Evolution

Evolution

  • Craig Dremann 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?

    Craig Dremann · The Reveg Edge

    Perhaps ANY plant or animal, once disconnected from its country of origin for a long enough period of time, so that it is no longer exchanging genes with the original population, can spin off in isolation to evolve not only new species, but entirely new genera, like how the silversword and two other Hawaiian plant genera evolved from their California tarweed ancestor, that you can read about at http://www.sherwincarlquist.com/tarweed-silversword.html

  • Leandro R. Jones added an answer:
    Does anyone know of any clear cases of molecular convergence?

    In my teaching I discuss the importance of convergence in evolutionary studies. Of course we can use cases of convergence to discover the selection pressure(s) responsible for particular adaptations, so convergence is our “friend.” But convergence is also our “enemy” because it can make taxonomy more difficult: Do taxa share a trait due to convergence or common ancestry?  I tell my students they don't have to worry about convergence distorting their taxonomies if they use traits below the level of the surface phenotype, e.g., molecular structures such as amino acid sequences or (ideally) A-C-T-G sequences. Since it's good to doubt one's claims, does anyone know any clear cases of molecular convergence?

    Leandro R. Jones · National Scientific and Technical Research Council

    DNA sequences are highly convergent (I would prefer the term homoplasious in fact) because there are only four possible states (i.e. A, T, C, G). Thus, the farther two branches are in a phylogenetic tree the larger the likelihood for a given nucleotide position to mutate towards the same state (say from any nuclotide to, for example, an A). In my opinion, this should not to be seen as a "bad" thing. Perhaps the perception that it is "bad" comes from its morphological counterpart. In morphology based phylogenies, a "convergence" is an ad-hoc explanation for homoplasia, which is to say that in this context the "convergence" is not an empirical observation. Furthemore, convergence, and homoplasy in general, in morphological data is almost always attributable to bad character interpretations: A non-homologous convergence (e.g. fly and bat wings) must be split in two different characters; by the other side a homologous convergence (e.g. bird and bat wings) should be recoded as two different character states. Neither of these problems apply to a homoplasious nt site.

  • James R Knaub added an answer:
    Is the scientific method natural to humans, or does it require a special effort? What about other animals?
    Take the average person you meet - how do they make decisions? What about evolution - has the scientific method ever had any influence on genetic mutation, or has any other aspect of evolution had any influence on living beings?
    James R Knaub · Energy Information Administration

    Edward -

    The "What about other animals?" caught my attention, and reading through the other answers first, I think that Aliza came closest to what I was thinking. You do see the basics of experimentation by other animals. A lot if it had to be accidental at first, like a large bird dropping a clam on a rock to open it, or just having fun, like a parrot or similar bird I saw had taught itself to use a peanut shell as a bucket from which it drank. But other primates use tools, and some examples of basic elements of scientific methodology have to be found in large numbers in other animals.

    Perhaps the disappointment we feel is that humans have learned something about 'perfecting' the scientific method, yet often seem to avoid it. However, I think that many use it more than they realize. Someone who didn't want to take high school algebra may claim for the rest of their lives that they "never used it," without being fully conscious of the many thousands of subtle uses of logic they made that may have been inspired by abilities they honed in that experience with algebra. However, you could say this is more related to the Ancient Greek Philosophy of logic, which fell short of full science or they would possible have gone beyond the 'four elements.' But it is something and it gave modern science a start.

    However, it is true that there is a great deal of interference with science in modern society. I heard or read that in North Carolina, the legislature decided that climate change was not to be considered in official documents, due to its inconvenience, so in effect it was outlawed. At one point the US Bureau of the Census, trying to avoid undercounting minorities, was criticized by Congress, at least one member going so far as to say that "sampling" was some kind of magic, not to be trusted. As a statistician, I was very embarrassed for the US. I've seen office politics that I had to struggle with and often lose against while trying to take the most clearly correct actions. The foolishness, irrationality, and too often selfish and hateful nature of humans can sometimes drown rational and socially progressive views, which you would think would contradict the evolutionary progress that was part of the inquiry Edward made. But perhaps we are just overreacting when we see it that way. Perhaps when we see irrational behavior (or otherwise disappointing behavior that I realize I mixed in here) we weigh that too heavily, and do not give enough credit to the scientific nature that is present in humans and other animals. It isn't perfect, but it's there.

    Jim 

  • Louis Brassard added an answer:
    When do you think art first developed?
    The 40,800 year old cave paintings from El Castillo cave in Spain are the oldest examples of human painting. Shells containing 100,000 year old pigments possibly used for body painting have been found in Southern Africa. 200,000 year old ostrich shell jewelry was found in Librya. Older still, a 350,000 year old rose quartz hand axe was found in a burial pit in Spain. This seems to be the oldest example of symbolism in a human species. But when did art first appear? Captive great apes and monkeys--young and old--have shown a facility for painting (they even have color preferences). However, no wild individuals have ever been shown to do art in their natural habitats. This is most likely because it does not give them any type of survival advantage. They obviously have more important things to deal with in their daily lives. But since humans and chimps have a capacity for art, this means our last common ancestor probably had it as well. It's possible unambiguous expressions of art probably didn't come about until an increase in our brain size gave us greater cognitive abilities. A friend of mine has speculated that art sprung forth from our need to pass on learned information that did not come naturally to us. I would say art was closely tied to spirituality early on. Now the question is whether art first developed in the genus Homo or sometime earlier?

    David,

    I personally think that our primate ancestors had almost all that we have to become us but did not had conscious access to it.  The communal practice that gave them access to what I call self-enactment was communal singing-dancing: our first religion and from that first communal art all others came.  All these self-enactments already existed for our primate but where used subconsciously as part of their perceptual processes.  Pre-music self-enactment was developed early in mammalian brain for interpreting animal sounds and in order to do that they harnessed their motor control system by self-enacting it for maching sound to the type of rythms that they used to move their own body.  Birds and some marine mammals went further and used this pre-music self-enactment for communal emotional control with musical expression and body movement and for female courtship etc. Dance is intimatly linked to it.  The history of the use of music in cinema, in animation re-discovered the importance of music for us to understand emotionally and for us to really perceive movement.  Walt Disney had understood that it was critical for his animation movie for the whale.  Look at all these shamanic dancing practices all around the world and singing and dancing as it used to be is well alive. And all the major social revolutionary movement are centered on communal dancing singing together. So it is as true today as when it created us. The story is getting too long.   Regards

  • Jordi Salmona 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?

    Jordi Salmona · Instituto Gulbenkian de Ciência (IGC)

    Dear all,

    There is an opinion paper by  Erik Meijaard published today, that touch the subject in an interesting way (link below).

    Have a good time reading it.

    Cheers.

    https://www.researchgate.net/publication/269109620_Humanity_Is_Too_Selfish_to_Save_Each_Other_or_Our_Environment

  • Leonard Greenfield added an answer:
    Why did we develop different from other species?

    There are many theories about homo sapiens development compared to others. And I know why but it´s not so easy to Google I have notice.

    So my question is how many know this, and is logically simple but it´s not so easy like we learned to use tools.

    THERMAL ENERGY, AND WE GET MORE TIME  TO DO OTHER THING´S.

    Leonard Greenfield · Temple University

    The simplest answer to your question is that every population and species evolves  differently, genetically and phenotyically,  from other populations and  species once natural interbreeding ceases. Each of the isolated  populations, if they are humans or apes  have approximately 66,000 nuclear DNA loci  (estimating 22,000 promoters, 22,000 operators, and 22, 000 protein coding)  any of which can base pair mutate into many thousands of permutations.  Thus, first , there is guaranteed to be different mutations occurring in each isolate each generation. Second, the environments in which the populations live, including the members of each population who are genetically and behaviorally unique,   are also going to be different - thus, without gene flow, there is a natural tendency for all populations and later their descendant species,  to go unique ways.

    Now, trying to identify more than just a skeleton (pun intended, lol) of a sequence of the   unique events in our lineage over the past 6 million years will be a great challenge. The enormity and depth of this  real sequence will probably never be known sufficiently enough to use the discovered fraction as the basis for causal explanations. You would have to have god-like omnicience to have access to this knowledge  and, we do not yet understand  the machinations of even  a  single human  brain. 

  • Marc Verhaegen added an answer:
    Are there evolutionary advantages to having mild schizophrenia?
    If so, what are they and why might they arise?
    Marc Verhaegen · Study Center Anthropology

    The late David Horrobin wrote a whole book (very readable, but speculative) on this: "The madness of Adam & Eve - How shcizophrenia shaped humanity" (Bantam Press 2001), partly based on human waterside evolution.

  • Jingjing Li 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.
    Jingjing Li · Chinese Academy of Sciences

    This problem has been solved. 

    http://scholar.google.co.nz/scholar?oi=bibs&hl=en&cluster=9003460531033052764

  • David Peris 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
    David Peris · University of Wisconsin, Madison

    I've found an interesting software, developed by Jessica W. Leigh: popART (http://popart.otago.ac.nz/index.shtml).

  • WOJCIECH BORKOWSKI added an answer:
    How serious are the constraints on the genetic code?

    Is DNA the only way to do hereditary business?  Once there are "replicators" that differ in "fertility", evolution by natural selection is unleashed--with, arguably, limitless possibilities. The integrated complexity of the DNA-RNA-ribosome-etc. based hereditary system we see on earth strongly implies a long history of selection on this machinery to make it very efficient at inter-generational information transfer.

    My question concerns the range of possible structure(s) for such a hereditary system. Let me pose it this way: If we were to discover biotic systems elsewhere (in our solar system, in our galaxy, or in our universe), A) How likely would they be to use DNA to transmit their developmental recipes, and B) If they did use DNA, would that be because B1) DNA is the optimal way to pass such information, or B2) life is so improbable that it must have a single origin and hence a shared hereditary system wherever it exists.

    I fully expect that this question will open up more than any of us bargained for.

    WOJCIECH BORKOWSKI · University of Social Sciences and Humanities & University of Warsaw

    It may be interested for you:

    What is Artificial Life?

    Christopher G Langton
    Editor of the Artificial Life journal


    http://www.biota.org/papers/cglalife.html

    http://en.wikipedia.org/wiki/Christopher_Langton

  • Luc Bulot added an answer:
    Do you have access to ammonoid evolution papers?
    I'm looking for 'contemporary' phylogenetic hypotheses for major ammonoid groups, I'm particularly eager to get hold of the "Towards a phylogenetic classification of the Cretaceous ammonites" series, if anyone has access?

    Cheers!
    Luc Bulot · Centre Européen de Recherche et d’Enseignement des Géosciences de l’Environnement

    Hello Tim,

    I guess that you refer to Mike Cooper work when it comes to : Towards a phylogenetic classification of the Cretaceous ammonites... Am I correct ?

    I have already atteched here the most recent ones with Hugh Owen as a co-author.

    I have all of the older ones as paper copies and will ask a friend in Germany if he has pdf of them...

    Hope this helps

    Luc

  • Reinhard Stindl 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?
    Reinhard Stindl · Alpharm, Perchtoldsdorf, Austria

    Thanks Pavel for your interesting and detailed comment. I did not say that I agree with the Nature article, I just mentioned it to show that other colleagues request an update of evolutionary theory too (in Nature!). So, I am not alone... ;-)

    I agree that everything must be programmed somewhere. Evo-devo is just a new name for an old problem, every embryologist was aware of (including Lovtrup): namely that embryonic development is highly regulated (and interconnected) and at these early stages you cannot simply mutate around...and hope that some "fitter adult organism" develops...you would just end up with a bunch of cells.

    Lastly, I did not use the argument of independent origins, I just cited an article and asked colleagues here at ResearchGate. ;-)

  • Is there any feasible solution to the taxonomic chicken-and-egg problem?
    This is probably a fun question with the chance of a strong headache. If we define a species biologically as a population of (potentially) interbreeding individuals, then at the very basis of this theorem is the notion that parents and offspring belong to the same species. It follows logically that if we could assemble a complete phylogeny of all individuals of all species that ever lived on Earth, they would all belong to the same species, because they represent a continuum of parents and offspring and there would be no possibility to define vertical limits. It does not even matter if reproduction was sexual or asexual. How can this paradox be resolved, if at all? Should taxonomy only be done horizontally to avoid this paradox?
    Chingangbam Dhananjoy Meitei · Central Agricultural University

    As far as my understanding goes egg is an evolutionary mode of reproduction and chicken is a taxon of particular identity. Egg developed into chicken exclusively after fertilization and without fertilization the particular does not developed into a chicken. So in order to produced the chicken, both male and female parents are required. So egg might developed latter the chicken. In short chicken is far ahead of chicken.

  • Christophe Menant 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.

    Louis,
    If you mean that love can limit anxiety, I of course agree. And it is not an opposite hypothesis to mine. Human love has probably been developed by our ancestors to limit the anxiety increase encountered when self-consciousness came in during evolution.
    You remember how anxiety is positioned in the scenario about self-consciousness (http://philpapers.org/rec/MENCOO).
    The evolution of inter-subjectivity carried by our primate ancestors brought them to identify with their conspecifics, represented as existing in the environment.By this process the limited representation of themselves that our ancestors had became about an entity existing in the environment, it became an elementary and embryonic representation of themselves as existing entities that can be named ‘ancestral self-consciousness’.
    But identification with conspecifics was also an identification with endangered or suffering conspecifics which has generated an important anxiety increase. To limit that anxiety our ancestors have developed performances which have procured significant evolutionary advantages favoring the evolution of ancestral self-consciousness toward our human full-fledged self-consciousness (and human love is probably part of these performances). This process brings to introduce an evolutionary engine based on a phylogenetic anxiety management which has been a root in human evolution and which is still active in our today human minds.
    So the scenario proposes that the evolutionary advantages come mostly from the performances developed to limit the anxiety increase, not that much from self-consciousness per se.

  • Steingrimur Stefansson added an answer:
    Darwin's Theory of Evolution: How to reconcile religious teaching with evolution? What is your view on this?
    Charles Robert Darwin (1809–1882) was a British naturalist and geologist, famous for his contributions to the theory of evolution. Darwin recognized that all living species have descended from common ancestors in a timely manner. Together with Alfred Russel Wallace, he released a joint publication in which he introduced his scientific theory that stipulates that such a branching pattern of evolution has been ensued from a process that he named “natural selection”.

    In 1859, Darwin published his Theory of Evolution in his famous book “On the Origin of Species”, overcoming the scientific rejection pertaining to earlier concepts of transmutation of species. In the 1870s much of the scientific community and the majority of the general public had accepted evolution as a fact. However, it was not until the emergence of the modern evolutionary synthesis when a broad consensus developed, between the 1930s to the 1950s, and in which natural selection was accepted as the basic mechanism of evolution.

    Charles Robert Darwin’s Theory of Evolution – How to reconcile religious teaching with evolution?
    Steingrimur Stefansson · HeMemics Biotechnologies Inc

    Hi Emmanuel, I forgot to add that science progresses by a process called the Scientific Method.

    Here is a good description:

    http://en.wikipedia.org/wiki/Scientific_method

  • Krzysztof Lastowski added an answer:
    Evolution
    Do lamarck's theory of adaptation has any validity or acceptance? Or It is the darwin's theory of natural selection that is 100% true and valid.?
    Krzysztof Lastowski · Adam Mickiewicz University

    The Lamarck's theory (LT) describe the process of organism's evolution (individual). The Darwinian Theory of natural selection (DT) describe evolution of species (sets of organisms). The LT assumes that evolution of organism carry on to adaptation, but DT assumes that good adaptation carry on to evolutionary success of species. LT describe valuable individual evolutionary behaviour of individuals, DT describe valuable the historical and phylogenetical process of species of evolution. Cif. K. Łastowski, The idealizational status of the contemporary theory of evolution, in: `Theoria`, San Sebastian, Mayo de 1994, Numero 20, ano IX, . 29-51 [ISSN 0495-4548]. 

  • Harald Gruber-Vodicka added an answer:
    From an evolutionary point of view which genes are rapidly evolving nuclear or mitochondrial genes and why? and what is selection pressure?
    I am working on the taxonomy of Nematodes, so for molecular characterization I want to choose molecular markers from mitochondrial genes or nuclear genes or have to work on both the genes.
    Harald Gruber-Vodicka · Max Planck Institute for Marine Microbiology

    The 18S rRNA (SSU) has been broadly sequenced for many nematode taxa and has a resolution down to the species level in most groups, but also resolves higher relationships quite well. General primers usually work and it is quite easy to get good sequences for the SSU. Apart from the SSU the mitochondrial COI would likely be your second choice, see the second papers I have attached. The paper nicely shows that a combination of the SSU with a second (e.g. LSU, COI) marker sufficently resolves species level complexes in root knot nematodes.

  • Marc Verhaegen added an answer:
    There are quite a few hypotheses to explain early human evolution: Are there ANY that explain the evolution of H. neand. and H. sapience?
    Negative answers will also be appreciated. See Anton and Snodgrass 2012, Wrangham 1999, Ungar 2006, Bunn 2007, Stanford 2001
    Marc Verhaegen · Study Center Anthropology

    Sorry, I forgot 'Homo' in '... when Pleistocene Homo dispersed globally along the coasts ...'

  • Steingrimur Stefansson added an answer:
    How do you introduce evolution to children?
    What is your practice of your first explanation or teaching with children (<10 years old) ? I mean the very first sentences.
    Steingrimur Stefansson · HeMemics Biotechnologies Inc

    Hi all. Sorry again to revive a thread that is dormant.

    If you show children documentaries about the unique life forms that exist in remote and isolated habitats and are not found anywhere else on earth, they will inevitably ask this question:

    Why do these animals only exist in these places and nowhere else?

    You have to explain that these animals have been isolated on islands, in caves, on mountains, in valleys, etc, for millennia.

    Since science only deals with natural explanations for natural processes, the only answer that does not invoke the supernatural is Natural Selection.

    Mutations that are beneficial to any animal's survival and reproduction in these habitats are selected for.

    That is the best explanation we have so far for eyeless animals found in dark caves, flightless birds in habitats with no land predators, marsupials thriving and diversifying on isolated islands with no mammalian competitors, lemurs thriving in the isolate island of Madagascar, etc, etc.

    And yes, the unique animals found only on the isolated Galapagos Islands that prompted Darwin to formulate his hypothesis on the origin of species.

  • How do you measure phylogenetic signal vs noise in a multiple sequence alignment?

    I know of a couple of measures of signal:noise ration in phylogenetic analyses, such as the consistency index and the retention index, but most phylogenetic reconstruction software packages do not compute these values and include them with the tree output.  Bootstrap values can be somewhat related to phylogenetic signal, but more often are related to the ratio of informative to noninformative (invariant within a clade) sites in the data set.

    With different data sets, I would expect that the consistency index or retention index value for good data would be different.  For example, with perfect sequencing (no sequencing errors at all) of human, chimpanzee, gorilla and orangutan I would expect CI values close to 1.  But for perfect sequencing of of the same DNA region from mammal, frog, salamander, fish, insect, the best value expected might be closer to .6 or so.  And it might be different if we have 10 widely diverse samples from each organism than if we have just one of each (10 mammals, 10 frogs etc).

    For most phylogenetic discussions I see here in ResearchGate and many other places, the focus is on the models and methods of analysis.  But in my experience, troubles with phylogenetic reconstruction giving impossible results is essentially always due to problems in the data, rather than problems in the model or method.  Good data will create a reasonable tree with any method, but it is frighteningly easy to come up with a bad data set for example due to misannotation of genes or organisms in GenBank.   And even with "perfect data" there can be problems with saturation of variable sites if we for example compare sequences from all lentiviruses, or DNA polymerase from bacteria, plants, animals, fungi.

    So, if you know of good review articles covering this topic, or you know of software that is useful for checking multiple sequence alignments for various types of quality, please post them here in the answers.

    Maximiliano Manuel Maronna · University of São Paulo

    AliGROOVE – visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support

    http://www.biomedcentral.com/1471-2105/15/294

  • Ravi Kant Upadhyay 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.

    Ravi Kant Upadhyay · Deen Dayal Upadhyaya Gorakhpur University

    Yes, plant viruses infect human beings also, there are viruses which are released into water and soil from fallen leaves of the plants, these rotting leaves possess inclusion viruses basically viruses which infect human skin. Other viruses which are important infectious agents are rotaviruses and phytorheo viruses which show their growth in pond scum, garbage vegetation, and polluted water drain inside the soil. Really, leaf curl virus is transformed into poliovirus in a long period of evolution, because it infest vein inside leaves, similarly, they attack on photosensory cells, these are nothing but neuro-epithelial receptors. Baculoviruses and Topsvirus are very near to human viruses. There is no example available on symbiosis in visruses. These are true parasites, with a parasitic assimilatory and recombining genome.  It is the transformation and addition of new environment induced mutations which have generated host specificities, but basic nature of integration to the host genome is quite similar. 

  • Manoj Kumar Jaiswal added an answer:
    How is roughness exponent calculated from power spectrum is related to rms roughness in surface evolution?

    Please suggest

    Manoj Kumar Jaiswal · Guru Gobind Singh Indraprastha University, Delhi, India

    Thanks

  • Chithan C Kandaswami added an answer:
    Why do plants synthesize substances beneficial to human health?
    Howitz and Sinclair state in a brilliant manner: “Our xenohormesis hypothesis proposes that animals and fungi (heterotrophs) have evolved the ability to sense signaling and stress-induced molecules from other species, and that they are under selective pressure to do so. In essence, xenohormesis refers to inter-species hormesis, such that an animal or fungal species uses chemical cues from other species about the status of its environment or food supply to mount a preemptive defense response that increases its chances of survival” Can anybody provide examples in which this hypothesis is unlikely?
    Chithan C Kandaswami · University at Buffalo, The State University of New York

    Metabolic pathways and  enzyme systems catalyzing the generation of polyphenolic flavonoid molecules such as quercetin and luteolin by the two crucial, ancient pathways have been conserved for millions of years, and these molecules are not merely produced in response to stressful factors.

  • Vivek Kempraj 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.
    Vivek Kempraj · National Fellow Lab, Indian Institute of Horticultural Research

    Yes Dr. Ritzel.. All possibilities are to be considered !! The interactions in nature is too complex to look at it with a single view point !! 

  • Eduardo Guillin added an answer:
    Can anybody please explain to me why Kimura's neutral theory is the inverse of effective population size?
    I read in a paper that "mutation close to neutrality accumulate independently of selection at constant rate, which is the inverse of the effective population size".
    Eduardo Guillin · Instituto Nacional de Tecnología Agropecuaria

    Hola Lucas,  

    la mutación es la generadora, en última instancia, de variabilidad; ésta se pierde por deriva génica. Cuanto mayor es Ne, menor será la deriva, y por tanto una mutación tendrá menos chances de perderse, y viceversa. La tasa de mutación es constante (en términos generales) para un locus dado. Si esa mutación es neutral (ó casi) entonces las únicas variables de las que depende la acumulación de una mutación dada (ponele que recurrente) son la tasa de mutación y el tamaño efectivo. Bajo un modelo de sitios infinitos, sólo tenés ésta última variable, ya que no hay mutaciones recurrentes.  Te sugiero leer algún review sobre teoría del coalescente. Allí se entiende muy bien esta temática. 

    Saludos, EG

  • Andrea Gazzola added an answer:
    What kind of relation is there between the Hutchinson Niche Concept and norm of reaction for phenotypic plasticity?
    The Hutchinson niche is an n-dimensional hypervolume, where the dimensions are environmental conditions and resources, that define the requirements of an individual or a species to practice its way of life. The pattern of phenotypes produced by a given genotype under different environmental conditions is the norm of reaction.
    Andrea Gazzola · University of Pavia

    Thank you for your suggestion, It seems to be an interesting page

  • Aimer Díaz added an answer:
    Are there any recent investigations into inversion theories in evolutionary biology?
    Inversion hypotheses suggest that during the course of evolution structures along the dorsoventral (DV) axis have taken on an orientation opposite that of an ancestral form.
    Aimer Díaz · National University of Colombia

    That theory have reached a great evidence support, the current investigations have focused in the regulatory and functional networks of the genes implies in the dorsoventrla axis determination. For that reason i think there's little recent theoretical additions.
    The hot topic related to the dorsoventral inversion theory in the evo-devo is the evolution and the number of origin events of the nervous system... I think these papers show this research tendency:
    http://link.springer.com/article/10.1007/s13127-011-0044-4
    http://www.nature.com/nrn/journal/v10/n10/abs/nrn2703.html
    http://onlinelibrary.wiley.com/doi/10.1111/j.1525-142X.2010.00460.x/abstract;jsessionid=4B7D2F58D4FC0BAC520DE090C40A5E44.f02t01?deniedAccessCustomisedMessage=&userIsAuthenticated=false
    http://www.biomedcentral.com/content/pdf/2041-9139-4-27.pdf

  • Aimer Díaz added an answer:
    What is the limit of DNA evolution in any trend?

    Every cell and organism depending on the exposed environment, are in a continuous process of evolution, is there any limit.If yes what are those factors.

    Aimer Díaz · National University of Colombia

    There's a lot of ambiguity
    I understand your question like this: ¿If we develop a RNA or DNA self replicating molecule, and we left them into a million years experiment, would be appear an primitive organism, a primitive cell?
    Well if your question is something similar to the last one.. So my answer is that NO. The evolutionary dynamics at the genetic level is not enough to build anything with certain level order or organization. There is a little contribution of genetic change in the major evolutionary transitions.
    One example of another factors needed, could be the concept of membranome proposed by Cavalier Smith, that refers to the positional information of the lipid and protein components of the cell membranes

  • Lahcen Benomar added an answer:
    What is the difference between plasticity and acclimation? Is acclimation mediated by plasticity?
    I'd like to know if there's a clear criterion for the differences
    Lahcen Benomar · Laval University

    Dear Matesanz

    Broadly, acclimation is a special case of phenotypic plasticity. Acclimation refers specially  to physiological process. Thus, long term thermal acclimation of photosynthesis is a case of plasticity 

  • Leonardo Maurici Borges added an answer:
    Can orthologous sequences be symplesiomorphic?
    As I understand, both are "homologous". Is the term "ortholog" used only for referring to a synapomorphic character state?
    Leonardo Maurici Borges · University of São Paulo

    Nikolaus, I think we are more or less saying the same thing. I need to check Patterson 1998 again to be sure, however.

    Anyway, what you said is that paralogy fails the conjunction test, in other words, there is a relation of homonomy between the regions. A orthologous sequences passed all tests and are, hence, homologous.

    If I am not mistaken, you can also have duplication events followed by deletion events and what looks like a single copy will show itself paralogous only after phylogentic analysis. If my memory don't fail me, there is a Nelson paper discussing that issue.

    Cheers,

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