Comprehensive molecular sampling yields a robust phylogeny for geometrid moths (Lepidoptera: Geometridae)

Background

The moth family Geometridae (inchworms or loopers), with approximately 23 000 described species, is the second most diverse family of the Lepidoptera. Apart from a few recent attempts based on morphology and molecular studies, the phylogeny of these moths has remained largely uninvestigated.

Methodology/Principal Findings

We performed a rigorous and extensive molecular analysis of eight genes to examine the geometrid affinities in a global context, including a search for its potential sister-taxa. Our maximum likelihood analyses included 164 taxa distributed worldwide, of which 150 belong to the Geometridae. The selected taxa represent all previously recognized subfamilies and nearly 90% of recognized tribes, and originate from all over world. We found the Geometridae to be monophyletic with the Sematuridae+Epicopeiidae clade potentially being its sister-taxon. We found all previously recognized subfamilies to be monophyletic, with a few taxa misplaced, except the Oenochrominae+Desmobathrinae complex that is a polyphyletic assemblage of taxa and the Orthostixinae, which was positioned within the Ennominae. The Sterrhinae and Larentiinae were found to be sister to the remaining taxa, followed by Archiearinae, the polyphyletic assemblage of Oenochrominae+Desmobathrinae moths, Geometrinae and Ennominae.

Conclusions/Significance

Our study provides the first comprehensive phylogeny of the Geometridae in a global context. Our results generally agree with the other, more restricted studies, suggesting that the general phylogenetic patterns of the Geometridae are now well-established. Generally the subfamilies, many tribes, and assemblages of tribes were well supported but their interrelationships were often weakly supported by our data. The Eumeleini were particularly difficult to place in the current system, and several tribes were found to be para- or polyphyletic.     

A nuclear gene for higher level phylogenetics: phosphoenolpyruvate carboxykinase tracks mesozoic-age divergences within Lepidoptera (Insecta)

The sequence of phosphoenolpyruvate carboxykinase (PEPCK) has been previously identified as a promising candidate for reconstructing Mesozoic-age divergences (Friedlander, Regier, and Mitter 1992, 1994). To test this hypothesis more rigorously, 597 nucleotides of aligned PEPCK coding sequence (approximately 30% of the coding region) were generated from 18 species representing Mesozoic-age lineages of moths (Insecta: Lepidoptera) and outgroup taxa. Relationships among basal Lepidoptera are well established by morphological analysis, providing a strong test for the utility of a gene which has not previously been used in systematics. Parsimony and other phylogenetic analyses were conducted on nucleotides by codon positions (nt1, nt2, nt3) separately and in combination, and on amino acids, for comparison to the test phylogeny. The highest concordance was achieved with nt1 + nt2, for which one of two most-parsimonious trees was identical to the test phylogeny, and with all nucleotides when nt3 was down-weighted sevenfold or higher, for which a single most-parsimonious tree identical to the test phylogeny resulted. Substitutions in nt3 approached saturation in many, but not all, pairwise comparisons and their exclusion or severe downweighting greatly increased the degree of concordance with the test phylogeny. Neighbor-joining analysis confirms this finding. The utility of PEPCK for phylogenetics is demonstrated over a time span for which few other suitable genes are currently available.      

Macroevolution of hoverflies (Diptera: Syrphidae): the effect of using higher‐level taxa in studies of biodiversity,and correlates of species richness

We test a near‐complete genus level phylogeny of hoverflies (Diptera: Syrphidae) for consistency with a null model of clade growth having uniform probabilities of speciation and extinction among contemporaneous species. The phylogeny is too unbalanced for this null model. Importantly, the degree of imbalance in the phylogeny depends on whether the phylogeny is analysed at the genus level or species level, suggesting that genera ought not to be used uncritically as surrogates for species in large‐scale evolutionary analyses. Tests for a range of morphological, life‐history and ecological correlates of diversity give equivocal results, but suggest that high species‐richness may be associated with sexual selection and diet breadth. We find no correlation between species‐richness and either body size or reproductive rate.     

Sequential sampling plan for Cameraria ohridella (Lepidoptera: Gracillariidae) on horse chestnut tree

A fixed precision sequential sampling plan for estimating the density of the horse chestnut, Aesculus hippocastanum L., leafminer Cameraria ohridella Deschka & Dimic (Lepidoptera: Gracillariidae) was developed. Data were collected from 2002 to 2004 in Turin, northwestern Italy, with the aim of developing a sampling strategy for estimating populations of C. ohridella mines. Taylor's power law was used as a regression model. Sampling parameters were estimated from 216 data sets, and an additional 110 independent data sets were used to validate the fixed precision sequential sampling plan with resampling software. Covariance analysis indicated that there were not significant differences in the coefficient of Taylor's power law between heights of the foliage, months, and years. Dispersion patterns of C. ohridella were determined to be aggregated. The parameters of the Taylor's power law were used to calculate minimum sample sizes and sampling stop lines for different precision levels. Considering a mean density value of five mines per leaf, an average sample number of only 49 leaves was necessary to achieve a desired precision level of 0.25. As the precision level was increased to 0.10, the average sample size increased to 303 leaves. The sequential sampling plan should provide an effective management of C. ohridella in the urban areas, minimizing sampling time and cost, and at the same should be an effective tool to reduce insecticide applications and prevent the esthetic damage.     

A new nuclear gene for insect phylogenetics: dopa decarboxylase is informative of relationships within Heliothinae (Lepidoptera: Noctuidae)

The lack of a readily accessible roster of nuclear genes informative at various taxonomic levels is a bottleneck for molecular systematics. In this report, we describe the first phylogenetic application of the sequence that encodes the enzyme dopa decarboxylase (DDC). For 14 test species within the noctuid moth subfamily Heliothinae that represent the previously best-supported groupings, a 690-bp fragment of DDC resolved relationships that are largely concordant with prior evidence from elongation factor-1 alpha (EF-1 alpha), morphology, and allozymes. Although both synonymous and nonsynonymous changes occur in DDC substantially more rapidly than they do in EF-1 alpha, DDC divergences within Heliothinae are below saturation at all codon positions. Analysis of DDC and EF-1 alpha in combination resulted in increased bootstrap support for several groupings. As a first estimate of previously unresolved relationships, DDC sequences were analyzed from 16 additional heliothines, for a total of 30 heliothine species plus outgroups. Previous relationships based on DDC were generally stable with increased taxon sampling, although a two- to eightfold downweighting of codon position 3 was required for complete concordance with the 14-species result. The weighted strict consensus trees were largely resolved and were congruent with most although not all previous hypotheses based on either morphology or EF-1 alpha. The proposed phylogeny suggests that the major agricultural pest heliothines belong to a single clade, characterized by polyphagy and associated life history traits, within this largely host-specific moth subfamily. DDC holds much promise for phylogenetic analysis of Tertiary-age animal groups.     

Dispersion statistics and a sampling plan for Helicoverpa (Lepidoptera: Noctuidae) on fresh-market tomatoes (Lycopersicon esculentum)

Abstract  Helicoverpa spp. is the primary pest in the Australian fresh-market tomato industry. We describe the spatial distribution of Helicoverpa spp. eggs on fresh-market tomato crops in the Goulburn Valley region of Victoria, and present a sequential sampling plan for monitoring population densities. The distribution of Helicoverpa spp. eggs was highly contagious, as indicated by a Taylor's b -value of 1.59. This high level of contagion meant that relatively large sample sizes would need to be collected to obtain an estimate of population density. High-precision sampling plans generally necessitated impractical sample sizes, and thus the plan we present is a relatively low-precision level plan (SE/mean = 0.3). Nonetheless, this level of precision is considered adequate for most agronomic scenarios. The plan was validated using a statistical re-sampling approach. The level of precision achieved was generally close to the nominal level. Likewise, the number of samples collected generally showed little departure from the theoretically calculated minimum sample size.     

Exploration of data partitioning in an eight‐gene data set: phylogeny of metalmark moths (Lepidoptera,Choreutidae)

Rota, J. & Wahlberg, N. (2012). Exploration of data partitioning in an eight‐gene data set: phylogeny of metalmark moths (Lepidoptera, Choreutidae). —Zoologica Scripta, 41, 536–546. Molecular data sets for phylogenetic inference continue to increase in size, especially with respect to the number of genes sampled. As more and more genes are included in analyses, the importance of partitioning the data to avoid problems that can arise from underparameterization becomes more apparent. With an eight‐gene data set from 38 metalmark moth species (12 genera represented) and three outgroups, we explored different data partitioning strategies and their influence on convergence and mixing of Markov Chains Monte Carlo in a Bayesian setting. We found that in larger data sets, with an increase in the number of partitions that are made a priori (e.g. by gene and codon position), convergence and mixing become poor. This problem can be overcome by using a recently published algorithm in which homologous sites are grouped into blocks with similar evolutionary rates that can then be modelled as separate data subsets. Using this novel approach to data partitioning, our analyses resolve with strong support relationships among the genera of metalmark moths. Support for the monophyly of the family, the two subfamilies and all genera except Hemerophila is strong. Hemerophila is broken into two separate clades, Hemerophila sensu stricto and another well‐supported clade. To render Hemerophila monophyletic, we describe a new genus, Ornarantia Rota, gen. nov., and transfer 18 species from Hemerophila to it. The type species of Ornarantia is Hemerophila laciniosella Busck, 1914.     

Larval Case Architecture and Implications of Host‐Plant Associations for North American Coleophora (Lepidoptera; Coleophoridae)1

The case‐bearing moths of North America are represented by a single genus, Coleophora, which contains approximately 144 described species. All are external seed or leaf miners that inhabit portable silk cases during most of the larval stage. Architectural and ecological characters from larval cases were used in cladistic analysis to investigate existing case groups for 32 North American species of Coleophora. Cladistic analysis confirmed monophyly of certain case groups, but not of others. Host‐plant preferences were also examined. The pattern of host plant use reflects more closely preference for certain plant tissues (seeds versus leaves) and growth forms (herbaceous versus woody) with exploitation of different plant taxa, rather than preference for certain plant taxa with exploitation of different plant tissues.     

False codling moth Thaumatotibia leucotreta (Lepidoptera,Tortricidae) larvae are chill‐susceptible

Abstract This study reports on the low temperature tolerance and cold hardiness of larvae of false codling moth, Thaumatotibia leucotreta. We found that larvae have mean critical thermal minima (lower limits of activity) of 6.7°C which was influenced by feeding status. The effects of low temperature exposure and duration of exposure on larval survival were assessed and showed that the temperature at which 50% of the population survives is ?11.5 ± 0.3°C after 2 h exposure. The supercooling point (SCP, i.e., freezing temperature) was investigated using a range of cooling rates and under different conditions (feeding and hydration status) and using inoculative freezing treatments (in contact with water or orange juice). The SCP decreased significantly from ?15.6°C to ?17.4°C after larvae were fasted for 24 h. Twenty‐four hour treatments at either high or low relative humidity (95.9% or 2.4%) also significantly decreased SCP to ?17.2°C and ?18.2°C respectively. Inoculative freezing (by water contact) raised SCP from ?15.6°C to ?6.8°C which could have important implications for post‐harvest sterilization. Cooling rates did not affect SCP which suggests that there is limited phenotypic plasticity of SCP during the larval life‐stage, at least over the short time‐scales investigated here. In conclusion, larvae of T. leucotreta are chill‐susceptible and die upon freezing. These results are important in understanding this pest's response to temperature variation, understanding pest risk status and improving post‐harvest sterilization efficacy.     

A sampling plan for population dynamics studies on currant clearwing,Synanthedon tipuliformis (Lepidoptera: Sesiidae)

Abstract

Sampling techniques for eggs, larvae, and pupae of the currant clearwing, Synanthedon tipuliformis (Clerck), attacking blackcurrant were developed, and their precision was evaluated. Reliable population estimates for the egg and early larval stages (standard error < 10%) were obtained by sampling one cane with at least two age groups of wood from the north and south halves of seven bushes in nine blocks. Similar precision was obtained for post-winter larvae from samples comprising three canes from each half of the bushes, but using this sampling scheme a lower precision (S.E.?25–30%) had to be accepted for overwintering mortality factors. The pupal population was estimated from the numbers of live larvae at the end of the post-winter feeding stage, and cross-checked from the number of emergence holes in the 1-year-old wood taken for egg sampling the following year. This procedure gave estimates of similar reliability to those for the egg and larval stages.     

Interleukin‐6 (G‐174C) and tumour necrosis factor‐alpha (G‐308A) gene polymorphisms in geriatric patients with chronic periodontitis

doi:10.1111/j.1741‐2358.2009.00291.x
Interleukin‐6 (G‐174C) and tumour necrosis factor‐alpha (G‐308A) gene polymorphisms in geriatric patients with chronic periodontitis Background and objective: Periodontitis is a chronic inflammatory disease, and genetic factors may have an important role in its severity. Polymorphisms in the promoter regions of the interleukin‐6 (IL‐6) and tumour necrosis factor‐α (TNF‐α) genes have been reported to cause changes in the production of these cytokines. The aim of this study was to evaluate the possible role of IL‐6 (G?174C) and tumour necrosis factor (G?308A) polymorphisms, in the severity of chronic periodontitis in an elderly population. Materials and methods: In this study, a group of 65 elderly women, comprising 17 patients with moderate chronic periodontitis, 21 with severe chronic periodontitis and 27 healthy patients were selected. DNA was isolated from all subjects, and polymerase chain reaction was used to study the IL‐6 and TNF‐α gene polymorphisms. Results: The results of this study showed a significant difference in the allele and genotype frequencies of IL‐6 gene polymorphism between patients with periodontal disease and controls. Subjects carrying the G/G genotype of IL‐6 were most severely affected by periodontitis. The TNF‐α gene polymorphism showed no association with chronic periodontitis between patients and controls. Conclusion: The results suggest that the IL‐6 gene polymorphism may be associated with chronic periodontitis, and that TNF‐α gene polymorphism may not be involved in the progression of chronic periodontitis in the population of elderly Brazilian women.     

A robust method for estimating gene expression states using Affymetrix microarray probe level data

Background  

Microarray technology is a high-throughput method for measuring the expression levels of thousand of genes simultaneously. The observed intensities combine a non-specific binding, which is a major disadvantage with microarray data. The Affymetrix GeneChip assigned a mismatch (MM) probe with the intention of measuring non-specific binding, but various opinions exist regarding usefulness of MM measures. It should be noted that not all observed intensities are associated with expressed genes and many of those are associated with unexpressed genes, of which measured values express mere noise due to non-specific binding, cross-hybridization, or stray signals. The implicit assumption that all genes are expressed leads to poor performance of microarray data analyses. We assume two functional states of a gene - expressed or unexpressed - and propose a robust method to estimate gene expression states using an order relationship between PM and MM measures.     

A multi‐gene phylogeny disentangles the chat‐flycatcher complex (Aves: Muscicapidae)

Zuccon, D. & Ericson, P. G. P. (2010). A multi‐gene phylogeny disentangles the chat‐flycatcher complex (Aves: Muscicapidae).—Zoologica Scripta, 39, 213–224. We reconstructed the first well‐sampled phylogenetic hypothesis in the chat‐flycatcher complex combining nuclear and mitochondrial sequences. The dichotomy between chats‐terrestrial feeders and flycatchers‐aerial feeders does not reflect monophyletic groups. The flycatching behaviour and morphological adaptations to aerial feeding (short tarsi, broad bill, rictal bristles) evolved independently from chat ancestors in three different lineages. The genera Alethe, Brachypteryx, and Myiophonus are nested within the Muscicapidae radiation and their morphological and behavioural similarities with the true thrushes Turdidae are presumably the result of convergence. The postulated close relationships among Erithacus, Luscinia and Tarsiger cannot be confirmed. Erithacus is part of the African forest robin assemblage (Cichladusa, Cossypha, Pogonocichla, Pseudalethe, Sheppardia, Stiphrornis), while Luscinia and Tarsiger belong to a large, mainly Asian radiation. Enicurus belongs to the same Asian clade and it does not deserve the recognition as a distinct subfamily or tribe. We found good support also for an assemblage of chats adapted to arid habitats (Monticola, Oenanthe, Thamnolaea, Myrmecocichla, Pentholaea, Cercomela, Saxicola, Campicoloides, Pinarochroa) and a redstart clade (Phoenicurus, Chaimarrornis and Rhyacornis). Five genera (Muscicapa, Copsychus, Thamnolaea, Luscinia and Ficedula) are polyphyletic and in need of taxonomic revision.     

Increased positive selection pressure within the complementarity determining regions of the T‐cell receptor β gene in New World monkeys

Because of the long‐term co‐evolution of TCR and MHC molecules, numerous nucleotide substitutions have accumulated within the domains of TCRβ genes. We previously found that nonsynonymous nucleotide substitutions occurred more frequently in complementarity determining region (CDR)β than in CDRα, even though only a limited number of common marmoset (Callithrix jacchus) and human T‐cell receptor β variable (TRBV) sequences were compared. This interesting finding raised the question of whether the increased selective pressure within CDRβ was species‐specific. In this study, we identified 21 TRBV region sequences from the common marmoset and performed comparative sequence analyses of the T‐cell receptor α variable (TRAV) and TRBV regions from human, chimpanzee, rhesus monkey, cotton‐top tamarin, Ma's night monkey, and common marmoset. The ratios of the number of nonsynonymous nucleotide substitutions per site (d_N) to the d_S values (d_N/d_S) were less than 1 within the framework regions (FRs) of TRAV and TRBV region sequences, suggesting that purifying selection is largely dominant within the FRs. In contrast, the d_N values were statistically significantly greater for CDRβ than for CDRα only in New World monkeys. Also, increased d_N/d_S ratios (d_N/d_S>1) were observed within CDRβ between humans and New World monkeys and, interestingly, between New World monkeys, which share a relatively recent common ancestor. Moreover, phylogenetic analysis by maximum likelihood analysis provided firm evidence to support that positive selection occurred within CDRβ along New World monkey lineages. These results suggest that increased positive selection pressure within CDRβ is common in New World monkeys rather than being species‐specific. This study provides an intriguing insight into the co‐evolution of TCR and MHC molecules within primates. Am. J. Primatol. 73:1082–1092, 2011. © 2011 Wiley‐Liss, Inc.     

Speciation in Mediterranean refugia and post‐glacial expansion of Zerynthia polyxena (Lepidoptera,Papilionidae)

Migration of populations to and from glacial refugia is responsible for various cases of speciation and subspeciation in Europe. The pattern of distribution and the degree of diversification between lineages originated by isolation in different glacial refugia usually depends on ecological traits, especially to their dispersal ability. Zerynthia polyxena is a philopatric species, scattered in small populations and rarely colonizing mountain areas. These characteristics probably caused repeated isolation during the Quaternary and may have favoured diversification. Actually two studies, based on both morphological and genetic data, suggest the existence of two highly distinct lineages in Europe having in Northern Italy their contact zone. In this study, I applied geometric morphometrics to male genitalia and demonstrated that (i) two morphotypes exist in Europe approximately facing on the two sides of the Po River; (ii) the two lineages probably survived glaciations in Italy and the Balkan Peninsula, respectively; then the Balkans lineage expanded to Central and Eastern Europe; (iii) no hybrid populations seem to exist in the contact area and, in one locality at least, the two lineages live in sympatry without any evidence of intermediates. These results suggest that (i) two sister species of Zerynthia exist in Europe. Accordingly, Papilio cassandra Geyer, 1828 is reinstated, as Zerynthia cassandra stat. rev., as the species to which the Zerynthia from Italy South of the Po River belong. Male genitalia differences with Zerynthia polyxena are described.     

Estimating temperature‐dependent developmental rates of potato tuberworm,Phthorimaea operculella (Lepidoptera: Gelechiidae)

Abstract The potato tuberworm, Phthorimaea operculella (Zeller) (Lepidoptera: Gelechiidae), is the most destructive pest of potato, Solanum tuberosum L. (Solanaceae), in tropical and subtropical regions in both field and storeroom situations. The modeling of temperature‐dependent development can be useful in forecasting occurrence and population dynamics of the pests. Published developmental parameters for this pest vary greatly for many reasons. We determined temperature‐dependent development of P. operculella at seven constant temperatures (16, 20, 24, 28, 32, 34 and 36 °C). Developmental period of whole immature stage (egg to the end of the pupal stage) varied from 75.5 days at 16 °C to 17 days at 32 °C. The population failed to survive at 36 °C. The observed data was modeled to determine mathematical functions for simulating P. operculella development in each stage of development and overall. Two linear models, ordinary linear regression and the Ikemoto linear model were used to describe the relationship between temperature and development rate of the different stages of P. operculella and estimating the thermal constant and lower temperature threshold. The lower temperature threshold (t) and thermal constant (k) of whole immature stage were estimated to be 11.6 °C and 338.5 DD by Ikemoto linear model, and the estimated parameters were not substantially different with those estimated by ordinary linear models. Different models provided a better fit to the various developmental stages. Of the eleven nonlinear models fitted, the Beriere‐1, Logan‐6 and Lactin‐1 model was found to be the best for modeling development rate of egg, larva and pupa of P. operculella, respectively. Phenological models based on these findings can be part of a decision‐support tool to improve the efficiency of pest management programs.     

A dynamic binomial sequential sampling plan for Plutella xylostella (Lepidoptera: Plutellidae) on broccoli and cauliflower in Australia

Binomial sequential sampling plans have been used widely for monitoring invertebrate pest populations. Such plans are typically based upon a single action threshold (AT), which represents the level of infestation that the grower is prepared to accept before using a control measure. For many cropping systems this acceptable infestation level is likely to vary, being dependent on factors such as the growth stage of the crop and the value or demands of the destination market (e.g., local or high-quality export). We developed and validated a computer-assisted plan that uses a dynamic AT. The plan has been developed for monitoring diamondback moth, Plutella xylostella (L.) on broccoli (Brassica oleracea variety botrytis L.) and cauliflower (Brassica oleracea variety botrytis L.), but the concepts and methodologies could be readily applied to other systems.     

Evaluation of sequential presence-absence sampling plans for the diamondback moth (Plutellidae: Lepidoptera) in cruciferous crops in Australia

Two sets of sequential presence-absence sampling plans for decision-making in the management of diamondback moth, Plutella xylostella (L.), were developed and evaluated. One set of sampling plans targeted the classification of proportions of infested plants, and the other set of sampling plans targeted the classification of larval density. The action thresholds investigated were 0.15, 0.25, 0.35, and 0.45 proportion of plants infested with larvae, and 0.2, 0.4, 0.6, and 0.8 larvae per plant. They are representative of the action thresholds currently practiced by Australian crucifer growers. For each sampling plan, the population range within which a minimal correct decision rate of 95% can be expected at a maximal average sample size of 50 plants (OC95ASN50) was specified. The closeness of an OC95ASN50 range to the target action threshold is a measure of the expected performance of the sampling plan. A closer distance reflects better performance. The OC95ASN50 ranges of the proportion-classification sampling plans were within 33-53% of the target action thresholds. The width of these OC95ASN50 ranges represents 73-87% of the entire population range (0-1). For the classification of larval density, an empirical proportion-density model was first established using data from different states and different cruciferous crops. The OC95ASN50 ranges of the density-classification sampling plans were within 57-75% of the target action threshold. Simulated sampling of 20 independent data sets showed that for most data sets the correct classification rate was at least 98% and the matching average sample size was <50 plants.     

Biology of Mastrus ridibundus (Gravenhorst), a potential biological control agent for area‐wide management of Cydia pomonella (Linneaus) (Lepidoptera: Tortricidae)

The codling moth Cydia pomonella (Linnaeus) (Lepidoptera: Tortricidae) is a serious pest of pome fruit crops. A natural enemy of codling moth, the larval ectoparasitoid Mastrus ridibundus (Gravenhorst) (Hymenoptera: Ichneumonidae) has been imported into South America from the USA but little is known about the biology and ecology of the wasp, knowledge that is needed to design an efficient strategy of release and establishment. Experiments were carried out to assess important traits of the biology of the parasitoid in relation to its possible use as a biocontrol agent for codling moth. When M. ridibundus females were offered larvae ranging in weight from 37 to 78 mg, they oviposited more eggs on heavier hosts. In another study, the adult wasps were offered honey, diluted honey (10%) or pollen in paired choice tests and both males and females preferred honey over the other two foods. Females preferred 10% honey over pollen, while the males showed the opposite preference. Honey‐fed females lived longer than starved females. Adults died rapidly at 35°C, while they lived 20 days at 25°C and 12–17 days at 15°C. Female wasps had on average 25 ± 14 and 18 ± 11 progeny at 15 and 25°C, respectively, but they did not had progeny at 35°C. The development time (egg to adult emergence) was on average 44 ± 7 and 24 ± 2 days at 15 and 25°C respectively. Immature insects did not reach the adult stage at 35°C.