Interspecific gene flow obscures phylogenetic relationships in an important insect pest species complex.

As genomic data proliferates, the prevalence of post-speciation gene flow is making species boundaries and relationships increasingly ambiguous. Although current approaches inferring fully bifurcating phylogenies based on concatenated datasets provide simple and robust answers to many species relationships, they may be inaccurate because the models ignore inter-specific gene flow and incomplete lineage sorting. To examine the potential error resulting from ignoring gene flow, we generated both a RAD-seq and a 500 protein-coding loci highly multiplexed amplicon (HiMAP) dataset for a monophyletic group of 12 species defined as the Bactrocera dorsalis sensu lato clade. With some of the world's worst agricultural pests, the taxonomy of the B. dorsalis s.l. clade is important for trade and quarantines. However, taxonomic confusion confounds resolution due to intra- and interspecific phenotypic variation and convergence, mitochondrial introgression across half of the species, and viable hybrids. We compared the topological convergence of our datasets using concatenated phylogenetic and various multispecies coalescent approaches, some of which account for gene flow. All analyses agreed on species delimitation, but there was incongruence between species relationships. Under concatenation, both datasets suggest identical species relationships with mostly high statistical support. However, multispecies coalescent and multispecies network approaches suggest markedly different hypotheses and detected significant gene flow. We suggest that the network approaches are likely more accurate because gene flow violates the assumptions of the concatenated phylogenetic analyses, but the data-reductive requirements of network approaches resulted in reduced statistical support and could not unambiguously resolve gene flow directions. Our study highlights the importance of testing for gene flow, particularly with phylogenomic datasets, even when concatenated approaches receive high statistical support.

Controlling anisotropic properties by manipulating the orientation of chiral small molecules.

Chiral π-conjugated molecules bring new functionality to technological applications and represent an exciting, rapidly expanding area of research. Their functional properties, such as the absorption and emission of circularly polarized light or the transport of spin-polarized electrons, are highly anisotropic. As a result, the orientation of chiral molecules critically determines the functionality and efficiency of chiral devices. Here we present a strategy to control the orientation of a small chiral molecule (2,2'-dicyano[6]helicene) by the use of organic and inorganic templating layers. Such templating layers can either force 2,2'-dicyano[6]helicene to adopt a face-on orientation and self-assemble into upright supramolecular columns oriented with their helical axis perpendicular to the substrate, or an edge-on orientation with parallel-lying supramolecular columns. Through such control, we show that low- and high-energy chiroptical responses can be independently 'turned on' or 'turned off'. The templating methodologies described here provide a simple way to engineer orientational control and, by association, anisotropic functional properties of chiral molecular systems for a range of emerging technologies.

A Universal Force Field for Materials, Periodic GFN-FF: Implementation and Examination.

In this study, the adaption of the recently published molecular GFN-FF for periodic boundary conditions (pGFN-FF) is described through the use of neighbor lists combined with appropriate charge sums to handle any dimensionality from 1D polymers to 2D surfaces and 3D solids. Numerical integration over the Brillouin zone for the calculation of π bond orders of periodic fragments is also included. Aside from adapting the GFN-FF method to handle periodicity, improvements to the method are proposed in regard to the calculation of topological charges through the inclusion of a screened Coulomb term that leads to more physical charges and avoids a number of pathological cases. Short-range damping of three-body dispersion is also included to avoid collapse of some structures. Analytic second derivatives are also formulated with respect to both Cartesian and strain variables, including prescreening of terms to accelerate the dispersion/coordination number contribution to the Hessian. The modified pGFN-FF scheme is then applied to a wide range of different materials in order to examine how well this universal model performs.

Novel lures and COI sequences reveal cryptic new species of Bactrocera fruit flies in the Solomon Islands (Diptera, Tephritidae, Dacini).

Results from a snap-shot survey of Dacine fruit flies carried out on three of the Solomon Islands in April 2018 are reported. Using traps baited with the male lures cue-lure, methyl eugenol, and zingerone, 30 of the 48 species previously known to occur in the Solomon Islands were collected. Six species are newly described here: Bactroceraallodistincta sp. nov., B.geminosimulata sp. nov., B.kolombangarae sp. nov., B.quasienochra sp. nov., B.tsatsiai sp. nov., and B.vargasi sp. nov., all authored by Leblanc & Doorenweerd. An illustrated key to the 54 species now known to be present in the country is provided.

Highly variable COI haplotype diversity between three species of invasive pest fruit fly reflects remarkably incongruent demographic histories.

Distance decay principles predict that species with larger geographic ranges would have greater intraspecific genetic diversity than more restricted species. However, invasive pest species may not follow this prediction, with confounding implications for tracking phenomena including original ranges, invasion pathways and source populations. We sequenced an 815 base-pair section of the COI gene for 441 specimens of Bactrocera correcta, 214 B. zonata and 372 Zeugodacus cucurbitae; three invasive pest fruit fly species with overlapping hostplants. For each species, we explored how many individuals would need to be included in a study to sample the majority of their haplotype diversity. We also tested for phylogeographic signal and used demographic estimators as a proxy for invasion potency. We find contrasting patterns of haplotype diversity amongst the species, where B. zonata has the highest diversity but most haplotypes were represented by singletons; B. correcta has ~7 dominant haplotypes more evenly distributed; Z. cucurbitae has a single dominant haplotype with closely related singletons in a 'star-shape' surrounding it. We discuss how these differing patterns relate to their invasion histories. None of the species showed meaningful phylogeographic patterns, possibly due to gene-flow between areas across their distributions, obscuring or eliminating substructure.

What is "many-body" dispersion and should I worry about it?

Inclusion of dispersion effects in density-functional calculations is now standard practice in computational chemistry. In many dispersion models, the dispersion energy is written as a sum of pairwise atomic interactions consisting of a damped asymptotic expansion from perturbation theory. There has been much recent attention drawn to the importance of "many-body" dispersion effects, which by their name imply limitations with a pairwise atomic expansion. In this perspective, we clarify what is meant by many-body dispersion, as this term has previously referred to two very different physical phenomena, here classified as electronic and atomic many-body effects. Atomic many-body effects refer to the terms in the perturbation-theory expansion of the dispersion energy involving more than two atoms, the leading contribution being the Axilrod-Teller-Muto three-body term. Conversely, electronic many-body effects refer to changes in the dispersion coefficients of the pairwise terms induced by the atomic environment. Regardless of their nature, many-body effects cause pairwise non-additivity in the dispersion energy, such that the dispersion energy of a system does not equal the sum of the dispersion energies of its atomic pairs taken in isolation. A series of examples using the exchange-hole dipole moment (XDM) method are presented to assess the relative importance of electronic and atomic many-body effects on the dispersion energy. Electronic many-body effects can result in variation in the leading-order C6 dispersion coefficients by as much as 50%; hence, their inclusion is critical for good performance of a pairwise asymptotic dispersion correction. Conversely, atomic many-body effects represent less than 1% of the total dispersion energy and are much less significant than higher-order (C8 and C10) pairwise terms. Their importance has been previously overestimated through empirical fitting, where they can offset underlying errors stemming either from neglect of higher-order pairwise terms or from the base density functional.

Asymptotic Pairwise Dispersion Corrections Can Describe Layered Materials Accurately.

A recent study by Tawfik et al. [ Phys. Rev. Mater. 2018, 2, 034005] found that few density functionals, none of which are asymptotic pairwise dispersion methods, describe the geometry and binding of layered materials accurately. Here, we show that the exchange-hole dipole moment (XDM) dispersion model attains excellent results for graphite, hexagonal BN, and transition-metal dichalcogenides. Contrary to what has been argued, successful modeling of layered materials does not necessitate meta-GGA exchange, nonlocal correlation functionals, or the inclusion of three-body dispersion terms. Rather, a GGA functional, combined with a simple asymptotic pairwise dispersion correction, can be reliably used, provided that it properly accounts for the geometric dependence of the dispersion coefficients. The overwhelming contribution to the variation of the pairwise dispersion coefficients comes from the immediate vicinity of an atom and is already present for single layers. Longer-range and interlayer effects are examined in detail for graphite.

Six years of fruit fly surveys in Bangladesh: a new species, 33 new country records and discovery of the highly invasive Bactrocera carambolae (Diptera, Tephritidae).

We engaged in six years of snap-shot surveys for fruit flies in rural environments and ten protected forest areas of Bangladesh, using traps baited with male lures (cue-lure, methyl eugenol, zingerone). Our work has increased the recorded number of species of Tephritidae in the country from seven to 37. We summarize these surveys and report eight new country occurrence records, and a new species (Zeugodacus madhupuri Leblanc & Doorenweerd, sp. nov.) is described. The highlight among the new records is the discovery, and significant westward range extension, of Bactrocera carambolae Drew & Hancock, a major fruit pest detected in the Chattogram and Sylhet Divisions. We rectify the previously published erroneous record of Bactrocera bogorensis (Hardy), which was based on a misidentification of Zeugodacus diaphorus (Hendel). We also report the occurrence in Bangladesh of nine other Tephritidae, the rearing of three primary fruit fly parasitoids from Zeugodacus, and records of non-target attraction to fruit fly lures.

Dispersion XDM with Hybrid Functionals: Delocalization Error and Halogen Bonding in Molecular Crystals.

The accurate calculation of relative lattice energies of molecular crystals is important in polymorph ranking and crystal structure prediction. Delocalization error has been shown to affect calculated intermolecular binding energies in DFT and is similarly expected to affect the lattice energies of some classes of molecular crystals. In this work, we explore the use of dispersion-corrected hybrid functionals in the planewave-pseudopotentials approach to reduce delocalization error. We combine several hybrid functionals with the exchange-hole dipole moment (XDM) model for dispersion and show that they generally outperform GGA functionals in the calculation of both gas-phase binding energies and molecular crystal lattice energies. We apply the resulting XDM-corrected functionals to four halogen-bonded crystals: Cl2, Br2, I2, and ICl. GGA functionals severely overestimate their lattice energies, while hybrid functionals give accurate values. The preference of GGA functionals for monatomic structures in the Br2 and Cl2 crystals is also explained. Finally, we apply a recently developed method to calculate Bader's delocalization indices to examine the extent of intermolecular delocalization in the halogen molecular crystals. It is shown that intermolecular delocalization indices can be used to measure the strength of halogen bonds within the crystal, as well as detect the presence of delocalization error.

Clusters in Liquid Fatty Acids: Structure and Role in Nucleation.

Saturated fatty acids are used in many consumer products and have considerable promise as phase change materials for thermal energy storage, in part because they crystallize with minimal supercooling. The latter property correlates with the existence of molecular clusters in the liquid; when heated above a threshold temperature, clusters do not immediately re-form on cooling, and supercooling results. Raman spectroscopy, density functional theory calculations, and small-angle X-ray scattering were used to reveal the size, structure, and temperature dependence of the clusters. We found that the liquid phases of fatty acids contain some ordering at all temperatures, with the molecules showing, on average, short-range alignment along their long axes. At temperatures below the threshold temperature for increased susceptibility to supercooling, clusters of more highly ordered fatty acid dimers, several hundred molecules in size, exist in the liquid. Within these clusters, the alkyl chains of the fatty acid dimers are essentially completely inserted between the alkyl chains of their longitudinal neighbors. Above the threshold temperature, fatty acid clusters are smaller in size and number. We explored how the fatty acid clusters promote bulk crystallization and show quantitatively that their presence reduces the energy barrier to crystal growth, likely by a particle-attachment-type mechanism.

Descriptions of four new species of Bactrocera and new country records highlight the high biodiversity of fruit flies in Vietnam (Diptera, Tephritidae, Dacinae).

Recent snap-shot surveys for fruit flies in Vietnam in 2015 and 2017 using traps baited with the male Dacinae fruit fly lures methyl eugenol, cue-lure and zingerone, collected 56 species, including 11 new country records and another 11 undescribed species, four of which are described in this paper. This increases the number of described species known to occur in Vietnam from 78 to 93. Species accumulation curves, based on the Chao 2 mean estimate, suggest that we collected 60-85 % of the local fauna at the sites sampled, and that species diversity decreases with increasing latitude. The four new species are named: Bactrocera (Tetradacus) ernesti Leblanc & Doorenweerd sp. n., B. (Asiadacus) connecta Leblanc & Doorenweerd sp. n., B. (Parazeugodacus) clarifemur Leblanc & Doorenweerd sp. n., and B. (Bactrocera) adamantea Leblanc & Doorenweerd sp. n. In addition to morphological data COI DNA sequence data of both the COI-5P and COI-3P mitochondrial DNA gene regions is provided. Three of the four newly described species are morphologically and genetically easily distinguished from all other members of Dacini. Bactroceraclarifemur sp. n. is superficially similar to B.pendleburyi (Perkins) based on morphology, but there are several apomorphic characters to distinguish the two. Both COI and a segment of the nuclear gene Elongation Factor 1 alpha separate the two species as well.

Description of a new species of Dacus from Sri Lanka, and new country distribution records (Diptera, Tephritidae, Dacinae).

A fruit fly survey in the Sinharaja and Knuckles National Parks in Sri Lanka (2016), using traps baited with the male lures methyl eugenol, cue-lure, and zingerone, yielded 21 species of Dacini fruit flies. Of these, three species, viz. Bactroceraamarambalensis Drew, B.dongnaiae Drew & Romig, and B.rubigina (Wang & Zhao), are new country occurrence records, and Dacus (Mellesis) ancoralis Leblanc & Doorenweerd, sp. n. is described as a new species. The Sri Lankan Dacini fruit fly fauna is now comprised of 39 species.

Non-Covalent Interactions in Molecular Crystals: Exploring the Accuracy of the Exchange-Hole Dipole Moment Model with Local Orbitals.

We present the first implementation of the exchange-hole dipole moment (XDM) model in combination with a numerical finite-support local orbital method (the SIESTA method) for the modeling of non-covalent interactions in periodic solids. The XDM model is parametrized for both the B86bPBE and PBE functionals using double-ζ- and triple-ζ-quality basis sets (DZP and TZP). The use of finite-support local orbitals is shown to have minimal impact on the computed dispersion coefficients for van der Waals molecular dimers and small molecular solids. However, the quality of the basis set affects the accuracy of calculated dimer binding energies and molecular-crystal lattice energies quite significantly; the size of the counterpoise correction indicates that this is caused by basis-set incompleteness error. In the case of the DZP basis set, its performance for weakly bound gas-phase dimers is similar to that of a double-ζ Gaussian basis set without diffuse functions. The new XDM implementation was tested on graphite and phosphorene exfoliation, and on the X23 benchmark set of molecular-crystal lattice energies. Our results indicate that lattice energies similar to plane-wave calculations can be obtained only if the counterpoise correction is applied. Alternatively, the calculated equilibrium geometries are reasonably close to the plane-wave equivalents, and composite approaches in which a single-point plane-wave calculation is used at the XDM/DZP equilibrium geometry yield good accuracy at a significantly lower computational cost.

Tracking the Origins of Fly Invasions; Using Mitochondrial Haplotype Diversity to Identify Potential Source Populations in Two Genetically Intertwined Fruit Fly Species (Bactrocera carambolae and Bactrocera dorsalis [Diptera: Tephritidae]).

Bactrocera carambolae Drew and Hancock and Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) are important pests of many fruits. These flies have been spread across the world through global travel and trade, and new areas are at risk of invasion. Whenever new invasive populations are discovered, quick and accurate identification is needed to mitigate the damage they can cause. Determining invasive pathways can prevent further spread of pests as well as subsequent reinvasions through the same pathway. Molecular markers can be used for both species identification and pathway analysis. We analyzed 1,601 individuals from 19 populations using 765 base pairs of the mitochondrial cytochrome oxidase I (COI) gene to infer the haplotype diversity and population structure within these flies from across their native and invasive ranges. We analyzed these samples by either grouping by species or geographic populations due to the genetic similarity in the mitochondrial genome. We found no genetic structure between B. dorsalis and B. carambolae and our findings suggest recent and most likely ongoing, genetic exchange between these two species in the wild. Hyper-diverse mitochondrial genetic diversity in the native range suggests large population sizes and relatively high mutation rates. Only 52% of the haplotypes found in the trap captures from California are shared with haplotypes from flies found in our global survey, indicating significant genetic diversity in the native range that is missing from our samples. However, these results provide a foundation for the accurate determination of the provenance of invasive populations around the world.

Pervasive Delocalisation Error Causes Spurious Proton Transfer in Organic Acid-Base Co-Crystals.

Dispersion-corrected density-functional theory (DFT-D) methods have become the workhorse of many computational protocols for molecular crystal structure prediction due to their efficiency and convenience. However, certain limitations of DFT, such as delocalisation error, are often overlooked or are too expensive to remedy in solid-state applications. This error can lead to artificial stabilisation of charge transfer and, in this work, it is found to affect the correct identification of the protonation site in multicomponent acid-base crystals. As such, commonly used DFT-D methods cannot be applied with any reliability to the study of acid-base co-crystals or salts, while hybrid functionals remain too restrictive for routine use. This presents an impetus for the development of new functionals with reduced delocalisation error for solid-state applications; the structures studied herein constitute an excellent benchmark for this purpose.

Correction: A computational exploration of the crystal energy and charge-carrier mobility landscapes of the chiral [6]helicene molecule.

Correction for 'A computational exploration of the crystal energy and charge-carrier mobility landscapes of the chiral [6]helicene molecule' by Beth Rice et al., Nanoscale, 2018, 10, 1865-1876.

HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing.

High-throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50- to 100-fold more loci than those generated using traditional Sanger sequencing-based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single-tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon-based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically important agricultural insect pests. The resulting filtered data set (>150,000-bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting data set provides into relationships of this diverse insect group.

Composite and Low-Cost Approaches for Molecular Crystal Structure Prediction.

Molecular crystal structure prediction (CSP) requires evaluating differences in lattice energy between candidate crystal structures accurately and efficiently. In this work, we explore and compare several low-cost alternatives to dispersion-corrected density-functional theory (DFT) in the plane-waves/pseudopotential approximation, the most accurate and general approach used for CSP at present. Three types of low-cost methods are considered: DFT with a small basis set of finite-support numerical orbitals (the SIESTA method), dispersion-corrected Gaussian small or minimal-basis-set Hartree-Fock and DFT with additional empirical corrections (HF-3c and PBEh-3c), and self-consistent-charge dispersion-corrected density-functional tight binding (SCC-DFTB3-D3). In addition, we study the performance of composite methods that comprise a geometry optimization using a low-cost approach followed by a single-point calculation using the accurate but comparatively expensive B86bPBE-XDM functional. All methods were tested for their abilities to produce absolute lattice energies, relative lattice energies, and crystal geometries. We show that assessing various methods by their ability to produce absolute lattice energies can be misleading and that relative lattice energies are a much better indicator of performance in CSP. The EE14 set of relative solubilities of homochiral and heterochiral chiral crystals is proposed for relative lattice-energy benchmarking. Our results show that PBE-D2 plus a DZP basis set of numerical orbitals coupled with a final B86bPBE-XDM single-point calculation gives excellent performance at a fraction of the cost of a full B86bPBE-XDM calculation, although the results are sensitive to the particular details of the computational protocol. The B86bPBE-XDM//PBE-D2/DZP method was subsequently tested in a practical CSP application from our recent work on the crystal structure of the enantiopure and racemate forms of 1-aza[6]helicene, a chiral organic semiconductor. Our results show that this multilevel method is able to correctly reproduce the energy ranking of both crystal forms.

A global checklist of the 932 fruit fly species in the tribe Dacini (Diptera, Tephritidae).

The correct application of the scientific names of species is neither easy nor trivial. Mistakes can lead to the wrong interpretation of research results or, when pest species are involved, inappropriate regulations and limits on trade, and possibly quarantine failures that permit the invasion of new pest species. Names are particularly challenging to manage when groups of organisms encompass a large number of species, when different workers employ different philosophical views, or when species are in a state of taxonomic flux. The fruit fly tribe Dacini is a species-rich taxon within Tephritidae and contains around a fifth of all known species in the family. About 10% of the 932 currently recognized species are pests of commercial fruits and vegetables, precipitating quarantines and trade embargos. Authoritative species lists consist largely of scattered regional treatments and outdated online resources. The checklist presented here is the first global overview of valid species names for the Dacini in almost two decades, and includes new lure records. By publishing this list both in paper and digitally, we aim to provide a resource for those studying fruit flies as well as researchers studying components of their impact on agriculture. The list is largely a consolidation of previous works, but following the results from recent phylogenetic work, we transfer one subgenus and eight species to different genera: members of the Bactrocera subgenus Javadacus Hardy, considered to belong to the Zeugodacus group of subgenera, are transferred to genus Zeugodacus; Bactrocera pseudocucurbitae White, 1999, stat. rev., is transferred back to Bactrocera from Zeugodacus; Zeugodacus arisanicus Shiraki, 1933, stat. rev., is transferred back to Zeugodacus from Bactrocera; and Z. brevipunctatus (David & Hancock, 2017), comb. n.; Z. javanensis (Perkins, 1938), comb. n.; Z. montanus (Hardy, 1983), comb. n.; Z. papuaensis (Malloch, 1939), comb. n.; Z. scutellarius (Bezzi, 1916), comb. n.; Z. semisurstyli (Drew & Romig, 2013), comb. n.; and Z. trilineatus (Hardy, 1955), comb. n. are transferred from Bactrocera to Zeugodacus.

A computational exploration of the crystal energy and charge-carrier mobility landscapes of the chiral [6]helicene molecule.

The potential of a given π-conjugated organic molecule in an organic semiconductor device is highly dependent on molecular packing, as it strongly influences the charge-carrier mobility of the material. Such solid-state packing is sensitive to subtle differences in their intermolecular interactions and is challenging to predict. Chirality of the organic molecule adds an additional element of complexity to intuitive packing prediction. Here we use crystal structure prediction to explore the lattice-energy landscape of a potential chiral organic semiconductor, [6]helicene. We reproduce the experimentally observed enantiopure crystal structure and explain the absence of an experimentally observed racemate structure. By exploring how the hole and electron-mobility varies across the energy-structure-function landscape for [6]helicene, we find that an energetically favourable and frequently occurring packing motif is particularly promising for electron-mobility, with a highest calculated mobility of 2.9 cm2 V-1 s-1 (assuming a reorganization energy of 0.46 eV). We also calculate relatively high hole-mobility in some structures, with a highest calculated mobility of 2.0 cm2 V-1 s-1 found for chains of helicenes packed in a herringbone fashion. Neither the energetically favourable nor high charge-carrier mobility packing motifs are intuitively obvious, and this demonstrates the utility of our approach to computationally explore the energy-structure-function landscape for organic semiconductors. Our work demonstrates a route for the use of computational simulations to aid in the design of new molecules for organic electronics, through the a priori prediction of their likely solid-state form and properties.