The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci
Open accessAbstract
Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Patterson's D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole-genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic ƒ(d), a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. ƒ(d) is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and ƒ(d) outliers tend to cluster in regions of low absolute divergence (d(XY)), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.
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Cites
Ancient Admixture in Human History
Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., Genschoreck, T., Webster, T., & Reich, D. (2012) · Genetics · doi:10.1534/genetics.112.145037 · Cited by 2,848
Abbott, R., Albach, D., Ansell, S., Arntzen, J. W., Baird, S. J. E., Bierne, N., Boughman, J., Brelsford, A., Buerkle, C. A., Buggs, R., et al. (2013) · Journal of Evolutionary Biology · doi:10.1111/j.1420-9101.2012.02599.x · Cited by 2,194
Self-citationReconstructing Indian population history
Reich, D., Thangaraj, K., Patterson, N., Price, A. L., & Singh, L. (2009) · Nature · doi:10.1038/nature08365 · Cited by 1,674
Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA
Huerta-Sánchez, E., Jin, X., Asan, Bianba, Z., Peter, B. M., Vinckenbosch, N., Liang, Y., Yi, X., He, M., Somel, M., et al. (2014) · Nature · doi:10.1038/nature13408 · Cited by 1,208
Inference of Population Structure using Dense Haplotype Data
Lawson, D. J., Hellenthal, G., Myers, S., & Falush, D. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002453 · Cited by 1,188
The genomic landscape of Neanderthal ancestry in present-day humans
Sankararaman, S., Mallick, S., Dannemann, M., Prüfer, K., Kelso, J., Pääbo, S., Patterson, N., & Reich, D. (2014) · Nature · doi:10.1038/nature12961 · Cited by 1,107
Sensitive detection of chromosomal segments of distinct ancestry in admixed populations
Price, A. L., Tandon, A., Patterson, N., Barnes, K. C., Rafaels, N., Ruczinski, I., Beaty, T. H., Mathias, R., Reich, D., & Myers, S. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000519 · Cited by 539
Genomic Ancestry of North Africans Supports Back-to-Africa Migrations
Henn, B. M., Botigué, L. R., Gravel, S., Wang, W., Brisbin, A., Byrnes, J. K., Fadhlaoui-Zid, K., Zalloua, P. A., Moreno-Estrada, A., Bertranpetit, J., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002397 · Cited by 331
Higher Levels of Neanderthal Ancestry in East Asians than in Europeans
Wall, J. D., Yang, M. A., Jay, F., Kim, S. K., Durand, E. Y., Stevison, L. S., Gignoux, C., Woerner, A., Hammer, M. F., & Slatkin, M. (2013) · Genetics · doi:10.1534/genetics.112.148213 · Cited by 249
Ancient Structure in Africa Unlikely to Explain Neanderthal and Non-African Genetic Similarity
Yang, M. A., Malaspinas, A.-S., Durand, E. Y., & Slatkin, M. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss117 · Cited by 101
Cited by
Dsuite ‐ Fast D ‐statistics and related admixture evidence from VCF files
Malinsky, M., Matschiner, M., & Svardal, H. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13265 · Cited by 992
Evidence for archaic adaptive introgression in humans
Racimo, F., Sankararaman, S., Nielsen, R., & Huerta-Sánchez, E. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3936 · Cited by 521
Phylogenomics reveals three sources of adaptive variation during a rapid radiation
Pease, J. B., Haak, D. C., Hahn, M. W., & Moyle, L. C. (2016) · PLOS Biology · doi:10.1371/journal.pbio.1002379 · Cited by 432
Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake
Malinsky, M., Challis, R. J., Tyers, A. M., Schiffels, S., Terai, Y., Ngatunga, B. P., Miska, E. A., Durbin, R., Genner, M. J., & Turner, G. F. (2015) · Science · doi:10.1126/science.aac9927 · Cited by 420
Adaptive introgression: a plant perspective
Suarez-Gonzalez, A., Lexer, C., & Cronk, Q. C. B. (2018) · Biology Letters · doi:10.1098/rsbl.2017.0688 · Cited by 389
Metadata
- Authors
- Martin, S. H., Davey, J. W., & Jiggins, C. D.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-09-22
- Volume
- 32
- Issue
- 1
- Pages
- 244-257
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2022984183
- Cited by
- 742
- References
- 10
- FWCI
- 13.47
- Type
- journal article
- Language
- en
- Open access
- hybrid
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