Biodiversity Informatics - Science method

As part of the technological advances that have been taking place in recent years, which are also rapidly advancing as part of the development of ICT information technologies and Industry 4.0, more and more sophisticated analytical instruments and research techniques are being developed to carry out increasingly complex, multifaceted and Big Data-based analyses of the various processes taking place in nature and to obtain increasingly precise results from the research conducted. With the combination of ICT information technology and Industry 4.0 with satellite analysis technology, the analyses of changes in the biodiversity of the planet's various natural ecosystems carried out using satellites placed in planetary orbit are also being improved. Taking into account the negative human impact on the biodiversity of the planet's natural ecosystems that has been taking place since the beginning of the development of the first technological and industrial revolution, and especially in the Anthropocene epoch from the mid-20th century onwards, there is a growing need to counteract these negative processes, a need to increase the scale and outlays allocated to the improvement of nature conservation systems and instruments, including the protection of the biodiversity of the planet's natural ecosystems.

Improving nature conservation and biodiversity protection systems also requires cyclic surveys of the state of biodiversity of individual terrestrial and marine natural ecosystems of the planet and analyses of progressive environmental degradation and the rate of biodiversity loss. In the situation of obtaining more precise results of research concerning changes in the state of the natural environment and the rate of loss of biodiversity of particular terrestrial and marine natural ecosystems of the planet occurring in various climate zones, changes in the state of the climate and diagnosing key civilisational determinants generating those changes, it is possible to apply specific actions and systemic solutions within the framework of counteracting negative processes of degradation of the natural environment and loss of biodiversity within the framework of improving nature protection techniques more effectively and adapted to the specific nature of a given local biosphere, climate conditions, diagnosed processes of the aforementioned changes but also economic factors. In this connection, the technology of artificial intelligence, which has been developing particularly rapidly in recent years, can also prove helpful in the process of improving the planning, design, management and restoration of natural ecosystems, taking into account a high degree of sustainability, biodiversity and naturalness, i.e. the restoration of natural ecosystems that existed in a specific area centuries ago. In the process of the aforementioned restoration of sustainable, highly biodiverse terrestrial and marine natural ecosystems of the planet, many primary factors must also be taken into account, including geological and climatic factors as well as the modifications previously applied to the area by man concerning geology, land irrigation, drainage, microclimate, soil quality, environmental pollution, the presence of certain invasive species of flora, fauna, fungi and microorganisms. Therefore, the process of planning, design, management and restoration of biodiverse natural ecosystems should take into account many of the above-mentioned factors that are a mix of natural biotic, climatic, geological and abiotic factors and changes in these factors that have taken place over the last centuries or millennia, i.e. changes and side-effects of the development of human, unsustainable civilisation, the development of a robber economy based on intensive industrial development with ignoring the issue of negative externalities towards the surrounding natural environment.

Considering how this should be a complex, multifaceted process of planning, designing, arranging and restoring the planet's biodiverse, natural ecosystems, the application in this process of the new generations of Industry 4.0 technologies, including, above all, artificial intelligence based on large sets of data, information and knowledge concerning many different aspects of nature, ecology, climate, civilisation, etc., collected and processed on Big Data Analytics platforms, can be of great help. On the other hand, artificial intelligence technology combined with satellite analytics can also be of great help in improving research processes aimed at investigating changes in the state of the planet's biosphere, including analysis of the decline in biodiversity of individual ecosystems occurring in specific natural areas and precise diagnosis of the rate of the aforementioned negative changes resulting in environmental degradation and the key determinants causing specific changes.

I will write more about this in the book I am currently writing. In this monograph, I will include the results of my research on this issue. I invite you to join me in scientific cooperation on this issue.

Counting on your opinions, on getting to know your personal opinion, on an honest approach to discussions in scientific problems, and not on ready-made answers generated in ChatGPT, I deliberately used the phrase "in your opinion" in the question.

In view of the above, I address the following question to the esteemed community of scientists and researchers:

What do you think about this topic?

What is your opinion on this subject?

Please respond,

I invite you all to discuss,

Counting on your opinions, on getting to know your personal opinion, on an honest approach to discussing scientific issues and not ChatGPT-generated ready-made answers, I deliberately used the phrase "in your opinion" in the question.

The above text is entirely my own work written by me on the basis of my research.

I have not used other sources or automatic text generation systems such as ChatGPT in writing this text.

Copyright by Dariusz Prokopowicz

Thank you very much,

Warm regards,

Dariusz Prokopowicz

On 16.11.2022 at the UN Climate Summit COP27 in Sharm el-Sheikh, Egypt, debates and speakers address, among other things, the issue of the loss of biodiversity of the planet's natural ecosystems caused by the increasingly rapid process of global warming caused by anthropogenic factors, i.e., primarily by civilization's greenhouse gas emissions. Due to the accelerating deforestation of forests, the burning and clearing of rainforests to create more areas to grow crops for export, the planet's biodiversity is rapidly declining. In addition, also due to the increasing scale of land and sea pollution, oceanic pollution and the accelerating process of global warming, the level of biodiversity of the planet's natural ecosystems is rapidly declining. Due to the predatory management of burning and clearing of the Amazon rainforest, the area of these natural boreal forests described as the natural lungs of the planet has been declining rapidly in recent years. In addition, due to the greenhouse effect, ocean water temperatures are also rising and coral reefs, including the Great Barrier Reef in Oceania, are dying. The decline in biodiversity noted in recent years correlates with the rapid mass die-off of many species of flora and fauna. In view of the above, it is necessary to urgently stop forest deforestation, including the burning and clearing of tropical rainforests and also other forest formations and natural ecosystems located in all climate zones. It is necessary to increase the scale of implementation of afforestation programs for civilization-degraded areas, post-mining heaps, wastelands, and the creation of additional urban parks in urban agglomerations. Besides, it is necessary to urgently carry out a full green transformation of the economy, including a pro-climate transformation of the energy sector by replacing the dirty energy of burning fossil fuels with clean energy based on renewable and emission-free energy sources. With the rapid development of ICT information technology, Industry 4.0, satellite analytics, 5G big data transfer, etc. as important elements of the current fourth technological revolution, it is possible to improve techniques and systems for monitoring the state of biodiversity of natural ecosystems.

In view of the above, I address the following question to the esteemed community of researchers and scientists:

What is your opinion on this issue?

Please answer with reasons,

I invite everyone to join the discussion,

Thank you very much,

Warm regards,

Dariusz Prokopowicz

What kind of scientific research dominate in the field of The importance of biodiversity, the environment, environmental protection?

Please reply. I invite you to the discussion

-Inaturalist

-Orthoptera Species File (OSF)

-Tettigoniidae (Orthoptera) species from Argentina and Uruguay

-The Catalogue of Life (COL)

-Global Biodiversity Information (GBIF)

-Berkeley Ecoinformatics Engine (Ecoengine)

-Encyclopedia of Life (EOL)

-Integrated Digitized Biocollections (IDigBio)

-NBNatlas

-System of Information on Brazilian Biodiversity (Sibbr)

-Ocean Biodiversity Information System (OBIS)

-VertNet

I need more suggestions please!

The current technological revolution, known as Industry 4.0, is determined by the development of the following technologies of advanced information processing: Big Data database technologies, cloud computing, machine learning, Internet of Things, artificial intelligence, Business Intelligence and other advanced data mining technologies.

In view of the above, what kind of information technologies from the Industry 4.0 range and how will they help to protect the natural environment and biodiversity?

Please reply

Best wishes

What kind of scientific research dominate in the field of Protection of biodiversity and natural ecosystems?

Please, provide your suggestions for a question, problem or research thesis in the issues: Protection of biodiversity and natural ecosystems.

Please reply.

I invite you to the discussion

Thank you very much

Best wishes

Can you share any interesting photo concerning butterflies you'd met in nature in your country or during your voyages abroad?

Can you also comment it shortly with a place and date you'd spot it? Also its name. If you are not sure you may ask other participants about the specy name, instead.

E.g.: In May 2019 I'd spend my holidays in Greece, and met there the above Epicallia villica, the cream-spot tiger, a moth of the family Erebidae.

Can you share any interesting photo concerning insects you'd met in nature in your region, country or during your voyages?

Can you also comment it shortly with a place and date you'd spot it? Also its name. If you are not sure you may ask the other participants about the specy name, instead.

During one of my holidays in Dolomiti I've spot the above Panorpa sp. (Mecoptera: Panorpidae) at wild flower of lily in Cortina d"Ampezzo Valley.

Dear Friends

Is there a simple method for evaluating ecoSystem servcices of Urban Tree and any research on linking Ecosystem Services to Urban Corridor Management?

Best Regards

Olivier

Virgin nature rapidly invides our abandon constructions as demonstrates photography including the attached photo. How long could survive traces of our civilisation if its development would crush? Does not invasive species like heracleum, biodiversity, and especially plant biodiversity, plants conservation, plants biology, plant ecology, botany, flowers biology, even actinobacteria and microbiology, phytogeography, vegetation ecology, biodiversity informatics tell us that it would proceed very rapidly?

I am currently looking for Invasive Alien Plant Species (IAPS) Occurrence-Data for mainly the Tropics including Africa, South America, & Asia tropical regions. If you know any research-networks or sources (published and/or Unpublished) of this data, please point me to it. The data would be mainly used for IAPS - Species Distribution Modelling.

NB: I have already gone through most of the data from International Databases (e.g.GBIF and GISD), however.. it is abit lacking.

I thank you in advance for your responses.

Sincerely,

NM

According to Global Biodiversity Information Facility (GBIF), the following nine major groups: Animalia, Archaea, Bacteria, Chromista, Fungi, Plantae, Protozoa, Viruses and Incertae Sedis are alphabetically arranged. What is the correct order (not the alphabetical order) of the phylogeny and evolutionary hierarchy of such major groups?

Best wishes and regards.

Furhan T. Mhaisen

I have been working on a project to collate species occurrence data inherent from unpublished student theses in an integrated database (currently published in GBIF) and still working on a systematic protocol of data validation. Expert review is really subjective and I got many findings that said "expert" estimation were not always more consistent than amateurs, student, or even public enthusiasts (feel free to message me for the papers I collected regarding this), thus my team was still struggling to find a way. Our current method is just independently evaluate the scientific names through taxonomic checklists and the geographic distribution were validated through available published literature mentioning the geographic distribution of each species. We occasionally ask experts but as we are working on many understudied taxa and geographical area, there was not many around.

Please reply

Thank you very much

I am pretty confused about the use of taxonomic diversity and taxonomic distinctness.

Taxonomic diversity can be defined as the average taxonomic path between randomly chosen individuals. It takes into consideration taxonomic differences and heterogeneity (species richness and evenness). Why should we not just decide to use taxonomic diversity instead of Simpson’s index/Shannon index when we know the taxonomy of each species? Moreover, isn’t calculating the taxonomic diversity across different areas more appropriate than other beta diversity indices such as Jaccard Similarity?

Taxonomic distinctness can be defined as the average taxonomic path between two individuals from different species. I don’t understand the point of this index. It doesn’t give us information about the heterogeneity (which taxonomic diversity does), but at the same time it is not an index of the how the different species are related taxonomically (which is delta+). Which information gives us? When is the use of taxonomic distinctness more appropriate than the one of taxonomic diversity? 

Thank you for anyone who will help, I really appreciate it!

Understanding what drives the large-scale pattern of biodiversity is the vital part of macroecology and conservation. The basis of this study is obtaining high-quality data of abiotic /biotic variables. Nowadays, we are in the big-data era, there are a lot of resources for available data. However, the quality and resolution of these data are uneven which may let many novices feel confused. Therefore, we could discuss this topic here.

I wrote a list of several resources on my website that I have knew until now for reference:

Here are some example:

WorldClim (v1, v2): http://www.worldclim.org/

CHELSA (2017): http://chelsa-climate.org/

EarthEnv: http://www.earthenv.org/

Hi,

I have used RDP classifier in my pipeline to assign 16S sequence to their corresponding taxonomy.

I'd like to know if a similar function would exist to assign CO1 (cytochrome oxydase 1) sequences to their corresponding taxonomy.

Another way to solve my problem would be to download a database containing only CO1 sequence files (wether from BOLD or Genbank) and use the Usearch function but I was unable to find such a database yet.

many thanx for your help!

What is the best method to estimate the species richness of birds if we have multiple bird surveys from a single site?  Same method  (line transect) is employed, with same effort in each survey.

Is species accumulation curve useful in this case, considering each survey as an effort?

And should we use the same curve for migratory species (which are only at that site for few months) and resident species, or we should use different curves for both?

 

I need to estimate effective population size of a grasshopper species using AFLP data. However, the methods I reviewed so far only work for SNP or microsatellite data. Is there any tool/software that you used for AFLP? Thanks.

Hello there!

We have been working on sequencing proteins from different sampling points, located a few kilometers away one from another. Now we want to make an analysis to see if there is any significant difference in these and environmental factors among the sampling points due to their geographical location (distances among sites), but we do not know which method use.

I think that any method that should apply for DNA sequences will work on protein data, am I wrong? BTW, we are working with Metaproteomics data.

Thanks a lot

Geographic data (in the form of latitude/longitude co-ordinates) are severely lacking for many specimens/species within the Barcode of Life Data Systems (BOLD). Interspecific (nearest-neighbour) distances can likely serve as a good proxy, but there is a high degree of uncertainty.

due to the each taxonomic level is important in the distinctness indices I need to take the best decision and I have few organisms in my database.  

I have a 3-dimensional NMDS of avian community composition, and I have built predictive models linking site scores to environmental covariates (one for each axis/dimension, so three models) to make spatial predictions across a landscape that estimate a given site's position within the ordination combining predictions for each dimension.  Given this, I was hoping to then be able to estimate a given site's avian composition based on it's position (sites scores) within the ordination.  I am familiar with OMI, but was hoping to use my existing models to extract or estimate community composition given that I know the site's site scores.

I am following the generalized string below, hardly having any clue to change color, line and symbol types to give contrast to the plot. No good tutorial on par function :(  

please help

##Biodiversity.R ##Kindt & Coe 2005

##follow the string below

ranka = rankabundance(data.all)

ranka

rankabunplot(x, scale='abundance', addit= F, specnames= c(1,2,3)) rankabuncomp(data.all, y=data.env, factor='Site', scale ='accumfreq', legend=F, labels(T), lty=2)

Dear friends

Part of my work is the creation of species inventories by analyzing the relevant literature. Reasons of this are to have an update information for the area i work, to have such lists with coordinates (if possible for all data) in order to be used in maritime spatial planning and for comparisons with neighbour areas. Apart from the traditional statistical analysis (number of species per class, family, etc.), any zoogeographical analysis (after having such a list for the larger area), habitat analysis (where these have been found in terms of substrate) which other analysis could be included in such a work in order to become more modern and attactive? Do taxonomic diversity indices (Δ+, Λ+) can be used for comparison with larger datasets (e.c. local species list with Mediterranean species list)?

Any idea - proposition is welcome.

Best

Conducting experiment on differences in biodiversity of micro-atolls between day/night. I am wondering when conducting the shannon index if I should remove species that remained the same in numbers. For example coral and rock boring urchins remained the same. Thanks for any help! 

I need to know how to ensure that calibration and projection (future) raster stacks have the same names for layers

Swaziland's Biodiversity: I am currently working on compiling a dataset of all Swaziland's flora and fauna observations and collections. I am looking for anyone who has records of any flora or fauna from Swaziland which are currently not included in GBIF or SANBI datasets. The information we would need would be the basic record data (date, collector/observer, identification information, locality, latitude/longitude, and any other collection notes). The information will be used by the Swaziland National Trust Commission as part of a project to upgrade and expand the protected area network in Swaziland.

I am working with species richness on a plant group and for my discussion, I would like to compare my results with the results obtained in different published studies. Do you know any statistical method to do it?

Most of the papers just give the number of species, other provide a species list but only with a number of total individuals.

I have just tried comparing the species richness/total area (sum of plots) and then extrapolate it to 1 ha to have the same measure in all the studies.

Why do you suggest?

For example, if a survey of an area is done, we want to decide how important it is to conserve the area based on species diversity. However, a criticism of diversity is that the diversity index is great but the species could all be common species. Is there a way to place greater weightage on rare species to make the diversity index more relevant?

I have the coordinates of the area and also installed qgis but i cant find any tutorials for making a good study area figure which usually i found in several research articles. please assist me regarding this.

I've been trying iNaturalist and a few other mobile phone apps (Map of Life, eBird, PlantNet, Urubu, SISS-Geo) for over a year and found that many users start but do not continue using them. Moreover, due to the existence of several apps, none of them has a complete list of species and none has all desired functions and features.Citizen perspective:In your experience, do you believe common citizens find the apps user friendly and are able to use them effectively to learn and add data to science?Science perspective:Are scientists, mainly taxonomists, engaging in this initiative to help people learn about nature? If not, why? Is the data generated by citizens, useful for science (biogeography, conservation)?

I have two groups of species and four principal components of ecological niche space. I want to find (a single) the pairwise Mahalanobis distance in 4D space between the groups.

Hi, I want to submit an application for financial support, mainly about pollination biology and plant-insect-relationships, but including also biodiversity statistical analyses, as well as pollination network analyses. Does anybody have advanced experience in statistical analyses of pollinator networks and biodiversity methods and can spare some time to review my application for financial support and give me some expert advice, please? As I am new in the field of network analyses and modelling and only used quite basic statistical analyses for my PhD yet, I am in need for some expert advices concerning the statistical and network methods as well as the hypotheses I included in my application. Thank you very much in advance!!!

If biodiversity indices applied at genus level? what are problems and disadvantages expected out of it.

I am working with some data from botanical records. But I only measure the presence-absence of the species. I am interested in compare three habitats (natural, disturbed and secondary) with herbaceous angiosperms along an altitudinal gradient.

It is a known fact that there are differences between Shannon-Weaver and Simpson's diversity index. I just can find a paper which breaks it down and can be cited in a work. Any help is welcome!

Thanks in advance!

Peter

I would like to know how to use MEGA and other softwares to do the analysis done in this paper; such as Haplotype diversity and  the mean nucleotide diversity (Pi).

Thanks in advance

I am in need of calculating Shannon's diversity index of my identified diatom species using Excel with the formula H'= - Σpiln(pi)

Thank you in advance!

A referee asks me to do an haplotype network for concatenated sequences of two gene fragments from coding and non-coding regions (control region and cytochrome b). However, I think that it's better to keep as separate haplotype networks. He argues it can be done in NETWORK 4.6 but I think that to concatenate means the construction of "chimeric" mtDNA haplotypes.

I calculated diversity index of DGGE profile by using bionumerics software. the index range for Shannon wiener is the following for five different rhizopshere

                 SW index        

sample1:    1.2435              

sample 2:   1.2280

sample 3:   1.1189

sample 4:   1.1533

sample 5:    0.7559

how to interpret the results and the method of correlation of data. any suggestions.

I mean this for any nexus multiple tree-file and not the dot-star file given by MRBAYES for a consensus tree-file

I'm interested in knowing how the estimates of the numbers of species present in an ecosystem are made, and how the biodiversity losses are evaluated. In particular:

* is it based on the macrofauna/macroflora only, or does it also include microbes?

* does the advent of metagenomics/barcoding technologies change the estimates, as new species /OTUs are constantly being described?

I am working on a superfamily which has different types of genes. I would like to compare their similarity within this family. I am wondering if the distance in the Mega program is suitable for protein similarity calculation? What approaches can I use just for the genetic distance between species or populations? There is another way to measure protein similarity by ClustWal (http://www.genome.jp/tools-bin/clustalw).

(modelling of species number in a region by using ecological variables)