Temporal genetic analysis of the endangered tidewater goby: extinction–colonization dynamics or drift in isolation?
Extinction and colonization dynamics are critical to understanding the evolution and conservation of metapopulations. However, traditional field studies of extinction–colonization are potentially fraught with detection bias and have rarely been validated. Here, we provide a comparison of molecular a...
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| Published in | Molecular ecology Vol. 24; no. 22; pp. 5544 - 5560 |
|---|---|
| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Blackwell Scientific Publications
01.11.2015
Blackwell Publishing Ltd |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0962-1083 1365-294X 1365-294X |
| DOI | 10.1111/mec.13424 |
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| Abstract | Extinction and colonization dynamics are critical to understanding the evolution and conservation of metapopulations. However, traditional field studies of extinction–colonization are potentially fraught with detection bias and have rarely been validated. Here, we provide a comparison of molecular and field‐based approaches for assessment of the extinction–colonization dynamics of tidewater goby (Eucyclogobius newberryi) in northern California. Our analysis of temporal genetic variation across 14 northern California tidewater goby populations failed to recover genetic change expected with extinction–colonization cycles. Similarly, analysis of site occupancy data from field studies (94 sites) indicated that extinction and colonization are very infrequent for our study populations. Comparison of the approaches indicated field data were subject to imperfect detection, and falsely implied extinction–colonization cycles in several instances. For northern California populations of tidewater goby, we interpret the strong genetic differentiation between populations and high degree of within‐site temporal stability as consistent with a model of drift in the absence of migration, at least over the past 20–30 years. Our findings show that tidewater goby exhibit different population structures across their geographic range (extinction–colonization dynamics in the south vs. drift in isolation in the north). For northern populations, natural dispersal is too infrequent to be considered a viable approach for recolonizing extirpated populations, suggesting that species recovery will likely depend on artificial translocation in this region. More broadly, this work illustrates that temporal genetic analysis can be used in combination with field data to strengthen inference of extinction–colonization dynamics or as a stand‐alone tool when field data are lacking. |
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| AbstractList | Extinction and colonization dynamics are critical to understanding the evolution and conservation of metapopulations. However, traditional field studies of extinction-colonization are potentially fraught with detection bias and have rarely been validated. Here, we provide a comparison of molecular and field-based approaches for assessment of the extinction-colonization dynamics of tidewater goby (Eucyclogobius newberryi) in northern California. Our analysis of temporal genetic variation across 14 northern California tidewater goby populations failed to recover genetic change expected with extinction-colonization cycles. Similarly, analysis of site occupancy data from field studies (94 sites) indicated that extinction and colonization are very infrequent for our study populations. Comparison of the approaches indicated field data were subject to imperfect detection, and falsely implied extinction-colonization cycles in several instances. For northern California populations of tidewater goby, we interpret the strong genetic differentiation between populations and high degree of within-site temporal stability as consistent with a model of drift in the absence of migration, at least over the past 20-30 years. Our findings show that tidewater goby exhibit different population structures across their geographic range (extinction-colonization dynamics in the south vs. drift in isolation in the north). For northern populations, natural dispersal is too infrequent to be considered a viable approach for recolonizing extirpated populations, suggesting that species recovery will likely depend on artificial translocation in this region. More broadly, this work illustrates that temporal genetic analysis can be used in combination with field data to strengthen inference of extinction-colonization dynamics or as a stand-alone tool when field data are lacking. Extinction and colonization dynamics are critical to understanding the evolution and conservation of metapopulations. However, traditional field studies of extinction–colonization are potentially fraught with detection bias and have rarely been validated. Here, we provide a comparison of molecular and field‐based approaches for assessment of the extinction–colonization dynamics of tidewater goby (Eucyclogobius newberryi) in northern California. Our analysis of temporal genetic variation across 14 northern California tidewater goby populations failed to recover genetic change expected with extinction–colonization cycles. Similarly, analysis of site occupancy data from field studies (94 sites) indicated that extinction and colonization are very infrequent for our study populations. Comparison of the approaches indicated field data were subject to imperfect detection, and falsely implied extinction–colonization cycles in several instances. For northern California populations of tidewater goby, we interpret the strong genetic differentiation between populations and high degree of within‐site temporal stability as consistent with a model of drift in the absence of migration, at least over the past 20–30 years. Our findings show that tidewater goby exhibit different population structures across their geographic range (extinction–colonization dynamics in the south vs. drift in isolation in the north). For northern populations, natural dispersal is too infrequent to be considered a viable approach for recolonizing extirpated populations, suggesting that species recovery will likely depend on artificial translocation in this region. More broadly, this work illustrates that temporal genetic analysis can be used in combination with field data to strengthen inference of extinction–colonization dynamics or as a stand‐alone tool when field data are lacking. Extinction and colonization dynamics are critical to understanding the evolution and conservation of metapopulations. However, traditional field studies of extinction-colonization are potentially fraught with detection bias and have rarely been validated. Here, we provide a comparison of molecular and field-based approaches for assessment of the extinction-colonization dynamics of tidewater goby (Eucyclogobius newberryi) in northern California. Our analysis of temporal genetic variation across 14 northern California tidewater goby populations failed to recover genetic change expected with extinction-colonization cycles. Similarly, analysis of site occupancy data from field studies (94 sites) indicated that extinction and colonization are very infrequent for our study populations. Comparison of the approaches indicated field data were subject to imperfect detection, and falsely implied extinction-colonization cycles in several instances. For northern California populations of tidewater goby, we interpret the strong genetic differentiation between populations and high degree of within-site temporal stability as consistent with a model of drift in the absence of migration, at least over the past 20-30 years. Our findings show that tidewater goby exhibit different population structures across their geographic range (extinction-colonization dynamics in the south vs. drift in isolation in the north). For northern populations, natural dispersal is too infrequent to be considered a viable approach for recolonizing extirpated populations, suggesting that species recovery will likely depend on artificial translocation in this region. More broadly, this work illustrates that temporal genetic analysis can be used in combination with field data to strengthen inference of extinction-colonization dynamics or as a stand-alone tool when field data are lacking.Extinction and colonization dynamics are critical to understanding the evolution and conservation of metapopulations. However, traditional field studies of extinction-colonization are potentially fraught with detection bias and have rarely been validated. Here, we provide a comparison of molecular and field-based approaches for assessment of the extinction-colonization dynamics of tidewater goby (Eucyclogobius newberryi) in northern California. Our analysis of temporal genetic variation across 14 northern California tidewater goby populations failed to recover genetic change expected with extinction-colonization cycles. Similarly, analysis of site occupancy data from field studies (94 sites) indicated that extinction and colonization are very infrequent for our study populations. Comparison of the approaches indicated field data were subject to imperfect detection, and falsely implied extinction-colonization cycles in several instances. For northern California populations of tidewater goby, we interpret the strong genetic differentiation between populations and high degree of within-site temporal stability as consistent with a model of drift in the absence of migration, at least over the past 20-30 years. Our findings show that tidewater goby exhibit different population structures across their geographic range (extinction-colonization dynamics in the south vs. drift in isolation in the north). For northern populations, natural dispersal is too infrequent to be considered a viable approach for recolonizing extirpated populations, suggesting that species recovery will likely depend on artificial translocation in this region. More broadly, this work illustrates that temporal genetic analysis can be used in combination with field data to strengthen inference of extinction-colonization dynamics or as a stand-alone tool when field data are lacking. Extinction and colonization dynamics are critical to understanding the evolution and conservation of metapopulations. However, traditional field studies of extinction–colonization are potentially fraught with detection bias and have rarely been validated. Here, we provide a comparison of molecular and field‐based approaches for assessment of the extinction–colonization dynamics of tidewater goby ( Eucyclogobius newberryi ) in northern California. Our analysis of temporal genetic variation across 14 northern California tidewater goby populations failed to recover genetic change expected with extinction–colonization cycles. Similarly, analysis of site occupancy data from field studies (94 sites) indicated that extinction and colonization are very infrequent for our study populations. Comparison of the approaches indicated field data were subject to imperfect detection, and falsely implied extinction–colonization cycles in several instances. For northern California populations of tidewater goby, we interpret the strong genetic differentiation between populations and high degree of within‐site temporal stability as consistent with a model of drift in the absence of migration, at least over the past 20–30 years. Our findings show that tidewater goby exhibit different population structures across their geographic range (extinction–colonization dynamics in the south vs. drift in isolation in the north). For northern populations, natural dispersal is too infrequent to be considered a viable approach for recolonizing extirpated populations, suggesting that species recovery will likely depend on artificial translocation in this region. More broadly, this work illustrates that temporal genetic analysis can be used in combination with field data to strengthen inference of extinction–colonization dynamics or as a stand‐alone tool when field data are lacking. |
| Author | Hellmair, Michael Goldsmith, Greg McCraney, W. Tyler Kinziger, Andrew P. Jacobs, David K. |
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| Copyright | 2015 John Wiley & Sons Ltd 2015 John Wiley & Sons Ltd. Copyright © 2015 John Wiley & Sons Ltd |
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| Keywords | microsatellites metapopulation tidewater goby conservation extinction colonization |
| Language | English |
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| Notes | http://dx.doi.org/10.1111/mec.13424 Fig. S1. Summary of repeat field surveys and temporal genetic analysis for 10 sites with multiple years of collections, including (i) site occupancy histories from field surveys, tabulated on an annual basis (1 = occupied, 0 = unoccupied, * indicates year of genetic tissue collection), (ii) estimates of genetic diversity within each temporal genetic collection (N = sample size, Ho = observed heterozygosity, He = expected heterozygosity, A = allelic richness, Ar = rarefied allelic richness, Ap = rarefied private allelic richness), (iii) results from site-specific Bayesian cluster analysis using structure assuming the data were composed of two genetically distinct clusters, (iv) Genetic differentiation (FST) between population pairs (below diagonal) and P-values from permutation tests for significance (above diagonal).Appendix S1. Probability of at least one site going extinct by year n across m sites. Table S1. Microsatellite loci details including allelic richness across all populations, size range (including amplified flanking regions and microsatellite repeats) in base pairs (bp), Hardy-Weinberg expected heterozygosity (He), and references. Table S2. Genetic differentiation (FST) between population pairs (below diagonal) and p-values from permutation tests for significance (above diagonal). Table S3. Summary of the 16 time intervals for which both temporal genetic and repeat field collections are available, including the site, time interval, interpretation from temporal genetic analysis, findings from naïve inspection of repeat field survey data, and inference to extinction-colonization dynamics for the time interval. ArticleID:MEC13424 istex:12C35BA6EEA0F67EFC9678887C9655EAA221D5B9 ark:/67375/WNG-18H2Q382-S United States Fish and Wildlife Service ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 |
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| Snippet | Extinction and colonization dynamics are critical to understanding the evolution and conservation of metapopulations. However, traditional field studies of... |
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| SubjectTerms | Animals California Cluster Analysis Colonization conservation Eucyclogobius newberryi extinction Extinction, Biological field experimentation Gene Flow Gene Frequency Genetic diversity Genetic Drift genetic techniques and protocols Genetic Variation Genetics, Population Genotype metapopulation Metapopulations Microsatellite Repeats microsatellites Models, Genetic Perciformes - genetics Population Density Population Dynamics Sequence Analysis, DNA Spatio-Temporal Analysis Species extinction Tidewater tidewater goby Translocation |
| Title | Temporal genetic analysis of the endangered tidewater goby: extinction–colonization dynamics or drift in isolation? |
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