Molecular anthropological studies of the populations in and around East Asia have resulted in the discovery that most of the Y-chromosome lineages of East Asians came from Southeast Asia. However, very few Southeast Asian populations had been investigated, and therefore, little was known about the purported migrations from Southeast Asia into East Asia and their roles in shaping the genetic structure of East Asian populations. Here, we present the Y-chromosome data from 1,652 individuals belonging to 47 Mon-Khmer (MK) and Hmong-Mien (HM) speaking populations that are distributed primarily across Southeast Asia and extend into East Asia. Haplogroup O3a3b-M7, which appears mainly in MK and HM, indicates a strong tie between the two groups. The short tandem repeat network of O3a3b-M7 displayed a hierarchical expansion structure , with MK haplotypes being located at the original point, and the HM and the Tibeto-Burman haplotypes distributed further away from core of the network. Moreover, the East Asian dominant haplogroup O3a3c1-M117 shows a network structure similar to that of O3a3b-M7. These patterns indicate an early unidirectional diffusion from Southeast Asia into East Asia, which might have resulted from the genetic drift of East Asian ancestors carrying these two haplogroups through many small bottle-necks formed by the complicated landscape between Southeast Asia and East Asia. The ages of O3a3b-M7 and O3a3c1-M117 were estimated to be approximately 19 thousand years, followed by the emergence of the ancestors of HM lineages out of MK and the unidirectional northward migrations into East Asia. The origin of early East Asians, and particularly their point of entry into the region, remains ambiguous Mon-Khmer (MK) and Hmong-Mien (HM) speaking populations live in the area where the expansion towards East Asia from Southeast Asia is thought to have occurred . DespiteIn addition, among the three derived haplogroups, O2a-M95 and O3-M122 are the most abundant in Southeast Asia. However, M95 , they were still useful by pooling them in the analyses.We collected fingertip blood samples and kept the samples dry on the filter paper. Whole genome amplification was performed with the filter paper samples using the published method Thirty Y chromosome biallelic loci were screened according to the population specificity of East and Southeast Asia. Genotyping of DE*-YAP was conducted by agarose gel electrophoresis directly after PCR. O*-M175, O3a1-M121, O3a3c-M134, O3a3c1-M117, and D1-M15 were scanned on the ABI 3130×l genetic analyzer after Y chromosome PCR with fluorescent primers . C-M130, F*-M89, K*-M9, O3*-M122, O3a3b-M7, O3a2-M164, O3a3a-M159, O1a*-M119, O1a1a-M101, O1a2-M110, O2a*-M95, O2a1-M88, Q1a1-M120, P*-M45, and D3-P47 were typed using a PCR-RFLP assay  [15]. D-Seventeen Y chromosome microsatellites were also typed for further study on the diversity of samples. These include DYS456, DYS389I, DYS389II, DYS390, DYS458, DYS19, DYS385I, DYS385II, DYS393, DYS391, DYS439, DYS635, DYS392, YGATAH4, DYS437, DYS438, and DYS448. Multiple-touchdown PCR was adopted . The scaThe frequency contour maps for haplogroups were constructed by Golden Software Surfer7.0. Clustering analyses were performed based on the haplogroup frequency data of various East Asian populations, including principal component analysis and neighbor-joining hierarchical cluster analysis, using SPSS 15.0.The networks of Y-STR haplotypes of the individual samples with haplogroups O2a-M95, O3a3b-M7, and O3a3c1-M117  were con−4−4 per locus per 25 years i is the average squared difference in the number of repeats for the ith STR between pairs of alleles sampled within haplogroup; m is the number of STRs investigated, µi is the mutation rate for ith STR.Based on the Y-STR diversity of the haplogroups O2a, O3a3b, and O3a3c1, the time depth of haplogroups within Network was estimated from the ρ statistic (the mean number of mutations from the assumed root of the network), using a 25-year generation time and a mean per-locus, per-generation mutation rate of 6.9×10We analyzed the correlation between the geographic locations and the ages of the STR haplotype samples, to address the origin and diffusion of M7 and M117. The age of a haplotype is mostly related to its location in certain Y-STR network when the network includes sufficient samples, e.g., the haplotypes closer to the center of the network are most probably older. Therefore, in the analysis, we did not use the absolute ages, but the mutation step numbers counted from the center of the network. Coordinate planes were then set up with the mutation steps as x-coordinate and the latitude of each sample as y-coordinate . The PeaTo show the result in more animate way, we turned the coordinate planes into two flashes using Adobe ImageReady CS2. In these flashes, the samples occurred on the maps in turn of the ages .The haplogroup frequencies of the HM and MK populations are listed in History of the large populations such as East Asians was always complicated. The population was formed by many demographic evens, represented by different Y chromosome haplogroups. However, the haplogroups with the highest frequencies were most probably related to the mainstream of the population migration event. Other haplogroups with different genetic structure might have not involved in the same migration, e.g., came from other neighboring population groups in much recent time.Haplogroups C and D were less frequent in the region, but both were found in MK and HM groups. The TK abundant haplogroup O1a2-M110 was observed only in one sample of Palyu which is known to have been genetically influenced by Kadai populations In order to illustrate the close relationships between these two populations, HM and MK, and the distances to the other populations in East Asia, we collected the published haplotype frequency data from six other ethnic phyla Furthermore, we also performed the hierarchical cluster analysis. Additional data of Indians (Dravidians and Indo-Aryans) were added as an outer group. The STR diversity of a certain haplogroup is usually informative for the origin and diffusion of the relevant genetic markers. We analyzed STRs of the Y chromosomes belonging to O2a-M95, O3a3b-M7, and O3a3c1-M117 see  to furthA clear hierarchical structure  emerged in the network of O3a3b-M7 , in whicIn the O2a-M95 STR network , most ofO3a3c1-M117 is another sub-haplogroup of O3-M122 and is much younger than M95. In the STR network of O3a3c1, more th−17). Therefore, we propose that the O3a3b might have originated in the ancestors of MK populations, and they migrated northward unidirectionally into the ancestors of HM and ST populations sequentially. Moreover, a similar case happens to O3a3c1-M117 (−14), supporting the unidirectional northward migration suggested by the analyses on O3a3b.Geographically, MK, HM, and ST populations are distributed across the border of Southeast Asia and East Asia in sequence from south to north. Thus, to examine the correlation between sample locations and STR haplotype structure of O3a3b, we plotted the latitude of each sample location against the STR mutation step number of each haplotype from the origin of the network . InteresHowever, we failed to construct this kind of annual ring shaped network from other haplogroups , becauseThere are several statistics for genetic time estimation. Here we calculated the ages of the O2a, O3a3b and O3a3c1 using the ρ statistic and average squared difference (ASD) which are suitable for the Y chromosome STR data . The ageThe age of O3a3c1 is 24352±7325 years by ρ statistic and 18786±4565 years by ASD, a little bit older than that of O3a3b, just before the Last Glacial Maximum when early people migrated into East Asia through the Yun-Gui Plateau. Little diversity had been accumulated during the short time between its emergence and the start of migration. The unidirectional passage therefore has also left an effect on the STR structure of O3a3c1 although not as perspicuous as that of O3a3b. The oldest haplogroup O2a occurred thousands of years before the migration, and too much diversity had been accumulated to show any signals of the bottlenecks into East Asia. The subsequent ethnic diversification distributed most of the O2a STR haplotypes into different ethnic groups.We had also implemented BATWING calculation. However, the result showed a much broader confidence interval , and is not coincident with the known history of modern human. Therefore, we omitted the BATWING results.The two population groups studied in this paper, i.e., the MK and HM, are indigenous populations of mainland Southeast Asia and Southwest China, respectively. This study has shown that MK and HM groups are closely related genetically and share high frequencies of haplogroups O2a-M95, O3a3b-M7, and O3a3c1-M117. The O3a3b-M7 is rare in neighboring populations, i.e. Tibeto-Burman and TK, while almost absent in the other East/Southeast Asian populations. The STR network of O3a3b-M7  exhibitsThe annual ring shape of the network or tree is not strange in human evolutionary studies. If we transform the Y haplogroup tree Several studies have revealed that the genetic diversity is much higher in the southern populations than in the northern populations of East Asia, as the haplogroups found in the south include almost all the haplogroups in the north Unlike previous studies on the peopling of East Asia which focused on Y-SNP frequency In an effort to interpret these findings, we need to take into account the topographic conditions at the time modern human arrived in Southeast Asia. In this regard, there were several geographic barriers to the distribution of human populations in Southeast Asia and South China, and these may have shaped the subsequent ethnic diversifications. For instance, the Annamese Cordillera segregated the ancestors of TK and MK in the Ice Age Judging from the structure of the O3a3b and O3a3c1 STR networks, the ancestral population size was changing during this migration but growing eventually, e.g. decreased through the bottlenecks and increased after the bottlenecks, enabling the rising of different diversity patterns. Moreover, the diffusion was very slow and dispersive because of the cold climate and complicated landforms through which it had to move. Consequently, genetic drift frequently occurred when populations moved from one valley to another, resulting in the loss of the old haplotypes and the emergence of the novel haplotypes in the new populations. Therefore, the STR haplotypes found at the forefront of the migrating population(s) would have gone through more steps averagely from the root of the network. It is likely that the STR diversity of O3a3b and O3a3c1 dispersed northward along a unidirectional passage, allowing more new haplotypes to evolve and move ahead eventually into new regions. This passage may extend through to North China, the homeland of modern Chinese and Tibetan, and O3a3b was almost lost during the long distance migration of those northern ST populations while O3a3c1 was increased by chance. This unidirectional passage is the combination of many collateral bottleneck effects, which resulted in the unique genetic structure and physical characteristics of East Asians and caused the genetic differences between East Asians and Southeast Asians At the same time, the unidirectional MK-HM-ST route through the Yun-Gui Plateau might not be the only route by which early people entered East Asia. The ancestors of TK and Austronesians might have entered East Asia through a different coastal route Protocol S1The primers and protocols for the SNPs and STRs genotyping used in this paper.(DOC)Click here for additional data file.Figure S1STR networks for the minor haplogroups found in MK and HM.(TIF)Click here for additional data file.Table S1Y chromosome STR data of the MK and HM samples and topology showing the hierarchy between SNPs. Note: Y-STR data of following populations are unavailable due to poor sample quality or lack of data from references: Pahng, Northern Bunu, Mien Western, Guizhou Miao, Yunnan Miao, Blang, Ava, Kinh, Muong. Hence only 1360 sets of Y-STR data were listed.(XLS)Click here for additional data file.Information S1The action map reproducing a unidirectional diffusion northward from the population of MK to HM and ST according to the individual STR mutations of O3a3b-M7 and latitude of each population.(GIF)Click here for additional data file.Information S2The action map reproducing a unidirectional diffusion northward from the population of MK to HM and ST according to the individual STR mutations of O3a3c1-M117 and latitude of each population.(GIF)Click here for additional data file.


Acer takesimense, an anagenetically derived species endemic to Ullung Island, Korea, and its continental progenitor A. pseudosieboldianum on the Korean Peninsula. Microsatellite data reveal a clear genetic distinction between the two species. A high F value in the cluster of A. takesimense was found by Bayesian clustering analysis, suggesting a strong episode of genetic drift during colonization and speciation. In comparison with A. pseudosieboldianum, A. takesimense has slightly lower genetic diversity and possesses less than half the number of private and rare alleles. Consistent with predictions, weak geographical genetic structure within the island was found in A. takesimense. These results imply that anagenetic speciation leads to a different pattern of specific and genetic diversity than often seen with cladogenesis.Anagenetic speciation is an important mode of speciation in oceanic islands; one-fourth of the endemic plants are estimated to have been derived via this process. Few studies, however, have critically examined the genetic consequences of anagenesis in comparison with cladogenesis (involved with adaptive radiation). We hypothesize that endemic species originating via anagenetic speciation in a relatively uniform environment should accumulate genetic variation with limited populational differentiation. We undertook a population genetic analysis using nine nuclear microsatellite loci of  Oceanic islands have long been recognized as fascinating natural laboratories for the study of evolution (Bramwell and Caujapé-Castells Echium (Boraginaceae) of the Canary Islands . During anagenetic speciation, an initial founder lineage simply transforms genetically and morphologically through time without further specific differentiation  species, A. okamotoanum Nakai and A. takesimense Nakai, occur on Ullung Island. Morphological and phylogenetic studies have shown that these two endemics are not closely related to each other but rather have had independent anagenetic origins from different continental progenitors, A. mono Maxim. and A. pseudosieboldianum Kom., respectively  Is there clear genetic differentiation between the two species? (2) How much genetic diversity exists within island populations of A. takesimense in comparison to continental populations of A. pseudosieboldianum? (3) Is there any geographic structuring of genetic variation among populations of A. takesimense within the island?In this study we investigate genetic consequences of anagenetic speciation of Acer takesimense from seven populations in Ullung Island, and 133 individuals of A. pseudosieboldianum from seven populations in the Korean Peninsula . We selected ten microsatellite markers, which were isolated from The statistical significance of deviation from Hardy–Weinberg equilibrium (HWE), and linkage disequilibrium between loci in each population, were conducted with the Markov chain method  using GENEPOP 4.0 (Raymond and Rousset AR), observed proportion of heterozygotes (HO), expected proportion of heterozygotes (HE), and total number of alleles, was evaluated for each species and population using FSTAT 2.9.3.2 (Goudet FIS) was calculated in the program. We also counted the number of private alleles (unique to one group), and rare alleles  per individuals in each group. Three categories were constructed for these estimates: (i) each species is treated as a group; (ii) the seven populations of A. takesimense as a group and the seven populations of A. pseudosieboldianum as seven different groups; and (iii) each population in both species as a group.Genetic diversity, in terms of allelic richness  A. pseudosieboldianum. Statistical significance of the variance components was tested by calculating their probabilities based on 1,023 permutations. Genetic distance among populations was calculated by DA genetic distance  A. pseudosieboldianum. We used an admixture model with correlated allele frequency . 20,000 ‘‘burn-in’’ steps of Chain Monte Carlo searches, followed by 10,000 iterations, and 20 replicate runs were performed at each K from 1 to 10 under the F-model. We adopted the hierarchical approach for the STRUCTURE analysis employing ∆K to determine the uppermost level of structure  after Bonferroni correction. All the deviating cases were related to the positive FIS, indicating HWE deviation due to heterozygote deficit. Therefore, we estimated the frequency of null alleles across populations and loci using Micro-Checker, resulting in an average frequency from 0.228 (BDG7D) to 0.036 (A88LE), and 0.135 in all of the nine loci. For loci that showed significant heterozygote deficit, we generated corrected genotypic frequencies for putative null alleles using Micro-Checker. We performed population genetic analyses  using both the corrected and non-corrected data sets. Significant linkage disequilibrium was not found between any pairwise loci in all populations (P < 0.05) after Bonferroni correction.Ten microsatellite loci were used to genotype 263 individuals from 14 populations in A. takesimense generally showed lower levels of genetic diversity than populations of A. pseudosieboldianum in allelic richness, expected heterozygosity, and total number of alleles according to the Mann–Whitney U test (P < 0.05). FIS values were significantly positive in 11 populations, four of A. takesimense and all of A. pseudosieboldianum (P < 0.05) after Bonferroni correction. At the specific level, A. takesimense possessed half the number of private and rare alleles of A. pseudosieboldianum. If A. takesimense is treated as one population, then this population shows a large number of private and rare alleles in comparison with each of the seven populations of A. pseudosieboldianum.Genetic diversity parameters estimated by the nine microsatellite loci are shown in Table A. takesimense.Genetic variation among and within populations was examined by AMOVA at different hierarchical levels with three categories using the corrected and non-corrected data sets Table . The twoDA genetic distance  than in A. pseudosieboldianum  according to the Mann–Whitney U test (P < 0.05). The mean genetic distance between populations of the two species was 0.260 (SD 0.036).A neighbour-joining tree of the two species was constructed based on nce Fig. . The corK = 2 based on ΔK value in two categories, (a) all samples from the two species, and (c) A. pseudosieboldianum  was higher than that of cluster II . In the separate analysis performed for each category, no clear populational subdivisions were found in each species  after Bonferroni correction. In Population 14 excess heterozygosity was detected under TPM as well. As a result, Populations 9 and 14 of A. pseudosieboldianum detected recent reduction of population size in multiple analyses (or mutation models).We tested bottleneck effects using the corrected and non-corrected data sets. They showed much the same results, and therefore again we dealt with results from the non-corrected data only. The mode-shift test detected the evidence of a bottleneck in Population 9 of um Table . Excess Acer takesimense and its progenitor A. pseudosieboldianum was clear in both the STRUCTURE analyses and neighbour joining tree. In the STRUCTURE analyses, most individuals were assigned to each of the species clusters, but there were a few individuals that had intermediate genetic components between the two species  being much higher than that among populations of A. pseudosieboldianum (DA = 0.152); (2) the populations of A. takesimense accumulate some private and rare alleles, suggesting genetic uniqueness; and (3) the two populational systems are completely geographically isolated.The two species differ in morphological features, with Acer takesimense in comparison with those of A. pseudosieboldianum. A smaller number of alleles in populations of A. takesimense was also revealed by AFLP analysis , another endemic species in Ullung Island, which showed a slightly higher level of genetic diversity of AFLPs than its continental progenitor D. ibukiensis in the Japanese archipelago , the number of alleles in A. takesimense is relatively high. Over generations, genetic variation in A. takesimense may indeed have accumulated through mutation and recombination followed by changes in allelic frequencies through drift and/or selection. The seven populations of A. takesimense analysed were collected broadly at different elevations (120–900 m) on Ullung Island, but only weak geographical genetic structure was detected in STRUCTURE analysis. The level of genetic variation among populations was also quite low as documented with AMOVA. Such a weak geographical genetic structure within Ullung Island has also been reported in the anagenetically derived species, A. okamotoanum and Dystaenia takesimana  bottleneck signals were detected in the two populations (9 and 14) of A. pseudosieboldianum, which could support the concept of recent dramatic distributional changes within this species. Further study will be required to provide a foundation for phylogeographic evolutionary insight into progenitor species in the Peninsula.In the structure analysis, the compositions of clusters between Populations 9 and 13 were quite different from each other, but there were also multiple clusters mixed together within the other populations. It is difficult, therefore, to see any trend in geographic structure due to genetic variation. This complex geographic structure could be the result of their ability for long distance dispersal of seeds (via the well-known winged samara fruits) and subsequent genetic exchange, and also changes in population sizes and distribution throughout the Quaternary glacial period. Macrofossils and pollen data from the Korean Peninsula indicate that temperate deciduous broad-leaved forests broadly declined between ca. 20,700 and 11,500 years BP, and increased after ca. 11,500 years BP in response to dramatic climate change during the late Pleistocene and early Holocene (Chung et al. This study adds important new data on the genetic consequences of anagenetic speciation in oceanic islands. In cladogenesis, several lines of speciation occur from founder populations by selection within markedly different ecological zones that results in different morphological and physiological traits, and also in genetic portioning of the founder populations. In anagenetic speciation, as shown in this study, after a founder event the initial population expands its distribution range across the entire island, and in the process accumulates genetic variation through mutation and recombination. No eco-geographic partitioning of genetic variation results. Over many generations, island populations simply diverge in genetic and morphological composition from progenitor populations, and a new species arises.


AS3MT (the major arsenic-metabolizing gene) haplotype associated with reduced health risks due to rapid arsenic excretion and lower urinary fraction of the monomethylated metabolite.Background: Arsenic in drinking water causes severe health effects. Indigenous people in the South American Andes have likely lived with arsenic-contaminated drinking water for thousands of years. Inhabitants of San Antonio de los Cobres (SAC) in the Argentinean highlands generally carry an AS3MT variants and compared AS3MT haplotype frequencies among different indigenous groups.Objectives: We hypothesized an adaptation to high-arsenic living conditions via a possible positive selection for protective a) inhabitants of SAC and villages near Salta in northern Argentina (n = 346), b) three Native American populations from the Human Genome Diversity Project , and c) five Peruvian populations (n = 97). The last two groups have presumably lower historical exposure to arsenic.Methods: Indigenous groups we evaluated were AS3MT haplotype in the SAC population (68.7%) compared with the HGDP  and Peruvian  populations. Genome-wide microsatellite (n = 671) analysis showed no detectable level of population structure between SAC and Peruvian populations (measure of population differentiation FST = 0.006) and low levels of structure between SAC and HGDP populations .Results: We found a significantly higher frequency of the protective AS3MT haplotype frequencies, our data raise the possibility that, during a few thousand years, natural selection for tolerance to the environmental stressor arsenic may have increased the frequency of protective variants of AS3MT. Further studies are needed to investigate this hypothesis.Conclusions: Because population stratification seems unlikely to explain the differences in  The widespread occurrence of arsenic-resistance genes in bacteria and archaea, and in eukaryotes such as yeast and plants , reflectIncreased concentrations of inorganic arsenic  in drinking water are frequently found in Argentina, Bangladesh, Chile, China, Hungary, India, Mexico, Romania, Taiwan, and different parts of the United States  were also included and analyzed separately. No urine samples were collected from the HGDP populations.HGDP populations. Samples for assessing worldwide genetic diversity were collected for the HGDP, and the provided cell lines are maintained at the Centre d’Étude du Polymorphisme Humain  for use in population genetic studies . A previn = 97) were students at the University of San Marcos in Lima; participants who identified themselves as second-generation Quechua migrants currently living in Lima; participants currently living in the Andean highland cities of Cerro de Pasco and Huancayo; and participants from a village near Pucallpa in the jungle area of Peru. The Peruvians were mestizos determined to have predominately native ancestry. No urine samples were taken from the Peruvian subjects.Peru. The Peruvian study subjects . The protocol was approved by the Ministry of Health  and the ethics committees of the Karolinska Institutet , the University of Oklahoma , and the Universidad Nacional Mayor de San Marcos .Arsenic analysis. Exposure to inorganic arsenic was assessed by the concentration of arsenic in water and total arsenic in urine, that is, the sum of inorganic arsenic, MMA, and DMA. Speciation of arsenic metabolites in urine was performed using HPLC hyphened with hydride generation and inductively coupled plasma mass spectrometry , employing adequate quality control  or by Sequenom™ SNP Genotyping  according to the manufacturer’s protocol. The Peruvian participants were genotyped by TaqMan assays for rs3740393 , rs3740390 (C/T), and rs10748835 (A/G), each containing a protective allele  associated with less MMA and more DMA  .abolism) . These SImputations. Genotype imputation is a technique that allows accurate estimation of associations with genetic markers that are not directly genotyped. When a particular stretch of a chromosome is examined in at least one participant, the genotypes of many others who inherit that same stretch of markers are also identified. We analyzed SNPs in linkage disequilibrium with other neighboring SNPs in the AS3MT region that could reliably be used to impute genotypes of SNPs that were not genotyped. The HGDP panel has previously been genotyped for a panel of genome-wide SNPs , and these SNPs were used to impute the three untyped SNPs associated with arsenic metabolism for the three Native American populations and eight East Asian populations typed by http://dx.doi.org/10.1289/ehp.1205504)]. For imputation, we used a reference panel from the HapMap Phase 2 Project  were selected to be typed by PreventionGenetics (http://www.preventiongenetics.com) for 806 short tandem repeat polymorphic markers. Participants included in the microsatellite analysis had sufficient DNA of good quality (260:280 ratio > 1.8) for analysis, were born in the study area, and were not first-degree relatives of other participants included in the analysis (based on self-report). The marker data were integrated with previously published data following the procedure described by n = 73), SAC (n = 14), and an expanded set of participants from the three HGDP Native American populations .Relationships between pairs of participants were inferred with Relpair version 2.0.1  and firsulations  , from K = 3 to K = 10. The 10 replicates for each choice of K were summarized using CLUMPP , with a median age of 31 years  and 32 years of age . Fourteen percent of the women in SAC were pregnant. Median (range) arsenic concentrations in urine were 268 µg/L  for participants from SAC and 19 µg/L (3.0–606) for those from near Salta.AS3MT haplotype in SAC was C-T-A , which was found in 68.7% of the evaluated participants (p = 2.20 × 10–16), the Peruvians , and the 23 participants who lived near Salta . This most frequent AS3MT haplotype appeared to have a strong effect on the arsenic metabolite pattern in urine in the SAC group : Increasing copies of the C-T-A haplotype were associated with a smaller percentage of MMA  and a higher percentage of DMA .The most frequent icipants . The C-Thttp://dx.doi.org/10.1289/ehp.1205504)]. The phased and imputed haplotypes (both 3-SNP and 6-SNP haplotypes) in HGDP East Asians compared well to the known haplotypes in the HapMap JPT and CHB groups , and it was assumed that phasing and imputation were likely to be reasonably accurate for Native Americans too.The C-T-A haplotype in SAC was also higher than the inferred frequencies in the East Asian (range = 8.1–37%), Native American HGDP (12–17%), and the European populations [5.8% in the HapMap CEU (Utah residents with ancestry from northern and western Europe) group] [see Supplemental Material, Table S2 (p = 5.16 × 10–10 compared with SAC), and occurred at intermediate frequency in Peruvians  and in the population near Salta .The G-C-G haplotype, which contains no protective alleles, was the second most frequent in the SAC population (26%) , but it Population structure analysis of Native American groups. Pairwise FST based on the 671 microsatellites showed low levels of differentiation between SAC and Peruvian populations (FST = 0.006) and slightly higher levels of differentiation between SAC and the three Native American HGDP groups (FST 0.012–0.054) (2–0.054) .K), whereas the variation attributable to European and African contribution were fixed to clusters 1 and 2 and the remaining clusters were available to represent remaining population structure in the data set through hierarchical clustering. Although the SAC and Peruvian populations showed slight differences in contribution from the European cluster (blue) and the African cluster (yellow), the remaining variation belongs to the main Native American cluster (orange). This cluster is constant from K = 3 to K = 10, with no additional clustering within the main Native American cluster. Among the HGDP Native American populations, the Maya and the Piapoco fell in the same cluster (orange) as SAC and the Peruvian populations. The Pima showed partial contribution from another group (green) compared with the SAC and the Peruvian populations for K = 7 to K = 10.The results from a supervised STRUCTURE analysis  demonstrAS3MT, associated with a more efficient arsenic metabolism and a probably lower formation of the most toxic metabolite, may have undergone positive selection in populations who have lived for a very long time in areas with high arsenic concentrations in the drinking water. This study presents a number of findings that are in support of the hypothesis for positive selection:The findings from this study raise the possibility that haplotypes in AS3MT haplotypes between SAC participants versus Peruvians and Native Americans from the HGDP panel.We observed significant differences in the frequencies of The haplotype that contained three protective alleles (C-T-A), previously associated with more efficient arsenic methylation , was sigAS3MT haplotypes between SAC and villages near Salta may reflect the more pronounced Hispanic genetic influence in the latter groups and, thus, these populations have been exposed to arsenic only during the last few centuries.The difference in The absence of population structure between the Peruvian groups and SAC (and the low levels of population structure between SAC and the HGDP Native American groups) indicates that the difference cannot be explained by population differentiation attributed to genetic drift.FST) between SAC and Peruvian groups was about 10 times as large for the AS3MT gene (0.053) compared with the genome-wide average .The differentiation  and found that expression was significantly altered in association with an increasing number of AS3MT protective alleles . Furthermore, Mexican populations of indigenous American ancestry that live in areas with historically high arsenic content have repeatedly been shown to have lower urinary percent MMA compared with populations of European ancestry  in Africa and Europe (AMY1), improving the capacity to digest starch-rich diets  PDFClick here for additional data file.


Houttuynia cordata is an important traditional Chinese herb with unresolved genetics and taxonomy, which lead to potential problems in the conservation and utilization of the resource. Inter-simple sequence repeat (ISSR) markers were used to assess the level and distribution of genetic diversity in 226 individuals from 15 populations of H. cordata in China. ISSR analysis revealed low genetic variations within populations but high genetic differentiations among populations. This genetic structure probably mainly reflects the historical association among populations. Genetic cluster analysis showed that the basal clade is composed of populations from Southwest China, and the other populations have continuous and eastward distributions. The structure of genetic diversity in H. cordata demonstrated that this species might have survived in Southwest China during the glacial age, and subsequently experienced an eastern postglacial expansion. Based on the results of genetic analysis, it was proposed that as many as possible targeted populations for conservation be included. It plays a unique role in improving the immune system of patients with severe acute respiratory syndrome (SARS) [H. cordata is also consumed as a vegetable in China for its special aroma. Although H. cordata is of high medicinal and economic value, wild H. cordata population resources are limited, which is a main hurdle for the breeding of new cultivated varieties. Therefore, it is critical to arrest this dearth of information on this important natural resource and study the genetic diversity of the remaining population.Saururaceae, a member of paleoherbs, is an ancient family with six species in four genera, Saururus . H. corduttuynia ,3. This uttuynia ,5, althoe (SARS) , and thee (SARS) . H. cordet al. [H. cordata, as well as the relationship between its genetic variation and life history based on morphological features, isozyme, chromosome number and RAMP markers. However, samples in these studies were collected from limited areas in the Sichuan Basin of China, and the genetic information was not sufficient for the conservation of the rare but valuable species.Knowledge of population genetic structure provides evolutionary perspectives of a species, allows for the prediction of population response to natural and artificial changes in the future , and is et al. ,11 have H. cordata based on ISSRs using a large number of individuals sampled from wide areas including central, southeastern and southwestern China. The purposes of this study are to address the following questions. What is the level of genetic diversity and the degree of differentiation among populations in H. cordata from its main range? What does the genetic structure imply for the evolutionary history? How can the species be conserved and used effectively based on the revealed genetic information?Because large numbers of polymorphic fragments can be produced by inter-simple sequence repeats (ISSR)-PCR at a relatively low cost ,13, thisPp) was 30.49% on average, ranging from 12.17% to 42.61% at the population level. Nei’s genetic diversity (H) was estimated to be 0.0923 at the population level and 0.2820 at the species level, while Shannon indices (I) were 0.1413 and 0.4338 at these levels, respectively. Among the 15 populations, population KM exhibited the highest level of variability , while population LX exhibited the lowest level of variability .The 10 selected primers amplified a total of 115 reproducible and distinct ISSR bands with a percentage of polymorphic markers of 97.39%. Among the 115 bands scored, 25 bands (21.7%) were found in 50–100% of samples, 27 bands (23.5%) were found in 30–49% of samples, and 63 bands (54.8%) were found in less than 30% of samples. A few population-specific bands were observed in the data set. ST, estimated by partitioning of the total gene diversity) was 0.6728. The level of gene flow among populations (Nm) was estimated to be 0.2431, indicating that there was a low migration rate among populations. This finding was consistent with the type of genetic structure predicted by the Shannon’s diversity index analysis, which suggested that 67.42% of the total variation was partitioned among populations. GI) and genetic distance (GD) for each pairwise comparison between two populations. Genetic identities between populations varied from 0.6936 to 0.9184 with a mean of 0.7764 ± 0.0437. Correlative analysis with SAS software showed that there was no significant correlation either between genetic differentiation and latitude (p = 0.9408), or between genetic differentiation and longitude (p = 0.3368). The AMOVA indicated that most (77%) of the molecular variation in H. cordata populations existed among populations, with lesser amounts within populations (23%). Permutation tests (based on 999 permutations) suggest that the overall ΦPT was significantly different from the null distribution  (Differentiation among populations was significant in this species. The coefficient of genetic differentiation among populations (G= 0.010) , which iH. cordata .A UPGMA dendrogram based on Nei’s (1972) genetic distance indicated that the 15 populations were clustered into four geographically distinct groups, including Sichuan basin , Yungui Plateau (KM and HX), central south China  and southeast China  . The ManH. cordata was generally characterized by high genetic variation at species level (Shannon indices of 0.4338 and Nei’s gene diversity of 0.2820) and low genetic variation within population . These results were similar to those obtained using other molecular markers (such as RAPD and SSR) previously in a much smaller sample size [H. cordata was restricted to refugia with an endurable temperature, and such areas were expected to be small. One of the major genetic consequences of long-term habitation at a small population size is high levels of genetic drift [The genetic structure of plant populations reflects interactions amongst a range of different processes, including the long-term evolutionary history of the species , mutation, genetic drift, mating systems, as well as gene flow and selection . In thisple size . This heic drift ,18. ThisGST) of the species was 0.6728, the proportion of diversity among populations based on the Shannon indices was similarly high (67.42%); correspondingly, the estimate of gene flow (Nm) is low (0.2431); and the AMOVA test also showed that there was high genetic diversity among populations (77%) and low genetic diversity within the population (23%). H. cordata is a relic of its agamic race [H. cordata is a polyploidy complex with 36 to 126 chromosomes [H. cordata might have survived in Southwest China during the last Pleistocene glaciation. The route extended southeastward of Southwest China along the Yungui Plateau Range, where the present distribution pattern appeared. The strong differentiation among populations may be mainly due to subsequent genetic drift and natural selection. Genetic drift changes the distribution of genetic variation either by reducing variation within a population or by increasing the differentiation among populations [H. cordata in China took on an overall pattern of eastward expansion, the lack of significant correlation between genetic distance and geographical distance supports the hypothesis of historical relationships and the subsequent action of genetic drift accounts for current-day patterns of variation.The individuals in different regions were not from the same migratory routes derived from distinct sister groups that once lived in the refuge. In the present study, 15 sampled populations were collected from 13 provinces in China. Latitude and longitude of the areas vary from 21°12′ (N) to 34°36′ (N) and from 101°31′ (E) to 119°36′ (E), respectively. Different geographical distribution ranges, the intricate landform and the weather conditions of the sampled populations might have limited migration. In this study, the coefficient of genetic differentiation  did not stand alone in these analyses, it is necessary to deliberate in classifying it as a new species.A new species nd bract . HoweverH. cordata in China, to ensure that as many as possible separate populations are targeted for conservation rather than a few selected populations. Ex situ conservation may also be appropriate, because the total genetic diversity in a population of H. cordata may be adequately captured in only a few plants from the wild, which would not be the case for species with high levels of genetic diversity within a population. It would be beneficial to find ways to strengthen the gene flow between populations to maintain the natural genetic variation of H. cordata. Considering the high genetic differentiation among the wild populations, preservation of only a few populations may not adequately protect the genetic variation within the species in central China. Therefore, several populations throughout the entire range of the species in the country should be considered for conservation.Our results also provide theory for further protection of the germplasm resources. The low levels of genetic diversity within a population and the low gene flow among populations point towards the possibility of the possession of unique genotypes in a single population that are not found in other populations. It is therefore imperative for conservation planners, when designing conservation strategies for wild populations of H. cordata Thunb from 15 populations located in the natural distribution of the species in 13 provinces of China 8C, #810(GA)8, # 811(GA)8C, #812(GA)8A, #825(AC)8T, #826(AC)8C, #848(CA)8RG, #850(GT)8YC, and #873(GACA)4) that produced clear bands were chosen for all the 266 individuals in subsequent PCR reactions. For each primer analyzed, amplification was repeated once in the same situation to test the reproducibility of the ISSR bands, with a sample composed of two or three individuals selected randomly from each population.Genomic DNA was extracted from the leaves of each individual using CTAB protocol , dissolv2, 0.21 mM dNTPs, 200 nM primers, 1.0 unit of Taq polymerase and double-distilled water. Amplification was performed in a PTC-100 thermal cycler  programmed for an initial step of 3 min at 94 °C, followed by 35 cycles of 1 min at 94 °C, 1 min at 50 °C or 52 °C and 1.5 min at 72 °C, and a final 8 min extension at 72 °C. A negative control reaction without template DNA was also included to verify the absence of contamination. PCR products were separated in 1.2% agarose gels buffered with 1× TBE. Only bands reproducible in different PCR reactions were further analyzed. Bands with similar migration distance amplified from different individuals were considered homologous. A positive control  and a Gene Ruler DNA 100 bp ladder (Bio Basic Inc.) were run on each gel for homology assessments of PCR products on different gels.PCR amplification was performed in a 10-μL reaction volume containing about 20 ng of template DNA, 1.0 μL 10× PCR buffer, 2.0–2.2 mM MgClThe presence or absence of a PCR band was scored as 1 or 0, respectively. Two people scored the bands together in order to minimize the scoring of artificial bands. Only bands that were consistently amplified were considered, while smearing and weak bands were excluded. We refrained from pruning the loci that fulfilled Lynch and Milligan’s  criterioNe), Nei’s gene diversity (H) [I) [Pp). To examine population genetic structure, the proportion of genetic divergence was estimated within and among populations as described by Nei [GST was designated as the coefficient of gene differentiation among populations. The genetic identity (GI) and the genetic distance (GD) among populations were also computed using the model presented by Nei [Nm) were calculated as Nm = (1 – GST)/4GST [et al. 1992, which estimates and partitions total molecular variance within and between populations and then tests the significance of partitioned variance components using permutational testing procedures. When the data are binary, AMOVA calculates the ΦPT value, which is analogous to Fst representing the proportion of the total variance among populations [Four genetic diversity parameters were analyzed using POPGENE (version 1.31) : effectisity (H) , Shannon (H) [I) , and perd by Nei , and GSTd by Nei . Gene flST)/4GST . Differeulations –32.http://www.oup-usa.org/sc/0195135857). The relationship between latitude and longitude and the molecular indices was calculated as a two-polynomial regression. Correlations were calculated with software SAS version 6.12.An unweighted pair group method using an arithmetic average (UPGMA) dendrogram was performed on the data matrix of mean character difference between pairs of samples with software MEGA version 2.1 (downloaded from the website at Finally, a Mantel correlation test  was applH. cordata in China. This genetic structure probably reflected the historical association among populations, and subsequent severe genetic drift of small and isolated populations further promoting random divergence among populations. The observed genetic structure of the populations implies that as many populations as possible should be considered for both in situ and ex situ conservation practices on this species.In summary, ISSR analysis revealed low genetic variations within a population but high genetic differentiations among populations in the medical herb


Principal Components Analysis showed that the Xavante Indians are concentrated in the Amerindian axis near other populations of known Amerindian ancestry such as Karitiana, Pima, Surui and Maya and a low degree of genetic admixture was observed. This is consistent with the historical records of bottlenecks experience and cultural isolation. By calculating pair-wise Fst statistics we characterized the genetic differentiation between Xavante Indians and representative populations of the HapMap and from HGDP-CEPH project. We found that the genetic differentiation between Xavante Indians and populations of Ameridian, Asian, European, and African ancestry increased progressively. Our results indicate that the Xavante is a population that remained genetically isolated over the past decades and can offer advantages for genome-wide mapping studies of inherited disorders.Characterization of population genetic variation and structure can be used as tools for research in human genetics and population isolates are of great interest. The aim of the present study was to characterize the genetic structure of Xavante Indians and compare it with other populations. The Xavante, an indigenous population living in Brazilian Central Plateau, is one of the largest native groups in Brazil. A subset of 53 unrelated subjects was selected from the initial sample of 300 Xavante Indians. Using 86,197 markers, Xavante were compared with all populations of HapMap Phase III and HGDP-CEPH projects and with a Southeast Brazilian population sample to establish its population structure Knowledge of genetic diversity patterns of human populations provides important insights of their evolutionary history and is useful in genetic mapping studies of complex diseases and their component traits th century in the Brazilian Central Plateau and this period was marked by epidemics, armed conflicts and forced labor imposed by the Portuguese colonial government. In the middle of 19th century, in an attempt to escape mistreatment, they moved westward to their present habitat and remained relatively isolated until the early 20th century. In the 1940s Brazilian government decided to stimulate settlements in its central region, considered a sparsely populated area, aiming to promote greater integration of this area with the rest of the country. As a result of this political decision the Xavante groups were forced to deal with the settlers and the post-contact period was characterized by epidemics and conflicts that resulted in a severe reduction of their population. By the end of the 1950s, the Xavante were reduced to small patches of settlements. However, in the last decades with the demarcation of their lands, health programs and establishment of peaceful contacts with non-Indians they experienced an increase in their population. Importantly, despite of the interaction with the outsiders, the Xavante maintain their own complex social organization and cultural values that were preserved over the years Xavante is an indigenous population living in Mato Grosso state, Central Brazil. They comprise approximately 10,000 individuals, one of the largest indigenous groups in Brazil, and are Jê-speaking people The aim of the present study was to characterize the genetic structure in Xavante Indians providing valuable baseline data for future genetic studies and to compare it with a Southeast Brazilian population A cross-sectional study was conducted in the Sangradouro Reservation, Mato Grosso state, Brazil. The initial sample of Xavante Indians was comprised of 300 individuals and blood samples were collected from each subject. Genomic DNA was extracted from peripheral blood leukocytes using a commercial kit .http://pngu.mgh.harvard.edu/~purcell/plink/) confirmed the presence of related individuals in this sample. Genetic data were used for obtaining maximum likelihood estimates of relationship among pairs of individuals using the ML-Relate software http://www.montana.edu/kalinowski/Software/MLRelate.htm). This approach uses simulation to determine which relationships are consistent with the empirical genotype data, comparing putative relationships with possible alternatives. Only main pairs of individuals, such as parent-offspring, full-siblings, and half-siblings, are identified by the software. The ML-Relate software was unable to estimate the relationships using the complete panel of SNPs , therefore we selected a set of approximately 10% independent markers (730 SNPs) to perform this analysis. The selection of unrelated individuals was conducted in several steps. The individual with the greatest number of relationships was identified and removed from the Xavante sample. Next, the relatedness was recalculated, generating other relationship structures. Again, the individual with the higher number of relatedness was removed and the relatedness was recalculated. This process was repeatedly made until we had only an unrelated sample. We identified 53 unrelated Xavante Indians in our sample.Individuals were genotyped in 731,442 SNPs using Human Omni Express Bead Chip plataform . Genome-wide pair-wise identity-by-descent (IBD) estimated using the PLINK package Genotype data from the HapMap project (Phase 3) The Indian leaders and the study participants were informed about the purposes of this study and gave their consent. The majority of the population gave their written consent, for the ones who were illiterate (14%), fingerprint impressions were used to document their approval. A Xavante health agent worked as an interpreter when necessary. This study was approved by Ethics Committee of Escola Paulista de Medicina, Universidade Federal de São Paulo and Brazilian National Ethics Commision (CONEP).Principal component analysis (PCA) was applied to genotype data to infer continuous axes of genetic variation using the SmartPCA program of the Eigensoft package st estimates were also computed by SmartPCA program to characterize the genetic differentiation between Xavante Indians and the populations of the final dataset.Pair-wise Fhttp://evolution.genetics.washington.edu/phylip.html) and visualized with HyperTree http://kinase.com/tools/HyperTree.html).Next, we investigate the genome-wide genetic distance among individuals of all populations using a distance matrix computed by the PLINK package We knew there was a familial structure in the Xavante Indians sample. Genealogical relationships can be represented mathematically as probabilities that individuals share zero, one, or two alleles identical-by-descent. All 731.442 markers were used to estimate the genome-wide pair-wise identity-by-descent using the PLINK package, confirming the presence of related individuals in our sample, as shown in The ML-Relate software was used to select unrelated individuals. Estimates of relatedness and relationship of main related pairs  are computed by maximum likelihood approach. After the removing process, a subset of 53 unrelated Xavante Indians were selected for the genetic population structure analysis. In The group of 53 Xavante Indians was merged with HapMap, HGDP-CEPH, and São Paulo databases and the set of markers genotyped in all datasets was determined. The merged dataset is composed of 2,363 individuals  genotyped in 86,197 markers.. Although the São Paulo sample has been removed from our final dataset, we plotted the first three eigenvectors including it to illustrate the ancestry of the general Brazilian population, as shown in Ten continuous axes of genetic variation (eigenvectors) were computed using the Eigensoft package. Principal component analyses (PCA) using different subsets of populations were firstly performed to investigate which populations were important for determine the genetic structure of the Xavante Indians. These datasets were composed by Xavante Indians and, respectively: (a) only Amerindians samples; (b) Amerindians and Asians samples; (c) Amerindians, Asians and São Paulo samples; (d) the complete dataset. Three-dimensional plots were provided to all analyses, considering the first three principal components. Comparing plots of each subset of populations, we decided to remove São Paulo and GHI samples from the final dataset for PCA, since these two populations do not enhance the determination of the eigenvectors of the Xavante sample. Thus the final dataset for PCA was composed by Xavante Indians and all populations of HAPMAP and HGDP projects, excluding only São Paulo and GHI samples. A principal component analysis was then performed using this final datasetWe also studied the genetic similarity at the individual level from a genetic distance matrix obtained by calculating the complementary values of the genome-wide average proportion of alleles identical-by-state shared among pairs of individuals from all studied samples. The results of a neighbour-joining tree analysis are shown in st estimates were also computed by the SmartPCA program of the Eigensoft package for all populations of our final dataset with more than 6 sampled individuals. The genetic differentiation between Xavante Indians and representative populations of the European, Asian, African, and Amerindian ancestry are shown in Pair-wise FIn this study we compared the genetic variation of 2,363 individuals  genotyped in 86,197 markers. Our results showed that the Xavante population has a low level of genetic admixture. This is consistent with the historical records of bottlenecks experience, cultural isolation with subsequent reduced gene flow. Despite using different methodologies, which difficult the comparison, our data are consistent with previous studies that have shown low level of admixture in the Xavante population suggesting that no significant changes in this villagés gene pool has occurred over last decades Genetic studies of isolated populations have been subject of interest since they may help to map genes underlying simple monogenic, as well as, complex diseases. In isolated populations, monogenic disorders are less likely to show non-allelic heterogeneity Principal component analyses demonstrate that the Xavante population is a distinct ethnic group more closely related to individuals of Amerindian ancestry and genetically distinct from other HapMap and HGDP populations and from São Paulo individuals.st statistics, we found that the genetic differentiation between the Xavante population and representative populations of Amerindian, Asian, European and African ancestry increased progressively. These results are consistent with the Americas history of peopling that suggests a main colonization event from Siberia. The migration of humans from Eurasia to the Americas took place via Bering Strait and spread throughout North, Central and South Americas, diversifying into several culturally distinct native populations By calculating pairwise FThe findings from this study add to our understanding of genomic variation across the South American native populations and confirm that the Xavante is a closed Indian population that can provide a unique opportunity for genome-wide mapping studies of inherited disorders.


Trypanosoma cruzi, the causative agent of Chagas disease, is subdivided into six discrete typing units  of which TcI is ubiquitous and genetically highly variable. While clonality is the dominant mode of propagation, recombinant events play a significant evolutive role. Recently, foci of wild Triatoma infestans have been described in Bolivia, mainly infected by TcI. Hence, for the first time, we evaluated the level of genetic exchange within TcI natural potentially panmictic populations . T. infestans, belonging to six populations were characterized at eight microsatellite loci. For each population, Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD), and presence of repeated multilocus genotypes (MLG) were analyzed by using a total of seven statistics, to test the null hypothesis of panmixia (H0). Seventy-nine TcI stocks from wild 0; for another one the low size did not allow us to conclude, and for the two others the tests have given contradictory results. Interestingly, apparent panmixia was only observed in very restricted areas, and was not observed when grouping populations distant of only two kilometers or more. Nevertheless it is worth stressing that for the statistic tests of "HWE", in order to minimize the type I error (i. e. incorrect rejection of a true H0), we used the Bonferroni correction (BC) known to considerably increase the type II error . For the other tests (LD and MLG), we did not use BC and the risk of type II error in these cases was acceptable. Thus, these results should be considered as a good indicator of the existence of panmixia in wild environment but this must be confirmed on larger samples to reduce the risk of type II error.For three populations, none of the seven statistics allowed to rejecting H Trypanosoma cruzi is the causative agent of Chagas disease, which affects about eight million people in Latin America, of whom 30–40% either suffers or will develop cardiomyopathy, digestive megasyndromes, or both. Moreover, Chagas disease is becoming an emerging health problem in nonendemic areas because of the increasing number of migrants from endemic areas [T. cruzi species exhibits a very high genetic variability similar to that observed within different species of other kinetoplastidae such as Leishmania [T. cruzi [ic areas . The T. ishmania . ConsensT. cruzi ; TcI is T. cruzi . The lonT. cruzi –9, mitocT. cruzi ,11, and T. cruzi –14. In aT. cruzi , occurreT. cruzi . SeveralT. cruzi  and are T. cruzi : “From aT. cruzi at the DTU level [Triatoma infestans vectors mainly infected by TcI have been recently described in Bolivia [T. cruzi TcI populations isolated from sylvatic T. infestans in Bolivia.In general terms, to test panmixia, two prerequisites are needed: (i) the use of an appropriate genetic marker not subjected to selection and with a sufficient level of polymorphism and (ii) populations isolated in restricted areas where parasites are assumed to be in sympatry. Our previous work showed that microsatellite markers are relevant for studying the population genetics of TU level . Moreove Bolivia ,21; hencT. cruzi stocks, previously assigned to the DTU TcI using the multiplex miniexon PCR method [T. infestans populations (see T. infestans vector can move freely (maximum distance between two stocks less than five hundred meters). Four of them are located in La Paz department , while the other two populations are located in Cochabamba department . The distances between the populations are given in ® software  was used to characterize the alleles.Seventy-nine R method  and isolions see  were comions see . These pFis, while genetic recombination was explored through linkage disequilibrium analysis  and the presence / absence of repeated multilocus genotypes (MLG). A previous study, based on simulations and aiming to estimate the level of clonal reproduction in diploids [Fis (mean and variance) and LD estimators.“For a majority of pathogens, including the Trypanosomatidae family, the reproductive strategy was mainly deduced from population genetics analysis” . Here, tdiploids  advised Fis is a measure of inbreeding of individuals within a subsample; it also represents the deviation from random union of gametes and varies from −1 (fixed heterozygous) to +1 (fixed homozygous) via Fis = 0 (Hardy-Weinberg equilibrium). This Wright F-statistic [f. Negative values of Fis (excess heterozygosity) can be caused by accumulation of mutations in an ancient clonal lineage, a phenomenon called the Meselson effect [Fis correspond to inbreeding within the sample, a particular case being the Wahlund effect, when the sample comes from heterogeneous and structured populations. It is worth noting that if the mean Fis values are good estimators of HWE, low Fis values associated with substantial variance of Fis among loci (with some loci displaying an extreme heterozygote deficit and others an extreme excess) can reveal very low levels of sex (cryptic sex) [0 = panmixia) were generated by randomizing the relevant unit . Here, to test HWE within the subsamples, the alleles were permuted among individuals within each subsample and Fis was used as a HWE estimator, while for testing the overall HWE, alleles were permuted among subsamples and Fit was used as an estimator. Moreover, since the presence of null alleles artificially increases Fis estimations, we tested the impact of null alleles on the increased Fis values.tatistic  was estitatistic  called fn effect , and aren effect . Positivtic sex) . All staA [d) which is independent of the number of loci [G-statistics [P-value of this test is obtained as follows: genotypes at the 2 loci are associated at random a number of times and the statistic is recalculated on the randomized data set; the P-value is estimated as the proportion of statistics from randomized data sets that are larger or equal to the observed and (iii) by comparing the observed number of MLGs and the frequency of the most frequent MLG to the expected ones in simulated panmixia. As for Fis, all the LD statistical tests are based on H0 = panmixia .Linkage disequilibrium (LD) is another measure of deviation from panmixia. Here it was estimated in three different ways: (i) by the classical index IA , which h of loci ; (ii) byatistics ; the P-vp-value , which is the threshold for rejecting H0, by the number of comparisons. For example, testing eight loci within seven different populations leads to 56 comparisons and theoretically α (0.05) would become α′ = α / 56 = 0.00089. Nevertheless, the Bonferroni correction entails a high risk of falsely accepting H0 (bias towards Type II error) and therefore masking real deviations from panmixia. Teriokhin et al. [0 is rejected, and if it is not true, H0 is not rejected ; for example here with 8 loci, to test the genotype association at two loci by using G-statistics there are 26 comparisons and hence 26 values of G-Statistics: if 3 of them are below 0.05 the binomial test ”) give a no significant P-value of 0.1386, meaning that 3 values under 0.05 out of 26 are not sufficient to reject Ho; in reality we need 4 values below 0.05 out of 26 to reject significantly H0 . Because rejecting or accepting the null hypothesis is crucial here, we chose to use and discuss all the p-values .LD and HWE tests are based on multiple comparisons, so the Bonferroni corrections should be applied; this consists in dividing the n et al.  suggesteFis, LD, and MLG, we examined nine subsamples: the six populations under study ; the subsample “overall Sapini,” which clusters the two populations from Sapini (Sap-Sap + Sap-Cosi); the subsample “overall Quillacollo,” which clusters the two populations from Quillacollo (Qui-Urk + Qui-Bsia); and the “overall” sample including all stocks (N = 79). The different indices and p-values were associated with their level of significance . As several tests were applied for Fis, LD, and repeated MLG, a decision about accepting or rejecting H0 is proposed in each case, namely “reject H0” or “not reject H0” when all tests are congruent, and “ambiguous” when at least one of the tests gave a discordant result.To test Fis, (ii) the “binom.test” function in R to test the null hypothesis about the probability of success in Bernoulli’s experiments, (iii) MicroChecker v.2.2.3 [A and ȓd indices and to test the probabilities of repeated MLG and different MLG, (v) Populations  to build a general clustering analysis between all stocks using the Cavalli-Sforza and Edwards’ chord genetic distances [To process the data, different programs were used: (i) the HierFstat package  in R 3636 to com v.2.2.3  to test  v.2.2.3  for IA aistances , and  and within the 21 reference strains. Details of the origin and allelic microsatellite composition of each stock studied are listed in Genetic diversity was explored within the six local wild Fis over 1264 alleles, hence 3.40%, which is already very low. The proportion of observed null alleles in this sample  is lower than expected . Thus, the role of null alleles in inflated Fis may be considered here as negligible.Null alleles: Only two stocks from the Luribay population did not amplify at locus MCL08 and one reference stock at locus A427. Analyzing the six potentially panmictic populations with MicroChecker, 43 null alleles were expected at loci presenting high Fis by locus and by population are listed in n = 21) is by far the most polymorphic. Moreover, 42 alleles out of 82  were specific to reference strains  to 1.00 , while only positive Fis values were observed for the reference population (ranging from 0.30 to 0.82) as is expected when pooling differentiated reproductive units within a single subpopulation [Overall polymorphism: The main indices of genetic diversity as well as observed and expected heterozygotes and ains see . Eighty-ains see . The numpulation . The meaFis among populations: Fis values per population and their 95% confidence intervals are shown in Fis values were also examined by grouping the most adjacent populations, Sap-Sap with Sap-Cosi (1.9 km apart), Qui-Urk with Qui-Bsia (3.3 km apart), and all the populations . Fis varied from −0.08 (Qui-Urk population) to 0.29 . Considering the significance using the Bonferroni correction (BC), none of the Fis were significant , a direct measure of LD, and (iii) a special index (ȓd) derived from IA. These indices and their associated significance are given in 0 was not rejected in four of them ; two results were ambiguous  and three rejected H0 .Linkage disequilibrium (LD): three parameters were tested: (i) the proportion of significant LD tests over the total number of comparisons by pairs of loci, using the binomial test, (ii) the association index , not rejected in five populations  and ambiguous in three populations .Repeated multilocus genotypes: We tested two parameters, the number of different MLGs and the maximum frequency of the most repeated MLG. The results showed  that H0 Fis, LD, and MLG were “no rejecting H0” , while in the two others (Mecapaca and Sap-Sap) contradictory results were observed between the different tests of panmixia. Nevertheless, for the only Fis tests within the populations from Luribay and Sap-Cosi, there is a potential risk of type II errorConsidering only the six potentially panmictic populations under study, in four of them  the decisions for T. cruzi populations  sampled in restricted areas, true panmixia cannot be excluded. In the case of Luribay and Sap-Cosi, the FIS tests required the Bonferroni correction to lead to the decision “no rejecting Ho”, carrying a high risk of Type II error. However, as Qui-Bsia has a small size (N = 4) and that we cannot rule out a statistical type II error in this case, we must consider only three panmictic populations Luribay, Sap-Cosi, and Qui-Urk. For the two other populations, the tests gave contradictory results in Sap-Sap and ambiguous results for LD tests in Mecapaca, which appears “more panmictic” than Sap-Sap. In this case we could infer a lack of power of the tests to explain these results; nevertheless, and except for Qui-Bsia where the sample size is very small, a high β error value (type II error) is unlikely because for comparable population sizes the tests can reject or not reject H0. Moreover, multiplying the tests decreases the probability of type II error and increases the power of the test. Hence we can consider that no rejection of H0 is equivalent to accepting panmixia, possibly except for Qui-Bsia. Moreover, it is interesting to note that the tests were very sensitive to the Wahlund effect (sampling from heterogeneous populations): when we grouped all six populations , all the tests became highly significant, proving the heterogeneity between populations at the regional level. This was true to a lesser extent for overall Sapini and overall Quillacollo, showing a genetic structure at a very low geographic scale (a few kilometers).As previously recommended , we used0. As nobody knows precisely what sympatry means for this parasite, we picked up the populations within a very small area, not more than 1 ha, in which the triatomes and mammal hosts are assumed to move enough to allow parasite transmission from one host to another and hence generate opportunities for genetic exchanges; we named these populations “potentially panmictic” and tested them. Consequently, in such populations, when H0 is not rejected, and excluding a type II error discussed above, we can consider, a posteriori, that these populations were truly sympatric. Inversely, when H0 is rejected by some tests, as is the case for the Sap-Sap population and to a lesser extent for Mecapaca, a Wahlund effect due to a hidden genetic structure (itself possibly due to a lack of sympatry) could be inferred. Interestingly, when we analyzed the microsatellite data by the software Structure [0 for some tests within these two populations (data not shown). Meanwhile for these two populations, choosing between the two alternative hypotheses  is almost impossible. Sampling in areas that are not actually sympatric may therefore result in falsely rejecting H0. Inversely, as previously stated by others [0 rejection cannot be attributed to this sampling bias. All these remarks emphasize the importance of sampling design to test the hypothesis under study, for example here, to test panmixia, we need potential sympatric areas, not allopatric areas.To test panmixia, the first condition is natural sympatry; indeed, a nonsympatric sample may lead to genetic structuring and generate a Wahlund effect and consequently a false rejection of Htructure , we showy others , selectiT. cruzi has been considered by most authors to have a basically clonal population structure, with occasional bouts of genetic exchange or hybridization. These facts were confirmed on many occasions with other genetic markers and a clonal theory of parasitic protozoa was proposed [Plasmodium falciparum in which sex occurs [Trypanosoma and Leishmania genera [T. cruzi is not trivial, nor needless. Because of a reduced or absent gene flow, clonality must have a major impact on the biological and medical properties of the parasites, which has been explored [in vitro [T. cruzi evolution (generating new DTUs). It is generally admitted that two hybridization events have defined the population structure of T. cruzi [in vitro hybrids showed a fusion of parental genotypes, loss of alleles, homologous recombination, and uniparental inheritance of kinetoplast maxicircle DNA [FIS, LD, etc., like here). Because we do not know the cytological mechanisms involved, we named these events “recombination-like” in order to differentiate them from the known genetic exchanges involving meiosis in sexual diploids. One of the first studies regarding this event [T. cruzi, (i) using genomic CNV (copy number variation) [T. cruzi has definitively became obsolete; this species obviously has used both mechanisms to evolve and probably to adapt to its multiple hosts, associated with an extraordinarily plastic genome shaped by clonal evolution and several kinds of genetic exchanges. The mode of reproduction of T. cruzi could oscillate between clonality and sexuality and the true questions are why, when, how, and to what extent T. cruzi recombines? Nevertheless, we agree with Tibayrenc and Ayala’s [T. cruzi since the same MLGs can be sampled at different times and in distant regions. The same authors stated that “recombination seems easier between closely related genotypes pertaining to the same near-clade in both fungi and parasitic protozoa”; this probably constitutes the most parsimonious explanation for the co-occurrence of recombination at restricted space / time levels and of clonality at larger space / time scales. Interestingly, in bacteria “the probability of acceptance of a recombination event decreases exponentially with genetic distance between the donor and recipient DNA” [T. cruzi and should be further investigated.Since the pioneering studies using isoenzymes , T. cruzproposed ,42 with x occurs ; the thea genera  and extea genera . The queexplored ,47. On tin vitro  and has rcle DNA , and it rcle DNA . In addircle DNA ,11 and ercle DNA  using thrcle DNA . The lasis event , reporteis event , TcI in is event , and TcIis event : in the riation) ; (ii) anriation)  reportedriation)  showed t Ayala’s  definitient DNA” , which ient DNA” ; this coT. cruzi TcI populations isolated from wild T. infestans in Bolivia. In absence of additional studies involving other sylvatic vectors, it is not possible to associate panmixia with the sylvatic biotopes; further studies of panmixia should be conducted in other biotopes where parasites should be sympatric. As previously mentioned, “mixed clonal / sexual reproduction is nearly indistinguishable from strict sexual reproduction as long as the proportion of clonal reproduction is not strongly predominant” [Leishmania genome is aneuploid [T. cruzi, as suspected [Fis in the trisomic state (excess heterozygosity) and artificially increasing Fis in the monosomic state (excess homozygosity). Hence, all the Fis results should be interpreted with caution, especially when there is a substantial variance of Fis between loci. Moreover, Fis is not linearly related to the rate of clonal reproduction [For the first time we report panmixia, notably through linkage disequilibrium statistics, in ominant” , so, altneuploid , every cuspected , there coduction . As statoduction , “taking


Eumetopina flavipes), through an archipelago of significant Australian quarantine concern. Analysis of eight microsatellite loci from 648 individuals suggests that frequent, wind-assisted immigration from multiple sources in Papua New Guinea contributes significantly to repeated colonization of far northern islands. However, intermittent wind-assisted immigration better explains patterns of genetic diversity and structure in the southern islands and on the tip of mainland Australia. Significant population structuring associated with the presence of clusters of highly related individuals results from breeding in-situ following colonization, with little postestablishment movement. Results also suggest that less important secondary movements occur between islands; these appear to be human mediated and restricted by quarantine zones. Control of the planthopper may be very difficult on islands close to Papua New Guinea given the apparent propensity for multiple invasion, but may be achievable further south where local populations appear highly independent and isolated.The use of a multidisciplinary approach is becoming increasingly important when developing management strategies that mitigate the economic and biological costs associated with invasive pests. A framework of simulated dispersal is combined with life-history information and analyses of population genetic structure to investigate the invasion dynamics of a plant disease vector, the island sugarcane planthopper ( The environmental and economic costs of biological invasions and pest management are key issues for many countries  is a significant invasive agricultural pest because it is the only known vector for Ramu stunt disease of sugarcane  and in the northern peninsula area (NPA) of Cape York  . Whole insects were sent to the Australian Genome Research Facility Limited for their standard DNA extraction, PCR amplification and microsatellite genotyping at eight polymorphic loci. For PCR, initial denaturing was at 94°C for 5 min, 35 amplification cycles of 94°C for 30 s, annealing temperature  and observed heterozygosity (HO) in Arlequin. Locus-by-locus departure from Hardy–Weinberg equilibrium was tested by determining significance of the inbreeding coefficient FIS (heterozygosity deficit), with 10 000 permutations in Arlequin. All multiple comparison P values were corrected for false discovery rate , therefore, FST was suitable.Population genetic characterization was done by calculating the expected (FST [FST/(1−FST)] and the natural log of pairwise geographical distances between locations in the TS/NPA  mainland Australia (NPA) (Bamaga and New Mapoon), (ii) Special Quarantine Zone  and (iii) Torres Strait Protected Zone . Significance of P was assessed with 10 000 permutations in Arlequin.Overall genetic differentiation throughout the TS/NPA was assessed with T Wright  using anFST analyses, the Bayesian clustering method implemented in Structure v 2.2.3  in our data was unknown, Structure was used to assign individuals into the most likely K. We evaluated results for K = 1 to K = 33, being no genetic structure at all (K = 1) to every sampled population being genetically distinct (K = 31). Estimates of K were based on 10 iterations, each with a burn in of 50 000, and Markov Chain Monte Carlo (MCMC) lengths of 100 000 using the admixture model and correlated allele frequencies. The optimal value of K was based on both log probabilities [Pr (X|K)] and ΔK  were pooled, and an allelic dropout rate of 0.1%, and 1.5% for other errors were assumed. Female monogamy and male polygamy were selected because it appears unlikely that female planthoppers mate repeatedly, whereas multiple mating by males is common . Running analyses with and without 1-TER-327 did not significantly change any outcomes, so this locus was included in all analyses.A total of 648 individuals from 31 populations were sampled from locations throughout the TS/NPA . All eignificant . HoweverFIS value at 6-TER-827 was an order of magnitude larger than that of other loci . Isolation by distance calculations were conducted with and without these three populations. In no instance did their inclusion alter result significance, so results presented are from analyses containing all populations.The her loci . FurtherSignificant linkage disequilibrium occurred in most populations even after correction. This result was not unexpected, given that populations in this study may have been influenced by evolutionary processes such as founder effects and inbreeding following introduction, which are known to cause linkage disequilibrium Slatkin . ImportaFST and the natural log of geographical distance   . DespiteR2 = 0.75, F1, 29 = 91.57, P < 0.001; R2 = 0.32, F1, 29 = 13.81, P = 0.001). Thus, population genetic diversity decreases with increasing distance from PNG. Conversely, mean population FST significantly increased with distance from PNG, which explains 77% of the variation in FST  suggests that significant population genetic differentiation occurs throughout the TS/NPA. Of the total variation, 68% occurred within populations, with the remaining 32% variation among populations also significant. After correction for false discovery rate, 463 of the 465 population pairwise FST comparisons were significant. Populations sampled in both years from the same host plant patch were significantly genetically different between years of sampling . Only Badu 1 and 2 (both sampled 2006) and Saibai 3 and 4 (both sampled 2008) were not significantly different from each other . Results of the hierarchical amova indicated that significant regional structuring also occurs, where 16.6% of the overall variation was attributed to quarantine zone. However, only 20.06% variation occurs among populations within quarantine zones, which is low when compared with the 63.34% of variation that occurs within populations . So although significant, grouping populations by quarantine zone only weakly explains population genetic structuring in the TS/NPA. The majority of genetic differentiation is explained at the individual population level.A global K = 26 (−11745.70) (K statistic peaked at K = 26 (3.93)  and K = 10 (2.88)  . Using t1745.70) , the ΔK 6 (3.93) . Examinapatterns A. First,patterns A. Secondpatterns A. ΔK als0 (2.88) . K = 3 wthey did B. Evannothey did  note thathey did  warn thaThe Colony analysis suggests the presence of significant family structure throughout the TS/NPA; a total of 10 845 dyads  occurred with over 0.9 probability. Plots of the change in Log-likelihood values as a function of the number of iterations from each of the replicate runs were consistent, indicating that the annealing procedure produced convergence and was powerful , and many individuals sampled at the two locations were half-sibs. Waiben and Ngurupai islands are geographically ‘next door’. When the owner of the sugarcane plants at Ngurupai 3 was interviewed, she stated that she had obtained her plants from Waiben 1. Similar linear sib-ships occur across New Mapoon 1–2, Waiben 1 and Ngurupai 1–2, as well as between Ngurupai 1, 2 and 3. Further examples of such directional across-location sib-ships are evident between Badu 1–2 and Saibai 1, 2 and 3, where a number of individuals from Saibai are related at both full- and half-sib level to the majority of individuals at Badu 1–2.Colony suggests that two individuals sampled from Waiben 1 were full-sibs to the majority of individuals at Ngurupai 3  is removed from the stalk, dried in the sun and then burned, while the stalks are cut into smaller pieces and replanted. Levels of postplanting care varied, and appeared to determine whether the stalk would successfully grow. Long-term detection records indicate that E. flavipes has been present in the TS/NPA for at least 28 years, despite such cultivation practices. Intensive sampling during this study revealed that within a 2-year period local extinction/recolonization events occur and may be driven by cultivation practices as described above that remove entire host plants, causing the distribution and abundance of E. flavipes populations to change in both space and time  could significantly reduce E. flavipes infestation, and if publicly encouraged could achieve local or even regional eradication (Anderson et al. E. flavipes is unlikely, especially on islands close to PNG given the apparent propensity for successful invasion.In other systems, eliminating the dispersal pathway and/or a focus on reducing the size of the source population have been suggested for pest management (Russell et al. E. flavipes should be location specific. This is implied because populations in the northern TS that exhibit higher levels of genetic diversity will be more difficult to manage than those on the NPA, principally because of much higher levels of propagule pressure (Lockwood et al. E. flavipes favoured host material, and then followed by annual monitoring and further location-specific tip pruning if recolonization is detected, may achieve longer lasting control. Such a strategy may achieve permanent eradication in the southern TS given the apparent lower invasion pressure and reproductive isolation. There is some evidence that quarantine zones restrict gene flow throughout the region, but ultimately, anthropogenic movement cannot be prevented. However, a continuing tip-pruning management strategy would reduce the likelihood of an infested stalk being moved.Our results suggest that the type of management employed for E. flavipes is no exception. This study thus demonstrates how population genetics can inform an understanding of the drivers of dispersal and dynamics of population growth, and the relative importance of such factors in a system with multiple immigration pathways, differing levels of multidirectional movement and extinction/recolonization dynamics all placed within a highly fragmented landscape. By definition, invasive pest species exhibit characteristics such as high levels of propagule pressure promoted by the use of multiple dispersal pathways and genetic and life-history characteristics that favour establishment success and persistence (Lockwood et al. Invasions are often complex; results from this research show that


Aedes aegypti from the Brazilian Amazon, by using a 380 bp fragment of the mitochocondrial NADH dehydrogenase subunit 4 (ND4) gene. A total of 123 individuals were analyzed, whereby 13 haplotypes were found. Mean genetic diversity was slightly high . Two AMOVA analyses indicated that most of the variation (~70%-72%) occurred within populations. The variation found among and between populations within the groups disclosed lower, but even so, highly significant values. FST values were not significant in most of the comparisons, except for the samples from Pacaraima and Rio Branco. The isolation by distance (IBD) model was not significant  when the samples from Pacaraima and Rio Branco were excluded from the analyses, this indicating that genetic distance is not related to geographic distance. This result may be explained either by passive dispersal patterns  or be due to the recent expansion of this mosquito in the Brazilian Amazon. Phylogenetic relationship analysis showed two genetically distinct groups (lineages) within the Brazilian Amazon, each sharing haplotypes with populations from West Africa and Asia. Genetic variation was estimated in ten samples populations of  Aedes aegypti is the main vector of urban yellow fever and four dengue virus serotypes (DENV-1 to DENV-4). This mosquito is also involved in the transmission of other arboviruses and filarial helminthes which affect humans and several other animal species , pronounced rainy seasons and complex environmental and social factors. Currently, this vector is found in virtually all the towns of the Brazilian Amazon , its dispersion possibly having occurred via river traffic, a major travel route for persons and commercial trade between many localities of the region. Thus, studies in population genetics of these Ae. aegypti populations could provide knowledge on gene-flow patterns and colonization events, which would be important parameters for outlining new strategies for local and regional vector control.The Amazon region possesses ideal characteristics favoring rapid development of the life cycle, proliferation and longevity of ND4) gene has shown to be an excellent marker for analyzing the genetic population structure and colonization events in Ae. aegypti , Boa Vista and Pacaraima (state of Roraima), Rio Branco (state of Acre), and Coari and Manaus (state of Amazonas). With a view to micro-geographic analysis, individuals from four suburban neighborhoods of Manaus were sampled: Coroado, Praça 14 de Janeiro, Compensa, and Tancredo Neves . All individuals were sequenced in both directions.Genomic DNA was extracted individually from 4h) and nucleotides (π), the number of variable sites (NV) and the average number of nucleotide differences (K), were calculated by using the DnaSP program (D (Fs (h) and nucleotide (π) diversities, the average number of nucleotide differences (K) and sequence divergence (D) calculated between the two haplotype groups, were also obtained through the DnaSP program.Sequences were edited and aligned by means of the BioEdit  and Chroogram , were calculated using the Arlequin program (FST statistics (Nm), which provides an estimate of gene flow between sub-populations, was obtained through FST values. The correlation between genetic (FST) and geographic (km) distances was estimated by using Mantel's test . Geographic distances for this analysis were obtained from the GPS and those in the Google Earth program. Levels of significance were adjusted by the Bonferroni correction whenever there were multiple tests  and Anopheles marajoara (GenBank accession number: AY846347) were employed as outgroups.Phylogenetic relationships among haplotypes were estimated by using the Mega program  in all the samples, this suggesting that these populations are in genetic equilibrium (The highest levels of both haplotype and nucleotide diversity were detected in the samples from Belém and two suburbs of Manaus (Coroado and Praça 14 de Janeiro) . The samilibrium .FST = 0.273; p < 10-5). In the second AMOVA test, the populations were grouped according to their respective states, the Amazonas group, comprising the four suburbs of Manaus  and Coari, the Pará group, comprising Santarém and Belém, the Roraima group with Boa Vista and Pacaraima, and the Acre group with Rio Branco. Similar to the first AMOVA analysis, the greater part of variation (70.66%) occurred within the populations themselves, with a highly significant value . The percentage of variation between populations within the states (18.87%) was also highly significant , whereas among the states, the percentage of variation (10.47%) was low and insignificant  (data not shown).Two analyses levels were used in the AMOVA test to verify the origin of genetic variation in the different hierarchical levels and groups. In the first, all the populations analyzed were considered as constituting a single group (island model), the highest variation occurring within the populations themselves (72.69%). Nevertheless, the percentage of variation was lower among samples (27.31%), even though highly significant  were observed, after Bonferroni correction, in most of the comparisons involving samples from Rio Branco, with the corresponding Nm values varying from 0.0 to 1.0, thereby indicating from an absent to a reduced gene flow  was obtained between samples from Compensa and Tancredo Neves, which was not significant after Bonferroni correction. This could be explained on considering that in Compensa only group II haplotypes were found, whereas in the samples from Tancredo Neves, haplotypes of two groups in similar frequencies were sampled.Significant ene flow . FST valr = 0.5815; p = 0.006) when taking all the populations into consideration, thereby suggesting isolation by distance (IBD). However, when the samples from Pacaraima and Rio Branco, the most genetically structured, were removed from the analysis, correlation was non-significant , thus indicating that gene flow is not related to geographic distance.The correlation between genetic and geographic distances was statistically significant  between groups I and II was 10.308, whereas nucleotide divergence (D) was 0.02713.Haplotype diversity within groups I and II was 0.6571 and 0.5276, respectively, whereas nucleotide diversity was 0.00590 and 0.00325, respectively. The average number of nucleotide differences , Boa Vista (83%) and Santarém (79%), it was totally absent in those from Tancredo Neves, Belém and Rio Branco. These findings suggest that gene flow is absent between Pacaraima and Rio Branco, and reduced between Pacaraima and Belém, and Boa Vista and Rio Branco see . H1 was On the contrary, H6 was absent in the samples from Pacaraima and Boa Vista, but was detected in all the others in this study. In an extensive study on the Americas, Africa and Asia, et al., 2002), Venezuela  may be coincident with demographic density being the highest in these two port-towns in north Brazil, besides their both being situated on the banks of two large rivers (Amazon and Negro), thereby being exposed to an intense flow of both persons and trade. Furthermore, the industrial center of Manaus is one of the largest in Brazil. These factors are likely to favor multiple introductions and/or the dispersal of Ae. aegypti from the Brazilian Amazon. Similar results were found in Mexico , which can probably be attributed to the presence of two genetically distinct sympatric haplotype lineages. The significant variation (27.31%) among populations (non-grouped) could be primarily due to the high genetic differentiation found between Pacaraima and Rio Branco, whereas the significant variation (18.87%) between populations within the states themselves could result mainly from the differentiation observed between Belém and Santarém (Pará group). This indicates that a significant genetic structure occurs in Nm = 35.1) due to the high frequency of H1 in both populations. The free gene flow (Nm = 13.1) between Belém and Tancredo Neves, about 1,284 km apart, was directly related to H6 frequency. Nevertheless, this result may indicate distinct introduction events followed by the recent expansion of Ae. aegypti in the Brazilian Amazon (less than 25 years) rather than the current gene flow.In this study, the gene flow pattern was related to H1 and H6 frequencies. In spite of the great distance between Santarém and Boa Vista (~880 km), gene flow was extensive  and have maintained low effective population sizes; or 2) the sizes of these populations were reduced due to the constant use of insecticides, thereby generating repeated bottleneck effects and/or populations founded by few individuals through cycles of extinction and re-colonization. Both effects could imply the reduction of genetic variability through genetic drift  the Rio Branco and Pacaraima ic drift , thus poAe. aegypti populations of five Brazilian states with RAPD markers, and found high levels of genetic differentiation and reduced gene flow at both the macro-geographic (Nm = 0.54) and micro-geographic (Nm = 0.69) levels. Nm = 0.65), even though from the same state (Nm = 0.83). Compared to the present study, these results suggest that levels of genetic variability and differentiation among Brazilian Ae. aegypti populations are relatively high. Nevertheless, most of the populations of the Brazilian Amazon analyzed here manifested higher gene flow, probably due to human migration and river or land trading movement, thereby favoring the dispersal of this vector in the region. Alternatively, this could indicate the recent expansion of Ae. aegypti throughout this area. The absence of isolation by distance, when the samples from Pacaraima and Rio Branco were removed from the analyses, supports these hypotheses. Identical results were found in samples from Mexico , this dispersal mechanism obviously not being a possible explanation for our results.All told, we observed higher rates of gene flow for populations of the Brazilian Amazon when compared to the two previous studies undertaken in Brazil. et al., 2002; COI gene in most of our samples (K (12.015) and D (0.03207) between the two haplotype groups than those disclosed in the present study. This could be related to the colonization history of these populations (Two haplotype groups were indicated through phylogenetic relationship analysis, which is in accordance with previous studies (Gorrrochotegui-Escalante Ae. aegypti into the Brazilian Amazon. Cluster analysis clearly showed two genetic lineages, each of which sharing haplotypes with West Africa and Asia, thereby suggesting that Brazilian Amazon populations probably originated from these regions. The existence of distinct lineages within the Brazilian Amazon could imply differences in the susceptibility for transmitting dengue and urban yellow fever viruses (Concluding, the data in this study indicate multiple introductions of