Birding and DNA: species for the new millennium

Capsule Based on the 1999 Witherby Memorial Lecture – reviews how developments in molecular and population genetics have led to a reappraisal of species limits in birds.

The taxonomy of birds of the West Palearctic has moved from the comparative stability of the ‘Voous List’ into a period of serious activity, with new data emerging in almost every issue of every evolutionary and avian journal! This activity comes from two directions. Firstly, developments in population genetics, molecular biology, acoustics, behaviour and distributional studies have opened new avenues to measuring differentiation among groups of birds. This, in turn, has led to the recognition that earlier views of what constitutes a ‘species’ are in need of modification (‘improvement’), and the emergence of the ‘lineage concept’ of species. I review some of the species concepts most relevant to avian studies, and attempt to show how and why this change has happened, and its consequences for taxonomy and species limits. Examples are given in the form of ‘case studies’, and include Carrion/Hooded Crows Corvus corone/cornix, Green-winged/Eurasian Teals Anas carolinensis/crecca and Phylloscopus warblers.     

G. Ledyard Stebbins, Jr. and the evolutionary synthesis (1924-1950)

This is an historical paper examining the scientific background of George Ledyard Stebbins, Jr. (b. 1906), one of the foremost botanists of this century and one of the architects of the evolutionary synthesis, the intellectual event that brought together genetics and selection theory in the interval between 1920 and 1950. It considers his scientific influence and research, beginning with his Harvard education in 1924 and ending in 1950 with the publication of his book Variation and Evolution in Plants. The paper also more broadly assesses the contributions of other botanists to the evolutionary synthesis, including discussion of the work of Edgar Anderson (1897-1967) and others. It also traces the larger historical patterns of American botany, which saw a shift from East Coast botany as exemplified by Harvard botany, to West Coast botany, as exemplified by California botany.     

Is xenodontine snake reproduction shaped by ancestry,more than by ecology?

One of the current challenges of evolutionary ecology is to understand the effects of phylogenetic history (PH) and/or ecological factors (EF) on the life‐history traits of the species. Here, the effects of environment and phylogeny are tested for the first time on the reproductive biology of South American xenodontine snakes. We studied 60% of the tribes of this endemic and most representative clade in a temperate region of South America. A comparative method (canonical phylogenetic ordination—CPO) was used to find the relative contributions of EF and PH upon life‐history aspects of snakes, comparing the reproductive mode, mean fecundity, reproductive potential, and frequency of nearly 1,000 specimens. CPO analysis showed that PH or ancestry explained most of the variation in reproduction, whereas EF explained little of this variation. The reproductive traits under study are suggested to have a strong phylogenetic signal in this clade, the ancestry playing a big role in reproduction. The EF also influenced the reproduction of South American xenodontines, although to a lesser extent. Our finding provides new evidence of how the evolutionary history is embodied in the traits of living species.     

Scratching beneath the surface: Bandicoot bioturbation contributes to ecosystem processes

Animals that forage for food or dig burrows by biopedturbation can alter the biotic and abiotic characteristics of their habitat. The digging activities of such ecosystem engineers, although small at a local scale, may be important for broader scale landscape processes by influencing soil and litter properties, trapping organic matter and seeds, and subsequently altering seedling recruitment. We examined environmental characteristics (soil moisture content, hydrophobicity and litter composition) of foraging pits created by the southern brown bandicoot (Isoodon obesulus; Peramelidae), a digging Australian marsupial, over a 6‐month period. Fresh diggings typically contained a higher moisture content and lower hydrophobicity than undisturbed soil. A month later, foraging pits contained greater amounts of fine litter and lower amounts of coarse litter than adjacent undug surfaces, indicating that foraging pits may provide a conducive microhabitat for litter decomposition, potentially reducing litter loads and enhancing nutrient decomposition. We tested whether diggings might affect seedling recruitment (seed removal by seed harvesters and seed germination rates) by artificially mimicking diggings. Although there were no differences in the removal of seeds, seedling recruitment for three native plant species (Acacia saligna, Kennedia prostrata and Eucalyptus gomphocephala) was higher in plots containing artificial diggings compared with undug sites. The digging actions of bandicoots influenced soil moisture and hydrophobicity, the size distribution of litter and seedling recruitment at a local scale. The majority of Australian digging mammals are threatened, with many suffering substantial population and range contraction. However, their persistence in landscapes plays an important role in maintaining the health and function of ecosystems.     

Engineering Saccharomyces cerevisiae for high yield production of α-amyrin via synergistic remodeling of α-amyrin synthase and expanding the storage pool

α-Amyrin is a plant-originated high-valued triterpene that is highly effective against several pathological ailments. α-Amyrin production by engineered Saccharomyces cerevisiae has been achieved by introducing α-amyrin synthase (αAS). However, the low yield of α-amyrin highly limits its industrial application; the low catalytic activity of αAS and the toxic effect of α-amyrin have been considered key elements. In this study, the highest yield of α-amyrin was obtained in engineered S. cerevisiae by remodeling α-amyrin synthase MdOSC1 and expanding the storage pool. The yield of α-amyrin was increased to 11-fold higher than that of the control by the triple mutant MdOSC1^{N11T/P250H/P373A} obtained based on the modeling analysis. Furthermore, key genes of MVA pathway were overexpressed to provide sufficient precursors, and DGA1 (Diacylglycerol acyltransferase) was overexpressed to expand the intracellular storage capacity. Finally, the as-constructed aAM12 strain produced 213.7 ± 12.4 mg/L α-amyrin in the shake flask and 1107.9 ± 76.8 mg/L in fed-batch fermentation; the fermentation yield was 106-fold higher than that of the original aAM1 strain under the same conditions, representing the highest α-amyrin yield in yeast reported to date. Microbial production of α-amyrin with over 1 g/L will be suitable for commercialization and can accelerate the industrial production of α-amyrin in yeast.     

Modular Skeletal Evolution in Sticklebacks Is Controlled by Additive and Clustered Quantitative Trait Loci

Understanding the genetic architecture of evolutionary change remains a long-standing goal in biology. In vertebrates, skeletal evolution has contributed greatly to adaptation in body form and function in response to changing ecological variables like diet and predation. Here we use genome-wide linkage mapping in threespine stickleback fish to investigate the genetic architecture of evolved changes in many armor and trophic traits. We identify >100 quantitative trait loci (QTL) controlling the pattern of serially repeating skeletal elements, including gill rakers, teeth, branchial bones, jaws, median fin spines, and vertebrae. We use this large collection of QTL to address long-standing questions about the anatomical specificity, genetic dominance, and genomic clustering of loci controlling skeletal differences in evolving populations. We find that most QTL (76%) that influence serially repeating skeletal elements have anatomically regional effects. In addition, most QTL (71%) have at least partially additive effects, regardless of whether the QTL controls evolved loss or gain of skeletal elements. Finally, many QTL with high LOD scores cluster on chromosomes 4, 20, and 21. These results identify a modular system that can control highly specific aspects of skeletal form. Because of the general additivity and genomic clustering of major QTL, concerted changes in both protective armor and trophic traits may occur when sticklebacks inherit either marine or freshwater alleles at linked or possible “supergene” regions of the stickleback genome. Further study of these regions will help identify the molecular basis of both modular and coordinated changes in the vertebrate skeleton.     

Timentin as an alternative antibiotic for suppression of Agrobacterium tumefaciens in genetic transformation

The effects of timentin on shoot regeneration of tobacco (Nicotiana tabaccum) and Siberian elm (Ulmus pumila L.) and its use for the suppression of Agrobacterium tumefaciens in Agrobacterium-mediated genetic transformation were determined. Timentin is a mixture of ticarcillin and clavulanic acid, and at concentrations of 200–500 mg/l with ratios of ticarcillin:clavulanic acid of 50:1 and 100:1, it had little effect on shoot regeneration of tobacco or Siberian elm. Timentin was as effective in suppressing A. tumefaciens as carbenicillin and cefatoxime at concentrations commonly used in transformation. The disarmed A. tumefaciens strain LBA4404 in infected tobacco leaf tissues was visually undetectable after three subcultures on medium with 500 mg/l of timentin and 250 mg/l carbenicillin. Timentin was stable in solid agar medium and remained effective for at least 70 days, but was unstable when stored as a mixed stock solution or as separate ticarcillin and clavulanic acid stock solutions at –20°C or –80°C freezer for 4 weeks. Timentin may be an alternative antibiotic for the effective suppression of A. tumefaciens in genetic transformation. Received: 8 September 1997 / Revision received: 19 November 1997 / Accepted: 2 December 1997     

Functional characterization of an anti-estradiol antibody by site-directed mutagenesis and molecular modelling: modulation of binding properties and prominent role of the V(L) domain in estradiol recognition

The high-affinity monoclonal anti-estradiol antibody 9D3 presents a specificity defect towards estradiol-3-sulphate and 3-glucuronide conjugates incompatible with use in direct immunoassays. The corresponding single-chain variable fragment (scFv), cloned and produced in E. coli, exhibited a 10-fold lower affinity for estradiol (K(a)=1.2 x 10(9) M (-1)) and a slightly increased specificity defect for the 3-position. Site-directed mutagenesis revealed critical residues involved in estradiol recognition and produced mutants exhibiting up to a 3-fold increase of the binding affinity for estradiol and up to a 2-fold decrease of the cross-reactivity with estradiol-3-sulphate. A comparative model of the antibody 9D3-estradiol complex was built in which the estradiol D-ring is buried into the binding pocket while the 3-, 6- and 7-positions are solvent exposed, agreeing with the lack of specificity for these three positions. Two potential alternative orientations of the A-ring, one close to CDR H3 and L2 loops, and the other one close to CDR H2 and L3 loops, have been considered for the docking of estradiol, none of which could be unambiguously privileged taking into account data from cross-reactivity measurements, photolabelling and mutagenesis studies. For both orientations, estradiol is stabilized by hydrogen bonding of the 17beta-OH group with TyrL36, His89 and GlnH35 in the first case, or TyrL36, only, in the second case and by van der Waals contacts from TyrL91 with alpha- or beta-face of estradiol, respectively, and from ValH95 and GlyH97 with the opposite face. To elucidate the molecular basis of antibody 9D3 specificity, as compared with that of another anti-estradiol antibody 15H11, single variable domains (V(H) and V(L)) and scFv hybrids have been constructed. The binding activity of V(L)9D3 as well as the specificity of the V(L)9D3/V(H)15H11 hybrid, both similar to antibody 9D3, revealed a prominent role of V(L) in estradiol recognition. These findings establish premises for antibody engineering to reduce cross-reactivity, especially with estradiol-3-conjugates.     

褐藻寡糖生物法制备研究进展 *

褐藻寡糖(alginate oligosaccharides,AOS)是褐藻胶的降解产物,具有抗氧化、调节免疫、调节血脂、促进细胞生长等生理活性,应用范围广泛。现有的AOS 制备法主要分为物理法、化学法和生物法。介绍AOS的生物法制备包括酶解、微生物全细胞发酵和生物合成法,基因工程的应用在改造产褐藻胶裂解酶的菌株以提高生物法效率方面具有重要意义。此外,规模化的AOS生物法制备案例进行了科学引证,并展望了未来 AOS规模化制备的发展方向,以期为 AOS 的工业化制备和应用提供参考。     

Population persistence under high mutation rate: From evolutionary rescue to lethal mutagenesis

Populations may genetically adapt to severe stress that would otherwise cause their extirpation. Recent theoretical work, combining stochastic demography with Fisher's geometric model of adaptation, has shown how evolutionary rescue becomes unlikely beyond some critical intensity of stress. Increasing mutation rates may however allow adaptation to more intense stress, raising concerns about the effectiveness of treatments against pathogens. This previous work assumes that populations are rescued by the rise of a single resistance mutation. However, even in asexual organisms, rescue can also stem from the accumulation of multiple mutations in a single genome. Here, we extend previous work to study the rescue process in an asexual population where the mutation rate is sufficiently high so that such events may be common. We predict both the ultimate extinction probability of the population and the distribution of extinction times. We compare the accuracy of different approximations covering a large range of mutation rates. Moderate increase in mutation rates favors evolutionary rescue. However, larger increase leads to extinction by the accumulation of a large mutation load, a process called lethal mutagenesis. We discuss how these results could help design “evolution‐proof” antipathogen treatments that even highly mutable strains could not overcome.