Hiya again, Connie. I agree with your choice to remove the information in that earlier post. Since I'd replied to the topic, I received it via email. I'll make some general comments here that don't reveal any of the data.
First things first. Step one is to make certain we're looking at the returned data we want to look at. It isn't immediately obvious.
What you posted looked like it was taken from the very bottom of the reported results. Logically, that's where you'd think you should look, right?
But if you scroll up a bit from there, you'll see the heading, "The following percentages are for individual homozygous SNPs, not just those in ROHs." So that bottom section is looking at all locations on the chromosomes that show the same nucleic acid: we only have four of 'em--A, C, G, and T--so a bunch of the locations, locations that don't mean anything about pedigree collapse because they aren't in sequential runs, will be doubled-up, i.e., AA, CC, GG, TT.
These are reporting as homozygous SNPs, but we're only interested in them if they're strung together, a lot of them occurring contiguously, for example: AA, GG, GG, AA, CC, TT, etc.
Just above that heading about individual SNPs you should see three lines that look like:
Total ROH Mb: [number]
Total genome Mb: [number]
The detected ROHs account for [number]% of the reported genome
What we're interested in is that percentage, as well as the per-chromosome ROH sizes listed above it.
(Ed's Nerd Note [meaning this can be completely ignored]: That percentage is a measure of individual autozygosity--usually written as Froh--which is the proportion of the autosomal genome in runs of homozygosity above a specified length threshold. ROH are contiguous pieces of a chromosome that exist because parents passed down identical segments. Autozygosity is the degree to which both copies of a chromosome an individual carries have identical genetic sequences.)
Okay. Still with me? As I mentioned before, several studies have indicated that we all show some level of autozygosity--makes sense because all our DNA came from somewhere, and the whole "can't split-up genes that actively code for important stuff" thing. They found that the length of a run of homozygosity was important in determining whether or not that segment indicated recent pedigree collapse, or was simply inherited from longer ago...a population-level indicator. And the population-level genetic origins of the test-taker make a difference in evaluating the results.
The (somewhat) bad news: this means there really is no one hard-and-fast rule in using ROH to estimate pedigree collapse if the consanguinity is more than a few degrees of relationship removed; it's more assured if it's recent. If Aaron reads this, he might want to give us an idea of what evaluation thresholds GEDmatch uses.
African, East Asian, and European populations tend to show the shortest length of ROH, and smallest total genomic ROH (Kirin, et. al., "Genomic Runs of Homozygosity Record Population History and Consanguinity." PLoS One, Nov 2010; https://doi.org/10.1371/journal.pone.0013996).
Click the chart for a full-sized version.
(Ed's Nerd Note [meaning this can be completely ignored]: There is always discussion on G2G about Native American DNA and our common, inexpensive microarray tests. There has been--and will probably continue to be--little interest among the NA People regarding DNA; it isn't something that defines their ethnicity, and a single interaction with colonial European uniparental DNA--yDNA or mtDNA--will remove NA indicators for those anthropological-timeframe markers. However, the study linked above, though dated by current standards, found that NA populations as sampled from Central and South America showed the longest stretches of homozygosity for all ROH length categories, as shown in the chart. Of the NA samples evaluated, 67% showed at least one ROH longer than 10 megabase pairs. I don't really research NA genetics, and don't know if there have been other studies that looked specifically at this population-level ROH/autozygosity and whether it might be a reasonable indicator of NA descent within, say, five to 10 generations. For those involved, that could be worth some research.)
<coughcough> So... David Pike's utility will report short runs of homozygosity that, depending upon the circumstances and population-level genetics, may very well not be informative about pedigree collapse. You might choose to disregard very small ROH segments; your call. And because the utility includes the X-chromosome, we have to do some of our own math.
We males are odd, and that throws some folks for a curve when looking at data like these. Males have only one Y chromosome, only one X chromosome, and then two tiny little areas, called the pseudoautosomal regions (PAR), that allow the Y and X chromosomes to link up. But because almost all of the formats the testing companies use for our microarray raw DNA results contain two columns of alleles (the A, C, G, and T) for each locus on a chromosome, they simply double-up the values of the X chromosome for us guys so that both columns are filled (i.e., every allele will simply be displayed twice, for instance: AA, GG, AA, CC). That's why Pike's utility is showing your husband's X chromosome as 99.988% homozygous: the only bits that can't be homozygous are in the PAR...which can have medical importance, but does absolutely nuthin' for genealogy. So we ignore everything but chromosomes 1 through 22.
I'll (gasp) reveal my actual results so you can follow along:
- Chr 2 has a ROH of length 464 ( 0.20 Mb)
- Chr 2 has a ROH of length 217 ( 0.03 Mb)
- Chr 2 has a ROH of length 252 ( 0.09 Mb)
- Chr 3 has a ROH of length 313 ( 0.09 Mb)
- Chr 6 has a ROH of length 961 ( 0.48 Mb)
- Chr 7 has a ROH of length 628 ( 0.12 Mb)
- Chr 9 has a ROH of length 524 ( 2.66 Mb)
- Chr 10 has a ROH of length 209 ( 0.91 Mb)
- Chr 11 has a ROH of length 334 ( 0.12 Mb)
- Chr 11 has a ROH of length 221 ( 0.89 Mb)
- Chr 13 has a ROH of length 251 ( 0.02 Mb)
- Chr 14 has a ROH of length 338 ( 0.13 Mb)
- Chr 15 has a ROH of length 232 ( 0.15 Mb)
- Chr 16 has a ROH of length 200 ( 1.39 Mb)
- Chr 17 has a ROH of length 243 ( 0.10 Mb)
- Chr 19 has a ROH of length 449 ( 5.81 Mb)
- Chr X has a ROH of length 8878 (87.44 Mb)
- Chr X has a ROH of length 7096 (62.90 Mb)
- Total ROH Mb: 163.52
- Total genome Mb: 2884.10
- The detected ROHs account for 5.670% of the reported genome.
The utility is taking the total of all identified ROH segments (163.52 megabase pairs) and comparing that to the total genome estimate (2884.1 Mb) and showing that as a percentage. But I'm a male. There's no such thing as ROH on the X chromosome for me. So that has to go away.
My X is showing 150.34 Mb in total ROH. So we take 163.52 and subtract 150.34 for an actual total of 13.18 Mb...and an adjusted percentage of 0.47%. Big difference!
Barring any significant population-level differences, what can you expect with recent pedigree collapse? We can look to a 2011 article in the medical journal The Lancet for some info. Referring back to what I mentioned uptopic, the Coefficient of Inbreeding (CoF), a mating of 1st-degree relatives (CoF of 1/4; father/daughter, brother/sister), would be expected to show a total ROH of about 716 Mb....or about 25% of the genome.
A pairing of 2nd-degree relatives (e.g., double 1st cousins, an uncle and a niece; a CoF of 1/8), would be expected to show a total ROH of about 358 Mb...or, ta dah!, about 12.5% of the genome.
Similarly, a child of 3rd-degree relatives, like full 1st cousins, would have a CoF of 1/16 and be expected to show a total ROH of about 179 Mb...or about 6.25% of the genome. On David Pike's page for his ROH utility, he uses as an example one set of results where "ROHs were found on five different chromosomes of a person whose parents were first cousins." The total of those ROHs are 171.32 Mb. Pretty darned close to 179.
Connie, only looking at the numbers you initially posted I can't offer an informed opinion. I think you need to either check the results from David's utility if you saved them, or run the analysis again. But if I were forced to make a guess, I'd say you'll find that your husband has no significant autozygosity and that there is no close-relation inbreeding in his past between his patrilineal and matrilineal lines.
Back to my confusion over the actual scenarios involved, that doesn't tell you anything about a paternal grandfather impregnating his son's otherwise unrelated wife, or a maternal grandmother who was impregnated by someone related to her but unrelated to the son's patrilineal line.
Autozygosity also won't show in your husband if his father were, say, the product of two 1st cousins but his mother was biologically unrelated to the father's line. So Hubby's paternal grandfather might be the result of relational consanguinity, and the father's results would show indicative ROH...but the son's, Hubby's, ROH results wouldn't reveal that because he inherited one set of chromosomes from his father, and one from his mother. ROH happens only if segments of the father's and mother's genetic sequences match. If the mother is not biologically related to the father, the resultant ROH will look like a standard, outbred population.