ) along a salinity cline. Wild populations differing in salinity tolerance revealed differential methylation (pop-DMS) at genes enriched for osmoregulatory processes. A two-generation experiment demonstrated that 62% of these pop-DMS were noninducible by salinity manipulation, suggesting that they are the result of either direct selection or associated genomic divergence at cis- or trans-regulatory sites. Two-thirds of the remaining inducible pop-DMS increased in similarity to patterns detected in wild populations from corresponding salinities. The level of similarity accentuated over consecutive generations, indicating a mechanism of transgenerational plasticity. While we can attribute natural DNA methylation patterns to the two information channels, their interplay with genomic variation in salinity adaptation is still unresolved.
    Type: Article , PeerReviewed
    Format: text
    Format: text
    Format: text
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    OceanRep: Article in a Scientific Journal - peer-reviewed
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