Phenotypic data
We randomly selected individuals from each habitat type for phenotyping
and genome sequencing from the frozen subset of the long-term monitoring
samples. Individuals were thawed, weighed on an electronic balance (wet
mass, nearest mg) and their total length (TL) measured using a ruler (to
the nearest mm). The right pectoral fin was then cut and stored in 96%
ethanol for DNA isolation. We measured traits typically under selection
in stickleback: body size, defence traits (armour plate number and
length of spines) and dietary traits (gill raker morphology and gut
length) . Specifically, for each individual we measured the following 10
traits: total length (TL), total gut length (gut length), number of
lateral armour plates (plate number), length of the first dorsal spine
(DS1), length of the second dorsal spine (DS2), length of the pelvic
spine (PS), length of the second gill raker on the first gill arch
(GRL2), length of third gill raker on the first gill arch (GRL3), gap
width between second and third gill rakers (GRW), and number of long
gill rakers on the first gill arch (GRN) (see below). Note that we
measured the second and third gill rakers, rather than the first (which
is usually used in studies of stickleback trophic phenotype), because in
some cases gill arches broke during dissection. After measurement of TL,
each individual was dissected to remove the stomach and the gut, and any
tapeworm (Schistocephalus solidus) parasites. Gut length (from
the sphincter at the end of the oesophagus to the end of the digestive
tract) was measured (to the nearest mm) using a ruler.
To aid morphological measurements, fish were stained with alizarine red
using standard protocols (Millet et al. 2013). Fish were bleached using
a 1:1 ratio of 3% H2O2 and 1% KOH and
then stained in a solution of alizarin red and 1% KOH . After staining,
digital images were taken of the left side of the fish with a Canon EOS
600D digital camera, with mm paper for scale. From these images, plate
number was counted and the length of the spines (DS1, DS2 and PS)
measured to the nearest hundredth of a millimetre. After imaging, we
dissected the first gill arch and, where necessary, re-stained before
mounting it between two glass plates and photographing using a digital
camera (Nikon Coolpix 4500) mounted to a stereomicroscope (Leica MZ12)
with mm paper for scale. We used the digital images of gill arches to
measure GRL2, GRL3 and GRW (in mm) and counted GRN. All measurements
were taken from the digital images were done using segmented tool in
ImageJ .