- Jackson Achankunju added an answer:Can anyone suggest me the various soft wares by which we can study evolution of plant viruses?
software names especially for geminivirus evolution
Sequence analysis of the nucleic acid using the softwares available on National Centre for Biotechnology Information (NCBI) database.The genetic distance in nucleotide substitutions can be calculated using MEGA 4.0 and then plot against time [Ferguson et al., 2003].Hope the attached paper will be helpful.
- Raúl E. González-Ittig added an answer:Any software that could infer stages of hybridization, aside from NewHybrids?I am currently studying hybridization between 2 plant species using dominant genetic markers (ISSR markers), and would like to infer the stages of hybridization (infer with confidence that a certain individual is an F1 hybrid, F2, or backcross). So far the only one I have found is NewHybrids by Anderson and Thompson 2002 (http://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm). Does anyone know if there are other softwares that could do a similar job, probably with a different model or inference method?
Dear Dr Wei Lung Ng
we have tried to use the program Newhybrids and we could not.
We put the glut32.dll file in the same folder of the program. In Windows the program opens, but when we try to use the program it crashes in the graphical interphase option.
Without the graphical interphase we can continue a little bit more; after setting the burnin and the number of iterations after that period, the program crashes with the following message:
unhandled exception: c0000005
At adress: 0040b097
We also tried to install the OpenGl v1.1 software but we couldn't.
We tried all the procedure in a Windows7-64bits computer and in a windowXP-32bits computer.
We follow the instructions of the program, but it doesn´t work
Could you please help us?
Thank you very much.
- András Bozsik added an answer:Are there evolutionary advantages to having mild schizophrenia?If so, what are they and why might they arise?
It seems that participants and the question owner have abandoned the thread. As you put it above the connotation of this disorder is much more complicated than to arrange it with the expression of “mild schizophrenia”. By the way, I agree with your rephrasing of the question.Following
- Robert Grumbine added an answer:What does it mean to you that the global conc. of atmospheric CO2 crossed 400 ppm mark for the first time in recorded history?What would be the consequence? Practically is there any way out? Soliciting inputs from the experts.Following
- Daniel R Brooks added an answer:Is there any experimental or reproducible proof sample about microevolution?
to show in the class as a simple experiment?
And, is there any receiving scientific answer or objection answer of it from the creationist approach?
Have a look at John Endler's classic "Natural Selection in the Wild" in the Princeton series.Following
- Sundaresan Muthuswamy added an answer:Is consciousness giving human beings an evolutionary advantage?While having the concept of Self as opposed to others or to the environment seems good for focusing the organism functions on survivability and on DNA spreading, is there any evidence that consciousness has an evolutionary advantage?
To elaborate further, here I'm talking about consciousness as the first person experience. And for "first person experience" I'm not talking about "experience OF first person": conversly, I'm specifically addressing the "experience IN first person MODALITY" (as a corollary to this question, I'm proposing that the word "consciousness" refers to too many concepts). In this view, I consider self-consciousness "experience of first person in first person modality".
If we embrace the assumption that consciousness is always consciousness of something, we still lack an explanation for the nature and the purpose ("what is/what's for" rather than "how is it") of the first person experience, and as such why evolution favored it.
In a lot of other Q/A about self and consciousness people are talking about consctructs that may function even without consciousness. Two examples:
-self: a neural network comprising semantic concepts about the world could very well include the concept of self as a non-other or non-environment, or even a concept of self as an independent organism with such and such features; why do we need consciousness to conceptualize it? Would a machine decoding all the concepts coming across the node of (or the distributed knowledge about) self be considered conscious? We do not have to attribute consciousness to the machine to explain the machine processing its concept of self.
-thinking: processing is certainly different from consciously elaborate something, as all the studies on automatic and subconscious processing show. On the other hand, this point address the free will problem: when we consciously elaborate something, does it mean we are voluntarly doing so? Or are we just experiencing a first person "show" of something already happened subconsciously (as Libet's studies suggest)? Without touching upon the ad infinitum regression problems, this poses the question if consciousness is useful without free will: if the conscious experience is just a screen on which things are projected, no free will is needed and thus what's the whole point of consciousness? As such, do we also need free will for accepting consciousness? If we are working with the least number of assumptions, it seems unlikely the we can accept consciousness.
It seems to me that the general attitude of cognitive theories in a biological information processing/computational theory of mind framework is to try to explain everything without putting consciousness in the equation. And indeed it seems to me that no one is actually putting consciousness in the equation, when explaining cognition or behaviour (at least in modern times).
All in all, it seems to me that all the above reasonings bring the suggestion that consciousness is not needed and has no evolutionary advantage over automatic non-conscious entities. Or that we should make more and more assumptions (such as accepting free will) to make sense of consciousness.
I think that asking why we have consciousness could lead us to understand it better.
Two distinct differences exist between humans and animals. One is our conscious emotions and the other is that humans can stand and deliver with his hands..I am sure no one will like to dwell on the aspect of superiority of man over animals and plants as the language of discussion can only be between like species. Differences in various living beings exist by the Will of Nature or due to evolutionary aspects and is a fact many will agree. The problem of relating the created from the inanimate is the one that will bother man till eternity. I am sure most scientists will not like to believe man has originated from nowhere nor can anyone meaningfully trace the millions of living creatures and its variety with its origin in a simple manner that a common man can understand. It is only by intuition that a scientist or a sage who dares to reveal the possible likely mode practically with little evidence..
Even to the believers of evolution , can understand that there is a common living Factor which unites and unties all living matter. There has to be continuity in evolution with a common link in a evolutionary process.We describe that from space we see a bright or dark cloud leading to fiery burning mass which condenses to water vapor and later solidifies into earthy material. The life then originated. How can all happen without a common factor? Is this not primitive evolution which man can never see or physically prove but with surmises, theories, telescopes, astronomy etc etc, we all believe. What justice is it scientific or spiritual? Man has no option but to believe this theory as it rises from intuition which is themain element of of consciousness or Awareness which alone dictates or paints an evolutionary picture captured by the human mind with the very consciousness dwelling in it. One may coin various words , phrases and definitions which a simple person can never understand. Scientists also need not assume that knowledge of high degree mathematics and advanced physics alone can explain this wonderful creation.Following
- Sai GOPAL Dvr added an answer:Are plant viruses infectious to animals?
Phytoreo viruses are being recognized the insects and able to multiply in insects, it means plant viruses may also multiply in invertebrate animals. In the evolution of the viruses there will be a chance for the above.
Human and animal viruses are being recognized them selves, examples of Zoonotic viruses, but in the plant system it is not like that, enterogroup of viruses attach on the surface of the vegetable leaves, tubers causes the oral entry, but this is not a true transmission. Animal and human cells should recognize by the plant virus then only it become true transmission.Following
- Alexander Makhrov added an answer:What are the main factors in gradual evolution?
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?
A selection is single factor of gradual evolution (see, for example, famous book: Simpson, G. G. (1944) Tempo and Mode in Evolution. New York: Columbia Univ. Press).Following
- Anuj Guruvacharya added an answer:Is there a software that can compare two phylogenetic trees to each othe (face to face comparison)?I want to compare the results I obtained using two different phylogenetic trees. I would like to have some lines between the species in the two trees.The phylogenetic trees or the dendograms are constructed using molecular markers.
Go to CRAN, phylogenetics task view and under the subsection called tree comparison you will find a list of R packages that do tree comparison, here is the copy paste of that paragraph :
Tree Comparison: Tree-tree distances can be evaluated, and used in additional analyses, in distory and Rphylip. ape can compute tree-tree distances and also create a plot showing two trees with links between associated tips. kdetrees implements a non-parametric method for identifying potential outlying observations in a collection of phylogenetic trees, which could represent inference problems or processes such as horizontal gene transfer. dendextend can evaluate multiple measures comparing dendrograms.Following
- Edward Patrick added an answer:Any discussion of biological evolution applied to life beyond Earth preceding Wallace in 1903?
A quick question about history of science. Alfred Wallace's 1903 book "Man's Place in the Universe" is usually considered the earliest precursor of contemporary astrobiology, since it applies the Darwinian (-Wallacean :o)) theory of biological evolution to life at large, beyond the boundaries of our planet. However, I wonder was there any previous discussion of it in the 1859-1903 period? After all, those were more than 4 decades of very vigorous scientific activity and speculation in the time when most educated people believed in life and intelligence beyond Earth. Do you know of any such reference? (I'm interested in specifically evolutionary discussions, not just any mention of extraterrestrial life, channels on Mars, etc. there were many of those.)
Edgars, the chemistry that is taking place in the upper atmosphere of Titan is occurring due to two-body collisions between particles with mean free paths on the order of kilometers. This is not wet chemistry. No fluids are required. This is in free molecular flow. I'm not sure what this has to do with fluid boundaries that are prevalent, say, at the magma-ocean boundary where mid-ocean ridge basalts (MORBs) are formed and the electron donor chemistry is marvelously pumped by a limitless energy source, but the results at Titan are at pressures many orders of magnitude lower that those occurring in these submarine, fluid environments you are describing.Following
- Romeu Guimaraes added an answer:How did the genetic code evolve?I attached a page of a thought provoking book written by A. E. Wilder-Smith and published in 1981. Does anyone know, if his criticism is still valid?
Are there any convincing models, why the genetic code (in the nucleus) of all cells is almost always the same.
Shouldn't it evolve based on currently accepted models? If it does not evolve anymore, how did it evolve in the first place?
Such "by chance" reasoning is not part of nature. (1) It's mathematical - probabilistic modeling to establish 'zero-flat' background data against which to evaluate natural probabilities. Natural things invariably have tendencies in reactivity. (2) The space of probabilities is also limited in nature, never infinite (also a mathematical model). (3) In the origin of life studies we work with compartments, limiting spaces even more, which are, e. g., pores, interlaminal watery layers or microholes inside minerals whose surfaces serve as catalysts and attachment sites for chemical reactions, all this contributing to generate concentration effects of solutes. (4) We also take profit from natural gradients of various kinds, such as material gradients or of energy, e. g., in serpentinization generating H2, submarine vents etc. (5) We don't feel like being in a Ship of Fools, or using Perpetui Mobilia...We work with energy transfers, conservation in chemicals, and so on...At your orders for specific questions on natural models, not for statements of faith. Yours, Romeu.Following
- prof V.S Muralidharan added an answer:What do you think of MSc and PhD theses written in languages other than English?For non-native speakers it can be easier to write in their mother tongue. Moreover, pride in ones language can play a role. However, the language of science is English and writing science in other languages has, therefore, drawbacks. I wonder how this issue is navigated internationally.
i received an e mail stating thatFollowing
- Ivan V. Zmitrovich added an answer:What are the origins of atavisms and retrograde evolution in biology and recent organisms?
I am a paleontologist interested by atavisms and retrograde evolution.
I found interesting indications in the literature concerning reverse evolution
in the limbs of snakes, eyes of ostracods, mandibles in collembola, wings in phasmids and ancestral digits of guinea pigs, but no explanations of those phenomena. Could you indicate me some papers about the origin of such retrograde evolutions?
thanks in advance and all the best
Valentin Krassilov, paleobotanist from Israel, is the author of term "retroconvergence" (there are some papers and chapters, particularly in the book "Evolutionary theory and processes: the modern horizons" dedicated to honour of Prof. Eviatar Nevo, 2004). In my book "Epimorphology and tectomorphology of higher fungi" (2010) the phenomenon of retroconvergency is associated to limited field of modules (hystiones) combinatorics.Following
- Caner Aktas added an answer:Is there a convenient software package for drawing minimum spanning networks for phylogenetic studies?I have struggled to do this with Powerpoint, but am sure that there must be simpler, better, more efficient software programmes for this purpose. Any suggestions? How have others done this? This is a good examples: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146880/pdf/1471-2148-11-172.pdf
My pleasure, feel free to ask further questions.Following
- Robert A D Cameron added an answer:Why are common ancestors extinct?Look at any phylogenetic tree we will find the internal nodes. However, do we have the common ancestors which are occupying those internal nodes in the real world? Sometimes we come up with fossils of missing links. But why the common ancestors of the missing links are mostly extinct?
When we deal with terminal branches, species alive now, the question seems to me to be a matter of definition only. An ancestral species may split into two or more lineages over time. We can separate the lineages, but since we do not have the relevant data for the actual ancestor, we do not know to what extent each has changed. It is likely that the various lineages have changed to different extents, as well as in different ways, relative to their common ancestor, especially if selection has influenced which changes persist. Whether you call any terminal lineage "ancestral" depends on your assessment of the amount of change that has happened, and on your sense of how much (or how little) change permits you to regard forms as being the same or different species. And you don't have real data for the actual ancestor!Following
- Livio Provenzi added an answer:Is there any article on Relationship between DNA Methylation and Human Evolution?
DNA methylation was involved in the evolution of duplicate genes, gene expression, miRNA network stability. Question, Is there any great article to discuss The Relationship between DNA Methylation and Human Evoluation?
- Fangluan Gao added an answer:How to do extended Bayesian skyline plot analyses?I want to use BEAST to do EBSP analyses with two loci. I open two "input.nex" files in BEAUti to generate a "output.xml" file (In the Trees panel select Extended Bayesian skyline plot for the tree prior), and then run BEAST. I do not know if this is right and I do not know what to do next. I can not construct the trend of demographic history in Tracer just like BSP. I got one log file but two trees files (for each locus), and I do not know how to import both tree files into Tracer.
Hi Yong Shi,
I got it. Thank you for your help.Following
- Shian-Loong Bernard Lew added an answer:Can pollution trigger evolution in some species?We are all aware of the evils of pollution and its impact on ecology. Among all the destruction it causes, is there any chance that it may actually lead to evolution of some species? Are there any examples?
If evolution implies increased complexity, then the answer is No. If evolution implies fitness to an inferior target, then the answer is Yes. As advanced by devolution hypotheses. Because genetic entropy may "discount" evolution's selection for the fittest (measured to a prior yardstick) due to pollution:
Following from which info-centric views of genetics and evolution may be used to explain:
- Pollution causing mutation in frog -devolution
- The link between pesticides and Alzheimer's-devolution
Just because somethings thrive tells us little of its fitness-.Especially if that fitness is a moving target. If we eat "heavy metal tuna" and become cognitively- impaired how fit are we compared to our ancestors, even though our average life expectancy is higher? Where are we on the global fitness landscape?Following
- Janine Wonnacott added an answer:Is the war an adaptive behaviour for men?Is the war a way to rationalize the natural human violence ?
You don't have to interpret the "posture / submit" response as a result of man's good nature.
For wolves, it is in the best interest of the pack that all wolves be healthy and uninjured. If conflict and issues of rank and dominance can be settled through posturing rather than fighting, that's better for the group. Fighting can mean injury, even for the victor, which weakens the pack.Following
- Timothy D Smith added an answer:What is the state of current evidence about the existence of a vomero-nasal organ in birds?The literature on whether birds have vomero-nasal organs (VNO) in birds is confusing, with little hard evidence supporting the presence of the organ, but equally few firm rejections of its presence. The situation regarding dinosaurs is equally confusing; Tyrannosaurus rex apparently did not have a VNO, but some pterosaurs might have had one (at least, they have two currently unexplained palatal fossae). Is there any recognised definitive literature on this matter?
The question of living birds possessing a VNS is one for histological research. This is so because of the microscopic size of the elements. In the periphery, one hopes to find a neuroepithelium in the form of a duct or patch, and Kurt summarizes the necessary evidence on the accessory olfactory bulb. So the very nice images provided above on the grey parrot and other birds are simply too macroscopic for the job.
A pitfall in the search for vomeronasal structures is that serial histological sections are needed because sampling regions can lead to falsely proclaiming a VNS structure is absent (when in fact it remains hidden in unsampled regions). So, there may well be birds that have not been studied thoroughly enough. See the literature on the VNO in primates and bats to get a sense of the enormity of the task.
That said, I would definitely agree with Kurt that a VNS in birds is highly unlikely. What seems possible though, is that some vestige of the peripheral receptor organ (the VNO) may remain in at least some birds, as is the case for some mammals.Following
- Georgi Gladyshev added an answer:Can somebody advise a big, widely used and comprehensive resource on studies related to origin of life?Can somebody advise a big, widely used and comprehensive resource on studies related to origin of life? Or maybe there are some institutions/individuals constantly working on that problem?
And another question is what happened to Eigen and Schuster's Hypercycle Theory? Is it a fundamental for today's understanding of the basic realisation of inorganic-->organic transition concept?
Georgi P. Gladyshev (2015) Natural Selection and Thermodynamics of Biological Evolution. Natural Science, 2015, 7, 117-126 Published Online March 2015 Pub. Date: March 9, 2015
DOI: 10.4236/ns.2015.73013 http://dx.doi.org/10.4236/ns.2015.73013
Abstract The author of this article proposes that the representation of Charles Darwin and Alfred Wallace’s theory on “variation and selection” in the living world is a reflection of the action of hierarchical thermodynamics...Following
- Ashley W. Poust added an answer:Can someone recommend books or articles with information on mammalian evolution?I am currently doing my presentation on mammals and their evolution, I would like to have books where I could get information.
I think one of the best books to think about evolution in mammals is GG Simpson's 1953 Condon lecture "Evolution and Geography, An essay on Historical Biogeography with special reference to Mammals".
You'll have to take it with a grain of salt - this was written before phylogenetics or plate tectonics caught on. And to echo other authors it depends on the level you are looking. Simpson's paper is amazing if you want to start thinking about how evolution happens, but it is not just a retelling of the history of mammal evolution. For that look for books by Prothero, Kurten, DR Wallace, or for more general books on the history of life and turn to the last few chapters (almost invariably mammals are at the end).Following
- Brian Thomas Foley added an answer:Are you teaching evolution using Evolutionary Analysis?
(4th or 5th edition) I would like to create a forum for the exchange of ideas, questions, and teaching experiences. What works, in your teaching? What doesn't work? Have you used any "active learning" methods in your course? Do you use virtual laboratory exercises (such as those from SimBio) in your course?
For molecular evolution and phylogenetic analysis, the Phyobabble group is very nice. http://phylobabble.org/ It is well organized and has a lot of experts in phylogenetic analysis. For data sets, and looking for interesting data and stories of evolution, the TreeBase is pretty interesting. http://treebase.org/treebase-web/home.html
For looking at "the tree of life" I really like the OneZoom site. http://www.onezoom.org/ the tutorial there is really worth taking, for example to learn that you can switch between common names of the organisms and Latin names.
In GOOGLE+ (google plus) there are a lot of "communities" for sharing thoughts, ideas, resources for studying evolution. https://plus.google.com/communities/108054924267127040453 for one example.
On YouTube, COncOrdance and AronRa have done some very nice videos: https://www.youtube.com/user/C0nc0rdance https://www.youtube.com/results?search_query=aronra+evolutionFollowing
- Iuliana Vasian (born Budae) added an answer:Are "sex pheromones" really produced by insects?I had previously asked a question "Can bacteria mediate "mating" in insects?" for which i had received wonderful answers from my peers. Taking all answers and reference into consideration we performed certain experiments to ascertain our hypothesis. We cultured a germ-free line (GFL) of B. dorsalis females. Virgin males were given a dual-choice between GFL and Non-GFL B. dorsalis females in a customized olfactometer. We were astonished as males were significantly (P < 0.0001) attracted to non-GFL B. dorsalis females.
We had previously identified 9 bacteria from the reproductive organ of the females and each bacteria was checked for their attractiveness. Two out of nine were attractive to virgin males. Is there a possibility that these bacteria produce "sex pheromones" that attract male towards female flies? Further work is under-process.
Nice work. Good lookFollowing
- Craig Dremann added an answer:Conservation biology: a fixist view of life?
All too often, people talking about biodiversity or ecosystem preservation (be it in the frame of climate/global change or of mitigation of other human activities, like agriculture or urbanisation) convey a message that we should basically maintain the current state, implying that any change would be for the worse and that human actions can only damage nature, not improve it. This somehow ignores the very principle of evolution - which means (in Darwin's words) change through descent with modification. There are attempts in conservation biology to use evolutionary processes (like in the dynamic management of genetic ressources used for some agricultural species), but these are marginal compared to the dominant 'preservation as identical' position. Aren't we missing the whole point of life evolution and of man being part of it when advocating to preserve the current status, rather than allow nature to evolve with us?
I think we can divide the planet into the human-habitat and the natural habitat, which in generally is divided into a 90:10 split. And until recently we believed that we could have it all, but we may be coming to the conclusion that we need more than 10% to remain, to maintain the other 90% for us--like providing the annual rainfall that we need to survive.
My guess is that we need to set aside and restore at least 35% of the natural areas as Ecological Restoration Preserves, that is what I am asking at https://www.researchgate.net/post/Do_we_need_to_set_aside_35_of_the_planet_as_Ecological_Restoration_Preserves?
So biodiversity and conservation as independent considerations are not the issue, but how much of the natural world do we need to keep around us, so that we can maintain our human-portion of the planet?Following
- John Grehan added an answer:How much influence would you say Dolf Seilacher had on Gould and Lewontin's "spandrels" paper, particularly on their critique of 'panadapationism'?
See Hallam's obituary for Seilacher in the Geoscientist 24(7):28.
I would agree that Gould had a fuzzy view of constraints, and more I would say very fuzzy as much of his thinking about evolution lacked an integrated coherence. As to the impact of his paper, given his prominence his paper received similar prominence - at least in the English speaking world. But whether it was much of a paper is another matter. It was not very deep in its analysis, far less than potential influences such as Leon Croizat whom Gould read, but never cited even though he seems to have borrowed on Croizat;s work in this respect.
- Brenden S Holland added an answer:Exotic plants or animals evolving into new species?
In California we have over 1,000 exotic plants that have become naturalized and exotic animals like the Argentine ant in California, lives a very different lifestyle than in its original country. Anybody looking into the possibility that these exotic plants and exotic animals may be evolving into new species, in the new lands they now live in?
Well yes if we want to consider insular islands as natural examples of how, and how fast species evolve to become unique entities from their "parental" lineages, the Hawaiian Islands are rife with examples, and a rich literature, as to how lineages phyletically evolve in reproductive isolation (due first to major GEOGRAPHIC ISOLATION) from source populations.
So given sufficient time, habitat diversity, and starting genetic variation, multiple lineages can arise from a single introduction event. Silverswords are a great example, as well as hundreds of species within the Hawaiian Drosophila, the case-building Hyposmocoma (micromoths with maybe 400 species), Tree Snails (endemic subfamily Achatinellinae with 100 species), and an entire family of snails with diverse biology, morphology, habitat preferences and around 350 endemic species called the Amastridae. This is in fact the only endemic FAMILY in Hawaii. So yes, certainly, deeper taxa than species can evolve following colonization/introduction events, given the right set of conditions!Following
- Simon Dellicour added an answer:A quantitative measurement of group assignment using mtDNA sequences, any advice?I'm working with two species using the mitochondrial cytb sequences from several localities and I want to obtain a continuous measurement of species assignation (i.e., one value for specimen/haplotype). I thought in use the program STRUCTURE to get the values of Q. But as far I know this approach could have several assumptions problems about LD and loci independence. Do you know another approach to get some estimator as Q from Structure? What about Geneland?
If you have a mono-locus dataset (for DNA sequences), I would recommend to try the SAMOVA clustering method of Dupanloup et al. (2002; doi:10.1046/j.1365-294X.2002.01650.x). This procedure assigns populations to groups based on geographical vicinity and sequence similarity. The most likely structure corresponds to the partition of populations that maximized among-group variation measured by the AMOVA ΦCT statistic (Excoffier et al. 1992; in Genetics).Following