Ecological segregation of systematically related stream insects

1969 ◽  
Vol 47 (4) ◽  
pp. 691-694 ◽  
Author(s):  
P. R. Grant ◽  
R. J. Mackay
Keyword(s):  
Jaccard Coefficient ◽  
Congeneric Species ◽  
Ecological Segregation ◽  
Stream Insects ◽  
Ecological Difference

Insects from a stream at Mont St. Hilaire, Quebec, were sampled monthly for 1 year. The degree of ecological difference between congeneric species in three orders was assessed by using a "coefficient of separation", similar to a modified Jaccard coefficient. It was found that species differed most in their season of occurrence, least in the substrates they occupied. The significance of this result in terms of the avoidance of competition is considered.

Erratum: Ecological segregation of systematically related stream insects

1970 ◽  
Vol 48 (1) ◽  
pp. 183-183
Author(s):  
P. R. Grant ◽  
R. J. Mackay
Keyword(s):  
Ecological Segregation ◽  
Stream Insects

Llandovery (Early Silurian) orthide brachiopod associations from Anticosti Island, eastern CanadaThis article is one of a series of papers published in this Special Issue on the theme The dynamic reef and shelly communities of the Paleozoic. This Special is in honour of our colleague and friend Paul Copper.

2008 ◽  
Vol 45 (2) ◽  
pp. 189-201 ◽  
Author(s):  
Rong-Yu Li ◽  
Trevor Allen
Keyword(s):  
Cluster Analysis ◽  
Water Depth ◽  
Binary Data ◽  
Species Level ◽  
Jaccard Coefficient ◽  
Congeneric Species ◽  
Special Issue ◽  
Storm Wave ◽  
Anticosti Island ◽  
Future Reference

Five Llandovery orthide brachiopod associations, through cluster analysis, are delineated on Anticosti Island. The Levenea – Dicoelosia Association (A), occurring in the Goéland and Richardson members of the lower Jupiter Formation, represents a deep-water setting around or below the maximum storm wave base. The Flabellitesia – Dalejina Association (B), appearing in the Cybèle, Ferrum, and Pavillon members of the upper Jupiter Formation, indicates water depth in between the maximum and normal storm wave bases. The Isorthis ( Ovalella ) Association (C1), present in the Fox Point Member of Becscie Formation, corresponds to the shallower water setting around the normal storm wave base. The Mendacella bleikeriensis Association (C2), occurring in the Innommée, Sandtop, and Macgilvray members of Gun River Formation, characterizes the water depth slightly below the normal storm wave base. The Mendacella udauberis Association (D), appearing in the Merrimack Formation, signifies a water depth around the maximum storm wave base. The water depth indication of these associations may bear potential as future reference for other regions, but attention should be paid to the species level as some congeneric species can belong to different associations of different depth. The cluster analysis on orthide collections based on binary data demonstrates that statistical methods, Jaccard coefficient and Ward’s method of clustering, are practical and effective to delineate large brachiopod collections on Anticosti Island.

Optimal Model-Free Approach Based on MDL and CHL for Active Brain Identification in fMRI Data Analysis

2020 ◽  
Vol 16 ◽  
Author(s):  
Hussain A. Jaber ◽  
Ilyas Çankaya ◽  
Hadeel K. Aljobouri ◽  
Orhan M. Koçak ◽  
Oktay Algin
Keyword(s):  
Data Analysis ◽  
Time Course ◽  
Extreme Values ◽  
Statistical Parametric Mapping ◽  
Fmri Data ◽  
Cluster Center ◽  
Jaccard Coefficient ◽  
Neural Gas ◽  
Model Free ◽  
Clustering Approach

Background: Cluster analysis is a robust tool for exploring the underlining structures in data and grouping them with similar objects. In the researches of Functional Magnetic Resonance Imaging (fMRI), clustering approaches attempt to classify voxels depending on their time-course signals into a similar hemodynamic response over time. Objective: In this work, a novel unsupervised learning approach is proposed that relies on using Enhanced Neural Gas (ENG) algorithm in fMRI data for comparison with Neural Gas (NG) method, which has yet to be utilized for that aim. The ENG algorithm depends on the network structure of the NG and concentrates on an efficacious prototype-based clustering approach. Methods: The comparison outcomes on real auditory fMRI data show that ENG outperforms the NG and statistical parametric mapping (SPM) methods due to its insensitivity to the ordering of input data sequence, various initializations for selecting a set of neurons, and the existence of extreme values (outliers). The findings also prove its capability to discover the exact and real values of a cluster number effectively. Results: Four validation indices are applied to evaluate the performance of the proposed ENG method with fMRI and compare it with a clustering approach (NG algorithm) and model-based data analysis (SPM). These validation indices include the Jaccard Coefficient (JC), Receiver Operating Characteristic (ROC), Minimum Description Length (MDL) value, and Minimum Square Error (MSE). Conclusion: The ENG technique can tackle all shortcomings of NG application with fMRI data, identify the active area of the human brain effectively, and determine the locations of the cluster center based on the MDL value during the process of network learning.

scholarly journals Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yuping Li ◽  
Xiaoju Liang ◽  
Xuguo Zhou ◽  
Yu An ◽  
Ming Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Stage ◽  
Reference Genes ◽  
Developmental Stages ◽  
Individual Factors ◽  
Congeneric Species ◽  
Spatio Temporal ◽  
The Stability ◽  
Different Tissues ◽  
Selection Of

AbstractGlycyrrhiza, a genus of perennial medicinal herbs, has been traditionally used to treat human diseases, including respiratory disorders. Functional analysis of genes involved in the synthesis, accumulation, and degradation of bioactive compounds in these medicinal plants requires accurate measurement of their expression profiles. Reverse transcription quantitative real-time PCR (RT-qPCR) is a primary tool, which requires stably expressed reference genes to serve as the internal references to normalize the target gene expression. In this study, the stability of 14 candidate reference genes from the two congeneric species G. uralensis and G. inflata, including ACT, CAC, CYP, DNAJ, DREB, EF1, RAN, TIF1, TUB, UBC2, ABCC2, COPS3, CS, R3HDM2, were evaluated across different tissues and throughout various developmental stages. More importantly, we investigated the impact of interactions between tissue and developmental stage on the performance of candidate reference genes. Four algorithms, including geNorm, NormFinder, BestKeeper, and Delta Ct, were used to analyze the expression stability and RefFinder, a comprehensive software, provided the final recommendation. Based on previous research and our preliminary data, we hypothesized that internal references for spatio-temporal gene expression are different from the reference genes suited for individual factors. In G. uralensis, the top three most stable reference genes across different tissues were R3HDM2, CAC and TUB, while CAC, CYP and ABCC2 were most suited for different developmental stages. CAC is the only candidate recommended for both biotic factors, which is reflected in the stability ranking for the spatio (tissue)-temporal (developmental stage) interactions (CAC, R3HDM2 and DNAJ). Similarly, in G. inflata, COPS3, R3HDM2 and DREB were selected for tissues, while RAN, COPS3 and CS were recommended for developmental stages. For the tissue-developmental stage interactions, COPS3, DREB and ABCC2 were the most suited reference genes. In both species, only one of the top three candidates was shared between the individual factors and their interactions, specifically, CAC in G. uralensis and COPS3 in G. inflata, which supports our overarching hypothesis. In summary, spatio-temporal selection of reference genes not only lays the foundation for functional genomics research in Glycyrrhiza, but also facilitates these traditional medicinal herbs to reach/maximize their pharmaceutical potential.

scholarly journals Limitation of current probe design for oligo-cross-FISH, exemplified by chromosome evolution studies in duckweeds

Chromosoma ◽  
2021 ◽  
Vol 130 (1) ◽  
pp. 15-25
Author(s):  
Phuong T. N. Hoang ◽  
Jean-Marie Rouillard ◽  
Jiří Macas ◽  
Ivona Kubalová ◽  
Veit Schubert ◽  
...  
Keyword(s):  
Growth Rate ◽  
Chromosome Number ◽  
Chromosome Evolution ◽  
Sequence Similarity ◽  
Flowering Plants ◽  
The Other ◽  
Probe Design ◽  
Congeneric Species ◽  
Specific Design ◽  
Spirodela Polyrhiza

AbstractDuckweeds represent a small, free-floating aquatic family (Lemnaceae) of the monocot order Alismatales with the fastest growth rate among flowering plants. They comprise five genera (Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia) varying in genome size and chromosome number. Spirodela polyrhiza had the first sequenced duckweed genome. Cytogenetic maps are available for both species of the genus Spirodela (S. polyrhiza and S. intermedia). However, elucidation of chromosome homeology and evolutionary chromosome rearrangements by cross-FISH using Spirodela BAC probes to species of other duckweed genera has not been successful so far. We investigated the potential of chromosome-specific oligo-FISH probes to address these topics. We designed oligo-FISH probes specific for one S. intermedia and one S. polyrhiza chromosome (Fig. 1a). Our results show that these oligo-probes cross-hybridize with the homeologous regions of the other congeneric species, but are not suitable to uncover chromosomal homeology across duckweeds genera. This is most likely due to too low sequence similarity between the investigated genera and/or too low probe density on the target genomes. Finally, we suggest genus-specific design of oligo-probes to elucidate chromosome evolution across duckweed genera.

scholarly journals Riparian forestry management and adult stream insects

2004 ◽  
Vol 8 (3) ◽  
pp. 545-549 ◽  
Author(s):  
R. A. Briers ◽  
J. H. R. Gee
Keyword(s):  
Riparian Vegetation ◽  
Management Practices ◽  
Food Sources ◽  
Tree Cover ◽  
Strong Impact ◽  
Riparian Management ◽  
Stream Insects ◽  
Larval Stages ◽  
Forestry Management ◽  
Coniferous Plantation

Abstract. The impacts of coniferous plantation forestry on the biology of upland streams in the UK are firmly established. Whilst benthic communities have been well studied, very little research has considered the impacts of riparian forestry management on adult stream insects, yet the essentially terrestrial adult (reproductive) phase may be important in determining the abundance and distribution of larval stages. Riparian vegetation has a potentially strong impact on survival and success of adult stages through alteration of microclimate, habitat structure and potential food sources, in addition to effects carried over from larval stages. Here, current riparian management strategies are analysed in the light of available information on the ecology of adult stream insects. On the whole, management practices appear to favour adult stream insects, although an increase in tree cover in riparian areas could be beneficial, by providing more favourable microclimatic conditions for adults. This conclusion is drawn based on rather limited information, and the need for further research into the effects of riparian forestry management on adult stream insects is highlighted. Keywords: microclimate, plantation, life history, riparian vegetation

A modelling approach to the investigation of the effects of the Minoan supervolcanic eruption on Aegian sand fly diversity

The Holocene ◽  
2021 ◽  
pp. 095968362110259
Author(s):  
Attila J Trájer
Keyword(s):  
Bronze Age ◽  
Coefficient Matrix ◽  
Climatic Conditions ◽  
Sand Fly ◽  
Jaccard Coefficient ◽  
Catastrophic Event ◽  
Heat Map ◽  
Aegean Islands ◽  
Minoan Eruption ◽  
Modelling Approach

The late Bronze Age eruption of the Thera volcano was among the largest eruptions of the Holocene era. This catastrophic event might perish all organisms from the ancient Santorini and could seriously impact the sand fly fauna of the Aegean islands. To investigate these effects, the survival possibility of the sand fly fauna in the Santorini islands and the biogeographic investigation of the sand fly fauna of eleven Aegean islands were conducted. It was found that only the south and east slopes of the massifs of Thira could provide refuge for sand fly populations. The expression-based heat map of the Jaccard coefficient matrix data showed that the Santorini islands and their neighbouring Anafi, Folegandros had clearly different z-score patterns compared to the other islands. It could be a late sign of the devastating effect of the Minoan eruption and/or the consequence of the distance of these islands from the mainland. Neither the glacial seashore patterns nor the geographic-climatic conditions can explain the present sand fly fauna of the Aegean Archipelago. If the sand fly populations of ancient Santorini survived the Minoan cataclysm, it could indicate that the environmental tolerance and the resilience of the sand fly populations can be high, and local geological and geomorphological conditions can play a greater role in the survival of sand fly species than previously assumed.

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