Identifying mechanisms of genetic differentiation among populations in vagile species: historical factors dominate genetic differentiation in seabirds

Elucidating the factors underlying the origin and maintenance of genetic variation among populations is crucial for our understanding of their ecology and evolution, and also to help identify conservation priorities. While intrinsic movement has been hypothesized as the major determinant of population genetic structuring in abundant vagile species, growing evidence indicates that vagility does not always predict genetic differentiation. However, identifying the determinants of genetic structuring can be challenging, and these are largely unknown for most vagile species. Although, in principle, levels of gene flow can be inferred from neutral allele frequency divergence among populations, underlying assumptions may be unrealistic. Moreover, molecular studies have suggested that contemporary gene flow has often not overridden historical influences on population genetic structure, which indicates potential inadequacies of any interpretations that fail to consider the influence of history in shaping that structure. This exhaustive review of the theoretical and empirical literature investigates the determinants of population genetic differentiation using seabirds as a model system for vagile taxa. Seabirds provide a tractable group within which to identify the determinants of genetic differentiation, given their widespread distribution in marine habitats and an abundance of ecological and genetic studies conducted on this group. Herein we evaluate mitochondrial DNA (mtDNA) variation in 73 seabird species. Lack of mutation–drift equilibrium observed in 19% of species coincided with lower estimates of genetic differentiation, suggesting that dynamic demographic histories can often lead to erroneous interpretations of contemporary gene flow, even in vagile species. Presence of land across the species sampling range, or sampling of breeding colonies representing ice‐free Pleistocene refuge zones, appear to be associated with genetic differentiation in Tropical and Southern Temperate species, respectively, indicating that long‐term barriers and persistence of populations are important for their genetic structuring. Conversely, biotic factors commonly considered to influence population genetic structure, such as spatial segregation during foraging, were inconsistently associated with population genetic differentiation. In light of these results, we recommend that genetic studies should consider potential historical events when identifying determinants of genetic differentiation among populations to avoid overestimating the role of contemporary factors, even for highly vagile taxa.     

Reaction equilibrium for lipase-catalyzed condensation in organic solvent systems

Lipase-catalyzed condensation in an organic solvent is useful for the syntheses of esters. To reasonably design and optimize the reaction conditions, knowledge of the reaction equilibrium is required. The interaction of water with other reactants and the quantitative predictions for adsorption of water by a desiccant are discussed. The solvent effects on the reaction equilibrium are also elucidated in mixtures of nitrile and tert-alcohol.     

Metal-binding ability of histidine-containing peptidehydroxamic acids: Imidazole versus hydroxamate coordination

Three new peptidehydroxamic acids (l-alanyl-l-histidinehydroxamic acid, l-Ala-l-HisNHOH, l-alanyl-l-alanyl-l-histidinehydroxamic acid, l-Ala-l-Ala-l-HisNHOH and l-histidyl-l-alaninehydroxamic acid, l-His-l-AlaNHOH) were synthesized and their complexation with Cu(II), Ni(II) and Zn(II) were studied by pH-potentiometric, UV-Vis, CD, ¹H NMR, EPR and ESI-MS methods. Each of the studied peptide derivatives involves one side-chain imidazole unit and the effect of this group on the metal binding of the hydroxamic moiety is evaluated in the paper. The obtained results are compared to those of the complexes of some histidine-containing di- or tripeptides and also to those of hydroxamic derivatives of aliphatic peptides.A competition between the hydroxamate and imidazole functions occurs in all systems, but the extent differs from metal to metal, from ligand to ligand and depends very much on the pH. The imidazole was found to play the most determinant role in the Cu(II) complexes, somewhat less in the Ni(II)-containing ones, while (except the case of l-Ala-l-HisNHOH) negligible role was found in the Zn(II)-complexes. Common feature of the Ni(II)- and especially Cu(II)-containing systems is that if an imidazole-N is displaced by a hydroxamate, imidazole-bridged di- and polynuclear complexes are formed.     

The maturation of HIV‐1 protease precursor studied by discrete molecular dynamics

The equilibrium properties of a HIV‐1‐protease precursor are studied by means of an efficient molecular dynamics scheme, which allows for the simulation of the folding of the protein monomers and their dimerization into an active form and compare them with those of the mature protein. The results of the model provide, with atomic detail, an overall account of several experimental findings, including the NMR conformation of the mature dimer, the calorimetric properties of the system, the effects of the precursor tail on the dimerization constant, the secondary chemical shifts of the monomer, and the paramagnetic relaxation enhancement data associated with the conformations of the precursor. It is found that although the mature protein can dimerize in a unique, single way, the precursor populates several dimeric conformations in which monomers are always native‐like, but their binding can be non‐native. Proteins 2014; 82:633–639. © 2013 Wiley Periodicals, Inc.     

Concluding remarks: historical perspective and the future of island biogeography theory

MacArthur and Wilson’s equilibrium theory revolutionized the field of island biogeography and, to a large degree, ecology as well. The theory, which quickly became the ruling paradigm of island biogeography, has changed little over the past three decades. It has not kept pace with relevant theory and our growing appreciation for the complexity of nature, especially with empirical findings that species diversity on many islands: 1) is not in equilibrium; 2) is influenced by differences in speciation, colonization, and extinction among taxa; and 3) is influenced by differences among islands in characteristics other than area and isolation. The discipline of biogeography, itself, is in a state of disequilibrium. We may again be about to witness another paradigm shift, which will see the replacement of MacArthur and Wilson’s theory. Wherever this shift may take us, we are confident that the next generation of biogeographers will still look to islands for insights into the forces that shape biological diversity.     

A call for a new paradigm of island biogeography

MacArthur and Wilson’s equilibrium theory of island biogeography quickly became the paradigm of the field in the 1960s and has strongly influenced this and other disciplines of ecology and conservation biology for the past three decades. Recently, however, a growing number of ecologists have begun to question whether the theory remains a useful paradigm for modern ecology. We now have a much better appreciation for the complexity of nature and we study patterns that span a very broad range in spatial, temporal and ecological scales. At such scales, assumptions that communities are in equilibrium, that species, islands and intervening landscapes or seascapes are equivalent or homogeneous with respect to factors influencing immigration and extinction, and that in situ speciation can be overlooked become very tenuous. With this in mind, this and other papers of this special feature discuss the principal, conceptual shortcomings of the equilibrium theory and offer some modifications or alternatives to the theory that we hope will eventually lead to a more comprehensive understanding of the forces structuring insular communities.     

A Method for Assessing Leaching Potential for Petroleum Hydrocarbons Release Sites: Multiphase and Multisubstance Equilibrium Partitioning

This article presents the rationale for the mathematical fate and transport model, which has been provided in the accompanying spreadsheet (GWProt). This spreadsheet model may be used as a simple and scientifically defensible regulatory tool for determining the risk-based soil clean up level of petroleum release sites to protect groundwater quality. The model incorporates either a three- or four-phase partitioning equilibrium mechanism, depending on the detection of Non-Aqueous Phase Liquid phase presence mathematically, as well as Raoult's Law convention and default dilution and attenuation factors. A database of contaminant-specific parameters, including solubility and organic-carbon partition-coefficient, molecular weight, and Henry's Law constant, is assembled for benzene, toluene, ethylbenzene, xylenes, and 12 other TPH equivalent carbon fractions. In addition to distributing organic chemicals among aqueous, sorbed solid, air, and NAPL phases, according to traditional partitioning equations, the algorithm incorporates equations for the conservation of mass and volume. A unique solution is obtained by solving a series of mass balance equations simultaneously using the iterative spreadsheet routine built in MICROSOFT EXCEL^TM Solver — with the restrictions that the volume is conserved and the sum of the mole fractions is equal to one. Sample calculations are presented for a range of parameter values to illustrate the use of the model and the relative leach-ability of a wide range of representative fuels. Sensitivity analysis was also performed to quantify the effects of uncertainty in the estimates of the key model parameters on model results. Model predictions were compared with the results from a water-fuel experiment. The noncar-cinogenic Hazard Index (HI) for groundwater through direct ingestion was calculated using predetermined oral reference dose (R_fd) values. Applications and limitations of the model are also discussed.