Citations are helpful, rather than having people chase thru videos for the actual source.
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I actually know enough about paternity testing to be fairly confident BLAST has nothing to do with it, UNLESS it corresponds to one of the common markers used. 
The pdf will be behind a paywall for anyone without a subscription, so please contact me privately if youâd like to see the full paper (nelsonpa@alumni.uchicago.edu).
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I was hoping that was something we could all agree on. 
Is the KALIGN program used in paternity testing?
ERVs?
I mean if all humans share the same ERVs, canât we look at their ERVs and create a phylogeny of the human family tree? Perhaps you and I are more closely related than either of us would be comfortable with.
I already explained it in a previous post:
I would think that the sequences are assumed to be identical between PCR fragments of equal length when using the same PCR primers.
If there was enough variation in ERVâs this would be possible.
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Iâm not sure what cousins and siblings have to do with it. Wonât any two humans share orthologous ERVâs through common ancestry?
Are we going to be able to discuss the actual methodologies employed when inferring phlyogenetic relationships and the methodologies employed in paternity testing and compare them?
DNA can be used for comparison purposes. Thatâs not in dispute.
VERY briefly, given a child and a man who might be the father (a prior assumption that the man and the mother ⌠well ⌠you know), look to see how many common Loci/Markers the man and child have in common. Based on those markers, calculate the probability two people would share those markers at random. Calculate a posterior probability that THIS man is the father.
There are a lot of details I left out, but the basic calculations can be done on a spreadsheet.
More info here: http://dna-view.com/promeg89.htm
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Wonât any two primates share orthologous ERVâs, for the same reason?
Thatâs exactly what I am discussing. The method used for comparing STR alleles is analogous to comparing ERV insertions.
Letâs look at one of the STR sequences:
https://strbase.nist.gov/images/se33.pdf
This section of DNA has multiple repeats of AAAG. Different people have different numbers of these repeats. This means that when you amplify that section the DNA strand will be a different length when run on a gel. They are using the size of the fragment as a proxy for comparing sequence. If there are 4 alleles for this section of DNA in the human population and even mixing then the chances of two people having the same allele is 1 in 4. As you increase the number of STR loci you multiply that probability until it is 1 in several million or billion. If you share a lot of STR alleles then the best explanation is common ancestry instead of random chance.
The same logic applies to ERVâs. Retroviruses insert randomly, so the chances of sharing the same ERV at the same location is small, and the probability nears zero when you look at thousands and hundreds of thousands of ERVâs. As in the case of sharing STR alleles, the low probability of randomly sharing ERVâs supports common descent.
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Is that why these cases never go to a jury trial? Could you imagine having to explain that to a jury, lol.
I donât suppose they use that program or other similar programs for constructing phylogenies.
Can you say more about the âmarkersâ that are used? Itâs not just raw DNA comparison, correct?
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Donât take this personally, itâs not directed at you, but it sounds like a probability argument.
It starts with some really exciting reading of ⌠PROBABILITY TABLES!
No phylogenies or complicated programs that I am aware of. Paternity testing is only interested in the father (rarely, the mother), not cousins or distant relatives.
When these tests come back positive, they are almost foolproof, so this question is unlikely to go to trial. Identical twins can cause problems, but only if both are potential fathers. Sometimes genetic weirdness can happen (like 3 copies of DNA instead of 2), which can change the correct calculations, or sometimes remove all doubt.
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Thatâs exactly what DNA fingerprinting is. It is a probability argument. That is also what the ERV argument is for common ancestry between humans and chimps.
Letâs say that we are looking at 20 loci with 4 alleles at each loci for DNA fingerprinting. If there is even mixing, the chances of a match at each loci is 1 in 4. The chances of a match at all 20 loci is 4^20, or about 1 in 1 trillion. Since there are only 7 billion people a match between 20 loci is enough to indicate ancestry or the same source if we are talking about forensics at a crime scene.
For retroviruses, the chances of a virus inserting at the same base is about 1 in 50,000 in the most favorable conditions. Therefore, the chances of having more than 99.9% of 200,000 ERVâs at the same location in two genomes is beyond what we would expect by random insertions in two genomes. Therefore, the probabilities favor a single source, or single insertion that occurred in a single common ancestor.
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Just to make sure I am reading this right . . .
The underlined headers are the loci.
The number under the allele heading is the number of repeats.
The 0.xxx is the percentage of people with a specific allele at a specific loci for a specific population (US African Americans in this case).
Is this correct?
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Of course. And sometimes it is lacking in phylogenetic conclusiveness.
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A paternity test seeks markers that are so unlikely to be a coincidence that observers can confidently state a man is (or is not) the contributor to an offspringâs genome ⌠or perhaps merely related or not to the father.
This IS an example of testing common descent.
There are different scales involved in testing descent from a population compared to descent from an individual. What makes you think the science radically differs between the two exercises?
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I donât know what you mean by âradically differs.â Itâs not a term that i have used. What I have argued is that the methods are different. Iâve also argued that we can test the one using known relationships between fathers and children.
There is no DNA sample that we can take from the âcommon ancestorâ of two extant species.
Can we agree on that?
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You got my vote. 
That seems right ⌠I made that slide 10 years ago, and my memory is a bit hazy
The Lenski experiments? Finding them in the wild depends on your definition of species.
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The methods are indeed different, although many of the concepts are the same. For something like tracking closely related flu viruses, on the other hand, the methods can be the same as those used in constructing phylogenies.
Probably true for animals and probably false for plants, which can sometimes speciate at the drop of a proverbial hat (which is, now that I think of it, a really odd phrase).
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