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When analyzing how the human species evolved and will continue to evolve over time, what evidence and tools (theory/models) do we have available to derive the rate at which this happens? Is it even possible to set reasonable bounds on such a rate?

Also, how large is the available dataset? And how does the dataset match with theory? I would especially like to get an idea of how well statistical (Bayesian/likelihood) analysis matches with empirical data and more conceptual models.

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there are several such clocks, but a main methodology is to watch the number of mutations that appear in genomic dna over time. Their sequence divergence varies over time at varying rates, but overall that's the clock. –  shigeta Feb 25 at 21:52
    
And is there a good database containing such data, or is it mostly to be found separately in published papers? –  Sander Feb 25 at 22:09

4 Answers 4

This question is very broad. And because of its broadness, I am afraid you won't find a database that will give you what you're looking for.

  • Are you interested in some specific phenotypic traits?
  • Or in some specific genes?
  • What time scale are you interested in?
  • Do you want to know about the time that a given allele needed to reach fixation?
  • Do you want to compare the number of mutations that accumulated in a given DNA sequence between human and close relatives (apes, primates, mammals, ..)?
  • Do you want to compare the evolution of the mitochondrial DNA between human populations that have different mating systems?
  • Evolution in response to HIV?

If there is one specific gene or trait (including traits such as the mutation rate) that interest you, you might want to ask a more specific question on another post.

Concerning the methodology, I agree with shigeta that probably the main methodology you'd be interested in is molecular clock. The ratio of synonymous over non-synonymous mutations are also of interest to compare rates of evolution. Comparisons of mutations accumulation between different sequences. But you might also be interested in fossil records (depending on the trait and the time scale you're interested in). Or more interestingly in selective sweeps. Selective sweep is the reduction in polymorphism and heterozygosity of linked loci to the locus under selection. In humans examples exist in the microcephalin gene or in the lactase gene for example. You might also be interested into allele frequency cline over spatial distribution and things like that. Comparison of evolutionary rates between populations of different size might also give you some insights in how quick does evolution occurs in humans. There are probably tons of other methodologies one could use.

You talk about comparisons between empirical data and theoretical model. But again the question is too broad I think. There a tons of different models to be considered depending on what you are interested in.

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Let me expand on my comment...

There are several such clocks, there are a couple of methods in use.

The oldest and primary methodology is to look at the bodies of the plants and animals and assemble the evolutionary tree by how closely these animals resemble each other (taxonomy). There are several authoritative databases on this data. The encyclopedia of life is a major aggregator for taxonomic analysis. They are tied into the Integrated Taxonomic Information system (ITIS). The millions of species known have not been sequenced and this is probably the most comprehensive overview of life as we know it on earth. The ITIS data is downloadable.

On the other hand the taxonomic record has many known problems. For example Rodentia (rodents) are known to be a bit of a dumping ground where hard to classify mammals are put because we just don't really know where they go.

In cases where there is money and energy to resolve an issue like this, a main methodology to gauge the evolutionary distance is to observe the number of mutations that appear in genomic dna over time. Their sequence divergence varies over time at varying rates, but overall that's the clock. This is pretty indisputable, but the coverage over the phylogenetic tree is low. There are a few databases focused on bacteria for instance and fungi, but you have to know what you are looking for. Often such evidence is entered into databases such as ITIS over time.

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There are currently 7 billion human organisms on the planet. We each have genome of about 3 billion letters, and we all have millions of differences in our DNA from each other. Some of these differences are private, only found in one individual, some are found in only one family, some only found in some larger kin groups. Over time, more novel polymorphisms will arise, and those and the existing ones will change proportion in sub populations, and in the human species as a whole. Some will have phenotype effects that we can measure.

You think the changing of those millions of DNA sequences in a population of 7 billion can be meaningfully summed up in some single measurement?

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I'd argue against using models of any sort, because the answer will be way off even if you use it on existing hard facts. Common sense is required here, I personally think it's silly to be trying to find a model for evolution when it is known evolution isn't a constant process and has no intent. Also, evolution can lead to a dead end.

The main reason why common sense is needed is that only then you can know when a species stopped evolving because there's no selective pressure. There are very few human groups today which are still evolving, but the species as a whole isn't evolving anymore and it won't in the future. There - just saved you the trouble of modeling future evolution because there won't be any.

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