Phylogeography of the black fly Simulium tani (Diptera: Simuliidae) from Thailand as inferred from mtDNA sequences

Intraspecific phylogeography has been used widely as a tool to infer population history. However, little attention has been paid to Southeast Asia despite its importance in terms of biodiversity. Here we used the cytochrome oxidase I gene of mitochondrial DNA (mtDNA) for a phylogeographic study of 147 individuals of the black fly Simulium tani from Thailand. The mtDNA revealed high genetic differentiation between the major geographical regions of north, east and central/south Thailand. Mismatch distributions indicate population expansions during the mid-Pleistocene and the late Pleistocene suggesting that current population structure and diversity may be due in part to the species' response to Pleistocene climatic fluctuations. The genealogical structure of the haplotypes, high northern diversity and maximum-likelihood inference of historical migration rates, suggest that the eastern and central/southern populations originated from northern populations in the mid-Pleistocene. Subsequently, the eastern region had had a largely independent history but the central/southern population may be largely the result of recent (c. 100,000 years ago) expansion, either from the north again, or from a relictual population in the central region. Cytological investigation revealed that populations from the south and east have two overlapping fixed chromosomal inversions. Since these populations also share ecological characteristics it suggests that inversions are involved in ecological adaptation. In conclusion both contemporary and historical ecological conditions are playing an important role in determining population genetic structure and diversity.     

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.     

河南纺蚋多线染色体研究

目的对河南纺蚋多线染色体核型及带型进行描述,对稳定且可作为该种重要鉴别依据的结构特征加以识别,并提供表示多线染色体相对长度、着丝粒位置和重要界标的模式图。方法取成熟幼虫分离出唾液腺,经苯酚品红染色、压片后,镜检、摄影和测量,作统计学处理。结果与结论河南纺蚋多线染色体数目为3条,第Ⅰ号具中央着丝粒,第Ⅱ、Ⅲ号为亚中央着丝粒,臂比值(着丝粒位置)高度稳定;ⅠS、ⅠL、ⅡS、ⅡL、ⅢS游离端均钝圆深染,ⅢL末端疏松膨大为扇形呈颗粒状浅染;核仁组织原、巴氏环、双泡、宽深带以及浅染膨大区等主要特征性结构的位置及形态恒定一致,可作为该种的重要鉴别特征。     

Cytogenetics of Simulium siamense Takaoka and Suzuki, 1984 (Diptera: Simuliidae) in northeastern Thailand

We analysed salivary gland polytene chromosomes of 796 larvae from 17 populations of Simulium siamense in northeastern Thailand. Seventeen floating and two fixed chromosome inversions were recorded. Three cytoforms (A, F and G) were recognised and two of them are new (F and G). Cytoform F is distinguished by a fixed inversion on the long arm of chromosome II (IIL-8) and cytoform G by fixed inversions on the long arm of chromosome II (IIL-8) and short arm of chromosome III (IIIS-2). Significant departures from Hardy–Weinberg equilibrium due to heterozygote deficiency in geographically intermediate populations and absence of shared polymorphic inversions of the cytoforms indicate separation of the gene pool. Morphometric analysis of the larvae revealed significant differences in body length (F = 5.00, p =0.007) and head capsule width (F = 4.68, p = 0.010) among cytoforms.     

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

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Isolation and characterization of 11 microsatellite loci from the black fly, Simulium negativum (Diptera: Simuliidae)

Eleven polymorphic microsatellite loci were isolated and developed from the black fly, Simulium negativum, a member of the Simulium arcticum sibling species complex. The observed heterozygosity of the 11 loci ranged from 0.03 to 0.83. The number of alleles per locus ranged from 8 to 19. Significant linkage disequilibria were encountered only for the primer pairs BF7-1 with BF7-5 and BF6-32 with BF7-16. Presumably, these microsatellite loci can be used to study genetic structure within the entire S. arcticum complex.     

Population genetics of the black ant Formica lemani (Hymenoptera: Formicidae)

Colony kin structure and spatial population structure were studied in multiple populations of the ant Formica lemani , using allozymes and DNA microsatellites. Average genetic relatedness between nestmate workers varied little between populations ( r  = 0.51–0.76), indicating that the average colony kin structure was relatively simple. Worker genotypes could not be explained with a single breeding pair in all nests, however, and the distribution of relatedness estimates across nests was bimodal, suggesting that single- and multi-queen colonies co-occur. We studied spatial population structure in a successional boreal forest system, which is a mixture of different aged habitats. Newly clear-cut open habitat patches are quickly colonized by F. lemani , where it is able to persist for a limited number of generations. Newly-founded populations showed signs of a founder effect and spatial substructuring, whereas older populations were more homogenous. This suggests that new populations are founded by a limited number of colonizers arriving from more than one source. Genetic differentiation among local populations was minor, indicating strong migration between them. There were, however, indications of both isolation by distance and populations becoming more isolated as habitat patches grew older.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 247–258.     

Larval polytene chromosomes of black flies (Simulium) from Thailand. I. Comparison among five species in the subgenus Gomphostilbia enderlein

Larval polytene chromosome maps of Simulium (G.) asakoae and S. (G.) sp. g in the ceylonicum-group and S. (G.) angulistylum, S. (G.) decuplum and S. (G.) siamense in the batoense-group of the subgenus Gomphostilbia from Thailand are presented. These species have three pairs of chromosomes (2n = 6). Light stained centromeric bands were observed in the chromosomes of S. (G.) asakoae, S. (G.) sp. g, S. (G.) decuplum and S. (G.) siamense, whereas heavy dark centromeric bands were present in S. (G.) angulistylum. The best distinguishing character of Simulium species in the subgenus Gomphostilbia is the position of the nucleolar organizer in the short arm of chromosome I. The Ring of Balbiani and the double bubble are located in chromosome arm IIS in all species except for S. (G.) angulistylum, which showed these cytological markers in chromosome arm IIIS. A low chromosomal polymorphism was recorded in all species except for S. (G.) sp. g, which exhibited a standard polytene chromosome. Inversion polymorphisms found in this study conformed to Hardy–Weinberg equilibrium and were not associated with sex. These species have different specific markers and banding patterns although homologous banding sequences were found in chromosome arm IIS in S. (G.) asakoae, S. (G.) sp. g, S. (G.) decuplum and S. (G.) siamense and chromosome arm IIIS in S. (G.) angulistylum. Our results showed no evidence of a sibling species complex within any taxon.     

基于线粒体COI基因的桔小实蝇种群遗传分化研究

【目的】推测桔小实蝇Bactrocera dorsalis在中国的扩散路径和新发生地区的入侵来源。【方法】本研究测序获得来自中国、泰国、日本、老挝、孟加拉国和美国等地31个种群的192头桔小实蝇个体的COI序列（1 496 bp,占COI基因全长97.3%）,并以软件DnaSP 5.0, MEGA 6.0和Arlequin 3.5等完成各种群的遗传多样性、种群间的遗传分化以及单倍型分析。【结果】所测31个桔小实蝇种群总体表现出较高水平的核苷酸多样性（0.00663）和高水平的单倍型多样性（0.98069）。以F-统计法度量种群间遗传分化程度, 结果显示中国桔小实蝇地理种群间遗传分化较弱, 中国种群与泰国、日本、老挝、孟加拉国、美国种群间的遗传分化程度不同, 中国种群与美国种群及日本种群的遗传分化最大。而Mantel检验发现,中国、泰国、日本、老挝、孟加拉国和美国种群间的遗传分化与空间距离有关（R=0.670, P<0.0001）, 中国种群间的遗传分化不是地理隔离所造成的（R=0.038, P=0.534）。中国种群与泰国、日本、老挝、孟加拉国和美国种群间不存在共享单倍型。根据种群系统发育树,可将中国原发生地区种群划分为西南、东南两大分支。中性检验和错配分析结果均表明桔小实蝇曾存在大规模的扩张。【结论】桔小实蝇以东南地区和西南地区为源头向中国内陆扩散,其中广东、福建、广西和贵州种群为中国内陆种群较为有影响力的源头。根据遗传多样性、遗传分化、单倍型分析,推测新发生地区桔小实蝇的来源, 例如安徽合肥桔小实蝇种群主要来源于福建长乐、广东珠海和上海。     

Phylogenetic analysis based on multiple gene sequences revealing cryptic biodiversity in Simulium multistriatum group (Diptera: Simuliidae) in Thailand

Phylogenetic relationships among four species of the Simulium multistriatum group (Diptera: Simuliidae) in Thailand were examined based on two mitochondrial genes (COI, COII) and one nuclear gene (18S/ITS1). Simulium takense was found to be genetically divergent (>20.3% for COI) from the other species, consistent with their distinctive morphology. Simulium chainarongi and S. chaliowae were monophyletic but were included in paraphyletic S. fenestratum. Simulium fenestratum was divided into three distinct lineages with high levels of genetic divergence. This suggests that S. fenestratum is a species complex. Neither morphological nor cytological examinations revealed evidence of sibling species. The clades derived from phylogenetic analyses were found to be correlated with the ecological conditions of larval habitat. Therefore, ecological adaptation may have played a role in black fly diversification and evolution. These results suggest the use of integrated, multidisciplinary approaches for fully understanding black fly biodiversity and systematics.     

Cytosystematics of the Simulium tuberosum group (Diptera: Simuliidae) in Thailand

The polytene chromosomes of 3347 larvae of the Simulium tuberosum group in Asia were analysed, representing the largest ever cytogenetic study of black flies in the Oriental Region. Band‐by‐band comparisons, relative to the established standard chromosome map for the subgenus Simulium, revealed 17 cytogenetically distinct taxa in Thailand, plus an 18th in China. Six of these taxa correspond to morphologically described species (S. doipuiense, S. rufibasis, S. setsukoae, S. tani, S. yuphae and S. weji). Recognition of the 18 taxa is based largely on unique inversions, either fixed or sex linked, primarily in the long arm of chromosome III. The greatest cytological diversity was discovered in the S. tani lineage, with ten cytoforms. This marked chromosomal diversification within S. tani is based largely on two inversions that have assumed different roles over evolutionary time, variously functioning in different combinations as fixed inversions, sex‐linked inversions and autosomal polymorphisms. Shared unique chromosomal features, relative to the subgeneric standard chromosome map, allowed evolutionary relationships among the cytotaxa to be inferred. Fluctuations in climate during the Pleistocene might have promoted differentiation of the Southeast Asian S. tuberosum group in isolated refugia such as mountains. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 289–315.     

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.     

基于线粒体COI基因分析钩手水母的群体遗传结构

钩手水母(Gonionemus vertens)为大西洋和太平洋广布种, 是我国习见的有毒水母种类之一。本文对采自黄渤海海域4个地理群体的104个钩手水母线粒体COI基因序列进行扩增, 并结合GenBank上其他182个钩手水母同源序列进行序列变异分析。在286个基因序列中共检测出52个多态位点, 定义了14种单倍型。总群体的单倍型多样性和核苷酸多样性分别为0.743 ± 0.012和1.046% ± 0.097%, 与其他几种大型水母相比, 钩手水母总群体的遗传多样性处于较高水平。AMOVA结果显示, 60.17%的分子变异源于群组间, 13.37%的分子变异源于群体内, 26.46%的分子变异源于组内群体间, 群组间、群体内和组内群体间的遗传分化均极显著。F_st值统计检验表明, 中国厦门群体与乐亭、东营、烟台、大连群体间存在显著的遗传分化, 大连与东营、烟台群体间也存在显著的遗传分化。系统分析结果显示, 钩手水母群体间存在2个明显的单倍型谱系分支。不同的钩手水母地理群体间具有复杂的遗传模式, 钩手水母复杂的生活史、扩散能力、地理隔离和海流分布可能是影响钩手水母遗传结构的重要因素。     

兴义维蚋多线染色体研究（英文）

首次在国内对兴义维蚋Simulium (Wilhelmia) xingyiense的多线染色体进行研究, 并提供其多线染色体标准图。选取兴义维蚋的成熟幼虫, 用改良苯酚品红染色法进行唾腺多线染色体制备, 并进行测量、 描述及分析。结果表明： 兴义维蚋多线染色体数目为3对（2n=6）。Ⅰ号染色体具中央着丝粒, Ⅱ和Ⅲ号染色体均为亚中央着丝粒染色体。核仁组织者区位于Ⅰ号染色体短臂近着丝粒端。巴尔比尼氏环和双泡位于Ⅱ号染色体短臂近中央位置。3对染色体的着丝粒区可形成明显的染色中心。兴义维蚋多线染色体具有多态性的倒位, 倒位频率为0.64。兴义维蚋多线染色体的着丝粒、 核仁组织区、 巴氏环、 双泡等主要特征性结构的位置及形态恒定一致,可作为该种的重要鉴别特征。其多态性的倒位可为该蚋种在细胞水平上进行蚋类分类鉴别和系统发育等研究提供基础资料。     

A new species of Simulium (Nevermannia) (Diptera, Simuliidae) from Thailand, with keys to members of the Simulium feuerborni species-group in Thailand

Simulium (Nevermannia) maeaiensesp. n. is described on the basis of female, male, pupal and larval specimens collected from Chiang Mai Province, Thailand. This species is assigned to the feuerborni species-group of the subgenus Simulium (Nevermannia), and is distinctive among this species-group in having the female cibarium furnished with numerous dark minute conical processes on the lower part, the female genital fork with a strongly sclerotized horizontal bar on each arm, and six long pupal gill filaments arising nearly at the same level from the common basal stalk and lying in a horizontal plane. Identification keys to seven species of the feuerborni species-group reported from Thailand are provided for females, males, pupae and mature larvae.     

植物病原物的群体遗传学

品种单一化、生产密集型和一年多茬的现代农业特点导致病原物呈现出进化速度加快、致病力增强及流行风险增大趋势。深入研究病原物群体遗传学对认识病害的流行、有效选育和使用抗性品种乃至控制病害具有重要意义。文章阐述了植物病原物群体遗传学的研究目标和内容、突变、基因迁移、基因重组、随机遗传漂变和自然选择5大遗传机制在植物病原物进化过程中的作用,以及目前植物病原物群体遗传学研究的现状。     

植物病原物的群体遗传学

品种单一化、生产密集型和一年多茬的现代农业特点导致病原物呈现出进化速度加快、致病力增强及流行风险增大趋势。深入研究病原物群体遗传学对认识病害的流行、有效选育和使用抗性品种乃至控制病害具有重要意义。文章阐述了植物病原物群体遗传学的研究目标和内容、突变、基因迁移、基因重组、随机遗传漂变和自然选择5大遗传机制在植物病原物进化过程中的作用, 以及目前植物病原物群体遗传学研究的现状。     

DNA barcoding of tropical black flies (Diptera: Simuliidae) of Thailand

The ecological and medical importance of black flies drives the need for rapid and reliable identification of these minute, structurally uniform insects. We assessed the efficiency of DNA barcoding for species identification of tropical black flies. A total of 351 cytochrome c oxidase subunit 1 sequences were obtained from 41 species in six subgenera of the genus Simulium in Thailand. Despite high intraspecific genetic divergence (mean = 2.00%, maximum = 9.27%), DNA barcodes provided 96% correct identification. Barcodes also differentiated cytoforms of selected species complexes, albeit with varying levels of success. Perfect differentiation was achieved for two cytoforms of Simulium feuerborni, and 91% correct identification was obtained for the Simulium angulistylum complex. Low success (33%), however, was obtained for the Simulium siamense complex. The differential efficiency of DNA barcodes to discriminate cytoforms was attributed to different levels of genetic structure and demographic histories of the taxa. DNA barcode trees were largely congruent with phylogenies based on previous molecular, chromosomal and morphological analyses, but revealed inconsistencies that will require further evaluation.