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Author Topic:   Question concerning evolution
Modulous
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 Message 16 of 21 (834895) 06-14-2018 3:02 PM Reply to: Message 15 by Faith06-14-2018 9:15 AM

 You'd have to have a very reliable rate of accumulation of those "neutral variations," by which I suppose you mean mutations, right? But how reliable could such a number be?

It doesn't need to be that reliable. It's an average over quite a long time - short term deviations lasting even thousands of years would be smoothed out.

Think of it like this. Let's say I eat 2 steaks a year. I'm in my late 30s and we can safely ignore my childhood as the average would likely be different so let's say I've eaten about 70 steaks in my life and that's how I derived the average. If I say 'I've eaten 3 steaks since last we met' you could guess that its been 18 months, but this would be unreliable. I could eat 5 steaks one year and none another year.

However, if I say 'I've eaten 30 steaks since last we met', you'd be on safer grounds to say it must have been about 10 years.

It's like flipping a coin. On one or two trials, it'd be difficult to be confident what the distribution of heads would be. After a thousand trials you probably wouldn't be too far wrong if you guessed it was about 500.

So we calculate based on observations and understanding of the mechanisms how many mitochondrial mutations there are per generation. When we're only examining a 100 generations, the error margin is likely to be high. When we're examining 10,000 generations (ie., for humans about 200,000 years) the error margins are smaller. The more trials, the smaller the error margin.

As ever, there are always complications and confounding factors, but that's the gist of it.

Edited by Modulous, : No reason given.

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Faith
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 Message 17 of 21 (834903) 06-14-2018 4:45 PM Reply to: Message 16 by Modulous06-14-2018 3:02 PM

 So we calculate based on observations and understanding of the mechanisms how many mitochondrial mutations there are per generation. When we're only examining a 100 generations, the error margin is likely to be high. When we're examining 10,000 generations (ie., for humans about 200,000 years) the error margins are smaller. The more trials, the smaller the error margin. As ever, there are always complications and confounding factors, but that's the gist of it.

thanks for the explanation.

So it appears your calculations rest on the assumption of the 200,000 years evolution imputes to the existence of the human race. What if the biblical timing happened to be right, what would the calculations look like then?

 This message is a reply to: Message 16 by Modulous, posted 06-14-2018 3:02 PM Modulous has not yet responded

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 Message 18 of 21 (834916) 06-14-2018 8:17 PM

Yeah, when I read the paper I thought the same as Paul: they're not measuring time since speciation, they're measuring time since the Mitochondrial Eve of each species. There's no way their methods let them do anything else.

Without even considering (as caffeine does) bottlenecks and selective sweeps, drift alone would create the same effect given long enough. How long would depend on population size; I have some spare time coming up, I'll do some simulations.

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 Message 19 of 21 (834960) 06-15-2018 4:37 PM Reply to: Message 17 by Faith06-14-2018 4:45 PM

Well in that case there'd be a greater element of chance, so any particular species could look like the Flood bottleneck was 6000 years ago or 2000 years ago instead of 4000. Of course you could get round this by just looking at a large number of species and averaging. (Just don't use kosher species because there were more animals per species of them on the Ark.)
 This message is a reply to: Message 17 by Faith, posted 06-14-2018 4:45 PM Faith has not yet responded

caffeine
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 Message 20 of 21 (834962) 06-15-2018 4:47 PM Reply to: Message 18 by Dr Adequate06-14-2018 8:17 PM

 Yeah, when I read the paper I thought the same as Paul: they're not measuring time since speciation, they're measuring time since the Mitochondrial Eve of each species. There's no way their methods let them do anything else.Without even considering (as caffeine does) bottlenecks and selective sweeps, drift alone would create the same effect given long enough. How long would depend on population size; I have some spare time coming up, I'll do some simulations.

Human genetic diversity is much less than it "should" be assuming constant population size and the absence of selection. That is, of course, not surprising since we know those assumptions are false. If I've understood the paper correct then they're arguing that the same is true of most animal species.

A mitochondrial haplotype could of course drift to fixation, but the argument is that if drift alone was the primary explanation for mtDNA variation; we would expect, when comparing tens of thousands of species, to see a much wider range of genetic diversity between species and some correlation between population size and diversity (since fixation due to drift would be less likely the larger the population). They're claiming this is not the case - the below is Figure 7 from the paper, plotting population size and average intrapecific pairwise difference in the DNA barcode region for 117 bird species and humans:

I think the above is a bit cherry-picked to make their point - if you look at the plots in Fig 1 you can see that some species are outliers with high variation, but the point is that these are the exception.

 This message is a reply to: Message 18 by Dr Adequate, posted 06-14-2018 8:17 PM Dr Adequate has not yet responded

Taq
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 Message 21 of 21 (835340) 06-21-2018 5:53 PM Reply to: Message 3 by Faith06-11-2018 8:29 PM

 Faith writes:I hope Taq or another geneticist will explain this. What I'd like explained among other things is how they get the 100,000 years by looking at DNA. Also what a DNA barcode is..

The DNA barcode they are talking about is a stretch of DNA from the mitochondrial genome (mtDNA). Mitochondria carry their own genomes that are separate from the genome in the cell nucleus, and it is passed down through maternal lineages because you inherit the mitochondria from the egg but not sperm.

The basic approach is to see how many differences there are between several mitochondrial genomes and then determine how long ago the common ancestor of those genomes lived by using the mutation rate and generation time. As it turns out, the most recent common ancestor (MRCA) for a lot of the species they looked at lived about 100,000 to 200,000 years. If they had looked at other genes in the autosomal genome (the DNA in the cell nucleus) I suspect they would have found a wide range of MRCAs for those genes.

Population genetics is my bag, but from what I think I do understand this isn't too much of a surprise. Even in a population of constant size you will get mitochondrial lineages that come to dominate a population over time. This is because not all mothers have daughters. Just by random luck you will get some mtDNA lineages that spread and become dominant and others that disappear. This is often called lineage sorting.

As the authors of the paper discuss, the simplest explanation is a population bottleneck for most species over the last 100,000 to 200,000 years, but they also state that there are other mechanisms, like lineage sorting, that could have produced the same observations.

 This message is a reply to: Message 3 by Faith, posted 06-11-2018 8:29 PM Faith has not yet responded

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