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Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
..., or the genetic relatedness matrix (GRM), which stores pairwise genetic similarity based on variants. GLMMs complement this approach by simultaneously accounting for population structure and cryptic relatedness by modeling a random effect whose covariance structure is defined by the estimated GRM. Both PC...
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Research: Most chromatin interactions are not in linkage disequilibrium
- Sean Whalen and
- Katherine S. Pollard
Genome Res. March 2019 29: 334-343; Published in Advance January 7, 2019, doi:10.1101/gr.238022.118
...Francisco, San Francisco, California 94158, USA; 3Chan-Zuckerberg Biohub, San Francisco, California 94158, USA Corresponding author: kpollard@gladstone.ucsf.eduAbstractChromatin interactions and linkage disequilibrium (LD) are both pairwise measurements between genomic loci that show block patterns along...
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Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
- Paige A. Byerly,
- Alina von Thaden,
- Evgeny Leushkin,
- Leon Hilgers,
- Shenglin Liu,
- Sven Winter,
- Tilman Schell,
- Charlotte Gerheim,
- Alexander Ben Hamadou,
- Carola Greve,
- Christian Betz,
- Hanno J. Bolz,
- Sven Büchner,
- Johannes Lang,
- Holger Meinig,
- Evax Marie Famira-Parcsetich,
- Sarah P. Stubbe,
- Alice Mouton,
- Sandro Bertolino,
- Goedele Verbeylen,
- Thomas Briner,
- Lídia Freixas,
- Lorenzo Vinciguerra,
- Sarah A. Mueller,
- Carsten Nowak,
- and Michael Hiller
Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
...in the Miocene (23–5.3 Mya) (Nadachoswki and Daoud 1995).View larger version: In this window In a new window Figure 3. Demographic history of the garden dormouse. Effective population size (Ne) of E. quercinus as estimated with PSMC. Ne in 10,000 is shown on the y-axis and time in years ago on the x-axis. Faint...
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Research: Human population dispersal “Out of Africa” estimated from linkage disequilibrium and allele frequencies of SNPs
- Brian P. McEvoy,
- Joseph E. Powell,
- Michael E. Goddard,
- and Peter M. Visscher
Genome Res. June 2011 21: 821-829; Published in Advance April 25, 2011, doi:10.1101/gr.119636.110
...of population genetics, 4th ed. Sinauer Associates, Sunderland, MA. Hayes BJ, Visscher PM,McPartlan HC, GoddardME. 2003. Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res 13: 635–643. Hill WG. 1975. Linkage disequilibrium among multiple neutral alleles...
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Method: Leveraging family data to design Mendelian randomization that is provably robust to population stratification
- Nathan LaPierre,
- Boyang Fu,
- Steven Turnbull,
- Eleazar Eskin,
- and Sriram Sankararaman
Genome Res. July 2023 33: 1032-1041; Published in Advance May 17, 2023, doi:10.1101/gr.277664.123
..., the MR effect estimate of the exposure on the outcome will be valid even if there are unobserved confounders of the exposure–outcome relationship. The independence assumption, however, is often violated by population stratification (Fig. 1A) or horizontal pleiotropy, as these phenomena cause the genetic...
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Research: Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States
- Greta Bellinzona,
- Tiago Nardi,
- Michele Castelli,
- Gherard Batisti Biffignandi,
- Karim Adjou,
- Martha Betson,
- Yannick Blanchard,
- Ioana Bujila,
- Rachel Chalmers,
- Rebecca Davidson,
- Nicoletta D'Avino,
- Tuulia Enbom,
- Jacinto Gomes,
- Gregory Karadjian,
- Christian Klotz,
- Emma Östlund,
- Judith Plutzer,
- Ruska Rimhanen-Finne,
- Guy Robinson,
- Anna Rosa Sannella,
- Jacek Sroka,
- Christen Rune Stensvold,
- Karin Troell,
- Paolo Vatta,
- Barbora Zalewska,
- Claudio Bandi,
- Davide Sassera,
- and Simone M. Cacciò
Genome Res. June 2024 34: 877-887; Published in Advance July 8, 2024, doi:10.1101/gr.278830.123
....Within-population genetic indicesTo gain further insight into the genetic differentiation of the two populations in the “Western” lineage (i.e., populations 2 and 3), we calculated linkage disequilibrium (LD) decay, Tajima's D values, and nucleotide diversity (π).We found that population 3 had a slower...
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Method: Haplotype and population structure inference using neural networks in whole-genome sequencing data
- Jonas Meisner and
- Anders Albrechtsen
Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
...the estimated ancestry proportions from our HaploNet clustering algorithm against results from ADMIXTURE based on signal-to-noise ratio measures (Supplemental Table S1) and their ability to separate ancestry sources. We further compare the inferred population structure from our PCA approach to the PCA from...
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Research: Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits
- Olivia Corradin,
- Alina Saiakhova,
- Batool Akhtar-Zaidi,
- Lois Myeroff,
- Joseph Willis,
- Richard Cowper-Sal·lari,
- Mathieu Lupien,
- Sanford Markowitz,
- and Peter C. Scacheri
Genome Res. January 2014 24: 1-13; Published in Advance November 6, 2013, doi:10.1101/gr.164079.113
...Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits Olivia Corradin 1 , Alina Saiakhova 1 , Batool Akhtar-Zaidi 1 , Lois Myeroff 2 , Joseph...
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Research: Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome
- Jessica Stapley,
- Tim R. Birkhead,
- Terry Burke,
- and Jon Slate
Genome Res. April 2010 20: 496-502; Published in Advance March 31, 2010, doi:10.1101/gr.102095.109
...and consistency across generations of linkage disequilibrium in commercial layer chickenbreedingpopulations.Genetics171:1173–1181. Hill WG. 1981. Estimation of effective population-size from data on linkage disequilibrium. Genet Res 38: 209–216. International Chicken Genome Sequencing Consortium. 2004. Sequence...
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METHODS: Novel Multilocus Measure of Linkage Disequilibrium to Estimate Past Effective Population Size
- Ben J. Hayes,
- Peter M. Visscher,
- Helen C. McPartlan,
- and Mike E. Goddard
Genome Res. April 1, 2003 13: 635-643; Published in Advance March 12, 2003, doi:10.1101/gr.387103
...Novel Multilocus Measure of Linkage Disequilibrium to Estimate Past Effective Population Size Ben J. Hayes 1 , 4 , Peter M. Visscher 2 , Helen C. McPartlan 1 , and Mike E. Goddard 1 , 3 1Victorian Institute of Animal Science...

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