3.1 Population sampling
Mosquitoes were collected from 23 locations in the ROK; however, 266 An. kleini were identified at only 10 sites, which are malaria-risk areas (Table 1). All An. kleini samples were confirmed using multiplex PCR assays. Only 249 samples from three regions, Baekyeon-ri (BY), Josan-ri (JS), and Yanggu (YG), were used for population genetic analysis since the sample sizes from these regions had more than five individuals (Figure 1).
Table 1. Geographical information on the sampling sites and sizes (n).
Division
|
Province
|
Sample site
|
Location ID
|
Collection n
|
Analysis n
|
Coordinate
|
Malaria Risk
Area
|
Gangwon-do
|
Cheorwon
|
CW
|
3
|
|
38°15'49.0"N 127°09'51.7"E
|
Chuncheon
|
CC
|
1
|
|
37°57'27.7"N 127°43'45.1"E
|
Goseong
|
GS
|
1
|
|
38°32'43.7"N 128°23'59.4"E
|
Hwacheon
|
HC
|
3
|
|
38°06'44.6"N 127°41'40.4"E
|
Inje
|
IJ
|
3
|
|
38°05'36.6"N 128°10'55.3"E
|
Yanggu
|
YG
|
20
|
20
|
38°04'38.4"N 128°00'15.9"E
|
Gyeonggi-do
|
Gimpo
|
GP
|
|
|
37°38'56.9"N 126°34'54.7"E
|
Paju (Baekyeon-ri)
|
BY
|
20
|
20
|
37°55'08.0"N 126°44'03.3"E
|
Paju (Josan-ri)
|
JS
|
209
|
209
|
37°54'37.3"N 126°43'53.0"E
|
Paju (Majeong-ri)
|
MJ
|
3
|
|
37°53'29.4"N 126°45'28.2"E
|
Uijeongbu
|
UB
|
|
|
37°42'36.2"N 127°05'47.3"E
|
Yeoncheon
|
YC
|
|
|
38°11'17.8"N 127°06'29.2"E
|
Incheon
|
Ganghwa
|
GH
|
3
|
|
37°47'04.1"N 126°16'58.7"E
|
Gyeyang
|
GY
|
|
|
37°34'49.0"N 126°44'51.6"E
|
Junggu
|
JG
|
|
|
37°29'42.8"N 126°32'15.3"E
|
Ongjin
|
OJ
|
|
|
37°57'28.9"N 124°39'52.5"E
|
Seogu
|
SG
|
|
|
37°31'42.6"N 126°39'31.7"E
|
Malaria Non
Risk Area
|
Busan
|
Gijang
|
GJ
|
|
|
35°11'55.7"N 129°12'09.1"E
|
Chungcheongnam-do
|
Yesan
|
YS
|
|
|
36°40'27.5"N 126°41'39.4"E
|
Gangwon-do
|
Gangneung
|
GN
|
|
|
37°48'44.5"N 128°51'59.9"E
|
Gyeongsangbuk-do
|
Hampyeong
|
HP
|
|
|
35°01'25.8"N 126°33'07.1"E
|
Gyeongsangnam-do
|
Jinju
|
JJ
|
|
|
35°09'23.3"N 128°07'36.1"E
|
Jeollabuk-do
|
Jeonju
|
JJu
|
|
|
35°48'14.5"N 127°11'36.5"E
|
Jeollanam-do
|
Gyeongsan
|
GSa
|
|
|
35°57'22.9"N 128°50'13.6"E
|
3.2 Sequence characteristics
The mtDNA COI gene was successfully amplified from individual An. kleini. Compared with the sequences from a previous study [26-28], 594 bp out of a total of 710 bp were analyzed. There were 499 conserved and 95 variable sites.
The number of segregating sites (S), JS was the highest at 85, followed by YG at 48 and BY at 34. The average number of nucleotide differences (K) was 10.41218 ± 1.39397 and the average number of mutations per sequence (θ) was 13.39431 ± 3.05977. Haplotype diversity (Hd) was high in all three analysis regions, from 0.92105 (YG) to 0.97895 (BY), whereas nucleotide diversity (Pi) was low, from 0.01543 (JS) to 0.02006 (YG) (Table 2).
Table 2. Sequence characteristics of Anopheles kleini in the three malaria-risk areas.
Location ID
|
n
|
H/Percentage
|
S
|
K
|
θ
|
Hd
|
Pi
|
BY
|
20
|
17 / 85.00
|
34
|
10.15789
|
10.14731
|
0.97895
|
0.01710
|
JS
|
209
|
119 / 56.94
|
85
|
9.16286
|
16.22401
|
0.97221
|
0.01543
|
YG
|
20
|
15 / 75.00
|
48
|
11.91579
|
13.81161
|
0.92105
|
0.02006
|
n: sample size; H: Number of haplotypes; S: Number of segregating sites; K: Average number of nucleotide difference; θ: Average number of mutations per sequence; Hd: Haplotype diversity; Pi: Nucleotide diversity; BY: Baekyeon-ri; JS: Josan-ri; YG: Yanggu.
3.3 Haplotype network analysis
A total of 140 haplotypes were identified in 249 An. kleini individuals. The haplotype percentages for each collection area were BY 85.00% (17/20), YG 75.00% (15/20), and JS 56.94% (119/209) (Table 2). There were three dominant haplotypes with more than ten individuals: H_12 (n = 28), H_2 (n = 25), and H_1 (n = 15). Haplotypes with more than two individuals were confirmed as 25 (17.86%), and the rest were found from only one individual. Region-specific haplotypes from one individual were detected in all three analysis regions but were especially abundant in JS.
Three clusters were identified in the COⅠ haplotype network and some haplotypes (median vectors) were not detected (Figure 2). Cluster I contained 75 haplotypes, including the dominant haplotypes (H_12, H_2, and H_1). Furthermore, 59 haplotypes belonged to Cluster II and six haplotypes belonged to Cluster III. When all haplotypes were compared with the existing foreign reference sequence, H_101 in Cluster II was identical to the Chinese sequence (OP311323), and H_105 was identical to the Russian sequence (KC855655).
3.4 Genetic structure among population
Pairwise genetic distance (FST) was used to evaluate the genetic distance between populations in the analysis region. The FST values between YG and BY were 0.08899 and 0.74900 for JS.
In other words, we confirmed that the two groups, Gangwon-do (YG) and Paju, Gyeonggi-do (BY and JS), had high genetic divergence and were regionally differentiated [29]. However, the genetic distinction of populations was difficult to analyze because the FST value between BY and JS was negative, and gene flow (Nm) was not available (Table 3).
Table 3. Pairwise genetic distance (FST) and gene flow (Nm) values among populations.
Nm
FST
|
BY
|
JS
|
YG
|
BY
|
-
|
-31.50000
|
2.55930
|
JS
|
-0.00800
|
-
|
0.08378
|
YG
|
0.08899
|
0.74900
|
-
|
BY: Baekyeon-ri; JS: Josan-ri; YG: Yanggu.
AMOVA was analyzed by dividing into two groups as Gangwon-do (YG) and Gyeonggi-do Paju (BY, JS). As a result, “within populations” was noticeably higher than “among groups” and “among populations within groups” (Table 4), which implies that individuals within a population have a substantial influence on the total variation than “among groups” and “among populations within groups.”
Table 4. Analysis of molecular variance (AMOVA) for geographic variation of Anopheles kleini in three malaria-risk areas.
Source of variation
|
Degrees of freedom
|
Sum of squares
|
Variance components
|
Percentage of variance (%)
|
F-index
|
Among groups
|
1
|
22.019
|
0.49755
|
9.58
|
0.0958
|
Among populations within groups
|
1
|
3.636
|
-0.02985
|
-0.57
|
-0.00636
|
Within populations
|
246
|
1162.638
|
4.72617
|
91.00
|
0.09005
|
Total
|
248
|
1188.293
|
5.19387
|
100.00
|
|
3.5 Neutrality test
The neutrality test was calculated using DnaSP with three methods: Fu’s Fs, Fu and Li’s D, and Fu and Li’s F. All data showed negative values, suggesting that the population was expanding and had many low-frequency mutations (Table 5). In particular, strong negative values (P < 0.05) of Fu and Li’s D and Fu and Li’s F were identified in the JS population, and the neutrality deviation was more sensitive than that in other regions.
Table 5. Neutrality test of Anopheles kleini in the three malaria-risk areas.
Location ID
|
Neutrality tests
|
Fu's Fs
|
Fu and Li's D
|
Fu and Li's F
|
BY
|
-5.29600
|
-0.05019
|
-0.03960
|
JS
|
-130.06000
|
-3.25408*
|
-2.82976*
|
YG
|
-2.05300
|
-0.40959
|
-0.52717
|
*P < 0.05
BY: Baekyeon-ri; JS: Josan-ri; YG: Yanggu.