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We model the process of breed formation and show that the probability of two or three adjacent marker loci showing a spurious signal of selection within at least one breed (i.e., Type I error or false-positive rate) is low if highly variable and moderately spaced markers are utilized. We also use simulations with selection to demonstrate that even a moderately spaced set of highly polymorphic markers (e.g., one every 0.8 cM) has high power to detect regions targeted by strong artificial selection in dogs. Further, we show that a gene responsible for black coat color in the Large Munsterlander has a 40-Mb region surrounding the gene that is very low in heterozygosity for microsatellite markers. Similarly, we survey 302 microsatellite markers in the Dachshund and find three linked monomorphic microsatellite markers all within a 10-Mb region on chromosome 3. This region contains the <jats:italic>FGFR3<\/jats:italic> gene, which is responsible for achondroplasia in humans, but not in dogs. Consequently, our results suggest that the causative mutation is a gene or regulatory region closely linked to <jats:italic>FGFR3<\/jats:italic>.<\/jats:p>","DOI":"10.1101\/gr.4374505","type":"journal-article","created":{"date-parts":[[2005,12,8]],"date-time":"2005-12-08T19:03:03Z","timestamp":1134068583000},"page":"1809-1819","source":"Crossref","is-referenced-by-count":91,"title":["Selective sweep mapping of genes with large phenotypic effects"],"prefix":"10.1101","volume":"15","author":[{"given":"John P.","family":"Pollinger","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos D.","family":"Bustamante","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adi","family":"Fledel-Alon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheila","family":"Schmutz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melissa M.","family":"Gray","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert K.","family":"Wayne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"246","published-online":{"date-parts":[[2005,12,8]]},"reference":[{"key":"2021111811011309000_15.12.1809.1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0306582101"},{"key":"2021111811011309000_15.12.1809.2","first-page":"1591","volume":"2","year":"2004","journal-title":"PLoS Biol."},{"key":"2021111811011309000_15.12.1809.3","unstructured":"American Kennel Club. 1997. 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