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Author Topic:   No genetic bottleneck proves no global flood
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 7 of 140 (655741)
03-13-2012 9:05 AM
Reply to: Message 6 by Tangle
03-13-2012 3:54 AM


Perhaps a discussion of what a bottleneck looks like:
quote:
Population Bottleneck:
A population bottleneck (or genetic bottleneck) is an evolutionary event in which a significant percentage of a population or species is killed or otherwise prevented from reproducing.[1]
A slightly different sort of genetic bottleneck can occur if a small group becomes reproductively separated from the main population. This is called a founder effect.
Population bottlenecks reduce the genetic variation and, therefore, the population's ability to adapt to new selective pressures, such as climatic change or shift in available resources. Genetic drift can eliminate alleles that could have been positively selected on by the environment if they had not already drifted out of the population.[2]
Population bottlenecks increase genetic drift, as the rate of drift is inversely proportional to the population size. The reduction in a population's dispersal leads, over time, to increased genetic homogeneity. If severe, population bottlenecks can also markedly increase inbreeding due to the reduced pool of possible mates (see small population size).
... The golden hamster is a similarly bottlenecked species, with the vast majority descended from a single litter found in the Syrian desert around 1930. And cheetahs are sufficiently closely related to one another that transplanted skin grafts do not provoke immune responses,[9] thus suggesting an extreme population bottleneck in the past.
The genome of the giant panda shows evidence of a severe bottleneck that took place about 43,000 years ago.[10] There is also evidence of at least one primate species, the golden snub-nosed monkey, that also suffered from a bottleneck around this time.
Further deductions can sometimes be inferred from an observed population bottleneck. Among the Galpagos Islands giant tortoises themselves a prime example of a bottleneck the comparatively large population on the slopes of Alcedo volcano is significantly less diverse than four other tortoise populations on the same island. DNA analyses date the bottleneck to around 88,000 years before present (YBP).[11]
We can also see that this would apply to any species taken off the endangered species list.
So we have the ability to see bottlenecks in populations: how do they line up in timing?
quote:
Dating the genetic bottleneck of the African cheetah
... The timing of a bottleneck is difficult to assess, but certain aspects of the cheetah's natural history suggest it may have occurred near the end of the last ice age (late Pleistocene, approximately 10,000 years ago), when a remarkable extinction of large vertebrates occurred on several continents. To further define the timing of such a bottleneck, the character of genetic diversity for two rapidly evolving DNA sequences, mitochondrial DNA and hypervariable minisatellite loci, was examined. Moderate levels of genetic diversity were observed for both of these indices in surveys of two cheetah subspecies, one from South Africa and one from East Africa. Back calculation from the extent of accumulation of DNA diversity based on observed mutation rates for VNTR (variable number of tandem repeats) loci and mitochondrial DNA supports a hypothesis of an ancient Pleistocene bottleneck ...
Of course genetic information cannot give you accurate timing (estimates can be made, but they are at best relative dates that tell the sequence of what occurred rather than the dates), so this needs to be tied back to fossil evidence for dating the events.
Enjoy.

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 13 of 140 (655787)
03-13-2012 2:15 PM
Reply to: Message 8 by Tangle
03-13-2012 12:40 PM


Hi Tangle,
As we don't look likely to get any opinion at all now from the creation side of the argument, ...
Not really a surprise, imho: first they need to understand the process, and they are not likely to get that information from creationist sources.
... can we dream up any defence at all for them?
Well, just from this information in Message 7 we have two possibilities:
(1) a bottleneck "about 43,000 years ago" in the Giant Panda lineage, and
(2) a bottleneck "approximately 10,000 years ago" in the Cheetah lineage.
For the creationist this means that (a) either the age measurements are off (SOP - as both these need to be crammed into ~5,000 years ago), or there is something else for which they don't have a clue.
Is it possible for a genetic bottleneck to be masked?
Well, I would think that the "approximately 10,000 years ago" event could mask the effects of the "about 43,000 years ago" ... if we found more evidence of bottleneck events at this later period.
Of course, then we go to the Toba Event
Toba catastrophe theory - Wikipedia
quote:
The Toba supereruption (Youngest Toba Tuff or simply YTT[1]) was a supervolcanic eruption that occurred some time between 69,000 and 77,000 years ago at Lake Toba (Sumatra, Indonesia). It is recognized as one of the Earth's largest known eruptions ...
The Toba event is the most closely studied supereruption. In 1993, science journalist Ann Gibbons first suggested a link between the eruption and a bottleneck in human evolution. Michael R. Rampino of New York University and Stephen Self of the University of Hawaii at Manoa quickly lent their support to the idea. The theory was further developed in 1998 by Stanley H. Ambrose of the University of Illinois at Urbana-Champaign.
So now the ~10,000 year ago and the ~43,000 year ago events mask the ~70,000 year ago event, and further analysis of the bottleneck patterns in other species will likely produce older dates for their most recent bottleneck events, creating an ever increasing problem for the YEC timing issues.
Enjoy.

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 29 of 140 (720308)
02-21-2014 1:31 PM
Reply to: Message 28 by Tangle
02-21-2014 1:16 PM


Re: Bottleneck
Well the rabbits certainly could have been on the ark and not show a bottleneck - according to these findings. Speed of reproduction and an empty ecosystem seems to be a big consideration.
13 is rather larger than 2 for starters, and it would also depend on the male\female mix (1 male to 12 females, mates with each one etc), although one would expect a founder effect unless ...
Second -- did the introduced rabbits from domesticated rabbit stock ... so they would already have reduced genetic variations compared to all rabbits ... and then compared back to that stock? If so I would not expect much change -- especially if there is no selection pressure to change.

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This message is a reply to:
 Message 28 by Tangle, posted 02-21-2014 1:16 PM Tangle has replied

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(2)
Message 45 of 140 (720448)
02-23-2014 7:21 PM
Reply to: Message 43 by Tangle
02-23-2014 2:09 PM


Yes Faith a change in gene frequency is the very definition of evolution but we don't expect to see phenotypic change - rabbits turning blue - just because there's been a bottleneck.
What we expect to see are rabbits being born that are like their parents.
And now you will be lectured with Faith's fantasy ... where hidden phenotypes suddenly pop up because they were never mixed that way before ...

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 47 of 140 (720475)
02-24-2014 8:32 AM
Reply to: Message 46 by Tangle
02-24-2014 3:38 AM


Biologists do not expect new phenotypes to pop into existence after a bottleneck and the two extreme examples of the rabbits and the deer demonstrate that. Similarly cheetahs, seals and bison are still cheetahs, seals and bison.
A little overstated imho. Small phenotypic change - fur color, length, curliness, some increase or decrease in size, for example - can occur and would not be unexpected.
Yes, reproductive rate is identified by both papers as likely being the reason that both the deer and the rabbits recovered gentic diversity. Note that Faith, recovered genetic diversity - not developed new phenotypes.
Significant new phenotypes, such as new subspecies, which is what Faith is thinking, are not expected, they could occur but don't have to occur without selection pressure for such changes.

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This message is a reply to:
 Message 46 by Tangle, posted 02-24-2014 3:38 AM Tangle has replied

Replies to this message:
 Message 48 by Faith, posted 02-24-2014 10:21 AM RAZD has replied
 Message 52 by Tangle, posted 02-24-2014 6:22 PM RAZD has replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 50 of 140 (720521)
02-24-2014 4:19 PM
Reply to: Message 48 by Faith
02-24-2014 10:21 AM


I'm thinking small phenotypic changes, and as you agree, those should be expected from new gene frequencies -- or, as you say, "would not be unexpected" though I think they should actually be expected.
Within a stable ecology selection would be towards the population average, both by survival and by reproduction. This is why stasis occurs. Thus any changes would necessarily be relegated to fairly minor aspects that would not decrease survival or reproduction, such as the types of variations I mentioned.
The idea that I'm expecting some large "significant" change, no, I'm just expecting typical microevolution of external traits. But I'm thinking of subspecies as simply a new population that has been worked through by the new gene frequencies over enough generations to get a characteristic appearance to the group. I don't consider that a "large" change. Nothing new is added, it's just the gene frequencies doing their thing.
A new subpopulation is a larger change in phenotype than I would expect, as it means that some selection is occurring to isolate variations into a breeding group.
That you don't consider it "large" is inconsequential to me, seeing as it is just your opinion, based on a fantasy that you have concocted which is not only unsupported, but the actual evidence points the other way: that such changes are due to mutations not pre-existing hidden never before seen alleles.
Let's take another example: the Galapagos\Darwin finches as studied by the Grants:
Evolution: Library: Finch Beak Data Sheet
quote:
The Grants wanted to find out whether they could see the force of natural selection at work, judging by which birds survived the changing environment. For the finches, body size and the size and shape of their beaks are traits that vary in adapting to environmental niches or changes in those niches. Body and beak variation occurs randomly. The birds with the best-suited bodies and beaks for the particular environment survive and pass along the successful adaptation from one generation to another through natural selection.
Natural selection at its most powerful winnowed certain finches harshly during a severe drought in 1977. That year, the vegetation withered. Seeds of all kinds were scarce. The small, soft ones were quickly exhausted by the birds, leaving mainly large, tough seeds that the finches normally ignore. Under these drastically changing conditions, the struggle to survive favored the larger birds with deep, strong beaks for opening the hard seeds.
Smaller finches with less-powerful beaks perished.
So the birds that were the winners in the game of natural selection lived to reproduce. The big-beaked finches just happened to be the ones favored by the particular set of conditions Nature imposed that year.
Now the next step: evolution. The Grants found that the offspring of the birds that survived the 1977 drought tended to be larger, with bigger beaks. So the adaptation to a changed environment led to a larger-beaked finch population in the following generation.
Adaptation can go either way, of course. As the Grants later found, unusually rainy weather in 1984-85 resulted in more small, soft seeds on the menu and fewer of the large, tough ones. Sure enough, the birds best adapted to eat those seeds because of their smaller beaks were the ones that survived and produced the most offspring.
Evolution had cycled back the other direction.
Note that only beak size changed, and this is a fairly minor phenotypical change.
These are larger changes to the phenotypes than we should expect for the Australian rabbits, because (a) the populations were smaller and (b) the ecology changed to the point that small beaked finches could not survive, and it was only when the ecology changed back that small beaks reappeared.
This is also similar to the Peppered Moths -- shifting populations in response to ecological stress.
Apparently there are some species where this doesn't happen, such as rabbits, due to their rapid reproductive cycle and their habit of forming small groups instead of mixing their genes by breeding through the main population as, say, herd animals would do.
And a lack of selection pressure.
There is still gene flow between family groups as mates are usually taken from outside families, and this leads to gene flow throughout the breeding population and prevents in-breeding.
The numbers Tangle gave for percentage of heterozygosity I'm going to have to spend some time on, because they are very large compared to my understanding that the human percentage is only around 7%.
I'll let you and Tangle sort this out.
Edited by RAZD, : ..

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 51 of 140 (720522)
02-24-2014 4:37 PM
Reply to: Message 49 by Faith
02-24-2014 10:30 AM


Selection pressure is not needed when you have such a significant bottleneck ...
Selection pressure may be reduced but it would still likely be prevalent. The major pressure would be for survival, as reproductive selection would be reduced.
... To which genetic drift would also contribute, ...
Which normally reduces available genotypes. particularly the rarer alleles.
... a significant bottleneck which would produce dramatically new gene frequencies. ...
The gene frequencies would match the original population if the selection pressure is reduced, especially for sexual selection: alleles that do not exist cannot be selected, and normally would most likely not include rare alleles from before the bottleneck -- hence the expected reduction.
My feeling is that if the rabbits came from a domesticated stock (highly likely imho) that then selection for domestic use has already reduced variability before going to Australia, and thus would not be much affected compared to the original domestic stock.

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 55 of 140 (720591)
02-25-2014 10:06 AM
Reply to: Message 52 by Tangle
02-24-2014 6:22 PM


I wouldn't expect anything new from a sub-population would you?
What is "new" ? I would expect some variation/s outside an "average" phenotype, but minor (does eye color affect reproduction? survival?) but most mutations would be neutral.
And as I've noted before, in a stable ecology I expect selection to favor the "average" phenotype as preferred sexual selection.
Take two mice out of a population and I'd expect them to produce mice with the characteristics of some of the mice within the population. These differences may become more fixed with time if they're not deleterious - like we expect more red headed Scots than English redheads (caution, maybe apocryphal!).
Curiously, I was doing some reading last night on heterozygosity, and one article said that the predicted\expected heterozygosity from two individuals was 0.75. It seems that the way this is measured does not really quantify what we think it does from a first look, because of the way it deals with population size. And it doesn't seem to count the degree of genetic variation in the parent population.
With two mice you would have somewhere between 2 and 4 possible alleles at each loci, depending on whether the two copies of DNA strings in each individual are the same or different (one maternal the other paternal). If we take an off the cuff "average" value for all alleles at 3, then 3 out of a potential 4 would be 0.75.
But, as you say, these irrelevant differences in average phenotypes is not what Faith is looking for, she thinks that species level changes come from isolation and bottlenecks almost instantly and biology knows that it doesn't.
Exactly, as you can see from her reply. Part of this is her belief that there are hidden alleles tucked away that are somehow suppressed in normal population reproduction but become freed to act in small populations. It's her alternative explanation to mutations creating new alleles.
Plus, the examples we have of even severe bottlenecks - rabbits, deer, cheetah, bison, seal haven't produced materially different phenotypes. I wonder if it's possible to tell the difference between an Austarlian rabbit and a French rabbit - even with a DNA sample?
And the starling population in the US compared to the UK -- introduced in NY and spread to the whole US is

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 Message 57 by Faith, posted 02-25-2014 10:21 PM RAZD has replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 58 of 140 (720675)
02-26-2014 7:49 AM
Reply to: Message 57 by Faith
02-25-2014 10:21 PM


I don't think I'm describing anything hidden or strange at all, just that new gene frequencies is likely to mean that recessives that weren't expressed in the former population may occur more frequently and therefore pair up more frequently in the new ...
Yes, the new look of the new population isn't new in the sense that nothing like it has ever appeared before, but it's a new combination of alleles that may affect a number of traits so that where the original population was brown and long haired and green eyes with short noses and ears and tails, the new population after a number of generations of blending may be mottled short haired with blue eyes and long noses, ears and tails and a larger body and so on. It's going to be recognizably different. A new race, "species" or subspecies.
Curiously, I am reminded of Monty Python's Flying Circus "and now for something completely new" ...
I'm thinking standard Mendelian combinations of course, not mutations. Since most mutations ARE neutral there's no reason to expect them to produce new combinations, but there are plenty of built in alleles that can do just that.
In "standard Mendelian combinations" each of these traits would have appeared in the general population, not just rarely but rather commonly for the alleles to be so well distributed in the population that any small contingent would have them.
And this also means that there would likely be combinations of blue eyes and mottled short haired, etc.
Furthermore, in "standard Mendelian combinations" there is no mathematical reason for these to suddenly all become sorted into certain individuals that would then become reproductively isolated within the rest of the population sufficiently to form such a sub-population. Nor would there be an evolutionary cause for this - there would be no positive selection for such combinations in an ecology with static selection pressure, and sexual selection would much more likely act to reduce the numbers of such random occurrences of such mathematically rare combinations.

we are limited in our ability to understand
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This message is a reply to:
 Message 57 by Faith, posted 02-25-2014 10:21 PM Faith has replied

Replies to this message:
 Message 64 by Faith, posted 02-27-2014 2:26 AM RAZD has replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 59 of 140 (720681)
02-26-2014 10:29 AM
Reply to: Message 57 by Faith
02-25-2014 10:21 PM


heterozygosity measurements - a (long) evaluation
Take two mice out of a population and I'd expect them to produce mice with the characteristics of some of the mice within the population. These differences may become more fixed with time if they're not deleterious - like we expect more red headed Scots than English redheads (caution, maybe apocryphal!).
Curiously, I was doing some reading last night on heterozygosity, and one article said that the predicted\expected heterozygosity from two individuals was 0.75. It seems that the way this is measured does not really quantify what we think it does from a first look, because of the way it deals with population size. And it doesn't seem to count the degree of genetic variation in the parent population.
This could use some more information and discussion and I've been doing some searches. I'm not sure what you are saying here, but the heterozygosity that COUNTS is at the EVOLVING LOCI, and I can't tell from any of the discussion about these things so far if that's even taken into account. The cheetah's heterozygosity must be near zero because of all their fixed (homozygous) genes for instance.
The article I was reading was:
Population Bottlenecks: Heterozygosity vs. Allelic Diversity
quote:
Question: How do we measure loss of genetic variation? Do the different measures yield similar estimates of the amount of variation lost?
Variables:
H heterozygosity
N population size during bottleneck
n original number of alleles
n' number of alleles remaining after bottleneck
pj frequency of the jth allele
A allelic diversity
t number of generations
Methods: The two measures of genetic variation examined by Allendorf (1986) were heterozygosity (proportion of individuals heterozygous at a locus) and allelic diversity (the actual number of alleles present at a locus). The expected heterozygosity following a bottleneck lasting a single generation is expressed as a proportion of the original heterozygosity:
1 - 1/(2N)
As N (the population size during the bottleneck) increases the second term (1/[2N]) decreases, and the proportion of the original heterozygosity remaining increases. In general, a bottleneck lasting one generation has a fairly small effect on heterozygosity; even if the population is reduced to 2 individuals the expected proportion of heterozygosity is 0.75 (1 - 1/[2*2] = 0.75). ...
This is a rather rudimentary estimate of expected heterozygosity (proportion of individuals heterozygous at a locus), basically like an order of magnitude calculation, as it doesn't include the number of alleles involved.
Note that this is looking at only one locus, one gene, and the number of alleles for that one locus\gene. The number 2N is the number of DNA strings in the population size N, and the maximum possible number would be obtained when there is a different allele in each DNA strand for that locus\gene.
Next they look at how this stacks up for different numbers of alleles in the original population for the various loci, and the math, unfortunately, gets a little more involved:
quote:
... Calculating the expected number of alleles present at a locus is more complicated, because it depends on the number and frequencies of alleles present before the bottleneck. For a diploid locus with n alleles, the frequency of the jth allele is expressed as pj (for our purposes we will assume that the alleles are equally frequent; if n = 4 then the frequency of each allele will be 0.25). The number of alleles we would expect following a bottleneck (n') is calculated by the following equation:
E(n') = n - Σ(j=1→n){1 - pj}2N
For each of the n alleles, we subtract the frequency of that allele from 1 and raise the difference to the bottleneck population size (N) multiplied by 2. ...
To break it down, n is the original population number of alleles at a loci, pj is the frequency of the jth allele at that loci,
and (1-pj)2N is the probability of that allele being in the number of DNA strands (2N) of the bottleneck population,
The probability of each allele, from 1 to n, is calculated and then they are all added up and this sum is subtracted from the original population number of alleles at a loci, n, to derive the expected number of alleles, n', in the bottleneck population.
Applying this to a simplistic example where N = 2 again, and using n = 2, with each allele having the same frequency (pj = 0.5) in the original population, we get:
  1. the probability of allele #1 being in the number of DNA strands (2N = 4) of the bottleneck population:
    (1-pj)2N = (1-0.5)2N = 0.06 (rounded)
  2. the probability of the other allele is the same (0.06)
  3. the sum of these probabilities is 0.12, so
  4. the expected number of alleles (n') after the bottleneck is:
    n' = n - 0.12 = 2 - 0.12 = 1.88
With N = 2 and n = 3 we get n' = 2.41
With N = 2 and n = 4 we get n' = 2.73
And this is STILL only one loci of the genetic sequence \ DNA strands \ genes.
quote:
... These values are summed for all n alleles, and the sum is subtracted from the original number of alleles (n). We can then use this number (n') to calculate the allelic diversity (A) after a bottleneck. A is the ratio between [the remaining number of alleles minus one] and [the original number of alleles minus one]:
A = (n'-1)/(n-1)
When all alleles are retained, A = 1. If only a single allele remains, A = 0. ...
For our first example this would be: A = (1.88-1)/(2-1) = 0.88
For our second example this would be: A = (2.41-1)/(3-1) = 0.70
For our third example this would be: A = (2.73-1)/(4-1) = 0.58
So there is significant variation depending on the numbers of alleles. For just one loci.
quote:
... The graph below (redrawn from Allendorf, 1986) illustrates the relationship between allelic diversity remaining after a single-generation bottleneck and the original number of alleles for different population sizes. The black dots indicate the expected proportion of heterozygosity remaining for each population size.
Note that although the proportion of heterozygosity retained for a bottleneck of N = 2 is 0.75, the proportion of allelic diversity retained when five or more equally frequent alleles are present before the bottleneck is less than 0.50.
Certainly when the original number of alleles, n, is greater than the number of DNA strings in the bottleneck population, 2N, there has to be some loss in allelic diversity, as it is mathematically impossible to have more alleles than strings.
From what I can see the black dots for the expected heterozygosity are just pasted on the curves at their values and don't have any calculated relationship to the original number of alleles.
And we can see that the proportion of heterozygosity is different from the expected allelic diversity, and the larger the number of original alleles the greater this difference will be.
Further, to get an idea of the overall effect these calculations would need to be repeated for every gene\loci and the results averaged. A lot of calculations.
They go on to calculate the effect over several generations (see graphs) and conclude:
quote:
Interpretation: As you can see from the above graphs, in most cases (with the exception of two equally frequent alleles originally present) the expected proportions of heterozygosity remaining (E(H)) indicate a higher retention of genetic variation than measured by allelic diversity (A). It is also apparent that the effects of bottlenecks on genetic variation are greatly increased as population size (N) decreases, and that the duration of the bottleneck (t) compounds these effects.
Conclusions: Heterozygosity can be used as a measure of a population's capacity to respond to selection immediately after a bottleneck. Allelic diversity, on the other hand, determines a population's ability to respond to long-term selection over many generations, and ultimately the survival of the population (perhaps even of the species). ...
So the expected heterozygosity is best used for initial evaluations, and more long term evaluations should use allelic diversity for a more accurate picture.
Genetic diversity, which would include evaluation for each gene\loci and integrating them into an overall picture would be even more complex a calculation.
If you have g genes do you multiply all the A values and then take the gth root? Do you average all the A values? Or is there some other metric that is used?
I don't know yet.
Edited by RAZD, : formula instead of hard to see image
Edited by RAZD, : ..

we are limited in our ability to understand
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 Message 57 by Faith, posted 02-25-2014 10:21 PM Faith has not replied

Replies to this message:
 Message 60 by Tangle, posted 02-26-2014 1:54 PM RAZD has replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 62 of 140 (720706)
02-26-2014 6:04 PM
Reply to: Message 60 by Tangle
02-26-2014 1:54 PM


Re: heterozygosity measurements - part 2
I don't know yet.
Wake me up when you do ;-)
Well the article does go into this a little bit:
Population Bottlenecks: Heterozygosity vs. Allelic Diversity ... continued ...
quote:
Another consideration is the duration of the bottleneck. For how many generations is the population size reduced? How does this affect heterozygosity and allelic diversity? We can calculate the expected proportion of heterozygosity retained after a bottleneck with population size N lasting for t generations:
{1 - 1/(2N)}t

Where t is the number of generations. This would generate an exponential decay curve ... assuming that the population size is static and there are no new mutations, both questionable assumptions, especially with rabbits ... ("had to keep telling the rabits, only two only two" - Bill Cosby on Noah ) ...
Back to the article:
quote:
Allendorf used computer simulations to examine the effect of multiple generations on allelic diversity. For each set of parameter values (N, n and t) the simulation was run 1,000 times, and the means of these simulations are graphed below. Each graph represents a different population size, N, with t on the x-axis and A on the y-axis. The different colored lines represent different numbers of alleles present (n) prior to the bottleneck (n = 2, 5, or 10). The dashed line represents the expected loss of heterozygosity (E(H)) for a population of size N over t generations. (Graphs redrawn from Allendorf 1986; values for A estimated from same).

Again it appears that the expected proportion of heterozygosity is a first approximation and the allelic diversity calculation is more representative ...
... however there is no reference to numbers of offspring, which I would think would be critical to hold on to the alleles from the original bottleneck population.
Instead these calculations seem to assume that the following generation is another bottleneck from the previous generation ???
Seems the models are missing something: I would expect that cheetahs would have a much larger bottleneck impact than rabbits due to the difference in numbers of offspring.
Edited by RAZD, : formula clarity

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
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Message 68 of 140 (720738)
02-27-2014 10:35 AM
Reply to: Message 64 by Faith
02-27-2014 2:26 AM


Yes there could have been all those varieties in the original population, but the effect of a change in gene frequencies is ...
What causes the change in gene frequencies Faith? If there is no difference in selection pressure from one generation to the next then there is no cause for a change in gene frequencies (other than drift which occurs over many generations).
Gene frequencies don't change spontaneously.
... the effect of a change in gene frequencies is that you DO get more of some and less of others and you DO get completely new combinations, ...
In response to selection pressure that favors some more and others less, without such pressure there is no mechanism to cause changes in frequencies.
... and you DO get completely new combinations, more mottled fur with fewer green eyes or whatever. ...
Ah the hopeful monster?
If each of these traits exist in the population beforehand, as you claim, but are not expressed frequently then they would necessarily be rare and recessive -- rare so that two matching recessive genes do not occur with any great frequency in the previous population, and recessive so that they can exist in sufficient numbers to stay in the population gene mix.
If these rare recessive genes also was deleterious (selected against) when occurring in both copies then that would also work to keep the allele suppressed in the general population before the bottleneck event.
Having this same scenario repeated for a number of different genes and then somehow magically combining them all into one individual would be a mathematically rare event.
Having it occur with no selection pressure to positively select any of these traits would be highly improbable.
Having it then become a dominant phenotype would be astounding.
... The point isn't that you get something that never existed before but that you get combinations that now CHARACTERIZE this new population and distinguish it from the mother population, a new "look," not brand new traits.
Magically?
What causes this change Faith?
I thought it was pretty well understood that a change in gene frequencies is a definition of evolution so that merely from such a change you should expect new phenotypes; it's rather surprising to see this foundational principle challenged and misrepresented.
In response to selection pressure, in response to changes in the ecology. It is a response mechanism not a causal one. The new phenotype occurs (by mutation) before the frequencies change in the breeding population and they cause the frequency change through selection.
The process of evolution involves changes in the composition of hereditary traits, and changes to the frequency of their distributions within breeding populations from generation to generation, in response to ecological challenges and opportunities.
"Suddenly" is not a word I've used; "sorted into certain individuals" also reflects nothing I've said; ...
They are implicit in your fantasy. You have a bunch of phenotypic changes all occurring at the same time and forming a subpopulation ... that is suddenly in ecological terms.
... and you have it backwards, saying that after such sorting "then" these "sorted individuals" "become reproductively isolated," which gets everything out of order that I've been talking about. Reproductive isolation of a portion of a population is the FIRST thing that happens in my scenario, although in reality there may not be such perfect isolation; but isolation all by itself should produce the effects I'm talking about, because it gives you new gene frequencies that now work their way through the new isolated population.
And you are the one that has it backwards, Faith.
Reproductive isolation does not happen spontaneously, nor is it necessarily are result from geographic isolation. Reproductive isolation is something that occurs by accumulated changes in breeding subpopulations when gene flow is interrupted or severely restricted. Ring species demonstrate this: several subpopulations in a ring, spreading from an original population around a geological feature, forming subpopulations capable of reproduction with the neighboring subpopulations, but gene flow between these subpopulations is less than inside each subpopulation, and where two ends meet they do not interbreed.
New combinations that form a new characteristic look to a subpopulation are not necessarily "mathematically rare," ...
This is you not understanding what you are saying.
... at least the components of the combinations are not although the particular combination MAY be brand new, based on as many as half a dozen or more traits in a combination that didn't occur in the parent population, ...
Which would be a mathematically rare occurrence in the parent population and no different in the bottleneck population without selection pressure cause them all to be positively selected -- also a mathematically rare occurrence.
... or maybe very occasionally did but was overwhelmed by combinations that occurred in greater frequency there. The new "look" is based on a new mix of alleles. ...
ie -- rare and recessive traits in the original population ... suddenly all getting sorted together with no causal pressure.
... This is elementary, RAZD, you really shouldn't be fighting it.
No Faith, it is fantasy, made up hokum. Phenotypic change of a single trait spread in a breeding population can occur in response to selection for that trait. A couple of traits selected at the same time would be unusual (ie Galapagos\Darwin Finches only changed beak size), and "as many as half a dozen or more traits" would be astounding.
And to have a whole subpopulation form with such traits in the absence of any selection pressure would be magic, not evolution.

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RAZD
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Posts: 20714
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Message 72 of 140 (720758)
02-27-2014 3:33 PM
Reply to: Message 70 by Stile
02-27-2014 2:53 PM


revitalized
Is there a reason the term "recovery" is used all the time when referencing this?
It would seem to me that for the genetic diversity to increase, brand new "genetic diversity" would have to be created.
That is:
Let's say genetic diversity was 6.2
Then there was a bottle neck and it dopped to 1.3
Then the genetic diversity worked it's way back up to 6.2 again.
I can see the use of the word "recovery" in this sense.
But I think it's important to note (especially in context with the EvC debate) that the "recovered" genetic diversity is entirely new. ...
Good point. Perhaps "revitalized" would be better terminology -- it has the connotations of reviving a species from decline without implying return to previous diversity.
... genetic diversity was 6.2
Are you referring to a specific metric that measures this, or just making up numbers?
The metrics I've seen seem to be normalized to numbers between zero (all genes have the same alleles throughout the population) and 1 (all genes have different alleles)
At least this applies to allelic diversity.
This should be rather simple to prove out as well by comparing the genetic information from before and after... if it's different, then new genetic information was obviously created. If the genetic information is exactly the same... then my idea is falsified.
There isn't a large record of before to work from at this time. With the current work on genomes this should not be as much of a problem for future studies.

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


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Message 93 of 140 (720894)
02-28-2014 9:24 AM
Reply to: Message 87 by Blue Jay
02-27-2014 10:32 PM


rabbit review
This article from CSIRO ...
So 24 wild european rabbits were introduced, not 13 (a big difference when dealing with loss of allelic diversity)
Not only that, but this article by an Australian pest control service ...
So six offspring 4 times a year is 24 offspring per year, and the probability that all the alleles in the founding population are passed on is extremely high -- there should be no further loss of allelic diversity than the stochastic loss of alleles that were not carried by the founding population.
Not only that, but this article by an Australian pest control service ...
And we have "immigration" from feral domestic rabbits that have different alleles from the wild population, thus increasing the overall mix of alleles.
So full revitalization of the allelic diversity is not really a big surprise.
Edited by RAZD, : .

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RAZD
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Posts: 20714
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Message 94 of 140 (720896)
02-28-2014 9:41 AM
Reply to: Message 89 by Faith
02-28-2014 1:15 AM


How evolution works ... again ...
Why should any particular mutation be expected, AZPaul? They ARE random "accidents" aren't they? Let alone one that turns out to be beneficial right when it's needed, at the very gene where it is needed, and it isn't a "neutral" mutation and so on and so forth. And if it DOES recur then that gives credence to my own theory of a recurring normal allele anyway.
You are making the post hoc ergo propter hoc error of assuming that the lava field somehow requires mice to evolve black fur.
Yes mutations are random, but changes to fur color can be caused by a number of different factors and mutations in many locations, some that affect the DNA directly and some that affect the fetal development (see silver foxes experiment).
... I figured and I still figure that it IS a normally recurring allele, but that most of the dark furred mousies that result from its occasional expression get eaten by the owl that likes them so much, because this occurs on the light colored sand among millions of his light-colored mousie brethren. Since it recurs from time to time, when the light mousies ventured onto the lava, its occasional appearance was selected, the light mousies all expired due to the owl's taste for them and the black mousies proliferated.
The process of evolution involves changes in the composition of hereditary traits, and changes to the frequency of their distributions within breeding populations from generation to generation, in response to ecological challenges and opportunities.
Now all we need is a random mutation that causes dark fur to occur randomly in an area where there are lava fields, and when it does then that mouse can take advantage of that opportunity to populate a lava field. It can still breed with the tan mice along the boundary, and new black mice can move further into the lava field as their subpopulation grows and the gene become fixed.
That is how evolution works.
It's not "just in time" or a "normally recurring allele" or ALL lava fields would be populated by black mice.

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