Population genetics and symbiont assemblages support opposing invasion scenarios for the red turpentine beetle (Dendroctonus valens)

Exotic forest insects and their symbionts pose an increasing threat to forest health. This is apparently true for the red turpentine beetle (Dendroctonus valens), which was unintentionally introduced to China, where the beetle has killed millions of healthy native pine trees. Previous population genetics studies that used cytochrome oxidase I as a marker concluded that the source of D. valens in China was western North America. In contrast, surveys of fungi associated with D. valens demonstrated that more fungal species are shared between China and eastern North America than between China and western North America, suggesting that the source population of D. valens could be eastern North America. In this study, we used microsatellite markers to determine population structure of D. valens in North America as well as the source population of the beetle in China. The analyses revealed that four genetically distinct populations (herein named the West, Central, Northeast and Mexico) represent the native range of D. valens. Clustering analyses and a simulation‐based approximate Bayesian computation (ABC) approach supported the hypothesis that western North America is the source of the invasive D. valens population. This study provides a demonstration of non‐congruence between patterns inferred by studies on population genetics and symbiont assemblages in an invasive bark beetle.     

Genomic evidence that resource‐based trade‐offs limit host‐range expansion in a seed beetle

Trade‐offs have often been invoked to explain the evolution of ecological specialization. Phytophagous insects have been especially well studied, but there has been little evidence that resource‐based trade‐offs contribute to the evolution of host specialization in this group. Here, we combine experimental evolution and partial genome resequencing of replicate seed beetle selection lines to test the trade‐off hypothesis and measure the repeatability of evolution. Bayesian estimates of selection coefficients suggest that rapid adaptation to a poor host (lentil) was mediated by standing genetic variation at multiple genetic loci and involved many of the same variants in replicate lines. Sublines that were then switched back to the ancestral host (mung bean) showed a more gradual and variable (less repeatable) loss of adaptation to lentil. We were able to obtain estimates of variance effective population sizes from genome‐wide differences in allele frequencies within and between lines. These estimates were relatively large, which suggests that the contribution of genetic drift to the loss of adaptation following reversion was small. Instead, we find that some alleles that were favored on lentil were selected against during reversion on mung bean, consistent with the genetic trade‐off hypothesis.     

Contemporary genetic structure and postglacial demographic history of the black scorpionfish,Scorpaena porcus,in the Mediterranean and the Black Seas

Understanding the distribution of genetic diversity in the light of past demographic events linked with climatic shifts will help to forecast evolutionary trajectories of ecosystems within the current context of climate change. In this study, mitochondrial sequences and microsatellite loci were analysed using traditional population genetic approaches together with Bayesian dating and the more recent approximate Bayesian computation scenario testing. The genetic structure and demographic history of a commercial fish, the black scorpionfish, Scorpaena porcus, was investigated throughout the Mediterranean and Black Seas. The results suggest that the species recently underwent population expansions, in both seas, likely concomitant with the warming period following the Last Glacial Maximum, 20 000 years ago. A weak contemporaneous genetic differentiation was identified between the Black Sea and the Mediterranean Sea. However, the genetic diversity was similar for populations of the two seas, suggesting a high number of colonizers entered the Black Sea during the interglacial period and/or the presence of a refugial population in the Black Sea during the glacial period. Finally, within seas, an east/west genetic differentiation in the Adriatic seems to prevail, whereas the Black Sea does not show any structured spatial genetic pattern of its population. Overall, these results suggest that the Black Sea is not that isolated from the Mediterranean, and both seas revealed similar evolutionary patterns related to climate change and changes in sea level.     

CoMuS: simulating coalescent histories and polymorphic data from multiple species

The simultaneous analysis of intra‐ and interspecies variation is challenging mainly because our knowledge about patterns of polymorphisms where both intra‐ and interspecies samples coexist is limited. In this study, we present CoMuS (Coalescent of Multiple Species), a multispecies coalescent software that can simulate intra‐ and interspecies polymorphisms. CoMuS supports a variety of speciation models and demographic scenarios related to the history of each species. In CoMuS, speciation can be accompanied by either instant or gradual isolation between sister species. Sampling may also occur in the past, and thus, we can study simultaneously extinct and extant species. Our software supports both the infinite‐ and the finite‐site model, with substitution rate heterogeneity among sites and a user‐defined proportion of invariable sites. We demonstrate the usage of CoMuS in various applications: species delimitation, software testing, model selection and parameter inference involving present‐day and ancestral samples, comparison between gradual and instantaneous isolation models, estimation of speciation time between human and chimpanzee using both intra‐ and interspecies variation. We expect that CoMuS will be particularly useful for studies where species have been separated recently from their common ancestor and phenomena such as incomplete lineage sorting or introgression still occur.     

Energetics of the structure and chain tilting of antiparallel beta-barrels in proteins

The preferred structural pattern of antiparallel beta-barrels in proteins, described as the right-handed tilting of the peptide strands with respect to the axis of the barrel, is accounted for in terms of intra- and interchain interaction energies. It is related to the preference of beta-sheets for right-handed twisting. Conformational energy computations have been carried out on three eight-stranded antiparallel beta-barrels composed of six-residue strands, in which L-Val and Gly alternate, and having a right-handed, a left-handed, or no tilt. After energy minimization, the relative energies of these structures were 0.0, 8.6, and 46.1 kcal/mol, respectively; i.e., the right-tilted beta-barrel is favored energetically, in agreement with anti-parallel beta-barrels observed in proteins. Tilting of the barrel is favored, relative to the nontilted structure, by both intra- and interstrand interactions, because tilting allows better packing of the bulky side chains. On the other hand, the energy difference between the left- and right-tilted barrels arises essentially from intrachain interactions. This is a consequence of the preference of beta-sheets for a right-handed twist. Space limitations inside the barrel are satisfied if there is an alternation of bulky residues and residues with small or no side chain (preferably Gly) in neighboring positions on adjacent strands. Such a pattern is seen frequently in antiparallel beta-barrels of globular proteins. The computations indicate that a structure with Val...Gly pairs can be accommodated in a beta-barrel with no distortion.     

An interactive microcomputer program for the computation of most probable number

An interactive computer program for the rapid computation of Most Probable Numbers (MPN) with 95% confidence intervals and goodness-of-fit, is presented. The program, written in ‘MICROSOFT BASIC’ employs an iterative algorithm based on a modification of the Newton-Raphson method and accomodates any number of replicates up to ten dilutions. It is applicable to most microcomputers with little or no modification. Since the computed MPN, confidence interval,a nd goodness-of-fit tests are displayed simultaneously, MPN tables are no longer required.     

Investigations on the structural,vibrational, computational,and molecular docking studies on potential antidiabetic chemical agent Diosmetin

In the present study, the harmonic vibrational frequencies of Diosmetin(5, 7 dihydroxy‐2(3‐hydroxy‐4 methoxyphenyl) chromen‐4‐one) have been investigated by both experimental (FTIR and FT‐Raman) and theoretical (HF and DFT/B3LYP) method. The calculated harmonic vibrational frequencies were compared with experimental data. A detailed interpretation of the vibrational spectra of the compound has been made on the basis of the calculated potential energy distribution (PED). The ¹H, ¹³C NMR chemical shifts and TD‐DFT calculations of the molecule were calculated and compared with the available experimental observations. A study on the molecular electrostatic potential surface (MEP) of the compound was performed, and the electrophilic and nucleophilic reactive sites were identified. Furthermore, the inhibition effect of compound against aldose reductase enzyme has been analyzed by molecular docking method, and the results were compared with the standard drug. The docking study indicates that the investigated compound shows better inhibitory activity toward aldose reductase enzyme than the standard drug, and hence this study may be supportive in the field of drug discovery to design more potential antidiabetic agents.     

Inferring the geographic origin of a range expansion: Latitudinal and longitudinal coordinates inferred from genomic data in an ABC framework with the program x‐origin

Climatic or environmental change is not only driving distributional shifts in species today, but it has also caused distributions to expand and contract in the past. Inferences about the geographic locations of past populations especially regions that served as refugia (i.e., source populations) and migratory routes are a challenging endeavour. Refugial areas may be evidenced from fossil records or regions of temporal stability inferred from ecological niche models. Genomic data offer an alternative and broadly applicable source of information about the locality of refugial areas, especially relative to fossil data, which are either unavailable or incomplete for most species. Here, we present a pipeline we developed (called x ‐origin ) for statistically inferring the geographic origin of range expansion using a spatially explicit coalescent model and an approximate Bayesian computation testing framework. In addition to assessing the probability of specific latitudinal and longitudinal coordinates of refugial or source populations, such inferences can also be made accounting for the effects of temporal and spatial environmental heterogeneity, which may impact migration routes. We demonstrate x ‐origin with an analysis of genomic data collected in the Collared pika that underwent postglacial expansion across Alaska, as well as present an assessment of its accuracy under a known model of expansion to validate the approach.     

Building up biogeography: Pattern to process

Linking pattern to process across spatial and temporal scales has been a key goal of the field of biogeography. In January 2017, the 8th biennial conference of the International Biogeography Society sponsored a symposium on Building up biogeography—process to pattern that aimed to review progress towards this goal. Here we present a summary of the symposium, in which we identified promising areas of current research and suggested future research directions. We focus on (1) emerging types of data such as behavioural observations and ancient DNA, (2) how to better incorporate historical data (such as fossils) to move beyond what we term “footprint measures” of past dynamics and (3) the role that novel modelling approaches (e.g. maximum entropy theory of ecology and approximate Bayesian computation) and conceptual frameworks can play in the unification of disciplines. We suggest that the gaps separating pattern and process are shrinking, and that we can better bridge these aspects by considering the dimensions of space and time simultaneously.     

From complexation to computation: Recent progress in molecular logic

The new thrusts in molecular logic are gathered together in this short review, while paying attention to the seeds from which these developments have arisen. The original demonstration of a few basic logic operations has now been extended to cover many of the one- and two-input varieties and even some of the three-input types. Many kinds of inputs and outputs have emerged, including various chemical species and some physical properties. The latter can include heat, light and, arguably, polarity. Reconfigurable logic has grown up to include a range of examples. Even superposable logic has proved possible with molecular systems. Numerical processors have flowered in recent years with several diverse approaches being revealed in recent years. Photochemical concepts such as photoinduced electron transfer (PET), internal charge transfer (ICT) and electronic energy transfer (EET) can be discerned among the designs in the field.