Abstract
BackgroundDemographic 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.ResultsWith large variance in reproductive success (Vk ≥ 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.ConclusionsOur 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.
Highlights
Demographic bottlenecks can severely reduce the genetic variation of a population or a species
We focus on type I error rates that may arise in bottleneck tests when the variance of reproductive success is larger than the Poisson variance assumed by simple models underlying the bottleneck detection methods
When Vk increases, we observe a trend of decreased genetic variation within each set of simulations with the same Ne, and this effect is stronger for K than for He
Summary
Demographic bottlenecks can severely reduce the genetic variation of a population or a species. 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). Bottlenecks may leave a population genetic signature, such as decreases in number of alleles and heterozygosity, and loss of rare alleles [5,6]. These signatures can be detected when temporal samples are available (e.g. museum specimens or fossil remains), so that contemporary genetic variation can be compared to historic levels. It is important to evaluate the statistical performance of these methods, especially as these tests are key components of many evolutionary, molecular ecology, and conservation genetic studies [13,14,15,16]
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.