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  #1  
Old 18th April 2018, 01:22 PM
FredH FredH is offline
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Chromosome Browser with1st Cousin

Hello,
I received my cousin results and the chromosome browser shows that I share a high level of match on chromosome 4; 173 cm from pos 10,686,414 to 185,524,516.
To my understanding all of that mean that I share around 84% of this chromosome 4.
My estimation is as follow:
chromosome 4 has 206.75 cm for full match then 173cm correspond to 173/206.75 = 84%.
84% looks rather high for a 1st cousin? since I suppose that 100% would be for a parent.
On another hand , I have 0 on chromosome 17 & 18.
Is it not rather low for a 1st cousin?
In fact what we should expect as maximum % per chromosome with a first cousin?
Thanks for your answers.

Last edited by FredH; 18th April 2018 at 01:32 PM.
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  #2  
Old 18th April 2018, 02:04 PM
John McCoy John McCoy is online now
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The assortment of homologous chromosomes as well as the process of recomgination are more or less random, so it is indeed perfectly possible to end up with a very long piece of a chromosome shared with a first cousin. Not a particularly common result, but entirely possible. The same is true for the much shorter chromosomes 17 and 18, it is entirely reasonable to find that a first cousin doesn't share any segments on a couple chromosomes. What is much more important is the total shared cM, which should be roughly in the range of 575 to 1330 cM.
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Old 18th April 2018, 06:00 PM
Fern Fern is offline
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John is absolutely correct

As a practical example, I share a total of 798cMs with my maternal first cousin. We have no matching segments on chromosomes 15 and 22, and matching is very light on chromosomes 12, 14 and 16. (I'm assuming the FTDNA chromosome-browser graphic is a reasonably accurate representation of the percentage of each chromosome that my cousin shares with me. I can't find a handy chart that tells me the number of cMs in each chromosome.) Likewise, it looks like my cousin and I share quite a high percentage of chromosomes 6 and 8, but I can't put a figure on it.
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Old 19th April 2018, 02:06 AM
FredH FredH is offline
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It looks like that the recombination is less random than I thought. To share 84% of a chromosome means that both my father and my uncle, then my cousin's father, inherited almost 100% of this same chromosome 4 from either their father(my G-father) or their mother (my G-mother) and this same chromosome 4 transmitted again almost entirely to me by my father and to my cousin by his father (my uncle). All of that is of course possible but looks also unlikely if it is purely random recombination process or I missed something. To share no cm on a chromosome is in fact more comprehensible. Here is an illustration of a random autosomal inheritance gene process to illustrate the problem

Last edited by FredH; 19th April 2018 at 02:16 AM.
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Old 19th April 2018, 02:32 AM
dna dna is offline
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Quote:
Originally Posted by FredH View Post
It looks like that the recombination is less random than I thought. [----]
It is random, but it is not on the level of individual SNPs.

One can think of chromosomes being divided into segments, and these segments participate in the random recombination. That is why it is so easy to get noticeably more or noticeably less than 50%, and if in the next generation randomness is not so random one could end with significantly more or significantly less of DNA from one of her or his grandparents. That could be on one of the chromosomes or across all of them (autosomal only).


Mr. W.

P.S.
I know what I meant to say but I am not sure whether I had properly composed my sentences above...
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  #6  
Old 19th April 2018, 09:23 AM
John McCoy John McCoy is online now
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Yes, recombination in the human genome involves a few dozen crossovers per generation. The result is that long segments from each parent are transmitted intact. The location of the crossovers on individual chromosomes is approximately random with respect to the "genetic map" expressed in centiMorgans -- because the centiMorgan metric is simply an expression of the probability that a crossover will occur between two markers. Over time, the random location of crossovers in successive generations has the effect of scrambling the chromosomes, but enough of the "original" configuration remains after, say, 5 generations that we can still detect matching segments between distant cousins. If SNP's were effectively scrambled at each generation, we would not be able to detect autosomal matches.
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Old 20th April 2018, 12:01 PM
FredH FredH is offline
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Quote:
Originally Posted by John McCoy View Post
Yes, recombination in the human genome involves a few dozen crossovers per generation.
Great thanks to clarify the problem. Is it Few dozen per generations in total or for each chromosomes? I still have difficulty with centimorgan , I understand that it is a mean number of crossovers between 2 markers. Could we say that this number of cm depends on the markers? then if we say you share 200 cm on a chromosome does this mean you share an ADN sequence from one specific marker to another in order to have 200 cm on this particular chromosome?
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Old 20th April 2018, 06:11 PM
John McCoy John McCoy is online now
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The rough figure of a "few dozen crossovers" is for the entire suite of human autosomes. By tradition (yes, classical genetics goes back far enough that is has traditions), chromosomes are numbered from the largest to the smallest, regardless of species. Usually, it is the genetic map expressed in centiMorgans (plenty of lore, in addition to traditions, goes back to Morgan himself) that is used to measure the "size" of the chromosomes. If two markers are located 1 cM from one another, that number (it is computed as a percent) expresses the fact that, on average, a crossover will occur between those markers only once in a hundred meiotic events. From the way the centiMorgan is defined, it follows that the longer (lower numbered) chromosomes have, on average, more crossovers than the smaller ones!

The length of a segment, expressed in cM, simply refers to the difference between the cM map positions of the beginning and end of the segment. A segment is only scored as a match if "essentially" ALL the SNP's that were tested within that segment match perfectly between two samples. Matching algorithms may have provisions for a small number of presumed data errors. However, it must be realized that the algorithms have to deal with the fact that there are two homologous copies of each chromosome, and hence each sample actually contains two separate sequences, which are probably not identical, for any given segment. The algorithm attempts to find long sequences where ONE value (A, T, G, or C) at each position matches ONE value for the same position in the other sample. Normally, the logic behind this process works very well, and we get consistent and reasonable matches for close relatives, for segments on the order of 10 cM or larger.

The discoveries of classical genetics are fascinating in themselves, well worth your study. The intricate process of meiosis, which is essentially the same throughout all organisms that have a nucleus, is possibly the most striking feature of life on Earth.
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Old 21st April 2018, 08:06 AM
FredH FredH is offline
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Quote:
Originally Posted by John McCoy View Post
The rough figure of a "few dozen crossovers" is for the entire suite of human autosomes. By tradition (yes, classical genetics goes back far enough that is has traditions), chromosomes are numbered from the largest to the smallest, regardless of species. Usually, it is the genetic map expressed in centiMorgans (plenty of lore, in addition to traditions, goes back to Morgan himself) that is used to measure the "size" of the chromosomes. If two markers are located 1 cM from one another, that number (it is computed as a percent) expresses the fact that, on average, a crossover will occur between those markers only once in a hundred meiotic events.
Ok! It 's getting clearer. To be concrete, Here is a cm map of chromosome 4
extract from article https://www.ncbi.nlm.nih.gov/pmc/art...83054/?page=10
then for ex. between marker D4S90 and D4S111 I have 0.5 cm then 0.5% of chance to have a cross over between these two markers.
the funny thing is that the cm map changes with sex. This is unexpected.no change for male, 1.3% for female...
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  #10  
Old 21st April 2018, 10:17 AM
John McCoy John McCoy is online now
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You are correct, the average rate of recombination is significantly higher for human females compared with that for human males. The standard maps used for genetic genealogy use the average of the results obtained from males and females. While you might think this has a major effect on the results of autosomal matching, that is apparently not the case, based on anecdotal reports by genetic genealogists.

However, it is important to consider that recombination must itself be under genetic control, and therefore subject to individual variation. Not only are the enzymes and control mechanisms under genetic control, there must also be some specificity built into the chromosomes and/or their supporting structures as well, because recombination is definitely not uniformly distributed across the physical structures of the chromosomes (as measured by the frequency of recombination per millions of base pairs). Whatever the signals are that enhance recombination at a particular place along a chromosome, those signals, too, should vary to some extent among individuals. Further, there is always the possibility of inversions or other rearrangements that could result in only the non-recombinant meiotic products being viable, though it would be extremely unlikely that any genetic genealogist would have enough evidence to be able to prove that one of these complicating factors had anything to do with a particular result.

Last edited by John McCoy; 21st April 2018 at 10:18 AM. Reason: correction!
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