scholarly journals Evaluation of the estimate bias magnitude of the Rao’s quadratic diversity index

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5211
Author(s):  
Youhua Chen ◽  
Yongbin Wu ◽  
Tsung-Jen Shen
Keyword(s):  
Diversity Index ◽  
Species Abundance ◽  
Diversity Indices ◽  
Ecological Community ◽  
Practical Applications ◽  
True Value ◽  
Standard Calculation ◽  
Number Of Individuals ◽  
Phylogenetic Ecology ◽  
Species Abundance Data

Rao’s quadratic diversity index is one of the most widely applied diversity indices in functional and phylogenetic ecology. The standard way of computing Rao’s quadratic diversity index for an ecological assemblage with a group of species with varying abundances is to sum the functional or phylogenetic distances between a pair of species in the assemblage, weighted by their relative abundances. Here, using both theoretically derived and observed empirical datasets, we show that this standard calculation routine in practical applications will statistically underestimate the true value, and the bias magnitude is derived accordingly. The underestimation will become worse when the studied ecological community contains more species or the pairwise species distance is large. For species abundance data measured using the number of individuals, we suggest calculating the unbiased Rao’s quadratic diversity index.

scholarly journals Distance Effects on Diversity and Abundance of the Flower Visitors of Ocimum kilimandscharicum in the Kakamega Forest Ecosystem

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Hellen K. Mandela ◽  
Mugatsia H. Tsingalia ◽  
Mary Gikungu ◽  
Wilbur M. Lwande
Keyword(s):  
Species Diversity ◽  
Diversity Index ◽  
Land Use Changes ◽  
Species Abundance ◽  
Diversity Indices ◽  
Forest Edge ◽  
Flower Visitors ◽  
Kakamega Forest ◽  
Species Invasions ◽  
Wiener Diversity Index

Pollination is an important ecosystem service in the maintenance of biodiversity and most importantly in food production. Pollination is on the decline due to habitat loss, exotic species invasions, pollution, overharvesting, and land use changes. This study analyzed the abundance and diversity of flower visitors’ of Ocimum kilimandscharicum in Kakamega forest with increasing distance from the forest edge. Data were collected through direct observation and sweep netting. Six study sites were identified along two transects each 2.5 km long and labeled A to F. Distance in metres from the forest edge to each site was A=221, B=72, C=83, D=198, E=113, and F=50. Sampling was done from 7:30 am to 4:00 pm, three days in a week for five months consecutively. Diversity indices of different flower visitors were calculated using the Shannon-Wiener diversity index. One-way analysis of variance was used to compare differences between sites and a two-sample t-test was used to identify mean significant differences in species diversity between the closest and the furthest sites. A total of 645 individuals belonging to 35 species were captured from 4 families. The highest diversity was at site F (H’= 2.38) which was closest to the forest edge and the lowest diversity was from site A (H’=1.44) which was furthest from the forest edge. Distance from the forest edge significantly influenced species diversity (F(3, 20)=14.67, p=0.024). Distance from the forest edge also significantly influenced species abundance between the furthest sites A, D, and E and the nearest sites F, B, and C to the forest edge (t=4.177; p=0.0312) and species richness (t=3.2893; p=0.0187). This study clearly demonstrates that Ocimum kilimandscharicum flower visitors play essential roles in pollination and their higher number of visits translates into higher numbers of seeds set. Many of these pollinators are associated with the forest and hence the need to conserve the Kakamega forest as a source pool for pollinators.

scholarly journals Diversitas Tumbuhan Liar Pada Lahan Jagung (Zea mays L.) di Desa Bungbungan Kecamatan Bluto Kabupaten Sumenep

2020 ◽  
Vol 6 (1) ◽  
pp. 54-60
Author(s):  
Khoiratul Hasanah ◽  
Ari Hayati ◽  
Hasan Zayadi
Keyword(s):  
Zea Mays ◽  
Agricultural Land ◽  
Zea Mays L ◽  
Crop Yields ◽  
Diversity Index ◽  
Diversity Indices ◽  
Wild Plants ◽  
Wild Plant ◽  
Cultivated Plants ◽  
Number Of Individuals

Wild plants are plants whose presence on agricultural land can reduce crop yields. Losses due to wild plants to cultivated plants vary depending on the type of plant cultivated, climate, species of wild plants and technical cultivation applied. This study aims to determine the diversity of wild plants in the land of maize (Zea mays L.) in Bung-bungan Village Bluto District Sumenep Regency. This method uses a descriptive exploratory method, for each wild plant found in ± 3600 m2 of corn land. Sampling of wild plants using a 4x4 m plot method. The measured data includes the number of species and the number of individuals calculating important values ​​and diversity indices. The results of the study showed that the Shannon-Wienner Diversity Index analysis of the highest value in maize plants in plantations was found in land II, which was 2.678 indicating moderate diversity, categorized as moderate because there were not too many wild plants on maize.  Keywords: Corn, diversity, wild plants,  ABSTRAK Tumbuhan liar merupakan tumbuhan yang kehadirannya pada lahan pertanian dapat menurunkan hasil tanaman. Kerugian akibat tumbuhan  liar terhadap tanaman budidaya beragam bergantung dari jenis tanaman yang diusahakan, iklim, jenis tumbuhan  liar dan teknis budidaya yang diterapkan. Penelitian ini bertujuan untuk mengetahui diversitas tumbuhan liar di lahan jagung (Zea mays L.) di Desa Bung-bungan Kecamatan Bluto Kabupaten Sumenep. Metode ini menggunakan metode deskriptif eksploratif, terhadap setiap tumbuhan liar yang ditemukan pada lahan jagung seluas ±3600 m2. Pengambilan sampel tumbuhan liar menggunakan metode plot berukuran 4x4 m. Data yang diukur meliputi jumlah spesies dan jumlah individu menghitung nilai penting dan indeks diversitas. Hasil penelitian menunjukkan analisis Indeks Keanekaragaman Shannon-Wienner tumbuhan liar nilai tertinggi pada tanaman jagung di lkebun terdapat pada lahan II yaitu 2,678 menunjukkan keanekaragaman sedang, di kategorikan sedang karena jenis tanaman liar yang ada pada lahan jagung tidak terlalu banyak. Kata kunci: Jagung, Diversitas, Tanaman liar

scholarly journals Tree species diversity in the forest of Renikhayong para village in Bandarban, Bangladesh: a case study

2020 ◽  
Vol 5 (2) ◽  
pp. 115-126 ◽  
Author(s):  
M Jannat ◽  
M Kamruzzaman ◽  
MA Hossain ◽  
MK Hossain
Keyword(s):  
Species Diversity ◽  
Tree Species ◽  
Diversity Index ◽  
Sustainable Use ◽  
Tree Height ◽  
Diversity Indices ◽  
Tree Species Diversity ◽  
Height Range ◽  
Hill District ◽  
Number Of Individuals

The study was conducted to explore tree species diversity of Renikhayong para Village Common Forest (VCF) of Bandarban hill district. Stratified random sampling was carried out to assess the tree species diversity of the VCF. Renikhayong Para VCF with an area of 40 acres of land has more than 85 tree species belonging to 31 families, where Euphorbiaceae family was dominant containing 11 species followed by Rubiaceae (7 species), Moraceae (7 species), Meliaceae (5 species), Mimosaceae (5 species), Combretaceae (4 species), Lauraceae (4 species) and Anacardiaceae (3 species). Dominant tree species was Grewia nervosa. Renikhayong para VCF has diverse floristic resources that are known from the Shannon-Wiener’s diversity index (4.007), Simpson’s diversity index (0.028), Margalef’s richness index (13.21) and Species evenness index (0.90). However, number of species and number of individuals both were highest in the height range of 5 - <10 m. Similar trend was observed in dbh classes. Number of individuals were highest in dbh range of 5 - <15 cm and the lowest in ≥ 55 cm. The results depict the presence of maximum small trees in the VCF and decreasing the number of trees with the increase of tree height (m) and dbh (cm). Presence of diverse tree species and diversity indices indicate the importance and potential of the VCF for conservation and sustainable use. J. Biodivers. Conserv. Bioresour. Manag. 2019, 5(2): 115-126

scholarly journals Transposable element diversity remains high in gigantic genomes

2021 ◽  
Author(s):  
Ava Louise Haley ◽  
Rachel Lockridge Mueller
Keyword(s):  
Diversity Index ◽  
Repetitive Sequences ◽  
Diversity Indices ◽  
Community Diversity ◽  
Pairwise Comparisons ◽  
Ecological Community ◽  
Oxford Nanopore ◽  
A Genome ◽  
Diverse Community ◽  
Low Coverage

ABSTRACTTransposable elements (TEs) are repetitive sequences of DNA that replicate and proliferate throughout genomes. Taken together, all the TEs in a genome form a diverse community of sequences, which can be studied to draw conclusions about genome evolution. TE diversity can be measured using models for ecological community diversity that consider species richness and evenness. Several models predict TE diversity decreasing as genomes expand because of selection against ectopic recombination and/or competition among TEs to garner host replicative machinery and evade host silencing mechanisms. Salamanders have some of the largest vertebrate genomes and highest TE loads. Salamanders of the genus Plethodon, in particular, have genomes that range in size from 20 to 70 Gb. Here, we use Oxford Nanopore sequencing to generate low-coverage genomic sequences for four species of Plethodon that encompass two independent genome expansion events, one in the eastern clade (P. cinereus, 29.3 Gb vs. P. glutinosus, 38.9 Gb) and one in the western clade (P. vehiculum, 46.4 Gb vs P. idahoensis, 67.0 Gb). We classified the TEs in these genomes and found ~52 TE superfamilies, accounting for 27-32% of the genomes. We calculated Simpson’s and Shannon’s diversity indices to quantify overall TE diversity. In both pairwise comparisons, the diversity index values for the smaller and larger genome were almost identical. This result indicates that, when genomes reach extremely large sizes, they maintain high levels of TE diversity at the superfamily level, in contrast to predictions made by previous studies on smaller genomes.

scholarly journals FLORISTIC STUDY ON ANGIOSPERMS SURROUNDING THE MEDAVAKKAM LAKE, CHENGALPATTU DISTRICT, TAMIL NADU, INDIA

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Amzad Basha Kolar ◽  
Palanivel. S, ◽  
M. Sheik Noor Mohamed ◽  
S. Sheik Mohamed ◽  
M. Shareef Khan ◽  
...  
Keyword(s):  
Native Species ◽  
Tamil Nadu ◽  
Diversity Index ◽  
Species Abundance ◽  
Wiener Index ◽  
Diversity Indices ◽  
Economic Importance ◽  
The Family ◽  
Species Diversity Indices

Biodiversity plays a significant role in maintaining the ecosystem for their sustainable utilization. A preliminary survey was conducted to document the diversity and economic importance of the angiosperms around the Medavakkam Lake, Chengalpattu district, Tamil Nadu. The study area act as a seed bank for native species and provide suitable conditions to endemic and certain endangered species. Diversity indices of the study area was found significant, in which the species abundance, richness and evenness were found. A total of 71 species belonging to 36 families of angiosperms were documented. Among which the Dicotyledons plants were 87.32% and monocotyledon plants were 12.67% of total flora reported. The study area was dominated by the family fabaceae (14.1%) with ten species. Habit wise classification of plants reveal that trees are predominant with 32%, followed by hers (25%), Shrubs (21%), Climbers (13%), undershrubs (6%) and grasses (3%). The Simpson Diversity Index, Shannon Wiener Index and evenness index of the study area is 0.777, 1.5634 and 0.8725 respectively. These plants was found with enormous benefits to the mankind such as medicinal, edible, timber, ornamental, oil and other sources. This investigation divulges that the Medavakkam Lake has substantial angiosperm diversity served as major source for native plants having greater economic importance.

scholarly journals DIVERSITY OF MOLLUSCA BIVALVIA ALONG THE BEACHES SAND OF KARANG MAS, MUARA GADING MAS, MARINGGAI REGENCY, EAST OF LAMPUNG

2021 ◽  
Vol 6 (2) ◽  
pp. 83-90
Author(s):  
Aprilia Indah M Riani ◽  
Suparmono Suparmono ◽  
Darma Yuliana ◽  
Henny Wijayanti
Keyword(s):  
Sampling Method ◽  
Sea Water ◽  
Diversity Index ◽  
Species Abundance ◽  
Quality Standards ◽  
Chemical Physics ◽  
Water Quality Standards ◽  
Chemical Conditions ◽  
Method Analysis ◽  
Species Abundance Data

East Lampung Regency has a coastal area of East Lampung with 316 ha. One of the coastal tourist areas owned by East Lampung Regency is Shells Mas Beach. This beach has a fairly long coastline where there are a lot of bivalves, but the inventory of the types of bivalves on the beach.The purpose of the research is to analyze both the species diversities of bivalves and physical also chemical conditions of the waters. The research methodology used purposive sampling method analysis of species abundance data, diversity index, and index dominance. From the result of the bivalve diversities on the coast, bivalve the most common found are is Matra grandis,it is found out that there is no dominating bivalve amongst them due to below normal dominating rate that is 0,08-0,16 to be considered low level (00,00<C≤0,30); middle with diversity index 2,18–2,70 (2<H’≤3); high with index diversity 0,85–0,94 (E>0,6). The highest abundance value at station 1 is 4787.01 ind/m3 and the lowest species abundance value at station 3 is138.75 ind/m3. From the results of the chemical physics measurements, it shows that it still is in the range of sea water quality standards. The Bivalve diversity relationship shows a positive correlation to the parameters of salinity, grain size, and sediment TSS. Meanwhile, it shows negative correlation for parameters DO, pH and temperature.

scholarly journals Coral Fishes of Chaetodontidae in North Salawaty and South Batanta Districts, Raja Ampat Regency, West Papua Province

2017 ◽  
Vol 5 (1) ◽  
pp. 97
Author(s):  
Ari B. Rondonuwu ◽  
Lawrence J. L. Lumingas ◽  
Nego E. Bataragoa
Keyword(s):  
Diversity Index ◽  
Species Abundance ◽  
Ecological Indices ◽  
Total Abundance ◽  
Visual Census ◽  
Number Of Species ◽  
West Papua ◽  
Coral Fish ◽  
The Right ◽  
Number Of Individuals

The objective of this study was to examine the general condition of Chaetodontidae fish in North Salawati and South Batanta Districts, i.e. species composition and number of species, abundance and density of individuals, as well as ecological indices.  Data were collected by using Visual Census method with a 70 m-transect, width 2.5 m to the left and 2.5 m to the right. Therefore, the total area observed was 350 m2. This study found 6 (six) genera with 32 species and total abundance of 791 individuals, Chaetodon, Chelmon, Coradion, Heniochus, Hemitaurichthys and Forcipiger.  Based on number of species, the studied area had highly diverse coral fish species.  Chaetodon lunulatus and C. kleinii were the most species found with the highest number of individuals. Station KBS01 had highest number of species and individual abundance. Diversity index was 2 < H’ < 3 meaning that the coral fish communities in both districts were stable.Keywords : Coral Fishes, Chaetodontidae, Raja Ampat Island. Abstrak Tujuan penelitian ini secara umum adalah untuk mengkaji kondisi existing ikan karang famili chaetodontidae di Kecamatan Salawati Utara dan Kecamatan Batanta Selatan, yaitu komposisi dan jumlah spesies, kelimpahan individu, dan indeks ekologi. Pengambilan data dilakukan menggunakan metode Sensus Visual dengan panjang garis transek 70 m, lebar pengamatan 2,5 meter ke kiri dan 2,5 meter ke kanan.  Dengan demikian, luas areal pengamatan adalah 350 m2. Penelitian ini menemukan  6 (enam) genera dengan 32 spesies dan kelimpahan individu total 791 individu terdiri dari Chaetodon, Chelmon, Coradion, Heniochus, Hemitaurichthys dan Forcipiger dengan 32 spesies. Oleh Karena itu, wilayah ini  memiliki keanekaragaman jenis ikan karang yang tinggi dimana Chaetodon lunulatus dan C. kleinii  paling sering ditemukan dengan jumlah individu tertinggi.   Stasiun KBS01 memiliki jumlah spesies dan kelimpahan individu tertinggi. Nilai indeks keanekaragaman berada pada kisaran    2 < H’< 3 yang berarti bahwa komunitas ikan karang di kecamatan ini  dinyatakan stabil.  

scholarly journals Diversity of the Arthropod edaphic fauna in preserved and managed with pasture areas in Teresina-Piauí-Brazil

2013 ◽  
Vol 73 (3) ◽  
pp. 483-489 ◽  
Author(s):  
RA. Luz ◽  
LS. Fontes ◽  
SRS. Cardoso ◽  
ÉFB. Lima
Keyword(s):  
Diversity Index ◽  
Diversity Indices ◽  
Similarity Coefficient ◽  
The State ◽  
Lack Of Information ◽  
Composition And Structure ◽  
Arthropod Fauna ◽  
Pasture Area ◽  
Number Of Individuals ◽  
The City

The soil fauna plays an important function over the processes of organic matter decomposition, nutrient cycling, ground aeration and fertility. Thus, studies on the composition and structure of such communities are important, considering moreover the lack of information in different regions of Brazil and mainly related to the state of Piauí. This study aimed to evaluate the density and diversity of the soil arthropod fauna in a Cerrado area in preservation conditions and in a pasture area. Both are situated in the city of Teresina, capital of the state of Piauí. Pitfall traps were used for sampling. Five stations with four traps were placed in each area. The traps were constituted by a 500 mL plastic cup containing a preserving solution made with 70% alcohol and 40% formalin. The traps were weekly changed by occasion of the collections. Eight samples were performed in the period between March and April 2007. The results were evaluated using the following variables: number of orders, number of families, total of species and total number of individuals. Evaluation of the Diversity Index and Similarity Coefficient were also performed. As result, the variables and diversity indices were slightly higher in the preserved area. However, the similarity coefficient showed only 10% similarity between both areas.

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

Entropy ◽  
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.

scholarly journals Can Habitat Quality Index Measured Using the InVEST Model Explain Variations in Bird Diversity in an Urban Area?

2021 ◽  
Vol 13 (10) ◽  
pp. 5747
Author(s):  
Dehuan Li ◽  
Wei Sun ◽  
Fan Xia ◽  
Yixuan Yang ◽  
Yujing Xie
Keyword(s):  
Habitat Quality ◽  
Quality Index ◽  
Empirical Studies ◽  
Species Abundance ◽  
Diversity Indices ◽  
Local Scale ◽  
Data Availability ◽  
Bird Diversity ◽  
Invest Model ◽  
Trade Offs

Biodiversity maintenance is a crucial ecosystem service. Due to time limits and data availability, assessing biodiversity using indicators or models has become a hot topic in recent decades. However, whether some proposed indicators can explain biodiversity well at the local scale is still unclear. This study attempted to test whether the habitat quality index (HQI) as measured using the integrated valuation of ecosystem services and trade-offs (InVEST) model could explain variations in bird diversity in New Jiangwan Town, a rapidly urbanized region of Shanghai, China. The relationships from 2002 to 2013 among HQI and the two diversity indices, species richness and species abundance, were analyzed using Fisher’s exact test and gray correlation analysis. No significant association was found. Habitat connectivity was then integrated to develop a new combined indicator of habitat quality and connectivity index (HQCI). The associations between HQCI and the two diversity indices were improved significantly. The results indicated that connectivity may be an important factor explaining the diversity of certain species at a local scale. More empirical studies should be conducted to provide scientific evidence relating habitat quality to biodiversity.

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