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Speciation - Science topic

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Hello everyone:
Like Darwin reading Malthus "for amusement", I've been reading the 2nd chapter, "Systematics and Evolution", of the 3rd edition of "Vertebrate Biology", by Donald W. Linzey (2020).
When reading the section on "Species and Speciation" in this chapter, and more specifically when reading about the founder effect and its relationship with the origin of new species, I found the following sentence: "(...) speciation can proceed rapidly since only a portion of the original gene pool is normally present in the small, newly relocated population, and NATURAL SELECTION CAN WORK MORE QUICKLY ON SMALLER GENE POOLS" (capital letters are mine).
To the best of my knowledge, mathematical models of natural selection include parameters like relative fitness and/or selection coefficients, whereas population size is included in models for the evolutionary effects of random genetic drift.
So, do you have any idea on the reasons why natural selection could go faster in small populations (i.e., small gene pools)?
Any help will be welcome. Best regards, and thanks in advance:
Jose.
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Hello; Small samples taken from a large pool will not reflect the gene distribution of the larger pool. Founders' effects, genetic bottlenecks, etc. are what are under discussion and the basis for many examples of speciation. The extreme example might be parthenogenetic species arising from hybridization. Fun stuff! Cheers, Jim Des Lauriers
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I have got an procedure in which (HPLC and GF-AAS) coupled instrument is required. I want to know about the laboratory which has this coupled instrument. Or Please suggest any other procedures.
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ICP-MS is the best option for speciation even at PPB level
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I need to get some equilibrium constants for speciation diagrams. I was planning to use HypSpec 2014 but I haven't received a reply from the e-mail given in the HyperQuad webpage. Does anyone know how to get it?
I also would appreciate input on other programs that would allow me to get equilibrium constants and/or speciation diagrams.
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There are several databases. You need to google. For example
HyperSpec has its own database. While using Hiss you should type the stability constants for your system.
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anyone can introduce some papers about the effect of Mycorrhiza on phosphorus speciation and dynamic?
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@Anoop Kumar Srivastava
Yes! But I am looking for more specific papers like the effect if Mycorrhiza in P isotherms! Sorption and desorption
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In a normal population, we assume the allele A could mutate into allele a, which is a typical speciation gene (bring the direct reproduction isolation), thus the hybrid of Aa will be death or underdominance in reproduction. And how is the allele aa fixed in a new population/species, like typical speciation genes, such as, PRMD9, Odysseus (Ods) locus?
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James Des Lauriers Hi, Prof Lauriers. Several cases were here, like locus Odysseus (Ods) with DOI: 10.1126/science.282.5393.1501, and gene PRMD9 with DOI: 10.1126/science.1163601
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Hello everyone,
I have a question regarding the As speciation in root iron plaque. Based on my reading DCB extraction is a well-known method however, it is an alkaline medium and I am facing problems to use ICP-MS and ICP-OES that runs on acidic digestion which will lead to dilution problems.
Is there a modified DCB extraction method that is compatible with ICP-MS/ICP-OES? Or is there a method where root iron plaque is digested in an acidic solution for As speciation measurement?
Also, I am not sure if my country has an X-ray absorption spectroscopy that is usually used to identify As species in iron plaque.
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Its very interesting question
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Speciation is not an overnight process and leaves many intermediates between the two extremes. Taxonomists failed to address these variations or do not have material to link the variations or not have the infrastructure to interpret at various level or tempted to publish new species in heist for improving cv.
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Hello D. K; There is certainly a variety of definitions for the species concept and most of them seem to be pretty taxon specific. At some point I assembled a little list of published definitions. Here is part of that list. Enjoy, Jim Des Lauriers
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NORMAN; A species is what a competent botanist thinks it is.
A species is a group of individuals or populations with the same or similar morphological characteristics.
BURMA; A species, be it plant or animal, is a mental construction without objective existence.
HATCH; The species is one thing only, the concept that the taxonomist develops on the basis of his data.
GILMOUR; A species is a group of individuals which, in the sum total of their attributes, resemble each other to a degree usually accepted as specific, the exact degree being ultimately determined by the more or less arbitrary judgment of taxonomists.
SIMPSON; A species is the smallest persistent unit in nature.
A species is the largest group with non-arbitrary exclusion and the smallest group with non-arbitrary inclusion.
WILHELM; Species (of helminths) may be defined tentatively as a group of organisms the lipid-free antigen of which, when diluted to 1:4000 or more, yields a positive precipitation test within one hour with rabbit antiserum produced by injecting one 40 mg. of dry-wt., lipid-free antigenic material and withdrawn 10-12 days after the last of four intravenous injections administered every third day.
MAYR; Species are groups of naturally or potentially interbreeding natural populations which are reproductively isolated from other such populations.
THORPE; A population of individuals prevented from interbreeding with all other populations by physiological differences whether or not structural differences are present.
KINSEY; Species are populations having access to a common stock of genes.
LOTSE; A species is a group of genetically identical individuals.
DOBZHANSKY; species are formed at that stage of the evolutionary process at which the once actually or potentially interbreeding array of forms becomes segregated into two or more separate arrays which are physiologically incapable of interbreeding.
DU RIETZ; Species are the smallest natural population permanently separated from each other by a distinct discontinuity in the series of biotypes.
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Across major geological boundaries (ex. KTB or others) some taxa often referred by various authors to Dwarfed taxa / Excursion taxa etc. get evolved through respective age boundaries and continue in the younger sequences. Sometimes there is a significant difference in their specific characters / morphological features when compared to the type species. This may prompt a thought whether so called dwarfed taxa are same as the quoted species or a product of normal evolution by way of speciation? In case the species remains same, what should be the limit of morphological variation within that species or it's author's own judgement to define the range of variation.
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Hello Sudhir; Paleontologists are stuck with a purely morphological definition for species and generally limited numbers of specimens. As a result, Professional judgement remains as the criterion for "how different is different enough". And so, the debate rages on endlessly.
When the evidence is weak or limited, perhaps it is best not to formally describe new species and wait for more evidence. Among ant taxonomists it is common to discuss such taxa in a standardized informal way. For instanace one ant, Strumigenys ca-01 is known from only a single specimen. It is discussed using that moniker without cluttering the literature with a formal name that might get sunk later, when more specimens are discovered. Best regards, Jim Des Lauriers
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Hi all, I am searching for a way to use UV-Vis spec. to speciate copper as in smooth muscle cells for a) cell viability/cell toxicity b) oxidation state changes
Because UV damages cells, I am having a hard time constructing an experiment where using UV-Vis won't affect the cells and copper environment which would skew my data. I'd appreciate any feedback and/or other approaches to tracking Cu+2/Cu+ in cell cultures!
For context, I am planning to use XANES/EXAFS in the second aspect of this study, but I need to know the oxidation state before hand.
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Dear Researcher, I appreciate your view to determine the oxidation state of copper. Since you want the UV radiation to cause any damage to the cells. So you can see by putting traces of silver nanoparticles in the cells. And what you are planning for oxidation state detection is fine.
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In Phreeqc, the "Saturation indices" section only presents the Saturation Index, Log Ion Activity Product, and Log K for each mineral. Is it possible to output the amount, relative amount, precipitate amount, or concentration of each mineral formed?
I have worked with the EQUILIBRIUM_PHASES function. Unfortunately, that function only works if you specify the mineral you want to model. Ultimately I would like to run a simple reaction and have the amount of each mineral calculated for each step.
Any insight into this issue is greatly appreciated!
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SOLUTION 1 # NaHCO3 solution
temp 25
pH 7 charge
Na 2
C(4) 1
END
USE SOLUTION 1
REACTION 1
CaCl2 1
0.004 mol in 10 steps
EQUILIBRIUM_PHASES 1
Calcite 0 0
USER_PUNCH
-headings CaCl2_addition_mol Calcite_precipitation_mol/kgw
-start
10 PUNCH RXN
20 PUNCH EQUI("Calcite")
-end
SELECTED_OUTPUT
-reset false
-file Calcite_precipitation.txt
-user_punch true
END
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Mostly the Neutral mutations are taking place in the non-Coding sequences.
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Neutral mutations or Silent point mutations, are neutral because they do not change the amino acids in the proteins they encode. Many other mutations have no effects on the organism because they are repaired before protein synthesis occurs.
90 percent of DNA expected to be non-functional, and mutations occur there usually have no effect. The other 10 percent functional, and have influence on the properties of the organism, as those used to direct the synthesis of proteins that guide the metabolism of the organism. So many examples color of white bears, size of ears, color of eyes etc. etc.
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This beetle (species X) consist of four eco-morphologically diversified populations. Each population depends on specific host plant and showed a very strict preference to their original host plant. It was known that host plant specialisation play a critical role in the speciation process of this beetle. Case in sympatric area has shown that two populations that rely on two different host plants were reproductively isolated only by habitat isolation and the populations showed a restricted but a degree of gene flow.
Recent findings in another sympatric area in different island, shown that two populations that depend on two different host plant, showed no specialisation yet. Both accept the original and alternative host plant. The questions are, how to know if this is a case of recent host shift? how to know that this beetle are the natural hybrid of these host races? or this is just a generalist population of this species?
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It is a large project. You could start by performing a good sampling of the populations of interest including a good outgroup, eg.: a species of the same genus that clusters outside the group of interest. Second, you need whole-genome sequencing, to get enough nuclear data to test your hypothesis. NextRAD sequencing can provide enough signal to address hybridization hypotheses. Floragenex claims they can even provide analysis for 80 US dollars a sample.
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This species of beetle (species X) consist of four eco-morphologically diversified populations. Each population depends on specific host plant species. (In fact, recently, we discover beetle populations on two different host plant in sympatric area and it turns out that these populations showed no specialisation yet and might be a case of recent host shift). So, we think that host shift played an important role (perhaps initiates) the speciation and radiation of this beetle.
The question is, if we interested to know the ancestral host plant of this species, what kind of approaches or methods can be done to resolve this problem?
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Hello Arif; Your example is very similar to the evolution of Ragolitis sp. The ancestral species was a host-specific parasite on Hawthorn. At some point in the 1800s, the fly had colonized Cherry trees as a host-specific parasite of that host. It was later discovered on apples.
Reading some of that literature might be helpful. Best regards, Jim Des Lauriers
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Hi everyone,
I am having some ideas to conduct a set of analyses concerning insect speciation and phenotypic diversification. For this, I will need a species-level phylogeny with complete taxon sampling (or as close as possible to this) - that is, few known species will be lacking in the tree. ANY group of insects is fine. I also need the phylogeny to be as big as possible, say at least 80-90 terminal taxa. Any thoughts?
ps. I also welcome collaborators, please contact if you like these topics :)
bruno
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Hi Bruno. This is really not the case. I'll check if there is something for Cicadidae but I don't think so. Cheers!
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I have an EDGAR emissions data-set. I would like to speciate the VOC emissions for CBMZ mechanism. Could anybody help? thanks
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I developed an R package to download and speciate EDGAR emissions data. The R package is eixport
chem_edgar speciates emissions data for several chemical mechanisms
Here a solution on StackOverflow
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As I know PE theory raised a typhoon for evolutionary scientists that time. The authors were proud of its novelty. I found, however, the punctuation giving abrupt speciation had originated from quantum evolution by G.G.Simpson as well as founder effect by E.Mayr. I don't think the idea of PE theory embodies any originality, I mean, novelty. I am a biologist but not paleontologist by training. I just wonder weather there exist any answer definitive yes or no.. still in debate.
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I think that the important thing to consider in relation to the punctuated equilibrium hypothesis is not the rate of speciation, but the long periods of stasis (lack of significant evolutionary change in morphological features detectable in the fossil record). One requires a very complete fossil record to be able to discriminate among alternatives, and the evidence is therefore almost always equivocal.
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Which aqueous chemistry modelling would you recommend for studying silica speciation (dissolution & polymerization) and silicate compounds precipitation in a given water (non-geothermal but concentrates of a type of groundwater treated by RO) ?
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Thanks Kirill Boldyrev and Can Ertekin . The water is concentrates ( rejects or retentates) of a type of groundwater treated with Reverse Osmosis. I have tried PHEREEQC, it seems the outcome does not match with experimental results ; for example it says my amorphous silica is under-saturated which does not support the results from experiment as we have colloidal silica (so it is supersaturated)...
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Hi I'm looking for method of metal speciation in soil. I came across with two most commonly used techniques which are ICP-MS and X-ray absorption near edge structure (XANES). Any metal analyst there, kindly suggest me which one is better and feasible. If there's any other method more flexible and less costly method with easy sample preparation technique kindly suggest me. It will be great help in my research
Thanks in advance
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I do not what you are aiming at.
The ICP-MS is mass spectrometry. Here you are able to evaluate the concentration.
With XANES you can address the absorption edge of an element and you have access to the oxidation number. You will also have some access to the concentration depending on which detection mode you perform.
However I would suggest X-ray fluorescence (XRF), a technique which is able to give you the elemental concentration. It is often used in soil analysis. Results are quite ok when the system is appropriately calibrated.
Just 'google' for 'XRF and soil'.
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Hi there,
I have ddRADseq data, with RAD-loci assembled de-novo using the STACKS pipeline for two species and their hybrids. As such, I was wondering how I could estimate Fst for each of those putative loci without using BayeScan. This is because many of my samples are hybrids which violate the model assumptions of the program.
I have seen a method mentioned which uses the ' Bayesian implementation of the F-model' by Gompert et al 2012, but I am unsure how to practically put this into use. I have also tried using outFLANK, but it needs a data-set containing no missing data.
Thanks a lot.
Rowan
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Hey! this is a super old question, but still here my answer in case someone else stumbles upon your question.
Fst per Locus can be calculated directly with STACKs in the population function/pipeline. Then, you can use that stuff to run OutFlank in R either using this script and your FST values: https://github.com/whitlock/OutFLANK/blob/master/R/OutFLANK.R
our run OutFlank on a genind object that you can convert in R from a genepop or structure input file using the import2genind function and then this other script to calculate all the parameters required from there: https://rpubs.com/lotterhos/outflank
Hope this helps! PS: I prefer the second...
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As most speciation events are said too be allopathic are there some good examples of sympatric speciation say by ecological isolationvor some other means barring poloploidy in plants. I am more interested in this event if it does occur commonly in sexually reproducing animals.
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Hello gentlemen; Here are some more examples that I can find off hand.
1. Time shifts in breeding time. Megacylene spp. Cerambycidae
2. Pheromone changes in the % distribution of two components. Noctuidae
3. Hybridization. Mosquitoes,
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Is there any free software to calculate the speciation distribution?
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I have different ions and complexes formed at elevated temperature and would like to know about their stability constant at that temperature, can anybody help me to know that please?
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Thanks for your kind information Professor Jean-François Gal
Will find away to find these species experimentally.
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Can someone provide suggestions on which methods / softwares can perform fast and reliable estimates of diversification rates (speciation - extinction) using very large phylogenetic trees (> 10 000 tips)? 
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BAMM, LASER, and APE
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What is the best practice for assessing recovery of a speciation technique when one of the species is below DL (e.g. Cr speciation)? Do you omit the <DL species from the calculation? Are there any good references for best practice in writing?
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Hi Elliot,
I think peaks below the DL should be omitted. Just as you wouldn’t report values below DL for any type of analysis.
It shouldn’t make much difference to your column recoveries.
Cheers
Mark
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And what are the implications? There are a variety of benchmarks for computer processing. An article in September 2019 Science Advances, Different languages, similar encoding efficiency, by Coupe et al estimates human information transmission at 39 bits per second. A 2007 PNAS article by Allen, Gillooly, Savage and Brown estimates correlation between metabolic rate and speciation. One would think that the rate of genetic change is far slower than human information transmission. Are there other possible sources of comparison?
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Dr Nepal,
Thank you for your reply.
The September 2019 article referred to in the question suggests an average information transmission rate of 39 bits per second.
Suppose this approximates the average individual human processing rate. For certain kinds of problems, computer processing rates are must faster. Another rate is the rate at which DNA changes. Different rates of change for different systems imply different emergent attributes, and different ways that they interact with each other. For example, given the processing rate of computers, human societies obtain economic advantages by investing in faster computer processing. Given the slowness of individual human processing, networked human societies have processing advantages over individuals. Given the rate at which generic change occurs, networked human cultural change has advantages over the evolution of new species.
You ask, about the context. I am not sure where a comparison of rates leads, the question posed is for now still amorphous and I hope perhaps some readers will improve the context.
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Hi All,
I just start working on X-ray adsorption spectroscopy.
I noticed that people use EXAFS-LCF for Zn and Pb, but XANES-LCF for Ni, P and Cd. Clearly, XANES-LCF is much faster and easier.
Can anyone let me know why people choose above approaches. If I want identify speciation of one element, how should I determine which approach I need to use?
Thanks!
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Any kind of LCF is useful only if the sample contains a mixture of known signals, such as spectra that correspond to specific coordination structures or crystal phases. The bigger the differences between signals for each component of the mixture, the clearer the LCF result will be. If the signals are too similar, then the uncertainty in the result may be too high to draw a strong conclusion.
XANES LCF is especially useful when differences in oxidation state or coordination of the element lead to significant changes in XANES, such as the appearance of a pre-edge feature, a significant shift in binding energy, or a significant change in the white line intensity. For many elements, however, there are only subtle differences in XANES for chemically distinct species. Take a look at published XANES spectra for the materials you're trying to distinguish. Do you see features that would clearly identify each phase if all the signals were added together?
An EXAFS spectrum contains more information about the coordination environment than XANES. However, one reason EXAFS LCF can be more tricky than XANES LCF is that the EXAFS data is more processed, which can introduce artifacts into the LCF. The shape of the EXAFS spectrum can be affected by the initial spline fitting and the choice of binding energy offset. The high energy (high k) region of EXAFS is also usually very noisy, which can cause problems for LCF. Finally, it might be difficult to find, measure, or simulate standard EXAFS spectra for each component in the sample. The properties of the standard samples, such as crystallite size and local disorder, should be as close as possible to the same properties of the corresponding material in the mixed-phase sample. If these conditions can be met, then EXAFS LCF is a good option.
I recommend joining the IFEFFIT mailing list, where there is a lot of discussion about best practices for data analysis between new EXAFS/XANES users and experts: http://cars9.uchicago.edu/mailman/listinfo/ifeffit/
Some examples of using EXAFS LCF to distinguish different structures of the same element are linked here. Good luck!
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We invite you to take a short survey about key concepts used in the field of speciation research. Through a series of questions, this survey is designed to capture people’s thoughts about concepts that are central to speciation research. We plan to use the answers to understand why researchers think about speciation differently, and to help people understand one another’s perspectives.  
The survey is anonymous, and open to anyone that would like to take it, though we are primarily targeting researchers that study speciation. The summarized results may be circulated and published and answers will ultimately be available to anyone that wants to use them. The country of origin will only be used to measure the spread of the survey.  Please circulate the link to anyone that you think may be interested in taking part!
The survey was written by Dr. Sean Stankowski, a research scientist from the department of Animal and Plant Sciences at the University of Sheffield (https://www.sheffield.ac.uk/aps), and Dr. Mark Ravinet, a research scientist from the Centre for Ecological and Evolutionary Synthesis (https://www.mn.uio.no/cees/english/). The survey has received ethical approval from the Department of Animal and Plant Sciences, University of Sheffield. In the event of any concern or complaint about this survey, please contact the Head of Department, of Animal and Plant Sciences, University of Sheffield. You can take the survey here:
Please forward it to any colleagues or students that you think would like to take part!
If you have any general questions about the survey, please email: s.stankowski@sheffield.ac.uk and/or mark.ravinet@ibv.uio.no
Sean Stankowski and Mark Ravinet
📷
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Maybe you can share some results on RG in due course.
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Aluminium is the third most abundant element in the Earth's crust. Can anyone let me know if any speciation state of Al has positive role in any living organism? I do find several reports of Al3+ toxicity to wide range of organisms.
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I attached conclusion of 3 articles about Aluminium
Article 1. Aluminum and Alzheimer's Disease: After a Century of Controversy, Is there a Plausible Link?
Review Article
Tomljenovic, Lucija
Journal: Journal of Alzheimer's Disease, vol. 23, no. 4, pp. 567-598, 2011
Conclusion of the author
Experimental evidence has repeatedly demonstrated that chronic Al intoxication reproduces neuropathological hallmarks of Alzheimer's disease ( AD). Misconceptions about Al bioavailability may have misled scientists regarding the significance of Al in the pathogenesis of Alzheimer's disease (AD). The hypothesis that Al significantly contributes to AD is built upon very solid experimental evidence and should not be dismissed. Immediate steps should be taken to lessen human exposure to Al, which may be the single most aggravating and avoidable factor related to AD.
Article 2. Aluminum and Alzheimer's disease: A new look
Article type: Research Article
Authors: Miu, Andrei C.; * | Benga, Oana
Journal: Journal of Alzheimer's Disease, vol. 10, no. 2-3, pp. 179-201, 2006
Conclusion of the authors
The involvement of Al in the pathogenesis of AD should not be discarded, especially in these times when the amyloid dogma of AD etiology shows its myopia.
Article 3. The meaning of aluminium exposure on human health and aluminium-related diseases
BioMol Concepts 2013; 4(1): 77–87 
Review
Guido Crisponi * , Daniela Fanni , Clara Gerosa , Sonia Nemolato , Valeria M. Nurchi , Miriam Crespo-Alonso , Joanna I. Lachowicz and Gavino Faa
Conclusion of the authors
Aluminium represents a significant component of exposure of humans to xenobiotics and contaminants and that newborns are at risk of aluminium-related toxicity not only in the perinatal period, but also in childhood and in adulthood.
To alert the medical community about the risk humans are experiencing from aluminium exposure represents an ambitious but measured plan that could be initiated, extending with caution information to pregnant women and to mothers about the vulnerability of infants to early exposure to this contaminant.
Moreover, food manufacturers should be forced to indicate on labels the level of aluminium contained in every food product, with particular care for neonatal products, to reduce aluminium-related human pathologies, with the hope of halting the epidemic increase of neurodegenerative diseases in elderly people.
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The aim of speciation procedures is to maintain the integrity of heavy metals species and minimise sample preparation procedures that may alter heavy metals speciaton. There is a tendency for laboratories to choose methods they are familiar with rather than the most appropriate procedures likely to obtain accurate and unambiguous speciation data.
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Chemical Speciation and Potential Mobility of Heavy Metals ...
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I would like to ask you for help with interpretation of abgd results. According to morphology and phylogenetical tree clades, I should have here 6 species. ABGD gives me some weird results, with no barcoding gap, moreover I don't know how to connect the plot with partitions with the histogram of distances, because the scales are in different orders of magnitude. Anyone has some ideas what's wrong here?
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This method sort sequences into putative species based on pairwise distance, you can work with distance matrix or you can use. the alignment that the ABDG web serve make the distance matrix before analyzes. The ABDG web serve separates the species based on a range of maximum intraspecific distance. I mean, the ABDG consider different value of maximum intraspecific divergence to separete species (graph below) .You can click each point (yellow or red) to see which species were delimited for each maximum intraspecific divergence. If you know the intraspecific divergence of the gene in your taxonomic group, you can modify the parameter on web serve and maybe you get better results. Other important point is: the ABDG works better if you use the sequences closer phylogenetic each others(for e.g use sequences from the same class or genus). Because the substitutions rates (consequently intraspecific distance ) can vary among taxonomy groups. For this reason, I recommend exclude the outgroup from alignment before analyses. Since the greater pairwise distance between ingroup and outgroup can "confuse " ABDG.
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I am working on chromium detection and removal from aqueous medium. I also want to study about the speciation. Kindly suggest me, is there any instrument available for detection of both species separately.
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Hi! You can determinate Cr (VI) by UV-vis method with diphenylcarbazide (see the article ).
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The use of the phrase "physiologic pH" is ubiquitous. Yet, if their is heterogeneity of the microenvironment, the phrase is grossly-misleading, by suggesting that "healthy pH" is invariably 7.4. Whereas, we know that the speciation of biomolecules is pH-dependent and solvent dependent.
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One aspect of the variation of pH within a tissue is related to distance if cells from microcapillaries. This has been examined a lot in tumors, for example. https://pdfs.semanticscholar.org/4827/bdcbfcc0e67550a17e3c661a29d19f35f9e2.pdf
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Hi I have been doing some potentiometric (pH-metric) titrations on copper complexes with two different bidentate ligands and I need to determine the stability constants and generate speciation curves using Hyperquad software. The problem is that I cannot figure out how use the software for bidentate ligands and for ternary complexes. Does anybody know of a guide or manual for this software that can help with this problem?
Thank you.
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Hi, you may find some answers in Coord Chem Rev. article of Hyperquad authors
as well in in Talanta
In principle, one bidentate ligand is marked as L1 another as L2. Then you provide constants for Cu-L1 and CuL2 complexes as fixed (constant). In the end you need to suggest constants for Cu-L1-L2 species (as refine) and run fitting step by step to get best model.
Good luck!
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While performing Phylogenetic and evolutionary analysis of a gene family what should be the sample ?
I am working on a gene family that has undergone various duplication & speciation events giving rise to orthologs as well as paralogs. I want to do selection pressure analysis. My question is :
Should I do selection pressure analysis using the different members of the gene family in my organism of interest ? (Kind of paralogs, however their Fxs have diverged during duplication events giving rise to different family members)
OR
Should I do selection pressure analysis using one family member across 10s of different species.
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The two methods should answer rather different questions In the first case if the families are similar enough to align you might get differential selection coefficients across the families: some transitions from one family to another may have stronger selection coefficients across the families. This might give you insight into the order in which the families appear a particular species - I am thinking off the top of my head on this one and would welcome other answers.
The second seems more conventional: to find the relative strength of selection across the speciation events: which species show profound changes within each gene family.
I think I would do both and treat it as an exploratory analysis.
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I am working on lateral root (LR) formation and I want to understand the relationship the phosphorus in the rhizosphere as a signal to elicit the (LR) development.
Does anyone know if the amount of nutrients, especially phosphorus, in surrounding rhizosphere is an important factor to stimulate the LR differentiation? If so, there is a speciation of the phosphorus?
Thanks for your help.
Regards,
Dr. João Paulo R. Marques
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As Hayat Essalmani suggested much of emphasis on lateral rooting has involved Phosphorus uptake which limited by immobility issues. The ability to greatly stimulate phosphorus mobility is by optimizing the mycorrhizal relationship with conclusive mycorrhizal relationship the Phosphorus optimization can by reduced by 70 to 80% of nonmycorrhizal plants. Another issue of practical concern is that humic materials are able to work as growth regulators. Growth factors and symbiotic relationship of mycorrhizae are all synergistic in their capacity to optimize results while minimizing the need for nutrient additions.
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Hello, everyone. The production of methlymercury (MeHg) was primarily conducted by anaerobic microorganisms including sulfate- and iron-reducing bacteria, methanogens, and other syntrophs. Thus, the amount of inorganic mercury (Hg(II)) that is bioavailable to these organisms is an important factor for controlling Hg(II) methylation. Due to the complexity of Hg speciation in sediments, quantification of the bioavailable fraction remains a great challenge. So, which method would be potential strategies ? the concentrations of Hg(II) in pore water ? the contents of low-molecular-weight (LMW) thiols (e.g. cysteine, thioglycolic acid) which could affect its bioavailability and thus MeHg production? passive sampling like diffusive gradients in thin films (DGT)? a selective model organism using to stimulate the Hg uptake process into methylating microbes?
I don't know the performance difference between those methods. So if anyone can share your opinion or scientific story, I'd be most grateful.
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The potential strategies for predicting or quantifying the amount of bioavailable ( Hg(II ) in water and sediment include measurements of the " dissolved" or filter-passing phase ( typically 0.2 or 0.45 microns nominal pore size ) or the solid - aqueous Hg partition coefficient where the aqueous fraction is defined by this filter - passing phase. Despite this widely employed approach, the filter - passing Hg concentraion rarely correlate with Hg methylation rates or MeHg concentration. Another approach is to infer Hg speciation using chemical equilibrium speciation models and assume the subset of dissolved species are available. For details consult Environmental Science and Tecchnology. Vol. 52 issue 15: pp. 8510 - 8520. http://dol.org/10121/acs.est.8b02515
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Good day everyone!
I would like to ask for your suggestions relative to Genus primers.
Can anyone recommend primers that would capture genus for Cryptosporidium spp. and Cyclospora spp.
I am currently working on water reservoir samples with various environmental profiles so I need to identify at a genus level first before i venture into speciating any isolates.
Your suggestions are greatly appreciated!
Please recommend papers also that you believe will help in profiling for these organisms.
Thank you in advance for your assistance!
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Hello Asif! Thank you for taking time with my question.
Well, there are several markers that have been identified for my organisms.
Example:
Cryptosporidium parvum:
60kD glycoprotein gene (gp60)
Full-length SSu rRNA (1733-1750 bp)
Cyckospora cayetanensis:
70 kD Heat shock protein (HSP70)
But these are specific primers up to the species level...
Since my samples are water and sediments, the idea is if there is the presence of the target organisms there, then one should expect multi species of that genus (Cryptosporidium spp. or Cyclopspora spp.).
If I will be using specific primers then I would be able (if present) identify Cryptosporidium parvum and Cyclospora cayetanensis only.
So in effect, other cryptosporidium spp. and other Cyclopspora spp. will be left out.
More so, if I use these specific primers only, then there is a big possible that the results would come out negative for the parvum and cayetanensis species but the samples may be have other species that cannot be detected by the specific primer set used.
So in effect, the use of specific primers enhances the specificity of the researchers result but the trade off is there is a big chance of not identfying other species present.
On the other hand, using non specific primers (18S rRNA) primers would be able to catch a broader spectrum of eukaryotic organisms but how would the researcher then resolve each species contained therein the sample.
I am a newbie in molecular techniques and have a difficult time understanding the protocols I am reading from my RRLs.
Which brings us back to my concern.
Is it possible for us to be able to use a primer which can catch all Cryptosporidium species and a primer which will catch all Cyclospora species? how do we do these?
Your suggestions would be most valuable for the progress of the molecular part of my research and is deeply appreciated!
Can you suggest any protocol, paper, or primer sets to identify these organisms at a genus level? and later on resolve the PCR products for species identification?
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I wonder what an average time-span of genera may be for evolutionary lineages of various supergeneric taxonomical level across the tree of life (e.g. fish, mammals, vertebrates, beetles, insects, ecdysozoans, metazoans, flowering plants, embryophytes, fungi etc.). In other words, how long on average may genera live in certain lineages? I am aware of the subjectivity of higher taxonomic categories, but there must be some time-span in which the genus is being found in the paleontological record. Similarly, using molecular clocks calibrated with fossils, we may assume the age of extant genera. Does anyone have some tips for relevant literature?
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I'm afraid this depends entirely on what you're look at! Of course, there will be an average (mean, median, etc.), but it will be meaningless because it is measuring different things in different groups.
Of course, a genus is an entirely artificial concept - a genus of a well-studied group of birds is nothing like the same as a genus of nematodes. Recognising genera is the next problem: the features used to define them may not be recognisable in the fossil record. So, for example, we get Lingula going back to the Ordovician, although the soft tissue anatomy is likely to have changed dramatically.
Then there are apparently very long-lived genera such as the pterobranch Rhabdopleura, which appears in near-identical form (including soft tissues, from what we can see) in the Cambrian. Is that because it was morphologically very stable, or because we don't properly understand it?
I know that's not very helpful, though, so here's my perspective on fossil sponges. In most cases, fossil genera appear to last for a few tens of millions, up to around 100 million years. There are, however, many genera recorded from only a single site, so we can't say how long they lasted, but this broad range also covers most of the molecular clock predictions for generic divergence dates. However, there are also some remarkably long-ranging fossil sponges like Nucha (300 million years, apparently)... and we don't yet have a clue what was going on in the deep sea, where the very long-lived sponges tend to thrive (but watch this space...).
As a final thought, I have seen a tendency of some palaeontologists to name new genera for fossils that are out the 'expected' time range--despite morphological similarity. This, of course, will result in shorter ranges in the fossil record than the the true ages based on divergence of living species within extant genera. So many problems!
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Hello,
I am looking to obtain a contig of atleast 1500 bp to identify fungi on the species level. Is there any publications or recomendations of primers to amplify the ITS region and the flanking regions to obtain a longer read than 400-600 bp?
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I am trying to find the right model to predict the hydroxyl radical concentration in water after hydrogen peroxide dosing. Tried MINEQL to model hydrogen peroxide speciation but what i really need is model to give me hydroxyl radical concentration as an output. Any suggestions will be appreciated.
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Dear Max,
It may be that your software does not express concentrations below a certain limit.
As I wrote, take pen and paper and calculate it.  If you are not able to do this, you should not be using any software, because you cannot check the answer.
Best,
Willem H. Koppenol
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Why transition from moneocious to Dioecious and different forms of  Dioecious were found in some plant families? Is this an evolutionary adaptation or due to some other reasons?
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I advise you to read:
Plant Breeding Systems by A. J. Richards, second edition 1997; Chapman & Hall. 
I think this will help you better understand the evolution of plant breeding systems. 
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I used K-medium (52 mM NaCl, 32 mM KCl, 5 µg/mL cholesterol), spiked with metals (CuCl2.2H2O, CdCl2.2.5H2O or ZnCl2). Furthermore, E. coli was added to the solution as feeding source for C. elegans.
I am interested in metal speciation.
Is there another programme, besides Visual MINTEQ, which takes organic compounds into account?
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You can try 
However, regardless of software you have to know the stability constants of metal/organic complexes
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Attach some journal papers listing the phytogeographical elements leads to speciation and endemism in plants?
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Occurrence of a complex of plant species in any geographic location is an indication of the adaptability of the species in that complex to the prevalent conditions in the location being studied. Adaptability, in turn, is an expression of genes for survival and reproduction  in the location. Initial lot of plants in this population might have come from diverse locations by way of dispersal or migration through various means available. Together, migration and survival make-up the adaptive radiation. At this stage, the change in genes in any species in the complex may not be much different from those prevailing in the parent populations from which they are derived. With advancing time and concurrent changes in climate, the genes for adaptation may change by way of recombining with related species in the vicinity, by mutation or by both. This results in a significant change in the expression of these genes in the next generation that may lead one to consider that new species are emerging. Sometimes, related species may interbreed and the resulting hybrids may tetraploidize as happened in the evolution of several crop species like coffee, wheat etc. In these cases speciation events are more clearly discernible.
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I use 15 specimens from 3 different islands separated by the sea using 17 microsatellite loci. If I can not use the data to assess the genetic diversity, then what can I discuss from data?
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Hi Dragos,
The attached file help me much. Thank you....
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Metal Extraction,  I have read article entilted "Solvent extraction of V(V) and Cr(III) from acidic leach liquors of ilmenite using Aliquat 336". I am unable to understand this diagram. Please do the needful.
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I advise you with program, that you will find it easily, will do it very fast and accurate, it is called MinteqA tried it strongly
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Hello, I would like to confirm that it is possible that ITS2 ribosomal DNA marker may indicate introgression and hybridization through inferred trees with this gene?
The tree recovered with this marker showed a polytomy with short branches between two sibling species, can I conclude that it is evidence of introgression only with this marker, in case the ITS2?
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Hi José. Usually polytomies indicate lack of resolution in your data.  A hypothesis of hybrid origin (introgression) cannot be rulled out, but the short terminal branches may also indicate weak support for a hypothesis of introgression. Why do you think that your particular tree indicate a hybrid origin of the ITS2? With a single marker it is easy to manually verify the origin of each mutation. For each polytomy select three specimens representing the suspected parent (monoclonal) populations, and the suspected hybrid, and visually compare their aligned sequences. Make a table classifying the various types of nucleotide similarities: positions with nucleotides unique to a each specimen, and positions with pairs of nuceotides shared by each of the three possible pairs of sequences. For ambiguous base calls (presumed polymorphic positions) consider the individual nucleotides comprising the ambigous call (but check the chromatograms to make sure that the polymorphisms are real and not the result of poor quality chromatograms).  If the frequency of pairs of shared nucleotides are large and close to 50%, 50%, 0%, the hypothesis of hybrid origin is preferred; otherwise alternative hypotheses, such as lack of ancestral resolution or stable polymorphism may be preferred.
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Where there are slight differences it often becomes very difficult in traditional/classical taxonomy to separate varieties (forms), subspecies, sister species or cryptic species especially where reproductive isolation or behavioural or other differences are difficult or impossible to see.I am in the habit of separating geographic variants as subspecies and sympatric variants as varieities/forma. However, I have read some comments on Researchgate that all geographic variants should be regarded as separate species while I believe that such differences if minor should be looked at as incipient speciation. Orshould it be left to the specialist to decide whether a taxon should be treated as a variety/subspecies/different species as Darwin suggested? 
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Classic taxonomy works well in deeper nodes where species no longer interbreed.  For cases with speciation in progress, DNA, ecological, and behavioral studies are needed to understand why, from who,  and how much the populations have diverged. We often don't have those studies in hand while needing to give a name to a new form.  So, we use classic taxonomy, but need to keep in mind that the name and placing of that form may change as new studies come along.  I see the use of morphological taxonomy in species that are being formed as a temporary placeholder.  
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I want to know whether speciation rate of any particular insect family is larger than others. How can I do that? What are the simplest and suitable bioinformatic tools to address the question.
Thanks 
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pretty much as above, probably want to check out what is available in the lit also!
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Climate change is slowly impacting species populations around the world, more pronounced in marine waters. On the other hand, rapid origin of new species through quicker adaptation to climate change of existing population is happening. Unless species are rapidly able to adapt there is likely to be a sharp increase in extinction rates as opined by International Institute for Environment and Development (IEED).  
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In my opinion, it is very important and well-timed question. At present, I write a detailed paper on this subject. I think that our PFO-CFO Theory of Solar System Formation contains the answer to this question. Today, I address you to our last publications of 2015-2013, where this theory is presented in its today form (the first publications relate to 2009). These works are available in my and Elena Kadyshevich pages at the ResearchGate site. 
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We discussed in class how the Galapagos finches have developed different beak sizes due to environmental conditions (sympatry, allopatry, available food resources), and gave rise to Geospiza fuliginosa, G. fortis, and G. magnirostris (small-, medium-, and large-beaked in order). However, how can one classify which species one belongs to if the determining factor is a polygenic trait such as beak size?
We have also defined "species" as a group of similar organisms who can interbreed and produce fertile offspring. Does this mean that small finches cannot mate with medium finches and produce fertile offspring? If yes, why is this so? Aside from changes in beak size due to adaptation, what genetic changes have occurred such that they cannot be considered to be of the same species?
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So you are asking how to tell when speciation is "complete"? This is actually a very difficult question, and one for which we don't really have a generalizable answer yet. The definition for "species" is not quite as simple as the one you gave. What you refer to is the "biological species concept", which defines species as discrete units which are reproductively isolated from other such units... And there is much debate surrounding the application of various species concepts (see attached commentary by John Avise).
One problem with answering the question you have posed, is that speciation itself is a continuous process, where the parameters used to define its "progress" vary along a gradient.. For example various types of reproductive isolation (extrinsic vs. intrinsic, premating vs postmating, etc) can exist to varying degrees between populations, or "subspecies", or recognized species, or even members of different genera. We can see examples of hybridization (thus "incomplete reproductive isolation") throughout nature- does this mean that these are not "true species"?
So, along this continuum, diverging populations accumulate mutations, and accumulate reproductive isolation, either as a result of allopatry+time (geographic separation), or via divergent selection (and the cumulative effect of many other processes). Things are more complicated when we consider that the net effects of these processes are heterogeneous throughout the genome- thus the "amount" of divergence will vary depending on which locus we assay... Attempting to delineate classifications (such as "species" or "sub-species") along this continuum requires that we either treat it as discrete, or determine some arbitrary threshold at which we consider speciation to have progressed (for example, we might say "2% sequence divergence at X locus constitutes species-level divergence).. I'm not sure how far you have made it in your class, but probably you can think of many ways that this sort of attempt to quantify speciation progress might not be generalizable. I've attached another paper by Sara Via which might be interesting to read.
TL;DR- You really can't quantitatively determine when speciation is "complete", because the term "species" (and other various classifications of biodiversity) are human constructs which attempt to apply discrete delineations on a continuous process.
Just my take though
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Dear All.
Speciation of Lipid
I extracted marine green algal using Hexane as solvent and got oily substance.  I would like to know the kind of lipid (speciation) that contain in my crude extract not only fatty acid, is it any methods and tools I can use to analyses it, without doing fractionation using column or solvent. Is  it GC-MS could  answer my question..?
Thank before
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Dear all, the best method to differenciate the lipid types is a combination of 1H and 13C NMR. Neutral and polar lipids as well as glycolipids and phospholipids can be analysed. Sterols and polyphenols as well. NMR is a good tool to analyse DHA and EPA quantitatively.
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Hello,
I am working on a project that uses HPLC to investigate the presence and speciation of vanadium in environmental samples. I have used vanadium standard and pre-treated my samples before injecting them into the column. I am using MeOH: Water (50:50). I normally let MeOH: Water (30:70) flow at a rate of 0.5 ml/minutes for sometime before injecting my sample.
 So far the qualitative part of the study is fine. My challenge now is the quantification, I feel that when running more than one sample in the same day, there is a contamination. Which means that the calculated concentration of sample2 will be affected by the previous sample1.
My questions are:
1- what can I do to ensure that the peak I am getting is from the sample and not from a previous run? (When I run the blanc, a peak from vanadium standard for example is still there)
2- Shall I wash the column after running each sample? and what can I use for the washing process and for how long?
3- would it be ok to run more than one type of samples in one day? (seawater samples and soil samples. Or seawater at different pH)
In general what I can do to avoid contamination in my actual run from the previous run?
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Thanks.
Effectively washing the column and running he blank few time eliminated the previously observed peak.
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How will you do the speciation of Cr+3 and Cr+6?
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The spectra is useful with pure solutions,.
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This is only a general comment.
Good taxonomists who erect species do not depend on minor floral structures only but consider more characters and now a days based on supplementary supporting characters. Good peer reviewed Taxonomic Journals publish species only after some good exercise to avoid  such situation.
There may be cases where  papers are published without genuine study, but they usually come in journals without any reputation and in due course get assessed in authentic revision studies.  
I wish to say that the situation is not so panic.
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Why Different Sps of one genus in some plants are naturally seen in an altitudanal difference between 250m to 2500m ?
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Hello Binoy
When members of same group are geographically isolated (isolation technically means the different members are no longer able to undergo sexual reproduction due to the presence of a barrier ie in case of plants the pollen is unable to travel to the stigma of the geographically isolated group) speciation can occur eventually.
Consider this example: seeds of a particular species can flow through the stream or river from mountain top to lower valley region and establish a new colony there. At this point of time both the plants (one on the mountain top (A) and other on the valley (B)) are same. But because of the long distance the pollen of these plants would not have the capacity to travel that long to fertilize each other and they become isolated (sexually) resulting in limited gene flow between these two groups.
Now gradually adaptive mutations better suited for life in the valley (depending on temperature, humidity, soil structure, availability of food, presence of pathogens, pollinators,foraging animals etc) will occur in the B group.  Over time(very long time), the accumulation of these mutations in B (occurring independently from A) will result in the formation of a new species.
And now if you take a member from B and go up the mountain and plant in there it will show stunted growth or it may not grow at all (Your plant is now showing altitude specificity).  
Hope this helps you
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How much RAM is recommended for "mothur" to run cluster for grouping the sequences in OTU ?
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The distance matrix contains 18 Gb? Well then you definitely need more than 4 Gb. A process can't access all of the memory available on the machine due to usage by the OS and other necessary processes, so I would say you should probably find a machine with 32 Gb of memory. You don't quite need that much but usually you don't see anything in between 16 Gb and 32. 
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What were the reasons for speciation in plants?
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This is a very broad question and the answer depends on the plant species. Wild relatives may have different levels of ploidy and cultivated forms can either have higher or lower levels of ploidy, again depending on the species. For instance, cultivated potatoes are tetraploid (mostly) but  you have wild relatives that go from diplods to hexaploids. Generation of poly- or disomic polyploids respond to diverse hypothesis that go from genome duplication to genome capture, there are several books/papers presenting this and again every plant species has its own history on these processes. 
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Attached is a pretty picture of what our current understanding of species looks like at the genome level (ie the big complete picture)
Generally the darker the colour the better the match between isolates.
This particular picture is of all the currently known genome sequenced isolates of S. epidermidis.
As you can see there is a lot of white space indicating genes outside a core genome and almost no black (close to 100% match).
This could be due to:
1) Misidentified isolates being called S. epidermidis by the authors of the sequence
2) Sequencing errors
3) Plasmids being forced into alignments inappropriately
4) There really is this much genetic variation at the species level.
Assuming 4) is true, there are a number of interesting consequential ideas:
a) All previous ideas regarding the concept of clonality need to be completely re-evaluated with all non-genomic previous papers claiming clonality disregarded in this aspect.
b) PCR tests and PCR sequencing tests, MMLVA, MLST of genes like rRNA, cytochrome oxidase and other housekeeping genes can be used to group isolates but these groupings only relate to evolutionary history and say very little about what a bacterial isolate currently is.
c) In terms of pathobiology, the term species is almost meaningless. A single base pair mutation in one regulatory gene can fundamentally change how a isolate interacts with a host and how easily it is triggered to cause disease. Given the huge number of differences between isolates of the same species, it is invalid logic to make any pathobiologic statements or assumptions at the species level.
d) Given the genomic differences at the species level, it is completely invalid logic to expect to make a single vaccine or antimicrobial to protect against an entire species of bacteria that do not burn down the house to keep warm (obligately virulent). At best we could hope to make a vaccine against a single isolate, or tight group of closely related, recently diverged isolates.
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Brian, Your answer echoes something of what is discussed by Nesse and by Williams in the book I mention and some other literature in evolutionary medicine.
The host switching idea is key and the book also discusses the correlation of pathogenicity to the ability of pathogens to spread from one host to another. If transmission is easy, the pathogen can completely exploit the current host and then expect to find another easily. An excellent example is the 1854 London water pump handle and the easy spread of cholera.
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I am working with a bacterial whole-cell biosensor for assessment of bioavailable arsenic in soil. For calibration, I use arsenite and arsenate standard solutions, respectively. Right now I prepared them as concentrated stocks and stored them in 0.2% HNO3 at -20°C. Just before the assay, I dilute them with MilliQ.
I was wondering, whether under these conditions speciation will be stable or whether I will have to prepare the standard solutions every time freshly.
Does anybody have any experience regarding stability of arsenite and arsenate solutions under these conditions?
Thank you very much already in advance!
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I used to make them fresh every day. No doubt there is a way to preserve them, but why bother when they are relatively cheap? I had one pot of sodium arsenite for my whole PhD and by the end it looked as though I'd barely used any. 
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Can I detect, speciate and quantify simultaneously by Real TIme using Sybr Green dye? I have done multiplexing and qPCR separately. Can both of these be combined in a single reaction?
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Hi Shehla,
In order to multiplex you will need different primer sets and matching probes with different fluorophores on each probe.  Additionally, you will need a multichannel qPCR detection system to simultaneously detect your different targets.  The SYBR-green method is only detectable on that one specific channel.  Hope this helps!
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sometimes, we can see ecological pressure effect in gradual evolution and sometimes, a kind of interaction gene-from-gene. Which of them is more important in gradual evolution?
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What do we understand as gradual evolution? Evolution occurs in all life forms from viruses to prokaryotes to diverse eukaryotes, such as invertebrates and vertebrates and plants. Prokaryotes evolve largely by means of horizontal gene transfer and natural selection, e.g. resistance to antibiotics. Vertebrates have many facilitators of evolution, such as whole genome duplications, point mutations, retroviral endogenisations, and  numerous others, together with natural selection. I take it that gradual evolution would mean adaptations rather than speciation or large innovations, such as the evolution of the placenta, for example . Intra-genomic potential* together with ecological pressure, both biotic and abiotic, and natural selection would be the main drivers of adaptation or gradual evolution in many eukaryotes. However, much evolution occurs in a punctuated equilibrium manner in eukaryotes. 
I hope this helps you,
Regards,
Keith
* Intra-genomic potential, as defined in the TE-Thrust hypothesis, is a continuum from realisable adaptive potential to realisable evolutionary potential.
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For molecular analysis of the largest genus of flowering plants (Astragalus: Fabaceae) containing about 3000 species, I focused on a section with more than 70 species, I used 4 or 5 specimens (including type ) for each species.
These species taxonomically are very distinct and easily separable from each others by morphologic characters,
 but the obtained tree showing that the specimens of the same area nested in a large polytomy!
I would like to know suggestion of the researchers in this matter and how can I interpret in the point of speciation and definition of species.
thank you so much in advance for your responds.
Ali
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I agree with all statements. Dr. Massoumi is expert in Astaragalus taxa, and I believe they are evolving so fast and therefore some polytomy occurs. However, gene flow is maintained possibly for long time among the new arising species and the older forms, therefore we observe molecular similarity between them. It is important to check the gene flow and geographical distance of these presumed new species.
Regards
Masoud Sheidai
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I'm looking for keys or descriptions to tarantulas of Mexico and North America,
I have this: Smith A. 1994. Tarantula Spiders: Tarantulas of the USA and México. Fitzgerald Publishing, London. 196 pp. but I'm also looking for this: Peters, H.-J., 2005. Tarantulas of the World: Amerika's Vogelspinne Insektuto, Konchuaikokai . or the most recent.
To be more specific I need these keys or descriptions:
Aphonopelma bicoloratum. Struchen, Brändle & Schmidt, 1996
Aphonopelma braunshausenii. Tesmoingt, 1996
Aphonopelma mooreae Smith, 1995
Bonnetina papalutlensis. Mendoza, 2012
Bonnetina cyaneifemur Vol, 2000 *
Bonnetina rudloffi Vol, 2001
Bonnetina tanzeri Schmidt, 2012
Brachypelma albiceps. Pocock, 1903
Brachypelma hamorii. Tesmoingt, Cleton & Verdez, 1997
Brachypelma kahlenbergi. Rudloff, 2008
Brachypelma schroederi. Rudloff, 2003
Brachypelma verdezi. Schmidt, 2003
Citharacanthus alvarezi. Estrada-Alvarez, Guadarrama Martínez, 2013
Cotztetlana omiltemi. Mendoza, 2012*
Cyclosternum obscurum. Simon, 1891
Cyclosternum palomeranum. West, 2000
Hapalopus aldanus. West, 2000
Hemirrhagus chilango. Pérez-Miles & Locht, 2003
Hemirrhagus coztic Pérez-Miles & Locht, 2003
Hemirrhagus elliotti (Gertsch, 1973)
Hemirrhagus eros Pérez-Miles & Locht, 2003
Hemirrhagus gertschi Pérez-Miles & Locht, 2003
Hemirrhagus grieta (Gertsch, 1982)
Hemirrhagus mitchelli (Gertsch, 1982)
Hemirrhagus nahuanus (Gertsch, 1982)
Hemirrhagus ocellatus Pérez-Miles & Locht, 2003
Hemirrhagus papalotl Pérez-Miles & Locht, 2003
Hemirrhagus perezmilesi García-Villafuerte & Locht, 2010
Schizopelma masculinum (Strand, 1907)
Sericopelma panamense (Simon, 1891)
Someone could help me?
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you have to check the taxonomic revision of Hemirrhagus that Jorge Mendoza publish the last year in Zootaxa, his email is: Jorge Mendoza <nomeireth@hotmail.com>, even he is working now with the phylogeny and taxonomy of Brachypelma also. About Bonnetina, David Ortiz is working   in the Universidad Nacional Autonoma de Mexico in Mexico City with the phylogeny and taxonomy of this genus, he can help you,
Regards
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I am working on speciation, transformation and mechanism of arsenic tolerance of different rice varieties, so I need some reviews of that topics .
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May be useful to you 
Good luck to you
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Now our laboratory do some research on bird's diversity in Hainan Island,China .I want to calculate simultaneously all three facets of diversity (taxonomic, functional and phylogenetic) to environmental gradients, and incorporating a spatial decomposition of diversity into α,β and γ components on birds.Can you give me some advice about which index is best for doing all this? How about Rao's quadratic entropy?could you tell me more details about the methods? I am just a green hand.
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To my knowledge the first tool (BAT package in R) to calculate these aspects and a discussion of all these dimensions was published recently in 2014 in Methods in Ecology and Evolution by Cardoso, Rigal and Carvalho.  It includes also valuable literature. You can find an accepted version on Research Gate (search by Pedro Cardoso): doi: 10.1111/2041-210X.12310 
Good luck,
Hubert Höfer
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Thank you in advance for your answers.
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Interesting question! Basically there should be no fundamental difference in utility for terrestrial vs. marine systems. However, keep in mind the long - standing notion (assumption) that there *tends* to be more gene flow, fewer obvious physical barriers to gene flow in the three dimensional marine ecosystem, especially for vagile and/or broadcast spawning taxa. 
But recently, the role of mitochondrial DNA (mtDNA) sequences in taxonomy and phylogenetic inference has become quite contentious:  two extreme viewpoints have
emerged. One which criticizes the use of mtDNA because the marker suggests 'misleading patterns of variation'; specifically, phylogenies that
are inconsistent with those derived from nuclear gene
sequences in the context of species relationships among
closely related taxa (Ballard and Whitlock, 2004; Shaw,
2002). The other extreme, the DNA “barcode” movement,
espouses the sole use of small fragments of a single
mtDNA gene, cytochrome c oxidase I (COI), to identify
most of life (Hebert et al., 2003).
In a review paper my colleague Dan Rubinoff and i published a few years back we present the disadvantages of these two extreme
viewpoints and argue for an integrated role for
mtDNA, one that takes advantage of mtDNA’s strengths
but also accounts for its shortcomings by using it in concert
with other independent data sources (e.g., nuclear
DNA, cytosystematic, morphological, behavioral). We
are against the abolition of the use of mtDNA in phylogenetics
but also against its narrow use in barcoding as currently
defined. We try to show why neither viewpoint
is particularly productive and emphasize how analysis
of mtDNA can be an important tool in the context of both
taxonomic and phylogenetic studies, and I would say equally for marine versus terrestrial organism systematics.  (for our review on this debate in general see:
Rubinoff, D. & B.S. Holland. 2005.  Between the two extremes: Mitochondrial DNA is neither the panacea nor the nemesis of phylogenetic and taxonomic inference. Systematic Biology, 54(6): 952-961). 
For a couple of additional papers that used mtDNA markers to examine and evaluate  systematic boundaries in closely related marine taxa:
Bird, C.E., B.S. Holland, B.W. Bowen & R.J. Toonen. 2011.  Diversification in broadcast-spawning sympatric Hawaiian limpets (Cellana spp.). Molecular Ecology. 20: 2128-2141
Bird, C.E., B.S. Holland, B.W. Bowen & R.J. Toonen. 2007. Contrasting phylogeography in three endemic Hawaiian limpets (Cellana spp.) with similar life histories. Molecular Ecology, 16(15): 3173-3187
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We have different levels in classification. One of them is subspecies. Subspecies explain the various definitions. Which of them is more complete and why?
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I always like to think of scientific theory as our 'map' for the 'territory' of nature. At present, reproductive isolation is generally considered valid for the definition of a species. However, one sometimes comes across a population of very different looking individuals, separated from the known population which are, nevertheless, identical in other respects to the main population. One obviously cannot describe these as separate species; nor can one ignore their existence: the need to give a name to them would arise from the need to refer to them in the course of discussing the species. Therefore, the category of sub-species was created. It is undefined and means different things under different circumstances. In the study of butterflies, they are sometimes called geographical variations, for the criterion that subspecies should not be sympatric is met by this definition and usually, the influence of local climatic conditions is the reason for the different appearance of the population.
There is a trend, a dangerous one i think, to raise all allopatric populations to species status, regardless of reproductive viability. However, one hopes that this trend and the 'justification', which is better focused conservation, will soon die out.
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Hi all,
I want to calculate the speciation and activity coefficient of the solution below by Phreeqc 3.1 but as far as know as the ionic strength of the solution is more than 0.1M then instead of Debye-Huckel I should use Davies equation. But I do not know how to change the settings in Phreeqc to do it. Would you please guide me?
The solution contains: 0.05M CaCl2.2H2O, 0.05M Na2SO4, 0.05M MgCl2.6H2O
My calculations in PhREEQC starts with
SOLUTION 1
temp 22
pH 7
pe 4
redox pe
units mmol/kgw
density 1
water 1 # kg
REACTION 1
CaCl2:2H2O 0.05
Na2SO4 0.05
MgCl2 0.05
1 moles in 1 teps
END
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The Davies equation is used to describe the activity of charged species by default.   (pg 11).
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Peripatric speciation as type of divergent evolution where a small subpopulation remains within the habitat of an original population but enters a different niche. Is there a way or a method of studying or observing this from protein sequences using a bioinformatic approach?
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Hi,
As from bioinformatics approach what you can do is find out the protein sequences of the sub-population and the original population and find out the conserved regions or domains in the sequences and and align them to see whether there is any mutation or changes, also you can build a phylogenetic tree for the same to visualize the effect of any change if present. Hope this helps
Regards
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How do I interpret them? In publications, which is the most important figure, or should I use all of them?
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Hi,
The figure on the bottom gives you the number of species for each prior. With the initial approach, it is very stable: 6 species. In the recursive approach, 1 or 2 additional species are recognized. Then to decide if you have finally 6, 7 or 8 species, you need to integrate other data, criteria or methods (anything that could support one or another partition).
Please note that each point on this figure (in the ABGD website) is clickable. It opens another page with the list of the species and the sequences included in it. If your dataset is less than 700 sequences, ABGD also provides a NJ tree (newick format, you just have to copy it in a document that you open with your favorite tree editor). In the tree, the species number as defined by ABGD is added at the end of each sequence title, at the tip of each branch.
All the best
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If I only have one single individual in one of the species analysed, is the analysis reliable. How do we interpret the results? Should we put each  three figures generated from the analysis into publication or just select the base partition?
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Hello
Generally spoken comparisons of distances within species to distances among species are more reliable if we have good proxies of intra- versus interspecific variability, thats clear.
If now among many compared species a single species is represented by only a single specimen I would nevertheless calculate the values. (By the way a higher number of representatives, if derived from a single Population often hide the fact, that the Proxy for intraspecific variability is not much better than in datasets containing a single specimen).
I would say more important is the way we discuss such data.
If you have a dataset that does not give a good estimate for intraspecific Variation, this should be clearly stated in your discussion of your data. then as a reviewer i would have no Problems with analyses that reflect our current knowledge.
greetings
nikola
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I have a big avian phylogenetic tree (rooted with branch length). The avian species on the big tree can be catergorized into two kinds, namely specialist birds and generalist birds. The I extract the generalist birds tree and specialist birds tree respectively from the big tree. I want to compare the speciation rate (which group evolves faster) of these two group of birds. I can get the distance matrix (using "ape" package in R, "cophenetic.phylo" to compute the pairwise distances between the pairs of tips from a phylogenetic tree with its branch lengths) for each of the trees. For example, I can calculate the average distance of each species towards other species for every avian species on generalist bird tree (same for the specialist tree) using the distance matrix, then compare theses two groups. Does it make sense if I want to compare the speciation rate of specialists and generalists birds in this way?  
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