Introduction
Model
The study in Bruneaux et al. (2013) focus on several freshwater and marine populations of ninespine stickleback from Fenno-Scandia. Those populations are relatively recent since this region was recolonized after the last glacial maximum (ca. 11000 years BP). They differ in several morphological, behavioural and physiological traits.
Figure 1: Sampling locations for ninespine stickleback (from Bruneaux et al. (2013)). Marine, pond and lake populations are marked as filled squares, filled circles and open circles, respectively.
In general, fish from the freshwater ponds where ninespine is the only fish species are larger, bolder and more aggressive than their marine counterparts, and also harbour reduced body armour. This is thought to be due to differences in intra and interspecific competition, and lab crosses have shown that the traits are at least partially genetically determined.
Figure 2: Gigantism in ninespine stickleback (from the Ecological Genetics Research Unit website). Some pond populations (top) harbour giant size compared to marine populations (bottom).
The aim of the study was to look for the genetic basis of differentiation between the different habitat types, and investigate if signals of parallel evolution could be found. For this species, no reference genome is available. However, the genome of the (relatively) closely related threespine stickleback is available and annotated in Ensembl.
Approach
Twenty individuals from each population were sampled and their DNA was extracted. The DNA was digested by two restriction enzymes and size-selected (ddRAD), and equal amounts of RAD fragments per individuals were then pooled into population-specific pools. Those pools were barcoded (one barcode per population pool) and sent for sequencing in an Illumina GAII system, using paired-end sequencing.
| Population | Location | Habitat | Drainage | Lane and barcode |
|---|---|---|---|---|
| ABB | Abbortjärn | Pond | Baltic Sea | 3_TTG |
| BYN | Bynastjärnen | Pond | Baltic Sea | 1_CAC |
| PYÖ | Pyöreälampi | Pond | White Sea | 3_CTT |
| RYT | Rytilampi | Pond | White Sea | 1_CTT |
| POR | Iso-Porontima | Lake | White Sea | 6_TTG |
| SKA | Västre-Skavträsket | Lake | Baltic Sea | 5_CAC |
| HKI | Helsinki | Marine | Baltic Sea | 2_TCT |
| LEV | Levin Navolok Bay | Marine | White Sea | 5_TCT |
Your work starts as the raw reads are sent back to you from the sequencing service.