Estimating pollen flow using SSR markers and paternity exclusion: accounting for mistyping

Highly informative genetic markers, such as simple sequence repeats (SSRs), can be used to directly measure pollen flow by parentage analysis. However, mistyping (i.e. false inference of genotypes caused by the occurrence of null alleles, mutations, and detection errors) can lead to substantial biases in the estimates obtained. Using computer simulations, we evaluated a direct method for estimating pollen immigration using SSR markers and a paternity exclusion approach. This method accounts for mistyping and does not rely on assumptions about the distribution of male reproductive success. If ignored, even minor rates of mistyping (1.5%) resulted in overestimating pollen immigration by up to 150%. When we required at least two mismatching loci before excluding candidate fathers from paternity, the resulting pollen immigration estimates had small biases for rates of mistyping up to 4.5%. Requiring at least three mismatches for exclusion was needed to minimize the upward biases of pollen immigration caused by rates of mistyping up to 10.5%. The minimum number of highly variable SSR loci needed to minimize cryptic gene flow and obtain reliable estimates of pollen immigration varied from five to seven for a sampling scheme applicable to most conifers (i.e. when paternal haplotypes can be unambiguously determined). Between five and nine highly variable SSR loci were needed for a more general sampling scheme that is applicable to all diploid seed plants. With moderately variable SSR markers, consistently accurate estimates of pollen immigration could be obtained only for rates of mistyping up to 4.5%. We developed the POLLEN FLOW (PFL) computer program which can be used to obtain unbiased and precise estimates of pollen immigration under a wide range of conditions, including population sizes as large as 600 parents and mistyping rates as high as 10.5%.     

Regionally isolated populations of an imperiled Caribbean coral, Acropora palmata

The movements of larvae between marine populations are difficult to follow directly and have been the subject of much controversy, especially in the Caribbean. The debate centres on the degree to which populations are demographically open, such that depleted populations can be replenished by recruitment from distant healthy populations, or demographically closed and thus in need of local management. Given the depressed state of many tropical reef populations, the understanding of these movements now bears critically on the number, placement, and size of marine reserves. Most genetic analyses assume that dispersal patterns have been stable for thousands of generations, thus they commonly reflect past colonization histories more than ongoing dispersal. Recently developed multilocus genotyping approaches, however, have the demonstrated ability to detect both migration and population isolation over far shorter timescales. Previously, we developed five microsatellite markers and demonstrated them to be both Mendelian and coral-specific. Using these markers and Bayesian analyses, we show here that populations of the imperiled reef-building coral, Acropora palmata, have experienced little or no recent genetic exchange between the western and the eastern Caribbean. Puerto Rico is identified as an area of mixing between the two subregions. As a consequence of this regional isolation, populations in the western and eastern Caribbean should have the potential to adapt to local conditions and will require population-specific management strategies.     

Landscape genetics of the blotched tiger salamander (Ambystoma tigrinum melanostictum)

The field of landscape genetics has great potential to identify habitat features that influence population genetic structure. To identify landscape correlates of genetic differentiation in a quantitative fashion, we developed a novel approach using geographical information systems analysis. We present data on blotched tiger salamanders (Ambystoma tigrinum melanostictum) from 10 sites across the northern range of Yellowstone National Park in Montana and Wyoming, USA. We used eight microsatellite loci to analyse population genetic structure. We tested whether landscape variables, including topographical distance, elevation, wetland likelihood, cover type and number of river and stream crossings, were correlated with genetic subdivision (F(ST)). We then compared five hypothetical dispersal routes with a straight-line distance model using two approaches: (i) partial Mantel tests using Akaike's information criterion scores to evaluate model robustness and (ii) the BIOENV procedure, which uses a Spearman rank correlation to determine the combination of environmental variables that best fits the genetic data. Overall, gene flow appears highly restricted among sites, with a global F(ST) of 0.24. While there is a significant isolation-by-distance pattern, incorporating landscape variables substantially improved the fit of the model (from an r2 of 0.3 to 0.8) explaining genetic differentiation. It appears that gene flow follows a straight-line topographic route, with river crossings and open shrub habitat correlated with lower F(ST) and thus, decreased differentiation, while distance and elevation difference appear to increase differentiation. This study demonstrates a general approach that can be used to determine the influence of landscape variables on population genetic structure.     

Tidal-Scale Hydrodynamics within Mangrove Swamps

Both the drag force and the horizontal eddy viscosity play a dominant role in the tidal-scale hydrodynamics in mangrove wetlands. Using field observations and basic fluid mechanics laws, the drag coefficient and the coefficient of dynamic eddy viscosity are found to be predictable as a function of the Reynolds Number based on the characteristic length scale of the vegetation. The characteristic length scale of the vegetation varies greatly with vegetation species, vegetation density and tidal elevation. Both these coefficients decrease with increasing values of the Reynolds Number. At the low range of the Reynolds Number both these coefficients reach much higher values than those typical of vegetation-poor estuaries and rivers. Consequently, the tidal flow within mangrove areas depends to a large degree upon the submerged vegetation density that varies with the tidal stage. These findings may be applied also in other vegetated tidal wetlands, including salt marshes.     

Comparison Between Tidally Driven Groundwater Flow and Flushing of Animal Burrows in Tropical Mangrove Swamps

Tidal groundwater in a mangrove swamp can return to the mangrove creek by one of two mechanisms: (a) it can either flow through the swamp soil due to the water table difference between the creek and the groundwater in the swamp; or (b) it can flow via tidal flushing of animal burrows. This paper compares the magnitude of these two mechanisms for different regions of a mangrove swamp. Direct groundwater flow rates resulting from water stored in the sediment as a consequence of infiltration, especially during and after tidal inundation, were calculated for every square meter in the surface of a mangrove forest from piezometer data. Flow rates of water due to burrow flushing were determined based on published surveys, by estimating the burrow volume and the percentage of the burrow water that is flushed at each tidal inundation. Although direct groundwater flux was found to decrease further away from the creek compared to close to the creek, it was also found to have a similar range as burrow flushing flow. Specifically, direct groundwater flow ranged from 0.004 to 0.04 m³/m²/day, whilst burrow flushing flux ranged from 0.01 to 0.04 m³/m²/day.Considering the errors involved in the experiments and calculations, these ranges can be considered as being the same and neither of the two processes can be considered as negligible compared to the other. As a consequence, surveys of groundwater processes in mangrove areas, and more generally in swamp and tidal areas where animal burrows are present, will need to consider both mechanisms. Investigations of the influence over flushing mechanisms of different residence times of the water in burrows and in the sediment body would also be recommended in order to establish salt and nutrient budget in mangrove swamps.     

Water uptake and transport in lianas and co-occurring trees of a seasonally dry tropical forest

Water uptake and transport were studied in eight liana species in a seasonally dry tropical forest on Barro Colorado Island, Panama. Stable hydrogen isotope composition (D) of xylem and soil water, soil volumetric water content (_v), and basal sap flow were measured during the 1997 and 1998 dry seasons. Sap flow of several neighboring trees was measured to assess differences between lianas and trees in magnitudes and patterns of daily sap flow. Little seasonal change in _v was observed at 90–120 cm depth in both years. Mean soil water D during the dry season was –19 at 0–30 cm, –34 at 30–60 cm, and –50 at 90–120 cm. Average values of xylem D among the liana species ranged from –28 to –44 during the middle of the dry season, suggesting that water uptake was restricted to intermediate soil layers (30–60 cm). By the end of the dry season, all species exhibited more negative xylem D values (–41 to –62), suggesting that they shifted to deeper water sources. Maximum sap flux density in co-occurring lianas and trees were comparable at similar stem diameter (DBH). Furthermore, lianas and trees conformed to the same linear relationship between daily sap flow and DBH. Our observations that lianas tap shallow sources of soil water at the beginning of the dry season and that sap flow is similar in lianas and trees of equivalent stem diameter do not support the common assumptions that lianas rely primarily on deep soil water and that they have higher rates of sap flow than co-occurring trees of similar stem size.     

Contrasting patterns of floral and molecular variation across a cline in Mimulus aurantiacus

Abstract Steep clines in ecologically important traits may be caused by divergent natural selection. However, processes that do not necessarily invoke ongoing selection, such as secondary contact or restricted gene flow, can also cause patterns of phenotypic differentiation over short spatial scales. Distinguishing among all possible scenarios is difficult, but an attainable goal is to establish whether scenarios that imply selection need to be invoked. We compared the extent of morphological and genetic differentiation between geographically structured red and yellow floral races of Mimulus aurantiacus (bush monkeyflower; Phrymacea). Flower color was assessed in a common garden as well as in the field to determine whether variation was genetic and to quantify the extent of geographical differentiation. Population genetic differentiation at marker loci was measured for both chloroplast and nuclear genomes, and the degree of population structure within and among the floral races was evaluated. Flower color shows both a strong genetic basis and a sharp geographic transition, with pure red-flowered populations in western San Diego County and pure yellow-flowered populations to the east. In the zone of contact, both pure and intermediate phenotypes occur. Patterns of genetic differentiation at marker loci are far less pronounced, as little of the variation is partitioned according to the differences in flower color. Phenotypic differentiation (Q_ST) between populations with different flower colors is much greater than neutral genetic differentiation (F_ST). When comparisons are made between populations of the same flower color, the opposite trend is evident. Limited neutral genetic structure between the floral races, combined with sharp differentiation in flower color, is consistent with the hypothesis that current or recent natural selection maintains the cline in flower color.     

Hydrodynamics and mass transfer coefficient in activated sludge aerated stirred column reactor: experimental analysis and modeling

The aerated stirred reactor (ASR) has been widely used in biochemical and wastewater treatment processes. The information describing how the activated sludge properties and operation conditions affect the hydrodynamics and mass transfer coefficient is missing in the literature. The aim of this study was to investigate the influence of flow regime, superficial gas velocity (U(G)), power consumption unit (P/V(L)), sludge loading, and apparent viscosity (mu(ap)) of activated sludge fluid on the mixing time (t(m)), gas hold-up (epsilon), and volumetric mass transfer coefficient (k(L)a) in an activated sludge aerated stirred column reactor (ASCR). The activated sludge fluid performed a non-Newtonian rheological behavior. The sludge loading significantly affected the fluid hydrodynamics and mass transfer. With an increase in the U(G) and P/V(L), the epsilon and k(L)a increased, and the t(m), decreased. The epsilon, k(L)a, and t(m), were influenced dramatically as the flow regime changed from homogeneous to heterogeneous patterns. The proposed mathematical models predicted the experimental results well under experimental conditions, indicating that the U(G), P/V(L), and mu(ap) had significant impact on the t(m), epsilon, and k(L)a. These models were able to give the t(m), epsilon, and k(L)a values with an error around +/-8%, and always less than +/-10%.     

Enhancing the electron transfer capacity and subsequent color removal in bioreactors by applying thermophilic anaerobic treatment and redox mediators

The effect of temperature, hydraulic retention time (HRT) and the redox mediator anthraquinone-2,6-disulfonate (AQDS), on electron transfer and subsequent color removal from textile wastewater was assessed in mesophilic and thermophilic anaerobic bioreactors. The results clearly show that compared with mesophilic anaerobic treatment, thermophilic treatment at 55 degrees C is an effective approach for increasing the electron transfer capacity in bioreactors, and thus improving the decolorization rates. Furthermore, similar color removals were found at 55 degrees C between the AQDS-free and AQDS-supplemented reactors, whereas a significant difference (up to 3.6-fold) on decolorization rates occurred at 30 degrees C. For instance, at an HRT of 2.5 h and in the absence of AQDS, the color removal was 5.3-fold higher at 55 degrees C compared with 30 degrees C. The impact of a mix of mediators with different redox potentials on the decolorization rate was investigated with both industrial textile wastewater and the azo dye Reactive Red 2 (RR2). Color removal of RR2 in the presence of anthraquinone-2-sulfonate (AQS) (standard redox potential E(0)' of -225 mV) was 3.8-fold and 2.3-fold higher at 30 degrees C and 55 degrees C, respectively, than the values found in the absence of AQS. Furthermore, when the mediators 1,4-benzoquinone (BQ) (E(0)' of +280 mV), and AQS were incubated together, there was no improvement on the decolorization rates compared with the bottles solely supplemented with AQS. Results imply that the use of mixed redox mediators with positive and negative E(0)' under anaerobic conditions is not an efficient approach to improve color removal in textile wastewaters.     

The use of multi-parameter flow cytometry to study the impact of limiting substrate, agitation intensity, and dilution rate on cell aggregation during Bacillus licheniformis CCMI 1034 aerobic continuous culture fermentations

The main objective of this work was to establish those factors either physical (power input) or chemical (limiting substrate or dilution rate) that enhance cell aggregation (biofilm or floc formation) and cell physiological state during aerobic continuous cultures of Bacillus licheniformis. Glucose-limited steady-state continuous cultures growing at a dilution rate between 0.64 and 0.87/h and 1,000 rpm (mean specific energy dissipation rate (epsilonT) = 6.5 W/kg), led to the formation of a thin biofilm on the vessel wall characterized by the presence of a high proportion of healthy cells in the broth (after aggregate disruption by sonication) defined as having intact polarized cytoplasmic membranes. An increased epsilonT (from 6.5 W/kg to 38 W/kg) was found to hinder cell aggregation under carbon limitation. The carbon recovery calculated from glucose indicated that additional extracellular polymer was being produced at dilution rates >0.87/h. B. licheniformis growth under nitrogen limitation led to floc formation which increased in size with dilution rate. Counter-intuitively the flocs became more substantial with an increase in epsilonT from 6.5 W/kg to 38 W/kg under nitrogen limitation. Indeed the best culture conditions for enhanced metabolically active cell aggregate formation was under nitrogen limitation at epsilonT = 6.5 W/kg (leading to floc formation), and under carbon limitation at a dilution rate of between 0.64 and 0.87/h, at epsilonT = 6.5 W/kg (leading to vessel wall biofilm formation). This information could be used to optimize culture conditions for improved cell aggregation and hence biomass separation, during thermophilic aerobic bioremediation processes.