Influence of molecular marker type on estimating effective population size and other genetic parameters in a critically endangered parrot.

Genetics is a fast-moving field, and for conservation practitioners or ecologists, it can be bewildering. The choice of marker used in studies is fundamental; in the literature, preference has recently shifted from microsatellites to single nucleotide polymorphism (SNP) loci. Understanding how marker type affects estimates of population genetic parameters is important in the context of conservation, especially because the accuracy of estimates has a bearing on the actions taken to protect threatened species. We compare parameter estimates between seven microsatellites, 3761 SNP loci, and a random subset of 100 SNPs for the exact same 324 individual swift parrots, Lathamus discolor, and also use 457 additional samples from subsequent years to compare SNP estimates. Both marker types estimated a lower H O than H E. We show that microsatellites and SNPs mainly indicate a lack of spatial genetic structure, except when a priori collection locations were used on the SNP data in a discriminant analysis of principal components (DAPC). The 100-SNP subset gave comparable results to when the full dataset was used. Estimates of effective population size (N e) were comparable between markers when the same individuals were considered, but SNPs had narrower confidence intervals. This is reassuring because conservation assessments that rely on population genetic estimates based on a few microsatellites are unlikely to be nullified by the general shift toward SNPs in the literature. However, estimates between markers and datasets varied considerably when only adult samples were considered; hence, including samples of all age groups is recommended to be used when available. The estimated N e was higher for the full SNP dataset (2010-2019) than the smaller comparison data (2010-2015), which might be a better reflection of the species status. The lower precision of microsatellites may not necessarily be a barrier for most conservation applications; however, SNPs will improve confidence limits, which may be useful for practitioners.

Wildlife Crime: Issues and Promising Solutions.

The poaching of wildlife for profit, pleasure, subsistence, or as a result of human-animal conflict has decimated wildlife populations-particularly those of at-risk species [...].

Threats of Longline Fishing to Global Albatross Diversity.

Albatrosses are among the most threatened seabird species. Often entangled in gillnets or hooked while longline fishing gear is being set, albatrosses are affected by fishing. This is assumed to be especially true in cases where illegal longline fishing vessels are involved, as they are less likely to implement the bycatch mitigation measures implemented to reduce the risk of albatrosses being caught on their hooks. This is the assumption that was tested in the current study, which uses environmental criminology as its guiding theoretical framework. Using the spatial units of one-half-degree by one-half-degree longitude/latitude cells, this research examined the patterns of concentration of potentially illegal longlining efforts and their relationships to commercially sought-out and illegally caught (i.e., CRAAVED-concealable, removable, abundant, accessible, valuable, enjoyable, disposable) fish species concentrations, as well as their effects on the average risk of albatrosses. The results indicated that (a) potentially illegal longlining activity is spatially concentrated; (b) this concentration is exhibited in areas with the highest concentrations of the presence of CRAAVED fish; and (c) the average risk score of albatrosses, as measured by their International Union for Conservation of Nature (IUCN) Red List status, is significantly higher in the areas where illegal longlining vessels are found controlling for the activities of legal longlining vessels. These findings provide strong grounding that illegal longline fishing poses a particularly serious threat to the survival of albatrosses. These activities, however, are not randomly spread across the vast oceans, but rather are highly spatially concentrated. Therefore, the bird conservation lobby should work closely with regional fisheries management organizations to devise and implement targeted interventions aimed at reducing potential illegal longline fishing, which, in turn, will likely have positive effects on albatrosses.

Global trends of habitat destruction and consequences for parrot conservation.

Human advance on natural habitats is a major cause of biodiversity loss. This transformation process represents a profound change in wooded environments, disrupting original communities of flora and fauna. Many species are highly dependent on forests, especially parrots (Psittaciformes) with almost a third of their species threatened by extinction. Most parrot species occur in tropical and subtropical forests, and given the forest dependence of most species, this is the main reason why habitat loss has been highlighted as the main threat for the group. Such habitat loss acts in synergy with other important threats (e.g., logging and poaching), which become especially problematic in certain developing countries along tropical latitudes. In this study, we used available information on parrot distributions, species traits, IUCN assessment, habitat loss and timber extraction for different periods, and distribution of protected areas, to determine conservation hotspots for the group, and analyze potential changes in the conservation status of these species. We detected four conservation hotspots for parrots: two in the Neotropics and two in Oceania, all of them facing different degrees of threat in regard of current habitat loss and agricultural trends. Our results suggest that the future of the group is subject to policymaking in specific regions, especially in the northeastern Andes and the Atlantic Forest. In addition, we predicted that agricultural expansion will have a further negative effect on the conservation status of parrots, pushing many parrot species to the edge of extinction in the near future. Our results have conservation implications by recommending protected areas in specific parrot conservation hotspots. Our recommendations to mitigate conservation risks to this group of umbrella species would also benefit many other coexisting species as well.

Genomic impact of severe population decline in a nomadic songbird.

Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained a SNP dataset from 64 museum specimens (date 1879-1960), 102 'recent' (1989-2012) and 52 'current' (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. Museum sampling showed population structure in regent honeyeaters was historically low, which remains the case despite a severe fragmentation of the breeding range. Population decline has led to minimal loss of genetic diversity since the 1980's. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. A rapid population decline, coupled with the regent honeyeater's high mobility, means a detectable genomic impact of this decline has not yet manifested. Extinction may occur in this nomadic species before a detectable genomic impact of small population size is realised. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

Sex ratio bias and shared paternity reduce individual fitness and population viability in a critically endangered parrot.

Sex-biased mortality can lead to altered adult sex ratios (ASRs), which may in turn lead to harassment and lower fitness of the rarer sex and changes in the mating system. Female critically endangered swift parrots (Lathamus discolor) suffer high predation while nesting due to an introduced mammalian predator, the sugar glider (Petaurus breviceps). High predation on females is causing severe population decline alongside strongly biased adult sex ratios (≥73% male). Our 6-year study showed that 50.5% of critically endangered swift parrot nests had shared paternity although the birds remained socially monogamous. Shared paternity increased significantly with the local rate of predation on breeding females, suggesting that rates of shared paternity increased when the ASR became more biased. Nests that were not predated produced fewer fledglings as the local ASR became more male-biased possibly due to higher interference during nesting from unpaired males. Population viability analyses showed that part of the predicted decline in the swift parrot population is due to reduced reproductive success when paternity is shared. The models predicted that the population would decline by 89.4% over three generations if the birds maintained the lowest observed rate of shared paternity. This compares with predicted population reductions of 92.1-94.9% under higher rates of shared paternity. We conclude that biases in the ASR, in this case caused by sex-specific predation from an introduced predator, can lead to changes in the mating system and negative impacts on both individual fitness and long-term population viability.

Efficient Reversible Hydrogen Carrier System Based on Amine Reforming of Methanol.

A novel hydrogen storage system based on the hydrogen release from catalytic dehydrogenative coupling of methanol and 1,2-diamine is demonstrated. The products of this reaction, N-formamide and N,N'-diformamide, are hydrogenated back to the free amine and methanol by a simple hydrogen pressure swing. Thus, an efficient one-pot hydrogen carrier system has been developed. The H2 generating step can be termed as "amine reforming of methanol" in analogy to the traditional steam reforming. It acts as a clean source of hydrogen without concurrent production of CO2 (unlike steam reforming) or CO (by complete methanol dehydrogenation). Therefore, a carbon neutral cycle is essentially achieved where no carbon capture is necessary as the carbon is trapped in the form of formamide (or urea in the case of primary amine). In theory, a hydrogen storage capacity as high as 6.6 wt % is achievable. Dehydrogenative coupling and the subsequent amide hydrogenation proceed with good yields (90% and >95% respectively, with methanol and N,N'-dimethylethylenediamine as dehydrogenative coupling partners).

Chemical Formation of Methanol and Hydrocarbon ("Organic") Derivatives from CO2 and H2-Carbon Sources for Subsequent Biological Cell Evolution and Life's Origin.

Formation of methanol and hydrocarbon derivatives from CO2 and H2, their simplest molecular building blocks, under biocompatible conditions is proposed. Alternate panspermia of similar extraterrestrially formed and observed hydrocarbons to earth is also discussed. The simple molecular building blocks derived from CO2 and H2 are carbon sources in the initial stage of biological evolution of cells leading to life's origin.

Relevance and Significance of Extraterrestrial Abiological Hydrocarbon Chemistry.

Astrophysical observations show similarity of observed abiological "organics"-i.e., hydrocarbons, their derivatives, and ions (carbocations and carbanions)-with studied terrestrial chemistry. Their formation pathways, their related extraterrestrial hydrocarbon chemistry originating from carbon and other elements after the Big Bang, their parent hydrocarbon and derivative (methane and methanol, respectively), and transportation of derived building blocks of life by meteorites or comets to planet Earth are discussed in this Perspective. Their subsequent evolution on Earth under favorable "Goldilocks" conditions led to more complex molecules and biological systems, and eventually to humans. The relevance and significance of extraterrestrial hydrocarbon chemistry to the limits of science in relation to the physical aspects of evolution on our planet Earth are also discussed.

Chemical Aspects of Astrophysically Observed Extraterrestrial Methanol, Hydrocarbon Derivatives, and Ions.

Astrophysically observed extraterrestrial molecular matter contains, besides hydrogen and water, methane and methanol as the most abundant species. Feasible pathways and chemical aspects of their formation as well as of derived hydrocarbon homologues and their ions (carbocations and carbanions) are discussed on the basis of observed similarities with our studied terrestrial chemistry. The preferred pathway for converting extraterrestrial methane according to Ali et al. is based on CH5(+) and Olah's related nonclassical carbonium ion chemistry. On the basis of the observed higher reactivity of methanol compared with methane in various chemical reactions, a feasible new pathway is proposed for the conversion of extraterrestrial methanol to hydrocarbons, their derivatives, and carbocations together with a possible connection with methonium ion-based chemistry.

Synthesis of 3-substituted isoindolin-1-ones via a tandem desilylation, cross-coupling, hydroamidation sequence under aqueous phase-transfer conditions.

A simple and expedient method for the synthesis of 3-methylene-isoindolin-1-ones 4 under aqueous phase-transfer conditions has been developed. Starting from 2-iodobenzamides 1 and (silyl)alkynes, the products are obtained in high yields and short reaction times (30 min) with the use of inexpensive CuCl/PPh3 catalyst system in the presence of n-Bu4NBr (TBAB) as a phase-transfer agent. Terminal alkynes are conveniently "unmasked" upon in situ desilylation under the reaction conditions. Alkynes possessing heterocyclic moieties were also found as amenable substrates. Furthermore, a one-pot process starting from 2-iodobenzamides 1, aryl halides (bromides or iodides) and trimethylsilylacetylene (TMSA) as a convenient acetylene surrogate was also shown to be feasible under Pd/Cu catalysis.

Conversion of CO2 from Air into Methanol Using a Polyamine and a Homogeneous Ruthenium Catalyst.

A highly efficient homogeneous catalyst system for the production of CH3OH from CO2 using pentaethylenehexamine and Ru-Macho-BH (1) at 125-165 °C in an ethereal solvent has been developed (initial turnover frequency = 70 h(-1) at 145 °C). Ease of separation of CH3OH is demonstrated by simple distillation from the reaction mixture. The robustness of the catalytic system was shown by recycling the catalyst over five runs without significant loss of activity (turnover number > 2000). Various sources of CO2 can be used for this reaction including air, despite its low CO2 concentration (400 ppm). For the first time, we have demonstrated that CO2 captured from air can be directly converted to CH3OH in 79% yield using a homogeneous catalytic system.

Ab initio/GIAO-CCSD(T) (13)C NMR study of the rearrangement and dynamic aspects of rapidly equilibrating tertiary carbocations, C6H13(+) and C7H15(+).

The rearrangement pathways of the equilibrating tertiary carbocations, 2,3-dimethyl-2-butyl cation (C6H13(+), 1), 2,3,3-trimethyl-2-butyl cation (C7H15(+), 5) and 2,3-dimethyl-2-pentyl cation (C7H15(+), 8 and 9) were investigated using the ab initio/GIAO-CCSD(T) (13)C NMR method. Comparing the calculated and experimental (13)C NMR chemical shifts of a series of carbocations indicates that excellent prediction of δ(13)C could be achieved through scaling. In the case of symmetrical equilibrating cations (1 and 5) the Wagner-Meerwein 1,2-hydride and 1,2-methide shifts, respectively, produce the same structure. This indicates that the overall (13)C NMR chemical shifts are conserved and independent of temperature. However, in the case of unsymmetrical equilibrating cations (8 and 9) the Wagner-Meerwein shift produces different tertiary structures, which have slightly different thermodynamic stabilities and, thus, different spectra. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level structure 8 is only 90 calories/mol more stable than structure 9. Based on computed (13)C NMR chemical shift calculations, mole fractions of these isomers were determined by assuming the observed chemical shifts are due to the weighted average of the chemical shifts of the static ions.

Superelectrophilic Activation of Crotonic/Methacrylic Acids: Direct Access to Thiochroman-4-ones from Benzenethiols by Microwave-Assisted One-Pot Alkylation/Cyclic Acylation.

An efficient microwave-assisted protocol for the synthesis of 2-/3-methylthiochroman-4-ones by superacid-catalyzed alkylation followed by cyclic acylation (cyclization via intramolecular acylation) is described. Using easily accessible benzenethiols and crotonic acid/methacrylic acid with triflic acid (as catalyst of choice for needed optimal acidity), the reaction was tuned toward the formation of the cyclized products in good selectivity and yield. A mechanism involving the formation of carbenium-carboxonium superelectrophilic species is suggested.

Single Step Bi-reforming and Oxidative Bi-reforming of Methane (Natural Gas) with Steam and Carbon Dioxide to Metgas (CO-2H2) for Methanol Synthesis: Self-Sufficient Effective and Exclusive Oxygenation of Methane to Methanol with Oxygen.

Catalysts based on suitable metal oxide supports, such as NiO/MgO and CoO/MgO, were shown to be active for single step bi-reforming, the combined steam and dry reforming of methane or natural gas with H2O and CO2 exclusively to metgas (CO-2H2) for efficient methanol synthesis. Reactions were carried out in a tubular flow reactor under pressures up to 42 bar at 830-910 °C. Using a CH4 to steam to CO2 ratio of ∼3:2:1 in the gas feed, the H2/CO ratio of 2:1 was achieved, which is desired for subsequent methanol synthesis. The needed 2/1 steam/CO2 feed ratio together with the reaction heat for the endothermic bi-reforming can be conveniently obtained by the complete combustion of a quarter part of the overall used methane (natural gas) with oxygen of the air (oxidative bi-reforming). Complete combustion of a part of methane followed by bi-reforming leads to the production of metgas (H2/CO in 2:1 mol ratio) for self-sufficient exclusive methanol synthesis. The long sought after but elusive efficient and selective oxygenation of methane to methanol is thus achieved in an effective and economic way without any oxidation byproduct formation according to CH4 + 1/2O2 → CH3OH.

MP2, CCSD(T), and Density Functional Theory Study of the 2-Butyl Cation: New Insight into the Methyl- and Hydrogen-Bridged Structures.

Using the MP2, CCSD(T), and DFT (B3LYP) methods, the structures and energies of the 2-butyl cation (C4H9(+)) were calculated. Energetically, the C-C hyperconjugated structure 1 and hydrogen-bridged structure 2 were found to be almost identical at all levels. The (13)C NMR chemical shifts of 1 and 2 were computed by the GIAO-CCSD(T) method using different geometries. On the basis of calculated relative energies and calculated (13)C NMR chemical shifts, an equilibrium involving 1 and 2 (in a 50:50 ratio) seemed likely responsible for the experimentally observed (13)C NMR chemical shifts in superacid solutions at -80 °C. However, on the basis of computed and experimental frequencies the hydrogen-bridged structure 2 is most likely responsible for the experimentally observed frequencies in the solid state at -125 °C.

Amine-free reversible hydrogen storage in formate salts catalyzed by ruthenium pincer complex without pH control or solvent change.

Due to the intermittent nature of most renewable energy sources, such as solar and wind, energy storage is increasingly required. Since electricity is difficult to store, hydrogen obtained by electrochemical water splitting has been proposed as an energy carrier. However, the handling and transportation of hydrogen in large quantities is in itself a challenge. We therefore present here a method for hydrogen storage based on a CO2 (HCO3 (-) )/H2 and formate equilibrium. This amine-free and efficient reversible system (>90 % yield in both directions) is catalyzed by well-defined and commercially available Ru pincer complexes. The formate dehydrogenation was triggered by simple pressure swing without requiring external pH control or the change of either the solvent or the catalyst. Up to six hydrogenation-dehydrogenation cycles were performed and the catalyst performance remained steady with high selectivity (CO free H2 /CO2 mixture was produced).

Paul von Ragué Schleyer (1930-2014).

Paul von Ragué Schleyer, Graham Perdue Professor at the University of Georgia passed away on November 21, 2014. Schleyer was an eminent and prolific physical organic chemist, whose pioneering contributions included the application of computational chemistry to broad fields of physical organic, inorganic, organometallic, and mechanistic chemistry concepts.

Long-lived trifluoromethanide anion: a key intermediate in nucleophilic trifluoromethylations.

The trifluoromethanide anion is the postulated key intermediate in nucleophilic trifluoromethylation reactions. However, for more than six decades, the trifluoromethanide anion was widely believed to exist only as a short-lived transient species in the condensed phase. It has now been prepared in bulk for the first time in THF solution. The trifluoromethanide anion with the [K(18-crown-6)](+) cation was unequivocally characterized by low-temperature (19)F and (13)C NMR spectroscopy. Its intermediacy in nucleophilic trifluoromethylation reactions was directly evident by its reaction chemistry with various electrophilic substrates. Variable-temperature NMR spectroscopy, along with quantum mechanical calculations, support the persistence of the trifluoromethanide anion.

The trifluoromethyl group as a conformational stabilizer and probe: conformational analysis of cinchona alkaloid scaffolds.

The introduction of the CF3 group on the C9 atom in quinidine can significantly increase the conformational interconversion barrier of the cinchona alkaloid scaffold. With this modification the conformational behavior of cinchona alkaloids in various solvents can be conveniently investigated via (19)F NMR spectroscopy. Based on the reliable conformational distribution information obtained, the accuracy of both theoretical (PCM) and empirical (Kamlet-Taft) solvation models has been assessed using linear free energy relationship methods. The empirical solvation model was found to provide accurate prediction of solvent effects, while PCM demonstrated a relatively low reliability in the present study. Utilizing similar empirical solvation models along with Karplus-type equations, the conformational behavior of quinidine and 9-epi-quinidine has also been investigated. A model SN2 reaction has been presented to reveal the important role of solvent-induced conformational behavior of cinchona alkaloids in their reactivity.