Distinct geographical structure across species units evidenced by chloroplast DNA haplotypes and nuclear ribosomal ITS genotypes of Corylopsis (Hamamelidaceae) in the Japanese islands

The geographical distribution of chloroplast DNA (cpDNA) haplotypes and nuclear ribosomal internal transcribed spacer (nrITS) genotypes of Japanese Corylopsis (Hamamelidaceae), which consists of four species, was investigated. Two hundred and five individuals belonging to four species from 30 populations, covering the entire geographical range, were studied. Based on approximately 1108 bp of the three non-coding regions of cpDNA, nine haplotypes were detected, and each was distinguished from adjacent haplotypes by one substitution. Based on approximately 507-bp nrITS sequences, 47 genotypes were detected, for which three clades were identified in the phylogenetic analysis. There was inconsistency between the cpDNA haplotypes, nrITS genotypes, and classification of Corylopsis taxa, possibly because of incomplete lineage sorting or introgressive hybridization. The distribution of the haplotypes was highly structured geographically, and N _ST (0.893) was significantly greater than G _ST (0.819), implying that the current distribution of Corylopsis species was structured phylogeographically during Quaternary climatic oscillations. The haplotype composition and results of analysis of molecular variance showed that the populations in Hokuriku were highly divergent, suggesting that they are long-term persistent populations arising from refugia during the Quaternary climatic oscillations. Refugial populations in Chugoku and Shikoku may have lost genetic diversity because of a bottleneck resulting from a small population size, followed by post-glacial range expansion. Pre-existing refugia may have been so small that the subsequent range expansion replaced the pre-existing genetic structure.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 501–518.     

Testing hypotheses of mitochondrial gene‐tree paraphyly: unravelling mitochondrial capture of the Streak‐breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (Pomatorhinus musicus)

Species‐level paraphyly inferred from mitochondrial gene trees is a prevalent phenomenon in taxonomy and systematics, but there are several potential causes that are not easily explained by currently used methods. This study aimed to test the underlying causes behind the observed paraphyly of Streak‐breasted Scimitar Babbler (Pomatorhinus ruficollis) via statistical analyses of four mitochondrial (mtDNA) and nine nuclear (nuDNA) genes. Mitochondrial gene trees show paraphyly of P. ruficollis with respect to the Taiwan Scimitar Babbler (Pomatorhinus musicus), but nuclear genealogies support a sister‐group relationship. Predictive coalescent simulations imply several hypothetical explanations, the most likely being mitochondrial capture of P. ruficollis by P. musicus for the observed cyto‐nuclear incongruence. Further approximate Bayesian computation suggests a unidirectional introgression model with substantial level of gene flow from P. ruficollis to P. musicus during their initial divergence during the Late Pleistocene. This specific observation frames several potential causes for incongruent outcomes of mitochondrial and nuclear introgression in general, and on the whole, our results underscore the strength of multiple independent loci for species delimitation and importance of testing hypotheses that explain disparate causes of mitochondrial gene‐tree paraphyly.     

Biogeography of the Indonesian archipelago: mitochondrial DNA variation in the fruit bat, Eonycteris spelaea

The fruit bat, Eonycteris spelaea , occurs from India through the Philippines to the southeast limit of its distribution in the Lesser Sunda islands of Indonesia. Mitochondrial DNA (mtDNA) variation was examined in Indonesian E. spelaea island populations by amplification of the D-loop and digestion with restriction endonucleases. In addition, microgeographic variation was assessed by investigation of three cave populations within one island. A total of 24 genotypes, comprising two broad clades, was detected. The pattern of mtDNA variation reflects the colonization history of E. spelaea with estimates of haplotype and sequence diversity highest in the older western populations and lowest at the eastern periphery of the species' distribution. These findings may also be associated with an environmental cline from west to east. There is also evidence that genetic distance between populations reflects geographic relationships, especially historical connectedness, as measured by Pleistocene sea-crossing distances. At the microgeographic level, cave populations were heterogeneous and composed of diverse lineages suggesting restricted local interchange.     

Speciation and mitochondrial DNA diversification of the diving beetles Agabus bipustulatus and A. wollastoni (Coleoptera, Dytiscidae) within Macaronesia

Diversification of populations of two morphologically similar diving beetles within the Agabus tristis group, A. wollastoni and A. bipustulatus, was investigated, with partial mtDNA cytochrome b (Cyt b) sequences, allozymes and landmark‐based morphometrics. The Madeiran endemic A. wollastoni was collected from 11 localities. Population genetic and morphological variation was compared to Scandinavian localities of the widespread west Palearctic A. bipustulatus, recorded also from the Azores. Agabus wollastoni and European A. bipustulatus specimens representing eight and 13 localities respectively, were used in evaluating their phylogenetic relationship. Maximum parsimony analysis of the Cyt b sequences showed that both the A. bipustulatus and A. wollastoni specimens form well‐supported monophyletic groups. Three lines of evidence suggest that Agabus wollastoni has speciated through a few founders: (1) a well‐supported mtDNA line; (2) the mean heterozygosity of A. wollastoni is lower when compared to A. bipustulatus on the mainland; and (3) several uncommon alleles of A. bipustulatus are missing in A. wollastoni. The Azorean A. bipustulatus population was drastically affected by the colonization event, since several loci have become fixed with a resulting lower mean heterozygosity. The colonization was relatively recent, as the mtDNA lineage represented in the Azores is deeply nested within the A. bipustulatus clade. Population structure shows moderate inbreeding of A. wollastoni, and extensive substructuring at all localities with moderate gene‐flow between them. Morphological variation in A. wollastoni showed significant differentiation among several populations. Island colonizations, population structure of A. wollastoni, and an observed pattern of variation of the α‐glycerophosphate dehydrogenase locus are discussed. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 79, 653–666.     

Recent volcanism and mitochondrial DNA structuring in the lizard Gallotia atlantica from the island of Lanzarote

The phylogeography of the lacertid lizard Gallotia atlantica from the small volcanic island of Lanzarote (Canary Islands) was analysed based on 1075 bp of mitochondrial DNA (mtDNA) sequence (partial cytochrome b and ND2) for 157 individuals from 27 sites (including three sites from neighbouring islets). Levels of sequence divergence were generally low, with the most distant haplotypes separated by only 14 mutational steps. MtDNA divergence appears to coincide with formation of the middle Pleistocene lowland that united formerly separate ancient islands to form the current island of Lanzarote, allowing rejection of a two-island model of phylogeographical structure. There was evidence of large-scale population expansion after island unification, consistent with the colonization of new areas. A nested clade phylogeographical analysis (NCPA) revealed significant phylogeographical structuring. Two-step and higher-level clades each had disjunct distributions, being found to the east and west of a common area with a north-south orientation that extends between coasts in the centre-east of the island (El Jable). Other clades were almost entirely restricted to the El Jable region alone. Bayesian Markov chain Monte Carlo analyses were used to separate ongoing gene flow from historical associations. These supported the NCPA by indicating recent (75,000-150,000 years ago) east-west vicariance across the El Jable region. Lava flows covered El Jable and other parts of the central lowland at this time and likely led to population extinctions and temporary dispersal barriers, although present-day evidence suggests some populations would have survived in small refugia. Expansion of the latter appears to explain the presence of a clade located between the eastern and western components of the disjunct clades. Direct relationships between mtDNA lineages and morphology were not found, although one of two morphological forms on the island has a disjunct distribution that is broadly concordant with east-west components of the phylogeographical pattern. This work demonstrates how recent volcanic activity can cause population fragmentation and thus shape genetic diversity on microgeographical scales.     

Molecular and plumage analyses indicate the incomplete separation of two woodpeckers (Aves,Picidae)

We evaluated the relationship between Celeus undatus and Celeus grammicus, with the objective of clarifying their evolutionary history. We analysed fragments of the mitochondrial and nuclear genes of 57 specimens. For comparative purposes, we inspected the plumage patterns of 77 skins. Our findings highlight the absence of reciprocal monophyly between the two taxa, given their reduced genetic divergence, and the lack of any clear separation of the two forms in the haplotype networks. A similar situation was found in the STRUCTURE analysis, with reciprocal contributions from the two taxa to the respective clusters, indicating that C. grammicus and C. undatus cannot be differentiated using the molecular markers. Corroborating the genetic data, our plumage analyses also failed to find any clear diagnostic characters between the polytypic C. undatus and C. grammicus, as they are defined at present. The genetic profile is consistent with either extensive historical gene flow between the species or, alternatively, incomplete lineage sorting, rather than recent secondary contact. The lack of monophyly between the two taxa impeded subspecies‐level phylogeographic inferences, with the subspecific variation being interpreted as a probable artefact of the phenotypic plasticity of the two forms. These findings indicate clearly that the two taxa form a single evolutionary unit, in which the morphological differentiation used to diagnose the species, combined with their geographic distribution, is at odds with the incomplete separation of the taxa. This may reflect disparities in the rates of differentiation between molecular and phenotypic markers, which is possibly due to the variation in selection pressures along a humidity gradient in Amazonia.     

Nuclear microsatellite and mitochondrial DNA analyses reveal the regional genetic structure and phylogeographical history of a sanguivorous land leech,Haemadipsa japonica,in Japan

Recent molecular studies have indicated that phylogeographical history of Japanese biota is likely shaped by geohistory along with biological events, such as distribution shifts, isolation, and divergence of populations. However, the genetic structure and phylogeographical history of terrestrial Annelida species, including leech species, are poorly understood. Therefore, we aimed to understand the genetic structure and phylogeographical history across the natural range of Haemadipsa japonica, a sanguivorous land leech species endemic to Japan, by using nine polymorphic nuclear microsatellites (nSSR) and cytochrome oxidase subunit one (COI) sequences of mitochondrial DNA (mtDNA). Analyses using nSSR revealed that H. japonica exhibited a stronger regional genetic differentiation among populations (G'_ST = 0.77) than other animal species, probably because of the low mobility of land leech. Analyses using mtDNA indicated that H. japonica exhibited two distinct lineages (A and B), which were estimated to have diverged in the middle Pleistocene and probably because of range fragmentation resulting from climatic change and glacial and interglacial cycles. Lineage A was widely distributed across Japan, and lineage B was found in southwestern Japan. Analyses using nSSR revealed that lineage A was roughly divided into two population groups (i.e., northeastern and southwestern Japan); these analyses also revealed a gradual decrease in genetic diversity with increasing latitude in lineage A and a strong genetic drift in populations of northeastern Japan. Combined with the largely unresolved shallow polytomies from the mtDNA phylogeny, these results implied that lineage A may have undergone a rapid northward migration, probably during the Holocene. Then, the regional genetic structure with local unique gene pools may have been formed within each lineage because of the low mobility of this leech species.     

Spatial and temporal population structure of sea trout at the Island of Gotland, Sweden, delineated from mitochondrial DNA

In a study of the genetic relationships among 879 anadromous brown trout Salmo trutta from 13 streams at the Island of Gotland, Sweden, using RFLP analysis of a mitochondrial DNA segment (NADH dehydrogenase-1 gene), six haplotypes were detected. Significant genetic divergence was observed among streams as well as between cohorts within streams. Approximately 8–9% of the total variation was due to differences between populations, and 4–5% was explained by differences between cohorts within populations. The female effective population size ( N _ef) was assessed from temporal haplotype frequency differences between consecutive cohorts; the estimated average N _ef over all populations was just below 30, suggesting that these populations were effectively quite small. With such small effective sizes the populations are expected to loose genetic variability quickly, but the observed levels do not appear particularly low. This indicates that female migration between streams occurs. The observed level of differentiation does not support the presumption that a particular pre-smolt migratory behaviour observed in Gotland streams, with large portions of fry leaving for the sea soon after hatching, results in a reduced homing ability. From a conservation management perspective the Gotland brown trout streams should be regarded as a population system where the vitality and survival of brown trout in one stream is dependent on the opportunity of contact and exchange of individuals from other streams.     

Taxonomic relationships between four species of the Mullidae family revealed by three genetic methods: allozymes, random amplified polymorpic DNA and mitochondrial DNA

Genetic distances were lower between Upeneus moluccensis and Pseudopeneus prayensis than between those species and Mullus barbatus and Mullus surmuletus . However, for allozymes, the two Mullus species were found genetically more distinct from U. moluccensis than from P. prayensis , but RAPD and mtDNA analysis showed the opposite. RAPDs revealed less interspecific divergence compared with allozymes and the results they produced were more consistent with mtDNA analysis. Although RAPDs did not add any supplementary taxonomic information, they proved valuable tools for quick and reliable species discrimination compared with allozymes and mtDNA.     

Relationship of Hypochaeris salzmanniana (Asteraceae, Lactuceae), an endangered species of the Iberian Peninsula, to H. radicata and H. glabra and biogeographical implications

Hypochaeris salzmanniana DC. (Asteraceae, Lactuceae) is an endangered species on the Iberian Peninsula, known from only eight coastal populations. Most authors have treated it as a variety, subspecies or simply as a synonym of H. glabra L. On the basis of morphological and cytological characters, Talavera recently separated H. salzmanniana (2n = 8) from H. glabra (2n = 10). Material of H. salzmanniana, H. glabra and H. radicata was collected from Spain, Italy, Sicily and Tunisia in order to assess taxonomic status and population relationships. Amplified Fragment Length Polymorphism (AFLP) analysis revealed three well-differentiated species. A close relationship between H. salzmanniana and H. radicata is also confirmed by AFLP analysis and chromosome number (2n = 8), morphology, and rDNA localization (FISH, fluorescence in situ hybridization). Hypochaeris salzmanniana and H. radicata share three fixed diagnostic AFLP fragments out of 348 fragments scored. The population structure of H. salzmanniana reveals distinct groups in southern Spain that are separated geographically. High differentiation among a western (Conil to Zahara), an intermediate (Punta Paloma and Los Algarbes) and an eastern (Algeciras and La Línea) group may reflect ancient separation. Population sizes and genetic compatibility differ greatly among populations and can be used to explain levels of within-population genetic diversity, together with recent documented loss of habitats resulting from tourist developments. Population structures of H. radicata and H. glabra show a similar geographical patterning: strongly differentiated populations from the Betic Cordillera and from the Iberian Massif, which are separated at present by the Guadalquivir river. Geological events at the end of the Tertiary (Tortonian–Messinian Miocene) might help explain patterns of differentiation in these three species of sect. Hypochaeris. © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society, 2004, 146 , 79–95.     

Karyological and allozyme survey of the Common shrew, Sorex araneus, from Macedonia

Karyotype and genetic variation of the common shrew (Sorex araneus) from Mt. Pelister in southern Macedonia has been studied. Whereas all autosomes in the chromosomal set (2 n_a, = 28, the only present metacentrics being af, bc, jl, and tu) were of the standard type as well as the sex chromosomes X and Y₂ in males, the Y₁ chromosome was a small metacentric. This chromosomal feature is unique among the common shrew populations studied cytogenetically so far. Three out of 33 loci analysed (Sdh, 6Pgd, Mdh-1) were discriminant between the Mt. Pelister population and Sorex araneus from Slovenia and two loci (Est-3, Ada) were partially discriminant. A relatively high value of Nei's genetic distance (D = 0.137) confirms unique character of the Pelister population.     

Genetic variation and population structure of the Japanese sika deer (Cervus nippon) in Hokkaido Island, based on mitochondrial D-loop sequences

Mitochondrial DNA (mtDNA) D -loop region sequences (602 bp) from 141 samples of the sika deer Cervus nippon collected from Hokkaido Island of Japan were investigated to elucidate population genetic structure. All animals possessed seven repeat units (38 or 39 bp each) in the sequences. Comparison of the 602-bp sequences showed four sites of transitional mutations (A↔G or C↔T). Based on combination of the substitutions, six D -loop haplotypes (a–f types) were identified in the Hokkaido population, suggesting the occurrence of at least six maternal lineages. Distribution maps of the haplotypes constructed using the Geographic Information System showed that the distribution patterns differed from haplotype to haplotype. In particular, distribution of the major three types (a-, b-, and c-types) almost overlapped with three main areas of coniferous forests in Hokkaido. These results suggest that expansion of the sika deer population could have occurred through the habitat of coniferous forests after the historical bottleneck in Hokkaido.     

The effect of deforestation on the genetic diversity and structure in <Emphasis Type="Italic">Acer saccharum</Emphasis> (Marsh): Evidence for the loss and restructuring of genetic variation in a natural system

The level and distribution of genetic diversity can be influenced by species life history traits and demographic factors, including perturbations that might produce population bottlenecks. Deforestation and forest fragmentation are common sources of population disturbance in contemporary populations of forest ecosystems. Although the genetic effects of forest fragmentation and deforestation have been examined by assessing levels of genetic variation in forest fragments that remain after logging, few considerations have been made of the populations that re-colonize once-cleared areas. Here we examine the effects of human-mediated population bottlenecks on the level and distribution of genetic diversity in natural populations of the long-lived forest tree species, Acer saccharum (sugar maple). We compared genetic variation and structure for populations of sugar maple found within old-growth forested area and in area that has re-colonized since logging. In this study the percent polymorphic loci and allelic richness estimates were reduced in the logged populations compared to old-growth populations. Jackknifed estimates of population genetic differentiation showed significantly higher differentiation among logged populations, with this result being consistently seen when individuals within populations were grouped according to diameter at breast height. The result of decreased genetic variation and higher levels of genetic structure among logged populations suggests that even one extensive bout of logging can alter the level and distribution of genetic variation in this forest tree species.     

Standing genetic variation as a potential mechanism of novel cave phenotype evolution in the freshwater isopod,Asellus aquaticus

Novel phenotypes can come about through a variety of mechanisms including standing genetic variation from a founding population. Cave animals are an excellent system in which to study the evolution of novel phenotypes such as loss of pigmentation and eyes. Asellus aquaticus is a freshwater isopod crustacean found in Europe and has both a surface and a cave ecomorph which vary in multiple phenotypic traits. An orange eye phenotype was previously revealed by F₂ crosses and backcrosses to the cave parent within two examined Slovenian cave populations. Complete loss of pigmentation, both in eye and body, is epistatic to the orange eye phenotype and therefore the orange eye phenotype is hidden within the cave populations. Our goal was to investigate the origin of the orange eye alleles within the Slovenian cave populations by examining A. aquaticus individuals from Slovenian and Romanian surface populations and Asellus aquaticus infernus individuals from a Romanian cave population. We found orange eye individuals present in lab raised surface populations of A. aquaticus from both Slovenia and Romania. Using a mapping approach with crosses between individuals of two surface populations, we found that the region known to be responsible for the orange eye phenotype within the two previously examined Slovenian cave populations was also responsible within both the Slovenian and the Romanian surface populations. Complementation crosses between orange eye Slovenian and orange eye Romanian surface individuals suggest that the same gene is responsible for the orange eye phenotype in both surface populations. Additionally, we observed a low frequency phenotype of eye loss in crosses generated between the two surface populations and also in the Romanian surface population. Finally, in a cave population from Romania, A. aquaticus infernus, we found that the same region is also responsible for the orange eye phenotype as the Slovenian cave populations and the Slovenian and Romanian surface populations. Therefore, we present evidence that variation present in the cave populations could originate from standing variation present in the surface populations and/or transgressive hybridization of different surface phylogenetic lineages rather than de novo mutations.     

Holocene chloroplast genetic variation of shrubs (Alnus alnobetula,Betula nana,Salix sp.) at the siberian tundra‐taiga ecotone inferred from modern chloroplast genome assembly and sedimentary ancient DNA analyses

Climate warming alters plant composition and population dynamics of arctic ecosystems. In particular, an increase in relative abundance and cover of deciduous shrub species (shrubification) has been recorded. We inferred genetic variation of common shrub species (Alnus alnobetula, Betula nana, Salix sp.) through time. Chloroplast genomes were assembled from modern plants (n = 15) from the Siberian forest‐tundra ecotone. Sedimentary ancient DNA (sedaDNA; n = 4) was retrieved from a lake on the southern Taymyr Peninsula and analyzed by metagenomics shotgun sequencing and a hybridization capture approach. For A. alnobetula, analyses of modern DNA showed low intraspecies genetic variability and a clear geographical structure in haplotype distribution. In contrast, B. nana showed high intraspecies genetic diversity and weak geographical structure. Analyses of sedaDNA revealed a decreasing relative abundance of Alnus since 5,400 cal yr BP, whereas Betula and Salix increased. A comparison between genetic variations identified in modern DNA and sedaDNA showed that Alnus variants were maintained over the last 6,700 years in the Taymyr region. In accordance with modern individuals, the variants retrieved from Betula and Salix sedaDNA showed higher genetic diversity. The success of the hybridization capture in retrieving diverged sequences demonstrates the high potential for future studies of plant biodiversity as well as specific genetic variation on ancient DNA from lake sediments. Overall, our results suggest that shrubification has species‐specific trajectories. The low genetic diversity in A. alnobetula suggests a local population recruitment and growth response of the already present communities, whereas the higher genetic variability and lack of geographical structure in B. nana may indicate a recruitment from different populations due to more efficient seed dispersal, increasing the genetic connectivity over long distances.     

Bridging two scholarly islands enriches both: COI DNA barcodes for species identification versus human mitochondrial variation for the study of migrations and pathologies

DNA barcodes for species identification and the analysis of human mitochondrial variation have developed as independent fields even though both are based on sequences from animal mitochondria. This study finds questions within each field that can be addressed by reference to the other. DNA barcodes are based on a 648‐bp segment of the mitochondrially encoded cytochrome oxidase I. From most species, this segment is the only sequence available. It is impossible to know whether it fairly represents overall mitochondrial variation. For modern humans, the entire mitochondrial genome is available from thousands of healthy individuals. SNPs in the human mitochondrial genome are evenly distributed across all protein‐encoding regions arguing that COI DNA barcode is representative. Barcode variation among related species is largely based on synonymous codons. Data on human mitochondrial variation support the interpretation that most – possibly all – synonymous substitutions in mitochondria are selectively neutral. DNA barcodes confirm reports of a low variance in modern humans compared to nonhuman primates. In addition, DNA barcodes allow the comparison of modern human variance to many other extant animal species. Birds are a well‐curated group in which DNA barcodes are coupled with census and geographic data. Putting modern human variation in the context of intraspecies variation among birds shows humans to be a single breeding population of average variance.     

Genetic differences among three colour morphotypes of the black rockfish,Sebastes inermis,inferred from mtDNA and AFLP analyses

The genetic differences among three colour morphotypes of the black rockish, Sebastes inermis, were determined from mitochondrial DNA (mtDNA) and amplified fragment length polymorphisms (AFLP) analyses. In the AFLP analysis, each morphotype could be distinguished by the presence or absence matrix of five AFLP loci. These diagnostic loci indicated that the three morphotypes represented independent gene pools, indicating reproductive isolation. Furthermore, 14 significant frequency differences in AFLP fragments were observed between morphotypes A and B, 12 between morphotypes A and C and six between morphotypes B and C. These significant differences also supported the likelihood of reproductive isolation among the morphotypes. In the mtDNA analysis, variations in partial sequences of the control region failed to distinguish clearly between the three morphotypes, but restrictions of gene flow and genetic differentiation among the morphotypes were supported by significant FST estimates. The absence of diagnostic mtDNA differences in this study may have been due to introgressive hybridization among the morphotypes and/or incomplete lineage sorting, due to the recency of speciation.     

MOTUs, Morphology, and Biodiversity Estimation: A Case Study Using Nematodes of the Suborder Criconematina and a Conserved 18S DNA Barcode

DNA barcodes are increasingly used to provide an estimate of biodiversity for small, cryptic organisms like nematodes. Nucleotide sequences generated by the barcoding process are often grouped, based on similarity, into molecular operational taxonomic units (MOTUs). In order to get a better understanding of the taxonomic resolution of a 3' 592-bp 18S rDNA barcode, we have analyzed 100 MOTUs generated from 214 specimens in the nematode suborder Criconematina. Previous research has demonstrated that the primer set for this barcode reliably amplifies all nematodes in the Phylum Nematoda. Included among the Criconematina specimens were 25 morphologically described species representing 12 genera. Using the most stringent definition of MOTU membership, where a single nucleotide difference is sufficient for the creation of a new MOTU, it was found that an MOTU can represent a subgroup of a species (e.g. Discocriconemella limitanea), a single species (Bakernema inaequale), or a species complex (MOTU 76). A maximum likelihood phylogenetic analysis of the MOTU dataset generated four major clades that were further analyzed by character-based barcode analysis. Fourteen of the 25 morphologically identified species had at least one putative diagnostic nucleotide identified by this character-based approach. These diagnostic nucleotides could be useful in biodiversity assessments when ambiguous results are encountered in database searches that use a distance-based metric for nucleotide sequence comparisons. Information and images regarding specimens examined during this study are available online.     

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.