CURSAT ver. 2.1: A Simple, Resampling-Based, Program to Generate Pseudoreplicates of Data and Calculate Rarefaction Curves

This study summarizes taxonomic information on polychaetes from Santa Catarina State, southern Brazil, between25º57'S and 29º23'S, and provides species distribution records together with information on habitats, based on historicaldata and novel records from primary surveys. Rarefaction curves showed that most species were found in the shallowsublittoral (to 60 m) rather than in deep sublittoral (>60 m) or estuarine habitats. Altogether, 228 valid species belongingto 141 genera and 44 families were recorded. This inventory adds 141 new records to previous regional reports. We founda shift in occurrence of species when comparing data from the study area with data from both southward (29–33º S) andnorthward (23–26º S) sites. Few species were shared between consecutive sites: this could be a response to the regionalbehaviour of the atmosphere and water masses, with a progressive increase in the influence of subantarctic waters and a decrease in the influence of subtropical waters.

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Construction of the Global Solutions to the Perturbed Riemann Problem for the Leroux System

Advances in Mathematical Physics ◽

10.1155/2016/4808610 ◽

2016 ◽

Vol 2016 ◽

pp. 1-13

Author(s):

Pengpeng Ji ◽

Chun Shen

Keyword(s):

Initial Data ◽

Riemann Problem ◽

Phase Plane ◽

Wave Interaction ◽

Global Solutions ◽

Geometrical Structures ◽

Small Perturbations ◽

Riemann Solutions ◽

Piecewise Constant ◽

Rarefaction Curves

The global solutions of the perturbed Riemann problem for the Leroux system are constructed explicitly under the suitable assumptions when the initial data are taken to be three piecewise constant states. The wave interaction problems are widely investigated during the process of constructing global solutions with the help of the geometrical structures of the shock and rarefaction curves in the phase plane. In addition, it is shown that the Riemann solutions are stable with respect to the specific small perturbations of the Riemann initial data.

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How Much is Enough? Improving Participatory Mapping Using Area Rarefaction Curves

Land ◽

10.3390/land8110166 ◽

2019 ◽

Vol 8 (11) ◽

pp. 166

Author(s):

Jennifer C. Selgrath ◽

Sarah E. Gergel

Keyword(s):

Human Activities ◽

Marine Ecosystem ◽

Spatial Extent ◽

Participatory Mapping ◽

Sample Sizes ◽

Rarefaction Curves ◽

Large Numbers ◽

A New Technique ◽

Number Of Individuals

Participatory mapping is a valuable approach for documenting the influence of human activities on species, ecosystems, and ecosystem services, as well as the variability of human activities over space and time. This method is particularly valuable in data-poor systems; however, there has never been a systematic approach for identifying the total number of respondents necessary to map the entire spatial extent of a particular human activity. Here, we develop a new technique for identifying sufficient respondent sample sizes for participatory mapping by adapting species rarefaction curves. With a case study from a heavily fished marine ecosystem in the central Philippines, we analyze participatory maps depicting locations of individuals’ fishing grounds across six decades. Within a specified area, we assessed how different sample sizes (i.e. small vs. large numbers of respondents) would influence the estimated extent of fishing for a specified area. The estimated extent of fishing demonstrated asymptotic behavior as after interviewing a sufficiently large number of individuals, additional respondents did not increase the estimated extent. We determined that 120 fishers were necessary to capture 90% of the maximum spatial extent of fishing within our study area from 1990 to 2010, equivalent to 1.1% of male fishers in the region. However, a higher number of elder fishers need to be interviewed to accurately map fishing extent in 1960 to 1980. Participatory maps can provide context for current ecosystem conditions and can support guidelines for management and conservation. Their utility is strengthened by better consideration of the impacts of respondent sample sizes and how this can vary over time for historical assessments.

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Rarefaction Curves

Encyclopedia of Statistical Sciences ◽

10.1002/0471667196.ess2195 ◽

2004 ◽

Author(s):

Andrew F. Siegel

Keyword(s):

Rarefaction Curves

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An approach to detecting species diversity of microfaunas in colonization surveys for marine bioassessment based on rarefaction curves

Marine Pollution Bulletin ◽

10.1016/j.marpolbul.2014.08.032 ◽

2014 ◽

Vol 88 (1-2) ◽

pp. 268-274 ◽

Cited By ~ 7

Author(s):

Guangjian Xu ◽

Xiaoxiao Zhong ◽

Yangfan Wang ◽

Henglong Xu

Keyword(s):

Species Diversity ◽

Rarefaction Curves

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Additive partitioning of rarefaction curves and species–area relationships: unifying α-, β- and γ-diversity with sample size and habitat area

Ecology Letters ◽

10.1111/j.1461-0248.2006.00941.x ◽

2006 ◽

Vol 9 (8) ◽

pp. 923-932 ◽

Cited By ~ 168

Author(s):

Thomas O. Crist ◽

Joseph A. Veech

Keyword(s):

Sample Size ◽

Additive Partitioning ◽

Rarefaction Curves ◽

Habitat Area ◽

Species Area

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Diversity and microhabitat use of benthic invertebrates in an urban forest stream (Southeastern Brazil)

Iheringia Série Zoologia ◽

10.1590/1678-4766e2021020 ◽

2021 ◽

Vol 111 ◽

Author(s):

Vitor Manuel B. Ferreira ◽

Nathália de O. Paiva ◽

Bruno E. Soares ◽

Maíra Moraes

Keyword(s):

Community Structure ◽

Benthic Invertebrates ◽

Urban Forest ◽

Repeated Measure ◽

Southeastern Brazil ◽

Microhabitat Use ◽

Taxonomic Richness ◽

Rarefaction Curves ◽

Forest Stream ◽

Structure Indices

ABSTRACT This work aimed to assess the diversity and microhabitat use of benthic invertebrates in an urban forest stream in southeastern Brazilian region. The invertebrates were sampled in a headwater stream, located at the Tijuca Forest, Rio de Janeiro. Three types of microhabitats were sampled (litter, sand and stone) using a Surber sampler. Specimens were identified to the family-level and rarefaction curves were constructed for the total sampling and for each type of microhabitat. Community structure indices (abundance, taxonomic richness, diversity, and dominance) were calculated for each microhabitat. Differences among indices were tested through a repeated measure ANOVA, and differences among microhabitatsʼ composition through a PerMANOVA. A total of 9,800 specimens were registered in which Chironomidae was the most abundant. The rarefaction curves did not reach the asymptote. Community structure indices exhibited differences (RM ANOVA; p < 0.001), as well as microhabitats’ composition (PerMANOVA; p < 0.001). Abundance and taxonomic richness were the highest in litter, diversity was higher both in litter and stone, and sand had the highest dominance. Results highlighted that the variety of microhabitats may enhance local diversity and that the differences in resources availability of each type of microhabitat determine the distribution of these invertebrates.

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Microbial Diversity Assessment in Milkfish Culture Ponds

Asian Journal of Fisheries and Aquatic Research ◽

10.9734/ajfar/2019/v5i330077 ◽

2020 ◽

pp. 1-12

Author(s):

L. M. M. Dalmacio ◽

B. L. Ramirez ◽

R. Estacio ◽

I. Borlongan ◽

J. M. Ramirez ◽

...

Keyword(s):

Sequence Analysis ◽

16S Rrna ◽

16S Rrna Gene ◽

Microbial Diversity ◽

Bacterial Diversity ◽

Dna Sequence ◽

Dna Sequence Analysis ◽

Rrna Gene ◽

Rarefaction Curves ◽

Distance Matrices

Aims: To determine bacterial diversity in milkfish culture ponds that contain different life-cycle stages of the milkfish (pond A: fry, pond B: juveniles and pond C: adults) by DNA sequence analysis of organisms and compare that microbial diversity to organisms found in soil adjacent to the ponds. Study Design: Comparative metagenomic study of aquatic and terrestrial biodiversity based on DNA sequence analysis of water and soil DNA. Place and Duration of Study: SEADEC milkfish ponds in Tingnauan, Iloilo. Philippines. All water and soil samples were collected over a three-day period. Methodology: DNA sequence analysis of nucleic acids extracted from water samples collected from the three types of milkfish ponds along with soil adjacent to the ponds. DNA was extracted and PCR was performed using the 11F-1492R primer pair to amplify 16S rRNA gene. Purified 16S rDNA amplicons were cloned in using the TOPO-TA cloning kit for DNA sequencing. 16s rRNA gene sequences were analyzed with the use of software tools at the National Center for Biotechnology Information website and imported into the ARB phylogenetic analysis software. Distance matrices were exported using the neighbor-joining algorithm in ARB, in the form of PHYLIP-formatted lower triangular matrices. The distance matrices were then used to calculate Shannon-Weaver and Simpson diversity indices to evaluate the richness and evenness of the sampled populations. Rarefaction curves were determined to evaluate sampling efficiency. Results: Rarefaction curves indicated that the sampling effort was sufficient to reveal the majority of phyla present in the sample. Shannon-Weaver and Simpson indices suggested that the diversities of all the groups were statistically different from each other. It was observed that pond A was least diverse, followed by pond C and pond B. The soil was most diverse. DNA sequence analysis identified the various species of bacteria in soil and water. Conclusion: All three pond communities were significantly different in diversity. This study did not identify any significant human pathogens such as Vibrios, Salmonella or Shigella. Bacterial diversity of sites decreased in the following order: soil > fry pond > fingerling pond > adult pond.

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Scaling of species distribution explains the vast potential marine prokaryote diversity

Scientific Reports ◽

10.1038/s41598-019-54936-y ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 3

Author(s):

Victor M. Eguíluz ◽

Guillem Salazar ◽

Juan Fernández-Gracia ◽

John K. Pearman ◽

Josep M. Gasol ◽

...

Keyword(s):

Red Sea ◽

Power Law ◽

Species Distribution ◽

Species Abundance ◽

Global Ocean ◽

Sampling Effort ◽

Power Law Distribution ◽

Rarefaction Curves ◽

The Earth ◽

Repeated Sampling

AbstractGlobal ocean expeditions have provided minimum estimates of ocean’s prokaryote diversity, supported by apparent asymptotes in the number of prokaryotes with sampling effort, of about 40,000 species, representing <1% of the species cataloged in the Earth Microbiome Project, despite being the largest habitat in the biosphere. Here we demonstrate that the abundance of prokaryote OTUs follows a scaling that can be represented by a power-law distribution, and as a consequence, we demonstrate, mathematically and through simulations, that the asymptote of rarefaction curves is an apparent one, which is only reached with sample sizes approaching the entire ecosystem. We experimentally confirm these findings using exhaustive repeated sampling of a prokaryote community in the Red Sea and the exploration of global assessments of prokaryote diversity in the ocean. Our findings indicate that, far from having achieved a thorough sampling of prokaryote species abundance in the ocean, global expeditions provide just a start for this quest as the richness in the global ocean is much larger than estimated.

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