The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Linkage Disequilibrium and Demographic History of Wild and Domestic Canids
Open accessAbstract
Assessing the extent of linkage disequilibrium (LD) in natural populations of a nonmodel species has been difficult due to the lack of available genomic markers. However, with advances in genotyping and genome sequencing, genomic characterization of natural populations has become feasible. Using sequence data and SNP genotypes, we measured LD and modeled the demographic history of wild canid populations and domestic dog breeds. In 11 gray wolf populations and one coyote population, we find that the extent of LD as measured by the distance at which r2 = 0.2 extends <10 kb in outbred populations to >1.7 Mb in populations that have experienced significant founder events and bottlenecks. This large range in the extent of LD parallels that observed in 18 dog breeds where the r2 value varies from ∼20 kb to >5 Mb. Furthermore, in modeling demographic history under a composite-likelihood framework, we find that two of five wild canid populations exhibit evidence of a historical population contraction. Five domestic dog breeds display evidence for a minor population contraction during domestication and a more severe contraction during breed formation. Only a 5% reduction in nucleotide diversity was observed as a result of domestication, whereas the loss of nucleotide diversity with breed formation averaged 35%.
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Cites
Principal components analysis corrects for stratification in genome-wide association studies
Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., & Reich, D. (2006) · Nature Genetics · doi:10.1038/ng1847 · Cited by 10,248
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
Population Structure and Eigenanalysis
Patterson, N., Price, A. L., & Reich, D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020190 · Cited by 5,280
Genome sequence, comparative analysis and haplotype structure of the domestic dog
members, B. S. P., Lindblad-Toh, K., Wade, C. M., Mikkelsen, T. S., Karlsson, E. K., Jaffe, D. B., Kamal, M., Clamp, M., Chang, J. L., Kulbokas, E. J., et al. (2005) · Nature · doi:10.1038/nature04338 · Cited by 2,568
Self-citationAssessing the evolutionary impact of amino acid mutations in the human genome.
Boyko, A. R., Williamson, S. H., Indap, A. R., Degenhardt, J. D., Hernandez, R. D., Lohmueller, K. E., Adams, M. D., Schmidt, S., Sninsky, J. J., Sunyaev, S. R., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000083 · Cited by 628
Self-citationMolecular and Evolutionary History of Melanism in North American Gray Wolves
Anderson, T. M., vonHoldt, B. M., Candille, S. I., Musiani, M., Greco, C., Stahler, D. R., Smith, D. W., Padhukasahasram, B., Randi, E., Leonard, J. A., et al. (2009) · Science · doi:10.1126/science.1165448 · Cited by 416
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Genome sequencing highlights the dynamic early history of dogs
Freedman, A. H., Gronau, I., Schweizer, R. M., Ortega-Del Vecchyo, D., Han, E., Silva, P. M., Galaverni, M., Fan, Z., Marx, P., Lorente-Galdos, B., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004016 · Cited by 624
Variation in recombination frequency and distribution across eukaryotes: patterns and processes
Stapley, J., Feulner, P. G. D., Johnston, S. E., Santure, A. W., & Smadja, C. M. (2017) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2016.0455 · Cited by 507
A Simple Genetic Architecture Underlies Morphological Variation in Dogs
Boyko, A. R., Quignon, P., Li, L., Schoenebeck, J. J., Degenhardt, J. D., Lohmueller, K. E., Zhao, K., Brisbin, A., Parker, H. G., vonHoldt, B. M., et al. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000451 · Cited by 494
Self-citationMarsden, C. D., Ortega-Del Vecchyo, D., O’Brien, D. P., Taylor, J. F., Ramirez, O., Vilà, C., Marques-Bonet, T., Schnabel, R. D., Wayne, R. K., & Lohmueller, K. E. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1512501113 · Cited by 333
Self-citationA genome-wide perspective on the evolutionary history of enigmatic wolf-like canids
vonHoldt, B. M., Pollinger, J. P., Earl, D. A., Knowles, J. C., Boyko, A. R., Parker, H., Geffen, E., Pilot, M., Jedrzejewski, W., Jedrzejewska, B., et al. (2011) · Genome Research · doi:10.1101/gr.116301.110 · Cited by 342
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Metadata
- Authors
- Gray, M. M., Granka, J. M., Bustamante, C. D., Sutter, N. B., Boyko, A. R., Zhu, L., Ostrander, E. A., & Wayne, R. K.
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-04-01
- Volume
- 181
- Issue
- 4
- Pages
- 1493-1505
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- OpenAlex
- W2087260514
- Cited by
- 172
- References
- 6
- FWCI
- 8.73
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Gray, M. M., Granka, J. M., Bustamante, C. D., Sutter, N. B., Boyko, A. R., Zhu, L., Ostrander, E. A., & Wayne, R. K. (2009). Linkage Disequilibrium and Demographic History of Wild and Domestic Canids. Genetics. https://doi.org/10.1534/genetics.108.098830
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