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Thread: About IBD segment size and TMRCA

  1. #1
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    About IBD segment size and TMRCA

    Hello all,

    Apparently the DNA companies (like MyHeritage) have made significant progress in order to remove the false positive matches, and now they confidently report matches with only 7 CM shared DNA segments or less.

    As I am interested in deep ancestry (historical timeframe) I intend to exploit these "small segments" (taken into account the number of SNP's too), especially for finding Anglo-Norman and Scandinavian matches before the 12th century.

    I have found some information on "ISOGG Wiki" and "The Geography of Recent Genetic Ancestry across Europe", but not accurate enough (I only got that "the segments > 4 CM come mostly from 500-1500 years ago)

    Where can I find a study establishing the IBD segment size distribution according to the TMRCA?

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  3. #2
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    Have not seen anything like what you are looking for.
    You have obviously done some reading, so the next comment is for others who are absolute beginners.
    A high proportion of small segments are false, because they disappear when phased against both parents.
    e.g. around 90% at 3cM (See https://isogg.org/wiki/Identical_by_descent)
    So the first thing that has to be done is to remove those by phasing against both parents.
    Then your search may have a chance.

    A number of commentators have mentioned small segments, but not quite in your context.
    They are: Dave Hamm and Jim Bartlett (see his Segmentology blog).
    And maybe Tim Janzen has commented too, but I can't remember where I saw those.

    Any work I have seen at the sort of distance you describe has been with Y DNA, which is not your interest.
    Last edited by Saetro; 01-06-2020 at 07:56 PM.

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    It is interesting:

    "Another aspect of this discussion has to do with what I call “sticky” segments. Per the Table above at 5 generations back we would see 386 segments – or 386 TGs – of about 18cM each. But going back one more generation – one more round of 68 crossover points would result in 454 segments. This means that 64 of the 386 segments were subdivided, and 322 segments were not! This means that 322 segments (TGs) were passed down intact (no recombination). The effect of this is that many TGs will persist, at the same size, for several generations." (segment-logy from Jim Bartlett)

    I think that the smaller the DNA segment is, the less is the likelihood of a recombination, which explains the presence of IBD segments with a reduced but still significant size and coming from the historical or anthropological timeframe.

    Concerning my MyHeritage matches, I am satisfied for 3 reasons:

    - First I was able to check the consistency of a lot of matches based on my knowledge of my recent and less recent ancestry.

    - Since 2018 they made great efforts to remove the false positive:

    https://blog.myheritage.com/2018/01/...-dna-matching/

    - I have compared the common DNA matches between me (test performed in 2018) and my father (test performed in 2019), and I have noticed a reduction of the shared segment size and triangulated matches number, which means that in 2019 the test was more accurate than in 2018.

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    Crossover interference and sex-specific maps shape IBD sharing in close relatives

    Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives
    Madison Caballero,Daniel N. Seidman,Ying Qiao,Jens Sannerud,Thomas D. Dyer ,Donna M. Lehman,Joanne E. Curran,Ravindranath Duggirala,John Blangero,Shai Carmi,Amy L. Williams


    Abstract
    Simulations of close relatives and identical by descent (IBD) segments are common in genetic studies, yet most past efforts have utilized sex averaged genetic maps and ignored crossover interference, thus omitting features known to affect the breakpoints of IBD segments. We developed Ped-sim, a method for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either a model of crossover interference or the traditional Poisson model for inter-crossover distances. To characterize the impact of previously ignored mechanisms, we simulated data for all four combinations of these factors. We found that modeling crossover interference decreases the standard deviation of pairwise IBD proportions by 10.4% on average in full siblings through second cousins. By contrast, sex-specific maps increase this standard deviation by 4.2% on average, and also impact the number of segments relatives share. Most notably, using sex-specific maps, the number of segments half-siblings share is bimodal; and when combined with interference modeling, the probability that sixth cousins have non-zero IBD sharing ranges from 9.0 to 13.1%, depending on the sexes of the individuals through which they are related. We present new analytical results for the distributions of IBD segments under these models and show they match results from simulations. Finally, we compared IBD sharing rates between simulated and real relatives and find that the combination of sex-specific maps and interference modeling most accurately captures IBD rates in real data. Ped-sim is open source and available from https://github.com/williamslab/ped-sim.

    Author summary
    Simulations are ubiquitous throughout statistical genetics in order to generate data with known properties, enabling tests of inference methods and analyses of real world processes in settings where experimental data are challenging to collect. Simulating genetic data for relatives in a pedigree requires the synthesis of chromosomes parents transmit to their children. These chromosomes form as a mosaic of a given parentís two chromosomes, with the location of switches between the two parental chromosomes known as crossovers. Detailed information about crossover generation based on real data from humans now exists, including the fact that men and women have overall different rates (women produce ∼1.6 times more crossovers) and that real crossovers are subject to interferenceówhereby crossovers are further apart from one another than expected under a model that selects their locations randomly. Our new method, Ped-sim, can simulate pedigree data using these less commonly modeled crossover features, and we used it to evaluate the impact of sex-specific rates and interference compared to real data. These comparisons show that both factors shape the amount of DNA two relatives share, and that their inclusion in models of crossover better fit data from real relatives.
    YFull: YF14620 (Dante Labs 2018)

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    I was thinking about new possible DNA ethnic breakdowns, that, as far as I know, have never been proposed by the DNA companies.

    Currently when looking at your DNA ethnic breakdown there is no distinction between recent, less recent and deep ancestry: all is mixed up in a single view.

    But it is clear that there is a probabilistic relationship between TMRCA and segment size.

    So it would be much more interesting to propose several ethnic breakdowns based on the different segment sizes, so that you will be able to see the evolution of your ethnic breakdown along the time.

    The current situation is not satisfactory: the ethnic computation is done whatever the segment sizes are, and so the short is added to the long, the old to the young, it is like adding apples and oranges.

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    I have processed the 245 MyHeritage matches of my father, classifying them according to the segment size and computing their average ethnical composition, considering 6 components: Italian, Iberian, Celtic, Germanic, English and Scandinavian:

    From 6 CM to 8 CM: Italian 4.2%, Iberian 16.9%, Celtic 11%, Germanic 20%, English 16.7%, Scandinavian 18.5

    From 8 CM to 9 CM: Italian 15.20%, Iberian 13.7%, Celtic 10.4%, Germanic 18%, English 14.5%, Scandinavian 12%

    From 9 CM to 11 CM: Italian 18.50%, Iberian 14%, Celtic 9.8%, Germanic 17.6%, English 10.6%, Scandinavian 11.75%

    From 11 CM to 60 CM: Italian 24%, Iberian 17%, Celtic 11.11%, Germanic 14%, English 9.98%, Scandinavian 7%

    My interpretation of these statistics according to my own genealogical knowledge:

    The old ancestry of my paternal lineage is well reflected between 6 and 8 CM, which corresponds to the 12th century Anglo-Norman colony in Tortosa: Iberian + English + Scandinavian. But the recent ancestry (Italian) is not.

    The increase of the Italian ancestry as the segment length grows corresponds to the eastward movement of my paternal lineage: the presence of my paternal lineage in Eastern Provence is attested at the end of the 15th century, when a massive Italian migration from Liguria occurred, mixing with the Provencal. This increase has continued as my paternal lineage settled in "Countea de Nissa" at the end of the 18th century.

    In parallel the Scandinavian and English components decrease continually as the segment size grows, which is normal, as the Provencal, and then Italian heritages have replaced the Nordic one, since the 13th century.
    Last edited by Phil1973; 01-10-2020 at 09:38 AM.

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