Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers

Information about the genetic diversity and population structure in elite breeding material is of fundamental importance for the improvement of crops. The objectives of our study were to (a) examine the population structure and the genetic diversity in elite maize germplasm based on simple sequence repeat (SSR) markers, (b) compare these results with those obtained from single nucleotide polymorphism (SNP) markers, and (c) compare the coancestry coefficient calculated from pedigree records with genetic distance estimates calculated from SSR and SNP markers. Our study was based on 1,537 elite maize inbred lines genotyped with 359 SSR and 8,244 SNP markers. The average number of alleles per locus, of group specific alleles, and the gene diversity (D) were higher for SSRs than for SNPs. Modified Roger’s distance (MRD) estimates and membership probabilities of the STRUCTURE matrices were higher for SSR than for SNP markers but the germplasm organization in four heterotic pools was consistent with STRUCTURE results based on SSRs and SNPs. MRD estimates calculated for the two marker systems were highly correlated (0.87). Our results suggested that the same conclusions regarding the structure and the diversity of heterotic pools could be drawn from both markers types. Furthermore, although our results suggested that the ratio of the number of SSRs and SNPs required to obtain MRD or D estimates with similar precision is not constant across the various precision levels, we propose that between 7 and 11 times more SNPs than SSRs should be used for analyzing population structure and genetic diversity.     

Populational structure of Schistosoma mansoni assessed by DNA microsatellites

DNA microsatellites were used as molecular markers to analyse the population structure of the laboratory LE strain and of 10 field isolates of Schistosoma mansoni, the aetiologic agent of schistosomiasis. Out of 16,000 DNA sequences analysed in databases, 622 microsatellite loci were identified in 481 sequences (3.0%). The AT repetitions were the most frequent, followed by AAT and AC. Six loci showing perfect repetitions were selected and used in the polymerase chain reaction to evaluate polymorphisms in the number of repeats. Two groups of worms were studied. The first group consisted of 78 individuals, 39 of each sex, of the LE strain. The second group of worms consisted of 10 field isolates: seven from humans and three from snails. Four of the six loci were polymorphic, containing 11-17 alleles per locus. No linkage disequilibrium was observed among loci and none of the loci was sex linked. In both groups of worms, a significant deviation from Hardy-Weinberg equilibrium was observed. The observed heterozygosity was always lower than the expected one. The polymerase chain reaction primers were S. mansoni specific. The LE strain showed a lower total number of alleles or a lower average number of alleles/polymorphic locus than the field isolates, suggesting that 41 years of laboratory maintenance exerted selective pressure on the LE strain. The S. mansoni populations from the field were most genetically undifferentiated (R(ST)<0.027), suggesting a high gene flow among them. Our results showed the usefulness of microsatellites for population analysis of S. mansoni, offering a new alternative for a better understanding of schistosomiasis epidemiology.     

Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites

Two hundred and sixty maize inbred lines, representative of the genetic diversity among essentially all public lines of importance to temperate breeding and many important tropical and subtropical lines, were assayed for polymorphism at 94 microsatellite loci. The 2039 alleles identified served as raw data for estimating genetic structure and diversity. A model-based clustering analysis placed the inbred lines in five clusters that correspond to major breeding groups plus a set of lines showing evidence of mixed origins. A "phylogenetic" tree was constructed to further assess the genetic structure of maize inbreds, showing good agreement with the pedigree information and the cluster analysis. Tropical and subtropical inbreds possess a greater number of alleles and greater gene diversity than their temperate counterparts. The temperate Stiff Stalk lines are on average the most divergent from all other inbred groups. Comparison of diversity in equivalent samples of inbreds and open-pollinated landraces revealed that maize inbreds capture <80% of the alleles in the landraces, suggesting that landraces can provide additional genetic diversity for maize breeding. The contributions of four different segments of the landrace gene pool to each inbred group's gene pool were estimated using a novel likelihood-based model. The estimates are largely consistent with known histories of the inbreds and indicate that tropical highland germplasm is poorly represented in maize inbreds. Core sets of inbreds that capture maximal allelic richness were defined. These or similar core sets can be used for a variety of genetic applications in maize.     

Population structure and genetic diversity of Ammodytes personatus in the Northwestern Pacific revealed by microsatellites markers

Genetic diversity and population structure of Ammodytes personatus in the Northwestern Pacific were investigated for 16 collections using eight highly variable microsatellite loci. Microsatellite analyses gave strong support for the presence of two distinct groups of genotypes. Pleistocene glaciations can cause significant geographical differentiation in A. personatus populations. However, microsatellite data cannot confirm completely reproductive isolation between north group and south group. About half of comparison values within the first and second cluster were significant after sequential Bonferroni corrections. Routine oceanic currents associated with strong wind condition may provide an excellent chance for connectivity of among populations within clusters. However, gene flow can be restricted by marine gyres due to complex geographical characteristic.     

An analysis of genetic diversity across the maize genome using microsatellites

How domestication bottlenecks and artificial selection shaped the amount and distribution of genetic variation in the genomes of modern crops is poorly understood. We analyzed diversity at 462 simple sequence repeats (SSRs) or microsatellites spread throughout the maize genome and compared the diversity observed at these SSRs in maize to that observed in its wild progenitor, teosinte. The results reveal a modest genome-wide deficit of diversity in maize relative to teosinte. The relative deficit of diversity is less for SSRs with dinucleotide repeat motifs than for SSRs with repeat motifs of more than two nucleotides, suggesting that the former with their higher mutation rate have partially recovered from the domestication bottleneck. We analyzed the relationship between SSR diversity and proximity to QTL for domestication traits and observed no relationship between these factors. However, we did observe a weak, although significant, spatial correlation for diversity statistics among SSRs within 2 cM of one another, suggesting that SSR diversity is weakly patterned across the genome. Twenty-four of 462 SSRs (5%) show some evidence of positive selection in maize under multiple tests. Overall, the pattern of genetic diversity at maize SSRs can be explained largely by a bottleneck effect with a smaller effect from selection.     

Population structure and genetic diversity of Lithocarpus litseifolius (Fagaceae) assessed using microsatellite markers

Lithocarpus litseifolius (Fagaceae), known as tree of Chinese sweet tea, is a native commercial plant distributed in south China and adjacent areas. This study used ten microsatellite markers to investigate the genetic variation and population structure of 11 populations of L. litseifolius from the main production regions in China. All of the tested loci proved to be effective for the species. The number of alleles per locus ranged between 3 and 39, and mean observed and expected heterozygosity was 0.43 and 0.52, respectively. The deficiency in heterozygosity may be the result of human interference and harvesting activities. Analysis of molecular variance revealed that most of the variation was within populations, whereas differentiation among populations was insignificant, and that there was no significant correlation between genetic distance and geographic distance (r = 0.4089, p = 0.9940). However, A Bayesian model‐based analysis sorted all 11 populations into two (when k = 2) or three (when k = 3) clusters with higher probabilities and showed a geographical pattern which is probably related to the topography of China. Our results provide important information for protecting, sustainably using, and improving the current resources of L. litseifolius.     

多基因联合揭示海南鲌的遗传结构与遗传多样性

海南鲌(Culter recurviceps)是我国华南地区重要经济鱼类, 由于受到近些年水利开发、过度捕捞、环境污染等诸多因素的影响, 其资源量快速下降, 亟需得到更多的关注和保护。为保护和合理开发海南鲌种质资源, 本研究采集了华南地区23个地理群体207尾海南鲌样本, 测定了2个线粒体基因(Cytb和ND2)并从Barcode of Life Data System数据库获得相对应线粒体COI基因, 结合多种分析方法(系统发育分析、分化时间估算、单倍型网状图、群体遗传分析和Mantel检验)对海南鲌的遗传结构和遗传多样性展开研究。系统发育分析和单倍型网状图表明华南地区海南鲌群体被分成3个谱系(I、II和III), 其中谱系I和III由珠江的群体组成, 谱系II由海南岛的群体组成。分化时间估算发现3个谱系之间的分化时间介于0.028-0.251 Ma之间, 表明华南地区更新世气候变化可能是造成海南鲌谱系分化的重要原因。群体遗传分析发现海南鲌群体之间存在极显著的遗传分化(F_ST = 0.511, P < 0.001), 并且符合距离隔离模式(R = 0.348, P = 0.0010)。群体动态历史分析表明, 海南鲌群体可能在0.010-0.025 Ma经历了群体扩张, 表明更新世的气候波动也影响了海南鲌的群体大小和分布。综上所述, 海南鲌群体由3个谱系组成, 更新世气候变化是导致3个谱系分化和影响海南鲌群体动态历史的重要因素。此外, 海南鲌群体之间的遗传分化也可能受到了空间距离的影响。     

Stability of population structure and genetic diversity across generations assessed by microsatellites among sympatric populations of landlocked Atlantic salmon (Salmo salar L.)

It may often be necessary to perform genetic analyses of temporal replicates to estimate the significance of spatial variation independently from that of temporal variation in order to ensure the reliability of estimates of a defined population structure. Nevertheless, temporal studies of genetic diversity remain scarce in the literature relative to the plethora of empirical studies of population structure. In vertebrates, a limited number of studies have specifically assessed the temporal stability of population structure for more than one generation. In this study, we performed a microsatellite analysis of DNA obtained from archived scales to compare the population structure among four sympatric landlocked populations of Atlantic salmon ( Salmo salar ) over a time frame of three to five generations. The same patterns of allele frequency distribution, θ, R _ST and genetic distance estimates were observed among populations for two time periods, confirming the temporal stability of the population structure. Despite population declines and stocking during this period, no statistically significant changes in intrapopulation genetic diversity were apparent. This study illustrates the feasibility and usefulness of microsatellite analysis of temporal samples, not only to infer changes of intrapopulation genetic diversity, but also to assess the stability of population structure over a time frame of several generations.     

Genetic diversity of Guangxi chicken breeds assessed with microsatellites and the mitochondrial DNA D-loop region

The domestic chicken (Gallus gallus domesticus) is an excellent model for genetic studies of phenotypic diversity. The Guangxi Region of China possesses several native chicken breeds displaying a broad range of phenotypes well adapted to the extreme hot-and-wet environments in the region. We thus evaluated the genetic diversity and relationships among six native chicken populations of the Guangxi region and also evaluated two commercial breeds (Arbor Acres and Roman chickens). We analyzed the sequences of the D-loop region of the mitochondrial DNA (mtDNA) and 18 microsatellite loci of 280 blood samples from six Guangxi native chicken breeds and from Arbor Acres and Roman chickens, and used the neighbor-joining method to construct the phylogenetic tree of these eight breeds. Our results showed that the genetic diversity of Guangxi native breeds was relatively rich. The phylogenetic tree using the unweighed pair-group method with arithmetic means (UPGAM) on microsatellite marks revealed two main clusters. Arbor Acres chicken and Roman chicken were in one cluster, while the Guangxi breeds were in the other cluster. Moreover, the UPGAM tree of Guangxi native breeds based on microsatellite loci was more consistent with the genesis, breeding history, differentiation and location than the mtDNA D-loop region. STRUCTURE analysis further confirmed the genetic structure of Guangxi native breeds in the Neighbor-Net dendrogram. The nomenclature of mtDNA sequence polymorphisms suggests that the Guangxi native chickens are distributed across four clades, but most of them are clustered in two main clades (B and E), with the other haplotypes within the clades A and C. The Guangxi native breeds revealed abundant genetic diversity not only on microsatellite loci but also on mtDNA D-loop region, and contained multiple maternal lineages, including one from China and another from Europe or the Middle East.     

Population structure and genetic diversity of moose in Alaska

Moose (Alces alces) are highly mobile mammals that occur across arboreal regions of North America, Europe, and Asia. Alaskan moose (Alces alces gigas) range across much of Alaska and are primary herbivore consumers, exerting a prominent influence on ecosystem structure and functioning. Increased knowledge gained from population genetics provides insights into their population dynamics, history, and dispersal of these unique large herbivores and can aid in conservation efforts. We examined the genetic diversity and population structure of moose (n = 141) with 8 polymorphic microsatellites from 6 regions spanning much of Alaska. Expected heterozygosity was moderate (H(E) = 0.483-0.612), and private alleles ranged from 0 to 6. Both F(ST) and R(ST) indicated significant population structure (P < 0.001) with F(ST) < 0.109 and R(ST) < 0.125. Results of analyses from STRUCTURE indicated 2 prominent population groups, a mix of moose from the Yakutat and Tetlin regions versus all other moose, with slight substructure observed among the second population. Estimates of dispersal differed between analytical approaches, indicating a high level of historical or current gene flow. Mantel tests indicated that isolation-by-distance partially explained observed structure among moose populations (R(2) = 0.45, P < 0.01). Finally, there was no evidence of bottlenecks either at the population level or overall. We conclude that weak population structure occurs among moose in Alaska with population expansion from interior Alaska westward toward the coast.     

Population structure, genetic diversity and linkage disequilibrium in elite winter wheat assessed with SNP and SSR markers

Modern genomics approaches rely on the availability of high-throughput and high-density genotyping platforms. A major breakthrough in wheat genotyping was the development of an SNP array. In this study, we used a diverse panel of 172 elite European winter wheat lines to evaluate the utility of the SNP array for genomic analyses in wheat germplasm derived from breeding programs. We investigated population structure and genetic relatedness and found that the results obtained with SNP and SSR markers differ. This suggests that additional research is required to determine the optimum approach for the investigation of population structure and kinship. Our analysis of linkage disequilibrium (LD) showed that LD decays within approximately 5–10 cM. Moreover, we found that LD is variable along chromosomes. Our results suggest that the number of SNPs needs to be increased further to obtain a higher coverage of the chromosomes. Taken together, SNPs can be a valuable tool for genomics approaches and for a knowledge-based improvement of wheat.     

Population genetic structure and diversity of the endangered Cantabrian capercaillie

The Cantabrian capercaillie (Tetrao urogallus cantabricus) occupies the southwestern edge of the grouse family distribution range in Eurasia. It is endemic to the Cantabrian Mountains in northwestern Spain and is geographically isolated and separated from the neighboring population in the Pyrenees by a distance of 300 km. Over the last decades, the population has undergone a dramatic decline and is now threatened with extinction. This study presents the genetic analysis of the Cantabrian capercaillie population using non-invasive samples. We performed genotyping of 45 individuals using 20 microsatellites and a sex marker. The data highlight the need for using a large number of markers when considering fragmented small populations. Genetic diversity (H_E = 0.50) and average number of alleles (3.40) in the population were low. The population is fragmented into 2 clusters (F_ST = 0.113) that fit with areas on both sides of the transportation ways that divide its range. Both clusters exhibited additional heterozygote deficits. Geographical distance was negatively correlated with genetic relatedness (r = −0.44, P ≤ 0.001). The data show a recent decline in effective population size that can be related to an ongoing process of population reduction and fragmentation. Conservation actions should focus on the protection of local demes by maintaining a dense network of suitable patches to maximize reproductive output and the number of potential dispersers to reconnect the 2 subpopulations. © 2012 The Wildlife Society.     

Population structure and genetic diversity of four Henan pig populations

To investigate the population structure and genetic diversity of Henan indigenous pig breeds, samples from a total of 78 pigs of 11 breeds were collected, including four pig populations from Henan Province, three Western commercial breeds, three Chinese native pig breeds from other provinces and one Asian wild boar. The genotyping datasets were obtained by genotyping‐by‐sequencing technology. We found a high degree of polymorphism and rapid linkage disequilibrium decay in Henan pigs. A neighbor‐joining tree, principal component analysis and structure analysis revealed that the Huainan and Erhualian pigs were clustered together and that the Queshan black pigs were clearly grouped together but that the Nanyang and Yuxi pigs were extensively admixed with Western pigs. In addition, heterozygosity values might indicate that Henan indigenous pigs, especially the Queshan black and Huainan pigs, were subjected to little selection during domestication. The results presented here indicate that Henan pig breeds were admixed from Western breeds, especially Nanyang and Yuxi pigs. Therefore, establishment of purification and rejuvenation systems to implement conservation strategies is urgent. In addition, it is also necessary to accelerate genetic resources improvement and utilization using modern breeding technologies, such as genomic selection and genome‐wide association studies.     

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...     

Population structure of Purple Sandpipers (Calidris maritima) as revealed by mitochondrial DNA and microsatellites

The Purple Sandpiper (Calidris maritima) is a medium‐sized shorebird that breeds in the Arctic and winters along northern Atlantic coastlines. Migration routes and affiliations between breeding grounds and wintering grounds are incompletely understood. Some populations appear to be declining, and future management policies for this species will benefit from understanding their migration patterns. This study used two mitochondrial DNA markers and 10 microsatellite loci to analyze current population structure and historical demographic trends. Samples were obtained from breeding locations in Nunavut (Canada), Iceland, and Svalbard (Norway) and from wintering locations along the coast of Maine (USA), Nova Scotia, New Brunswick, and Newfoundland (Canada), and Scotland (UK). Mitochondrial haplotypes displayed low genetic diversity, and a shallow phylogeny indicating recent divergence. With the exception of the two Canadian breeding populations from Nunavut, there was significant genetic differentiation among samples from all breeding locations; however, none of the breeding populations was a monophyletic group. We also found differentiation between both Iceland and Svalbard breeding populations and North American wintering populations. This pattern of divergence is consistent with a previously proposed migratory pathway between Canadian breeding locations and wintering grounds in the United Kingdom, but argues against migration between breeding grounds in Iceland and Svalbard and wintering grounds in North America. Breeding birds from Svalbard also showed a genetic signature intermediate between Canadian breeders and Icelandic breeders. Our results extend current knowledge of Purple Sandpiper population genetic structure and present new information regarding migration routes to wintering grounds in North America.     

Human genetic diversity and the nonexistence of biological races

Sewall Wright's population structure statistic, F(ST), measured among samples of world populations is often 15% or less. This would indicate that 85% of genetic variation occurs within groups while only 15% can be attributed to allele frequency differences among groups. In this paper, we show that this low value reflects strong biases that result from violating hidden assumptions that define F(ST). These limitations on F(ST) are demonstrated algebraically and in the context of analyzing dinucleotide repeat allele frequencies for a set of eight loci genotyped in eight human groups and in chimpanzees. In our analyses, estimates of F(ST) fail to identify important variation. For example, when the analysis includes only humans, F(ST) = 0.119, but adding the chimpanzees increases it only a little, F(ST) = 0.183. By relaxing the underlying statistical assumptions, the results for chimpanzees become consistent with common knowledge, and we see a richer pattern of human genetic diversity. Some human groups are far more diverged than would be implied by standard computations of F(ST), while other groups are much less diverged. We discuss the relevance of these findings to the application of biological race concepts to humans. Four different race concepts are considered: typological, population, taxonomic, and lineage. Surprisingly, a great deal of genetic variation within groups is consistent with each of these concepts. However, none of the race concepts is compatible with the patterns of variation revealed by our analyses.     

Temporal variation of the population structure and genetic diversity of Farfantepenaeus notialis assessed by allozyme loci

Population genetic studies carried out on penaeid shrimps have disclosed different patterns of population subdivision, revealing new aspects of shrimp biology as well as the effects of historical contingency molding those patterns. However, the stability of observed allele frequencies over time still remains untested. The objective of this article is to show the analysis of the temporal variation of allozymes in a shrimp species inhabiting Cuba which proves that the genetic structure of this species could significantly change in time. The study involves four populations of Farfantepenaeus notialis sampled in a period of 8 years. The significant statistics obtained from partitions observed in 1995 were not detected in 2003 (as suggested by AMOVA and F(ST)), whereas temporal genetic differentiation and heterozygosity became highly significant. The results strongly suggest that the effect of migrations could be the cause for the loss of F. notialis genetic structure in 2003. It is therefore imperative to call attention on the vulnerability of these populations when facing unstable environmental and habitat conditions.     

Population structure and genetic diversity in bottle gourd [Lagenaria siceraria (Mol.) Standl.] germplasm from India assessed by ISSR markers

Genetic diversity analysis was undertaken in 42 geographically distant genotypes accessions of bottle gourd (Lagenaria siceraria) from India northeastern (14) and northern region (28) using inter-simple sequence repeat (ISSR) markers. A total of 209 amplified bands were obtained from 20 ISSR primers used in this study, of which 186 were polymorphic with 89.00 % band polymorphism. Various parameters namely, observed number of alleles, effective number of alleles, Nei’s gene diversity/heterozygosity, resolving power, Shannon’s information index and gene flow were estimated under experiment. Jaccard’s similarity coefficient matrix was generated for pairwise comparisons between individual ISSR profiles and UPGMA cluster analysis based on this matrix showed clustering into six groups. Jaccard’s coefficient of similarity values ranged from 0.409 to 0.847, with a mean of 0.628 revealing a moderate level of genetic diversity. The Bayesian model-based approach to infer hidden genetic population structures using the multilocus ISSR markers revealed two populations among the 42 genotypes. This is the first report on the assessment of genetic variation using ISSR markers in this medicinal vegetable plant, and this study of diversity analysis will be helpful in analyzing future hybrid breeding strategy and devising effective germplasm exploration and conservation strategy.     

Population structure and genetic diversity in tristylous Narcissus triandrus: insights from microsatellite and chloroplast DNA variation

We investigated cpDNA sequence and nuclear microsatellite variation among populations of the wild daffodil Narcissus triandrus to examine the role of historical vs. contemporary forces in shaping population structure, morphological differentiation and sexual-system evolution. This wide-ranging heterostylous species of the Iberian Peninsula is largely composed of two allopatric varieties (vars. cernuus and triandrus), and populations with either stylar trimorphism or dimorphism. Dimorphic populations only occur in var. triandrus, are mainly restricted to the northwestern portion of the species range, and uniformly lack the mid-styled morph (M-morph). Chloroplast DNA (cpDNA) sequence variation revealed strong geographical structuring and evidence for a fragmentation event associated with differentiation of the two varieties. In var. triandrus, population fragmentation, restricted gene flow and isolation-by-distance were also inferred. Significant differences in genetic diversity and population structure between the two varieties likely reflect historical and contemporary differences in demography and gene flow among populations. Discordance between cpDNA markers and both microsatellite and morphological variation indicate that hybridization has occurred between the two varieties at contact zones. There were no differences in genetic diversity or population structure between dimorphic and trimorphic populations, and chloroplast haplotypes were not associated with either sexual system, indicating transitions in morph structure within each maternal lineage. M-morph frequencies were positively correlated with differentiation at microsatellite loci, indicating that the evolutionary processes influencing these neutral markers also influence alleles controlling the style morphs.     

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.