Do the effects of piscivorous largemouth bass cascade to the plankton?

Ecologists have hypothesized that an increase in the biomass of piscivorous fish in lakes will cause a decrease in populations of planktivorous fish, an increase in the size of herbivorous zooplankton and a decrease in the biomass of phytoplankton. Here we present an experimental test of whether the effects of largemouth bass (Micropterus salmoides) cascade to the planktivorous fish, zooplankton and phytoplankton of a 15-ha water storage reservoir. A pilot study indicated that the reservoir was eutrophic with dense populations of planktivorous fish dominated by threadfin shad (Dorosoma petenense). No piscovorous fish were present in the reservoir. We conducted a one-month mesocosm experiment using water and plankton from the reservoir showing that the presence of threadfin shad reduced large-sized zooplankton and increased the productivity and biomass of phytoplankton. To test whether the effects of piscivorous fish could cascade to the plankton, we assessed the effects of the addition of piscivorous largemouth bass on the planktivorous fish, zooplankton and biomass of phytoplankton of the reservoir by monitoring the reservoir during the year before and the two years after largemouth bass were stocked. In the second year after the addition of largemouth bass, the number of planktivorous fish decreased and the relative abundance of threadfin shad declined. Although the abundance of cladocerans increased after the addition of largemouth bass, the average size of zooplankton did not change. We did not detect changes in chlorophyll a, Secchi depth, or concentrations of total phosphorus and total nitrogen as a result of the addition of largemouth bass.     

Do lichens show latitudinal patterns of diversity?

No previous study has directly investigated whether lichens show latitudinal patterns of diversity. We used vouchered data and MaxEnt models to compile richness estimates (species, genera, and families) across the western coastal region of the US. Nonparametric multiplicative regression then sought the geographic factors or interactions of factors that explained the most variability in lichen richness. Collection density was the strongest predictor of raw estimates of richness at all taxonomic ranks. Latitude was the overall single-best predictor of MaxEnt modeled species, generic, and familial richness in all models. MaxEnt modeling was necessary to minimize collection bias, which otherwise obscured any other patterns of diversity. While geography explained a sizable portion of variance in lichen richness, it does not trend linearly with latitude. Instead, lichen diversity may be influenced by a compilation of regional and local factors including climate, disturbance, and competition.     

Do cladistic and morphometric data capture common patterns of morphological disparity?

The distinctly non‐random diversity of organismal form manifests itself in discrete clusters of taxa that share a common body plan. As a result, analyses of disparity require a scalable comparative framework. The difficulties of applying geometric morphometrics to disparity analyses of groups with vastly divergent body plans are overcome partly by the use of cladistic characters. Character‐based disparity analyses have become increasingly popular, but it is not clear how they are affected by character coding strategies or revisions of primary homology statements. Indeed, whether cladistic and morphometric data capture similar patterns of morphological variation remains a moot point. To address this issue, we employ both cladistic and geometric morphometric data in an exploratory study of disparity focussing on caecilian amphibians. Our results show no impact on relative intertaxon distances when different coding strategies for cladistic characters were used or when revised concepts of homology were considered. In all instances, we found no statistically significant difference between pairwise Euclidean and Procrustes distances, although the strength of the correlation among distance matrices varied. This suggests that cladistic and geometric morphometric data appear to summarize morphological variation in comparable ways. Our results support the use of cladistic data for characterizing organismal disparity.     

Do evolutionary processes minimize expected losses?

Evolution by variation and natural selection is often viewed as an optimization process that favors those organisms which are best adapted to their environment. This leaves open the issue of how to measure adaptation and what criterion is implied for optimization. This problem has been framed and analysed mathematically under the assumption that individuals compete to minimize expected losses across a series of decisions (e.g. choice of behavior), where each decision offers a stochastic payoff. But the fact that a particular analysis is tractable for a specified criterion does not imply the fidelity of that criterion. Computer simulations involving a version of the k -armed bandit problem can address the veracity of the hypothesis that individuals are selected to minimize expected losses. The results offered here do not support this hypothesis.     

Do modern humans and Neandertals have different patterns of cranial integration?

Studies of cranial differences between modern humans and Neandertals have identified several characteristics for which the two groups differ in their mean values, the proportional relationships with other traits, or both. However, the limited number of fairly complete Neandertals has hindered investigations into patterns of integration – covariance and correlation among traits – in this fossil group. Here, we use multiple approaches specifically designed to deal with fragmentary fossils to test if metric cranial traits in Neandertals fit modern human patterns of integration. Based on 37 traits collected from a sample of 2524 modern humans from Howells’ data set and 20 Neandertals, we show that overall patterns of cranial integration are significantly different between Neandertals and modern humans. However, at the same time, Neandertals are consistent with a modern human pattern of integration for more than three-quarters of the traits. Additionally, the differences between the predicted and actual values for the deviating traits are rather small, indicating that the differences in integration are subtle. Traits for which Neandertals deviate from modern human integration patterns tend to be found in regions where Neandertals and modern humans are known to also differ in their mean values. We conclude that the evolution of patterns of cranial integration is a cause for caution but also presents an opportunity for understanding cranial differences between modern humans and Neandertals.     

Do thyroid and testis modulate the effects of pineal and melatonin on haemopoietic variables inClarias batrachus?

Involvement of pineal and its major hormone, melatonin, in the process of erythropoiesis in a freshwater catfish,Clarias batrachus has been investigated. The study was conducted during four phases, namely preparatory phase, spawning phase, postspawning phase and late postspawning phase of its annual reproductive cycle. During each phase a fish received either melatonin injections or subjected to pinealectomy. In addition, each fish in all the groups, received either iopanoic acid or cyproterone acetate or vehicle in the morning or late afternoon. Results clearly indicate that melatonin stimulates the rate of erythropoiesis inClarias batrachus. It appears that the extent of stimulation depends upon the phase of the annual reproductive cycle. However, in general, the pineal-or melatonin-induced modulation of blood variables is gonad dependent and thyroid seems to play a time of the day dependent subtle role     

Darwin's error? Patrick Matthew and the catastrophic nature of the geologic record

In 1831, the Scottish horticulturalist Patrick Matthew (1790–1874) published a clear statement of the law of natural selection in an Appendix to his book Naval Timber and Arboriculture, which both Darwin and Wallace later acknowledged. Matthew, however, was a catastrophist, and he presented natural selection within the contemporary view that relatively long intervals of environmental stability were episodically punctuated by catastrophic mass extinctions of life. Modern studies support a similar picture of the division of geologic time into long periods of relative evolutionary stability ended by sudden extinction events. Mass extinctions are followed by recovery intervals during which surviving taxa radiate into vacated niches. This modern punctuated view of evolution and speciation is much more in line with Matthew's episodic catastrophism than the classical Lyellian–Darwinian gradualist view.     

Do vegetation patch spatial patterns disrupt the spatial organization of plant species?

The mechanisms that structure plant diversity and generate long-range correlated spatial patterns have important implications for the conservation of fragmented landscapes. The ability to disperse and persist influences a plant species’ capacity for spatial organization, which can play a critical role in structuring plant diversity in metacommunities. This study examined the spatial patterns of species diversity within a network of patches in Cabo de Gata Natural Park, southeastern Spain. The objectives were to understand how the spatial heterogeneity of species composition (beta diversity) varies in a structured landscape, and how the long-range spatial autocorrelation of plant species is affected by the spatial configuration of patches.The mechanisms underlying the spatial distribution of plants acted at two scales. Between patches, spatial variation in species distributions was greater than that expected based on spatial randomization, which indicated that movement among patches was restricted. Within patches, diffusion processes reduced spatial variability in species distributions, and the effect was more prominent in large patches. Small patch size negatively influenced the long-range spatial autocorrelation of characteristic species, whereas inter-patch distance had a stronger effect on species frequency than it had on the disruption of spatial organized patterns.The long-range spatial autocorrelation was evaluated based on the dispersal abilities of the species. Among the 106 species evaluated, 39% of the woody species, 17% of the forbs, and 12% of the grasses exhibited disrupted long-range spatial autocorrelation where patches were small. The species that are more vulnerable to the effects of fragmentation tended to be those that have restricted dispersal, such as those that have short-range dispersal (atelechoric), e.g., Phlomis purpurea, Cistus albidus, Teucrium pseudochamaepytis, Brachypodium retusum, and the ballistic species, Genista spartioides. Helianthemum almeriense is another vulnerable species that has actively restricted dispersal (antitelechory), which is common in arid regions. Wind dispersers such as Launaea lanifera were less vulnerable to the effects of fragmentation. Long-distance dispersers whose persistence depends on facilitative interactions with other individuals, e.g., allogamous species such as Thymus hyemalis, Ballota hirsuta, and Anthyllis cytisoides, exhibit disrupted long-range spatial autocorrelation when patch size is reduced.     

Exploring the common molecular basis for the universal DNA mutation bias: revival of Löwdin mutation model

Recently, numerous genome analyses revealed the existence of a universal G:C→A:T mutation bias in bacteria, fungi, plants and animals. To explore the molecular basis for this mutation bias, we examined the three well-known DNA mutation models, i.e., oxidative damage model, UV-radiation damage model and CpG hypermutation model. It was revealed that these models cannot provide a sufficient explanation to the universal mutation bias. Therefore, we resorted to a DNA mutation model proposed by L?wdin 40 years ago, which was based on inter-base double proton transfers (DPT). Since DPT is a fundamental and spontaneous chemical process and occurs much more frequently within GC pairs than AT pairs, L?wdin model offers a common explanation for the observed universal mutation bias and thus has broad biological implications.     

Where is the root of the universal tree of life?

The currently accepted universal tree of life based on molecular phylogenies is characterised by a prokaryotic root and the sisterhood of archaea and eukaryotes. The recent discovery that each domain (bacteria, archaea, and eucarya) represents a mosaic of the two others in terms of its gene content has suggested various alternatives in which eukaryotes were derived from the merging of bacteria and archaea. In all these scenarios, life evolved from simple prokaryotes to complex eukaryotes. We argue here that these models are biased by overconfidence in molecular phylogenies and prejudices regarding the primitive nature of prokaryotes. We propose instead a universal tree of life with the root in the eukaryotic branch and suggest that many prokaryotic features of the information processing mechanisms originated by simplification through gene loss and non-orthologous displacement.     

Are mutations usually deleterious? A perspective on the fitness effects of mutation accumulation

Evolutionary Ecology - All adaptive alleles in existence today began as mutations, but a common view in ecology, evolution, and genetics is that non-neutral mutations are much more likely to be...     

The effects of dispersal patterns on marine reserves: does the tail wag the dog?

The concept of marine reserves as a method of improving management of fisheries is gaining momentum. While the list of benefits from reserves is frequently promoted, precise formulations of theory to support reserve design are not fully developed. To determine the size of reserves and the distances between reserves an understanding of the requirements for persistence of local populations is required. Unfortunately, conditions for persistence are poorly characterized, as are the larval dispersal patterns on which persistence depends. With the current paucity of information regarding meroplanktonic larval transport processes, understanding the robustness of theoretical results to larval dispersal is of key importance. From this formulation a broad range of dispersal patterns are analyzed. Larval dispersal is represented by a probability distribution that defines the fraction of successful settlers from an arbitrary location, the origin of the distribution, to any other location along the coast. While the effects of specific dispersal patterns have been investigated for invasion processes, critical habitat size and persistence issues have generally been addressed with only one or two dispersal types. To that end, we formulate models based on integrodifference equations that are spatially continuous and temporally discrete. We consider a range of dispersal distributions from leptokurtic to platykurtic. The effect of different dispersal patterns is considered for a single isolated reserve of varying size receiving no external larvae, as well as multiple reserves with varying degrees of connectivity. While different patterns result in quantitative differences in persistence, qualitatively similar effects across all patterns are seen in both single- and multiple reserve models. Persistence in an isolated reserve requires a size that is approximately twice the mean dispersal distance and regardless of the dispersal pattern the population in a patch is not persistent if the reserve size is reduced to just the mean dispersal distance. With an idealized coastline structure consisting of an infinite line of equally spaced reserves separated by regions of coastline in which reproduction is nil, the relative settlement as a function of the fraction of coastline and size of reserve is qualitatively very similar over a broad range of dispersal patterns. The upper limit for the minimum fraction of coastline held in reserve is about 40%. As the fraction of coastline is reduced, the minimum size of reserve becomes no more than 1.25 times the mean dispersal distance.     

Do rodent and human brains have different N-glycosylation patterns?

A large number of studies on the structure of N-glycosidically linked oligosaccharides from glycoproteins of different organs and/or different species have been carried out in the past using various combinations of techniques such as monosaccharide analysis, permethylation, peracteylation, exoglycosidase sequencing, normal and reversed phase HPLC, mass spectrometry and nuclear magnetic resonance spectroscopy. Although it is widely accepted that the processing of N-glycans in the ER and Golgi of mammalian cells follows the same principal metabolic rules, analyses have revealed that the glycosylation pattern of a particular protein may differ depending on the cell type in which it is expressed. N-glycans from brain glycoproteins have been shown to include a variety of hybrid- and complex-type structures with structural features that are not so commonly found on glycoproteins from other organs and which have, therefore, been classified as 'brain-specific'. Comparison of the N-glycans of glycoproteins from homogenates of rat, mouse and human brains confirm that, in general, glycoproteins from human brain show a similar profile of brain-specific N-glycans as glycoproteins from mouse and rat brain.     

Studies of the effects of liquid holding on viability and mutation frequency in N-methyl-N′-nitro-N-nitrosoguanidine-treated halophiles

The capacities ofHalobacterium cutirubrum and a moderate halophile NRC 41227 to survive and recover from treatment with N-methyl-N-nitro-N-nitrosoguanidine have been compared.Halobacterium cutirubrum is resistant to this chemical and its mutation frequency is only slightly affected, whereas NRC 41227 is highly sensitive and its mutation frequency is markedly increased. The chemically treated extreme halophile fully regains viability during liquid holding, in notable contrast to its known failure to recover from the effects of ultraviolet irradiation.     

Do dams and levees impact nitrogen cycling? Simulating the effects of flood alterations on floodplain denitrification

A fundamental challenge in understanding the global nitrogen cycle is the quantification of denitrification on large heterogeneous landscapes. Because floodplains are important sites for denitrification and nitrogen retention, we developed a generalized floodplain biogeochemical model to determine whether dams and flood‐control levees affect floodplain denitrification by altering floodplain inundation. We combined a statistical model of floodplain topography with a model of hydrology and nitrogen biogeochemistry to simulate floods of different magnitude. The model predicted substantial decreases in NO₃‐N processing on floodplains whose overbank floods have been altered by levees and upstream dams. Our simulations suggest that dams may reduce nitrate processing more than setback levees. Levees increased areal floodplain denitrification rates, but this effect was offset by a reduction in the area inundated. Scenarios that involved a levee also resulted in more variability in N processing among replicate floodplains. Nitrate loss occurred rapidly and completely in our model floodplains. As a consequence, total flood volume and the initial mass of nitrate reaching a floodplain may provide reasonable estimates of total N processing on floodplains during floods. This finding suggests that quantifying the impact of dams and levees on floodplain denitrification may be possible using recent advances in remote sensing of floodplain topography and flood stage. Furthermore, when considering flooding over the long‐term, the cumulative N processed by frequent smaller floods was estimated to be quite large relative to that processed by larger, less frequent floods. Our results suggest that floodplain denitrification may be greatly influenced by the pervasive anthropogenic flood‐control measures that currently exist on most majors river floodplains throughout the world, and may have the potential to be impacted by future changes in flood probabilities that will likely occur as a result of climate shifts.     

Do the substituent effects affect conformational freedom of squalene in hopene biosynthesis?

The analysis of biochemical processes is one of the main challenges for modern computational chemistry. Probably the biggest issue facing scientists in this case is the number of factors that have to be taken into account, as even those factors that do not seem to be meaningful may eventually be crucial. Such a belief led to the investigation on the substituent effects during squalene cyclization process. We focused on the formation of lanosterol ring A through squalene epoxide and an analogue process observed in bacteria, leading to the hopene formation without an intermediate oxide. Interestingly, our results indicate that, opposite of chemical intuition, a more substituted chain is more likely to adopt a conformation suitable for the cyclization process. Presumably the rational for this behavior is the presence of intermolecular CH⋅⋅⋅π interactions between the hydrogen atoms from methyl groups and the squalene π bonds in the open-chain structure. The effect seems to have a firm impact on the hopene formation process. Calculations were performed using two different methods: MP2 and M06-2X, combined with the cc-pVDZ basis set.