Population genetic structure and demographic history of the black fly vector,Simulium nodosum in Thailand

An understanding of the genetic structure and diversity of vector species is crucial for effective control and management. In this study, mitochondrial DNA sequences were used to examine the genetic structure, diversity and demographic history of a black fly vector, Simulium nodosum Puri (Diptera: Simuliidae), in Thailand. A total of 145 sequences were obtained from 10 sampling locations collected across geographical ranges in the country. Low genetic diversity was found in populations of S. nodosum that could be explained by the recent population history of this species. Demographic history analysis revealed a signature of demographic expansion dating back to only 2600–5200 years ago. Recent population expansion in S. nodosum possibly followed an increase in agriculture that enabled its hosts', humans and domestic animals, densities to increase. Alternatively, the Thai populations could be a derivative of an older expansion event in the more northern populations. Mitochondrial DNA genealogy revealed no genetically divergent lineages, which agrees with the previous cytogenetic study. Genetic structure analyses found that only 27% of the pairwise comparisons were significantly different. The most likely explanation for the pattern of genetic structuring is the effect of genetic drift because of recent colonization.     

Analysis of the expressed genome of the lone star tick, Amblyomma americanum (Acari: Ixodidae) using an expressed sequence tag approach

An expressed sequence tag (EST) approach was used to study the genome of two developmental stages of the lone star tick, Amblyomma americanum. cDNA libraries were constructed from the larval and adult stages of A. americanum. In total, 1942 ESTs were sequenced (1462 adult ESTs and 480 larval ESTs) and analyzed using bioinformatic programs. Contig assembly using the CAPII program revealed 11% and 15% redundancy of sequences in the larval and adult ESTs, respectively. Of the 1942 ESTs, 1738 sequences were considered quality sequences and of these, 771 or approximately 44.4% of the sequences were putatively identified based on amino acid identity using the protein Basic Local Alignment Search Tool (BLAST) algorithm. Putatively identified sequences were classified according to their predicted gene function. In total, 967 sequences, or 55.6% of the quality sequences, had limited or no protein similarity to previously identified gene products. Sequences lacking protein homology were analyzed using an automated sequence annotation system for predicted protein characteristics such as open reading frames, signal peptides, protein motifs, and transmembrane regions. In this paper we describe the sequencing of the largest number of ESTs obtained from an arachnid species to date and the subsequent detailed analysis of these sequences.     

Population structure,population history and DNA barcoding of fruit fly Bactrocera latifrons (Hendel) (Diptera: Tephritidae)

The fruit fly Bactrocera latifrons (Hendel) is an important pest of commercially significant plants such as chili, tomato and eggplant. The species is native to South and Southeast Asia, but has now invaded Japan, Hawaii and Africa. In this study, mitochondrial DNA sequences were used to infer genetic structure and demographic history of B. latifrons. The efficiency of DNA barcodes for identification of B. latifrons was also tested. Ninety‐three specimens infesting four host‐plant species were obtained from 11 sampling locations in Thailand. The mitochondrial haplotype network revealed no major divergent lineage, which was consistent with a phylogenetic analysis that found strong support for the monophyly of B. latifrons. Population pairwise F_ST revealed that most (65%) comparisons were not significantly different, suggesting a high rate of gene flow. Analysis of molecular variance (amova ) found no significant genetic differentiation among populations from different host‐plant species. Sharing of several haplotypes among flies from different host‐plants indicates that the flies were moved freely across the plant species. Demographic history analysis revealed that the population has undergone recent expansion dating back to the end of the last glaciation. Thus, the results indicate that both ongoing and historical factors have played important roles in determining the genetic structure and diversity of B. latifrons. DNA barcoding analysis revealed that B. latifrons specimens were clearly differentiated from other species with 100% correct identification. Therefore, cytochrome oxidase I (COI) barcoding sequences could be effectively used to identify this important pest species, which could encourage monitoring and control efforts for this species.     

Inferring the population structure and demographic history of the tick, Amblyomma americanum Linnaeus.

A hierarchial population genetic study was conducted on 703 individual Amblyomma americanum from nine populations in Georgia, U.S.A. Populations were sampled from the Coastal Plain, midland Piedmont region, and the upper Piedmont region. Twenty-nine distinct haplotypes were found. A minimum spanning tree was constructed that indicated these haplotypes comprised two lineages, the root of which was distinctly star-like. The majority of the variation found was among ticks within each population, indicating high amounts of gene flow and little genetic differentiation between the three regions. An overall F(ST) value of 0.006 supported the lack of genetic structuring between collection sites in Georgia. Mantel regression analysis revealed no isolation by distance. Signatures of population expansion were detected in the shapes of the mismatch distribution and tests of neutrality. The absence of genetic differentiation combined with the rejection of the null model of isolation by distance may indicate recent range expansion in Georgia or insufficient time to reach an equilibrium where genetic drift may have affected allele frequencies. Alternatively, the high degree of panmixia found within A. americanum in Georgia may be due to bird-mediated dispersal of ticks increasing the genetic similarity between geographically separated populations.     

间颅鼠兔的种群遗传结构和历史演化动态

本研究基于多个线粒体基因（包括COI、Cyt b、tRNA-Thr、tRNA-Pro、D-loop控制区部分序列共计2417bp）对间颅鼠兔（Ochotona cansus）的种群遗传结构和历史演化动态进行了研究。基于线粒体基因联合数据构建的贝叶斯树显示,间颅鼠兔分为两大支系：来自岷山山系东部的甘肃白水江和四川唐家河的种群组成了支系一;其余采样点的种群组成了支系二。基于以上基因所构建的单倍型网络图显示的遗传结构与贝叶斯树一致。贝叶斯聚类分析（BAPS）将间颅鼠兔分为4个地理种群。A种群包括甘肃白水江（BSJ）和四川唐家河（TJH）的样本;B种群仅包括四川卧龙（WL）的样本;C种群包括青海北部种群（GC、MY、QL）、青海南部-四川北部种群（JW、JZ、ZK、RE）、四川康定（KD）和陕西太白山（TB）的样本;D种群包括山西娄烦（LF）以及陕西吴起（WQ）的样本。基于线粒体基因构建的物种树进行支系分化时间的推测,结果显示4个地理种群的分化时间约为0.72 Ma、0.32 Ma、0.12 Ma, 这与造成青藏高原剧烈隆起的昆黄运动（1.10-0.60Ma）和共和运动（0.15Ma）发生时间基本吻合。采用中性检验、错配分布、扩展贝叶斯天际线（EBSPs）3种方法对间颅鼠兔的种群历史动态进行预测,分析结果显示间颅鼠兔在历史上并没有经历过显著的种群扩张,而且在末次盛冰期后开始衰减。生态位模型（ENM）预测结果表明：末次盛冰期时间颅鼠兔的潜在分布区比其现今分布区小,末次盛冰期比末次间冰期潜在分布区略大,表明间颅鼠兔受末次盛冰期影响较大。气候因子分析显示降水比温度对间颅鼠兔种群影响更大,推测降水对植被的演化影响显著,从而影响间颅鼠兔的食物来源和栖息环境。     

Population genetic structure and demographic history of the endemic Formosan lesser horseshoe bat (Rhinolophus monoceros)

Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. Taiwan formed around 5 million years ago from tectonic uplift, and has been connected to mainland Asia several times since its emergence. A central mountain range runs north to south, bisecting the island, and potentially impedes gene flow along an east-west axis. The Formosan lesser horseshoe bat (Rhinolophus monoceros) is endemic to Taiwan, where it is found mainly at low altitude. To determine the population structure and the demographic and colonization history of this species, we examined variation in the mitochondrial DNA control region in 203 bats sampled at 26 sites. We found very high haplotype and nucleotide diversity, which decreased from the centre to the south and north. Population differentiation followed a pattern of isolation by distance, though most regional genetic variance was attributable to differences between the relatively isolated southern population and those from other regions. A haplotype network was consistent with these findings and also suggested a southward colonization, followed by subsequent secondary contact between the south and other regions. Mismatch distributions were used to infer a past population expansion predating the last glacial maximum, and a neighbour-joining tree showed that R. monoceros formed a monophyletic grouping with respect to its sister taxa. Taken together, our results suggest that this taxon arose from a single period of colonization, and that demographic growth followed in the late Pleistocene. Current genetic structure reflects limited gene flow, probably coupled with stepwise colonization in the past. We consider explanations for the persistence of the species through multiple glacial maxima.     

Biochemical differentiation of lone star tick,Amblyomma americanum (L), salivary glands: Effects of attachment,feeding and mating

Salivary glands of female Amblyomma americanum (L.) are stimulated to differentiate by attachment to a host, subsequent feeding and mating. Incorporation of [³H]uridine into ribosomal and transfer RNAs as well as the synthesis of poly(A⁺)mRNA and protein parallel the pattern of increasing enzymatic activity and secretory ability of the glands. Unfed ticks contained 3.5 ± 0.47 ng poly(A⁺)mRNA/gland pr. By the second day of feeding this had increased more than 5-fold. The greatest amount of poly(A⁺)mRNA found in rapid-feeding phase females (body wt > 100 mg) was 370 ± 80 ng/gland pr. Poly(A⁺)mRNA mass doubles on the final day of feeding, just as the ticks exceeded 100 mg in wt. Ticks attached 1 to 10 days had increasingly greater amounts of salivary monosomes, 60 and 40S ribosomal subunits, and polysomes. Polysomal mass/gland pr also attained its maximum above 100 mg tick wt at the slow/rapid-feeding phase boundary; exceeding by 20 times that of unfed ticks. Degenerating glands from replete ticks continued to synthesize protein. In vitro incorporation of [³H]leucine was greatest within 24 h of attachment. Fluorographs of [³H]leucine labeled protein showed that mating caused a drop in incorporation after the 4th day of feeding. Glands from unmated females attached the same number of days continued to incorporate [³H]leucine at higher levels than those from mated females.     

Responses of the tick, Amblyomma hebraeum (Acari: Ixodidae), to carbon dioxide

We investigated the effect of physiological state of adult ticks (Amblyomma hebraeum Koch; Acari: Ixodidae) on their responses to a CO2-enriched atmosphere. Ticks were exposed to CO2 or air in an experimental chamber; we measured the effects on questing, movement and latency (the time after exposure to CO2 or air when ticks began questing or moving). This study confirmed the hypothesis that responsiveness to CO2 is enhanced during host-seeking periods of the life cycle and reduced at other times. Thus, whereas newly moulted ticks quested infrequently when exposed to CO2, questing increased over the 6 week period following moulting. Likewise, in 6 week old ticks, movement in CO2 was significantly greater than in air. When a partially fed female below approximately ten times its unfed weight is removed from a host, it reattaches if subsequently presented to another host. Such females quested vigorously in CO2 but not in air. When a partially fed female above approximately ten times its unfed weight is removed from a host, it usually does not subsequently reattach. Such females quested infrequently, there being no significant difference between air and CO2. Males removed from a host at any stage of feeding reattach readily when given the opportunity. They quested frequently, moved readily and the latency was very low in air or CO2. Exp Appl Acarol 22: 667–681 © 1998 Kluwer Academic Publishers     

秦岭地区赤胸梳爪步甲种群的遗传多样性和扩张历史分析（英文）

赤胸梳爪步Dolichus halensis (Schaller)（鞘翅目：步甲科）是重要的捕食性天敌昆虫,在我国分布广泛。为揭示其种群遗传多样性和扩张机制, 本研究以秦岭地区为中心,以线粒体Cox1 tRNALeu Cox2基因片段为分子标记,对来自于24个采集点共191个个体进行了检测分析。在长度为1 601 bp的碱基中共检测到45个变异位点,定义了53个单倍型,单倍型多样性高（H_d=0.796）,而核苷酸多样性较低（P_i=0.0033）。系统发育分析结果表明该地区该物种存在两大进化枝。分子变异分析（AMOVA）表明86.61%的变异来源于种群内。SAMOVA和PERMUT分析结果一致,表明秦岭地区分布的赤胸梳爪步甲种群不存在明显的谱系地理结构。中性检验和错配分布分析的结果一致,表明该物种在秦岭地区曾经发生过种群扩张。综上,认为赤胸疏爪步甲种群经历过冰期后的扩散。     

Genetic structure and demographic history of the melon fly Zeugodacus cucurbitae (Coquillet) (Diptera: Tephritidae) in Thailand

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Distribution and molecular characterization of Wolbachia endosymbionts and filarial nematodes in Maryland populations of the lone star tick (Amblyomma americanum)

The lone star tick Amblyomma americanum is host to a wide diversity of endosymbiotic bacteria. We identified a novel Wolbachia symbiont infecting A. americanum. Multilocus sequence typing phylogenetically placed the endosymbiont in the increasingly diverse F supergroup. We assayed a total of 1031 ticks (119 females, 78 males and 834 nymphs in 89 pools) from 16 Maryland populations for infection. Infection frequencies in the natural populations were approximately 5% in females and <2% (minimum infection rate) in nymphs; infection was not detected in males. Infected populations were only observed in southern Maryland, suggesting the possibility that Wolbachia is currently invading Maryland A. americanum populations. Because F supergroup Wolbachia have been detected previously in filarial nematodes, tick samples were assayed for nematodes by PCR. Filarial nematodes were detected in 70% and 9% of Wolbachia-positive and Wolbachia-negative tick samples, respectively. While nematodes were more common in Wolbachia-positive tick samples, the lack of a strict infection concordance (Wolbachia-positive, nematode-negative and Wolbachia-negative, nematode-positive ticks) suggests that Wolbachia prevalence in ticks is not due to nematode infection. Supporting this hypothesis, phylogenetic analysis indicated that the nematodes were likely a novel species within the genus Acanthocheilonema, which has been previously shown to be Wolbachia-free.     

Genetic variation in the mitochondrial 16S rRNA gene of the American dog tick,Dermacentor variabilis (Acari: Ixodidae)

Genetic variation in the mitochondrial (mt) 16S ribosomal RNA (rRNA) gene was examined for the American dog tick, Dermacentor variabilis (Say, 1821). Nine different haplotypes were detected among 369 adult D. variabilis collected from four localities in Canada. There were eight variable nucleotide positions in the 404 bp sequence alignment. Individuals of haplotype 1 occurred at frequency of >75% at all localities. Five haplotypes were detected at only one of the four localities. High haplotype diversity and low nucleotide diversity, combined with significantly negative F_s values for ticks at three localities, suggest a recent population expansion. Genetic differences were found between populations at different localities, but a Mantel regression analysis revealed no association between genetic differences and geographical distances. There was also no association between tick haplotype and the prevalence of the bacterium, Rickettsia montanensis Weiss and Moulder, 1984, in D. variabilis among localities or on opposite sides of Blackstrap Lake (Saskatchewan). The 16S rDNA haplotypes from Canadian populations of D. variabilis formed a clade with those from the eastern and central U.S.A., to the exclusion of D. variabilis from geographically isolated populations in the western U.S.A. Although sample sizes for D. variabilis in the eastern U.S.A. are small, there may be genetic divergence between populations in Canada and those in the eastern U.S.A., which may have implications for studies on the pathogenic agents transmitted by D. variabilis to its hosts.     

Population structure, genetic diversity, and clone formation in Quercus chrysolepis (Fagaceae)

Stands of canyon live oak (Quercus chrysolepis, Fagaceae) are maintained for fuelwood, fire management, recreation, and as habitat for wildlife. Information about the link between the oak's reproductive ecology and its extent of genetic diversity is important in developing land management policies that will maintain the long-term viability of populations. Basal sprouting is the primary means of reproduction following fire or cutting, and stands frequently include groups of visibly connected trees in a clustered distribution that suggests cloning. We determined the extent to which clusters of trees were clonal and defined the spatial pattern and diversity of genotypes for six populations across nearly the entire east-west extent of the San Bernardino Mountains in southern California. We mapped over 100 trees at each of five sites and genotyped each tree for allozymes at seven polymorphic loci. We identified clones using these multilocus genotypes and detected an average of 34.4 ± 7.3 (SD) clones per site, most of which had unique genotypes. In general, clustered trees belong to single clones and most clones consist of few trees (mean = 3.4 ± 0.6 trees per clone). However, clone size increased significantly with increased individual heterozygosity, suggesting that selection may favor highly heterozygous clones. Clonal diversity and evenness were high relative to reports for most other clonal species; an average of 97% of clones had distinct genotypes, and Simpson's index of diversity averaged 0.95 ± 0.02. Population genetic analyses of 319 clones from six sites revealed high genetic diversity within sites (mean HS = 0.443). Only a small proportion of the total genetic diversity was explained by variation among sites (mean GST = 0.018), which is consistent with high gene flow among sites (Nm = 9.5). We found no significant substructure among plots within sites, and fixation indices within sites were generally small, suggesting that either little inbreeding occurs, and/or few inbred progeny survive. However, spatial autocorrelation analysis of clones indicated fine-scale genetic structure at distances under 4 m, possibly due to limited seed dispersal. Our data suggest that guidelines for seed collection of canyon live oak for use in restoration can be specified in a manner similar to that recommended for conifer species within the region studied.     

Microsatellite DNA analysis of northern pike (Esox lucius L.) populations: insights into the genetic structure and demographic history of a genetically depauperate species

The northern pike Esox lucius L. is a freshwater fish exhibiting pronounced population subdivision and low genetic variability. However, there is limited knowledge on phylogeographical patterns within the species, and it is not known whether the low genetic variability reflects primarily current low effective population sizes or historical bottlenecks. We analysed six microsatellite loci in ten populations from Europe and North America. Genetic variation was low, with the average number of alleles within populations ranging from 2.3 to 4.0 per locus. Genetic differentiation among populations was high (overall θ_ST = 0.51; overall ρ_ST = 0.50). Multidimensional scaling analysis of genetic distances between populations and spatial analysis of molecular variance suggested a single phylogeographical race within the sampled populations from northern Europe, whereas North American and southern European populations were highly distinct. A population from Ireland was monomorphic at all loci, presumably reflecting founder events associated with introduction of the species to the island in the sixteenth century. Bayesian analysis of demographic parameters showed differences in θ (a product of effective population size and mutation rate) among populations from large and small water bodies, but the relative differences in θ were smaller than expected, which could reflect population subdivision within the larger water bodies. Finally, the analyses showed drastic population declines on a time scale of several thousand years within European populations, which we ascribe to either glacial bottlenecks or postglacial founder events.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 91–101.     

Identification of SNARE and cell trafficking regulatory proteins in the salivary glands of the lone star tick,Amblyomma americanum (L.)

Prostaglandin E(2) (PGE(2)) stimulates secretion of tick salivary gland proteins via a phosphoinositide signaling pathway and mobilization of intracellular Ca(2+) (). Highly conserved intracellular SNARE (soluble NSF attachment protein receptors) complex proteins are associated with the mechanism of protein secretion in vertebrate and invertebrate neuronal and non-neuronal cells. Proteins in the salivary glands of partially fed female lone star ticks cross-react individually with antibodies to synaptobrevin-2 (vesicle (v)-SNARE), syntaxin-1A, syntaxin-2 and SNAP-25 (target (t)-SNAREs), cytosolic alpha/beta SNAP and NSF (N-ethylmaleimide-sensitive fusion protein), Ca(2+) sensitive synaptotagmin, vesicle associated synaptophysin, and regulatory cell trafficking GTPases Rab3A and nSec1. V-SNARE and t-SNARE proteins form an SDS-resistant, boiling sensitive core complex in the salivary glands. Antibodies to SNARE complex proteins inhibit PGE(2)-stimulated secretion of anticoagulant protein in permeabilized tick salivary glands. We conclude that SNARE and cell trafficking regulatory proteins are present and functioning in the process of PGE(2)-stimulated Ca(2+) regulated protein secretion in tick salivary glands.     

Fine structure of the foveae dorsales and foveal glands in the female tick Amblyomma americanum (acari: Ixodoidea: Ixodidae)

The fine structure of the paired foveae dorsales and foveal glands in the unfed female Amblyomma americanum is described and compared with that in other tick species. Each fovea opens to the exterior via pores which lead internally into a single cuticular tube, the pore-tube. This is surrounded by 2–3 epithelial cells. The pore-tube enlarges basally forming a large cavity possessing a cup-shaped cytoplasmic protrusion. The pore-tube cuticular lining extends downward to form an electron-dense, flaplike protrusion bracketing narrow cytoplasmic extensions filled with microtubules. These extensions form a previously undescribed valvelike structure that seems to control the flow of pheromone secretion from the foveal gland to the pore-tube. The single foveal gland lying beneath each pore-tube is composed of 2–3 inner, large, storage cells surrounded by outer, spindle-shaped cells; both types of cells have a characteristic feature of epithelia involved in secretory activity and ion transport. The outer cells extend upward to join the base of the poretube cells by septate desmosomes. A nerve, the foveal nerve, containing axons with neurosecretory vesicles occurs in the vicinity of the foveal gland. The secretory activity of the pheromone glands seems to be partially, if not entirely, under a neural regulation.