LOGIN

RSS Facebook Twitter YouTube
GLOSSARY       

SEARCHGLOSSARY

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

PROFILESEARCH

BillT

Forum Replies Created

Viewing 15 posts - 16 through 30 (of 154 total)
  • Author
    Posts
  • in reply to: Zootaxa 3994(1) #354971

    BillT
    Participant

    OK forgot about the synonyms.

    Are the listed names in the note section searchable?  If so that would work fine since one goal would be to find fish by search.

    Would the notes list include the most popular name also?

    Realistically, I am not sure it makes much sense to keep adding an increasing number of poorly applied names. Mostly I like the scientific names but its annoying when they change frequently.

    Presumably databases will have individual identifiers for each species which are not their scientific name so things remain easy to track through these changes. An official taxonomically determined identifier would be nice (because everyone could use the same one), but it would have to be separate from the scientific names which have additional (phylogenetic) meaning. Perhaps this would be like L- numbers which I don’t know a lot about.

     

    My idea answer to the situation of conflicting naming systems would be to find a way to present both with an explanation of their differences. Drawings, phylogenetic diagrams, and text with a bunch of parentheses (like this: (vs. So and So, date, Genus species)).

    Generally speaking, probably time consuming and only worth doing where there would seem to be some controversy on the subject.

    in reply to: Zootaxa 3994(1) #354967

    BillT
    Participant

    Thanks for the fix Matt.

    How many of these Chain Danios are available for hobbyists?

    Is Danio dangila the only one or are other species being mis-identified as that?

     

    General rant WRT your question:

    Since there seem to be an ever increasing number of sps in the Danio clade (meaning danios not including Devarios and their relatives), the splitting approach makes sense to me as it gives reasonable names to the sub-branches of the larger clade. To me these are names defining smaller parts but leaving the underlying phylogenetic relationships largely the same. The new genera, to my eye, make sense with the species they group together.

    On the other hand lots of people are confused by name changes, especially if they don’t know much of the fish to begin with.

    In the long run, it should go with what taxonomists say. How they come to a final decision as a group is a bit beyond me though.

    However, I think it would be helpful to have a list of scientific name synonyms (perhaps a historically based list), so one could identify the former names of the particular species.

    A similar list of common (or informal) names would be helpful. Many of theses should be called trade names, since that is the source of many and their purpose would seem to be promoting sales. In addition, many informal names are used for multiple species (like blue danio which I have seem attached to several different species). It would be useful that have a list of the different species a common name of multiple use refers to (to answer the question: what species have been referred to as blue danio?).


    BillT
    Participant

    Me too!

    in reply to: Zootaxa 3994(1) #354962

    BillT
    Participant

    For me (OSX/Firefox), both links go to the second (less interesting to me!) paper.

    in reply to: Danio and Barilius in an open tank – bound to fail? #354881

    BillT
    Participant

    Large and mid-sized danionins are certainly jumpers.

    Floating plants inhibit their jumping out.

    Lack of scarey stimuli (sudden noises, light changes, movements) also helps. Some tanks I have visually screened to keep them more calm.

    in reply to: Long fin pearl danio #354869

    BillT
    Participant

    Researchers would like them because they would provide a lot of genetic differences that could be used for molecular genetic mapping of mutants (mostly from zebrafish). This has not worked out, because of their reproductive problems.

    Certainly no true of all fish. Platies and swordtails are a good examples of fish that hybridize well and have produced nice fish, but that group has a recent evolutionary history of hybridization.

    in reply to: Long fin pearl danio #354867

    BillT
    Participant

    Its my recollection that Danio fertile hybrids (generally speaking) are not very common or robust.

    If you get some that can breed and breed, them they don’t improve much.

    It might be possible to backcross to one of the original species to get a more normal set of chromosomes and a more robust hybrid.

    in reply to: Long fin pearl danio #354860

    BillT
    Participant

    Sounds like you might have read this:

    abstract

    in reply to: A Glofish Selection Experiment #354813

    BillT
    Participant

    The entire mechanism is not clear since unlike other coloration in the fish it does not go through chromatophores but likely comes from a pigment present in every(?) normal cell. (When I raised GF the color showed up in larva earlier than chromatophores could develop)

    Glow fish glow because they have one or more gene(s) for a fluorescent protein inserted somewhere in their genome. Exactly where the gene goes in the genome affects where and at what age the gene turns on and off. If a cell has such a fluorescent protein in it, it will fluoresce.

    A molecule is fluorescent when it can absorb a photon of light, and then release a photon of lower energy (which has a shorter wavelength). Not all molecules can do this. The protein in glofish was first discovered in a jellyfish and was adapted for research uses. It was also modified to change the wavelength of light it releases. The proteins releasing different colored proteins have cleaver names like GFP (green fluorescent protein), RFP (red fluorescent protein), BFP (blue fluorscent protein).

    This has been done lots of times for research purposes. Here are pictures of GFP and some other colors in research zebrafish. One common research use is make a specific set of cells fluorescent (so they can easily bee seen) and then do something the affects them. This is most useful when very small numbers of cells are labeled. It often takes a microscope to see them. This could be something like change the shape of an axon of a neuron in the nervous system or where some group of cell.

    There are some lines of GFP fish which lay glowing eggs. They stayed glowing in most tissues through development and into adults. Other lines might fluoresce only at certain stages of development. If you look closely at some glofish you can see differences in the details of which parts are glowing.

     

    first there was an insertion of a recessive allele to suppress the normal coloration, this produced a (call this Base) form that is somewhat in the albino direction

    What you are calling the base form is just normal (not transgenic) mutations that are combined to make the fish more clear by suppressing normal pigment formation. This lets more of the light that activates the fluorescence in and more of the emitted light can get out to be seen.

    In labs these lines are fish are easy to get and would be used for this purpose. Here is an article on the current favorite line for doing this.

    in reply to: A Glofish Selection Experiment #354791

    BillT
    Participant

    OK, let me know your e-mail and I can send a copy of the article to you (or anyone else interested).

     

    I do not think there is a possibility of fading color, the line is likely the same as on day 1. (I bred them a few gens and did not see any color deterioration)

    There are at least two ways the expression of a gene inserted into a genome using techniques from around the turn of the century could get reduced soon after they are made. Genes were then added to ZF by injecting DNA encoding the genes into fertilized eggs. Enzymes in the egg recognize the cut DNA ends and “fix” them by sticking them to other cut ends or making a cut in the some chromosomal DNA and sticking the inserted DNA on to those cut ends. This can lead to multiple site in insertion on the same or different chromosomes.

    Fluorescence is thought to go up and down with gene copy number in a fish. Subsequent breeding and separate the different insertion sites such that they go to different sperm or eggs and pass on fewer copies of the genes to offspring. Strings of an inserted gene lined up at one site (is called concatenation) are subject to either increases or losses on the number of genes in the group by inexact crossing over among chromosome pairs which would add gene copies to one chromosome but remove from the other. These two mechanisms can remove gene copies and therefore reduce expression and therefore fluorescence early in the life of the transgenic line (first few generations). Usually these losses stabilize, perhaps because all the easy losses have occurred. There could still be differences between heterozygous (fluorescence is dominant) and homozygous fish.

    Modern transformation mechanisms for ZF use molecular techniques like Crisp3r to do more controlled inserts. So these problems may not be as significant now.

     

    I’m skeptical it is possible to reprogram the personality part of genome in a small number of generations…. otoh the difference between tank and wild raising has a huge impact. (As one current example on my end : Sew03 (loach) juveniles are way more accepting of me than the w/c adults… and one generation with no selection cannot possibly alter the genome.

    The paper (A potential model system for studying the genetics of domestication: behavioral variation among wild and domesticated strains of zebra danio (Danio rerio). Barrie D. Robison and William Rowland Can. J. Fish. Aquat. Sci. 62: 2046–2054 (2005).) is about the genetics basis of behavior as seen inn hybrids of the two lines they used. They crossed them together and mixed the genetics 50-50. So there is a lot of genetic change, but not, at that point, due to selection.

    One possible way selection could have an effect in one generation is if you got very few survivors in the first generation or two. Any survivors might be surviving because of some genetic advantage (perhaps a combination of low frequency alleles in several different genes) they have unbeknownst to you. They then pass this on to the next generation where the likelihood of these combinations being reproduced are increased because the alleles are now dominant in your breeding population. Suddenly the fish do better the next generation.

     

    Another tangentially relevant point about selection is that smaller selective differences will have a stronger effect in populations of larger size. Home aquarium population sizes are usually small, lab population sizes a bit larger, fish farms very much larger, and wild populations immense. Smaller selective advantages can have effects in large populations while they might be slower acting or be swamped out be drift in smaller populations. Selection in a small population would have to be very strong to act fast. Flat out survival would probably work.

    in reply to: A Glofish Selection Experiment #354788

    BillT
    Participant

    The glofish were first made in a lab in Singapore. They were intended to glow when exposed to some environment toxin as a bioassay. This did not work out well (they glowed without the toxin), so they eventually got re-purposed as pets.

    At least for the last few years glofish have been raised in one or more fish farms in Florida. It seems likely to me that they regenerate their large breeding populations periodically in order to maintain their high intensity glow. This would allow genetic changes to be made before the new group gets expanded to a production breeding population.

    It is likely they have been outcrossed to improve their husbandry traits etc. However, it is neither clear if this actually occurred nor how many times it might have been repeated.

    Outcrossing would make for big genetic changes (somewhhat random with respect to the environmental conditions). Selection in the fish farm environment would be much slower and would depend on pre-existing genetic diversity in the population or on the creation of new mutations which is usually slow. Selection would adapt the population to its current conditions.

     

    At least some of the traits are genetic. Here’s a paper on the Nadia line of WT fish which I got started sometime around 2000 claiming most are:

    A potential model system for studying the genetics of domestication: behavioral variation among wild and domesticated strains of zebra danio (Danio rerio). Barrie D. Robison and William Rowland Can. J. Fish. Aquat. Sci. 62: 2046–2054 (2005). This is behind a paywall, but I have a copy of this if you are interested.

    Abstract: The process of domestication in fish is fundamentally important to conservation efforts because of the extensive
    use of hatcheries to mitigate population declines. Research into the genetic changes associated with the domestication
    process in many endangered species is impeded by a lack of genomic tools, long generation times, and large space
    requirements. The study of the genetics of fish domestication could therefore benefit from the introduction of a model
    system. In this paper, we document behavioral and growth rate differences observed between a domesticated laboratory
    strain of zebra danio (Danio rerio) and a strain newly introduced into the laboratory from its native habitat in India.
    Domesticated zebra danio showed a higher degree of surface orientation, a reduced startle response, and higher growth
    rate compared with wild zebra danio. Wild–domesticated interstrain hybrids were intermediate in phenotype for all
    traits. When strains were reared together, most interstrain behavioral differences were maintained, indicating a genetic
    basis underlying the interstrain phenotypic variation. Phenotypic differences observed in this study are consistent with
    the effects of domestication in other fish species, indicating that the zebra danio can be used as a model system for
    studying the genetics of the domestication process in fish.

    in reply to: A Glofish Selection Experiment #354784

    BillT
    Participant

    Actually, once you make a hybrid however, the background genetics of the different lines will be blended together. Neither will win out totally. There are something like 20-30,000 genes. No set (from one parent or the other) is going to fully will out in competition, especially in new (to the fish) environments like living in an aquarium. Furthermore, you will only be able to assess and score visible mutations (unless you use molecular biology). You will not be able to determine the presence or absence of most of the background genes.

     

    The way I think of lab line genetis, there are three kinds of zebrafish lines: lab lines, fish farm lines, and lines recently started from fish collected from the wild.

    Lab lines are generally more inbred and are more difficult to handle (husbandry-wise) presumably for reasons typical of inbreeding problems, fixation of may slightly deleterious mutations in their genetic background. Most lab lines have breeding population sizes 20-200 fish/generation, with smaller numbers during selections. In addition, two of the most popular lines (AB and Tübengen) underwent very strong selections when they were established and have recently been shown to lack a significant part of their sex determination system.

    These fish have been selected to be breedable by squeezing out eggs and sperm. They were also selected for a reproducible look to their embryos and being raised in certain conditions. Some of these lines were made homozygous in two generations. This allows more deleterious mutations to be fixed because they are not being selected out of the line over many generations. Visible mutations however, (including those affecting embryo development) have often been selected out.

    Farm lines are often selected for fecundity (labs line were not until recently), can be larger than wild caught fish or lab lines. Often raised outside, but protected from large predators they tend to lose predator avoidance behaviors of wild fish.

    The way they breed their fish selects for fecundity (which until recently was not done in lab lines) and therefore large size. They have large breeding populations (probably 1,000 – 100,000) and therefore can maintain their genetic diversity better. They frequently carry background mutations. Fish farm fish can have diseases but are robust.

    Wild caught fish generated lines are smaller than fish farm lines. They come from populations that are presumably immense, but are then maintained with lab techniques using much smaller population sizes. Their genetic diversity will be undergoing reduction. Selection should be applied to maintain desired traits during this period, lest something undesirable get fixed.

    These lines (at least initially) have some obvious predator avoidance behaviors that are lost in the aquarium environment (because no predators makes them a waste of energy). These include:

    1) Feeding Behavior: The will mostly stay 4-8 inches below the surface, dash up to the water surface to grab a piece of food and then and then immediately back down to cruising depth. Reducing exposure to predators. More “domesticated” lines will “lawn mow” the surface, sucking in the food way more efficiently.

    2) Flee or Approach: In 30 G tanks with the ends towards the sides, wild caught fish lines will flee to the back 20% of the tank when some one approaches one side (such as when feeding). Fish from the more “domesticated” lines will often crowd toward the front in expectation of being fed.

    Living in an aquarium will put the fish from these different backgrounds, under different selections. Wild caught fish, for example, are often more difficult for the first few generations living in aquariums.

    in reply to: A Glofish Selection Experiment #354780

    BillT
    Participant

    Yes! This leaves a lot unanswered.

    Here are some possibilities:

    The original glofish were made many years ago and were probably done in a way where many copies of a gene are inserted end-to end at a single site in the genome, or in several different sites. This can change in the first few generations of breeding as some of the end-to-end duplicates get deleted and genes at separate sites could become separated as chromosomes sort out differently among an animal’s progeny.

    This can lead to a reduction of brightness. much of this should have happened many years ago. Fish from each generation should be selected for brightness before being bred. Not likely to happen in a big fishfarm population (hundreds of thousands of fish). This short blurb did not mention the source of the fish or details of their genetics.

    There are several colors of glofish, only one color was tested. Effects might vary with color.

    GM fish (in labs at least)  are often crossed to other lines and then crossed together to recover the homozygous state (2 copies) for the flourescent gene. Each out cross replaces half the genes not being selected for with those to the line being outcrossed to. This will tend to replace genes from the first line with some of those from the second line. The genes removed and replaced could have either a “good” or “bad” effect on the first line.

    To do a more perfect experiment of this type (which is done in mouse genetics labs) you would do backcrosses for about 20 generations. This would reduce the differences between the two strains to some small fraction of a percent, leaving only a relative few genes different between the strains. It takes years to go through these breeding steps before such a experiment could be done. The comparison could then be made between the two different strains with their genetics close to identical.

     

    Common assumptions (among scientists) of why these fish would lose out is that:

    1) Randomly throwing a gene into the genome could mess something up by inserting somewhere where it could break an gene or its controllers could have some negative effect.

    2) There will be an energetic burden on the animal because it has to produce an extra protein which provides no offsetting adaptive advantage.

    These hypotheses were not really addressed by the experiment. Each answer leads to more questions.

    in reply to: Nitrate levels up.. #354756

    BillT
    Participant

    Nitrates will naturally raise over time as ammonia is transformed to nitrites and nitrites are transformed to nitrate by bacteria in standard biofilter.

    The nitrates are the end of this aerobic degradation pathway so they pile up.

    Usually they are removed by water changes (which will also remove any other accumulating things that might also be accumulating from bacterial or fish metabolism).

    Alternatively, they can be reduced with more complex filtration systems that either have a anaerobic filter environment of additional unusual filter substrates (housed in a separate filter). These approaches favor bacteria that remove oxygen from the nitrates. This can lead to the generation of nitrogen gas (which diffuses out of the water) and the decrease of nitrates.

    This can also go on in little nitches in your aquarium that have low oxygen levels, such as in gravel where there is not a lot of water circulation.

    Of course the more food you throw, in the more nitrogen, (in the form of ammonia, nitrites, and nitrates you water system will have to deal with.

    You could also use a chemical filtration media to remove the offending compound(s). This would either require periodic money and labor for media replacement or labor for media regeneration.

    Personally, I would just change the water until you get your nitrates to your desired level.

    in reply to: Lab Diet for Danios #354746

    BillT
    Participant

    Opps. It is Skretting (an aquacultural fish food maker) that makes the larval diet:

    http://zebrafish.skrettingusa.com/

    The prices on these foods are not cheap you might notice.

     

    The larval diet apparently works great. Many labs can eliminate using live foods for larvae completely.

     

    ZM has been around for many years and a lot of people in European labs use it.

Viewing 15 posts - 16 through 30 (of 154 total)

     Next Entries »