Reliability of genetic bottleneck tests for detecting recent population declines

@article{Peery2012ReliabilityOG,
  title={Reliability of genetic bottleneck tests for detecting recent population declines},
  author={M. Zachariah Peery and Rebecca Kirby and Brendan N. Reid and Ricka E. Stoelting and Elena Doucet-B{\"e}er and Stacie J Robinson and Catalina V{\'a}squez‐Carrillo and Jonathan N. Pauli and PER J. Palsb{\o}ll},
  journal={Molecular Ecology},
  year={2012},
  volume={21}
}
The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and popular approach for determining if a population decline has occurred because they only require sampling at a single point in time, yet reflect demographic history over multiple generations. However, a… Expand
High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study
TLDR
The authors' results suggest caution when interpreting the results of bottleneck tests in species showing high variance in reproductive success, particularly in species with high fecundity, and computer simulations are recommended to confirm the occurrence of a population bottleneck. Expand
Inferring and outlining past population declines with linked microsatellites: a case study in two spruce species
TLDR
Simulation of the evolution of linked haploid SSR variation in populations submitted to different bottleneck regimes indicates that linked SSRs can be used as proxies to infer basic parameters related to strong population declines in species that lack adequate genomic resources. Expand
More precisely biased: increasing the number of markers is not a silver bullet in genetic bottleneck testing
In response to our review of the use of genetic bottleneck tests in the conservation literature (Peery et al. 2012, Molecular Ecology, 21, 3403–3418), Hoban et al. (2013, Molecular Ecology, in press)Expand
Challenges in analysis and interpretation of microsatellite data for population genetic studies
TLDR
This review assists with study design and molecular marker selection, facilitates sound interpretation of microsatellite data while fostering respect for their practical limitations, and identifies lessons that could be applied toward emerging markers and high-throughput technologies in population genetics. Expand
Ancient, but not recent, population declines have had a genetic impact on alpine yellow-bellied toad populations, suggesting potential for complete recovery
TLDR
This study investigated fine-scale population structure and tested for genetic signatures of historical and recent population decline, and suggested that genetic variation was shaped in all groups by a 7- to 45-fold demographic decline, which occurred between a few hundred and a few 1000 years ago. Expand
Disentangling genetic structure for genetic monitoring of complex populations
TLDR
Increased use of the SLFV model for genetic monitoring is supported by highlighting its benefits over traditional approaches and necessary future directions for model development to support large genomic datasets informing real‐world management and conservation issues are discussed. Expand
Genetics and the conservation of natural populations: allozymes to genomes
TLDR
I consider how the study of genetic variation has influenced efforts to conserve natural populations over the last 50 years and believes current training in conservation genetics focuses too much on the latest techniques and too little on understanding the conceptual basis which is needed to interpret data and ask good questions. Expand
Maximum-likelihood inference of population size contractions from microsatellite data.
TLDR
This work develops a maximum-likelihood method for the inference of past changes in population size from microsatellite allelic data, based on importance sampling of gene genealogies, extended for new mutation models, notably the generalized stepwise mutation model (GSM). Expand
Low bottleneck detection in long-lived species despite lost genetic diversity: a case study of tuatara and eastern massasauga rattlesnakes.
TLDR
The results suggest that reliance on commonly used bottleneck tests could lead to misguided species management decisions and heterozygosity excess and mode-shift tests often failed to detect bottlenecks in both species, even when large losses in genetic diversity had occurred. Expand
Inferring Demographic History Using Genomic Data
TLDR
This chapter discusses recent advancements in demographic inference made possible by genome sequence and new analytical tools and encourages users to recognize inherent limitations of model assumptions, use simulations to identify potential biases, and include complementary and supporting analyses. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 104 REFERENCES
Detecting past population bottlenecks using temporal genetic data
TLDR
Serial coalescent simulations were conducted to assess the extent to which temporal genetic data are informative regarding population bottlenecks and demonstrated that the power to reject a constant population size hypothesis using both ancient and modern genetic data is almost always higher than that based on modern data. Expand
Empirical Evaluation of a Test for Identifying Recently Bottlenecked Populations from Allele Frequency Data
TLDR
A statistical test (a sign test for heterozygosity excess) for detecting recent historical bottlenecks using allele frequency data (Cornuet & Luikart 1996) is developed and evaluated by analyzing 56 allozyme and 37 microsatellite data sets from bottlenecked and nonbottlenecked natural populations. Expand
Immigration and the ephemerality of a natural population bottleneck: evidence from molecular markers
TLDR
Results show that immigration at levels that are hard to measure in most field studies can lead to qualitatively very different genetic outcomes from those expected from mutations only, and suggest that future theoretical and empirical work on bottlenecks and metapopulations should address the impact of immigration. Expand
Evaluation of methodology for detection of genetic bottlenecks: inferences from temporally replicated lake trout populations.
TLDR
It is shown that single values of the M-ratio are not sufficient to unambiguously infer a bottleneck without knowledge of mutation rates and effective population size, and conclusions of the degree of population bottleneck would be best supported if analyses were conducted across plausible ranges of [symbol: see text] and by qualitative comparisons among population samples. Expand
Comparison of methods for detecting bottlenecks from microsatellite loci
TLDR
Simulation tests to compare methods for detecting recent bottlenecks using microsatellite data find that Mk was the method most likely to correctly identify a bottleneck when a bottleneck lasted several generations, the population had made a demographic recovery, and mutation rates were high or pre-bottleneck population sizes were large. Expand
Inferring Population Decline and Expansion From Microsatellite Data: A Simulation-Based Evaluation of the Msvar Method
TLDR
Using simulated data sets under various demographic scenarios, Msvar, a full-likelihood Bayesian method that infers past demographic change from microsatellite data, is evaluated and it is suggested that Msvar is robust to moderate departures from a strict stepwise mutation model. Expand
A Near-extinction Event in Lynx: Do Microsatellite Data Tell the Tale?
TLDR
The Scandinavian lynx population was hunted to the brink of extinction, with fewer than 100 animals remaining in the late 1920s, and despite this pronounced demographic bottleneck, no conclusive genetic evidence of a bottleneck was found using four of the recently developed tests for detecting such events. Expand
Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data.
TLDR
These analyses show that the most useful markers for bottleneck detection are those evolving under the infinite allele model (IAM) and they provide guidelines for selecting sample sizes of individuals and loci. Expand
Distortion of allele frequency distributions provides a test for recent population bottlenecks.
TLDR
It is demonstrated that population bottlenecks cause a characteristic mode-shift distortion in the distribution of allele frequencies at selectively neutral loci, and a qualitative graphical method is illustrated and evaluated for detecting a bottleneck-induced distortion of allele frequency distributions. Expand
Detection of reduction in population size using data from microsatellite loci
TLDR
It is demonstrated that the mean ratio of the number of alleles to the range in allele size, which is calculated from a population sample of microsatellite loci, can be used to detect reductions in population size and that the value of M consistently predicts the reported demographic history for these populations. Expand
...
1
2
3
4
5
...