The current state of insect molecular systematics: a thriving Tower of Babel

Phylogeography and genetic variation of Triatoma dimidiata, the main Chagas disease vector in Central America, and its position within the genus Triatoma

Background

Among Chagas disease triatomine vectors, the largest genus, Triatoma, includes species of high public health interest. Triatoma dimidiata, the main vector throughout Central America and up to Ecuador, presents extensive phenotypic, genotypic, and behavioral diversity in sylvatic, peridomestic and domestic habitats, and non-domiciliated populations acting as reinfestation sources. DNA sequence analyses, phylogenetic reconstruction methods, and genetic variation approaches are combined to investigate the haplotype profiling, genetic polymorphism, phylogeography, and evolutionary trends of T. dimidiata and its closest relatives within Triatoma. This is the largest interpopulational analysis performed on a triatomine species so far.

Methodology and Findings

Triatomines from Mexico, Guatemala, Honduras, Nicaragua, Panama, Cuba, Colombia, Ecuador, and Brazil were used. Triatoma dimidiata populations follow different evolutionary divergences in which geographical isolation appears to have had an important influence. A southern Mexican–northern Guatemalan ancestral form gave rise to two main clades. One clade remained confined to the Yucatan peninsula and northern parts of Chiapas State, Guatemala, and Honduras, with extant descendants deserving specific status. Within the second clade, extant subspecies diversity was shaped by adaptive radiation derived from Guatemalan ancestral populations. Central American populations correspond to subspecies T. d. dimidiata. A southern spread into Panama and Colombia gave the T. d. capitata forms, and a northwestern spread rising from Guatemala into Mexico gave the T. d. maculipennis forms. Triatoma hegneri appears as a subspecific insular form.

Conclusions

The comparison with very numerous Triatoma species allows us to reach highly supported conclusions not only about T. dimidiata, but also on different, important Triatoma species groupings and their evolution. The very large intraspecific genetic variability found in T. dimidiata sensu lato has never been detected in a triatomine species before. The distinction between the five different taxa furnishes a new frame for future analyses of the different vector transmission capacities and epidemiological characteristics of Chagas disease. Results indicate that T. dimidiata will offer problems for control, although dwelling insecticide spraying might be successful against introduced populations in Ecuador.

Chagas disease is a serious parasitic disease of Latin America. Human contamination in poor rural or periurban areas is mainly attributed to haematophagous triatomine insects. Triatoma includes important vector species, as T. dimidiata in Central and Meso-America. DNA sequences, phylogenetic methods and genetic variation analyses are combined in a large interpopulational approach to investigate T. dimidiata and its closest relatives within Triatoma. The phylogeography of Triatoma indicates two colonization lineages northward and southward of the Panama isthmus during ancient periods, with T. dimidiata presenting a large genetic variability related to evolutionary divergences from a Mexican-Guatemalan origin. One clade remained confined to Yucatan, Chiapas, Guatemala and Honduras, with extant descendants deserving species status: T. sp. aff. dimidiata. The second clade gave rise to four subspecies: T. d. dimidiata in Guatemala and Mexico (Chiapas) up to Honduras, Nicaragua, Providencia island, and introduced into Ecuador; T. d. capitata in Panama and Colombia; T. d. maculipennis in Mexico and Guatemala; and T. d. hegneri in Cozumel island. This taxa distinction may facilitate the understanding of the diversity of vectors formerly included under T. dimidiata, their different transmission capacities and the disease epidemiology. Triatoma dimidiata will offer more problems for control than T. infestans in Uruguay, Chile and Brazil, although populations in Ecuador are appropriate targets for insecticide-spraying.

18S rRNA hyper-elongation and the phylogeny of Euhemiptera (Insecta: Hemiptera)

The small subunit of nuclear ribosomal RNA (SSU nrRNA), whose sedimentation is mostly 18S in eukaryotes, is considered a relatively conservative marker for resolving phylogenetic relationship at the order level or higher. Length variation in SSU nrDNA is common, and can be rather large in some groups. In studies of Hexapoda phylogeny, the SSU nrDNA has been repeatedly used as a marker. Sternorrhyncha has been rarely included. The lengths of SSU nrDNAs of sternorrhynchids, the basal group of Hemiptera identified in the previous study are 0.3-0.6 kb longer than the usual ones in Hexapoda (1.8-1.9 kb). To use the entire SSU nrDNA sequences or the length-variable parts could cause alignment trouble and therefore affect phylogenetic results, as shown in this study of Euhemiptera phylogeny. Two problems are particularly noticeable. One is that two hyper-variable regions flanking a short length-conservative region could become overlapped in the alignment. This will destroy the positional homology over a larger range. The other is that, when a base pair in a stem of the secondary structure is located near the length-variable regions (LVRs), the simultaneous positional homology of these two bases in the pair is always lost in the alignment results. In this study, the secondary structure model of Hexapoda SSU nrRNA was slightly adjusted and the LVR distributions in it were finely positioned. The noise caused by the hyper LVRs was eliminated and the simultaneous homology for the paired bases was recovered based on the secondary structure model. These corrections improved the quality of the data matrix and hence improved the resolving behavior of the algorithm used. This study provided more convincing evidence for resolving the Euhemiptera suborders phylogeny as (Archaeorrhyncha+(Clypeorrhyncha+(Coleorrhyncha+Heteroptera))). This result provided a more solid background for outgroup determination according to the phylogenetic studies inside each suborder. The problems caused by LVRs have seldom been well addressed. As phylogenetic reconstruction depends more on the data matrix itself than on the algorithm, and length variation of SSU/LSU rRNA exists more or less in any group, it is necessary to closely investigate the effect of rRNA length variation on alignment and phylogenetic reconstruction in more groups.

Comparison of five allopatric fruit fly parasitoid populations (Psyttalia species) (Hymenoptera: Braconidae) from coffee fields using morphometric and molecular methods

Morphometric studies of five allopatric parasitoid populations (genus Psyttalia Walker) from coffee plantations in Cameroon (Nkolbisson), Ghana (Tafo) and Kenya (Rurima, Ruiru and Shimba Hills) and one non-coffee population (from Muhaka, Kenya) were compared with individuals of Psyttalia concolor (Szépligeti), a species released in several biological control programmes in the Mediterranean Region since the 20th Century. Analyses of wing vein measurements showed the second submarginal cell of the fore wing and its adjoining veins had the heaviest principal component weights and served as the main contributing variables in the diagnostic differentiation of the populations. Two populations (Rurima and Ruiru) were found to be the closest to each other and with the strongest phenetic affinity toward P. concolor (and forming one cluster). Populations from Shimba Hills (of unknown identity), Nkolbisson (P. perproximus (Silvestri)) and Tafo formed a second cluster and were separated from P. concolor. Comparison using amplified fragment length polymorphism (AFLP) also showed the Shimba, Nkolbisson and Tafo populations forming a cluster in a dendrogram generated from their genetic distances, with the Shimba and Tafo populations placed as the most closely related species. Based on consistent morphological similarities, morphometric and ecological data coupled with the genetic evidence from AFLP data, the Shimba population is suggested as belonging to the P. perproximus group and, thus, represents a new occurrence record in Kenya. Our results also support earlier conclusion from cross mating data that populations from Rurima and Ruiru belong to the Psyttalia concolor species-group.

Molecular characterization of Gonatocerus tuberculifemur (Ogloblin) (Hymenoptera: Mymaridae), a prospective Homalodisca vitripennis (Germar) (Hemiptera: Cicadellidae) biological control candidate agent from South America: divergent clades

We genetically characterized the prospective South American egg parasitoid candidate, Gonatocerus tuberculifemur, of the glassy-winged sharpshooter (GWSS), Homalodisca vitripennis, for a neoclassical biological control program in California. Two molecular methods, inter-simple sequence repeat-polymerase chain reaction DNA fingerprinting and a phylogeographic approach inferred from the mitochondrial cytochrome oxidase subunit I gene (COI), were utilized. Five geographic populations from South America were analyzed; in addition, a phylogenetic analysis was performed with several named and one unnamed Gonatocerus species using the COI gene. DNA fingerprinting demonstrated a fixed geographic banding pattern difference in the population from San Rafael, Mendoza Province, Argentina. The COI analysis uncovered haplotype or geographic structure in G. tuberculifemur. A neighbour-joining distance (NJ) and a single most parsimonious tree (MP) clustered the populations into two well-supported distinct clades with strong bootstrap values (97-99% and 92-99%, respectively) with populations from San Rafael clustering into clade 2 and the rest of the populations clustering into clade 1. No haplotype sharing was observed between individuals from the two clades. Phylogenetic analyses performed by NJ and MP methods with 15 Gonatocerus species confirmed species boundaries and again uncovered two distinct clades in G. tuberculifemur with strong bootstrap support (95-100% and 68-100%, respectively). However, the NJ tree supported the morphologically defined relationships better than the MP tree. The molecular evidence in the present study is suggestive of a species level divergence. Because G. tuberculifemur is under consideration as a potential biological control agent for GWSS in California, understanding cryptic variation in this species is critical.

Population structure of Cicada barbara Stål (Hemiptera, Cicadoidea) from the Iberian Peninsula and Morocco based on mitochondrial DNA analysis

We assess the genetic history and population structure of Cicada barbara in Morocco and the Iberian Peninsula, based on analysis of the mitochondrial cytochrome b gene. The divergence between Morocco and the Iberian Peninsula populations was strongly corroborated by the molecular data, suggesting genetically isolated populations with a low level of gene flow. The Ceuta population from Spanish North Africa was more similar to the Iberian populations than the surrounding Moroccan populations, suggesting that the Strait of Gibraltar has not been acting as a strict barrier to dispersal while the Rif Mountains have. The Iberian Peninsula specimens showed a signature of demographic expansion before that which occurred in Morocco, but some of the assumptions related to the demographic parameters should be considered with caution due to the small genetic variation found. The high haplotype diversity found in Morocco implies higher demographic stability than in the Iberian Peninsula populations. These results do not, however, suggest a Moroccan origin for Iberian cicadas; but the most northwest region in Africa, such as Ceuta, might have acted as a southern refuge for Iberian cicadas during the most severe climatic conditions, from where they could expand north when climate improved. The separation of two subspecies within C. barbara (C. barbara lusitanica and C. barbara barbara) finds support with these results.

Application of DNA-based methods in forensic entomology

A forensic entomological investigation can benefit from a variety of widely practiced molecular genotyping methods. The most commonly used is DNA-based specimen identification. Other applications include the identification of insect gut contents and the characterization of the population genetic structure of a forensically important insect species. The proper application of these procedures demands that the analyst be technically expert. However, one must also be aware of the extensive list of standards and expectations that many legal systems have developed for forensic DNA analysis. We summarize the DNA techniques that are currently used in, or have been proposed for, forensic entomology and review established genetic analyses from other scientific fields that address questions similar to those in forensic entomology. We describe how accepted standards for forensic DNA practice and method validation are likely to apply to insect evidence used in a death or other forensic entomological investigation.

The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths

The entire mitochondrial genome of the tobacco hornworm, Manduca sexta (Lepidoptera: Spinghidae) was sequenced -- a circular molecular 15516 bp in size. The arrangement of the protein coding genes (PCGs) was the same as that found in the ancestral insect, however Manduca possessed the derived tRNA arrangement of CR-M-I-Q which has been found in all Lepidoptera sequenced to date. Additionally, Manduca, like all lepidopteran mt genomes, has numerous large intergenic spacer regions and microsatellite-like repeat regions. Nucleotide composition is highly A+T biased, and the lepidopterans have the second most biased nucleotide composition of the insect orders after Hymenoptera. Secondary structural features of the PCGs identified in other Lepidoptera were present but highly modified by the presence of microsatellite-like repeat regions which may significantly alter their function in the post-transcriptional modification of pre-mRNAs. Secondary structure models of the ribosomal RNA genes of Manduca are presented and are similar to those proposed for other insect orders. Conserved regions were identified within non-translated spacer regions which correspond to sites for the origin and termination of replication and transcription. Comparisons of gene variability across the order suggest that the mitochondrial genes most frequently used in phylogenetic analysis of the Lepidoptera, cox1 and cox2, are amongst the least variable genes in the genome and phylogenetic resolution could be improved by using alternative, higher variability genes such as nad2, nad3, nad4 and nad5.

DNA based cladograms augment the discovery of a new Ips species from China (Coleoptera: Curculionidae: Scolytinae)

The implementation of DNA in taxonomic study is in its infancy because the association of the amount and type of nucleotide change with species boundaries has not been fully examined for most taxa. Mitochondrial cytochrome c oxidase I (COI) nucleotide data is currently the most popular molecular marker for delimiting species boundaries and a standard pair-wise nucleotide divergence between groups of individuals has been suggested for the recognition of new species. It is unlikely that such a standard would be applicable across animal species, but the association of the amount and type of nucleotide change with species boundaries could help with the establishment of a taxon-specific DNA taxonomy. This study utilizes DNA data from nuclear and mitochondrial genes to improve the taxonomy of an important forest beetle pest, Ips. Amount and type of nucleotide difference are associated with monophyletic species based on a cladistic analysis of these data. As a result, a new species from China is described for a clade of beetles whose nucleotide differences exceeded the amount of evolutionary change observed within currently recognized species. The COI data are analyzed independently with an expanded taxon data set, including pair-wise nucleotide differences between recognized sister species. The wide range of average intraspecific pair-wise nucleotide difference (0-10.0%) suggests limitations to the application of a standard percent nucleotide difference as a means to identify species boundaries. At most, average COI nucleotide intraspecific difference provides an informal guide to identify potential clades that may warrant further systematic investigation.

Limited performance of DNA barcoding in a diverse community of tropical butterflies

DNA 'barcoding' relies on a short fragment of mitochondrial DNA to infer identification of specimens. The method depends on genetic diversity being markedly lower within than between species. Closely related species are most likely to share genetic variation in communities where speciation rates are rapid and effective population sizes are large, such that coalescence times are long. We assessed the applicability of DNA barcoding (here the 5' half of the cytochrome c oxidase I) to a diverse community of butterflies from the upper Amazon, using a group with a well-established morphological taxonomy to serve as a reference. Only 77% of species could be accurately identified using the barcode data, a figure that dropped to 68% in species represented in the analyses by more than one geographical race and at least one congener. The use of additional mitochondrial sequence data hardly improved species identification, while a fragment of a nuclear gene resolved issues in some of the problematic species. We acknowledge the utility of barcodes when morphological characters are ambiguous or unknown, but we also recommend the addition of nuclear sequence data, and caution that species-level identification rates might be lower in the most diverse habitats of our planet.

Molecular phylogeny and dating of an insular endemic moth radiation inferred from mitochondrial and nuclear genes: The genus Galagete (Lepidoptera: Autostichidae) of the Galapagos Islands

Galagete is a genus of microlepidoptera including 12 nominate species endemic to the Galapagos Islands. In order to better understand the diversification of this endemic insular radiation, to unravel relationships among species and populations, and to get insight into the early stages of speciation, we developed a phylogenetic reconstruction based on the combined mitochondrial cytochrome oxidase I (555bp) and II (453bp), and the nuclear elongation factor-1alpha (711bp) and wingless (351bp) genes. Monophyly of the genus is strongly supported in the Bayesian and maximum likelihood analyses suggesting a single colonization event by a common ancestor. Two cases of paraphyly observed between species are hypothesized to represent imperfect species limits for G. espanolaensis nested within the G. turritella clade, and introgressive hybridization or lineage sorting in the case of the population of G. protozona from Santa Fe nested within the G. gnathodoxa clade. A geologically calibrated, relaxed molecular clock model was used for the first time to unravel the chronological sequence of an insular radiation. The first split occurring within the Galagete lineage on the archipelago is estimated at 3.3+/-0.4million years ago. The genus radiated relatively quickly in about 1.8million years, and gives an estimated speciation rate of 0.8 species per million years. Although the colonization scenario shows a stochastic dispersal pattern, the arrival of the ancestor and the diversification of the radiation coincide with the chronological emergence of the major islands.

A curious coincidence: mosquito biodiversity and the limits of the Japanese encephalitis virus in Australasia

BACKGROUND

The mosquito Culex annulirostris Skuse (Diptera: Culicidae) is the major vector of endemic arboviruses in Australia and is also responsible for the establishment of the Japanese encephalitis virus (JEV) in southern Papua New Guinea (PNG) as well as its incursions into northern Australia. Papua New Guinea and mainland Australia are separated by a small stretch of water, the Torres Strait, and its islands. While there has been regular JEV activity on these islands, JEV has not established on mainland Australia despite an abundance of Cx. annulirostris and porcine amplifying hosts. Despite the public health significance of this mosquito and the fact that its adults show overlapping morphology with close relative Cx. palpalis Taylor, its evolution and genetic structure remain undetermined. We address a hypothesis that there is significant genetic diversity in Cx. annulirostris and that the identification of this diversity will shed light on the paradox that JEV can cycle on an island 70 km from mainland Australia while not establishing in Australia itself.

RESULTS

We sequenced 538 bp of the mitochondrial DNA cytochrome oxidase I gene from 273 individuals collected from 43 localities in Australia and the southwest Pacific region to describe the phylogeography of Cx. annulirostris and its sister species Cx. palpalis. Maximum Likelihood and Bayesian analyses reveal supporting evidence for multiple divergent lineages that display geographic restriction. Culex palpalis contained three divergent lineages geographically restricted to southern Australia, northern Australia and Papua New Guinea (PNG). Culex annulirostris contained five geographically restricted divergent lineages, with one lineage restricted to the Solomon Islands and two identified mainly within Australia while two other lineages showed distributions in PNG and the Torres Strait Islands with a southern limit at the top of Australia's Cape York Peninsula.

CONCLUSION

The existence of divergent mitochondrial lineages within Cx. annulirostris and Cx. palpalis helps explain the difficulty of using adult morphology to identify Cx. annulirostris and its ecological diversity. Notably, the southern limit of the PNG lineages of Cx. annulirostris coincides exactly with the current southern limit of JEV activity in Australasia suggesting that variation in these COI lineages may be the key to why JEV has not yet established yet on mainland Australia.

Phylogeny and Bayesian divergence time estimations of small-headed flies (Diptera: Acroceridae) using multiple molecular markers

The first formal analysis of phylogenetic relationships among small-headed flies (Acroceridae) is presented based on DNA sequence data from two ribosomal (16S and 28S) and two protein-encoding genes: carbomoylphosphate synthase (CPS) domain of CAD (i.e., rudimentary locus) and cytochrome oxidase I (COI). DNA sequences from 40 species in 22 genera of Acroceridae (representing all three subfamilies) were compared with outgroup exemplars from Nemestrinidae, Stratiomyidae, Tabanidae, and Xylophagidae. Parsimony and Bayesian simultaneous analyses of the full data set recover a well-resolved and strongly supported hypothesis of phylogenetic relationships for major lineages within the family. Molecular evidence supports the monophyly of traditionally recognised subfamilies Philopotinae and Panopinae, but Acrocerinae are polyphyletic. Panopinae, sometimes considered "primitive" based on morphology and host-use, are always placed in a more derived position in the current study. Furthermore, these data support emerging morphological evidence that the type genus Acrocera Meigen, and its sister genus Sphaerops, are atypical acrocerids, comprising a sister lineage to all other Acroceridae. Based on the phylogeny generated in the simultaneous analysis, historical divergence times were estimated using Bayesian methodology constrained with fossil data. These estimates indicate Acroceridae likely evolved during the late Triassic but did not diversify greatly until the Cretaceous.

Monophyly and phylogenetic relationships of Thereva and therevine genus-groups (Insecta:Diptera:Therevidae) based on EF-1α, 28S rDNA and mitochondrial 16S rDNA sequences

Phylogenetic analyses using 28S rDNA, elongation factor (EF)-1α, and mt 16S rDNA sequences were performed to test the monophyly of Thereva Latreille. Two of the three Afrotropical Thereva species groups lack the genitalia characters that unambiguously diagnose Thereva in the Holarctic Region, but phylogenetic relationships among Thereva species groups and therevine genera are poorly understood. Using an extensive taxonomic sample (39 of the 62 therevine genera) and Thereva, sensu lato (15 spp.), simultaneous analyses of all three gene partitions recovered Nearctic and Palaearctic Thereva species in a well supported clade that includes the Afrotropical seminitida-group but excludes the Afrotropical analis- and turneri-groups. Stronger phylogenetic signal from the EF-1α partition, measured by the skewness statistic and proportion of total parsimony informative characters, dominated conflicting signal from the 16S partition and weaker, but more congruent, signal from 28S. Reducing the taxonomic sample in analyses of Therevinae reduced homoplasy, increased phylogenetic structure and partitioned Bremer support values and reduced incongruence with 28S for the 16S partition. Although molecular analyses yielded partial recovery of informal therevine genus-groups, morphological diagnoses of higher-level groups are poorly supported with the exception of Cyclotelini. The ‘Holarctic radiation’ refers to a diverse clade of genera closely related to Pandivirilia Irwin & Lyneborg and Acrosathe Irwin & Lyneborg widely distributed throughout the Holarctic Region that is the sister-group to Thereva, sensu stricto. Results from these analyses underscore the importance of male and female genitalia characters in recognising monophyletic groups and regional endemism in therevine diversification.

Molecular systematics of Dolichopodidae (Diptera) inferred from COI and 12S rDNA gene sequences based on European exemplars

With ~7000 species in ~220 genera, the Dolichopodidae is one of the most speciose families of Diptera. Though the family as such is well defined, knowledge on the internal phylogenetic relationships is generally poor and although authors of successive monographs and catalogues indifferently listed most genera in specific subfamilies, their decisions were rarely based on sound phylogenetic analyses and never on molecular data. In a first attempt to unravel the phylogeny of Dolichopodidae, a combined COI + 12S rDNA dataset (1199 characters) of 119 samples of 101 European species was used in Bayesian (BAY), neighbour joining (NJ) and weighted/unweighted maximum parsimony analyses (MP). At the subfamily level, our study supports the monophyly of Dolichopodinae, Sympycninae, and Hydrophorinae (including Machaerium Haliday, 1832). Ten (Campsicnemus Haliday, 1851, Chrysotus Meigen, 1824, Dolichopus Latreille, 1796, Gymnopternus Loew, 1857, Medetera Fischer von Waldheim, 1819, Poecilobothrus Mik, 1878, Rhaphium Meigen, 1803, Teuchophorus Loew, 1857, Sciapus Zeller, 1842, Syntormon Loew, 1857) of the 14 multispecies genera formed monophyletic assemblages in all analyses and relationships among Argyra Macquart, 1834 species were supported in most analyses. At the subgeneric level, seven of the nine stable species-groups in Dolichopus as established during previous research were supported in most analyses. The validity of the recent transfer of Hercostomus chrysozygos Wiedemann, 1817 to Poecilobothrus was clearly supported in all analyses. Within Argyra and Rhaphium, interspecific relationships reflected previously used subgeneric classifications (Lasiargyra Mik, 1878, Leucostola Loew, 1857 and Argyra s.s. in Argyra; Porphyrops Meigen, 1824, Rhaphium s.s. and Xiphandrium Loew, 1857 in Rhaphium). Further, subclades within Medetera corresponded to species-groups defined by other authors featuring a different morphology and ecology. Anepsiomyia flaviventris (Meigen, 1824) most probably does not belong to Sympycninae but its current position within Peloropeodinae could not be confirmed.

Phylogenetic relationships within the leaf-mining flies (Diptera: Agromyzidae) inferred from sequence data from multiple genes

The leaf-mining flies (Diptera: Agromyzidae) are a diverse group whose larvae feed internally in leaves, stems, flowers, seeds, and roots of a wide variety of plant hosts. The systematics of agromyzids has remained poorly known due to their small size and morphological homogeneity. We investigated the phylogenetic relationships among genera within the Agromyzidae using parsimony and Bayesian analyses of 2965 bp of DNA sequence data from the mitochondrial COI gene, the nuclear ribosomal 28S gene, and the single copy nuclear CAD gene. We included 86 species in 21 genera, including all but a few small genera, and spanning the diversity within the family. The results from parsimony and Bayesian analyses were largely similar, with major groupings of genera in common. Specifically, both analyses recovered a monophyletic Phytomyzinae and a monophyletic Agromyzinae. Within the subfamilies, genera found to be monophyletic given our sampling include Agromyza, Amauromyza, Calycomyza, Cerodontha, Liriomyza, Melanagromyza, Metopomyza, Nemorimyza, Phytobia, and Pseudonapomyza. Several genera were found to be polyphyletic or paraphyletic including Aulagromyza, Chromatomyia, Phytoliriomyza, Phytomyza, and Ophiomyia. We evaluate our findings and discuss host-use evolution in light of current agromyzid taxonomy and two recent hypotheses of relationships based on morphological data.

Patterns of evolution of mitochondrial cytochrome c oxidase I and II DNA and implications for DNA barcoding

DNA barcoding has focused increasing attention on the use of specific regions of mitochondrial cytochrome c oxidase I and II genes (COI-COII) to diagnose and delimit species. However, our understanding of patterns of molecular evolution within these genes is limited. Here we examine patterns of nucleotide divergence in COI-COII within species and between species pairs of Lepidoptera and Diptera using a sliding window analysis. We found that: (1) locations of maximum divergence within COI-COII were highly variable among taxa surveyed in this study; (2) there was major overlap in divergence within versus between species, including within individual COI-COII profiles; (3) graphical DNA saturation analysis showed variation in percent nucleotide transitions throughout COI-COII and only limited association with levels of DNA divergence. Ultimately, no single optimally informative 600 bp location was found within the 2.3 kb of COI-COII, and the DNA barcoding region was no better than other regions downstream in COI. Consequently, we recommend that researchers should maximize sequence length to increase the probability of sampling regions of high phylogenetic informativeness, and to minimize stochastic variation in estimating total divergence.

The history of early bee diversification based on five genes plus morphology

Bees, the largest (>16,000 species) and most important radiation of pollinating insects, originated in early to mid-Cretaceous, roughly in synchrony with the angiosperms (flowering plants). Understanding the diversification of the bees and the coevolutionary history of bees and angiosperms requires a well supported phylogeny of bees (as well as angiosperms). We reconstructed a robust phylogeny of bees at the family and subfamily levels using a data set of five genes (4,299 nucleotide sites) plus morphology (109 characters). The molecular data set included protein coding (elongation factor-1alpha, RNA polymerase II, and LW rhodopsin), as well as ribosomal (28S and 18S) nuclear gene data. Analyses of both the DNA data set and the DNA+morphology data set by parsimony and Bayesian methods yielded a single well supported family-level tree topology that places Melittidae as a paraphyletic group at the base of the phylogeny of bees. This topology ("Melittidae-LT basal") is significantly better than a previously proposed alternative topology ("Colletidae basal") based both on likelihood and Bayesian methods. Our results have important implications for understanding the early diversification, historical biogeography, host-plant evolution, and fossil record of bees. The earliest branches of bee phylogeny include lineages that are predominantly host-plant specialists, suggesting that host-plant specificity is an ancestral trait in bees. Our results suggest an African origin for bees, because the earliest branches of the tree include predominantly African lineages. These results also help explain the predominance of Melittidae, Apidae, and Megachilidae among the earliest fossil bees.

Utility of mitochondrial DNA barcodes in species conservation

Molecular tools are a standard part of many conservation studies and can be informative at many different levels of analysis, although there are inherent limitations and strengths of different genes or parts of genes to inform specific questions. Animal DNA barcodes, 600- to 800-base-pair segments of the mitochondrial gene cytochrome oxidase I, have been proposed as a means to quantify global biodiversity. Although mitochondrial (mt) DNA has a long history of use at the species level, recent analyses suggest that the use of a single gene, particularly mitochondrial, is unlikely to yield data that are balanced, universally acceptable, or sufficient in taxonomic scope to recognize many species lineages. Mitochondrial and nuclear genomes have different patterns of evolution and modes of inheritance, which can result in very different assessments of biodiversity. The ramifications of choosing a particular definition of species (species concept) need to be carefully considered because current efforts have designated DNA barcodes as the universal species concept without demonstrating its superiority over preexisting concepts. The results of such a barcoding paradigm may include a failure to recognize significant portions of biodiversity or nuclear/mitochondrial mixed lineages and could spuriously focus conservation resources on populations with relatively minor mtDNA divergence. DNA barcodes are most likely to provide potentially useful information for groups that are already well studied, and such taxa do not constitute the majority of biodiversity or those in most need of research attention. DNA barcode-length sequences are an important source of data but, when used alone or out of context, may offer only a fraction of the information needed to characterize species while taking resources from broader studies that could produce information essential to robust and informed conservation decisions.

Molecular systematics and phylogeography of the cryptic species complex Baetis rhodani (Ephemeroptera, Baetidae)

Genetic studies have highlighted cryptic diversity in many well-known taxa including aquatic insects, with the general implication that there are more species than are currently recognised. Baetis rhodani Pictet are among the most widespread, abundant and ecologically important of all European mayflies (Ephemeroptera), and used widely as biological indicators of stream quality. Traditional taxonomy and systematics have never fully resolved differences among suspected cryptic species in the B. rhodani complex because morphological characters alone do not allow reliable distinction. This is particularly true among larvae, the life-stage used most widely in monitoring. Here, we assess the molecular diversity of this complex in one of the largest such studies of cryptic species in the order Ephemeroptera to date. Phylogenies were constructed using data from the mitochondrial cytochrome oxidase subunit I (COI) gene. Two monophyletic groups were recovered consisting of one major haplogroup and a second clade of 6 smaller but distinct haplogroups. Haplogroup divergence ranged from 0.2-3% (within) to 8-19% (among) with the latter values surpassing maxima typically reported for other insects, and provides strong evidence for cryptic species in the B. rhodani complex. The taxonomic status of these seven haplogroups remains undefined. Their distributions across Western Europe reveal no obvious geographic pattern, suggesting widespread diffusion of genetic lineages since the last glacial maximum. The implications of these findings are far-reaching given the ecological and bioindicator significance of what now appears to be several taxa.

No sympatric speciation here: multiple data sources show that the ant Myrmica microrubra is not a separate species but an alternate reproductive morph of Myrmica rubra

No aspect of speciation is as controversial as the view that new species can evolve sympatrically, among populations in close physical contact. Social parasitism has been suggested to yield necessary disruptive selection for sympatric speciation. Recently, mitochondrial DNA phylogeography has shown that the ant Myrmica microrubra is closely related to its host, Myrmica rubra, leading to the suggestion that sympatric speciation has occurred. We investigated the relationships between the two ant forms using mitochondrial and nuclear DNA sequences, microsatellite genotyping and morphometrics. Molecular phylogenetic and population structure analyses showed that M. microrubra does not evolve separately to its host but rather shares a gene pool with it. Probability analysis showed that mitochondrial DNA data previously adduced in favour of sympatric speciation do not in fact do so. Morphometrically, M. microrubra is most readily interpreted as a miniature queen form of M. rubra, not a separate species. Myrmica microrubra is not an example of speciation. The large (typical M. rubra) and small (M. microrubra) queen forms are alternative reproductive strategies of the same species. Myrmica microrubraSeifert 1993 is consequently synonymized here with M. rubra Linnaeus, 1758.

Linking patterns and processes of species diversification in the cone flies Strobilomyia (Diptera: Anthomyiidae)

Phytophagous insects provide useful models for the study of ecological speciation. Much attention has been paid to host shifts, whereas situations where closely related lineages of insects use the same plant during different time periods have been relatively neglected in previous studies of insect diversification. Flies of the genus Strobilomyia are major pests of conifers in Eurasia and North America. They are specialized feeders in cones and seeds of Abies (fir), Larix (larch) ,and Picea (spruce). This close association is accompanied by a large number of sympatric Strobilomyia species coexisting within each tree genus. We constructed a molecular phylogeny with a 1320 base-pair fragment of mitochondrial DNA that demonstrated contrasting patterns of speciation in larch cone flies, as opposed to spruce and fir cone flies; this despite their comparable geographic distributions and similar resource quality of the host. Species diversity is the highest on larch, and speciation is primarily driven by within-host phenological shifts, followed by allopatric speciation during geographical expansion. By contrast, fewer species exploit spruce and fir, and within-host phenological shifts did not occur. This study illustrates within-host adaptive radiation through phenological shifts, a neglected mode of sympatric speciation.

Short‐term impact of disturbance on genetic diversity and structure of Indonesian populations of the butterflyDrupadia thedain East Kalimantan

We investigated the short-term impact of disturbance on genetic diversity and structure of the tropical butterfly Drupadia theda Felder (Lepidoptera: Lycaenidae). Populations were sampled from five landscapes in East Kalimantan (Borneo, Indonesia) which were differentially disturbed by selective logging and the 1997/1998 El Niño Southern Oscillation (ENSO)-induced drought and fires. Sampling occurred before (in 1997) and after the forest fires (in 1998, 1999, 2000, and 2004). Drupadia theda populations underwent serious population size reductions following the 1997/1998 ENSO event. For a total of 208 individuals, we sequenced a 509-bp segment of mtDNA containing the control region plus the 5' end of the 12S rDNA gene. Haplotype diversity in D. theda populations ranged from 0.468 to 0.953. Just after the 1997/1998 ENSO event, number of recorded individuals and genetic diversity were very low in D. theda populations sampled in the two severely burned areas and in a small pristine forest fragment that was surrounded by burned forest and thereby affected by drought. Interestingly, higher levels of genetic diversity were observed in logged forest compared to proximate pristine forest. After 1998, the genetic composition within the three ENSO-disturbed areas diverged. In the twice-burned forest, the genetic diversity in 1999 already approached pre-fire levels, while it remained nearly unchanged in proximate once-burned forest. Our data suggest that the 1997/1998 ENSO-induced drought and fires caused massive reductions in the genetic diversity of D. theda and that population recoveries were linked to their geographical position relative to patches of unburned forest (and thus to source populations).

Analysis of family-level relationships in bees (Hymenoptera: Apiformes) using 28S and two previously unexplored nuclear genes: CAD and RNA polymerase II

We analyzed a combined data set of two protein-coding nuclear genes (CAD and RNA polymerase II) and a nuclear ribosomal gene (28S D2-D4 region) for 68 bee species and 11 wasp outgroups. Our taxon sampling included all seven extant bee families, 17 of 20 subfamilies, and diverse tribes. Wasp outgroups included the two families most closely related to bees: Crabronidae and Sphecidae. We analyzed the combined and single gene data sets using parsimony and Bayesian methods, which yielded largely congruent results. Our results provide reasonably strong support for family and subfamily-level relationships among bees. Our data set strongly supports the sister-group relationship of the Colletidae and Stenotritidae, and places Halictidae as sister to this clade combined. Our analyses place the Melittidae and the long-tongued (LT) bee clade (Apidae+Megachilidae) near the base of the tree with Colletidae (and Stenotritidae) in a fairly highly derived position. This topology ("Melittidae-LT basal") was obtained in previous morphological studies under certain methods of character coding. A more widely accepted tree topology that places Colletidae (and/or Stenotritidae) as sister to all other bees ("Colletidae basal") is not supported by our data. The "Melittidae-LT basal" hypothesis may better explain patterns in the bee fossil record as well as historical biogeography of certain bee groups. Our results provide new insights into higher-level bee phylogeny and indicate that CAD, RNA polymerase II, and 28S are useful data sets for resolving Cretaceous-age divergences in bees and other Hymenoptera.

Phylogeny of the cricket subfamily Eneopterinae (Orthoptera, Grylloidea, Eneopteridae) based on four molecular loci and morphology

The phylogenetic relationships of 39 species of Eneopterinae crickets are reconstructed using four molecular markers (16S rRNA, 12S rRNA, cytochrome b, 18S rRNA) and a large morphological data set. Phylogenetic analysis via direct optimisation of DNA sequence data using parsimony as optimality criterion is done for six combinations of weighting parameter sets in a sensitivity analysis. The results are discussed in a twofold purpose: first, in term of significance of the molecular markers for phylogeny reconstruction in Ensifera, as our study represents the first molecular phylogeny performed for this insect suborder at this level of diversity; second, in term of corroboration of a previous phylogeny of Eneopterinae, built on morphological data alone. The four molecular markers all convey phylogenetic signal, although variously distributed on the tree. The monophyly of the subfamily, that of three over five tribes, and of 10 over 13 genera, are recovered. Finally, previous hypotheses on the evolution of acoustic devices and signals in the Eneopterinae clade are briefly tested, and supported, by our new data set.

Disturbed population genetics: suspected introgressive hybridization between two Mnais damselfly species (Odonata)

Mnais costalis and M. pruinosa are damselflies (Odonata: Calopterygidae) with low dispersal abilities, both during their aquatic stream-living immature stage and their flying adult stage. A previous nuclear DNA (nDNA) sequencing and morphology study showed that these two species are very closely related, and cohabit widely in western Japan. The two species, however, segregate microhabitats along a stream: M. costalis lives in the lower reaches, and M. pruinosa in the upper reaches. In this study, our analyses were based on mitochondrial DNA (mtDNA), which usually mutates faster and is more variable among individuals than nDNA, and which is inherited maternally. We found that most COI haplotypes were shared between the two species, and that for most study sites interspecific riverine genetic structures were not clarified by mtDNA analysis. Incongruent population genetic structures based on nDNA and mtDNA suggested hybridization and introgression of mtDNA between the two species.

Mitochondrial phylogeny of pine cone beetles (Scolytinae, Conophthorus) and their affiliation with geographic area and host

Pine cone beetles (Conophthorus spp.) feed and kill immature cones of Pinus species, thereby reducing seed production and seriously impairing reforestation of forest ecosystems. Population variation of Conophthorus reproductive behavior has hampered the development of semiochemical control of these pests. This difficulty is compounded by a lack of taxonomic knowledge and species diagnostic characters. Researchers and managers rely, in part, on host associations and geographic locality for species identifications and these have arguable taxonomic utility. However, host use and/or geographic separation may influence Conophthorus lineage diversification. To improve Conophthorus taxonomy and understand the association of host and geography with lineage diversification, a phylogeny of 43 individuals, including all valid species and a robust sample of C. ponderosae from different hosts, is reconstructed using 785 nucleotides of the 3'-end of the mitochondrial cytochrome oxidase I gene. Thirty trees were recovered in a parsimony analysis and the strict consensus was well resolved and supported by branch support measures. Conophthorus was monophyletic but mitochondrial polyphyly was uncovered for several species. The data also suggested an underestimation of species diversity. Phylogenetically related Conophthorus lineages were significantly associated with geographic proximity but not with host, as indicated by comparisons of character optimized geographic distributions and host associations against randomized distributions of these attributes on the parsimony tree. These results suggest that geographic separation better explains the mode of Conophthorus lineage diversification than does host specialization. Based on these results, researchers and managers of Conophthorus should consider populations as potentially different evolutionary entities until species boundaries are delineated via a robust phylogenetic revision of Conophthorus.

The invasive coconut mite Aceria guerreronis (Acari: Eriophyidae): origin and invasion sources inferred from mitochondrial (16S) and nuclear (ITS) sequences

Over the past 30 years the coconut mite Aceria guerreronis Keifer has emerged as one of the most important pests of coconut and has recently spread to most coconut production areas worldwide. The mite has not been recorded in the Indo-Pacific region, the area of origin of coconut, suggesting that it has infested coconut only recently. To investigate the geographical origin, ancestral host associations, and colonization history of the mite, DNA sequence data from two mitochondrial and one nuclear region were obtained from samples of 29 populations from the Americas, Africa and the Indo-ocean region. Mitochondrial DNA 16S ribosomal sequences were most diverse in Brazil, which contained six of a total of seven haplotypes. A single haplotype was shared by non-American mites. Patterns of nuclear ribosomal internal transcribed spacer (ITS) variation were similar, again with the highest nucleotide diversity found in Brazil. These results suggest an American origin of the mite and lend evidence to a previous hypothesis that the original host of the mite is a non-coconut palm. In contrast to the diversity in the Americas, all samples from Africa and Asia were identical or very similar, consistent with the hypothesis that the mite invaded these regions recently from a common source. Although the invasion routes of this mite are still only partially reconstructed, the study rules out coconut as the ancestral host of A. guerreronis, thus prompting a reassessment of efforts using quarantine and biological control to check the spread of the pest.

Validation of a DNA-based method for identifying Chrysomyinae (Diptera: Calliphoridae) used in a death investigation

Many authors have proposed DNA-based methods for identifying an insect specimen associated with human remains. However, almost no attempt has been made to validate these methods using additional observations. We tested a protocol for identifying insects in the blow fly subfamily Chrysomyinae (Diptera: Calliphoridae) often found to be associated with a human corpse in Canada or the USA. This method uses phylogenetic analysis of DNA sequence from a short segment of the mitochondrial gene for cytochrome oxidase one (COI). Test chrysomyine COI sequences were obtained from 245 newly sequenced specimens and 51 specimens from the published literature. Published sequences from representatives of nonchrysomyine genera were also included to check for the possibility of a false positive identification. All of the chrysomyine test haplotypes were correctly identified with strong statistical support, and there were no false positives. This method appears to be an accurate and robust technique for identifying chrysomyine species from a death investigation in this geographic region. The far northern species Protophormia atriceps was not evaluated; therefore, caution is required in applying this method at very high latitudes in North America.

DNA barcodes for biosecurity: invasive species identification

Biosecurity encompasses protecting against any risk through 'biological harm', not least being the economic impact from the spread of pest insects. Molecular diagnostic tools provide valuable support for the rapid and accurate identification of morphologically indistinct alien species. However, these tools currently lack standardization. They are not conducive to adaptation by multiple sectors or countries, or to coping with changing pest priorities. The data presented here identifies DNA barcodes as a very promising opportunity to address this. DNA of tussock moth and fruit fly specimens intercepted at the New Zealand border over the last decade were reanalysed using the cox1 sequence barcode approach. Species identifications were compared with the historical dataset obtained by PCR-RFLP of nuclear rDNA. There was 90 and 96% agreement between the methods for these species, respectively. Improvements included previous tussock moth 'unknowns' being placed to family, genera or species and further resolution within fruit fly species complexes. The analyses highlight several advantages of DNA barcodes, especially their adaptability and predictive value. This approach is a realistic platform on which to build a much more flexible system, with the potential to be adopted globally for the rapid and accurate identification of invasive alien species.

Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles)

Expressed sequence tag (EST) sequences can provide a wealth of data for phylogenetic and genomic studies, but the utility of these resources is restricted by poor taxonomic sampling. Here, we use small EST libraries (<1,000 clones) to generate phylogenetic markers across a broad sample of insects, focusing on the species-rich Coleoptera (beetles). We sequenced over 23,000 ESTs from 34 taxa, which produced 8,728 unique sequences after clustering nonredundant sequences. Between taxa, the sequences could be grouped into 731 gene clusters, with the largest corresponding to mitochondrial DNA transcripts and gene families chymotrypsin, actin, troponin, and tubulin. While levels of paralogy were high in most gene clusters, several midsized clusters including many ribosomal protein (RP) genes appeared to be free of expressed paralogs. To evaluate the utility of EST data for molecular systematics, we curated available transcripts for 66 RP genes from representatives of the major groups of Coleoptera. Using supertree and supermatrix approaches for phylogenetic analysis, the results were consistent with the emerging phylogenetic conclusions about basal relationships in Coleoptera. Numerous small EST libraries from a taxonomically densely sampled lineage can provide a core set of genes that together act as a scaffold in phylogenetic reconstruction, comparative genomics, and studies of gene evolution.

Molecular characterization of closely related species in the parasitic genus Encarsia (Hymenoptera: Aphelinidae) based on the mitochondrial cytochrome oxidase subunit I gene

The genus Encarsia Förster includes parasitoid species that are effective natural enemies of whitefly and armoured scale insect agricultural pests. Within this genus, several species groups have been recognized on the basis of morphological similarity, although their monophyly appears uncertain. It is often difficult to separate morphologically similar species, and there is evidence that some species could in fact be complexes of cryptic species. Their correct identification is fundamental for biological control purposes. Recently, due to unreliability of morphological characters, molecular techniques have been investigated to identify markers that differentiate closely related species. In this study, DNA variation in an approximately 900 bp segment of the mitochondrial cytochrome oxidase subunit I (COI) gene was examined by both sequencing and PCR-RFLP. Two pairs of species that are difficult to distinguish morphologically were analysed: Encarsia formosa Gahan and Encarsialuteola Howard, belonging to the luteola group, and two populations of Encarsiasophia (Girault & Dodd) from Pakistan and Spain, belonging to the strenua group, recently characterized as cryptic species. High sequence divergence and species-specific restriction patterns clearly differentiate both species pairs. Parsimony analysis of the nucleotide sequences was also performed, including Encarsiahispida De Santis (luteola group) and Encarsia protransvena Viggiani (strenua group). Two monophyletic clades supporting the two groups of species considered were resolved. The results of this study support the use of the COI gene as a useful marker in separating species of Encarsia, for which morphological differences are subtle. Moreover, the COI gene appears potentially useful for understanding phylogenetic relationships in this genus.

Phylogenetic relationships of the New World Troidini swallowtails (Lepidoptera: Papilionidae) based on COI, COII, and EF-1α genes

A phylogeny of the Neotropical members of the Tribe Troidini (Lepidoptera: Papilionidae) was obtained with sequences of three protein-coding genes: two mitochondrial (COI and COII), and one nuclear (EF-1alpha). Parsimony and Bayesian analyses of 33 taxa resulted in very similar trees regardless of method used with the 27 troidines always forming a monophyletic clade. Within Troidini, the genus Battus is sister group to the remaining troidines, followed by a clade formed by the Paleotropical taxa (here represented by three exemplars). The genus Euryades is the next branch, and sister group of Parides. The genus Parides is monophyletic, and is divided into four main groups by Maximum Parsimony analysis, with the most basal group composed of tailed species restricted to SE Brazil. Character optimization of ecological and morphological traits over the phylogeny proposed for troidines indicated that the use of several species of Aristolochia is ancestral over the use of few or a single host-plant. For the other three characters, the ancestral states were the absence of long tails, forest as the primary habitat and oviposition solitary or in loose group of several eggs.

Detection, identification and geographical distribution of European corn borer larval parasitoids using molecular markers

Biological control requires specific tools for the accurate detection and identification of natural enemies, and to detect unusual variations in their density, which may follow changes in agricultural practices. Here we have developed specific molecular markers to detect Lydella thompsoni (Herting) and Pseudoperichaeta nigrolineata (Walker) (Diptera: Tachinidae) within the European corn borer, Ostrinia nubilalis (Hübner) (Lepidoptera: Crambidae). Primers amplifying fragments of the mitochondrial COI gene were designed following alignment of comparable sequences for a range of parasitoid and host species. Each of the primer pairs proved to be species specific to a tachinid species, amplifying DNA fragments of 191 and 91 bp in length for L. thompsoni and P. nigrolineata, respectively. This DNA-based technique allowed molecular evaluation of parasitism in O. nubilalis natural populations. In order to study the geographical distribution of both species in France, O. nubilalis diapausing larvae in maize stalks were collected from 12 locations over the whole country. The molecular evaluation of parasitism was compared with the traditional method of maintaining O. nubilalis populations in controlled conditions before breaking off the diapause. The percentage parasitism found in both species of tachinids was higher--approximately three times--using the molecular method, suggesting an underestimation by the traditional rearing protocol. Tachinid parasitism on O. nubilalis was not significantly different between geographical areas (south, central and north France) for both species. This study shows that molecular methods are very promising for the correct detection and identification of tachinid parasitoids in natural field populations.