Noise-induced spatiotemporal patterns in Hodgkin–Huxley neuronal network

The effect of noise on the pattern selection in a regular network of Hodgkin–Huxley neurons is investigated, and the transition of pattern in the network is measured from subexcitable to excitable media. Extensive numerical results confirm that kinds of travelling wave such as spiral wave, circle wave and target wave could be developed and kept alive in the subexcitable network due to the noise. In the case of excitable media under noise, the developed spiral wave and target wave could coexist and new target-like wave is induced near to the border of media. The averaged membrane potentials over all neurons in the network are calculated to detect the periodicity of the time series and the generated traveling wave. Furthermore, the firing probabilities of neurons in networks are also calculated to analyze the collective behavior of networks.     

Diversity of developmental patterns in achelate lobsters—today and in the Mesozoic

Modern achelate lobsters, slipper and spiny lobsters, have a specific post-embryonic developmental pattern with the following phases: phyllosoma, nisto (slipper lobsters) or puerulus (spiny lobsters), juvenile and adult. The phyllosoma is a peculiar larva, which transforms through a metamorphic moult into another larval form, the nisto or puerulus which largely resembles the juvenile. Unlike the nisto and puerulus, the phyllosoma is characterised by numerous morphological differences to the adult, e.g. a thin head shield, elongate appendages, exopods on these appendages and a special claw. Our reinvestigation of the 85 million years old fossil “Eryoneicus sahelalmae” demonstrates that it represents an unusual type of achelatan lobster larva, characterised by a mixture of phyllosoma and post-phyllosoma characters. We ascribe it to its own genus: Polzicaris nov. gen. We study its significance by comparisons with other cases of Mesozoic fossil larvae also characterised by a mixture of characters. Accordingly, all these larvae are interpreted as ontogenetic intermediates between phyllosoma and post-phyllosoma morphology. Remarkably, most of the larvae show a unique mixture of retained larval and already developed post-larval features. Considering the different—and incompatible—mixture of characters of each of these larvae and their wide geographical and temporal distribution, we interpret all these larvae as belonging to distinct species. The particular character combinations in the different larvae make it currently difficult to reconstruct an evolutionary scenario with a stepwise character acquisition. Yet, it can be concluded that a larger diversity of larval forms and developmental patterns occurred in Mesozoic than in modern faunas.     

Are there general patterns in plant defence against megaherbivores?

Field surveys were conducted to test whether plants deploy structural defences in ways that match the distribution of megaherbivores. In Western Australian scrublands, where adult plants are within the reach of megaherbivores, structural defences increased vertically and were deployed preferentially by adult plants. Conversely, in woodlands of Eastern Australia and California, where adult plants grow above the reach of megaherbivores, structural defences decreased vertically. Populations of closely‐related taxa on offshore islands exhibited significant reductions in defence in the absence of megaherbivores. The results also demonstrate that island plant taxa can evolve vertical changes in defence after colonizing continents, where they are exposed to megaherbivores. Overall, the results of the present study illustrate a complex array of spatial patterns in plant defence that match the distribution and foraging behaviour of large mammals. When interpreted alongside previous work demonstrating similar spatial patterns in other types of plant defence, the results may help to unify our understanding of how megaherbivores have shaped the evolution of plant form and function. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 38–48.     

Phylogenetic patterns in the fleshy-fruited Myrtaceae – preliminary molecular evidence

A phylogenetic study of selected fleshy-fruited genera of the Myrtaceae was conducted using sequences from the ITS region of nuclear DNA and the psbA-trnH region of plastid DNA. Studies to date have suggested that the fleshy-fruited state has arisen on several occasions in the Myrtaceae. The previously accepted and predominantly Neotropical tribe Myrteae has traditionally been divided into three groups, the subtribes Myrtinae, Eugeniinae and Myrciinae. This subtribal arrangement is analysed in detail here for the first time. The monophyly of the tribe and subtribes are tested and relationships of the genera within them, in particular those of the Myrciinae and anomalous genera sometimes associated with it, are discussed. Combined analyses of these two DNA regions revealed 40 shortest trees, all of which resolve Myrteae (excluding the Acmena group) as monophyletic. Myrciinae appears to be monophyletic whereas Myrtinae and Eugeniinae appear polyphyletic. The phylogenetic positions and relationships of the anomalous genera Myrceugenia, Luma and Blepharocalyx are unclear, but Myrceugenia is never included within the Myrciinae s.str. A Myrciinae s.str. clade emerges within which Myrcia, Calyptranthes and Marlierea appear polyphyletic. Clades emerge, however, that may reflect some natural groupings within the subtribe.We thank David Simpson, Lazlo Csiba, Edith Kapinos and many others from Kew for invaluable advice and support. It would not have been possible to collect the Brazilian samples without the patience and careful guidance of Dr. Vinicius C. Souza, Fiorella F. Mazine (Universidade de São Paulo, ESALQ), Professor Gert Hatschbach, Joel M. de Silva (Museu Botânico Municipal, Curitiba) and many others from the ESA and MBM herbaria. Thanks also to Les Landrum, Andrew Salywon, Marcos Sobral and an anonymous reviewer for helpful comments at different stages of this work. British Airways are gratefully acknowledged for providing a flight to Brazil under their Community and Conservation programme.     

Spatial–temporal patterns of methane dynamics in Lake Taihu

Many European lakes are monitored according to the EU Water Framework Directive (WFD), with focus on phytoplankton biomass and species composition. However, the low-frequency WFD monitoring may miss short-term phytoplankton changes. This is an important issue because short-term extreme meteorological events (heat waves and heavy rain) are predicted to increase in frequency and intensity with climate change. We used records from Lake Mondsee (Austria) from 2009 to 2015 to test if a reduction from monthly to seasonal sampling affected the average annual phytoplankton biovolume. Furthermore, we combined inverted light microscopy, FlowCAM and flow cytometry to estimate the effect of sampling during extreme events on average phytoplankton biovolume. Relative to monthly sampling, seasonal sampling significantly overestimated phytoplankton biomass. A heat wave in 2015 and two episodes of heavy rain in 2015 and 2016 caused species-specific changes; biovolumes of chlorophytes and the filamentous cyanobacterium Planktothrix rubescens (De Candolle ex Gomont) Anagnostidis & Komárek increased significantly during the heat wave. Using live material with FlowCAM and flow cytometry, we detected small and fragile cells and colonies that were either ignored or underrepresented by analysing fixed samples with light microscopy. We suggest a modified sampling and analysis strategy to capture short-term changes within the phytoplankton community.     

Conservative ecological and evolutionary patterns in liverwort–fungal symbioses

Liverworts, the most ancient group of land plants, form a range of intimate associations with fungi that may be analogous to the mycorrhizas of vascular plants. Most thalloid liverworts contain arbuscular mycorrhizal glomeromycete fungi similar to most vascular plants. In contrast, a range of leafy liverwort genera and one simple thalloid liverwort family (the Aneuraceae) have switched to basidiomycete fungi. These liverwort switches away from glomeromycete fungi may be expected to parallel switches undergone by vascular plants that target diverse lineages of basidiomycete fungi to form ectomycorrhizas. To test this hypothesis, we used a cultivation-independent approach to examine the basidiomycete fungi associated with liverworts in varied worldwide locations by generating fungal DNA sequence data from over 200 field collections of over 30 species. Here we show that eight leafy liverwort genera predominantly and consistently associate with members of the Sebacina vermifera species complex and that Aneuraceae thalloid liverworts associate nearly exclusively with Tulasnella species. Furthermore, within sites where multiple liverwort species co-occur, they almost never share the same fungi. Our analyses reveal a strikingly conservative ecological and evolutionary pattern of liverwort symbioses with basidiomycete fungi that is unlike that of vascular plant mycorrhizas.     

Diagnostic potential of tear proteomic patterns in Sjögren's syndrome

Histological and functional changes of the lacrimal gland might be reflected in proteomic patterns in tear fluids. In this study, we carried out a determination of the disease biomarkers in tear fluid for Sj?gren's syndrome (SS) and a performance of noninvasive diagnostic test based on the proteomic patterns. Thirty-one SS patients and 57 control subjects were enrolled to this study. Their details were 23 cases with primary SS, 8 with secondary SS, 14 with dry eyes, 22 with miscellaneous ocular diseases, and 21 of healthy volunteers. Protein profiling in tear fluids was identified by surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS). Multiple protein changes were reproducibly detected in the primary SS group, including 10 potential novel biomarkers. Seven of the biomarkers (2094, 2743, 14191, 14702, 16429, 17453, 17792 m/z) were down-regulated and 3 biomarkers (3483, 4972, 10860 m/z) were up-regulated in primary SS group, comparing to the protein profiles of control subjects. When cutoff value of SS down-score was set less than 0.5, this result yielded 87% sensitivity and 100% specificity. The positive predictive value for this sample set was 100%. There was a significant inverse correlation between SS down-scores and epithelial damages of the ocular surface in primary SS patients. These findings support the potential of proteomic pattern technology in tear fluids as the noninvasive diagnostic test for primary SS.     

Do landscape processes predict phylogeographic patterns in the wood frog?

Understanding factors that influence population connectivity and the spatial distribution of genetic variation is a major goal in molecular ecology. Improvements in the availability of high-resolution geographic data have made it increasingly possible to quantify the effects of landscape features on dispersal and genetic structure. However, most studies examining such landscape effects have been conducted at very fine (e.g. landscape genetics) or broad (e.g. phylogeography) spatial scales. Thus, the extent to which processes operating at fine spatial scales are linked to patterns at larger scales remains unclear. Here, we test whether factors impacting wood frog dispersal at fine spatial scales are correlated with genetic structure at regional scales. Using recently developed methods borrowed from electrical circuit theory, we generated landscape resistance matrices among wood frog populations in eastern North America based on slope, a wetness index, land cover and absolute barriers to wood frog dispersal. We then determined whether these matrices are correlated with genetic structure based on six microsatellite markers and whether such correlations outperform a landscape-free model of isolation by resistance. We observed significant genetic structure at regional spatial scales. However, topography and landscape variables associated with the intervening habitat between sites provide little explanation for patterns of genetic structure. Instead, absolute dispersal barriers appear to be the best predictor of regional genetic structure in this species. Our results suggest that landscape variables that influence dispersal, microhabitat selection and population structure at fine spatial scales do not necessarily explain patterns of genetic structure at broader scales.     

Do changes in rainfall patterns affect semiarid annual plant communities?

Question: Climate change models forecast a reduction in annual precipitation and more extreme events (less rainy days and longer drought periods between rainfall events), which may have profound effects on terrestrial ecosystems. Plant growth, population and community dynamics in dry environments are likely to be affected by these changes since productivity is already limited by water availability. We tested the effects of reduced precipitation and fewer rain events on three semiarid plant communities dominated by annual species. Location: Three semiarid plant communities from Almería province (SE Spain). Methods: Rain‐out shelters were set up in each community and watering quantity and frequency were manipulated from autumn to early summer. Plant productivity, cover and diversity were measured at the end of the experimental period. Results: We found that a 50% reduction in watering reduced productivity, plant cover and diversity in all three communities. However, neither the 25% reduction in watering nor changes in the frequency of watering events affected these parameters. Conclusions: The lack of response to small reductions in water could be due to the identity and resistance of the plant communities involved, which are adapted to rainfall variability characteristic of arid environments. Therefore, a rainfall reduction of 25% or less may not affect these plant communities in the short term, although higher reductions or long‐term changes in water availability would probably reduce productivity and diversity in these communities.     

Can zebra mussels change stratification patterns in a small reservoir?

Colonization and proliferation of zebra mussel (Dreissena polymorpha) population in Hargus lake, a small thermally stratified reservoir in Ohio, U.S.A., caused a significant increase in water clarity and a remarkable decrease in phytoplankton biomass during the period from 1993 to 1995. Increased light penetration and reduced organic matter loading to the meta-and hypolimnion were reflected in the lake stratification patterns, particularly in the temperature and oxygen profiles in the metalimnion. The meta- and hypolimnetic water temperature increased significantly over three years, irrespective of variation in surface water temperature. The epilimnion depth (mixing depth) increased by about the same magnitude as did the average Secchi depth. However, the total heat content of the lake did not show a consistent trend to increasing zebra mussel abundance, as it was largely influenced by the temperature of the large water volumes near the surface, which were in turn affected by weather conditions. Concurrent with the thermal structure change, the dissolved oxygen structure also changed over three years, though to a lesser extent. The changes in oxygen stratification pattern were reflected by increased oxygen concentrations in the metalimnion and a lowered depth of 3 mg l^–1 DO isopleth. These observed changes were likely attributed to increased water mixing depth, metalimnion photosynthesis and reduced oxygen consumption by organic matter. With increased epilimnion thickness and improved oxygen conditions in the metalimnion, the habitable space for aquatic macro-organisms (including fish) expanded substantially. Our results suggest that the indirect impacts of zebra mussels on small lake stratification patterns may have much broader implications than do the direct trophic interactions to the whole ecosystem.     

Population biology patterns of commercially important mollusks in México

The need to propose recommendations for the management of over 80 species of bivalves and gastropod mollusks exploited commercially in Mexico, led to look for trends on the population and reproductive biology in relation to prevailing environmental conditions of the habitats where they are exploited. The reproductive cycle, growth parameters for the von Bertalanffy equation, mortality and recruitment of 18 populations of 14 species from 13 localities are compared and related to ambient temperature, precipitation, evaporation, geomorphology, tides, and water salinity and temperature. Localities were classified as influenced by landmasses or with marine influence, with a desert or tropical humid climate. With restricted or continuous communication to oceanic waters and with or without freshwater runoff. The reproductive cycles were classified in four groups in relation to intensity and duration of the spawning season: 1) limited to one annual spawning, 2) two or more defined spawning periods, 3) two or more extended spawning periods, and 4) continuous low intensity spawning. And three groups in relation to gonad recovery, and duration and intensity of gametogenesis: 1) post spawn and rest stages absent or restricted, 2) fast gametogenesis and a clear mature stage. and 3) extended gametogenesis and limited maturity stages. The population parameters were classified in relation to age structure and number of cohorts, intensity and duration of recruitment, and growth rates as expressed by infinity and K. In relation to their life cycle four types were found: 1) population represented by only one cohort, at least during part of the year, 2) with two or more cohorts at any time, 3) longevity under five years, and 4) longevity over live years. In relation to recruitment: 1) one recruitment period restricted to a short season, 2) two or more recruitment periods, 3) constant recruitment with one or more peaks, and 4) constant recruitment without periods of dominance.     

Spatial self-organisation in ecology: pretty patterns or robust reality?

Many seemingly plausible mathematical models of small-scale ecological interactions predict the self-organisation of dynamic, coherent and large scale spatial patterns (e.g. spirals). If true, such patterns would have important ecological and evolutionary consequences. For the most part, however, empirical studies have not corroborated their existence, suggesting erroneous dynamics in the models, shortcomings in empirical methodology, or both. Arguments for categorically dismissing self-organized patterns have been based on their assumed sensitivity to symmetry-breaking stochastic noise. However, many plausible mechanisms for generating patterns are robust to noise, and consequently broken symmetry is insufficient grounds for dismissing these self-organized patterns.     

Latitudinal and elevational patterns of phylogenetic structure in forest communities in China’s mountains

Science China Life Sciences - The phylogenetic structure incorporates both ecological and evolutionary processes to explain assembly of a local community. The “phylogenetic niche...     

Woody species patterns at forest–grassland boundaries in southern Brazil

Vegetation mosaics of grassland/savanna and forest can be found in tropical and subtropical regions of the world, as in southern Brazil, where climate conditions are suitable for forest. Changes in intensity or frequency of disturbances could enable woody species encroachment in grassland communities; however, the processes are related to site conditions and life history of pioneer species. In this paper, we study transition patterns of forest to grassland in the absence of grazing, but under different site conditions related to aspect (landscape position) and time since the last burn. Data are based on shrub and tree species composition and soil variables at forest–grassland boundaries. We found 119 woody species of 42 families along transects of 27 m into the forest and 31.5 m into the grassland. Gradients from forest to grassland were analysed as compositional trajectories in ordination space and differences in the spatial patterns depicted between distinct site aspects. The time since the last fire did not influence these patterns. Inside the forest, tree species diversity was significantly higher close to the edge, independent of the density of individuals. Two main mechanisms may promote forest expansion into the grassland. First, a gradual tree encroachment near the edge and, second, a mechanism linked to the recruitment of isolated pioneer trees within the grassland matrix, most frequently near rocky outcrops, where a decrease in grass biomass leads to low-intensity fires. Despite vegetation patterns at boundaries differing according to aspect, the most important explanatory factor was the distance from the forest border, not just by itself, but with all correlated parameters that are changing along the gradient.     

Methylation patterns in 5＇ terminal regions of pluripotency-related genes in bovine in vitro fertilized and cloned embryos

In order to investigate DNA methylation profiles of five pluripotency-related genes (Oct4, Sox2, Nanog, Rex1 and Fgf4) during bovine maternal to zygotic transition (MZT) in both in vitro fertilized (IVF) and nuclear transfer (NT) embryos, sodium bisulfite sequencing method was used to detect DNA methylation levels, accompanied by the statistical analysis of embryo developmental rates. The results showed that Oct4, Nanog, Rex1 and Fgf4 were respectively demethylated by 25.22% (P < 0.01), 3.84% (P > 0.05), 31.82% (P < 0.01) and 10% (P > 0.05) while Sox2 retained unmethylation during MZT in IVF embryos. By contrast, Oct4 and Rex1 respectively underwent demethylation by 23.04% (P < 0.01) and 6.02% (P > 0.05), and, reversely, Sox2, Nanog and Fgf4 respectively experienced remethylation by 0.84% (P > 0.05), 5.39% (P > 0.05) and 5.46% (P > 0.05) during MZT in NT embryos. Interestingly, the CpG 14 site of Sox2 was specifically methylated in both 8-cell and morula NT embryos. In addition, the development of blastocysts between IVF and NT embryos showed no significant difference. DNA methylation analysis showed that only Oct4 and Sox2 underwent the correct methylation reprogramming process, which may be responsible for the development of blastocysts of NT embryos to a certain extent. In conclusion, the five genes respectively experienced demethylation to different extents and incomplete DNA methylation reprogramming during bovine MZT in both IVF and NT embryos, suggesting that they may be used as indicators for bovine embryo developmental competence.     

Varying foraging patterns in response to competition? A multicolony approach in a generalist seabird

Reducing resource competition is a crucial requirement for colonial seabirds to ensure adequate self‐ and chick‐provisioning during breeding season. Spatial segregation is a common avoidance strategy among and within species from neighboring breeding colonies. We determined whether the foraging behaviors of incubating lesser black‐backed gulls (Larus fuscus) differed between six colonies varying in size and distance to mainland, and whether any differences could be related to the foraging habitats visited. Seventy‐nine incubating individuals from six study colonies along the German North Sea coast were equipped with GPS data loggers in multiple years. Dietary information was gained by sampling food pellets, and blood samples were taken for stable isotope analyses. Foraging patterns clearly differed among and within colonies. Foraging range increased with increasing colony size and decreased with increasing colony distance from the mainland, although the latter might be due to the inclusion of the only offshore colony. Gulls from larger colonies with consequently greater density‐dependent competition were more likely to forage at land instead of at sea. The diets of the gulls from the colonies furthest from each other differed, while the diets from the other colonies overlapped with each other. The spatial segregation and dietary similarities suggest that lesser black‐backed gulls foraged at different sites and utilized two main habitat types, although these were similar across foraging areas for all colonies except the single offshore island. The avoidance of intraspecific competition results in colony‐specific foraging patterns, potentially causing more intensive utilization of terrestrial foraging sites, which may offer more predictable and easily available foraging compared with the marine environment.