Editing Identity by descent (section)

=== IBD in population genetics ===
Detection of [[natural selection]] in the human genome is also possible via detected IBD segments. Selection will usually tend to increase the number of IBD segments among individuals in a population. By scanning for regions with excess IBD sharing, regions in the human genome that have been under strong, very recent selection can be identified.<ref name="Albrechtsen.2010">{{Cite journal
| last1 = Albrechtsen | first1 = A.
| last2 = Moltke | first2 = I.
| last3 = Nielsen | first3 = R.
| doi = 10.1534/genetics.110.113977
| title = Natural Selection and the Distribution of Identity-by-Descent in the Human Genome
| journal = Genetics
| volume = 186
| issue = 1
| pages = 295–308
| year = 2010
| pmid = 20592267
| pmc =2940294
}}</ref><ref name="Han.2013">{{Cite journal
| last1 = Han | first1 = L.
| last2 = Abney | first2 = M.
| doi = 10.1002/gepi.20606
| title = Identity by descent estimation with dense genome-wide genotype data
| journal = Genetic Epidemiology
| volume = 35
| issue = 6
| pages = 557–567
| year = 2011
| pmid = 21769932
| pmc =3587128
}}</ref>

In addition to that, IBD segments can be useful for measuring and identifying other influences on population structure.<ref name="Purcell.2007"/><ref name="Cockerham.1983">{{Cite journal
| last1 = Cockerham | first1 = C. C.
| last2 = Weir | first2 = B. S.
| title = Variance of actual inbreeding
| journal = Theoretical Population Biology
| volume = 23
| issue = 1
| pages = 85–109
| year = 1983
| pmid = 6857551
 | doi=10.1016/0040-5809(83)90006-0
| bibcode = 1983TPBio..23...85C
}}</ref><ref name="Gusev.2012b">{{Cite journal
| last1 = Gusev | first1 = A.
| last2 = Palamara | first2 = P. F.
| last3 = Aponte | first3 = G.
| last4 = Zhuang | first4 = Z.
| last5 = Darvasi | first5 = A.
| last6 = Gregersen | first6 = P.
| last7 = Pe'Er | first7 = I.
| doi = 10.1093/molbev/msr133
| title = The Architecture of Long-Range Haplotypes Shared within and across Populations
| journal = Molecular Biology and Evolution
| volume = 29
| issue = 2
| pages = 473–486
| year = 2011
| pmid = 21984068
| pmc =3350316
}}</ref><ref name="Palamara.2012">{{Cite journal
| last1 = Palamara | first1 = P. F.
| last2 = Lencz | first2 = T.
| last3 = Darvasi | first3 = A.
| last4 = Pe’Er | first4 = I.
| title = Length Distributions of Identity by Descent Reveal Fine-Scale Demographic History
| doi = 10.1016/j.ajhg.2012.08.030
| journal = The American Journal of Human Genetics
| volume = 91
| issue = 5
| pages = 809–822
| year = 2012
| pmid = 23103233
| pmc =3487132
}}</ref><ref name="Palamara.2013">{{Cite journal
| last1 = Palamara | first1 = P. F.
| last2 = Pe'Er | first2 = I.
| doi = 10.1093/bioinformatics/btt239
| title = Inference of historical migration rates via haplotype sharing
| journal = Bioinformatics
| volume = 29
| issue = 13
| pages = i180–i188
| year = 2013
| pmid = 23812983
| pmc =3694674
}}</ref> Gusev et al. showed that IBD segments can be used with additional modeling to estimate demographic history including [[Population bottleneck|bottlenecks]] and [[Genetic admixture|admixture]].<ref name="Gusev.2012b"/> Using similar models Palamara et al. and Carmi et al. reconstructed the [[Historical demography|demographic history]] of [[Ashkenazi Jewish]] and Kenyan [[Maasai people|Maasai]] individuals.<ref name="Palamara.2012"/><ref name="Palamara.2013"/><ref name="Carmi.2013">{{Cite journal
| last1 = Carmi | first1 = S.
| last2 = Palamara | first2 = P. F.
| last3 = Vacic | first3 = V.
| last4 = Lencz | first4 = T.
| last5 = Darvasi | first5 = A.
| last6 = Pe'Er | first6 = I.
| doi = 10.1534/genetics.112.147215
| title = The Variance of Identity-by-Descent Sharing in the Wright-Fisher Model
| journal = Genetics
| volume = 193
| issue = 3
| pages = 911–928
| year = 2013
| pmid = 23267057
| pmc =3584006
| arxiv = 1206.4745
}}</ref> Botigué et al. investigated differences in African ancestry among European populations.<ref name="Botigue.2013">{{Cite journal
| last1 = Botigue | first1 = L. R.
| last2 = Henn | first2 = B. M.
| last3 = Gravel | first3 = S.
| last4 = Maples | first4 = B. K.
| last5 = Gignoux | first5 = C. R.
| last6 = Corona | first6 = E.
| last7 = Atzmon | first7 = G.
| last8 = Burns | first8 = E.
| last9 = Ostrer | first9 = H.
| last10 = Flores | first10 = C.
| last11 = Bertranpetit | first11 = J.
| last12 = Comas | first12 = D.
| last13 = Bustamante | first13 = C. D.
| title = Gene flow from North Africa contributes to differential human genetic diversity in southern Europe
| doi = 10.1073/pnas.1306223110
| journal = Proceedings of the National Academy of Sciences
| volume = 110
| issue = 29
| pages = 11791–11796
| year = 2013
| pmid = 23733930
| pmc =3718088
| bibcode = 2013PNAS..11011791B
| doi-access = free
}}</ref> Ralph and Coop used IBD detection to quantify the common ancestry of different European populations<ref name="Ralph.2013">{{Cite journal
| last1 = Ralph | first1 = P.
| last2 = Coop | first2 = G.
| editor1-last = Tyler-Smith
| editor1-first = Chris
| doi = 10.1371/journal.pbio.1001555
| title = The Geography of Recent Genetic Ancestry across Europe
| journal = PLOS Biology
| volume = 11
| issue = 5
| pages = e1001555
| year = 2013
| pmid = 23667324
| pmc =3646727
| doi-access = free
}}</ref> and Gravel et al. similarly tried to draw conclusions of the genetic history of populations in the Americas.<ref name=" Gravel.2013">{{Cite journal
| last1 = Gravel | first1 = S.
| last2 = Zakharia | first2 = F.
| last3 = Moreno-Estrada | first3 = A.
| last4 = Byrnes | first4 = J. K.
| last5 = Muzzio | first5 = M.
| last6 = Rodriguez-Flores | first6 = J. L.
| last7 = Kenny | first7 = E. E.
| last8 = Gignoux | first8 = C. R.
| last9 = Maples | first9 = B. K.
| last10 = Guiblet | first10 = W.
| last11 = Dutil | first11 = J.
| last12 = Via | first12 = M.
| last13 = Sandoval | first13 = K.
| last14 = Bedoya | first14 = G.
| last15 = 1000 Genomes | first15 = T. K.
| last16 = Oleksyk | first16 = A.
| last17 = Ruiz-Linares | first17 = E. G.
| last18 = Burchard | first18 = J. C.
| last19 = Martinez-Cruzado | first19 = C. D.
| last20 = Bustamante | first20 = C. D.
| editor1-last = Williams
| editor1-first = Scott M
| title = Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data
| doi = 10.1371/journal.pgen.1004023
| journal = PLOS Genetics
| volume = 9
| issue = 12
| pages = e1004023
| year = 2013
| pmid = 24385924
| pmc =3873240
| arxiv = 1306.4021
| doi-access = free
}}</ref> Ringbauer et al. utilized geographic structure of IBD segments to estimate dispersal within Eastern Europe during the last centuries.<ref>{{Cite journal|last1=Ringbauer|first1=Harald|last2=Coop|first2=Graham|last3=Barton|first3=Nicholas H.|date=2017-03-01|title=Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks|url=http://www.genetics.org/content/205/3/1335|journal=Genetics|language=en|volume=205|issue=3|pages=1335–1351|doi=10.1534/genetics.116.196220|issn=0016-6731|pmid=28108588|pmc=5340342}}</ref> Using the [[1000 Genomes Project|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 hominin|Denisova]].<ref name="Hochreiter.2013">{{Cite journal
| last1 = Hochreiter | first1 = S.
| doi = 10.1093/nar/gkt1013
| title = HapFABIA: Identification of very short segments of identity by descent characterized by rare variants in large sequencing data
| journal = Nucleic Acids Research
| year = 2013
| pmid = 24174545
| pmc =3905877| volume=41
 | issue=22
 | pages=e202
}}</ref>