In defence of model‐based inference in phylogeography

Recent papers have promoted the view that model‐based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model‐based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method and highlight numerous deficiencies, either when used with single or multiple loci. We further show that the ages of clades are carelessly used to infer ages of demographic events, that these ages are estimated under a simple model of panmixia and population stationarity but are then used under different and unspecified models to test hypotheses, a usage the invalidates these testing procedures. We conclude by encouraging researchers to study and use model‐based inference in population genetics.     

Green Fluorescent Protein (GFP) as a Reporter Gene for the Plant Pathogenic Oomycete Phytophthora ramorum

ABSTRACT. Transgenic Phytophthora ramorum strains that produce green fluorescent protein (GFP) constitutively were obtained after stable DNA integration using a polyethylene glycol and CaCl₂-based transformation protocol. Green fluorescent protein production was studied in developing colonies and in different propagules of the pathogen to evaluate its use in molecular and physiological studies. About 12% of the GFP transformants produced GFP to a level detectable by a confocal laser scanning microscope. Green fluorescent protein could be visualized in structures with vital protoplasm, such as hyphal tips and germinating cysts. In infection studies with Rhododendron , one of the GFP expressing strains showed aggressiveness equal to that of the corresponding non-labelled isolate. Thus, GFP could be used as a reporter gene in P. ramorum . Limitations of the technology are discussed.     

Effects of Increasing Water Stress on Simulated Swards of Festuca arundinacea Schreb under Wind Tunnel Conditions

The effects of increasing water stress on water relations, leafconductance, leaf extension and leaf rolling of Festuca arundinaceain sward (I m²) were investigated under wind tunnel conditions.The plants were grown in a container 60 cm deep and the experimentwas conducted over a 36 d period. Upon cessation of watering(day 11), leaf extension and conductance were affected. Within8 d, the onset of leaf rolling helped to reduce transpirationand to maintain leaf water potential. Nocturnal recovery of turgor potential helped in maintainingleaf extension at a moderate level and in the final 5 d waterand osmotic potentials dropped sharply as leaf rolling becamemore acute and leaf extension stopped. The grass combines various morphological and physiological mechanismsto prevent water losses and maintain growth. Festuca arundinacea, tall fescue, wind tunnel, water stress, water potential, osmotic potential, conductance, leaf rolling, leaf extension     

Isocitrate Lyase from Germinating Soybean Cotyledons: Purification and Characterization

Ruchti, M. and Widmer, F. 1986. Isocitrate lyase from germinatingsoybean cotyledons: purification and characterization.—J.exp. Bot. 37: 1685–1690. Isocitrate lyase (E.C. 4.1.3.1 [EC] ) was purified from the cotyledonsof 7-d-old soybean seedlings. Three molecular forms were detectedwith pi values of 6·46, 6·25 and 6·0. Themain form (pl = 6·46) had an approximate Mr of 130000,a pH optimum of 8·0, a K_m (isocitrate) close to 2·0mol m^–3 and a molecular activity of 615 min ^–1 at25 °C. The purified enzyme is not a glycoprotein and isheat labile. Key words: Isocitrate lyase, soybean     

Organisation spatiale des fibres de collagène de la plaque basale des écailles des Téléostéens

Spatial organization of collagenous fibrils in the basal plate of elasmoid scales has been studied in 36 species among 24 teleost families which include the whole order. Angle measurements of the various fibrillary directions were performed on fracture surfaces in frozen scales observed with the scanning electron microscope. The organization of the basal plate is arrayed in three basic patterns. The most remarkable one, found in the more "primitive" families, is a double twisted plywood with a left-handed rotation of the fibrillary directions. The remaining two are an orthogonal plywood, more or less regular, and an "intermediate" plywood, both found among the more "advanced" families. However, an orthogonal plywood is also observed in some "primitive" families, for example in Clupeidae and Salmonidae. We tentatively interpret the left-handed double twisted plywood of the lower teleosteans and of Amiidae as a synapomorphy in relation to the primitive condition of an actinopterygian lineage. On the other hand, within the teleosts, we would consider that the double twisted plywood is a plesiomorphic condition and that the orthogonal plywood is an apomorphy among the "advanced" teleosts families.     

Evidence for Hybridization by Multilocus Enzyme Electrophoresis and Random Amplified Polymorphic DNA Between Leishmania braziliensis and Leishmania panamensis/guyanensis in Ecuador

ABSTRACT. The taxonomic attribution of four Leishmania stocks isolated from humans in Ecuador has been explored by both multilocus enzyme electrophoresis and random amplified polymorphic DNA. For three loci, MLEE results showed patterns suggesting a heterozygous state for a diploid organism, while the corresponding homozygous states are characteristic of the Leishmania panamensis/guyanensis complex and Leishmania braziliensis . RAPD profiles exhibited for several primers a combination of the Leishmania panmensis/guyanensis complex and L. braziliensis characters. These data hence suggest that the four stocks are the results of hybridization between L. panamensis/guyanensis and L. braziliensis . MLEE data show that the results cannot be attributed to either mixture of stocks, or an F1 in the framework of a simple Mendelian inheritance.     

Grass Leaf Elongation Rate as a Function of Developmental Stage and Temperature: Morphological Analysis and Modelling

Elongation of successive leaves was measured following defoliationof tall fescue plants in controlled environments. Measurementswere made under constant temperatures of 24 °C and 14 °C,and after temperature changes from 24 to 14 °C andvice versa.A morphological analysis of the growing leaf was made from thetime it was 1 mm long until it was fully elongated. The timeelapsed from initiation until the leaf was 1 mm long was estimated.Young leaves less than 1.5 mm long elongated slowly at a constantleaf elongation rate (LER). By extrapolating this LER back toleaf initiation from the apex it was calculated that elongationlasted 42.5 d at 24 °C and 51 d at 14 °C. Lengths ofthe division zone (DZ) and the extension-only zone (E-OZ) increasedto a maximum and then decreased during leaf development. Temperaturechange had an immediate effect on LER but the response varieddepending on the direction of the temperature change. To describethese different features, an empirical model of DZ and E-OZwas designed. Its five parameters were optimized at constanttemperature. The model was then used to simulate the LER ofplants subjected to temperature changes. Instant and lastingeffects of the initial temperature on mean LER in plants transferredfrom 14 to 24 °C andvice versawere well simulated. It wasconcluded that the major reason for differences was due to thegrowth stage (DZ and E-OZ lengths) at which the changes occurredat both temperatures.Copyright 1999 Annals of Botany Company Festuca arundinaceaSchreb., tall fescue, growth zone, division zone.