The DOI matches its Crossref record; 93 of the 93 references it cites were found in a registry or an index.
Reliability of genetic bottleneck tests for detecting recent population declines
Open accessAbstract
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 review of the published literature indicates that, as typically applied, microsatellite‐based bottleneck tests often do not detect bottlenecks in vertebrate populations known to have experienced declines. This observation was supported by simulations that revealed that bottleneck tests can have limited statistical power to detect bottlenecks largely as a result of limited sample sizes typically used in published studies. Moreover, commonly assumed values for mutation model parameters do not appear to encompass variation in microsatellite evolution observed in vertebrates and, on average, the proportion of multi‐step mutations is underestimated by a factor of approximately two. As a result, bottleneck tests can have a higher probability of ‘detecting’ bottlenecks in stable populations than expected based on the nominal significance level. We provide recommendations that could add rigor to inferences drawn from future bottleneck tests and highlight new directions for the characterization of demographic history.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Although no bottleneck was detected, we cannot exclude false negatives caused by small sample sizes and subsequent limited statistical power in this data set (Peery et al. 2012).”
From Population genetics of the brooding coral Seriatopora hystrix reveals patterns of strong genetic differentiation in the Western Indian Ocean (2021) · cites this paper as Peery et al. 2012
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
Tajima, F. (1989) · Genetics · doi:10.1093/genetics/123.3.585 · Cited by 14,056
BEAST: Bayesian evolutionary analysis by sampling trees
Drummond, A. J., & Rambaut, A. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-214 · Cited by 13,104
Cornuet, J. M., & Luikart, G. (1996) · Genetics · doi:10.1093/genetics/144.4.2001 · Cited by 4,365
Inbreeding effects in wild populations
Keller, L. F. (2002) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(02)02489-8 · Cited by 3,375
Piry, S., Luikart, G., & Cornuet, J. (1999) · Journal of Heredity · doi:10.1093/jhered/90.4.502 · Cited by 3,356
THE BOTTLENECK EFFECT AND GENETIC VARIABILITY IN POPULATIONS
Nei, M., Maruyama, T., & Chakraborty, R. (1975) · Evolution · doi:10.1111/j.1558-5646.1975.tb00807.x · Cited by 3,223
Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences
Drummond, A. J. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi103 · Cited by 3,094
Analysis and Management of Animal Populations
Grand, J. B., Williams, B. K., Nichols, J. D., & Conroy, M. J. (2003) · Journal of Wildlife Management · doi:10.2307/3802722 · Cited by 2,671
Genome-wide genetic marker discovery and genotyping using next-generation sequencing
Davey, J. W., Hohenlohe, P. A., Etter, P. D., Boone, J. Q., Catchen, J., & Blaxter, M. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3012 · Cited by 2,489
Microsatellites: simple sequences with complex evolution
Ellegren, H. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1348 · Cited by 2,429
Research works printed but not linked: 5
- Hudson RR, 1990, Oxford Survey in Evolutionary Biology, 1
- NMFS, 2010, Bi‐National Recovery Plan for the Kemp’s Ridley Sea Turtle (Lepidochelys kempii)
- Soulé ME, 1980, Conservation Biology: An Evolutionary‐Ecological Perspective, 151
- USFWS, 2010, Draft Revised Recovery Plan for the Northern Spotted Owl
- USFWS, 2010, Mexican Wolf Conservation Assessment
Cited by
Sorted by citations
Meta‐analysis reveals lower genetic diversity in overfished populations
Pinsky, M. L., & Palumbi, S. R. (2013) · Molecular Ecology · doi:10.1111/mec.12509 · Cited by 449
Challenges in analysis and interpretation of microsatellite data for population genetic studies
Putman, A. I., & Carbone, I. (2014) · Ecology and Evolution · doi:10.1002/ece3.1305 · Cited by 439
Genetics and the conservation of natural populations: allozymes to genomes
Allendorf, F. W. (2016) · Molecular Ecology · doi:10.1111/mec.13948 · Cited by 409
Flanagan, S. P., Forester, B. R., Latch, E. K., Aitken, S. N., & Hoban, S. (2017) · Evolutionary Applications · doi:10.1111/eva.12569 · Cited by 307
Genetic reconstructions of invasion history
Cristescu, M. E. (2015) · Molecular Ecology · doi:10.1111/mec.13117 · Cited by 230
Metadata
- Authors
- PEERY, M. Z., KIRBY, R., REID, B. N., STOELTING, R., DOUCET‐BËER, E., ROBINSON, S., VÁSQUEZ‐CARRILLO, C., PAULI, J. N., & PALSBØLL, P. J.
- Affiliations
- University of Wisconsin–Madison (US)
- Harvard University (US)
- Corresponding author
- PEERY, M. ZACHARIAH
- ORCID
- Venue
- Molecular Ecology
- Publisher
- Wiley
- Published
- 2012-05-30
- Volume
- 21
- Issue
- 14
- Pages
- 3403-3418
- ISSN
- 0962-1083 (ISSN-L)
- 1365-294X
- OpenAlex
- W2127249590
- Cited by
- 578
- References
- 93
- Citations by year
- 2026: 21 · 2025: 29 · 2024: 32 · 2023: 30 · 2022: 57 · 2021: 38 · 2020: 44 · 2019: 39 · 2018: 37 · 2017: 61 · 2016: 48 · 2015: 56 · 2014: 45 · 2013: 37 · 2012: 4
- FWCI
- 5.61
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Ecology (publishedVersion)
- PubMed (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, other-oa)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion)
- Funders
- National Science Foundation
- U.S. Environmental Protection Agency
- Harvard University
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- population decline detection, microsatellite markers, statistical power, mutation models, sample size, false positives, vertebrate populations, conservation genetics, demographic history
- MeSH terms
- Animals, Computer Simulation, Genetics, Population, Models, Genetic, Mutation, Population Dynamics, Vertebrates, Microsatellite Repeats
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
