Blackwell Publishing Ltd of closely linked SNPs
We consider an isolated population founded by a small number of individuals randomly chosen from a source population of known genetic composition at a known time in the past. We develop a Monte-Carlo maximum-likelihood method for estimating the number of founding individuals from the haplotype frequ...
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ftciteseerx:oai:CiteSeerX.psu:10.1.1.324.2268 2023-05-15T15:50:21+02:00 Blackwell Publishing Ltd of closely linked SNPs Raphaël Leblois Montgomery Slatkin The Pennsylvania State University CiteSeerX Archives 2007 application/pdf http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.324.2268 http://ib.berkeley.edu/labs/slatkin/monty/LebloisSlatkinMolEcol2007.pdf en eng http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.324.2268 http://ib.berkeley.edu/labs/slatkin/monty/LebloisSlatkinMolEcol2007.pdf Metadata may be used without restrictions as long as the oai identifier remains attached to it. http://ib.berkeley.edu/labs/slatkin/monty/LebloisSlatkinMolEcol2007.pdf coalescent theory founder effect gene genealogy linkage disequilibrium maximumlikelihood estimation text 2007 ftciteseerx 2016-09-04T00:26:07Z We consider an isolated population founded by a small number of individuals randomly chosen from a source population of known genetic composition at a known time in the past. We develop a Monte-Carlo maximum-likelihood method for estimating the number of founding individuals from the haplotype frequencies at several SNP (single nucleotide polymorphism) loci in a sample. We assume the isolated population was founded recently enough that that mutation can be ignored and that haplotype frequencies in the source population have not changed. We apply the method to simulated data and show that it is unbiased. With a reasonable number of individuals sampled, it is possible to estimate the number of founders within a factor of 2. We show that the performance of the method is not degraded substantially if the frequencies of the rare haplotypes in the source are not known precisely and if there is some recombination. We illustrate the use of our method by applying it to a previously published data set from a recently founded population of wolves (Canis lupus) in Scandinavia. Text Canis lupus Unknown |
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ftciteseerx |
language |
English |
topic |
coalescent theory founder effect gene genealogy linkage disequilibrium maximumlikelihood estimation |
spellingShingle |
coalescent theory founder effect gene genealogy linkage disequilibrium maximumlikelihood estimation Raphaël Leblois Montgomery Slatkin Blackwell Publishing Ltd of closely linked SNPs |
topic_facet |
coalescent theory founder effect gene genealogy linkage disequilibrium maximumlikelihood estimation |
description |
We consider an isolated population founded by a small number of individuals randomly chosen from a source population of known genetic composition at a known time in the past. We develop a Monte-Carlo maximum-likelihood method for estimating the number of founding individuals from the haplotype frequencies at several SNP (single nucleotide polymorphism) loci in a sample. We assume the isolated population was founded recently enough that that mutation can be ignored and that haplotype frequencies in the source population have not changed. We apply the method to simulated data and show that it is unbiased. With a reasonable number of individuals sampled, it is possible to estimate the number of founders within a factor of 2. We show that the performance of the method is not degraded substantially if the frequencies of the rare haplotypes in the source are not known precisely and if there is some recombination. We illustrate the use of our method by applying it to a previously published data set from a recently founded population of wolves (Canis lupus) in Scandinavia. |
author2 |
The Pennsylvania State University CiteSeerX Archives |
format |
Text |
author |
Raphaël Leblois Montgomery Slatkin |
author_facet |
Raphaël Leblois Montgomery Slatkin |
author_sort |
Raphaël Leblois |
title |
Blackwell Publishing Ltd of closely linked SNPs |
title_short |
Blackwell Publishing Ltd of closely linked SNPs |
title_full |
Blackwell Publishing Ltd of closely linked SNPs |
title_fullStr |
Blackwell Publishing Ltd of closely linked SNPs |
title_full_unstemmed |
Blackwell Publishing Ltd of closely linked SNPs |
title_sort |
blackwell publishing ltd of closely linked snps |
publishDate |
2007 |
url |
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.324.2268 http://ib.berkeley.edu/labs/slatkin/monty/LebloisSlatkinMolEcol2007.pdf |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_source |
http://ib.berkeley.edu/labs/slatkin/monty/LebloisSlatkinMolEcol2007.pdf |
op_relation |
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.324.2268 http://ib.berkeley.edu/labs/slatkin/monty/LebloisSlatkinMolEcol2007.pdf |
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Metadata may be used without restrictions as long as the oai identifier remains attached to it. |
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1766385312152420352 |