- Open Access
Genetic variations of ND5 gene of mtDNA in populations of Anopheles sinensis (Diptera: Culicidae) malaria vector in China
© Makhawi et al.; licensee BioMed Central Ltd. 2013
Received: 12 February 2013
Accepted: 24 September 2013
Published: 8 October 2013
Anopheles sinensis is a principal vector for Plasmodium vivax malaria in most parts of China. Understanding of genetic structure and genetic differentiation of the mosquito should contribute to the vector control and malaria elimination in China.
The present study investigated the genetic structure of An. sinensis populations using a 729 bp fragment of mtDNA ND5 among 10 populations collected from seven provinces in China.
ND5 was polymorphic by single mutations within three groups of An. sinensis that were collected from 10 different geographic populations in China. Out of 140 specimens collected from 10 representative sites, 84 haplotypes and 71 variable positions were determined. The overall level of genetic differentiation of An. sinensis varied from low to moderate across China and with a FST range of 0.00065 – 0.341. Genealogy analysis clustered the populations of An. sinensis into three main clusters. Each cluster shared one main haplotype. Pairwise variations within populations were higher (68.68%) than among populations (31.32%) and with high fixation index (FST = 0.313). The results of the present study support population growth and expansion in the An. sinensis populations from China. Three clusters of An. sinensis populations were detected in this study with each displaying different proportion patterns over seven Chinese provinces. No correlation between genetic and geographic distance was detected in overall populations of An. sinensis (R2 = 0.058; P = 0.301).
The results indicate that the ND5 gene of mtDNA is highly polymorphic in An. sinensis and has moderate genetic variability in the populations of this mosquito in China. Demographic and spatial results support evidence of expansion in An. sinensis populations.
Anopheles sinensis is a principal vector of malaria in many regions in China along with An. lesteri, An. minimus, and An. dirus[1, 2]. An. sinensis has also been identified as the major malaria vector in many parts of other Asian countries, such as in Indonesia, South Korea, Thailand and Japan . In China it was reported that 0.006-2.58% of An. sinensis was infected with P. vivax. The infection rate of An. sinensis in Taiwan was 0.02 % during 1947-1949 . However, malaria outbreaks and re-emergences in China occurred only in the areas where An. sinensis is the principal vector in recent years . Malaria was historically epidemic in the Huang-Huai River region of central China and the total malaria cases in these areas were 21.99 million, accounting for 91.2% of the total reported cases in the country in 1970s. With active implementation of malaria control measures for more than 30 years, considerable success had been achieved and the cases decreased dramatically and many counties in Huang-Huai River region reached the goals of the malaria elimination (the incidence is below 1/10,000). However, in the past decade, malaria has re-emerged in these areas, especially the Anhui Province, where a total of 26,873 malaria cases, 108,594 suspected cases and 23 deaths were reported by the annual case reporting system in 858 counties of 22 Provinces in 2008. The annual incidence was 0.21/10,000. Although, the re-emergence of malaria in central China was controlled in 2008, the number of malaria cases and the incidence of the disease in this region still accounts for 68% of the total cases reported in the country .
Although great success has been achieved since the launch of National Malaria Control Programme in 1955, malaria remains a serious public health problem in China [7–9]. Falciparum malaria, the most deadly among the four main types of human malaria, accounted for 14.9% of all blood-test confirmed malaria cases in 1998 . Falciparum malaria had been endemic in fifteen provinces of China in the early 1950s. The endemic area of falciparum malaria was restricted to eight provinces by 1980, and only to two provinces, Yunnan and Hainan, by 1998 . Consequently, knowledge regarding the distribution of this disease vector, the genetic characteristics of its populations in relation to local environmental conditions is valuable for malarial control.
An. sinensis belongs to Hyrcanus group that includes approximately 30 morphologically indistinguishable species. In China, 25 taxa, including synonyms, have been recorded . The study on the group in China can be traced back to the 1930s. Yao and Wu  and Yao and Ling  observed that An. sinensis could be separated into different forms on the basis of the egg deck width. Baisas and Hu  described the form with narrow decked eggs as a new species, An. lesteri. Ho et al.  also reported An. lesteri in China, but they noticed some distinct bionomic characters found in China as compared to those of the Philippine form. Particularly, the Chinese form of An. lesteri has a strong preference for human blood .
Cytogenetic studies have revealed two karyotypic forms, A (XY1) and B (XY2), in An. sinensis, which correspond to distinct sequences of the second internal transcribed spacer (ITS2) region . Both forms were present in Thailand , but only form B was observed in China and Korea [17, 18]. Analyses of microsatellites loci revealed high polymorphic nature of the An. sinensis populations in China, which indicates that An. sinensis could be divided at least into two populations . Recent molecular studies suggested that An. lesteri from Korea and Japan, An. lesteri from China and An. lesteri from the Philippines were all the same species . Ree et al.  reported an unknown Anopheles species that was morphologically identical to An. sinensis, and Li et al.  also observed two unknown species that were morphologically similar to An. sinensis. Rueda  designated these two species as new species, An. belenrae sp. Nov. and An. kleini sp. Nov, based on their same morphologically identity with An. pullus and An. sinensis, respectively. Morphological identification of sinensis complex is extremely difficult, so that some members of An. lesteri, An. pullus (including the form yatsushiroensis) and two species (at least) are mixed in the population of An. sinensis in Korea.
Various levels of population subdivision of the anopheline mosquito species have been observed from nearly panmictic across a wide geographic range to highly divergent within a short distance. A high rate of recurrent gene flow and/or recency of population expansion has made the populations of some anopheline species hardly differentiated [24–26]. However, other species are composed of highly structured populations, due primarily to geographic barriers, such as mountain chains or arid valleys [27–29]. These genetic data are of special value since it may enable planning of effective strategies for malaria control . For instance, the degree of dispersal of insecticide resistant individuals or genetically modified mosquitoes may provide insight for the development of novel mosquito control strategies. Therefore, understanding the genetic structures of vector species may contribute not only to predict the spread of genes of interest (such as insecticide resistant or refractory genes), but also to identify heterogeneities in disease transmission due to distinct vector populations.
A recent microsatellite study revealed two genetic pools indicating the coexistence of two genetic units in the sampled sites . In this study moderate genetic differentiation was identified in the An. sinensis populations in China and the population divergence was not correlated with geographic distance or barrier in the range . A better knowledge of the status of genetic structure in the local An. sinensis populations should benefit malaria control programs in China and enable more appropriate control strategies to be developed. Unfortunately, there is very limited information about An. sinensis population genetics.
Mitochondrial DNA remains one of the most powerful and reliable tools for detecting population structure and inferring population differences due to its high and rapid mutational rate compared with nuclear DNA . Interestingly, it has been found that within mtDNA, there are regions that diverge rapidly, while other regions that are highly conserved, making the different regions suitable for analysis of different taxonomic levels [33, 34]. Mitochondrial ND5 gene was previously used as a powerful tool in elucidating the level of genetic and phylogenetic divergence between closely related species . Herein, we provide data that describe/discuss the population structure, genetic variability and gene flow among An. sinensis populations from China based on NADH of dehydrogenase subunit 5 (ND5) gene of mitochondrial DNA (mtDNA).
Mosquito collection and identification
Collection data of An. sinensis populations in China
An. sinensis, obtained from different locations, were morphologically identified using keys described by Lu et al.. The identification was confirmed by specific-species PCR based on rDNA ITS2, according to the Ma et al. protocol. Total genomic DNA for individuals used in the study were isolated using extraction kit (QIAGEN, QIAamp DNA Mini Kit) following the manufacturer’s instructions.
Primer design, genomic DNA isolation, amplification and sequencing of rDNA ITS2 and ND5 of mtDNA fragments
A forward and reverse primer pair (5’-TGTGAACTGCAGGACACAT-3’ and 5’-GTTCTA CGGGCCTATCACC-3’), corresponding to ITS2 that was invariably conserved in An. sinensis regardless of the region of collection, was synthesized. This primer pair was used to amplify ITS2 fragment from genomic DNA samples followed by sequencing the amplified DNA fragment to verify the collected individual mosquitoes as true An. sinensis. Another forward and reverse primer pair (5’-TTGCGCCTAATCCTGCTAT-3’ and 5’-TGATTTGTGGTGTCAATGT-3’) were designed and synthesized for subsequent amplification of ND5 DNA fragments from An. sinensis genomic DNA samples. The ND5 primers were designed based on highly conserved regions of all available mosquito ND5 sequences from GenBank databases. Primer 3 software program was used to adjust the annealing temperature of two primer pairs. The primer pairs were used to amplify ND5 DNA fragments from genomic DNA samples extracted from An. sinensis collected from different regions to assess the polymorphism of the ND5 gene.
The PCR was conducted in a 50 μL reaction mixture containing 1 μL of a 1:200 diluted genomic DNA, 25 pmol primers, 5 μL 10X reaction buffer, 2.5 mM MgCl2, 200 μM of each dNTP, and 1 U Taq polymerase. The cycling condition was 5 minutes denaturation at 94°C, followed by 35 cycles of 15 seconds denaturation at 94°C, 15 seconds annealing at 50°C, and 1 minute extension at 72°C, ending with a final extension for 5 min at 72°C. Amplified PCR products were purified and then unidirectionally sequenced for both strands for each one of the two regions by Sangon Biotech (Shanghai Co., Ltd., Beijing, China).
Sequences alignment and analysis
The ND5 gene sequences from 140 An. sinensis individuals were aligned by using BioEdit program 5.0.9 . The Haplotype diversity, its variance and nucleotide diversity  among populations of An. sinensis from different provinces and/or sites, were estimated using the program DnaSP 4.9 . The Tajima  and the Fu and Li  tests were used to examine the hypothesis of selective neutrality of nucleotide substitutions. Tajima’s D test was utilized to examine whether the average number of pair-wise nucleotide differences (K) between sequences was larger or smaller than expected from the observed number of polymorphic sites (S).
Population pairwise net genetic distances based on Slatkin’s linearised F ST , and hierarchical analysis of molecular variance (AMOVA) [44, 45] were estimated Using Arlequin 3.5. 1.3 . The significance of F ST evaluated was based on 1023 random permutations. Demographic analysis and spatial parameters were assessed using the distribution of pair wise sequence differences (mismatch distribution) of Rogers and Harpending . We used Tajima’s D  and Fu’s Fs statistics . The significance of the D and F s values of Tajima and Fu, respectively, was evaluated by comparison with randomly generated values based on the observed (S) with 10,000 repeats. The Mantel test  was performed to test significant correlation between population genetic distance and linear straight geographical distances.
A TCS software program 2.1 [50, 51] was used to construct a haplotypes network and estimated genealogy relationship between haplotypes of An. sinensis populations collected from different sites in China.
We obtained ethical approval from the Ethical Review Committee of Chinese Center for Disease Control and Prevention (No.201214). Permission was also obtained from the directors and related departments of provincial CDC in seven provinces in China.
An. sinensis identification
All specimens used in this study were confirmed as An. sinensis either by PCR based on species-specific ITS2 sequences. Alignment of 30 representative ITS2 sequences of rDNA (accession number KC769646), in conjunction with different sites of collection, confirmed that only sequences of An. sinensis were used.
Characterization and Haplotypes estimation of ND5
A 836-bp segment of mitochondrial DNA (mtDNA), corresponding to coding region of NADH dehydrogenase gene subunit 5 (ND5), was successfully amplified. Analyses were carried out on 729 bp of mtDNA dehydrogenase gene subunit 5 (ND5) from 140 An. sinensis individuals collected from ten sites in seven Chinese Provinces. A total of 84 haplotypes of mtND5 were determined in An. sinensis individuals collected from China (GenBank accession numbers: KC565754 – KC565837), in which 71 polymorphic sites were detected within these populations. The partial nucleotide sequences of ND5 gene showed variable polymorphic sites within and among An. sinensis populations. The frequencies of haplotypes clearly divided these populations into three clusters. Among them, one cluster (n = 51) had low variable sites including ancestral populations, another cluster (n = 32) displayed moderate polymorphism (at least two main constant variable sites) with nucleotide substitutions at positions (55 and 325) respectively, and the third population (n = 57) showed many variable sites with one main constant site at position 529. No characteristics of heteroplasmy and insertion or deletion events were shown within the analysed mtDNA sequence.
The other nucleotide substitutions in ND5 gene of An. sinensis populations were synonymous (Additional file 1: Table S1). There were seven informative non-synonymous substituted sites with amino acids replacement. The first substitution site that corresponding to position 258 (N258S) only found in Yunnan population. Replacement corresponding to position 283 (K283N) occurred in seven populations (GX, HA, HE-N, HE-S, JX-J, JX-N and SH). Substitution at position 309 (N309S) was found in populations (JX-J, HE-S and SH). Substitutions at positions 379 and 385 (R379S; K385N), respectively, were detected in seven populations (HA, HE-S, JX-J, JX-N, SC-N, SH and YN). Substitution at position 529 (K529N) occurred in all populations except GX. Also substitution at position 687 (I687T) was detected in all sites except YN (Additional file 1: Table S1).
Genealogical relationships among populations groups of An. sinensis
Genetic differentiation of An. sinensis populations
Haplotypes and nucleotide diversity of An. sinensis populations collected from China
Hd ± SD
π ± SD
1.00 ± 0.05
0.0128 ± 0.003
1.00 ± 0.05
0.0053 ± 0.0007
0.988 ± 0.02
0.009 ± 0.002
1.00 ± 0.03
0.009 ± 0.002
1.00 ± 0.02
0.0086 ± 002
0.93 ± 0.08
0.005 ± 0.001
0.714 ± 0.13
0.0027 ± 0.0005
0.882 ± 0.07
0.0073 ± 0.002
0.991 ± 0.03
0.010 ± 0.002
0.849 ± 0.04
0.013 ± 0.001
0.981 ± 0.004
0.0098 ± 0.0007
Genetic differentiation and gene flow between populations of An. sinensis collected from China
Tajima’s D test of departures from the neutral expectations did not show significant deviation from neutrality. However, Fu and Li’s D and F statistics indicated a significant deviation from neutrality only for overall populations (P < 0.01), suggesting the existence of excessive rare nucleotide polymorphisms, with possible effects of purifying, selection, or population expansion. For other populations, all statistics tests did not reveal significant differences, suggesting that the nucleotide substitutions of the ND5 gene are consistent with neutral evolution theory.
Population structure of clustered groups of An. sinensis populations
AMOVA results among three clustered An. sinensis populations collected from China
Source of variation
Fixation Index (FST)
I & II:
I & III:
II & III:
Demographic and spatial history of An. sinensis populations in China
Mismatch and neutrality tests results of three clustered An. sinensis populations collected from China
Abundance of An. sinensis population groups in different Chinese provinces
It has generally been accepted that the degree of the polymorphisms of ND5 gene serves as a dependable representative for assessing the genetic variations in populations of a given species . The present study described an analysis of 729 bp sequence of ND5 mitochondrial DNA in An. sinensis populations obtained from 10 collection sites in seven Chinese provinces. The results indicate that An. sinensis populations in China were highly polymorphic in the ND5 gene. In most populations high level of polymorphism and moderate genetic differentiations were detected in this mosquito (F ST = 0.001 – 0.341). These results are comparable to previous findings on An. sinensis and its member group of Hyrcanus An. lesteri[19, 52, 53]. Also these results are in agreement with An. baimaii in India , An. darlingi malaria vector in Central and South America [55–57], An. albimanus in Latin America and African malaria vectors An. gambiae, An. arabiensis and An. funestus[44, 59, 60].
Neutrality tests of Tajima’s D, Fu and Li’s D and F did not detect deviation from neutrality theory in the ND5 gene within any population of An. sinensis. Only Fu and Li’s D and F tests were significant when all populations from different sites pooled together, and this perhaps is due to a high level of polymorphism within ND5 gene (71/140). These results support the neutral theory of mitochondrial gene evolution and suggested that there is a large effective population size of An. sinensis in these locations.
Generally, the results showed that there is low-to-moderate genetic differentiation and high gene flow within different populations except the YN population that displayed a significantly high level of genetic differentiation and restricted gene flow with all populations except Hainan population (F ST = 0.011; Nm = 42.33). This could be due to bias of low sample size in Hainan (n = 9) but similar samples were generated from (HE-N and SC-N), that give significant results with YN. Moreover, the two sites of Hainan and Yunnan are somehow similar in their conditions for mosquito habitats. Although distantly apart, both sites belong to typical temperate tropic zones where there are great seasonal variations in abundance of mosquito populations that reach their peak during summer . Yunnan is noted as centre of biodiversity [61–64]; because of it’s a highly complex region topographically due to its transitional position from tropical southern Himalayas to eastern Asia and from tropical Southeast Asia to subtropical China as well as at the junction of the India and Burmese plates, derived from Gondwanaland, and the Eurasian plate . Further studies in these areas could be established by collecting and analysing more An. sinensis samples over several seasons. The climatic condition could impose selection on An. sinensis populations. In addition, An. sinensis breeds in a wide range of habitats including natural and artificial [4, 64].
Interestingly, the results of haplotypes and genealogy revealed the presence of three clustered populations of An. sinensis across collection sites in China. In general cluster I approximately represented 36% (n = 51), cluster II includes relatively less samples 23% (n = 32) where 41% (n = 57) belong to cluster III. Cluster I was found in all populations collected across the study zone (ancestral), cluster two was found in 8 populations out of 10 (except HA and YN) where cluster III occured in 9 populations (except SC-C). The three clustered populations were assigned by at least one common haplotype or nucleotide substitution and/or amino acid(s) replacement. The proportion of the three clustered populations varied from site to site in China. For example, the cluster three of An. sinensis population is abundant in Hainan and Yunnan, but moderately abundant in Shanghai and Henan and absent in Guangxi. These results are similar to those reported in a previous study  that indicated that there were two gene pools found within An. sinensis populations collected across China from 20 collection sites (one pool included six populations and the second pool included eight populations). In that study the author reported that there was coexistence between two gene pools and specimens were assigned to one gene pool when it is remaining greater than 80%. A similar finding was reported in South Korea that An. sinensis includes two groups associated with the presence of a mountain functioning as a genetic barrier . Normally once there are two populations possible, there is, an intermediate group. In present study cluster II could be an intermediate group. In this cluster (C II) obviously only a few individuals share polymorphic sites with each one of the other two clusters (Additional file 1: Table S1), which could be due to an ancestral background.
An AMOVA analysis using the three clusters found that 31.32% of the variance was attributed to between populations and 68.68% to within populations. A similar phenomenon of variance pattern was observed in comparing three clusters. There is substantial significant genetic differentiation among populations of the three clusters (F ST = 0.313; P < 0.0001). The level of genetic differentiation is relatively similar to that previously detected in An. sinensis populations in China using microsatellites . The distribution of the three clusters does not seem to be attributable to geographical range because no correlation between genetic and geographic distance was detected based on the mantel test results. Moreover, sympatric occurrence of more than one clustered populations in the same study site is further evidence that distance has no major impact on genetic differentiation. Similar results have been reported for An. gambiae and An. arabiensis malaria vectors in Africa . In that report, the authors suggested that the high level of differences in these populations was likely due to some reproductive isolations rather than physical barrier or distance and also possibly due to demographic history or ecological diversification. The wide range of distributions for this mosquito population of An. sinensis is an importance factor for malaria control and that suggests further examining at a local level for microgeographic scales in lack of isolation by distance (IBD), for understanding population connectivity and vector dispersal across multiple spatial scales.
Mismatch distribution of demographic and spatial analyses were assessed using the distribution of pairwise sequence differences and suggested population expansion of An. sinensis in China. Both SSD and raggedness index supported the evidence of population expansion. Moreover, negative and significant values of Fu’s Fs are further indicators for population growth. These findings are also consistent with pervious reported results of An. sinensis in South Korea where two groups of An. sinensis have recently experienced expansion in population size based on mitochondrial control region .
Genetic diversity is a key factor that enables adaptation and persistence of a natural population towards changing or adverse environmental conditions. Its remains true that our analyses are based on a single marker, mtDNA, which may not be representative of the genome as a whole. Although most of the polymorphism in mtDNA sequences is likely to be neutral, positive or negative selection on any site within the mtDNA genome will influence the pattern of variation across the whole molecule . Our results emphasize the need for further investigation with deeper sampling (especially in the areas where there are more than one cluster) using more polymorphic nuclear markers to elucidate the forces that shape and maintain the population structure. Further studies are required to investigate the three clusters of An. sinensis regarding ecology and susceptibility to malaria transmission.
These results have implication for the interpretation of genetic population structure in An. sinensis. Our results revealed that the populations of An. sinensis in China are highly polymorphic within the ND5 gene of mitochondrial DNA with moderate genetic variability. There are at least three clustered populations with different abundance within Chinese provinces. The occurrence of more than one sympatric population could be due to adaption of the local environmental factors such as type of breeding sites and its availability in different seasons and/or as well as for control measures. Geographic range does not seem to have a major effect on the genetic variability of An. sinensis. Further exploring the mechanism for the absence of a given population may provide insight towards development of new vector control strategies.
We are grateful to Dr. Fengxia Meng, Dr. Yuhong Guo, Dr. Haixia Wu and Dr. Guichang Li from the Department of Vector Biology and Control, ICDC, China CDC for their support to the mosquito samples. We thank Dr. Jianyong Li from Virginia Tech for the revision of the manuscript. Also we thank Prof. Dia-Eldin A. El naiem from Department of Natural Sciences, University of Maryland Eastern Shore for extensive English and grammatical editing. This study was funded by the National Basic Research Program of China (973 Program) (Grant No.2012CB955500, 2012CB955504) and supported by Chinese Center for Disease Control and Prevention (China CDC). Most of the mosquito samples were collected through the National Selected Disease Vectors Surveillance Networks, China CDC. This study was also funded by the Postdoctoral Program for African Researchers of China-Africa Science and Technology Partnership Program (CASTEP; No. ZF2012021).
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