All individuals in a finite population are related if traced back long enough and will, therefore, share segments of their genomes IBD. During meiosis segments of IBD are broken up by recombination. Therefore, the expected length of an IBD segment depends on the number of generations since the most recent common ancestor at the locus of the segment. The length of IBD segments that result from a common ancestor n generations in the past (therefore involving 2n meiosis) is exponentially distributed with mean 1/(2n) Morgans (M). The expected number of IBD segments decreases as the number of generations since the common ancestor at this locus increases. For a specific DNA segment, the probability of being IBD decreases as 2−2n since in each meiosis the probability of transmitting this segment is 1/2.
Identified IBD segments can be used for a wide range of purposes. As noted above the amount (length and number) of IBD sharing depends on the familial relationships between the tested individuals. Therefore, one application of IBD segment detection is to quantify relatedness. Measurement of relatedness can be used in forensic genetics, but can also increase information in genetic linkage mapping and help to decrease bias by undocumented relationships in standard association studies.
Another application of IBD is genotype imputation and haplotype phase inference. Long shared segments of IBD, which are broken up by short regions may be indicative for phasing errors.: SI
IBD mapping is similar to linkage analysis, but can be performed without a known pedigree on a cohort of unrelated individuals. IBD mapping can be seen as a new form of association analysis that increases the power to map genes or genomic regions containing multiple rare disease susceptibility variants.
In addition to that, IBD segments can be useful for measuring and identifying other influences on population structure. Gusev et al. showed that IBD segments can be used with additional modeling to estimate demographic history including bottlenecks and admixture. Using similar models Palamara et al. and Carmi et al. reconstructed the demographic history of Ashkenazi Jewish and Kenyan Maasai individuals. Botigué et al. investigated differences in African ancestry among European populations. Ralph and Coop used IBD detection to quantify the common ancestry of different European populations and Gravel et al. similarly tried to draw conclusions of the genetic history of populations in the Americas. Ringbauer et al. utilized geographic structure of IBD segments to estimate dispersal within Eastern Europe during the last centuries. Using the 1000 Genomes data Hochreiter found differences in IBD sharing between African, Asian and European populations as well as IBD segments that are shared with ancient genomes like the Neanderthal or Denisova.
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