Putting Diversity Indices into Practice

Objective: To calculate the monthly relative abundance of Thysanoptera species, according to the Margalef, Simpson and Shannon-Wiener diversity indices. Design / Methodology / Approach: The work was carried out in three geographic units with conventional management, during January-December, 2019 in the Reserva de la Biosfera Zicuirán-Infiernillo (Biosphere Reserve), Michoacán, Mexico. In each unit, 10 trees were selected through simple random sampling. Thrips counts were performed on ten shoots per tree every 15 d, for a total of 7200 shoots in the three geographic units. Thysanoptera individuals were placed in entomological jars. The variables were: number of thrips collected per shoot in sampled tree and geographic unit (orchard). To estimate the specific richness and structure of species, the program "calculation of diversity indices DIVERS" was used. Results: In the three geographical units studied, the recorded presence of Thysanoptera accounted for 12 to 17 species. For Nueva Italia 12 recorded species, two were permanent (16.66%), five abundant (41.66%), one scarce (8.3%) and four rare (33.33%). In Zicuirán, three species were permanent (17.64%), six abundant (35.29%), two scarce (11.76%) and six rare (35.29%). In Los Hoyos, four species were permanent (26.66%), four abundant (26.66%) and seven rare (46.66%). The abundance of species was represented by the genus Frankliniella and the species Scolothrips sexmaculatus and Scirtothrips citri. The highest species richness and abundance was found from January to May. In October and November, the value of the calculated indices was zero, which shows less richness and abundance of individuals. The best species uniformity was recorded during January and December, which meant a more stable and homogeneous relation. Study limitations/Implications. Pest resurgence, presence of Candidatus Liberibacter spp. and its vector Diaphorina citri. Findings / Conclusions: in Nueva Italia, 12 species were taxonomically determined; in Los Hoyos 15, and in Zicuirán 17 species, which are reported for the first time in the state of Michoacán, Mexico. At the geographic unit "Los Hoyos" diversity was higher, uniform and stable.

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Climate resilience through natural regeneration in degraded natural forests of south-eastern hilly region of Bangladesh

Bangladesh Journal of Botany ◽

10.3329/bjb.v48i3.47720 ◽

2019 ◽

Vol 48 (3) ◽

pp. 417-425

Author(s):

Md Khayrul Alam Bhuiyan ◽

Md Akhter Hossain ◽

Abdul Kadir Ibne Kamal ◽

Mohammed Kamal Hossain ◽

Mohammed Jashimuddin ◽

...

Keyword(s):

Tree Species ◽

Natural Regeneration ◽

Diversity Indices ◽

Acacia Auriculiformis ◽

Quantitative Structure ◽

Natural Forests ◽

Climate Resilience ◽

Hilly Region ◽

Major Cluster ◽

Ecological Dominance

A study was conducted by using 5m × 5m sized 179 quadrates following multistage random sampling method for comparative regenerating tree species, quantitative structure, diversity, similarity and climate resilience in the degraded natural forests and plantations of Cox's Bazar North and South Forest Divisions. A total of 70 regenerating tree species were recorded representing maximum (47 species) from degraded natural forests followed by 43 species from 0.5 year 39 species from 1.5 year and 29 species from 2.5 year old plantations. Quantitative structure relating to ecological dominance indicated dominance of Acacia auriculiformis, Grewia nervosa and Lithocarpus elegans seedlings in the plantations whereas seedlings of Aporosa wallichii, Suregada multiflora and Grewia nervosa in degraded natural forests. The degraded natural forests possess higher natural regeneration potential as showed by different diversity indices. The dominance-based cluster analysis showed 2 major cluster of species under one of which multiple sub-clusters of species exists. Poor plant diversity and presence of regenerating exotic species in the plantations indicated poor climate resilience of forest ecosystem in terms of natural regeneration.

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Tree Diversity Conservation Initiatives in Sacred Groves of Kathmandu Valley, Nepal

Nepal Journal of Science and Technology ◽

10.3126/njst.v19i1.29768 ◽

2020 ◽

Vol 19 (1) ◽

pp. 60-68

Author(s):

Laxmi Joshi Shrestha ◽

Mohan Devkota ◽

Bhuvan Keshar Sharma

Keyword(s):

Tree Species ◽

Management System ◽

Survey Methods ◽

Belief Systems ◽

Decisive Role ◽

Diversity Indices ◽

Kathmandu Valley ◽

Sacred Grove ◽

Sacred Groves ◽

The Government

The study was conducted in two sacred groves of Kathmandu Valley, Pashupati Sacred Grove, and Bajrabarahi Sacred Grove, aiming to analyze the diversity of tree species and their role in conserving biodiversity. Parallel transects with concentric circular plot survey methods were applied for data collection. During the study, 23 tree species belonging to 22 genera and 15 families were recorded in Pashupati sacred grove, whereas only 19 tree species belonging to 16 genera and 13 families were recorded from Bajrabarahi Sacred Grove. The Shannon-Weiner diversity indices were higher (H=1.91) in Pashupati Sacred Grove compared to Bajrabarahi Sacred Grove, with 1.80 Shanon-Weiner Indices. Three types of forest were recorded from Pashupati Sacred Grove, namely the Schima-Pyrus forest, Myrsine-Persea forest, and Quercus-Myrsine forest, and only one Neolitsiacuipala forest from Bajrabarahi Sacred Grove. The sacred grove is one of the pioneers and community-based management regimes of the forest resource management system. It plays a decisive role in biodiversity conservation as it associated with many taboos and belief systems, thus providing a better opportunity for conservation compared to that of the government management system.

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Aquatic and semi aquatic Hemiptera community of Sonebeel, the largest wetland of Assam, northeastern India

Journal of Threatened Taxa ◽

10.11609/jott.3440.10.13.12792-12799 ◽

2018 ◽

Vol 10 (13) ◽

pp. 12792-12799

Author(s):

Anupama Saha ◽

Susmita Gupta

Keyword(s):

Species Richness ◽

Pest Control ◽

Relative Abundance ◽

Species Distribution ◽

Diversity Indices ◽

Environmental Data ◽

Northeastern India ◽

Ecological Roles

Aquatic and semiaquatic Hemiptera bugs play significant ecological roles, and they are important indicators and pest control agents. Little information is currently available concerning its populations in southern Assam. This study assessed hemipterans in four sites of Sonebeel, the largest wetland in Assam (3458.12 ha at full storage level), situated in Karimganj District. The major inflow and outflow of the wetland are the rivers Singla and Kachua, respectively (the Kachua drains into the Kushiyara River). Samples were trapped with pond nets and were seasonally recorded. This study recorded a total of 28 species of aquatic and semiaquatic hemipterans belonging to 20 genera under nine families. Population, geographical and environmental data (e.g., rainfall) were used to assess the relative abundance of species, species richness and different diversity indices, and species distribution.

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Microbiota identified from preserved Anopheles

Malaria Journal ◽

10.1186/s12936-021-03754-7 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Bianca E Silva ◽

Zvifadzo Matsena Zingoni ◽

Lizette L. Koekemoer ◽

Yael L. Dahan-Moss

Keyword(s):

Microbial Diversity ◽

Vector Competence ◽

Mosquito Species ◽

Anopheles Funestus ◽

Cost Effective ◽

Diversity Indices ◽

Malaria Vectors ◽

Microbial Composition ◽

Culture Independent ◽

Culture Dependent

Abstract Background Mosquito species from the Anopheles gambiae complex and the Anopheles funestus group are dominant African malaria vectors. Mosquito microbiota play vital roles in physiology and vector competence. Recent research has focused on investigating the mosquito microbiota, especially in wild populations. Wild mosquitoes are preserved and transported to a laboratory for analyses. Thus far, microbial characterization post-preservation has been investigated in only Aedes vexans and Culex pipiens. Investigating the efficacy of cost-effective preservatives has also been limited to AllProtect reagent, ethanol and nucleic acid preservation buffer. This study characterized the microbiota of African Anopheles vectors: Anopheles arabiensis (member of the An. gambiae complex) and An. funestus (member of the An. funestus group), preserved on silica desiccant and RNAlater® solution. Methods Microbial composition and diversity were characterized using culture-dependent (midgut dissections, culturomics, MALDI-TOF MS) and culture-independent techniques (abdominal dissections, DNA extraction, next-generation sequencing) from laboratory (colonized) and field-collected mosquitoes. Colonized mosquitoes were either fresh (non-preserved) or preserved for 4 and 12 weeks on silica or in RNAlater®. Microbiota were also characterized from field-collected An. arabiensis preserved on silica for 8, 12 and 16 weeks. Results Elizabethkingia anophelis and Serratia oryzae were common between both vector species, while Enterobacter cloacae and Staphylococcus epidermidis were specific to females and males, respectively. Microbial diversity was not influenced by sex, condition (fresh or preserved), preservative, or preservation time-period; however, the type of bacterial identification technique affected all microbial diversity indices. Conclusions This study broadly characterized the microbiota of An. arabiensis and An. funestus. Silica- and RNAlater®-preservation were appropriate when paired with culture-dependent and culture-independent techniques, respectively. These results broaden the selection of cost-effective methods available for handling vector samples for downstream microbial analyses.

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PSIX-6 Gastrointestinal microbiome of calves fed solid diets containing different levels and sources of NDF

Journal of Animal Science ◽

10.1093/jas/skaa278.729 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 418-419

Author(s):

Gercino F Virgínio Júnior ◽

Milaine Poczynek ◽

Ana Paula Silva ◽

Ariany Toledo ◽

Amanda Cezar ◽

...

Keyword(s):

Illumina Miseq ◽

Diversity Indices ◽

Dairy Calves ◽

Rrna Gene ◽

Gastrointestinal Microbiome ◽

Fecal Microbiome ◽

Miseq Platform ◽

Holstein Calves ◽

Ad Libitum ◽

Different Levels

Abstract Different levels and sources of NDF can modify the gastrointestinal microbiome. This study evaluated 18 Holstein calves housed in not-bedded suspended individual cages and fed one of three treatments: 22NDF - conventional starter containing 22% NDF (n = 7); 31NDF - starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22NDF+H - conventional starter with 22% NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily (24% CP; 18.5% fat; diluted to 12.5% solids), divided into two meals, being weaned at 8th week of age. After weaning, animals were housed in tropical shelters, fed with the respective solid diet and coast-cross hay ad libitum for all treatments. To evaluate the microbiome, ruminal fluid samples were collected using a modified Geishauser oral probe at weeks 2, 4, 6, 8 and 10, two hours after the morning feeding, and fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. Ruminal microbiome had no differences in diversity for the effects of weeks, treatments or interaction of both factors (Table 1). In feces, the diversity indices and evenness were higher for 22NDF+H when compared to 22NDF, with no difference for 31NDF. All indices were significantly affected by calves age. At birth, calves had the greatest diversity and richness. Week 1 and 2 had less evenness and diversity. Bacteroidota, Firmicutes_A and Firmicutes_C were the most abundant phylum in rumen and feces. The supply of hay was only effective in modifying the fecal microbiome of dairy calves, suggesting a resilience in the ruminal microbiome.

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Responses and Indicators of Composition, Diversity, and Productivity of Plant Communities at Different Levels of Disturbance in a Wetland Ecosystem

Diversity ◽

10.3390/d13060252 ◽

2021 ◽

Vol 13 (6) ◽

pp. 252

Author(s):

Tingting Duan ◽

Jing Zhang ◽

Zhengjun Wang

Keyword(s):

Plant Community ◽

Plant Communities ◽

Leisure Activity ◽

Local Environment ◽

Diversity Indices ◽

Soil Parameters ◽

Grazing Tolerance ◽

Organic Matter Concentration ◽

Drought Tolerant ◽

Different Levels

Grassland tourism is a very popular leisure activity in many parts of the world. However, the presence of people in these areas causes disturbance to the local environment and grassland resources. This study analyzes the composition, diversity, and productivity under different levels of disturbance of the plant communities in the Kangxi Grassland Tourist Area and the Yeyahu Wetland Nature Reserve of Beijing, China. It aims to identify indicators of plant communities and their responses to different levels of disturbance. Our analysis shows that the plant community density and coverage have a certain compensatory increase under disturbed conditions. With the increase in disturbances, more drought-tolerant species have appeared (increased by 5.7%), some of which have become the grazing-tolerance indicator species in the trampled grazed area (TGA). For plant community productivity, biomass and height are good indicators for distinguishing different disturbances (p < 0.05). In addition, several diversity indices reveal the change of plant communities from different perspectives (three of the four indices were significant at the p < 0.05 level). For soil parameters, soil water content and organic matter concentration help to indicate different disturbance levels (the former has a 64% change). Moreover, the standard deviation of the plant community and soil parameters is also a good indicator of their spatial variability and disturbance levels, especially for the TGA. Our analysis confirms that the indicators of productivity, diversity, and soil parameters can indicate the disturbance level in each subarea from different perspectives. However, under disturbed conditions, a comprehensive analysis of these indicators is needed before we can accurately understand the state of health of the plant community.

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On a Variational Definition for the Jensen-Shannon Symmetrization of Distances Based on the Information Radius

Entropy ◽

10.3390/e23040464 ◽

2021 ◽

Vol 23 (4) ◽

pp. 464

Author(s):

Frank Nielsen

Keyword(s):

Diversity Index ◽

Diversity Indices ◽

Shannon Diversity Index ◽

Probability Measures ◽

Variational Optimization ◽

Shannon Diversity ◽

Concept Of Information ◽

Jensen Shannon Divergence

We generalize the Jensen-Shannon divergence and the Jensen-Shannon diversity index by considering a variational definition with respect to a generic mean, thereby extending the notion of Sibson’s information radius. The variational definition applies to any arbitrary distance and yields a new way to define a Jensen-Shannon symmetrization of distances. When the variational optimization is further constrained to belong to prescribed families of probability measures, we get relative Jensen-Shannon divergences and their equivalent Jensen-Shannon symmetrizations of distances that generalize the concept of information projections. Finally, we touch upon applications of these variational Jensen-Shannon divergences and diversity indices to clustering and quantization tasks of probability measures, including statistical mixtures.

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Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus

Scientific Reports ◽

10.1038/s41598-021-81507-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hua Zha ◽

Fengping Liu ◽

Zongxin Ling ◽

Kevin Chang ◽

Jiezuan Yang ◽

...

Keyword(s):

Diabetes Mellitus ◽

Type 2 Diabetes ◽

Type 2 Diabetes Mellitus ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Diversity Indices ◽

Vital Role ◽

Rrna Gene ◽

Beta Glucosidase

AbstractType 2 diabetes mellitus (T2DM) influences the human health and can cause significant illnesses. The genitourinary microbiome profiles in the T2DM patients remain poorly understood. In the current study, a series of bioinformatic and statistical analyses were carried out to determine the multiple bacteria associated with the more dysbiotic genitourinary microbiomes (i.e., those with lower dysbiosis ratio) in T2DM patients, which were sequenced by Illumina-based 16S rRNA gene amplicon sequencing. All the genitourinary microbiomes from 70 patients with T2DM were clustered into three clusters of microbiome profiles, i.e., Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, with Cluster_3_T2DM at the most dysbiotic genitourinary microbial status. The three clustered T2DM microbiomes were determined with different levels of alpha diversity indices, and driven by distinct urinalysis variables. OTU12_Clostridiales and OTU28_Oscillospira were likely to drive the T2DM microbiomes to more dysbiotic status, while OTU34_Finegoldia could play a vital role in maintaining the least dysbiotic T2DM microbiome (i.e., Cluster_1_T2DM). The functional metabolites K08300_ribonuclease E, K01223_6-phospho-beta-glucosidase and K00029_malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) were most associated with Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, respectively. The characteristics and multiple bacteria associated with the more dysbiotic genitourinary microbiomes in T2DM patients may help with the better diagnosis and management of genitourinary dysbiosis in T2DM patients.

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Microbial community structure and trichloroethylene degradation in groundwater

Canadian Journal of Microbiology ◽

10.1139/w05-025 ◽

2005 ◽

Vol 51 (6) ◽

pp. 433-439 ◽

Cited By ~ 23

Author(s):

J A Humphries ◽

A M.H Ashe ◽

J A Smiley ◽

C G Johnston

Keyword(s):

Community Structure ◽

Clone Library ◽

Sequence Data ◽

Restriction Analysis ◽

Diversity Indices ◽

Department Of Energy ◽

Tetrazolium Chloride ◽

Degrading Bacteria ◽

Trichloroethylene Degradation ◽

Rdna Clone

Trichloroethylene (TCE) is a prevalent contaminant of groundwater that can be cometabolically degraded by indigenous microbes. Groundwater contaminated with TCE from a US Department of Energy site in Ohio was used to characterize the site-specific impact of phenol on the indigenous bacterial community for use as a possible remedial strategy. Incubations of14C-TCE-spiked groundwater amended with phenol showed increased TCE mineralization compared with unamended groundwater. Community structure was determined using DNA directly extracted from groundwater samples. This DNA was then analyzed by amplified ribosomal DNA restriction analysis. Unique restriction fragment length polymorphisms defined operational taxonomic units that were sequenced to determine phylogeny. DNA sequence data indicated that known TCE-degrading bacteria including relatives of Variovorax and Burkholderia were present in site water. Diversity of the amplified microbial rDNA clone library was lower in phenol-amended communities than in unamended groundwater (i.e., having Shannon–Weaver diversity indices of 2.0 and 2.2, respectively). Microbial activity was higher in phenol-amended ground water as determined by measuring the reduction of 2-(p-iodophenyl)-3(p-nitrophenyl)-5-phenyl tetrazolium chloride. Thus phenol amendments to groundwater correlated with increased TCE mineralization, a decrease in diversity of the amplified microbial rDNA clone library, and increased microbial activity.Key words: community structure, trichloroethylene, degradation, groundwater.

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