Distinguishing coevolution from covicariance in an obligate pollination mutualism: asynchronous divergence in Joshua tree and its pollinators

Obligate pollination mutualisms--in which both plants and their pollinators are reliant upon one another for reproduction--represent some of the most remarkable coevolutionary interactions in the natural world. The intimacy and specificity of these interactions have led to the prediction that the plants and their pollinators may be prone to cospeciation driven by coevolution. Several studies have identified patterns of phylogenetic congruence that are consistent with this prediction, but it is difficult to determine the evolutionary process that underlies these patterns. Phylogenetic congruence might also be produced by extrinsic factors, such as a shared biogeographic history. We examine the biogeographic history of a putative case of codivergence in the obligate pollination mutualism between Joshua trees (Yucca brevifolia) and two sister species of pollinating yucca moths (Tegeticula spp.) We employ molecular phylogenetic methods and coalescent-based approaches, in combination with relaxed-clock estimates of absolute rates of molecular evolution, to analyze multi-locus sequence data from more than 30 populations of Y. brevifolia and its pollinators. The results indicate that the moth species diverged significantly (p < 0.01) more recently than their corresponding host populations, suggesting that the apparent codivergence is not an artifact of a shared biogeographic history.     

Assessing the use of genomic DNA as a predictor of the maximum absorbance wavelength of avian SWS1 opsin visual pigments

Recently, in vitro mutation studies have made it possible to predict the wavelengths of maximum absorbance (λ_max) of avian UV/violet sensitive visual pigments (SWS1) from the identity of a few key amino acid residues in the opsin gene. Given that the absorbance spectrum of a cone’s visual pigment and of its pigmented oil droplet can be predicted from just the λ_max, it may become possible to predict the entire spectral sensitivity of a bird using genetic samples from live birds or museum specimens. However, whilst this concept is attractive, it must be validated to assess the reliability of the predictions of λ_max from opsin amino acid sequences. In this paper, we have obtained partial sequences covering three of the known spectral tuning sites in the SWS1 opsin and predicted λ_max of all bird species for which the spectral absorbance has been measured using microspectrophotometry. Our results validate the use of molecular data from genomic DNA to predict the gross differences in λ_max between the violet- and ultraviolet-sensitive subtypes of SWS1 opsin. Additionally, we demonstrate that a bird, the bobolink Dolichonyx oryzivorus L., can have more than one SWS1 visual pigment in its retina.     

Evolution of a carbohydrate binding module into a protein-specific binder

A carbohydrate binding module, CBM4-2, derived from the xylanase (Xyn 10A) of Rhodothermus marinus has been used as a scaffold for molecular diversification. Its binding specificity has been evolved to recognise a quite different target, a human monoclonal IgG4. In order to understand the basis for this drastic change in specificity we have further investigated the target recognition of the IgG4-specific CBMs. Firstly, we defined that the structure target recognised by the selected CBM-variants was the protein and not the carbohydrates attached to the glycoprotein. We also identified key residues involved in the new specificity and/or responsible for the swap in specificity, from xylan to human IgG4. Specific changes present in all these CBMs included mutations not introduced in the design of the library from which the specific clones were selected. Reversion of such mutations led to a complete loss of binding to the target molecule, suggesting that they are critical for the recognition of human IgG4. Together with the mutations introduced at will, they had transformed the CBM scaffold into a protein binder. We have thus shown that the scaffold of CBM4-2 is able to harbour molecular recognition for either carbohydrate or protein structures.     

Bromine oxidation of methyl α- and β-pyranosides of D-galactose,D-glucose,and D-mannose

Methyl α- and β-pyranosides of D-galactose, D-glucose, and D-mannose have been oxidized with bromine in aqueous solution at various pH values. The resulting keto glycosides were converted into their more-stable O-methyloxime derivatives which were characterized by spectroscopy and chromatography. Oxidation at a ring carbon atom where the hydrogen is axial is hindered by bulky substituents in syn (i.e., a 1,3) diaxial relationship. Thus, the aglycon group in the α anomers protects position 3, the axial HO-4 in galactopyranosides protects position 2, and the axial HO-2 in mannopyranosides protects position 4 from oxidation.     

Vegetation dynamics and disturbance history in three deciduous forests in boreal Sweden

Abstract. Remaining deciduous forests in the Fennoscandian boreal landscape have high ecological value, and are considered as key components of the forest landscape as well as remnants of a former natural forest type. To improve our understanding of the formation of deciduous forests, we studied past disturbance regimes and vegetation dynamics in three deciduous forests in boreal Sweden using dendro‐ecology, pollen analysis and charcoal analysis. We identified three stages in the development of the studied stands. Firstly, the coniferous period (pre 1800), a long‐lasting period characterized by frequent fires, livestock grazing and extensive agriculture during which Pinus sylvestris was dominant. Secondly, the transformation period (1800 ‐ 1900), when logging removed most pines from the sites while fire and grazing continued. At the time of the last fire, the sites lacked a local seed source of pines, resulting in a post‐fire succession dominated by deciduous species with the capacity to disperse over long distances. Thirdly, the deciduous period (1900 ‐ present), with little or no disturbance from fire, grazing or logging. Thus, the present deciduous stands have their origins in a complex interaction between changes in fire regime, extensive land use patterns and logging, contrary to earlier simplified explanations. We conclude that the complexity of historical patterns of land use, vegetation dynamics and disturbance should be acknowledged in the future when selecting areas for nature conservation and developing models for ecologically oriented forestry.     

Rapid population divergence linked with co-variation between coloration and sexual display in strawberry poison frogs

The likelihood of speciation is assumed to increase when sexually selected traits diverge together with ecologically important traits. According to sexual selection theory, the evolution of exaggerated display behavior is driven by increased mating success, but limited by natural selection, for example, through predation. However, the evolution of aposematic coloration (i.e., an ecologically important trait) could relieve the evolution of exaggerated display behavior from the bound of predation, resulting in joint divergence in aposematic coloration and sexual display behavior between populations. We tested this idea by examining conspicuousness, using color contrasts between individuals and their native backgrounds, and sexual display of 118 males from genetically diverged populations of the Strawberry poison frog, Dendrobates pumilio. Our results show that the level of conspicuousness of the population predicts the sexual display behavior of males. Males from conspicuous populations used more exposed calling sites. We argue that changes in aposematic coloration may rapidly cause not only postmating isolation due to poorly adapted hybrids, but also premating isolation through shifts in mating behaviors.     

Molecular tools for a molecular medicine: analyzing genes, transcripts and proteins using padlock and proximity probes

Procedures and reagents are needed to specifically detect all the macromolecules that are being identified in the course of genome projects. We discuss how this challenge may be met using a set of ligation-based reagents termed padlock probes and proximity ligation probes. These probes include elements with affinity for specific nucleic acid and protein molecules, respectively, along with unique identifier DNA sequence elements that encode the identity of the recognized target molecules. The information content of DNA strands that form in the detection reactions are recorded after amplification, allowing the recognized target molecules to be identified. The procedures permit highly specific solution-phase or localized analyses of large sets of target molecules as required in future molecular analyses.     

Isolation and characterization of a mixotrophic sulfur-oxidizing Thermus scotoductus

Thermophilic, faculatatively mixotrophic sulfur-oxidizing bacteria were isolated from a sulfide-rich, neutral hot spring in Iceland. The strain, IT-7254, used thiosulfate and elemental sulfur as electron donors, oxygen and nitrate as electron acceptors, and acetate and other organic compounds as carbon sources. After a few days of growth in the presence of thiosulfate, this strain formed sulfur globules. Comparison of intracellular enzymes and heme proteins of heterotrophically and mixotrophically grown cells showed some differences. The new isolate belonged to Thermus scotoductus because the small subunit (SSU) rRNA gene sequence analysis showed 98.6% sequence similarity and 84% DNA:DNA reassociation to Thermus scotoductus NMX2 A. 1. It is also close to Thermus antranikianii HN3-7, with 98.3% and 79% SSU rRNA sequence similarity and DNA:DNA reassociation, respectively. It was also found that both Thermus NMX2 A.1 and T. antranikianii HN3-7 were able to oxidize thiosulfate but that the T. scotoductus type strain SE-1 was not. This is the first report of Thermus strains that are capable of mixotrophic growth with sulfur oxidation.