Caputo et al. 2014, Supporting information
Table S1 –Anopheles coluzzii and An. gambiae samples along the Gambia river.
Anopheles coluzzii/M-form and An. gambiae/S-form samples collected in The Gambia and eastern
Senegal during 2006 rainy season. Areas=ecological areas and subareas along the sampling transect
(The Gambia: LRA-W=Western Lower River Area, LRA-S=South Bank Lower River Area, LRAN=North Bank Lower River Area, CRA=Central River Area, URA=Upper River Area; Senegal: EATAM= Eastern Area-Tambacounda, EA-WAS= Eastern Area-Wassadou, EA-KED= Eastern AreaKedougou); site code=site codes as in Caputo et al. (2008); new code=site codes for present
microsatellite analysis; karyotyped=samples scored for inversion polymorphisms; genotypes=samples
scored for 20 microsatellites.
Areas
LRA
LRA
LRA
LRA
LRA
LRA
LRA
LRA
LRA
LRA
LRA
LRA
CRA
CRA
CRA
URA
URA
URA
URA
URA
EA
EA
EA
EA
EA
EA
W
W
S
S
N
N
N
N
N
N
N
N
TAM
TAM
WAS
WAS
KED
KED
Village
Kartong
Mandinaba
Tankular
Keneba
Hamdalai
Sare Samba S
Sare Illo Buya
Dai Mandinka
Jajari
Yallal
Ker Madi
Kalataba
Teneng Fara
Wellingara K
Walikunda
Tinkinjo
Touba Tafsir
Limbanbulu Y
Kusunu
Kantel kunda
Jingoreh Mafy
Amdalaye pont
Wassadou
Laboya
Silling
Samecouta
Total
long
lat
-16,750000 13,083333
Rainfall Site New Karyotyped Genotyped
(mm) Code Code M
S
M
S
335,2
-16,583333 13,283333
335,2
-16,033333 13,416667
230,75
-16,016667 13,333333
230,75
-16,016667 13,566667
278,15
-15,900000 13,583333
278,15
-15,866667 13,583333
278,15
-15,816667 13,550000
278,15
na
na
278,15
-15,700000 13,550000
278,15
-15,616667 13,533333
278,15
-15,616667 13,550000
278,15
-15,016667 13,616667
241,65
-14,916667 13,550000
241,65
-14,916667 13,566667
241,65
-14,166667 13,300000
219,1
-14,150000 13,283333
219,1
-14,116667 13,416667
192,05
-13,916667 13,383333
192,05
-13,883333 13,400000
192,05
-13,666667 13,766667
179,3
-13,550000 13,583333
-13,350000 13,350000
179,3
na
-13,350000 13,300000
na
-12,266667 12,533333
na
-12,133333 12,600000
na
1
2
5
6
7
8
9
10
11
12
13
14
16
17
18
22
23
24
25
26
27
29
31
32
33
34
1
2
3
4
5
6
7
8
9
10
11
12
13
14
54
19
134
32
36
88
7
11
5
77
24
19
156
45
8
10
21
164
15
8
2
2
937
1
18
2
1
18
126
1
3
1
5
2
6
15
42
10
10
33
75
369
54
46
19
21
7
44
10
12
14
9
4
19
6
7
272
2
39
18
24
7
1
2
7
2
8
19
26
45
200
Caputo et al. 2014, Supporting information
Table S2- Anopheles coluzzii 2R-karyotypes
Frequencies of 2R-chromosomal arm karyotypes in Anopheles coluzzii/M-form along the Gambia
river. The observed 2R inversion karyotypes (indicated as whole arm arrangements on the each side of the
slash) are listed in order of decreasing frequencies in the overall sample. When the pairing of two
different homologues, each carrying different combinations of the 2R inversions, produced multiple
indistinguishable heterozygous configurations, the most probable ones are listed in the same row.
LRA-W =Western Lower River Area; LRA-S=South Bank Lower River Area; LRA-N=North Bank
Lower River Area, CRA=Central River Area; URA=Upper River Area, EA = Eastern Area.
N
Chromosome-2R
karyotypes
LRA-W
LRA-S
LRA-N
CRA
URA
EA
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
b/b
b/+
bd/+, b/d
d/+
d/d
bd/b
+/+
bd/d
bc/b
bd/bd
bc/+
bcd/+, b/cd
bcu/b, bu/bc
bcd/b, bd/bc
bc/bc
Total specimens
16.4
15.1
23.3
16.4
9.6
2.7
4.1
11.0
0.0
1.4
0.0
0.0
0.0
0.0
0.0
73
22.3
24.7
23.5
10.8
4.8
3.0
5.4
3.0
1.8
0.6
0.0
0.0
0.0
0.0
0.0
166
25.2
25.6
20.7
7.4
4.8
5.9
5.2
2.6
0.4
0.7
0.4
0.7
0.0
0.4
0.0
267
42.0
29.3
15.6
2.4
1.0
4.9
2.9
1.0
1.0
0.0
0.0
0.0
0.0
0.0
0.0
209
31.4
25.7
18.1
7.1
7.1
4.8
4.3
0.5
1.0
0.0
0.0
0.0
0.0
0.0
0.0
210
16.67
16.67
25.00
8.33
8.33
0.00
0.00
0.00
0.00
0.00
8.33
0.00
8.33
0.00
8.33
12
Caputo et al. 2014, Supporting information
Table S3- Anopheles gambiae 2R-karyotypes
Frequencies of 2R-chromosomal arm karyotypes in Anopheles gambiae/S-form along the Gambia
river. The observed 2R inversion karyotypes (indicated as whole arm arrangements on the each side of the
slash) are grouped for the West (West and Lower River areas of The Gambia) and East populations (Upper
River area in The Gambia and Eastern Senegal) and are listed in order of decreasing frequencies. When the
pairing of two different homologues, each carrying different combinations of the 2R inversions, produced
multiple indistinguishable heterozygous configurations, the most probable ones are listed in the same row.
* indicates karyotypes carrying new inversions, here detected for the first time [see text for details].
N
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
Chromosome-2R
karyotypes
+/d
+/+
bd/+, b/d
+/b
b/bd
b/b
bd/d
d/d
jbd/b,, jb/bd
jbd/bd
jbd/+, jb/d, j/bd
jbd/d,, jd/bd
bcu/+,, cu/b, bc/u
bd/bd
bcu/d,, bcd/u, bd/cu
jb/jbd
jbd/jbd
jbk/d, jd/bk
jb/b
cdu/+, cu/d
jbk/+, j/bk
jbd/bk, jbk/bd
jbd/jd
bcu/b
jb/+, j/b
cu/+
jbcd/+
jbcd/d, jd/bcd
jbd/j, jb/jd
jd/bk, jbk/d
jbd/jbk
bcd/b, bc/bd
jd/+, j/d
jcu/+, j/cu
jbd/cu, jcu/bd
jd/d
jbd/bcu, jbcu/d
jb/j
jbk/j
jcu/d, jd/cu
jbd/jcu, jbcu/jd
cu/cu
jb/jbk
jbd/jbcu
Total Specimens
West
East
23.9
22.7
14.8
15.3
8.5
6.3
5.1
3.4
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
176
2.6
1.0
8.3
4.7
6.2
6.7
3.6
2,1*
7,3*
5,7*
7.3
5.2
3.6
2.6
2,6*
2,6*
2,6*
2,1*
2.1
1.6
1.6
1.6
1.6
1.0
1.0
1.0
1,0*
1.0
1,0*
1.0
1.0
0.5
0.5
0.5
0.5
0.5
0,5*
0.5
0.5
0.5
0.5
0.5
0.5
0.5
193
Caputo et al. 2014, Supporting information
Table S4 – Exact tests of Linkage Disequilibrium.
The test of linkage disequilibrium (LD) for most common chromosome-2 inversions in Anopheles
coluzzii/M-form and An. gambiae/S-form along the Gambia river was performed using the sequential
Bonferroni correction to accommodate the number of tests. Significant tests are shown in bold. LRAW =Western Lower River Area; LRA-N=North Bank Lower River Area, CRA=Central River Area;
URA=Upper River Area, EA = Eastern Area.
LD
2Rj-2Rb
2Rj-2Rd
2Rb-2Rd
2Rj-2La
2Rb-2La
2Rd-2La
LRA-W
LRA-N
CRA
URA
EA
An.
An.
An.
An.
An.
An.
An.
An.
An.
coluzzii gambiae coluzzii gambiae coluzzii coluzzii gambiae coluzzii gambiae
0.482
0.000
0.210
0.000
0.845
0.161
0.185
0.249
0.000
0.000
0.000
0.000
0.000
0.229
0.784
0.105
0.068
0.544
0.945
0.106
0.425
0.240
0.044
0.001
0.028
0.594
0.121
0.622
0.050
0.003
0.490
0.311
0.479
Caputo et al. 2014, Supporting information
Table S5 – Microsatellite loci genotyped.
Locus=microsatellite locus code; Location= physical location on chromosome-X and chromosome-3
(chromosomal division); Repeat= type of repeat and size of cloned fragment (Zheng et al., 1996.
Genetics 143: 941-952; 45C1: Wang et al., 1999. Parasitology Today 15: 33-37); Dye= fluorescent
label in forward primer; Primers= f-forward (above) and r-reverse (below). TA= PCR annealing
temperature. Two to four amplified products, with different labels, were analysed per microplate well,
according to the following groups: Group I: H242, H128, H249 and H119; Group II: H55, H577, H59;
Group III: H758,H93, 45C. Group I: H145, H25, ND5B1, ND6U2; Group 2: H77, ND5C1, H678;
Group 3: H7, ND5D1, ND6U4.
Locus
Location
Repeat
Dye
AGXH145
X (4C)
(GT) 11
hex
AGXH77
X (4B)
(GT)10
6-fam
AGXH25
X (3A)
(GT)9
6-fam
AGXH7
X (1C)
(GT)8
hex
AGXND5B1
X (5B)
(CA)10
ned
AGXND5C1
X (5C)
(GT)10
6-fam*
AGXH678
X (5D)
(TC)7
hex
AGXND5D1
X (5D)
(CA)11
ned
AGXND6U2
X (6)
(CA)13
hex
AGXND6U4
X (6)
(AAC)3(AAT)32
6-fam
AG3H93
3R (29A)
(GT)4+7
ned
AG3H128
3R (29C)
(GT)21
6-fam
AG3H59
3R (29D)
(GT)9
hex
AG3H249
3R (30D)
(GT)15
ned
AG3H119
3R (31B)
(GT)6
Hex*
AG3H555
3R (32C)
(GT)8
ned
AG3H577
3L (42A)
(GT)16
6-fam
AG3H758
3L (43A)
(GT)11
6-fam
AG2H242
3L (45B)
(GT)8
hex
45C1
3L (45C)
(TG)4+7+4
Hex**
Primers
TGGTGGAATGTGAGACACAG
ATGATGGTCGATCCTTGTCC
TGGGACTGTAAGTGTCTCCC
TATCAGTGAGGCCGAGTTGC
GCCGAAAACATTCCAACAGG
CAGTTATGTCGGCATGCTAC
CACGATGGTTTTCGGTGTGG
ATTTGAGCTCTCCCGGGTG
CAACAGCGAAAGGGTTATCG
CAGCAGAACATACACGCACA
TCGCTTCGACAAATCATCAC
GGGCGAAAATTCGTACAGAG
CCTCTCCCCAGAATCGGTAC
AAGAGCAGAAACAACCGCAG
GGAAACCGACACCACAAAG
TGCCATTGAATGATGATGATG
TTGTTGCTCGGCTTGAAGTA
GAAGGAATCGAGGGTGCTCT
GTTGTGACTCACCTTTACTACGAA
GCTTAGGACTGATTTGCAACTGT
TCC CCA GCT CAC CCT TCA AG
GGT TGC ATG TTT GGA TAG CG
CGG GAC GGC TAG ATA AAG CG
CCG GGC GAC ATA ACC CAC CC
CCC CTA TTA AAC CCT GGA CG
TGT TGT TGC CCT GCG TTA CC
ATG TTC CGC ACT TCC GAC AC
GCG AGC TAC AAC AAT GGA GC
GGT TGA TGC TGA AGA GTG GG
ATG CCA GCG GAT ACG ATT CG
GCA GAG ACA CTT TCC GAA AC
TGT CAA CCC ACA TTT TGC GC
TTC AGC TTC AGG TTG GTC TC
GGG TTT TTT GGC TGC GAC TG
TGA TTT GCC AGT TCT GCC AG
GTG ATT GGA GTG GCT AGT GG
TTC ATT TCC ACC GCA GCT GC
GGC GAC ACT CAA TCC TTC C
AAA AGT GGT GAC CGA GTG AC
ATC TTC AAC ACT TCA GCA CG
TA
(ºC)
54
54
54
54
62
60
54
55
60
60
54
56
54
54
54
54
56
54
56
54
Caputo et al. 2014, Supporting information
Figure S1 – Intra-specific pairwise FST-values plotted against geographic distances.
FST based on: chromosomal data for Anopheles gambiae/S-form (a) and An. coluzzii/M-form (b) and
microsatellite data (c and d, respectively). Empty squares= intra-cluster comparisons; full triangles =
inter-cluster comparisons.
Caputo et al. 2014, Supporting information
Figure S2 - Neutrality tests based on inversion polymorphisms.
Single-locus FST estimates based on chromosomal inversion polymorphisms among populations of
Anopheles gambiae/S-form and An. coluzzii/M-form assembled in ecological areas/sub-areas along the
Gambia river, plotted against expected heterozygosity (Nei 1987). Outlier loci are referred to by their
acronyms. Lines represent the 99.5% confidence limits under the hypothesis of neutrality of the loci.