Reliability of genetic bottleneck tests for detecting recent population declines
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 popula...
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| Published in | Molecular ecology Vol. 21; no. 14; pp. 3403 - 3418 |
|---|---|
| Main Authors | , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Oxford, UK
Blackwell Publishing Ltd
01.07.2012
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| Subjects | |
| Online Access | Get full text |
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| Abstract | 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. |
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| AbstractList | 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.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. 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. 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. [PUBLICATION ABSTRACT] |
| Author | REID, BRENDAN N. VÁSQUEZ-CARRILLO, CATALINA ROBINSON, STACIE KIRBY, REBECCA PALSBØLL, PER J. DOUCET-BËER, ELENA PEERY, M. ZACHARIAH PAULI, JONATHAN N. STOELTING, RICKA |
| Author_xml | – sequence: 1 givenname: M. ZACHARIAH surname: PEERY fullname: PEERY, M. ZACHARIAH organization: Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, USA – sequence: 2 givenname: REBECCA surname: KIRBY fullname: KIRBY, REBECCA organization: Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, USA – sequence: 3 givenname: BRENDAN N. surname: REID fullname: REID, BRENDAN N. organization: Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, USA – sequence: 4 givenname: RICKA surname: STOELTING fullname: STOELTING, RICKA organization: Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, USA – sequence: 5 givenname: ELENA surname: DOUCET-BËER fullname: DOUCET-BËER, ELENA organization: Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, USA – sequence: 6 givenname: STACIE surname: ROBINSON fullname: ROBINSON, STACIE organization: Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, USA – sequence: 7 givenname: CATALINA surname: VÁSQUEZ-CARRILLO fullname: VÁSQUEZ-CARRILLO, CATALINA organization: Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, USA – sequence: 8 givenname: JONATHAN N. surname: PAULI fullname: PAULI, JONATHAN N. organization: Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, USA – sequence: 9 givenname: PER J. surname: PALSBØLL fullname: PALSBØLL, PER J. organization: Marine Evolution and Conservation, Centre of Evolutionary and Ecological Studies, University of Groningen, PO Box 11103, CC Groningen, The Netherlands |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/22646281$$D View this record in MEDLINE/PubMed |
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| Snippet | The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are... |
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| SubjectTerms | Animal populations Animals bottleneck test Computer Simulation extinction Genetic diversity genetics Genetics, Population Genetics, Population - methods heterozygosity M-ratio methods microsatellite Microsatellite Repeats Models, Genetic Mutation mutation model population bottleneck Population decline Population Dynamics Population genetics probability Reliability Reliability engineering Species extinction Vertebrates Vertebrates - genetics |
| Title | Reliability of genetic bottleneck tests for detecting recent population declines |
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