so, after all my rambling about the historic mating patterns amongst the native irish, how inbred are the irish really?

from Population structure and genome-wide patterns of variation in Ireland and Britain:

[O]ur results suggest that the Irish population has the largest proportion of the genome in ROH (as measured by FROH1), relative to the British and HapMap CEU populations examined here (Figure 3).”

the members of the ceu population are mormons in utah. here is figure 3 — click on images for LARGER view:

ireland - roh01 - o'dushlaine et al

Figure 3 – FROH1 patterning in Irish, British and Swedish populations. Box plots represent (a) the number and (b) the summed size of segments of the autosomal genome that exists in ROH of 1 Mb or greater in length (ie, FROH1). The bars represent mean and confidence intervals, as per a standard box plot (box indicating the 25th–75th percentile of the FROH1 distribution, line within box representing the median and ends of the whiskers representing the 5th–95th percentiles). Outliers are represented by diamonds.”

so the irish: more AND longer roh or runs of homozygosity (1 Mb in length or greater) than the english, the utah mormons, scots in aberdeen, or the swedes — in that order (if i’m not mistaken). so the english here are the most outbred (what have i been saying?), while the irish are the most inbred.

more from the paper:

“Overall, the Irish and Swedish populations seem slightly different from the others in the context of ROH. Both the Irish and Swedish populations showed, on an average, a greater number of ROH, an increased maximum ROH length, as well as an increased proportion of the genome in homozygous runs, compared with that of the Scottish, southern English and Utah populations. Similarly, the mean level of individual autozygosity per population as measured by FROH22 was highest for the Irish group (Figure 4). Together, these results suggest slightly increased autozygosity in the Irish cohort compared with the British and Swedish cohorts.”

here’s figure 4:

ireland - roh02 - o'dushlaine et al

Figure 4 – Mean FROH1 and FROH5 patterning in Irish, British and Swedish populations. See Figure 1 legend for population identifiers. Y-axis indicates the average proportion of the autosomal genome covered by FROH1 or FROH5 (see Materials and Methods for definition of FROH).

“Autozygosity is generated by increased levels of kinship, which in turn reflects the population history of Ireland. Although relatively undisturbed by secondary migrations, the population of Ireland has undergone expansions and contractions at numerous points in recent history (eg, two major famines since 1600, disease epidemics, expansion in the first half of the 19th century). Aside from these features, the increased autozygosity may also reflect legacies of Gaelic family structures and comparatively low levels of migration that are in part due to a lack of industrial revolution in Ireland.

“To test a hypothesis of increased autozygosity due to features of relatively recent population history, we examined the patterning of homozygosity looking for signals of parental relatedness over the last four or five generations. Previous work has illustrated that parental relatedness arising within four to six generations predominantly affects ROH over 5 Mb in length.22 We therefore compared this statistic across populations. Results show that the Irish and Swedish populations have around 10 times as much of their genomes in ROH over 5 Mb in length than the southern English, and 1.5–3 times as much as Scotland and Utah (Figure 4)….

“Analysis of ROH is a powerful method to gauge the extent of ancient kinship and recent parental relationship within a population. This is because ROH arise from shared parental ancestry in an individual’s pedigree. The offspring of cousins have very long ROH, commonly over 10 Mb, whereas at the other end of the spectrum, almost all Europeans have ROH of ∼2 Mb in length, reflecting shared ancestry from hundreds to thousands of years ago. By focussing on ROH of different lengths, it is therefore possible to infer aspects of demographic history at different time depths in the past.22 We used FROH measures to compare and contrast patterning across populations. These measures are genomic equivalents of the pedigree inbreeding coefficient, but do not suffer from problems of pedigree reconstruction. By varying the lengths of ROH that are counted, they may be tuned to assess parental kinship at different points in the past. We used two different measures, FROH1, which includes all ROH over 1 Mb and hence includes information on recent and background parental relatedness, and FROH5, which sums ROH over 5 Mb in length, more typical of a parental relationship in the last four to six generations.22 Our FROH1 results indicate slightly elevated levels in the Irish and Swedish populations (compared with southern England, Scotland and HapMap CEU) of both the overall number of ROH and the proportion of genome in ROH (see Figure 3). This pattern was exaggerated when we restricted analysis to ROH greater than 5 Mb in length (ie, FROH5, see Figure 4), indicating increased levels of parental relatedness in the last six generations in the Irish and Swedish populations compared with other populations tested in this study. When we remove individuals with ROH over 5 Mb from the FROH1 analysis (Supplementary Figure S5), Ireland remains as the population with the most homozygous runs and the longest sum length of homozygosity. This provides further evidence that the elevated proportion of shorter ROH, and hence the number of ancient pedigree loops in Ireland, is indeed real and not driven by a limited number of offspring of cousins.

recent cousin matings, they mean.

so, if you look at figure 4, both the irish and the swedes have way more roh of over 5 Mb in lenth than the english (who have a really miniscule amount), the scots in aberdeen, or the mormons in utah (ceu) — in that order. in this instance, the swedes appear to have the most roh over 5 Mb, but as the authors say, when they removed the over 5 Mb individuals from the samples (i.e. the individuals most likely to be the offspring of recent cousin marriages), the irish wind up having the most and the longest roh over 1 Mb in length, so they win the overall inbreeding prize for these groups.

what the authors overlook, i think, is the longer term mating patterns of these populations. i think that the english in this study (and, it should be noted, that these are described as individuals from the south and southeast of england) have miniscule amounts of roh in their genomes because, out of all these groups, they have been outbreeding the longest (see “mating patterns in europe series” ↓ below in left-hand column) — since the early part of the middle ages, in fact. the irish and the swedes, on the other hand, have more roh because they started outbreeding much later (and, probably, too, because, like other northern populations, they’re somewhat remote and small in size) — the swedes sometime after they converted to christianity in — when was it? — ca. 1000 a.d.? and the irish, as i’ve shown in the last few posts on irish mating patterns, not until sometime towards the late medieval period — as late as the 1500s possibly.

the implication of all this is, because the irish and the swedes (and other groups in europe) inbred for longer than the english (and some of the french and dutch and germans), their societies would’ve remained clan- or extended-family based for longer than those of the english et al., and so would’ve been under different sorts of selection pressures from their social environment.

update: Supplementary Figure S5 – when the researchers removed the individuals with roh over 5Mb, i.e. those individuals who were most likely to be the offspring of cousins (see comments):

ireland - roh03 - o'dushlaine et al

previously: runs of homozygosity and inbreeding (and outbreeding) and western europeans, runs of homozygosity (roh), and outbreeding and russians, eastern europeans, runs of homozygosity (roh), and inbreeding and early and late medieval irish mating practices and clannish medieval ireland and inbreeding in europe’s periphery and early modern and modern clannish ireland and meanwhile, in ireland… and drinkin’ and fightin’ songs and mating patterns, family types, and clannishness in twentieth century ireland and inbreeding in ireland in modern times

(note: comments do not require an email. clan map of ireland.)

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