Final Report Summary - SVASG (Structural Variation and Adaptation of the Stickleback Genome)
The project on 'structural variation and adaptation of the stickleback genome' is aiming to characterise structural variation (SV) such as deletions, insertions, duplications, translocations, and inversions within and between five geographically distinct lake-river population comparisons of the three-spined stickleback. Evaluating multiple parallel adaptations will infer the influence of SV on local adaptation and divergence in this prime study system for ecological speciation, adaptive radiation, and ecological genomics. Aim of this project is to develop a computational approach for the detection of SV from whole genome short read paired-end sequencing data. The computational approach will be further assessed in the laboratory. After building a comprehensive map of SV within and between stickleback populations, the role of SV for ecological speciation will be evaluated. Therefore molecular evolution and linkage pattern in the genomic regions affected by SV will be considered. Aim of the project is to contribute to the discussion about the adaptive role of SV of the genome.
Standing genetic variation and genomic architecture both have been speculated to contribute to recent adaptive radiations of sticklebacks. Since the end of the Pleistocene the three-spined stickleback has repeatedly colonised and adapted to various freshwater habitats probably fuelled by a marine population. As a first step within the project we characterised the SV amongst six marine stickleback genomes sampled from the North Sea (Denmark). We used this pilot study to establish bioinformatics pipelines for SV detection. We call SV based on three different signals present in the next generation sequencing data: paired end mapping, split read analysis, and depth of coverage evaluation. With this, we expand on the current genomic resources of this fish by providing extensive genome-wide variation data from six individuals from a marine (North Sea) stickleback population. Using next-generation sequencing and a combination of paired-end and mate-pair libraries, we detected a wide size range of genetic variation. Amongst the 6 individuals, we found more than 7 % of the genome is polymorphic, consisting of 2 599 111 SNPs, 233 464 indels, and structural variation (> 50 bp) such as 1054 copy-number variable regions (deletions and duplications) and 48 inversions. Many of these polymorphisms affect gene and coding sequences. We determined outlier regions based on SNP diversity concordant with signatures expected under adaptive evolution. As some of these outliers overlap with pronounced regions of copy-number variation, we propose the consideration of such structural variation when analysing SNP data from re-sequencing approaches. We further discuss the value of this resource on genome-wide variation for further investigation upon the relative contribution of standing variation on the parallel evolution of sticklebacks and the importance of the genomic architecture in adaptive radiation.
Currently, we are working on extend the SV detection and analysis onto the five parapatric lake-river population pairs we sampled and sequenced. Full genome sequences of 60 fish from 10 populations across two continents are evaluated for this. We will bring together data on the inferences of SV within and between these populations with diversity and differentiation estimates based on the SNP data. We use non-parametric statistics (multi-dimensional scaling) to contrast the divergence amongst the populations based on different inferred variations (SNPs, indels, deletions, inversions, translocations). We are estimating pairwise divergence between all five lake-river population pairs and search for correlations of extreme values with SV. Especially inversion and translocations are speculated to change the linkage pattern along the chromosome and potentially facilitate divergence between populations. These results will provide valuable contributions towards the discussion of genomic island of divergence in speciation research. To further strengthen our results with a good evaluation of the linkage pattern across one parapatric pair, we genotyped pedigree data from a crossing experiment. These pedigree data will allow us to assess recombination rates in details. Correlation of these recombination rates with the detected divergence signals and SV calls will further improve our understanding on the contribution of the genomic architecture during the divergence of populations.
In summary, the project on 'structural variation and adaptation of the stickleback genome' is stressing the importance of SV for adaptation and speciation. This will be achieved by:
(1) demonstrating the abundance of SV polymorphism within and between diverging populations;
(2) evaluating the impact of SV by inferring overlaps with annotated genes and their functions; and
(3) putting the observed variation pattern into the context of genomics of speciation due to the comparison with linkage pattern and diversity estimates across the genome.
Standing genetic variation and genomic architecture both have been speculated to contribute to recent adaptive radiations of sticklebacks. Since the end of the Pleistocene the three-spined stickleback has repeatedly colonised and adapted to various freshwater habitats probably fuelled by a marine population. As a first step within the project we characterised the SV amongst six marine stickleback genomes sampled from the North Sea (Denmark). We used this pilot study to establish bioinformatics pipelines for SV detection. We call SV based on three different signals present in the next generation sequencing data: paired end mapping, split read analysis, and depth of coverage evaluation. With this, we expand on the current genomic resources of this fish by providing extensive genome-wide variation data from six individuals from a marine (North Sea) stickleback population. Using next-generation sequencing and a combination of paired-end and mate-pair libraries, we detected a wide size range of genetic variation. Amongst the 6 individuals, we found more than 7 % of the genome is polymorphic, consisting of 2 599 111 SNPs, 233 464 indels, and structural variation (> 50 bp) such as 1054 copy-number variable regions (deletions and duplications) and 48 inversions. Many of these polymorphisms affect gene and coding sequences. We determined outlier regions based on SNP diversity concordant with signatures expected under adaptive evolution. As some of these outliers overlap with pronounced regions of copy-number variation, we propose the consideration of such structural variation when analysing SNP data from re-sequencing approaches. We further discuss the value of this resource on genome-wide variation for further investigation upon the relative contribution of standing variation on the parallel evolution of sticklebacks and the importance of the genomic architecture in adaptive radiation.
Currently, we are working on extend the SV detection and analysis onto the five parapatric lake-river population pairs we sampled and sequenced. Full genome sequences of 60 fish from 10 populations across two continents are evaluated for this. We will bring together data on the inferences of SV within and between these populations with diversity and differentiation estimates based on the SNP data. We use non-parametric statistics (multi-dimensional scaling) to contrast the divergence amongst the populations based on different inferred variations (SNPs, indels, deletions, inversions, translocations). We are estimating pairwise divergence between all five lake-river population pairs and search for correlations of extreme values with SV. Especially inversion and translocations are speculated to change the linkage pattern along the chromosome and potentially facilitate divergence between populations. These results will provide valuable contributions towards the discussion of genomic island of divergence in speciation research. To further strengthen our results with a good evaluation of the linkage pattern across one parapatric pair, we genotyped pedigree data from a crossing experiment. These pedigree data will allow us to assess recombination rates in details. Correlation of these recombination rates with the detected divergence signals and SV calls will further improve our understanding on the contribution of the genomic architecture during the divergence of populations.
In summary, the project on 'structural variation and adaptation of the stickleback genome' is stressing the importance of SV for adaptation and speciation. This will be achieved by:
(1) demonstrating the abundance of SV polymorphism within and between diverging populations;
(2) evaluating the impact of SV by inferring overlaps with annotated genes and their functions; and
(3) putting the observed variation pattern into the context of genomics of speciation due to the comparison with linkage pattern and diversity estimates across the genome.