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High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study

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hoban2013bmcbioinformatics309.pdf (537.0Kb)
Date
16/10/2013
Author
Hoban, Sean M.
Mezzavilla, Massimo
Gaggiotti, Oscar E.
Benazzo, Andrea
van Oosterhout, Cock
Bertorelle, Giorgio
Keywords
Conservation
Heterozygosity excess
M-ratio
MSVAR
FPR
Sweepstakes reproduction
Type I error
Variance in reproductive success
Allele frequency data
Coalescent processes
Life-history
Detecting bottlenecks
Microsatellite loci
Offspring number
Diversity
Variability
Program
QH426 Genetics
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Abstract
Background: Demographic bottlenecks can severely reduce the genetic variation of a population or a species. Establishing whether low genetic variation is caused by a bottleneck or a constantly low effective number of individuals is important to understand a species' ecology and evolution, and it has implications for conservation management. Recent studies have evaluated the power of several statistical methods developed to identify bottlenecks. However, the false positive rate, i.e. the rate with which a bottleneck signal is misidentified in demographically stable populations, has received little attention. We analyse this type of error (type I) in forward computer simulations of stable populations having greater than Poisson variance in reproductive success (i.e., variance in family sizes). The assumption of Poisson variance underlies bottleneck tests, yet it is commonly violated in species with high fecundity. Results: With large variance in reproductive success (V-k >= 40, corresponding to a ratio between effective and census size smaller than 0.1), tests based on allele frequencies, allelic sizes, and DNA sequence polymorphisms (heterozygosity excess, M-ratio, and Tajima's D test) tend to show erroneous signals of a bottleneck. Similarly, strong evidence of population decline is erroneously detected when ancestral and current population sizes are estimated with the model based method MSVAR. Conclusions: Our results suggest caution when interpreting the results of bottleneck tests in species showing high variance in reproductive success. Particularly in species with high fecundity, computer simulations are recommended to confirm the occurrence of a population bottleneck.
Citation
Hoban , S M , Mezzavilla , M , Gaggiotti , O E , Benazzo , A , van Oosterhout , C & Bertorelle , G 2013 , ' High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study ' , BMC Bioinformatics , vol. 14 , 309 . https://doi.org/10.1186/1471-2105-14-309
Publication
BMC Bioinformatics
Status
Peer reviewed
DOI
https://doi.org/10.1186/1471-2105-14-309
ISSN
1471-2105
Type
Journal article
Rights
© 2013 Hoban et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Description
Funding was provided by the University of Ferrara, Italy. CvO was funded by the Earth and Life Systems Alliance (ELSA), Norwich Research Park, UK
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  • University of St Andrews Research
URI
http://hdl.handle.net/10023/4646

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