Genetic Drift?

[Broccoli Head]

Cannabis breeding, if one wants to call it that these days, is the last frontier for the scientifically and mathematically challenged.

Nothing these hacks do now would be considered acceptable practices in any other breeding field......We have breeders taking clone onlys like Sour D and outcrossing them and saying they have an IBL...get real!

 

[John Public]

I was talking about Conservation of lines, not breeding.

Nail on the head! you gotta get up dam early to catch Sam out kids! He's on the roll

In fact, I was just thinking at this sentence of Sam before visiting the topic. And I think this assertion is very dependent of what you put in the definition of these words.

Wikipedia quotes "Plant breeding is the art and science of changing the genetics of plants for the benefit of humankind " whereas conservation (genetics) is described as "an interdisciplinary science that aims to apply genetic methods to the conservation and restoration of biodiversity. "

So how does this apply in the Cannabis context?

I think one misunderstanding is to want to conserve "statically" the gene pool of a sub species, implicitely believing that it is the case in the natural environment. But this is mostly false, depending of the context however. Most natural environments are indeed changing environments.

I'll detail here an example with a theoretical domesticated Cannabis line. I chose this kind of line because from what I read, THC production is supposed to be a man-related traits, selected by farmers in other words. And I think most people here are interested with drug lines and not with lines such as Carmagnola.

So suppose I visit an area somewhere in a nice tropical place of the world where the living is better than in my Western climate (when you have the western money to spend your hollidays there).

I find a nice sample of smoke there, very different from other areas that I could visit. Why is this line so special? I suppose it has evolved over the year to have this special gene combination that gives this special combination of cannabinoid production. And also, it has a special grow shape, a special flowering time, a special rate of hermies and so on... All that special traits come from a selection pressure that narrowed the gene pool so that the strain is stable for this traits and the farmer can know that when he plants the seeds he can expect this kind of special results.

How did this arrive? I think with a combination of selection pressures, both from man (manual selection of the best males and females) and also from the natural environment. We may say that the natural environment provides a first step of selection(some individuals won't flower because of some special conditions of the environment and from generation to generation, the gene pool will fit this special conditions) and the man will induce a second step by selecting not only those that can reproduce but those in them that fit the best his requirements.

I have to notice that the strain that I liked and that I obtained from seeds is just a picture of what is the state of the line at this moment, and at this place. If I went to another place, with another farmer, I would maybe obtain a strain that is very close but slightly different because the farmer preffered the individual leaning to the apple smell side rather than the orange smell side.

So now imagine the strain is in near to be extinct. What are the causes? Did the environment change or did the farmer choose another line to grow, or cross it to another line to obtain hybrid vigor? That is important to know that because it is not the same at all.

If the environment has changed or if the farmer has changed its practices on the field, then why should I try to conserve this line as it was 30 years ago? After all, that is a matter of human perception, as this line that I appreciated so much came via the natural selection as well, at least for some part. So to decide that this time, the nature should keep the older version is somewhat a morale choice. Then if I still decide to try to conserve the older version, then I just have to recreate the same environment and put the same selection pressure than the farmer in this tropical area and then the numbers arrive, according to the number of loci to have to preserve to keep the special traits alive and healthy in the gene pool, I have to define how many individuals I need each generation to do so.

And in this situation, I believe there will be still a genetic drift in the gene pool, even in a perfect greenhouse with heat and lights, because until now, we do not know how to re create the natural environment perfectly. We can make soil analysis, light analysis for spectra and intensity, heat analysis, humidity analysis, but it is still difficult to simulate all these factors perfectly at the same time. Many experiments have shown that for many species in the biological conservation science.

Genetic drift is a natural way of evolution. Whether you find it positive or negative is a man-based point of view. Believing that we can preserve perfectly a gene pool is imho something false in the current state of the art of conservation science.

I say that because we should not stop trying to preserve as we see the huge numbers that are necessary theoretically. Whether it may be true that 7 000 individuals are needed to make a 99% conservation of the genepool, I think we should first ask what are the priorities. It may be a good thing to try to avoid absolutely the genetic drift, but in our contexte, can we afford this really? How many people can reserve a greenhouse per year to reproduce 7000 individuals of a strain that takes more than 16 weeks to flower and produce less that the first dutch polyhybrid, in an illegal context?

So imho, conservation is a kind of breeding, in our current context.

Anyways, I'm frustrated that there's no 'how to preserve cannabis for dummies' like me that covers all (cannabis) relevant points.

I don't know it is possible to cover all relevant points of this subject, but here may be few starts:

- define how many traits have to be preserved (i.e. what makes this line so special?)

- define the natural environment of the line and the way it was farmed

- try to build the environment as close as the natural environement of the line

- try to recreate the selective pressure induced by the farmer, so that the global selective pressure on the line remain constant

- try to find other people to help you. Consider that a greenhouse with 1000 individuals represent a 500x500 potential combination of individuals if every male pollinate every female and the sex ratio is 1:1 (not mentionning how meiosis may increase this number). You can also obtain this number by using 100 friends that grow each 100 individuals of the same generation and share randomly the seeds.

- Freeze 10 000 seeds of each generation.

I think this shows that in our context, conservation of Cannabis is a matter of collective work between the Cannabis lovers. That's why it is impossible.

 

[Cuzin_Dave]

Brocolli, what would be great is someone is someone breeding out a great Diesel line.

 

[dank.frank]

^^^

A dream of mine as well...a rock solid basic diesel...


dank.Frank

 

[Sam_Skunkman]

In fact, I was just thinking at this sentence of Sam before visiting the topic. And I think this assertion is very dependent of what you put in the definition of these words.

I find a nice sample of smoke there, very different from other areas that I could visit. Why is this line so special? I suppose it has evolved over the year to have this special gene combination that gives this special combination of cannabinoid production. And also, it has a special grow shape, a special flowering time, a special rate of hermies and so on... All that special traits come from a selection pressure that narrowed the gene pool so that the strain is stable for this traits and the farmer can know that when he plants the seeds he can expect this kind of special results.

How did this arrive? I think with a combination of selection pressures, both from man (manual selection of the best males and females) and also from the natural environment. We may say that the natural environment provides a first step of selection(some individuals won't flower because of some special conditions of the environment and from generation to generation, the gene pool will fit this special conditions) and the man will induce a second step by selecting not only those that can reproduce but those in them that fit the best his requirements.

I have to notice that the strain that I liked and that I obtained from seeds is just a picture of what is the state of the line at this moment, and at this place. If I went to another place, with another farmer, I would maybe obtain a strain that is very close but slightly different because the farmer preffered the individual leaning to the apple smell side rather than the orange smell side.

So now imagine the strain is in near to be extinct. What are the causes? Did the environment change or did the farmer choose another line to grow, or cross it to another line to obtain hybrid vigor? That is important to know that because it is not the same at all.

If the environment has changed or if the farmer has changed its practices on the field, then why should I try to conserve this line as it was 30 years ago? After all, that is a matter of human perception, as this line that I appreciated so much came via the natural selection as well, at least for some part. So to decide that this time, the nature should keep the older version is somewhat a morale choice. Then if I still decide to try to conserve the older version, then I just have to recreate the same environment and put the same selection pressure than the farmer in this tropical area and then the numbers arrive, according to the number of loci to have to preserve to keep the special traits alive and healthy in the gene pool, I have to define how many individuals I need each generation to do so.

And in this situation, I believe there will be still a genetic drift in the gene pool, even in a perfect greenhouse with heat and lights, because until now, we do not know how to re create the natural environment perfectly. We can make soil analysis, light analysis for spectra and intensity, heat analysis, humidity analysis, but it is still difficult to simulate all these factors perfectly at the same time. Many experiments have shown that for many species in the biological conservation science.

Genetic drift is a natural way of evolution. Whether you find it positive or negative is a man-based point of view. Believing that we can preserve perfectly a gene pool is imho something false in the current state of the art of conservation science.

I say that because we should not stop trying to preserve as we see the huge numbers that are necessary theoretically. Whether it may be true that 7 000 individuals are needed to make a 99% conservation of the genepool, I think we should first ask what are the priorities. It may be a good thing to try to avoid absolutely the genetic drift, but in our contexte, can we afford this really? How many people can reserve a greenhouse per year to reproduce 7000 individuals of a strain that takes more than 16 weeks to flower and produce less that the first dutch polyhybrid, in an illegal context?

So imho, conservation is a kind of breeding, in our current context.



I don't know it is possible to cover all relevant points of this subject, but here may be few starts:

- define how many traits have to be preserved (i.e. what makes this line so special?)

- define the natural environment of the line and the way it was farmed

- try to build the environment as close as the natural environement of the line

- try to recreate the selective pressure induced by the farmer, so that the global selective pressure on the line remain constant

- try to find other people to help you. Consider that a greenhouse with 1000 individuals represent a 500x500 potential combination of individuals if every male pollinate every female and the sex ratio is 1:1 (not mentionning how meiosis may increase this number). You can also obtain this number by using 100 friends that grow each 100 individuals of the same generation and share randomly the seeds.

- Freeze 10 000 seeds of each generation.

I think this shows that in our context, conservation of Cannabis is a matter of collective work between the Cannabis lovers. That's why it is impossible.

You are much to concerned with environment, if you take a "variety" from an area, and try and allow the plants to fully finish in a greenhouse, you have the genes, and if the variety is taken back to the area it will express the same phenotypes as before, even if not fully expressed in the greenhouse. Concentrate on the genotype, be sure to use populations large enough to avoid gene loss. Keep it simple.
Of course the best way is to have traditional Cannabis production, large populations, in given areas, with no outside genes allowed in.

-SamS

 

[englishrick]

^^^ i agree,,,,,,the best way to breed is to extract the most desirable traits from our "global genepool", then isolate yourself and the genes

imo,,conserving supirior genotypes is the name of the game!!,,,im stll working out how to do it efficently

 

[Grat3fulh3ad]

You are much to concerned with environment, if you take a "variety" from an area, and try and allow the plants to fully finish in a greenhouse, you have the genes, and if the variety is taken back to the area it will express the same phenotypes as before, even if not fully expressed in the greenhouse. Concentrate on the genotype, be sure to use populations large enough to avoid gene loss. Keep it simple.
Of course the best way is to have traditional Cannabis production, large populations, in given areas, with no outside genes allowed in.

-SamS

 

[cannaboy]

^^^ i agree,,,,,,the best way to breed is to extract the most desirable traits from our "global genepool", then isolate yourself and the genes

imo,,conserving supirior genotypes is the name of the game!!,,,im stll working out how to do it efficently

All you do rick is make a clone its easy no math or owt to do..

 

[John Public]

You are much to concerned with environment, if you take a "variety" from an area, and try and allow the plants to fully finish in a greenhouse, you have the genes, and if the variety is taken back to the area it will express the same phenotypes as before, even if not fully expressed in the greenhouse. Concentrate on the genotype, be sure to use populations large enough to avoid gene loss. Keep it simple.
Of course the best way is to have traditional Cannabis production, large populations, in given areas, with no outside genes allowed in.

-SamS

I keep it simple

What I'm saying is about the "wild" strains which are not only in man hands, I say that even in the perfect greenhouse you'll have a genetic drift, even with 7000 individuals. Because in nature, the genetic diversity of such strain is most likely maintained between massive fields which exchange pollen coming from dozen of kilometers throug the wind. Most population viability analysis show that a metapopulation equilibrium has to be reached so that the diversity is maintained in the whole population. This exchange of genes from time to time from patch of populations having a slightly different environment and thus slightly different gene pools allow the strain (this time as a whole) to have a global diversity that is sufficient to face changing conditions and that is why "wild" strains have allways many phenos. I do not see why this process would not happen with sublines of Cannabis, which is an anemophilous and dioecious specis, as it is recognized for allmost all populations of any species, even mosses.

see this reference about selfing, metapopulation and inbreeding depression
A Metapopulation Perspective on Genetic Diversity and Differentiation in Partially Self-Fertilizing Plants
Pär K. Ingvarsson
Evolution, Vol. 56, No. 12 (Dec., 2002), pp. 2368-2373

this one for effect of metapopulation on genetic diversity

Genetic structure and gene flow in a metapopulation of an endangered plant species,Silene tatarica
N. TERO, J . ASPI, P. SIIKAMÄKI, A. JÄKÄLÄNIEMI and J . TUOMI
in Molecular ecology, 2003, 12, 2073–2085


I agree this may not be (or at least be less) the case for "farmer" strains that have been selected over centuries. My experience is that most "wild" strains I grew were in fact farmer strains and they were very homogeneous and had no inbreeding depression in the next 4 following generations grown indoor. This was not the case with the Nepalese/North Indian lines that I have grown, but I was not surprised as I read that these areas still contain wild cannabis stands.

Here is a discussion of what is a landrace:
http://books.google.fr/books?hl=fr&...zMDQdEQEYkO-SaokAIzKV3sRA#v=onepage&q&f=false

If you have only one place which is not the native place, with one kind of selective pressure for several generations, it is likely you'll have a genetic drift that will narrow the gene pool, compared with what happens in nature, with open pollination through the wind.

But I agree with you we do not have to work at this scale when talking about "drug strains". Moreover, I believe that with 100 individuals crossed together each generation, you're ok to preserve the most interesting traits of a farmer lines that has been already inbred over the years.

If you want to keep the whole diversity of a natural cannabis strain that open pollinates at a valley scale, then I agree with you when you say many individuals are needed, and even believe that you're underestimating the numbers and the pattern needed to have a long term preservation of the line.

Genetic evolution is a matter of "isolation then communication then isolation then communication" events between the sub populations, and it is almost impossible to recreate it, that's why I say that "to preserve" doesn't mean much if the objectives of what traits need to be preserved are'nt clearly stated. It is simple.

 

[Cuzin_Dave]

Sam is right on about the environment and genes thing. Equatorial sativas grow in conditions of 12/12 light cycles for example or a Pakistani Indica is adapted to low humidity and the ability or survive temperatures well above 40 Celsius. Plants have the right genetic information to thrive for their given environment.

 

[englishrick]

All you do rick is make a clone its easy no math or owt to do..

cloning is 1 good backup method ,,,but what if i want to shut down my mother room and i cant back-up my origonal mothers at another location,,,

what is the best thing to put in the freezer?...because selfed seed would defo be 1st on my list!!

1 day id hope to go back to the freezer and re aquire my be-loved traits

 

[cannaboy]

I hear you Rick but the day you stop a mother room will be the day you loose what you had!!!!

What other way other than clones is there?????

Fem is Bollocks way to save stuff,, Try some normal Male on female and you will get better stuff dude,,

Unless you are sam or shantibaba or a gene bank The best stuff for the freezer is food... Genetics should IMHO be in a jar to smoke a growroom or some soil somewhere growing not staying dormant to become unviable.. I however trust sam to be the holder of some NEW WORLD ORDER STUFF!!!

 

[Cuzin_Dave]

The basic concept with respect to genetic drift is that small isolated populations evolve in a very rapid and unsystematic fashion due to sampling error and habitat fragmentation.
Clones are genetically frozen, so to speak and they do not evolve as a population large or small would.
Population geneticists use the example of "founder effect" where an isolated population winds up with a high propensity for certain diseases due to the build up of a high frequency of negative recessive alleles consistently accumulating in the breeding population. Carriers mate with carriers until the allele becomes fixated at a very high frequency with detrimental consequences.

 

[englishrick]

it is possible to retain many priceless traits without cloning!!!,,,,,,

"selfing leads to very rapid increeses in homozygosity,,,,,starting with a heterozygote (F = 50) F takes the values 0.75, 0.875, 0.9375, 0.9688 , 0.9844, 0.9922..in sucsessive generations of selfing thus exeeding 0.90 in the third generation,,,

under continued mating of 2 inderviduals per family [full sibs] F is not expected to exeed 0.90 untill the 17th generation"

selfing schemes are by far the most comon in breeding outcrossing plants

you can take things from heterozygote to homozygote mutch quicker with selfing schemes ,,,,you can exeed 0.90 in the 3 genereation!!,,,,you gota go all the way to F17 to exeed 0.90 if you doing full sib mating

 

[Texicannibus]

The basic concept with respect to genetic drift is that small isolated populations evolve in a very rapid and unsystematic fashion due to sampling error and habitat fragmentation.
Clones are genetically frozen, so to speak and they do not evolve as a population large or small would.
Population geneticists use the example of "founder effect" where an isolated population winds up with a high propensity for certain diseases due to the build up of a high frequency of negative recessive alleles consistently accumulating in the breeding population. Carriers mate with carriers until the allele becomes fixated at a very high frequency with detrimental consequences.

Dave I know I sent you a PM thanking you for your posts in this thread. I find them very informative and easy to read and grasp. This makes alot of sense and is easy to understand. Im curious how small populations(plants) on islands dont suffer from these types of detrimental consequences or do they and I just havent taken notice. Thanks man

 

[Texicannibus]

To add to this ... from a article I have found about some sheep.
http://www.terradaily.com/reports/Remote_Sheep_Population_Resists_Genetic_Drift_999.html (external link)

Quote:
A whimsical attempt to establish a herd of mouflon for sport hunting on a remote island in the Indian Ocean 50 years ago has inadvertently created a laboratory for genetic researchers and led to a surprising discovery. A mouflon population, bred over dozens of generations from a single male and female pair transplanted to Haute Island from a Parisian zoo, has maintained the genetic diversity of its founding parents. This finding challenges the widely accepted theory of genetic drift, which states the genetic diversity of an inbred population will decrease over time.
"What is amazing is that models of genetic drift predict the genetic diversity of these animals should have been lost over time, but we've found that it has been maintained," said Dr. David Coltman, an evolutionary geneticist at the University of Alberta.

"We think this has happened because natural selection is more important to the evolutionary process than is commonly believed," he added.

 

[Cuzin_Dave]

Tex, the thing with small isolated populations is that they either survive and thrive or go extinct due to inability to survive environmental pressures or genetic bottlenecks. If the genetic adaptive complexes are not there then extinction is a possibility.

 

[Texicannibus]

Aye the article sites the tough conditions prevelant on that island as a possible reasoning for the population retaining the genetic diversity it started with. I just think its interesting and shows the possible relevance of 'natural selection' in our case though 'selection'.

Edit: I also think the article shows that models are helpful in determining genetic diversity inclinations but dont always accurately predict because of selection.

 

[Cuzin_Dave]

I was able to find a sample tableau on genetic drift. It is straightfoward, easy to understand and saves doing a lot of iterations on the calculator.

http://www.fao.org/docrep/006/x3840e/X3840E05.htm

 

[Yankee Grower]

Cannabis is an annual and not a perennial and that's part of the problem right there. In nature it goes to seed every year then starts over after being dormant over Winter. A breeder friend taught me that after a few years maintaining a cut you'll start seeing weaknesses like susceptibility to powdery mildew for starters. Some cuts can hang in there for years while others crap out faster.

Start looking for good males and build a library of genetics for future reference.