Questions related to Speciation
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:
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.
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.
anyone can introduce some papers about the effect of Mycorrhiza on phosphorus speciation and dynamic?
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?
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.
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.
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.
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.
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!
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?
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?
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 :)
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.
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) ?
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
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.
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.
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?
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)?
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?
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?
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?
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: email@example.com and/or firstname.lastname@example.org
Sean Stankowski and Mark Ravinet
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.
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.
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?
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.
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.
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?
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)
Should I do selection pressure analysis using one family member across 10s of different species.
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.
Dr. João Paulo R. Marques
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.
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!
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?
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?
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.
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?
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?
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?
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.
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?
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?
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.
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).
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?
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..?
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?
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.
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!
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?
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.
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?
I am working on speciation, transformation and mechanism of arsenic tolerance of different rice varieties, so I need some reviews of that topics .
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.
We have different levels in classification. One of them is subspecies. Subspecies explain the various definitions. Which of them is more complete and why?
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
water 1 # kg
1 moles in 1 teps
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?
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?
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?