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Solutions for PCR, cloning and sequencing errors in population genetic analysis

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Solutions for PCR, cloning and sequencing errors in population genetic analysis. / Cummings, SM; McMullan, M; Joyce, DA; Van Oosterhout, C.

In: Conservation Genetics, Vol. 11, No. 3, 2010, p. 1095-1097.

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Cummings, SM ; McMullan, M ; Joyce, DA ; Van Oosterhout, C. / Solutions for PCR, cloning and sequencing errors in population genetic analysis. In: Conservation Genetics. 2010 ; Vol. 11, No. 3. pp. 1095-1097.

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@article{1db71ebc8fc84731a5763c0521e9b5ec,
title = "Solutions for PCR, cloning and sequencing errors in population genetic analysis",
abstract = "PCR and sequencing artefacts can seriously bias population genetic analyses, particularly of populations with low genetic variation such as endangered vertebrate populations. Here, we estimate the error rates, discuss their population genetics implications, and propose a simple detection method that helps to reduce the risk of accepting such errors. We study the major histocompatibility complex (MHC) class IIB of guppies, Poecilia reticulata and find that PCR base misincorporations inflate the apparent sequence diversity. When analysing neutral genes, such bias can inflate estimates of effective population size. Previously suggested protocols for identifying genuine alleles are unlikely to exclude all sequencing errors, or they ignore genuine sequence diversity. We present a novel and statistically robust method that reduces the likelihood of accepting PCR artefacts as genuine alleles, and which minimises the necessity of repeated genotyping. Our method identifies sequences that are unlikely to be a PCR artefact, and which need to be independently confirmed through additional PCR of the same template DNA. The proposed methods are recommended particularly for population genetic studies that involve multi-template DNA and in studies on genes with low genetic diversity.",
author = "SM Cummings and M McMullan and DA Joyce and {Van Oosterhout}, C",
year = "2010",
doi = "10.1007/s10592-009-9864-6",
language = "English",
volume = "11",
pages = "1095--1097",
journal = "Conservation Genetics",
issn = "1566-0621",
publisher = "Springer",
number = "3",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Solutions for PCR, cloning and sequencing errors in population genetic analysis

AU - Cummings, SM

AU - McMullan, M

AU - Joyce, DA

AU - Van Oosterhout, C

PY - 2010

Y1 - 2010

N2 - PCR and sequencing artefacts can seriously bias population genetic analyses, particularly of populations with low genetic variation such as endangered vertebrate populations. Here, we estimate the error rates, discuss their population genetics implications, and propose a simple detection method that helps to reduce the risk of accepting such errors. We study the major histocompatibility complex (MHC) class IIB of guppies, Poecilia reticulata and find that PCR base misincorporations inflate the apparent sequence diversity. When analysing neutral genes, such bias can inflate estimates of effective population size. Previously suggested protocols for identifying genuine alleles are unlikely to exclude all sequencing errors, or they ignore genuine sequence diversity. We present a novel and statistically robust method that reduces the likelihood of accepting PCR artefacts as genuine alleles, and which minimises the necessity of repeated genotyping. Our method identifies sequences that are unlikely to be a PCR artefact, and which need to be independently confirmed through additional PCR of the same template DNA. The proposed methods are recommended particularly for population genetic studies that involve multi-template DNA and in studies on genes with low genetic diversity.

AB - PCR and sequencing artefacts can seriously bias population genetic analyses, particularly of populations with low genetic variation such as endangered vertebrate populations. Here, we estimate the error rates, discuss their population genetics implications, and propose a simple detection method that helps to reduce the risk of accepting such errors. We study the major histocompatibility complex (MHC) class IIB of guppies, Poecilia reticulata and find that PCR base misincorporations inflate the apparent sequence diversity. When analysing neutral genes, such bias can inflate estimates of effective population size. Previously suggested protocols for identifying genuine alleles are unlikely to exclude all sequencing errors, or they ignore genuine sequence diversity. We present a novel and statistically robust method that reduces the likelihood of accepting PCR artefacts as genuine alleles, and which minimises the necessity of repeated genotyping. Our method identifies sequences that are unlikely to be a PCR artefact, and which need to be independently confirmed through additional PCR of the same template DNA. The proposed methods are recommended particularly for population genetic studies that involve multi-template DNA and in studies on genes with low genetic diversity.

U2 - 10.1007/s10592-009-9864-6

DO - 10.1007/s10592-009-9864-6

M3 - Article

VL - 11

SP - 1095

EP - 1097

JO - Conservation Genetics

JF - Conservation Genetics

SN - 1566-0621

IS - 3

ER -

ID: 719380