scholarly journals Spatial analysis of phylogenetic community structure: New version of a classical method

2015 ◽  
Author(s):  
Carlo Ricotta ◽  
Eszter EA Ari ◽  
Giuliano Bonanomi ◽  
Francesco Giannino ◽  
Duncan Heathfield ◽  
...  
Keyword(s):  
Community Structure ◽  
Spatial Scales ◽  
Point Pattern ◽  
Maximum Deviation ◽  
Individual Plant ◽  
Phylogenetic Distance ◽  
Phylogenetic Structure ◽  
Phylogenetic Community Structure ◽  
Point Patterns ◽  
Wide Range

The increasing availability of phylogenetic information facilitates the use of evolutionary methods in community ecology to reveal the importance of evolution in the species assembly process. However, while several methods have been applied to a wide range of communities across different spatial scales with the purpose of detecting non-random phylogenetic patterns, the spatial aspects of phylogenetic community structure have received far less attention. Accordingly, the question for this study is: can point pattern analysis be used for revealing the phylogenetic structure of multi-species assemblages? We introduce a new individual-centered procedure for analyzing the scale-dependent phylogenetic structure of multi-species point patterns based on digitized field data. The method uses nested circular plots with increasing radii drawn around each individual plant and calculates the mean phylogenetic distance between the focal individual and all individuals located in the circular ring delimited by two successive radii. This scale-dependent value is then averaged over all individuals of the same species and the observed mean is compared to a null expectation with permutation procedures. The method detects particular radius values at which the point pattern of a single species exhibits maximum deviation from the expectation towards either phylogenetic aggregation or segregation. Its performance is illustrated using data from a grassland community in Hungary and simulated point patterns. The proposed method can be extended to virtually any distance function for species pairs, such as functional distances.

scholarly journals Spatial analysis of phylogenetic community structure: New version of a classical method

2015 ◽  
Author(s):  
Carlo Ricotta ◽  
Eszter EA Ari ◽  
Giuliano Bonanomi ◽  
Francesco Giannino ◽  
Duncan Heathfield ◽  
...  
Keyword(s):  
Community Structure ◽  
Spatial Scales ◽  
Point Pattern ◽  
Maximum Deviation ◽  
Individual Plant ◽  
Phylogenetic Distance ◽  
Phylogenetic Structure ◽  
Phylogenetic Community Structure ◽  
Point Patterns ◽  
Wide Range

The increasing availability of phylogenetic information facilitates the use of evolutionary methods in community ecology to reveal the importance of evolution in the species assembly process. However, while several methods have been applied to a wide range of communities across different spatial scales with the purpose of detecting non-random phylogenetic patterns, the spatial aspects of phylogenetic community structure have received far less attention. Accordingly, the question for this study is: can point pattern analysis be used for revealing the phylogenetic structure of multi-species assemblages? We introduce a new individual-centered procedure for analyzing the scale-dependent phylogenetic structure of multi-species point patterns based on digitized field data. The method uses nested circular plots with increasing radii drawn around each individual plant and calculates the mean phylogenetic distance between the focal individual and all individuals located in the circular ring delimited by two successive radii. This scale-dependent value is then averaged over all individuals of the same species and the observed mean is compared to a null expectation with permutation procedures. The method detects particular radius values at which the point pattern of a single species exhibits maximum deviation from the expectation towards either phylogenetic aggregation or segregation. Its performance is illustrated using data from a grassland community in Hungary and simulated point patterns. The proposed method can be extended to virtually any distance function for species pairs, such as functional distances.

Contributions of gopher mound and casting disturbances to plant community structure in a Cascade Range meadow complex

Botany ◽  
2013 ◽  
Vol 91 (8) ◽  
pp. 555-561 ◽  
Author(s):  
Madelon F. Case ◽  
Charles B. Halpern ◽  
Simon A. Levin
Keyword(s):  
Community Structure ◽  
Spatial Scales ◽  
Plant Cover ◽  
Small Scale ◽  
Individual Plant ◽  
Pocket Gopher ◽  
Community Patterns ◽  
Pocket Gophers ◽  
Mountain Meadows ◽  
Oregon Cascades

Pocket gophers (Geomyidae) are major agents of disturbance in North American grasslands. Gopher mounds bury existing plants and influence community structure through various mechanisms. However, in mountain meadows that experience winter snowpack, gophers also create winter castings, smaller tube-shaped deposits, previously ignored in studies of plant–gopher disturbance relationships. We studied the influences of the Mazama pocket gopher (Thomomys mazama Merriam, 1897) in montane meadows of the Oregon Cascades, quantifying community patterns at larger spatial scales than previously studied in this system and considering, for the first time, effects of both mounds and castings. We measured cover of disturbance and individual plant species along twenty 5 m transects in each of four plots with differing species composition. Total plant cover was negatively correlated with mounds and castings. However, only mounds influenced growth-form dominance, reducing graminoid cover and increasing the forb–graminoid ratio — effects attributable to the greater volume and longevity of mounds. Forb-disturbance relationships were variable among plots, likely due to differences in species’ tolerance of burial. Transect-scale richness and heterogeneity (variation in composition within transects) increased with disturbance. We conclude that frequent, small-scale disturbances create a shifting mosaic of vegetation states, reducing graminoid dominance and enhancing species richness and heterogeneity at larger spatial scales.

Testing the Stability of Crime Patterns: Implications for Theory and Policy

2010 ◽  
Vol 48 (1) ◽  
pp. 58-82 ◽  
Author(s):  
Martin A. Andresen ◽  
Nicolas Malleson
Keyword(s):  
Spatial Scales ◽  
Theoretical Development ◽  
Point Pattern ◽  
Crime Patterns ◽  
Point Patterns ◽  
Spatial Point ◽  
Spatial Point Patterns ◽  
Spatial Criminology ◽  
The Stability ◽  
Street Segments

Recent research in the ‘‘crime at places’’ literature is concerned with smaller units of analysis than conventional spatial criminology. An important issue is whether the spatial patterns observed in conventional spatial criminology focused on neighborhoods remain when the analysis shifts to street segments. In this article, the authors use a new spatial point pattern test that identifies the similarity in spatial point patterns. This test is local in nature such that the output can be mapped showing where differences are present. Using this test, the authors investigate the stability of crime patterns moving from census tracts to dissemination areas to street segments. The authors find that general crime patterns are somewhat similar at all spatial scales, but finer scales of analysis reveal significant variations within larger units. This result demonstrates the importance of analyzing crime patterns at small scales and has important implications for further theoretical development and policy implementation.

Relatedness and the composition of communities over time: Evaluating phylogenetic community structure in the late Cenozoic record of bivalves

Paleobiology ◽  
2020 ◽  
pp. 1-13
Author(s):  
Lucy M. Chang ◽  
Phillip L. Skipwith
Keyword(s):  
Community Structure ◽  
Competitive Exclusion ◽  
Critical Role ◽  
Environmental Filtering ◽  
Influential Factors ◽  
Phylogenetic Distance ◽  
Late Cenozoic ◽  
Phylogenetic Community Structure ◽  
Historical Perspectives ◽  
Over Time

Abstract Understanding the mechanisms that prevent or promote the coexistence of taxa at local scales is critical to understanding how biodiversity is maintained. Competitive exclusion and environmental filtering are two processes thought to limit which taxa become established in a community. However, determining the relative importance of the two processes is a complex task, especially when the critical initial stages of colonization cannot be directly observed. Here, we explore the use of phylogenetic community structure for identifying filtering mechanisms in a fossil community. We integrated a time-calibrated molecular phylogeny of bivalve genera with a spatial dataset of late Cenozoic bivalves from the Pacific coast of North America to characterize how the community that was present in the semirestricted San Joaquin Basin (SJB) embayment of present-day California was phylogenetically structured. We employed phylogenetic distance-based metrics across six time bins spanning 27–2.5 Ma and found no evidence of significant clustering or evenness in the SJB community when compared with communities randomly assembled from the regional source pool. Additionally, we found that new colonizers into the SJB were not significantly more or less closely related to native taxa than expected by chance. These findings suggest that neither competitive exclusion nor environmental filtering were overwhelmingly influential factors shaping the composition of the SJB community over time. We further discuss interpretations of these patterns in light of current understandings in community phylogenetics and reiterate the critical role historical perspectives play in how community assembly rules are assessed.

scholarly journals Does fluvial channel-belt clustering predict net sand to gross rock volume? Architectural metrics and point-pattern analysis of a digital outcrop model

2019 ◽  
Vol 89 (11) ◽  
pp. 1109-1126
Author(s):  
Alexander R. Koch ◽  
Cari L. Johnson ◽  
Lisa Stright
Keyword(s):  
Large Scale ◽  
Small Scale ◽  
Point Pattern ◽  
Point Patterns ◽  
Spatial Point ◽  
Channel Belt ◽  
John Henry Member ◽  
Scale Point ◽  
Belt Width ◽  
Digital Outcrop

ABSTRACT Spatial point-pattern analyses (PPAs) are used to quantify clustering, randomness, and uniformity of the distribution of channel belts in fluvial strata. Point patterns may reflect end-member fluvial architecture, e.g., uniform compensational stacking and avulsion-generated clustering, which may change laterally, especially at greater scales. To investigate spatial and temporal changes in fluvial systems, we performed PPA and architectural analyses on extensive outcrops of the Cretaceous John Henry Member of the Straight Cliffs Formation in southern Utah, USA. Digital outcrop models (DOMs) produced using unmanned aircraft system-based stereophotogrammetry form the basis of detailed interpretations of a 250-m-thick fluvial succession over a total outcrop length of 4.5 km. The outcrops are oriented roughly perpendicular to fluvial transport direction. This transverse cross-sectional exposure of the fluvial system allows a study of the system's variation along depositional strike. We developed a workflow that examines spatial point patterns using the quadrat method, and architectural metrics such as net sand to gross rock volume (NTG), amalgamation index, and channel-belt width and thickness within moving windows. Quadrat cell sizes that are ∼ 50% of the average channel-belt width-to-thickness ratio (16:1 aspect ratio) provide an optimized scale to investigate laterally elongate distributions of fluvial-channel-belt centroids. Large-scale quadrat point patterns were recognized using an array of four quadrat cells, each with 237× greater area than the median channel belt. Large-scale point patterns and NTG correlate negatively, which is a result of using centroid-based PPA on a dataset with disparately sized channel belts. Small-scale quadrat point patterns were recognized using an array of 16 quadrat cells, each with 21× greater area than the median channel belt. Small-scale point patterns and NTG correlate positively, and match previously observed stratigraphic trends in the fluvial John Henry Member, suggesting that these are regional trends. There are deviations from these trends in architectural statistics over small distances (hundreds of meters) which are interpreted to reflect autogenic avulsion processes. Small-scale autogenic processes result in architecture that is difficult to correlate between 1D datasets, for example when characterizing a reservoir using well logs. We show that 1D NTG provides the most accurate prediction for surrounding 2D architecture.

scholarly journals The OsERF115/AP2EREBP110 Transcription Factor Is Involved in the Multiple Stress Tolerance to Heat and Drought in Rice Plants

2021 ◽  
Vol 22 (13) ◽  
pp. 7181
Author(s):  
Seong-Im Park ◽  
Hyeok Jin Kwon ◽  
Mi Hyeon Cho ◽  
Ji Sun Song ◽  
Beom-Gi Kim ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Transcriptional Activation ◽  
Individual Plant ◽  
Hormone Signaling ◽  
Combined Stress ◽  
Drought Treatment ◽  
Wide Range ◽  
The Individual ◽  
Potential Use ◽  
Multiple Stress Tolerance

The AP2/EREBP family transcription factors play important roles in a wide range of stress tolerance and hormone signaling. In this study, a heat-inducible rice ERF gene was isolated and functionally characterized. The OsERF115/AP2EREBP110 was categorized to Group-IIIc of the rice AP2/EREBP family and strongly induced by heat and drought treatment. The OsERF115/AP2EREBP110 protein targeted to nuclei and suppressed the ABA-induced transcriptional activation of Rab16A promoter in rice protoplasts. Overexpression of OsERF115/AP2EREBP110 enhanced thermotolerance of seeds and vegetative growth stage plants. The OsERF115/AP2EREBP110 overexpressing (OE) plants exhibited higher proline level and increased expression of a proline biosynthesis P5CS1 gene. Phenotyping of water use dynamics of the individual plant indicates that the OsERF115/AP2EREBP110-OE plant exhibited better water saving traits under heat and drought combined stress. Our combined results suggest the potential use of OsERF115/AP2EREBP110 as a candidate gene for genetic engineering approaches to develop heat and drought stress-tolerant crops.

scholarly journals On the generation of internal waves by river plumes in subcritical initial conditions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
R. Mendes ◽  
J. C. B. da Silva ◽  
J. M. Magalhaes ◽  
B. St-Denis ◽  
D. Bourgault ◽  
...  
Keyword(s):  
Numerical Modeling ◽  
Internal Waves ◽  
Coastal Waters ◽  
Initial Conditions ◽  
Spatial Scales ◽  
River Plumes ◽  
Wide Range ◽  
Near Shore ◽  
Generation Mechanisms ◽  
Douro River

AbstractInternal waves (IWs) in the ocean span across a wide range of time and spatial scales and are now acknowledged as important sources of turbulence and mixing, with the largest observations having 200 m in amplitude and vertical velocities close to 0.5 m s−1. Their origin is mostly tidal, but an increasing number of non-tidal generation mechanisms have also been observed. For instance, river plumes provide horizontally propagating density fronts, which were observed to generate IWs when transitioning from supercritical to subcritical flow. In this study, satellite imagery and autonomous underwater measurements are combined with numerical modeling to investigate IW generation from an initial subcritical density front originating at the Douro River plume (western Iberian coast). These unprecedented results may have important implications in near-shore dynamics since that suggest that rivers of moderate flow may play an important role in IW generation between fresh riverine and coastal waters.

scholarly journals Archaeal ammonia oxidizers respond to soil factors at smaller spatial scales than the overall archaeal community does in a high Arctic polar oasis

2016 ◽  
Vol 62 (6) ◽  
pp. 485-491 ◽  
Author(s):  
Samiran Banerjee ◽  
Nabla Kennedy ◽  
Alan E. Richardson ◽  
Keith N. Egger ◽  
Steven D. Siciliano
Keyword(s):  
Community Structure ◽  
Spatial Scales ◽  
Archaeal Community ◽  
Diversity Indices ◽  
High Arctic ◽  
Total Carbon ◽  
Spatial Dependency ◽  
Edaphic Factors ◽  
Total Carbon Content ◽  
Arctic Soils

Archaea are ubiquitous and highly abundant in Arctic soils. Because of their oligotrophic nature, archaea play an important role in biogeochemical processes in nutrient-limited Arctic soils. With the existing knowledge of high archaeal abundance and functional potential in Arctic soils, this study employed terminal restriction fragment length polymorphism (t-RFLP) profiling and geostatistical analysis to explore spatial dependency and edaphic determinants of the overall archaeal (ARC) and ammonia-oxidizing archaeal (AOA) communities in a high Arctic polar oasis soil. ARC communities were spatially dependent at the 2–5 m scale (P < 0.05), whereas AOA communities were dependent at the ∼1 m scale (P < 0.0001). Soil moisture, pH, and total carbon content were key edaphic factors driving both the ARC and AOA community structure. However, AOA evenness had simultaneous correlations with dissolved organic nitrogen and mineral nitrogen, indicating a possible niche differentiation for AOA in which dry mineral and wet organic soil microsites support different AOA genotypes. Richness, evenness, and diversity indices of both ARC and AOA communities showed high spatial dependency along the landscape and resembled scaling of edaphic factors. The spatial link between archaeal community structure and soil resources found in this study has implications for predictive understanding of archaea-driven processes in polar oases.

scholarly journals Interaction between typical sulfonamides and bacterial diversity in drinking water

2018 ◽  
Vol 16 (6) ◽  
pp. 914-920 ◽  
Author(s):  
Qing Wu ◽  
Shuqun Li ◽  
Xiaofei Zhao ◽  
Xinhua Zhao
Keyword(s):  
Drinking Water ◽  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Microbial Community Structure ◽  
Antibiotic Use ◽  
Community Diversity ◽  
Wide Range ◽  
Growth Of Bacteria

Abstract The abuse of antibiotics is becoming more serious as antibiotic use has increased. The sulfa antibiotics, sulfamerazine (SM1) and sulfamethoxazole (SMZ), are frequently detected in a wide range of environments. The interaction between SM1/SMZ and bacterial diversity in drinking water was investigated in this study. The results showed that after treatment with SM1 or SMZ at four different concentrations, the microbial community structure of the drinking water changed statistically significantly compared to the blank sample. At the genus level, the proportions of the different bacteria in drinking water may affect the degradation of the SM1/SMZ. The growth of bacteria in drinking water can be inhibited after the addition of SM1/SMZ, and bacterial community diversity in drinking water declined in this study. Furthermore, the resistance gene sul2 was induced by SM1 in the drinking water.

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