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.     

Seasonal variation of black fly (Diptera: Simuliidae) species diversity and community structure in tropical streams of Thailand

Seasonal variation of the physicochemical conditions of streams plays an important role in aquatic insect diversity and community structure. Asian tropical streams profoundly change between seasons due to the effects of monsoons. However, little is known about how these changes affect aquatic insect diversity and community structure. The objectives of this study are to examine seasonal variations of the physicochemical conditions in tropical streams in Thailand and to assess the effects of these changes on black fly community structure and diversity. Black flies were sampled and physicochemical conditions recorded at eight sites between December 2007 and December 2008. A total of 10 black fly species were found. Comparisons of the streams between seasons revealed that physical conditions related to rainfall rate were significantly different. Canonical correspondence analysis differentiated sampling sites from each season. Streams in the rainy season were faster and deeper, with higher discharge and conductivity than those of the cold and dry seasons. Species richness was significantly higher in the rainy season than in the cold and dry seasons ( F  = 6.23, P  = 0.004). Community structure profoundly changed between the low-flow season (cold and dry) and high-flow season. Black fly species found predominantly in the low-flow season ( Simulium siamense "cytoform A", S. aureohirtum ) decreased dramatically during the high-flow season. In contrast, species found at high frequency during the high-flow season ( S. nakhonense , S. angulistylum ) disappeared in the low-flow season. The study demonstrates the importance of seasonal variation of stream conditions on black fly community structure and diversity.     

Genetic structure and diversity of Shorea obtusa (Dipterocarpaceae) in Thailand

Shorea obtusa is a keystone species of the dry deciduous dipterocarp forest in Thailand. In this study, the genetic structure and diversity of this species were evaluated by means of five microsatellite markers. A total of 146 trees were collected from five populations encompassing major forest regions of Thailand. High levels of genetic diversity were found among the five populations with the average He of 0.664. Genetic differentiations between populations, although significant, were low with approximately 3% of genetic variation partitioned among populations. This may indicate that the populations sampled were recently part of a continuous population. A tree constructed using the unweighted pair group method with arithmetic average, based on Nei's genetic distance, divided the populations into three groups. This separation was consistent with the altitudinal zonation of the populations, thus indicating that altitude might play a significant role in the genetic structure of S. obtusa. Areas of high genetic diversity were identified which could be considered priorities for conservation.     

Population genetics of the high elevation black fly Simulium (Nevermannia) feuerborni Edwards in Thailand

In this study, we examined the genetic structure and population history of the high elevation black fly Simulium feuerborni in Thailand at both cytogenetic and molecular genetic levels. Cytological examination revealed two cytoforms differentiated by fixed chromosome inversions. The distributions of the cytoforms were associated with geographic origins. Cytoform A was found in the lower north and northeast, and cytoform B was found in the upper northern region of Thailand. Molecular data based on the mitochondrial cytochrome oxidase subunit I (COI) barcoding sequence supports the separation of the cytoforms. The average sequence divergence between the two cytoforms was 3.75%, which is higher than the threshold value for the species level based on a COI barcoding sequence. Median joining network clearly differentiated the haplotypes of the cytoforms into different lineages. Population pairwise F_ST and amova analyses reveal significant genetic differentiation between cytoforms. This indicates that the low land areas separating these populations act as a gene flow barrier. No genetic differentiation was detected within cytoforms. This could be due to a recent sharing of population history. Mismatch distribution analysis revealed population expansion in the northern lineage of the cytoform B approximately 220 000 years ago. More recent expansion (32 000 years ago) was found in the lower north and northeast (cytoform A) lineage. The demographic history of S. feuerborni mirrored previous findings in black flies and other insect species in Thailand. This indicates the important role of Pleistocene climatic change on genetic structure and diversity of Southeast Asian mainland species.     

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.     

Host specificity and interaction networks of insects feeding on seeds and fruits in tropical rainforests

In the tropics, antagonistic seed predation networks may have different properties than mutualistic pollination and seed dispersal networks, but the former have been considerably less studied. We tested whether the structure of antagonistic tripartite networks composed of host plants, insects developing within seeds and fruits, and their insect parasitoids could be predicted from plant phylogenetic distance and plant traits. We considered subsets of the networks (‘subnetworks') at three rainforest locations (Panama, Thailand, Papua New Guinea), based on insect families, plant families or plant functional groups. We recorded 3197 interactions and observed a low percentage of realized interactions, especially in Panama, where insect host specificity was higher than in Thailand or New Guinea. Several factors may explain this, including insect faunal composition, incidence of dry fruits, high fruit production and high occurrence of Fabaceae at the Panamanian site. Host specificity was greater among seed-eaters than pulp-eaters and for insects feeding on dry fruits as opposed to insects feeding on fleshy fruits. Plant species richness within plant families did not influence insect host specificity, but site characteristics may be important in this regard. Most subnetworks were extremely specialized, such as those including Tortricidae and Bruchinae in Panama. Plant phylogenetic distance, plant basal area and plant traits (fruit length, number of seeds per fruit) had important effects on several network statistics in regressions weighted by sampling effort. A path analysis revealed a weak direct influence of plant phylogenetic distance on parasitoid richness, indicating limited support for the ‘nasty host hypothesis'. Our study emphasizes the duality between seed dispersal and seed predation networks in the tropics, as key plant species differ and host specificity tends to be low in the former and higher in the latter. This underlines the need to study both types of networks for sound practices of forest regeneration and conservation.     

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.     

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.     

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.