Low genetic diversity and lack of genetic structure in the giant jellyfish Nemopilema nomurai in Chinese coastal waters

The giant jellyfish Nemopilema nomurai is a scyphozoan species well-known in East Asian Marginal Seas for its damage to fisheries. The genetic diversity and population structure of N. nomurai, collected from five geographic regions in Chinese coastal seas, were examined based on mitochondrial cytochrome c oxidase subunit I (COI) gene and nuclear internal transcribed spacer one (ITS1) sequences. A total of 26 and five unique haplotypes were recovered from the COI and ITS1 genes, respectively. The overall genetic diversity of N. nomurai calculated by the COI and ITS1 sequences was low (haplotype diversity 0.727% and 0.108%, nucleotide diversity 0.212% and 0.039%). The median-joining network analysis revealed a star-like haplotype network. The hierarchical Analysis of Molecular Variance (AMOVA) of COI haplotypes showed that N. nomurai populations form a single population, with a low F_ST (0.0149, p?=?0.1036). The dispersal ability, together with the biological characteristics, could be important factors for the lack of a geographically structured pattern in N. nomurai in Chinese coastal waters.     

Population genetic diversity of Chinese sea bass (Lateolabrax maculatus) from southeast coastal regions of China based on mitochondrial COI gene sequences

Chinese sea bass (Lateolabrax maculatus), an important commercial and recreational fishery species in China, whose natural resources have decreased dramatically for decades due to overfishing and environmental changes. To provide guidelines for the source conservation and management, genetic diversity and population structure of L. maculatus were analyzed based on the mitochondrial cytochrome oxidase subunit I (COI) gene. Totally 192 individuals were sampled from five locations: Qingdao (QD), Chongming (CM), Dongtou (DT), Lieyu (LY) and Fangcheng (FC). After sequencing of a 586 bp fragment of COI gene, 20 haplotypes were defined. H4 (haplotype 4) and H8 were the dominant haplotypes and existed in all populations. Haplotype diversity (Hd) and nucleotide diversity (π) of each population ranged from 0.572 to 0.721 and from 0.00129 to 0.00271, respectively. The highest Hd and π were found in DT and LY populations, while the lowest value of Hd and π were in the QD population. Genetic distance ranged from 0.0031 to 0.0027 within populations and from 0.0018 to 0.0035 between populations. Analysis of molecular variance (AMOVA) revealed that significant genetic divergence was found in QD and FC populations. In addition, neutrality tests and mismatch distribution analysis indicated that this species experienced potential population expansion events.     

Genetic diversity of <Emphasis Type="Italic">Haemaphysalis qinghaiensis</Emphasis> (Acari: Ixodidae) in western China

Haemaphysalis qinghaiensis as an endemic species in China mainly infests domestic animals and causes great harm to animals and humans in Northwestern plateau. However, there is no information about genetic diversity within the recently established populations of this tick species. Therefore, the present study analyzed the fragments of mitochondrial 16S rDNA, COI and the nuclear gene ITS1 of 56 H. qinghaiensis ticks across four regions of China which are main endemic areas of this species. Analysis showed 98.1–100% (16S rDNA), 97.9–100% (COI), 99.7–100% (ITS1) identity within individuals. For these sequences, 9, 15 and 8 haplotypes were found for 16S rDNA, COI and ITS1, respectively. Ticks from Yongjing were the most variable group, followed by Lintan, Huangyuan, and Tianzhu. Based on parallel analysis of the mitochondrial and nuclear genetic diversity of H. qinghaiensis, our results indicated that mitochondrial markers (especially COI) were much more useful than nuclear ITS for intraspecific genetic variability analysis.     

Genetic diversity of the dung beetle,Copris tripartitus (Coleoptera: Scarabaeidae), that is endangered in Korea

The dung beetle, Copris tripartitus (Coleoptera: Scarabaeidae), is an endangered insect in Korea. In order to establish a conservation strategy, a preliminary investigation on the genetic diversity of Korean populations was performed using mitochondrial COI (658 bp), CytB (433 bp), and nuclear ITS2 (411 nucleotide positions). Sequencing of 69 individuals collected from five localities showed substantially higher variability (5.02% for COI, 4.62% for CytB, and 8.03% for ITS2). The resulting networks for mitochondrial DNA (mtDNA) haplotypes exhibited two star‐like phylogenies, which might indicate that Korean populations have recently expended from two small populations. The ITS2 network, which was presented in the form of a star‐like phylogeny, confirmed that a recent population expansion occurred. Considering the high genetic diversity and gene flow in C. tripartitus populations, one issue regarding conservation seems to be the recovery of previous habitats.     

Mitochondrial and nuclear markers reveal a lack of genetic structure in the entocommensal nemertean Malacobdella arrokeana in the Patagonian gulfs

Malacobdella arrokeana is an entocommensal nemertean exclusively found in the bivalve geoduck Panopea abbreviata, and it is the only representative of the genus in the southern hemisphere. To characterize its genetic diversity, population structure and recent demographic history, we conducted the first genetic survey on this species, using sequence data for the cytochrome oxidase I gene (COI), 16S rRNA (16S) and the internal transcribed spacer (ITS2). Only four different ITS2 genotypes were found in the whole sample, and the two main haplotypes identified in the mitochondrial dataset were present among all localities with a diversity ranging from 0.583 to 0.939. Nucleotide diversity was low (π = 0.001–0.002). No significant genetic structure was detected between populations, and mismatch distribution patterns and neutrality tests results are consistent with a population in expansion or under selection. Analysis of molecular variance (AMOVA) revealed that the largest level of variance observed was due to intrapopulation variation (100, 100 and 94.39 % for 16S, COI and ITS2, respectively). F _st values were also non-significant. The observed lack of population structure is likely due to high levels of genetic connectivity in combination with the lack or permeability of biogeographic barriers and episodes of habitat modification.     

Chloroplast DNA-based genetic diversity and phylogeography of Pyrus betulaefolia (Rosaceae) in Northern China

Pyrus betulaefolia Bunge, considered as an intermediate between oriental and occidental pear groups, is one of the most important wild pear species. The number of its populations is decreasing because of habitat destruction, fragmentation, and continuous exploitation, so protection and conservation measures are urgently needed. Assessment of its genetic diversity and phylogeography are imperative for its efficient conservation. Two chloroplast DNA intergenic fragments were used to detect genetic diversity and phylogeography of 320 individuals from 18 wild P. betulaefolia populations. Haplotype variation, genetic differentiation, and historical events of the populations were estimated. The results showed that P. betulaefolia populations sampled in northern China contained a high level of genetic diversity (H _T?=?0.826). A significant isolation-by-distance value (r?=?0.587, P?<?0.001, 1,000 permutations) among all 18 populations indicated a correlation between genetic divergence and geographic distance. Four population groups were identified in a neighbor-joining tree based on the genetic distance. Analyses of molecular variation showed that the genetic variation mainly existed among population groups, representing 64.61 % of the total variation. Phylogeographic analyses indicated that the populations of P. betulaefolia experienced a scenario of rapid range expansion, which probably occurred between 608,000 and 204,580 years ago. Meanwhile, both the restricted gene flow with isolation by distance and allopatric fragmentation were crucial processes responsible for shaping the genetic patterns of P. betulaefolia. The occurrence of specific haplotypes might be ascribed to an ancestral introgression or joint retention of an ancestral polymorphism with other Pyrus species at the northern edge of the distribution of P. betulaefolia. Three populations displaying a high level of haplotype diversity and unique haplotypes were assumed to be relict populations of Quaternary glaciation and should have conservation priority. Three additional large populations should also be preferentially protected by building natural preservation zones.     

Population genetic structure and phylogeography of the oak gall wasp Andricus chodjaii (Hymenoptera: Cynipidae) in Turkey as inferred from mitochondrial and nuclear DNA sequences

Sequence data of mitochondrial cytochrome b gene and nuclear ITS2 region were used to assess genetic diversity, intraspecific phylogeography and population genetic structure of the oak gall wasp Andricus chodjaii from Turkey. We examined 293 individuals from 21 localities which generated 57 cyt b haplotypes and 8 ITS2 alleles. The average genetic diversity was 0.575 for cyt b and 0.202 ITS2, and the average nucleotide diversity 0.015 for cyt b gene and 0.001 for the ITS2 region. Phylogenetic analyses of cyt b haplotypes produced mostly similar topologies with geographically significant groupings. The ITS2 data provided less resolution without robust and apparent geographic structure. Population demographic analysis indicated that some eastern populations expanded, however, some others underwent either expansion or decline resulting in genetically structured populations. Molecular clock applied to the mtDNA data indicated that ingroup haplotypes diversified from the outgroup haplotypes around Early Pliocene. Further diversification events throughout Pleistocene resulted in major clade formations. It appears that geographic formations and glacial and interglacial cycles of Pleistocene were crucial for shaping the phylogeographic structure of A. chodjaii in Turkey.     

Batrachochytrium dendrobatidis shows high genetic diversity and ecological niche specificity among haplotypes in the Maya Mountains of Belize

The amphibian pathogen Batrachochytrium dendrobatidis (Bd) has been implicated in amphibian declines around the globe. Although it has been found in most countries in Central America, its presence has never been assessed in Belize. We set out to determine the range, prevalence, and diversity of Bd using quantitative PCR (qPCR) and sequencing of a portion of the 5.8 s and ITS1-2 regions. Swabs were collected from 524 amphibians of at least 26 species in the protected areas of the Maya Mountains of Belize. We sequenced a subset of 72 samples that had tested positive for Bd by qPCR at least once; 30 samples were verified as Bd. Eight unique Bd haplotypes were identified in the Maya Mountains, five of which were previously undescribed. We identified unique ecological niches for the two most broadly distributed haplotypes. Combined with data showing differing virulence shown in different strains in other studies, the 5.8 s - ITS1-2 region diversity found in this study suggests that there may be substantial differences among populations or haplotypes. Future work should focus on whether specific haplotypes for other genomic regions and possibly pathogenicity can be associated with haplotypes at this locus, as well as the integration of molecular tools with other ecological tools to elucidate the ecology and pathogenicity of Bd.     

Genetic diversity and population connectivity of the Asian green mussel Perna viridis in South China Sea,inferred from mitochondria DNA markers

The Asian green mussel Perna viridis is ecologically and economically important in the coastal regions of China. In order to characterize the genetic diversity and population connectivity of P. viridis in South China Sea, a 664 bp region of mitochondrial COI gene and a 293 bp region of 16S rRNA gene were sequenced and analyzed for 78 and 92 individuals from four populations in South China Sea, respectively. A total of 15 haplotypes were defined by 14 variable nucleotide sites in COI gene, and 7 haplotypes by 6 variable nucleotide sites in 16S rRNA gene. High haplotype diversity and low nucleotide diversity were observed in COI gene, while moderate haplotype diversity and low nucleotide diversity were observed in 16S rRNA gene. Pairwise F_ST values of COI gene were all negative and those of 16S rRNA gene ranged from −0.01409 to 0.10289. The results showed that no significant genetic divergence (or shallow genetic structure) and high levels of population connectivity among the four populations of P. viridis in South China Sea.     

COI gene sequence analysis for testing cyclical mating in securing genetic diversity of Macrobrachium rosenbergii

In this study we analyzed sequences of the COI gene to investigate the genetic structure and diversity in four populations of the Giant Malaysian Prawn, Macrobrachium rosenbergii, and to test the effectiveness of cyclical mating as means of securing genetic diversity. Forty-three haplotypes were generated for the parental populations; most of these were unique, with moderate genetic and low nucleotide diversities. However Tajima's neutrality test indicated a significant (p < 0.05) departure of the Negeri Sembilan population from the mutation–drift equilibrium, suggesting that it may be losing genetic variability. To combat this problem we recommend a seasonal fishing ban. The AMOVA test results (5.45%, p < 0.00001), the networking of haplotypes and their phylogenetic tree all revealed clear population structuring between the populations. Genetic or haplotype diversity in the progeny groups had increased indicating that a cyclical mating system could be an effective means of maintaining it. The utilization of unique haplotypes in aquaculture, developing DNA barcodes for broods in genetic improvement programs as well as in evaluating restocking activities is recommended. For a better insight into the differences between and among the populations, further investigations using nuclear markers are required.     

Populations genetic structure of the razor clam Sinonovacula constricta from China,Korea and Vietnam

The population genetic structure of the razor clam Sinonovacula constricta was investigated between populations collected from China, Korea and Vietnam using cytochrome oxidase subunit 1 (COI) mtDNA and internal transcribed spacer 2 (ITS2) rDNA markers. A total of 622 bp of COI and 495 bp of ITS2 were sequenced. Highly significant Fst values and low rates of migration were observed from populations between Vietnam and China, (Fst = 0.7578, P < 0.001, Nm = 0.05 for COI; Fst = 0.91389, P < 0.001, Nm = 0.07 for ITS2) and Korea (Fst = 0.79783, P < 0.001, Nm = 0.07 for COI; Fst = 0.74143, P < 0.001, Nm = 0.03 for ITS2). However, lower Fst values and higher gene flow were detected between populations from China and Korea (Fst = 0.25733, P < 0.001, Nm = 0.73) based on COI analysis. The similar pattern was also captured by ITS2 rDNA marker. In addition, Neighbor-joining phylogenetic tree analysis of the two markers resulted in one cluster consisting of haplotypes from Vietnam, and a second group comprising haplotypes from China and Korea. This research revealed a closer genetic relationship between clam population from China and Korea but less similarity to population from Vietnam.     

A deep sequencing approach to estimate <Emphasis Type="Italic">Plasmodium falciparum</Emphasis> complexity of infection (COI) and explore apical membrane antigen 1 diversity

Background

Humans living in regions with high falciparum malaria transmission intensity harbour multi-strain infections comprised of several genetically distinct malaria haplotypes. The number of distinct malaria parasite haplotypes identified from an infected human host at a given time is referred to as the complexity of infection (COI). In this study, an amplicon-based deep sequencing method targeting the Plasmodium falciparum apical membrane antigen 1 (pfama1) was utilized to (1) investigate the relationship between P. falciparum prevalence and COI, (2) to explore the population genetic structure of P. falciparum parasites from malaria asymptomatic individuals participating in the 2007 Demographic and Health Survey (DHS) in the Democratic Republic of Congo (DRC), and (3) to explore selection pressures on geospatially divergent parasite populations by comparing AMA1 amino acid frequencies in the DRC and Mali.

Results

A total of 900 P. falciparum infections across 11 DRC provinces were examined. Deep sequencing of both individuals, for COI analysis, and pools of individuals, to examine population structure, identified 77 unique pfama1 haplotypes. The majority of individual infections (64.5%) contained polyclonal (COI > 1) malaria infections based on the presence of genetically distinct pfama1 haplotypes. A minimal correlation between COI and malaria prevalence as determined by sensitive real-time PCR was identified. Population genetic analyses revealed extensive haplotype diversity, the vast majority of which was shared across the sites. AMA1 amino acid frequencies were similar between parasite populations in the DRC and Mali.

Conclusions

Amplicon-based deep sequencing is a useful tool for the detection of multi-strain infections that can aid in the understanding of antigen heterogeneity of potential malaria vaccine candidates, population genetics of malaria parasites, and factors that influence complex, polyclonal malaria infections. While AMA1 and other diverse markers under balancing selection may perform well for understanding COI, they may offer little geographic or temporal discrimination between parasite populations.

     

外生菌根真菌土生空团菌种群遗传多样性与结构研究

土生空团菌Cenococcum geophilum是生态系统中广泛分布的外生菌根真菌,具有丰富的遗传多样性和重要的生态功能。为揭示土生空团菌的种群遗传多样性和结构,本研究对采集自中国10个森林地点的桦木科Betulaceae、壳斗科Fagaceae和松科Pinaceae植物根系219份样品高通量测序的土生空团菌ITS2序列进行分析。结果表明4 380条土生空团菌ITS2序列共划分为137个单倍型（Hap_1-Hap_137）,其中Hap_1是3科植物的优势单倍型并分布于所有地点,有48个单倍型分布于少数几个地点,但有88个单倍型仅分布于单个地点。非参数（Kruskal-Wallis）检验结果表明地点对土生空团菌单倍型的丰度和多样性具有显著影响,而宿主植物科对其无显著影响。分子方差分析（AMOVA）结果显示土生空团菌在10个地理种群间和3个植物科种群间的遗传分化均不明显,而遗传分化主要来自于种群内的个体差异。基于K-2P遗传距离的邻接法（NJ）树显示10个地理种群可以划分为3支,壳斗科土生空团菌种群的遗传距离比桦木科和松科远。土生空团菌单倍型组成在不同地点间和不同植物科间均有明显差异,有些土生空团菌单倍型具有地点和植物科的偏好性。研究结果为进一步揭示土生空团菌遗传多样性的生态功能提供科学依据。     

Chloroplast DNA variation and genetic structure of Miscanthus sinensis in southwest China

Miscanthus sinensis is a dominant perennial C4 grass with the potential to being a feedstock crop in North America, Europe, and China. Variation in chloroplast DNA sequence was used to obtain information regarding the genetic diversity and structure of populations of M. sinensis in southwest China. Chloroplast DNA, trnL-F and rpl20-rps12 sequences from seventy-five individuals representing 14 populations of M. sinensis were used to study the sequence variation. Seven haplotypes and 16 polymorphic sites (2.7%) were identified. Five substitutions, 6 indels, and 5 existing substitutions and indels sites, were detected through splicing these two gene segments. The genetic diversity within the studied populations (diversity of haploids, h = 0.561, nucleotide diversity, π = 0.00504) was low, this may be affected by the relatively larger effect of genetic drift on the chloroplast DNA, reflecting smaller effective populations than nuclear DNA. Genetic variance within the populations was higher than that between the populations, suggesting that higher gene flow may exist within these populations. The results of parsimony network in seven haplotypes indicated that H1 and H2 may be ancient haplotypes, which may help guide future research on the origin of M. sinensis. Our results provide information on the genetic diversity and structure of M. sinensis and may assist future studies on the phylogeography of M. sinensis.     

Genetic diversity and population structure of Sepiella japonica (Mollusca: Cephalopoda: Decapoda) inferred by mitochondrial DNA (COI) variations

In order to describe the genetic diversity of five geographical populations of cuttlefish (Sepiella japonica) along with Chinese coast and determined their phylogenetic relationship, partial mitochondrial COI gene (681bp in length) was amplified from 96 individuals collected from these populations and sequenced. The 5 populations of cuttlefish inhabit Yellow Sea, East China Sea and South China Sea. Out of 22 polymorphic nucleotides identified, 8 were represented by a single sequence, 12 were parsimony informative, which defined 22 haplotypes. Haplotype and nucleotide diversity were low among populations. Of 22 haplotypes, 15 appeared only in a single population, 6 appeared in 2 or 3 populations and 1 was shared by all populations. The COI gene was monomorphic in Qingdao population. The haplotypes identified clustered into 2 clades, each covered individuals from 5 populations each. Pairwise F_ST were not proportional to the geographical distances. Among the 5 populations, relatively high level of genetic diversity was found in Ningde population which was recommended to be the best choice of germplasm resources for artificial releasing project.     

Phylogeography of the widespread marine invader Microcosmus squamiger (Ascidiacea) reveals high genetic diversity of introduced populations and non-independent colonizations

The spread of non-indigenous species into new marine habitats represents an increasing threat to global diversity. Genetic techniques provide basic understanding of the invasion processes. The ascidian Microcosmus squamiger is considered to be native to Australia, having been spread worldwide via transoceanic vessels. It has successfully invaded artificial and natural habitats where it has become a pest. We studied phylogeography and genetic structure of 12 M. squamiger populations, including samples from its native range (Australia) and introduced populations from the Indian, Pacific, and Atlantic oceans, as well as the Mediterranean Sea. We amplified 574 bp of the mitochondrial COI gene in 258 individuals and found a total of 52 haplotypes. A haplotype tree revealed two main groups of haplotypes. The relative frequency of each group of haplotypes, multidimensional scaling, and analysis of molecular variance showed important differences between the western Australia localities and the remaining ones (eastern Australia and introduced populations). Furthermore, we found that the colonization of the different areas by M. squamiger has not occurred independently, as many introduced populations shared some low frequency alleles. A nested clade analysis showed a global pattern of restricted gene flow with isolation by distance, although we found episodes of long-distance dispersal in some clades. A contiguous range expansion was detected between Australian populations. We conclude that M. squamiger is native to Australia and has most likely expanded its range of distribution sequentially through worldwide shipping, especially from the harbours of the more populated eastern Australia. In introduced populations, we found a high genetic diversity which suggests enhanced invasive potential. Consequently, there is a need to control this species, as it outcompetes local biota and is an economic threat.     

Hotspots of diversity in a clonal world--the Mediterranean moss Pleurochaete squarrosa in Central Europe

Diversity patterns of the dioecious haploid Mediterranean moss Pleurochaete squarrosa were analysed from Central and Northwest Europe using nuclear and chloroplast DNA sequencing and enzyme electrophoresis. Across 69 populations, 38 distinct haploid multilocus genotypes (MLGs) were detected, but nearly all populations were clonal. Only five MLGs occurred in more than two regions, and two diversity hotspots were detected. The Kaiserstuhl mountains in Southwest Germany harboured 34 MLGs, 25 being endemic within Central Europe. Levels of linkage disequilibrium and population structure in Kaiserstuhl populations were similar to levels and structure in sexually reproducing populations in the Mediterranean Basin. In the Moselle-Nahe area, some 250 km north, a comparably high allelic diversity, but no evidence of recombination, was detected. Genetic diversity measures were significantly lower than estimates obtained in the Mediterranean Basin and a G _ST of 0.89 signified extreme population differentiation. Mantel tests identified a positive correlation on genetic and geographical distance for distances up to 50 km. Seven nrITS and three cpDNA haplotypes were detected, their geographical structure mirroring enzyme data set results. Comparative analysis with Mediterranean data demonstrated multiple recolonization of Central Europe from both the Iberian Peninsula and the Balkans. A suture zone of genotypes was detected along the border of Belgium/France and Germany. Despite P. squarrosa having haploid spore and/or vegetative propagules dispersal, we found patterns of postglacial recolonization of Central Europe comparable with those reported in flowering plants and animals. This study demonstrates the importance of comparative research on population genetics and phylogeography of a diverse range of organisms.     

Genetic variation and population structure of the carpet shell clam <Emphasis Type="Italic">Ruditapes decussatus</Emphasis> along the Tunisian coast inferred from mtDNA and ITS1 sequence analysis

Surveys of allozyme polymorphisms in the carpet shell clam Ruditapes decussatus have revealed sharp genetic differentiation of populations. Analysis of population structure in this species has now been extended to include nuclear and mitochondrial genes. A partial sequence of a mitochondrial COI gene and of the internal transcribed spacer region (ITS-1) were used to study haplotype distribution, the pattern of gene flow, and population genetic structure of R. decussatus. The samples were collected from twelve populations from the eastern and western Mediterranean coasts of Tunisia, one from Concarneau and one from Thau. A total of twenty and twenty-one haplotypes were detected in the examined COI and ITS1 regions respectively. The study revealed higher levels of genetic diversity for ITS1 compared to COI. The analysis of haplotype frequency distribution and molecular variation indicated that the majority of the genetic variation was distributed within populations (93% and 86% for COI and ITS1 respectively). No significant differentiation was found among eastern and western groups on either side of the Siculo-Tunisian strait. However, distinct and significant clinal changes in haplotypes frequencies between eastern and western samples were found at the most frequent COI haplotype and at three out of five major ITS1 haplotypes. These results suggest the relative importance of historical processes and contemporary hydrodynamic features on the observed patterns of genetic structure.     

Molecular diversity and phylogeography of Andricus curtisii (Hymenoptera,Cynipidae) in Turkey

A 433-bp fragment of the mitochondrial cytochrome b gene and the entire nuclear ITS2 region were sequenced in an oak gall wasp species, Andricus curtisii, which represents 21 populations across its range in Turkey. Forty cytochrome b haplotypes and 63 ITS2 alleles were discovered among the 161 individuals studied. Remarkable genetic variation was detected in the species, with an average haplotype diversity (h) of 0.72 and 0.76 and an average nucleotide diversity (π) of 0.06 and 0.01 for the cyt b gene and the ITS region, respectively. Most populations were genetically distinct, possessing unique cytochrome b haplotypes. Maximum likelihood and Bayesian phylogenetic analyses and application of the haplotype network to both datasets revealed that the most basally located haplotypes/alleles were from the eastern part of Turkey. The detection of older sequences in the phylogenetic trees of the easterly located populations implied an eastern origin of the species. The application of a conventional insect mitochondrial DNA clock to the dataset suggested a splitting of ingroup haplotypes from the outgroup lineages predating the Pleistocene epoch and the formation of two major haplogroups that coincided with the oscillation of the early Pleistocene glaciations.     

Population structure and genetic diversity of Aedes aegypti and Aedes albopictus in Penang as revealed by mitochondrial DNA cytochrome oxidase I

The population genetics study is crucial as it helps in understanding the epidemiological aspects of dengue and help improving a vector control measures. This research aims to investigate the population genetics structure of two common species of Aedes mosquitoes in Penang; Aedes aegypti and Aedes albopictus using Cytochrome Oxidase I (COI) mitochondrial DNA (mtDNA) marker. Molecular investigations were derived from 440 bp and 418 bp mtDNA COI on 125 and 334 larvae of Aedes aegypti and Aedes albopictus respectively, from 32 locations in Penang. All samples were employed in the BLASTn for species identification. The haplotype diversity, nucleotide diversity, neutrality test and mismatch distribution analysis were conducted in DnaSP version 5.10.1. AMOVA analysis was conducted in ARLEQUIN version 3.5 and the phylogenetic reconstructions based on maximum likelihood (ML) and neighbor-joining (NJ) methods were implemented in MEGA X. The relationships among haplotypes were further tested by creating a minimum spanning tree using Network version 4.6.1. All samples were genetically identified and clustered into six distinct species. Among the species, Ae. albopictus was the most abundant (67.2%), followed by Ae. aegypti (25.2%) and the rest were counted for Culex sp. and Toxorhynchites sp. Both Ae. aegypti and Ae. albopictus show low nucleotide diversity (π) and high haplotype diversity (h), while the neutrality test shows a negative value in most of the population for both species. There are a total of 39 and 64 haplotypes recorded for Ae. aegypti and Ae. albopictus respectively. AMOVA analysis revealed that most of the variation occurred within population for both species. Mismatch distribution analysis showed bimodal characteristic of population differentiation for Ae. aegypti but Ae. albopictus showed unimodal characteristics of population differentiation. Genetic distance based on Tamura-Nei parameter showed low genetic divergent within population and high genetic divergent among population for both species. The maximum likelihood tree showed no obvious pattern of population genetic structure for both Ae. aegypti and Ae. albopictus from Penang and a moderate to high bootstrap values has supported this conclusion. The minimum spanning network for Ae. aegypti and Ae. albopictus showed five and three dominant haplotypes respectively, which indicates a mixture of haplotypes from the regions analysed. This study revealed that there is no population genetic structure exhibited by both Ae. aegypti and Ae. albopictus in Penang. Mutation has occurred rapidly in both species and this will be challenging in controlling the populations. However, further analysis needed to confirm this statement.