Likelihood analysis of ongoing gene flow and historical association

Abstract.— We develop a Monte Carlo-based likelihood method for estimating migration rates and population divergence times from data at unlinked loci at which mutation rates are sufficiently low that, in the recent past, the effects of mutation can be ignored. The method is applicable to restriction fragment length polymorphisms (RFLPs) and single nucleotide polymorphisms (SNPs) sampled from a subdivided population. The method produces joint maximum-likelihood estimates of the migration rate and the time of population divergence, both scaled by population size, and provides a framework in which to test either for no ongoing gene flow or for population divergence in the distant past. We show the method performs well and provides reasonably accurate estimates of parameters even when the assumptions under which those estimates are obtained are not completely satisfied. Furthermore, we show that, provided that the number of polymorphic loci is sufficiently large, there is some power to distinguish between ongoing gene flow and historical association as causes of genetic similarity between pairs of populations.     

GRAZING OPTIMIZATION,NUTRIENT CYCLING,AND SPATIAL HETEROGENEITY OF PLANT‐HERBIVORE INTERACTIONS: SHOULD A PALATABLE PLANT EVOLVE?

Abstract.— Can the evolution of plant defense lead to an optimal primary production? In a general theoretical model, Loreau (1995) and de Mazancourt et al. (1998, 1999) have shown that herbivory could increase primary production up to a moderate rate of grazing intensity through recycling of a limiting nutrient, provided several conditions are fulfilled. In the present paper, we assume: (1) grazing intensity is controlled by plants through their level of palatability; and (2) plant fitness is determined by its productivity. We explore the conditions under which such an optimal production may be reached through natural selection. We model two competing plant types that differ only in palatability and are distributed in a patchy landscape determined by the plant‐herbivore interaction. Patch size is determined by herbivore behavior: herbivores recycle nutrient homogeneously within patches, but recycle nutrient proportionally to consumption between patches. The model shows that a strategy of intermediate palatability can be adaptive in response to a small herbivore that lives on and recycles nutrient around one or a few individual plants. For moderately small herbivores, plant palatability may evolve towards one of two local convergent strategies, depending on the initial conditions. For medium‐ to large‐sized herbivores, the nonpalatable strategy is always selected. We discuss the functional and evolutionary implications of these results, and suggest that the traditional dichotomy describing antagonistic and mutualistic interactions may be misleading.     

The temperature-dependent duration of development and parasitism of three cereal aphid parasitoids, Aphidius ervi, A. rhopalosiphi, and Praon volucre

Temperature dependencies were established for the egg-to-mummy and mummy-to-adult phases, for mummy mortality, and for parasitism of Aphidius ervi Haliday, Aphidius rhopalosiphi De Stefani-Perez, and Praon volucre (Haliday) (Hymenoptera, Aphidiidae), three parasitoids of Sitobion avenae (Fabricius) (Homoptera, Aphididae), at 8°C, 12°C, 16°C, 20°C, and 25°C on winter wheat (cv. Haven). A physiological model described temperature-dependent development over the full temperature range, whereas a linear model was fitted for data above 8°C and used to estimate the lower temperature thresholds and day-degrees (° D) required for development. The thresholds for A. ervi were 2.2°C for egg-mummy development and 6.6°C for mummy-adult development, those for A. rhopalosiphi were 4.5°C and 7.2°C, and those for P. volucre were 3.8°C and 5.5°C. The time to develop into mummies and adults differed significantly between the three species: A. ervi development into mummies required an average of 159 ° D, while development into adults took an average of 73 ° D. The corresponding average times required for A. rhopalosiphi and P. volucre to develop mummies were 124° D and 126° D, while their development into adults required an average of 70° D and 150° D, respectively. Mummy mortality was 25–35% at 8°C and less at the higher temperatures tested, but began to increase again at 25°C, showing a quadratic relationship between mortality and temperature. Parasitization was very low or, in the case of P. volucre, absent up to 12°C and thereafter increased with increasing temperature. The relationship between parasitization, recorded as percent aphids mummified, and temperature was linear at the temperatures tested and depended on species. A. ervisuperparasitized 11.1% aphids at 20°C and 16.6% aphids at 25°C, whereas superparasitism was low in A. rhopalosiphi and absent in P. volucre. From 16°C to 25°C the P. volucre sex ratio increased. For A. ervi and A. rhopalosiphi there was no trend with temperature, but at 20°C and 25°C it was close to even. Field data for 1996 and 1997 allowed for a comparison of actual and expected emergence of overwintering mummies. In both years, parasitoids were predicted to have emerged from overwintering mummies well in advance of the onset of aphid infestation, and more than a month earlier than the first parasitized aphids were found in winter wheat. Observations from trap plants in other crops supported the predictions of the models. Other factors that can affect biological control by cereal aphid parasitoids are discussed.     

A linear mixed-effects model for multivariate censored data

We apply a linear mixed-effects model to multivariate failure time data. Computation of the regression parameters involves the Buckley-James method in an iterated Monte Carlo expectation-maximization algorithm, wherein the Monte Carlo E-step is implemented using the Metropolis-Hastings algorithm. From simulation studies, this approach compares favorably with the marginal independence approach, especially when there is a strong within-cluster correlation.     

Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta): a critique of the subspecies concept

Subspecies have been considered artificial subdivisions of species, pattern classes, or incipient species. However, with more data and modern phylogenetic techniques, some subspecies may be found to represent true species. Mitochondrial DNA analysis of the polytypic snake, Elaphe obsoleta, yields well-supported clades that do not conform to any of the currently accepted subspecies. Complete nucleotide sequences of the cytochrome b gene and the mitochondrial control region produced robust maximum-parsimony and maximum-likelihood trees that do not differ statistically. Both trees were significantly shorter than a most parsimonious tree in which each subspecies was constrained to be monophyletic. Thus, the subspecies of E. obsoleta do not represent distinct genetic lineages. Instead, the evidence points to three well-supported mitochondrial DNA clades confined to particular geographic areas in the eastern United States. This research underscores the potential problems of recognizing subspecies based on one or a few characters.     

Limits to adaptive plasticity: temperature and photoperiod influence shade-avoidance responses

In plants, the ratio of red to far-red wavelengths (R:FR) reliably indicates neighbor proximity and influences stem elongation. Enhanced elongation increases light interception and fitness under crowded conditions. However, many environmental factors vary simultaneously such that responses to R:FR may be affected by abiotic conditions or maternal environmental conditions. This study examines the effects of temperature, photoperiod, and maternal environment on stem-elongation responses to R:FR. Four populations of Abutilon theophrasti (two from disturbed, weedy areas and two from cornfields) were used in factorial common-garden experiments of temperature × R:FR × population and photoperiod × R:FR × population. Seedling growth of greenhouse- and field-derived seed was compared to evaluate maternal effects. Maternal environment did not alter seedling elongation. Higher temperatures resulted in both a twofold increase in average elongation and increased responsiveness to R:FR. Significant three-way interactions in both experiments demonstrate that population responses to R:FR differ depending on temperature and photoperiod conditions. These results indicate that elongation responses to R:FR are more variable than previously realized. The observed variability in elongation also suggests that the outcome of competitive interactions in the natural environment will depend on ambient temperature, photoperiod length, and population origin.     

Exserohilum israeli, a new species isolated from soil from Timna Park (Israel), and its physiological properties

Fungi isolated from soil in Timna Park (Israel) were found to belong to a new species of Exserohilum for which the name Exserohilum israeli sp. nov. is proposed. The main physiological properties of members of this species are discussed and the influence of temperature and copper concentrations on the growth and morphology of the fungus were investigated.     

Cyclomorphosis in Daphnia lumholtzi induced by temperature

• 1 Cyclomorphosis is a well known phenomenon in Daphnia that involves a regular, seasonal, or induced change in body allometry. Long helmets and tail spines were induced in laboratory cultures of Daphnia lumholtzi with temperature of 31 °C as the proximal cue (temperature of locally occurring peak abundance in Kentucky Lake). The effect was greater in embryos than juveniles or adults exposed to the temperature cue.
• 2 The temperature cue appears to have a threshold value (animals cultured at 25 or 28 °C did not develop elongated helmets or spines). The helmet and spine length receded both with D. lumholtzi kept at a constant 31 °C temperature and when water temperature was decreased.
• 3 The induced helmet in this experiment (0.66 mm, 1.0 mm animal) was significantly longer than values reported in the literature for induction by planktivorous fish kairomones (0.25 mm, 1.2 mm animal). The strong response to a proximal cue of temperature may require the second weaker chemical cue for maintenance. It is suggested that a synergistic explanation with two cues may be more appropriate for cyclomorphosis induction and maintenance in Daphnia lumholtzi that could be tested with further studies.

     

Bacterial diversity and community composition in the chemocline of the meromictic alpine Lake Cadagno as revealed by 16S rDNA analysis

Using different techniques of molecular biology we investigated the bacterial diversity of the chemocline of the meromictic Lake Cadagno. Cloning of a total community 16S rDNA PCR product and subsequent screening with a combination of amplified ribosomal DNA restriction analysis and temporal temperature gradient gel electrophoresis (TTGE) analysis revealed that 30 of 47 randomly selected clones were unique. Partial sequencing and comparative analysis indicated a high bacterial diversity dominated by the gamma-Proteobacteria (33.3%). Most of these rDNA clone sequences were not closely related to any 16S rDNA sequence in the database. In a second approach, the TTGE pattern from an environmental sample was compared with the migration of the cloned 16S rDNA fragments. Four clone types were identified on the environmental pattern by excising and sequencing comigrating bands, three of which were well represented in the library: two Chromatiaceae species and one sequence affiliated with the Desulfobulbus assemblage. Using the fluorescent in situ hybridization technique we essentially confirmed the results of the cloning experiments and the TTGE analysis.     

CO2 efflux from a Mediterranean semi-arid forest soil. I. Seasonality and effects of stoniness

We studied the seasonality of total soil CO₂efflux and labeled C-CO₂ released from ¹⁴Clabeled straw incubated in the H horizon of asemi-arid Mediterranean forest soil. Fieldmeasurements were carried out over 520 days in aseries of reconstructed soil profiles with and withouta gravel layer below the H horizon. We monitored soilclimate and related this to soil CO₂ efflux.Seasonal variations in soil CO₂ efflux in asemiarid Mediterranean forest were mainly related tochanges in soil temperature. In spite of drought, highrespiration rates were observed in mid summer. Highsoil CO₂ efflux in hot and dry episodes wasattributed to increases in soil biological activity.The minimum soil CO₂ efflux occurred in latesummer also under dry conditions, probably related toa decrease in soil biological activity in deephorizons. Biological activity in organic layers waslimited by water potential () in summer and bytemperature in winter. Rewetting a dry soil resultedin large increases in soil CO₂ efflux only at hightemperatures. These large increases represented asignificant contribution to the decomposition oforganic matter in the uppermost horizons. Soilbiological activity in the uppermost horizons was moresensitive to changes in soil and hence tosummer rainstorms than the bulk soil microbialactivity. The presence of a layer of gravel improvedboth moisture and temperature conditions for thedecomposition of organic matter. As a result, soilCO₂ efflux increased in soils containing rockfragments. These effects were especially large for theorganic layers.