Comparing three different methods to detect selective loci using dominant markers

We carried out a simulation study to compare the efficiency of three alternative programs (dfdist , detseld and bayescan ) to detect loci under directional selection from genome‐wide scans using dominant markers. We also evaluated the efficiency of correcting for multiple testing those methods that use a classical probability approach. Under a wide range of scenarios, we conclude that bayescan appears to be more efficient than the other methods, detecting a usually high percentage of true selective loci as well as less than 1% of outliers (false positives) under a fully neutral model. In addition, the percentage of outliers detected by this software is always correlated with the true percentage of selective loci in the genome. Our results show, nevertheless, that false positives are common even with a combination of methods and multitest correction, suggesting that conclusions obtained from this approach should be taken with extreme caution.     

Pollinator shifts and the loss of style polymorphism in Narcissus papyraceus (Amaryllidaceae)

Darwin proposed that the driving force for the evolution of style polymorphisms is the promotion of cross‐pollination between style morphs, through accurate placement of pollen on the pollinator’s body. This hypothesis has received much attention, but the effect of different pollinators in the fitness of morphs remains poorly understood. Narcissus papyraceus is a style dimorphic species (long ‐L‐ and short ‐S‐ styled) with isoplethic (1 : 1) and L‐monomorphic populations, mainly visited by long‐tongued (LT) nocturnal and short‐tongued (ST) diurnal pollinators, respectively. We studied natural female fertility of morphs, and assessed the role of diurnal and nocturnal pollinators. We also quantified female fertility of the morphs in experimental populations with different morph ratio, exposed to predominately long‐ or short‐tongued pollinators. We found that with LT pollinators, both morphs were successfully pollinated in all morph ratio conditions, suggesting that these insects could be involved in maintenance of the polymorphism, although other factors may also play a role. However, with ST pollinators, S‐plants displayed less fertility than L‐plants, and mating among L‐plants was favoured, implying that the polymorphism is lost. These results underscore the role of pollinators on variations in style polymorphism.     

Hydrological and biogeochemical controls on the timing and magnitude of nitrous oxide flux across an agricultural landscape

Anticipated increases in precipitation intensity due to climate change may affect hydrological controls on soil N₂O fluxes, resulting in a feedback between climate change and soil greenhouse gas emissions. We evaluated soil hydrologic controls on N₂O emissions during experimental water table fluctuations in large, intact soil columns amended with 100 kg ha^?1 KNO₃‐N. Soil columns were collected from three landscape positions that vary in hydrological and biogeochemical properties (N= 12 columns). We flooded columns from bottom to surface to simulate water table fluctuations that are typical for this site, and expected to increase given future climate change scenarios. After the soil was saturated to the surface, we allowed the columns to drain freely while monitoring volumetric soil water content, matric potential and N₂O emissions over 96 h. Across all landscape positions and replicate soil columns, there was a positive linear relationship between total soil N and the log of cumulative N₂O emissions (r²= 0.47; P= 0.013). Within individual soil columns, N₂O flux was a Gaussian function of water‐filled pore space (WFPS) during drainage (mean r²= 0.90). However, instantaneous maximum N₂O flux rates did not occur at a consistent WFPS, ranging from 63% to 98% WFPS across landscape positions and replicate soil columns. In contrast, instantaneous maximum N₂O flux rates occurred within a narrow range (?1.88 to ?4.48 kPa) of soil matric potential that approximated field capacity. The relatively consistent relationship between maximum N₂O flux rates and matric potential indicates that water filled pore size is an important factor affecting soil N₂O fluxes. These data demonstrate that matric potential is the strongest predictor of the timing of N₂O fluxes across soils that differ in texture, structure and bulk density.     

Responses of macroinvertebrate communities to long‐term flow variability in a Sonoran Desert stream

Current global models predict a hotter and drier climate in the southwestern United States with anticipated increases in drought frequency and severity coupled with changes in flash flood regimes. Such changes would likely have important ecological consequences, particularly for stream and riparian ecosystems already subject to frequent hydrologic disturbance. This study assessed the potential response of aquatic macroinvertebrates to interannual variation in hydrology in a spatially intermittent desert stream (Sycamore Creek, AZ). We compiled data on the recovery of macroinvertebrate communities following spring floods, with successional sequences captured 11 times over a 16‐year period (1983–1999). This period encompassed a transition from perennial to intermittent flow in this system, and included a record drought in 1989–1990. Results show that while the size of floods initiating sequences had little explanatory power, changes in macroinvertebrate community structure during postflood succession were closely associated with antecedent flooding and drought. Year‐to‐year differences in benthic communities integrated taxon‐specific responses to antecedent disturbance, including differential resistance to channel drying, use of hyporheic refugia, and variable rates of recovery once stream flow resumed. The long‐term consequences of drying on community structure were only evident during later stages of postflood succession, illustrating an interaction between flood and drought recovery processes in this system. Our observations highlight the potential for predicted climate changes in this region to have marked and long‐lasting consequences for benthic communities in desert streams.     

Eutrophication and macroalgal blooms in temperate and tropical coastal waters: nutrient enrichment experiments with Ulva spp.

Receiving coastal waters and estuaries are among the most nutrient‐enriched environments on earth, and one of the symptoms of the resulting eutrophication is the proliferation of opportunistic, fast‐growing marine seaweeds. Here, we used a widespread macroalga often involved in blooms, Ulva spp., to investigate how supply of nitrogen (N) and phosphorus (P), the two main potential growth‐limiting nutrients, influence macroalgal growth in temperate and tropical coastal waters ranging from low‐ to high‐nutrient supplies. We carried out N and P enrichment field experiments on Ulva spp. in seven coastal systems, with one of these systems represented by three different subestuaries, for a total of nine sites. We showed that rate of growth of Ulva spp. was directly correlated to annual dissolved inorganic nitrogen (DIN) concentrations, where growth increased with increasing DIN concentration. Internal N pools of macroalgal fronds were also linked to increased DIN supply, and algal growth rates were tightly coupled to these internal N pools. The increases in DIN appeared to be related to greater inputs of wastewater to these coastal waters as indicated by high δ¹⁵N signatures of the algae as DIN increased. N and P enrichment experiments showed that rate of macroalgal growth was controlled by supply of DIN where ambient DIN concentrations were low, and by P where DIN concentrations were higher, regardless of latitude or geographic setting. These results suggest that understanding the basis for macroalgal blooms, and management of these harmful phenomena, will require information as to nutrient sources, and actions to reduce supply of N and P in coastal waters concerned.     

Grass invasion of a hardwood forest is associated with declines in belowground carbon pools

Invasive plant species affect a range of ecosystem processes but their impact on belowground carbon (C) pools is relatively unexplored. This is particularly true for grass invasions of forested ecosystems. Such invasions may alter both the quantity and quality of forest floor inputs. Dependent on both, two theories, ‘priming’ and ‘preferential substrate utilization’, suggest these changes may decrease, increase, or leave unchanged native plant‐derived soil C. Decreases are expected under ‘priming’ theory due to increased soil microbial activity. Under ‘preferential substrate utilization’, either an increase or no change is expected because the invasive plant's inputs are used by the microbial community instead of soil C. Here, we examine how Microstegium vimineum affects belowground C‐cycling in a southeastern US forest. Following predictions of priming theory, M. vimineum's presence is associated with decreases in native‐derived, C pools. For example, in September 2006 M. vimineum is associated with 24%, 34%, 36%, and 72% declines in total organic, particulate organic matter, mineralizable (a measure of microbially‐available C), and microbial biomass C, respectively. Soil C derived from M. vimineum does not compensate for these decreases, meaning that the sum of native‐ plus invasive‐derived C pools is smaller than native‐derived pools in uninvaded plots. Supporting our inferences that C‐cycling accelerates under invasion, the microbial community is more active per unit biomass: added ¹³C‐glucose is respired more rapidly in invaded plots. Our work suggests that this invader may accelerate C‐cycling in forest soils and deplete C stocks. The paucity of studies investigating impacts of grass invasion on C‐cycling in forests highlights the need to study further M. vimineum and other invasive grasses to assess their impacts on C sink strength and forest fertility.     

Turnover of labile and recalcitrant soil carbon differ in response to nitrate and ammonium deposition in an ombrotrophic peatland

The effects of 4 years of simulated nitrogen deposition, as nitrate (NO₃^?) and ammonium (NH₄⁺), on microbial carbon turnover were studied in an ombrotrophic peatland. We investigated the mineralization of simple forms of carbon using MicroResp^? measurements (a multiple substrate induced respiration technique) and the activities of four soil enzymes involved in the decomposition of more complex forms of carbon or in nutrient acquisition: N‐acetyl‐glucosaminidase (NAG), cellobiohydrolase (CBH), acid phosphatase (AP), and phenol oxidase (PO). The potential mineralization of labile forms of carbon was significantly enhanced at the higher N additions, especially with NH₄⁺ amendments, while potential enzyme activities involved in breakdown of more complex forms of carbon or nutrient acquisition decreased slightly (NAG and CBH) or remained unchanged (AP and PO) with N amendments. This study also showed the importance of distinguishing between NO₃^? and NH₄⁺ amendments, as their impact often differed. It is possible that the limited response on potential extracellular enzyme activity is due to other factors, such as limited exposure to the added N in the deeper soil or continued suboptimal functioning of the enzymes due to the low pH, possibly via the inhibitory effect of low phenol oxidase activity.     

Classifying the fire‐response traits of plants: How reliable are species‐level classifications?

Plant species in fire‐prone environments possess specific traits which allow them to survive fire. Species are commonly classified according to whether they survive fire and resprout or whether they are killed by fire and regenerate from seed. However, different populations of the same species have been shown to vary in their responses. Therefore, the classification of a species into a single category based on fire‐response traits may not necessarily be representative of every population under every circumstance. This study examined the extent of within‐species variation in fire‐response traits of woody plants in south‐eastern Australia after the 2003 fires. Species were then classified using two approaches: (i) using data from a field survey of fire‐response traits, taking into account within‐species variation; and (ii) using species' fire responses listed in a pre‐existing fire‐response database compiled from a variety of primary sources. Field data showed that the majority of species in the study area resprouted after fire with around one in 10 species variable in their resprouting response. Almost half of all species varied from site to site according to whether they regenerated from seed, either solely or in addition to resprouting. The numbers of species classified as resprouters and seed regenerators varied according to the classification method used. Differences were also found between the classification method when calculating the mean proportion of resprouters and seed regenerators across sites. The fire‐response traits for some species from the database were found to differ from the observed field responses. This study demonstrated that the application of a fire‐response trait, reported in a trait database, to an entire species, may not adequately represent the actual fire responses of the populations of interest. Rather than considering the fire‐response traits of a species, accurate prediction may be better achieved by considering how different populations of plants will respond to fire.     

Resource distribution and soil moisture content can regulate bait control in an ant assemblage in Central Amazonian forest

Resources influence population growth, interspecific interactions, territoriality and, in combination with moisture content, affect terrestrial arthropod distribution and abundance. Ants are usually described as interactive and compete in transitive hierarchies, where the dominants behaviourally exclude subordinate species from food resources. In this study, we evaluated the effects of (i) dominant ants, soil moisture and an artificial resource gradient on the number of ant species attracted to baits; and (ii) how soil moisture and an artificial resource gradient change the number of controlled baits in a Central Amazonian rain forest. We sampled 30 100‐m‐long transects, located at least 200 m apart. The transects were established with six different bait densities varying between six and 41 baits and the soil moisture content was measured at 10 points for each transect. Six ant species were considered dominant, and had negative correlations with the number of species at baits (r² = 0.186; F_1,28 = 6.419; P = 0.017). However, almost half of the transects showed low abundance of dominant species (<30%), and relatively high number of species (mean of 20.1 ± 8.75). Resource availability and soil moisture had negative and positive correlations, with number of controlled baits. These results suggest that, even though the dominance is relatively poorly developed on the floor of this tropical forest, both resource availability and soil moisture affect resource control, and thus, the number of species that use baits.     

Description of Paratetrahymena parawassi n. sp. using Morphological and Molecular Evidence and a Phylogenetic Analysis of Paratetrahymena and Other Taxonomically Ambiguous Genera in the Order Loxocephalida (Ciliophora,Oligohymenophorea)

ABSTRACT. The marine scuticociliate Paratetrahymena parawassi n. sp. is described on the basis of morphology, especially infraciliature, and the sequence of its small subunit (SSU) rRNA gene to become the second known member of its genus. Paratetrahymena and other ciliates in the order Loxocephalida possess a mixture of morphological and morphogenetic features characteristic of the subclasses Hymenostomatia and Scuticociliatia. Accordingly, we used SSU rRNA sequences to analyze the phylogeny of Paratetrahymena and three other loxocephalid genera. Paratetrahymena and Cardiostomatella vermiformis formed a moderately well‐supported clade that diverged at a deep level from all other scuticociliates, supporting separation of loxocephalids from other scuticociliates as a suprafamilial taxon. Sathrophilus holtae was a sister taxon to Paratetrahymena and Cardiostomatella in a poorly supported, unresolved relationship; nevertheless, association of all three genera into a single clade was supported by an approximately unbiased (AU) test. Any association of these genera singly or as a group with the Hymenostomatia was rejected decisively by AU tests and by a complete absence in the loxocephalids of the unique nucleotide identities that distinguish hymenostomes. Therefore, the morphological and morphogenetic similarities of loxocephalids to hymenostomes may be plesiomorphies, and the conflicting mix of scuticociliate and hymenostome characteristics seen in loxocephalids may result from differing rates of character evolution. Dexiotrichides pangi and Urocentrum, which is currently classified as a peniculid, formed a small clade that associated with hymenostomes and peritrichs. Monophyly of the Loxocephalida with Dexiotrichides and/or Urocentrum included was not rejected by AU; however, inclusion of Urocentrum in the Peniculia was rejected by AU tests. A hypothesis is offered to explain the lack of resolution of loxocephalid ciliates and Urocentrum in phylogenetic trees, namely that their phylogenetic positions are influenced by a combination of heterogeneous data and long‐branch attraction caused by poor representation of taxa in analyses. The well‐known genus Cyclidium, a member of the order Pleuronematida, was revealed to be polyphyletic as a byproduct of our analyses of loxocephalids. In particular, Cyclidium porcatum appears to fall outside the clade containing typical members of the subclass Scuticociliatia and thus invites investigation as a possible member of the order Loxocephalida.