Supporting information
S1 Substitution models
Best-fit models of nucleotide substitution were determined for MC1R and neutral loci
in jModeltest version 0.1.1 (Posada 2008), using likelihood calculations with
optimized ML and the Akaike information criterion (AIC). Calculations included
models with equal or unequal base frequencies (+F) and rate variation among sites
with a number of rate categories (+G) only, because models with a proportion of
invariable sites (+I) are not included in Arlequin version 3.5.1.2 (Excoffier & Lischer
2010), that was used for calculating nucleotide diversities. Either best-fit or the
nearest less-complex models were chosen (MC1R, Lamin and RP40: TrN+G, α =
0.01; MPP: TrN+G, α = 0.02 and mtDNA: JC).
S2 Probability of non-synonymous substitutions in MC1R being concentrated
near root of network in arctic skuas
7
6
5
4
NonSynonymous
3
Synonymous
2
1
0
0
1
2
3
Fig. S1 Frequency distribution of distance (x-axis) of non-synonymous and synonymous
substitutions from the ancestral haplotype in the arctic skua MC1R network (Figure 2). Total
number of substitutions = 17.
To calculate the exact probability of four mutations occupying the bins at 0 steps (2
mutations) and 1 step (2 mutations) from the root, we considered the potential paths in which
4 sequential randomly placed mutations would lead to the desired distribution. There are 6
possible paths (unoccupied bins are represented by ” –“ and dots represent mutations
occupying bins):
1. () → () → ( ) → ( )
2. () → ( ) → ( ) → ( )
3. () → ( ) → ( ) → ( )
4. (  ) → ( ) → ( ) → ( )
5. (  ) → ( ) → ( ) → ( )
6. (  ) → () → ( ) → ( )
Each of these paths has the same probability given by (1 x 2 x 7 x 8)/(17 x 16 x 15 x 14) =
1/510, so the total probability is 6 x 1/510 = 1/85 = 0.0118 (3 sig figs). This was verified by
calculating the total number of ways of placing 4 mutations in bins 0 and 1 divided by the
total number of ways 4 mutations could be distributed among the 4 bins.
Table S1: Sampling details
a
Location
Coordinates
Collection year
Number
of DNA
samples
Material
1
Colville
Rivera
70.00 N, 151.00 W
1998
17
2
Åland
60.13 N, 20.15 E
1999/2002
26
3
Slettnes
71.05 N, 28.13 E
1997/98
23
4
Bear Island
74.26 N, 19.10 E
2000
22
5
Spitsbergen
78.56 N, 11.53 E
2000
18
Tissue in
DSMObuffer
Blood in
SET-buffer
Blood in
SET-buffer
Blood in
SET-buffer
Blood in
SET-buffer
Number of
individuals
with
phenotypic
data
17
38
322
104
60
Tissue samples and plumage colour morph data obtained from Alaska Frozen Tissue Collection,
University of Alaska Museum, Fairbanks, USA
Table S2 MC1R and intron haplotypes and their frequencies in five arctic skua populations. Variable sites are shown. Dots indicate
identity with the first haplotype presented. Non-synonymous substitutions for MC1R are shown in bold. SP is arctic skua and SL is longtailed skua.
Nucleotide position
MC1R
Alleles
(Genbank
accessions
KF268961KF268987)
SP1 pale
SP2 pale
SP3 pale
SP4 pale
SP5 pale
SP6 pale
SP7 pale
SP10 pale
SP12 pale
SP13 pale
SP14 pale
SP15 pale
SP16 pale
SP8 melanic
SP9 melanic
SP11 melanic
SL1
000000000000000000000000000000000001
001111222222333333333455666667888990
890046055669012366789913366890299570
331402404234889039247207634268817742
CGCGTCGCCGGAACGCCCCCAGCGTCACCCCGCGGG
.................................A..
.............................T......
....................G...............
....................G.T.............
....................GA..............
.................T.....A....T.......
..........C.........................
....C...............................
....C........................T......
..G.................................
T...................................
T.........C.........................
............G.A...................A.
............G.A..................AA.
.......T....G.A...................A.
(1)
(2)
(3)
Alaska
Åland
Slettnes
7
0
0
6
0
1
0
1
0
0
0
0
0
15
0
4
8
0
0
6
0
0
0
2
0
0
0
0
0
32
1
3
12
4
0
5
1
0
0
1
0
0
2
1
20
0
0
(4)
Bear
Island
(5)
Spitzbergen
total
frequency
25
0
0
10
0
0
1
5
0
0
2
1
0
0
0
0
24
0
1
7
0
0
0
3
0
1
0
0
0
0
0
0
76
4
1
34
1
1
1
11
1
1
2
3
1
67
1
7
3
SL2
SL3
SL4
SL5
SL6
SL7
SL8
SL9
SL10
SL11
Lamin
Alleles
(Genbank
accessions
KF268999KF269006)
SP1
SP2
SP3
SP4
SP5
SP6
SP7
SP8
MPP Alleles
........G..GG...........C.G...T....A
........G..GG...........C.G.........
........G..GG....T......C.G.T.TA...A
........G..GG..T........CTGT........
........G..GGT..........C.G...T....A
........GA.GG...........C.G...T....A
......A.GA.GG...........C.G.........
......A.GA.GG.....T.....C.G.........
.....T..G..GG...T.TT....CTG.........
...A....G..GG...........CTG...T.....
.A......G..GG...........CTG.....T...
3
2
2
3
2
1
1
1
1
1
Nucleotide position
(1)
(2)
(3)
0000111
0589019
8087278
Alaska
Åland
CCACGGC
......T
....AAT
..G....
..G...T
..GG...
.T....T
T......
16
10
2
3
0
1
2
0
11
24
0
14
3
0
0
0
Nucleotide position
Gamvik
(4)
Bear
Island
(5)
Spitzbergen
total
frequency
22
17
0
4
1
2
0
0
28
5
0
8
0
1
0
2
16
17
0
2
0
0
0
1
93
73
2
31
4
4
2
3
(Genbank
accessions
KF269007KF269026)
SP1
SP2
SP3
SP4
SP5
SP6
SP7
SP8
SP9
SP10
SP11
SP12
SP13
SP14
SP15
SP16
SP17
SP18
SP19
SP20
*
00001112223
35991894792
15793998017
(1)
(2)
(3)
Alaska
Åland
AGACGAGGGCC
........A..
....A..A...
....A..A..T
..-........
G..........
G........T.
G.......A..
G.......AT.
G......A..T
G.....A....
G...A......
G...A..A...
G...A..A..T
G...AG.....
G..T.......
G.-........
GA.........
GA......A..
GA..A...A..
11
0
1
1
0
14
0
3
0
0
0
0
0
3
0
1
0
0
0
0
33
0
0
0
1
7
0
2
0
2
1
1
0
1
2
0
2
0
0
0
* deletion of 8 bp
RP40
Nucleotide position
Gamvik
(4)
Bear
Island
(5)
Spitzbergen
total
frequency
12
1
0
0
0
6
0
0
6
0
0
1
0
6
0
1
0
1
11
1
16
0
1
0
0
5
0
0
1
0
0
0
3
14
0
0
3
0
1
0
5
0
0
0
0
14
1
1
1
0
0
0
3
9
0
0
2
0
0
0
77
1
2
1
1
46
1
6
8
2
1
2
6
33
2
2
7
1
12
1
Alleles
(Genbank
accessions
KF268988KF268998)
SP1
SP2
SP3
SP4
SP5
SP6
SP7
SP8
SP9
SP10
SP11
(1)
(2)
(3)
Gamvik
(4)
Bear
Island
(5)
Spitzbergen
01111223
41126342
64778159
Alaska
Åland
total
frequency
ACGGGACC
......T.
....C.T.
...-..T.
...-.GT.
.T......
.T....T.
.T....TT
.TC...T.
.TC...TT
G.....T.
8
11
2
2
1
1
6
3
0
0
0
13
29
8
0
0
0
0
0
0
2
0
13
17
0
0
0
1
12
1
0
2
0
4
24
0
0
0
0
8
6
1
0
1
12
14
0
0
0
1
6
3
0
0
0
50
95
10
2
1
3
32
13
1
4
1
Table S3 Tajima’s D and Fu’s FS for five arctic skua populations, using standardized sample sizes (N = 17 individuals per population).
Alaska Åland
Slettnes Bear I. Spitz Overall
D MC1R
Lamin
MPP
RP40
mtDNA
0.805
-0.667
-0.048
-0.253
-0.973
0.625
1.897
-1.274
-0.835
-0.049
0.337
0.405
0.665
0.404
0.243
-1.179
-0.882
0.375
-0.176
-1.047
-0.769
-0.313
0.180
1.024
-0.991
FS MC1R
-0.882
-1.162
-1.290
-2.524
-6.952**
1.168
0.419
-5.859**
0.081
-0.357
0.032
-0.881
0.438
-1.101
-2.524
-1.458
-1.722
-0.721
-0.748
-2.461
-1.538 -2.583
-0.573 -1.938
-0.548 -6.186
-0.331 -2.775
-1.009 -25.320**
Lamin
MPP
RP40
mtDNA
**
p < 0.01
-0.735
-0.592
0.028
-0.241
-0.851