Recovering populations often must meet specific growth rate or abundance targets before their leg... more Recovering populations often must meet specific growth rate or abundance targets before their legal status can be changed from endangered or threatened. While the efficacy, power, and performance of population metrics to infer trends in declining populations has received considerable attention, how these same metrics perform when populations are increasing is less clear. We examined the ability of a one-sample effective population size (N e) estimator (LDNe) to discriminate between stable and increasing population trends across varying sample and initial population sizes. The performance of LDNe was compared to the Lincoln-Peterson (LP) abundance (N) estimator. The ability to identify stable and increasing populations varied widely across sample sizes and number of generations between sequentially collected samples, but LDNe outperformed LP. One-sample N e estimates show promise as an efficient method of detecting population increase when samples of 60-120 individuals are collected 5-10 generations apart.
Canadian Journal of Fisheries and Aquatic Sciences, Sep 1, 2017
Differential climate-induced shifts in phenology can create mismatches between predators and prey... more Differential climate-induced shifts in phenology can create mismatches between predators and prey, but few studies have examined predator–prey mismatch across multiple life-history stages. We used long-term data from a warming stream with shifting salmonid migration timings to quantify intra-annual migration synchrony between predatory Dolly Varden (Salvelinus malma) and Pacific salmon prey and examined how predator–prey synchrony has been influenced by climate change. We demonstrate that Dolly Varden have become increasingly mismatched with spring downstream migrations of abundant pink salmon (Oncorhynchus gorbuscha) juveniles. However, Dolly Varden have remained matched with fall upstream migrations of spawning Pacific salmon, including coho (Oncorhynchus kisutch), sockeye (Oncorhynchus nerka), and pink salmon. Downstream predator–prey migration synchrony decreased over time and with higher temperatures, particularly with pink salmon. In contrast, upstream migration synchrony was temporally stable and increased with rising temperatures. Differing trends in Dolly Varden predator–prey synchrony may be explained by the direct use of salmon to cue upstream migration, but not downstream migration. Overall, we show that climate change can have differing impacts on predator–prey synchrony across life-history stages.
We examined the genetic population structure of Long-Toed Salamanders (Ambystoma macrodactylum) f... more We examined the genetic population structure of Long-Toed Salamanders (Ambystoma macrodactylum) from the Bitterroot Mountains of Idaho and Montana to better understand their evolutionary history and genetic population structure. Populations show high levels of within-population genetic variation at six polymorphic allozyme loci (H s ؍ 0.09 for all 18 loci examined; range 0.04-0.14). There is very little divergence among populations within basins, suggesting panmixia within basins. In contrast, genetic differentiation among all populations is high (G st ؍ 0.30). We used computer simulations to examine population structures that could have led to the observed distribution of genetic variation, assuming selective neutrality of the allozymes. To test the assumption of selective neutrality of the markers used in this study, we compared the observed divergence among the allozymes to that expected from simulations of independently segregating and selectively neutral markers. The observed genetic divergence among populations is compatible with that expected for neutral genetic markers sampled from panmictic populations within basins that exchange less than one migrant among basins each generation.
JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, a... more JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact
Proceedings of the National Academy of Sciences of the United States of America, Nov 12, 2021
The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodive... more The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.
The estimation of effective population size from one sample of genotypes has been problematic bec... more The estimation of effective population size from one sample of genotypes has been problematic because most estimators have been proven imprecise or biased. We developed a web-based program, ONeSAMP that uses approximate Bayesian computation to estimate effective population size from a sample of microsatellite genotypes. ONeSAMP requires an input file of sampled individuals' microsatellite genotypes along with information about several sampling and biological parameters. ONeSAMP provides an estimate of effective population size, along with 95% credible limits. We illustrate the use of ONeSAMP with an example data set from a reintroduced population of ibex Capra ibex.
TOSSM (Testing of Spatial Structure Methods) is a package for testing the performance of genetic ... more TOSSM (Testing of Spatial Structure Methods) is a package for testing the performance of genetic analytical methods in a management context. In the TOSSM package, any method developed to detect population genetic structure can be combined with a mechanism for creating Management Units (MUs) based on the genetic analysis. The resulting Boundary-Setting Algorithm (BSA) dictates harvest boundaries with a genetic basis. These BSAs can be evaluated with respect to how well the MUs they define meet management objectives.
Bulletin of Environmental Contamination and Toxicology, May 7, 2009
We quantified imposex in file dogwinkles (Nucella lima) and tributyltin (TBT) contamination in ba... more We quantified imposex in file dogwinkles (Nucella lima) and tributyltin (TBT) contamination in bay mussels (Mytilus trossulus) from a number of sites in Auke Bay, Alaska, previously studied in the late 1980s. Imposex occurence and TBT contamination have generally declined in spatial extent and severity over time. However, high levels of TBT contamination (0.069 lg TBT/g wet tissue wt.) and imposex (100% of females affected) are still present near a large boat docking facility in the bay and deserve continued attention because of the importance of this bay to the local economy and fisheries.
We describe and evaluate a new estimator of the effective population size (N e), a critical param... more We describe and evaluate a new estimator of the effective population size (N e), a critical parameter in evolutionary and conservation biology. This new "SummStat" N e estimator is based upon the use of summary statistics in an approximate Bayesian computation framework to infer N e. Simulations of a Wright-Fisher population with known N e show that the SummStat estimator is useful across a realistic range of individuals and loci sampled, generations between samples, and N e values. We also address the paucity of information about the relative performance of N e estimators by comparing the SummStat estimator to two recently developed likelihood-based estimators and a traditional moment-based estimator. The SummStat estimator is the least biased of the four estimators compared. In 32 of 36 parameter combinations investigated using initial allele frequencies drawn from a Dirichlet distribution, it has the lowest bias. The relative mean square error (RMSE) of the SummStat estimator was generally intermediate to the others. All of the estimators had RMSE Ͼ 1 when small samples (n ϭ 20, five loci) were collected a generation apart. In contrast, when samples were separated by three or more generations and N e Յ 50, the SummStat and likelihood-based estimators all had greatly reduced RMSE. Under the conditions simulated, SummStat confidence intervals were more conservative than the likelihood-based estimators and more likely to include true N e. The greatest strength of the SummStat estimator is its flexible structure. This flexibility allows it to incorporate any potentially informative summary statistic from population genetic data.
Genetic rescue can increase the fitness of small, imperiled populations via immigration. A suite ... more Genetic rescue can increase the fitness of small, imperiled populations via immigration. A suite of studies from the past decade highlights the value of genetic rescue in increasing population fitness. Nonetheless, genetic rescue has not been widely applied to conserve many of the threatened populations that it could benefit. In this review, we highlight recent studies of genetic rescue and place it in the larger context of theoretical and empirical developments in evolutionary and conservation biology. We also propose directions to help shape future research on genetic rescue. Genetic rescue is a tool that can stem biodiversity loss more than has been appreciated, provides population resilience, and will become increasingly useful if integrated with molecular advances in population genomics. Review Glossary Absolute fitness: mean number of offspring per capita, measured as population growth rate (l) or abundance (N). Adaptive evolution: an increase in beneficial phenotypes in a population as a result of natural selection on genetic variation. Adaptive management: a structured, iterative process of decision-making that includes system monitoring to reduce uncertainty. Assisted gene flow: managed movement of individuals into populations to reduce local maladaptation to climate or other environmental change. Epistatic load: combinations of alleles at different loci that reduce fitness. Evolutionary rescue: an increase in population growth resulting from adaptation to otherwise extinction-causing environmental stress from standing genetic variation, de novo mutation or gene flow. Genetic load: the relative difference in fitness between the theoretically fittest genotype and the average genotype in a population. Caused by deleterious alleles in the case of mutational load. Other types of load include segregation, drift, epistatic, and migration. Genetic rescue: an increase in population fitness (growth) owing to immigration of new alleles. Genetic restoration: an increase in genetic variation and relative, but not absolute, fitness owing to immigration of new alleles. Heterosis: elevated fitness of offspring from matings between genetically divergent individuals. Invasive hybridization: cross-breeding between invasive and native species. Outbreeding depression: reduced fitness of offspring from matings between genetically divergent individuals. Transgressive hybridization: the creation of hybrids with phenotypes more extreme than their parental lines.
Proceedings of The Royal Society B: Biological Sciences, Jul 11, 2012
To predict how climate change will influence populations, it is necessary to understand the mecha... more To predict how climate change will influence populations, it is necessary to understand the mechanisms, particularly microevolution and phenotypic plasticity, that allow populations to persist in novel environmental conditions. Although evidence for climate-induced phenotypic change in populations is widespread, evidence documenting that these phenotypic changes are due to microevolution is exceedingly rare. In this study, we use 32 years of genetic data (17 complete generations) to determine whether there has been a genetic change towards earlier migration timing in a population of pink salmon that shows phenotypic change; average migration time occurs nearly two weeks earlier than it did 40 years ago. Experimental genetic data support the hypothesis that there has been directional selection for earlier migration timing, resulting in a substantial decrease in the late-migrating phenotype (from more than 30% to less than 10% of the total abundance). From 1983 to 2011, there was a significant decrease-over threefold-in the frequency of a genetic marker for late-migration timing, but there were minimal changes in allele frequencies at other neutral loci. These results demonstrate that there has been rapid microevolution for earlier migration timing in this population. Circadian rhythm genes, however, did not show any evidence for selective changes from 1993 to 2009.
Advances in molecular biology offer promise to the study of demographic characteristics of rare o... more Advances in molecular biology offer promise to the study of demographic characteristics of rare or hard-to-capture species, because individuals can now be identified through noninvasive sampling such as fecal collection or hair snags. However, individual genotyping using such methods currently leads to a novel problem that we call a ''shadow effect,'' because some animals not captured previously are believed to be recaptures due to their DNA profile being an indistinguishable shadow of previously captured animals. We evaluate the impact of the shadow effect on the two methods most commonly used in applied population ecology to estimate the size of closed populations: Lincoln-Petersen and multiple-recapture estimators in program CAPTURE. We find that the shadow effect can cause a negative bias in the estimates of both the number of different animals and the number of different genotypes. Furthermore, with Lincoln-Petersen estimators, the shadow effect can cause estimated confidence intervals to decrease even as bias increases. Because the bias arises from heterogeneity in apparent ''capture'' probabilities for animals with genetic shadows vs. those without, a model in program CAPTURE that is robust to capture heterogeneity (M h-jackknife) does not underestimate the number of genotypes in the population and only slightly underestimates the total number of individuals. As the shadow effect increases, CAPTURE is better able to correctly identify heterogeneity in capture probability and to pick M h-jackknife , so that the higher levels of shadow effect have less bias than medium levels. The shadow effect will occur in all estimates of demographic rates (including survival) that use DNA sampling to determine individual identity, but it can be minimized by increasing the number of individual loci sampled.
The effective population sizes (N e) of six populations of the long-toed salamander (Ambystoma ma... more The effective population sizes (N e) of six populations of the long-toed salamander (Ambystoma macrodactylum) from Montana and Idaho, USA were estimated from allozyme data from samples collected in 1978, 1996 and 1997 using the temporal allele frequency method. Five of the six estimates ranged from 23 to 207 (mean = 123 ± ± ± ± 79); one estimate was indistinguishable from infinity. In order to infer the actual N e of salamander populations, we compared the frequency distribution of our observed N e estimates with distributions obtained from simulated populations of known N e. Our observed N e estimate distribution was consistent with distributions from simulated populations with N e values of 10, 25, and 50, suggesting an actual N e for each of the six salamander populations of less than 100. This N e estimate agrees with most other N e estimates for amphibians. We conclude by discussing the conservation implications of small N e values in amphibians in the context of increasing isolation of populations due to habitat fragmentation.
Pacific salmon are a keystone resource in Alaska, generating annual revenues of well over ~US$500... more Pacific salmon are a keystone resource in Alaska, generating annual revenues of well over ~US$500 million/yr. Due to their anadromous life history, adult spawners distribute amongst thousands of streams, posing a huge management challenge. Currently, spawners are enumerated at just a few streams because of reliance on human counters and, rarely, sonar. The ability to detect organisms by shed tissue (environmental DNA, eDNA) promises a more efficient counting method. However, although eDNA correlates generally with local fish abundances, we do not know if eDNA can accurately enumerate salmon. Here we show that daily, and near-daily, flow-corrected eDNA rate closely tracks daily numbers of returning sockeye and coho spawners and outmigrating sockeye smolts. eDNA thus promises accurate and efficient enumeration, but to deliver the most robust numbers will need higher-resolution stream-flow data, at-least-daily sampling, and a focus on species with simple life histories, since shedding rate varies amongst jacks, juveniles, and adults.
Snakes have recently been proposed as model organisms for addressing both evolutionary and ecolog... more Snakes have recently been proposed as model organisms for addressing both evolutionary and ecological questions. Because of their middle position in many food webs they may be useful indicators of trophic complexity and dynamics. However, reliable data on snake populations are rare due to the challenges of sampling these patchily distributed, cryptic, and often nocturnal species and also due to their underrepresentation in the ecological literature. Studying a diurnally active stream-associated population of garter snakes has allowed us to avoid some of these problems so that we could focus on issues of sampling design and its influence on resulting demographic models and estimates. From 1986 to 2001, we gathered data on a population of the Pacific coast aquatic garter snake (Thamnophis atratus) in northwestern California by conducting 3-5 surveys of the population annually. We derived estimates for sex-specific survival rates and time-dependent capture probabilities using population analysis software and examined the relationship between our calculated capture probabilities and variability in sampling effort. We also developed population size and density estimates and compared these estimates to simple count data (often used for wildlife population monitoring). Over the 16-yr period of our study, we marked 1730 snakes and had annual recapture rates ranging from 13% to 32%. The best approximating demographic model for our data demonstrated higher survival rates for females than males and showed low and annually variable capture probabilities for both. Annual population size estimates (converted to linear densities), ranged from 58 to 131 snakes/km. Mean annual field counts typically accounted for only 5-10% of the total population size estimated using capture-recapture models. We found no evidence for a changing population size throughout the study. We found a positive relationship between sampling effort and capture probabilities. We evaluate survey design options that would help us approach recommended levels of capture probabilities and thus increase the precision of our estimates, allowing derivation of more complex demographic models. Our results should be useful in the development of monitoring programs for snakes and other secretive wildlife species and provide target demographic rate values for restoration of related at-risk snake species.
Recovering populations often must meet specific growth rate or abundance targets before their leg... more Recovering populations often must meet specific growth rate or abundance targets before their legal status can be changed from endangered or threatened. While the efficacy, power, and performance of population metrics to infer trends in declining populations has received considerable attention, how these same metrics perform when populations are increasing is less clear. We examined the ability of a one-sample effective population size (N e) estimator (LDNe) to discriminate between stable and increasing population trends across varying sample and initial population sizes. The performance of LDNe was compared to the Lincoln-Peterson (LP) abundance (N) estimator. The ability to identify stable and increasing populations varied widely across sample sizes and number of generations between sequentially collected samples, but LDNe outperformed LP. One-sample N e estimates show promise as an efficient method of detecting population increase when samples of 60-120 individuals are collected 5-10 generations apart.
Canadian Journal of Fisheries and Aquatic Sciences, Sep 1, 2017
Differential climate-induced shifts in phenology can create mismatches between predators and prey... more Differential climate-induced shifts in phenology can create mismatches between predators and prey, but few studies have examined predator–prey mismatch across multiple life-history stages. We used long-term data from a warming stream with shifting salmonid migration timings to quantify intra-annual migration synchrony between predatory Dolly Varden (Salvelinus malma) and Pacific salmon prey and examined how predator–prey synchrony has been influenced by climate change. We demonstrate that Dolly Varden have become increasingly mismatched with spring downstream migrations of abundant pink salmon (Oncorhynchus gorbuscha) juveniles. However, Dolly Varden have remained matched with fall upstream migrations of spawning Pacific salmon, including coho (Oncorhynchus kisutch), sockeye (Oncorhynchus nerka), and pink salmon. Downstream predator–prey migration synchrony decreased over time and with higher temperatures, particularly with pink salmon. In contrast, upstream migration synchrony was temporally stable and increased with rising temperatures. Differing trends in Dolly Varden predator–prey synchrony may be explained by the direct use of salmon to cue upstream migration, but not downstream migration. Overall, we show that climate change can have differing impacts on predator–prey synchrony across life-history stages.
We examined the genetic population structure of Long-Toed Salamanders (Ambystoma macrodactylum) f... more We examined the genetic population structure of Long-Toed Salamanders (Ambystoma macrodactylum) from the Bitterroot Mountains of Idaho and Montana to better understand their evolutionary history and genetic population structure. Populations show high levels of within-population genetic variation at six polymorphic allozyme loci (H s ؍ 0.09 for all 18 loci examined; range 0.04-0.14). There is very little divergence among populations within basins, suggesting panmixia within basins. In contrast, genetic differentiation among all populations is high (G st ؍ 0.30). We used computer simulations to examine population structures that could have led to the observed distribution of genetic variation, assuming selective neutrality of the allozymes. To test the assumption of selective neutrality of the markers used in this study, we compared the observed divergence among the allozymes to that expected from simulations of independently segregating and selectively neutral markers. The observed genetic divergence among populations is compatible with that expected for neutral genetic markers sampled from panmictic populations within basins that exchange less than one migrant among basins each generation.
JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, a... more JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact
Proceedings of the National Academy of Sciences of the United States of America, Nov 12, 2021
The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodive... more The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.
The estimation of effective population size from one sample of genotypes has been problematic bec... more The estimation of effective population size from one sample of genotypes has been problematic because most estimators have been proven imprecise or biased. We developed a web-based program, ONeSAMP that uses approximate Bayesian computation to estimate effective population size from a sample of microsatellite genotypes. ONeSAMP requires an input file of sampled individuals' microsatellite genotypes along with information about several sampling and biological parameters. ONeSAMP provides an estimate of effective population size, along with 95% credible limits. We illustrate the use of ONeSAMP with an example data set from a reintroduced population of ibex Capra ibex.
TOSSM (Testing of Spatial Structure Methods) is a package for testing the performance of genetic ... more TOSSM (Testing of Spatial Structure Methods) is a package for testing the performance of genetic analytical methods in a management context. In the TOSSM package, any method developed to detect population genetic structure can be combined with a mechanism for creating Management Units (MUs) based on the genetic analysis. The resulting Boundary-Setting Algorithm (BSA) dictates harvest boundaries with a genetic basis. These BSAs can be evaluated with respect to how well the MUs they define meet management objectives.
Bulletin of Environmental Contamination and Toxicology, May 7, 2009
We quantified imposex in file dogwinkles (Nucella lima) and tributyltin (TBT) contamination in ba... more We quantified imposex in file dogwinkles (Nucella lima) and tributyltin (TBT) contamination in bay mussels (Mytilus trossulus) from a number of sites in Auke Bay, Alaska, previously studied in the late 1980s. Imposex occurence and TBT contamination have generally declined in spatial extent and severity over time. However, high levels of TBT contamination (0.069 lg TBT/g wet tissue wt.) and imposex (100% of females affected) are still present near a large boat docking facility in the bay and deserve continued attention because of the importance of this bay to the local economy and fisheries.
We describe and evaluate a new estimator of the effective population size (N e), a critical param... more We describe and evaluate a new estimator of the effective population size (N e), a critical parameter in evolutionary and conservation biology. This new "SummStat" N e estimator is based upon the use of summary statistics in an approximate Bayesian computation framework to infer N e. Simulations of a Wright-Fisher population with known N e show that the SummStat estimator is useful across a realistic range of individuals and loci sampled, generations between samples, and N e values. We also address the paucity of information about the relative performance of N e estimators by comparing the SummStat estimator to two recently developed likelihood-based estimators and a traditional moment-based estimator. The SummStat estimator is the least biased of the four estimators compared. In 32 of 36 parameter combinations investigated using initial allele frequencies drawn from a Dirichlet distribution, it has the lowest bias. The relative mean square error (RMSE) of the SummStat estimator was generally intermediate to the others. All of the estimators had RMSE Ͼ 1 when small samples (n ϭ 20, five loci) were collected a generation apart. In contrast, when samples were separated by three or more generations and N e Յ 50, the SummStat and likelihood-based estimators all had greatly reduced RMSE. Under the conditions simulated, SummStat confidence intervals were more conservative than the likelihood-based estimators and more likely to include true N e. The greatest strength of the SummStat estimator is its flexible structure. This flexibility allows it to incorporate any potentially informative summary statistic from population genetic data.
Genetic rescue can increase the fitness of small, imperiled populations via immigration. A suite ... more Genetic rescue can increase the fitness of small, imperiled populations via immigration. A suite of studies from the past decade highlights the value of genetic rescue in increasing population fitness. Nonetheless, genetic rescue has not been widely applied to conserve many of the threatened populations that it could benefit. In this review, we highlight recent studies of genetic rescue and place it in the larger context of theoretical and empirical developments in evolutionary and conservation biology. We also propose directions to help shape future research on genetic rescue. Genetic rescue is a tool that can stem biodiversity loss more than has been appreciated, provides population resilience, and will become increasingly useful if integrated with molecular advances in population genomics. Review Glossary Absolute fitness: mean number of offspring per capita, measured as population growth rate (l) or abundance (N). Adaptive evolution: an increase in beneficial phenotypes in a population as a result of natural selection on genetic variation. Adaptive management: a structured, iterative process of decision-making that includes system monitoring to reduce uncertainty. Assisted gene flow: managed movement of individuals into populations to reduce local maladaptation to climate or other environmental change. Epistatic load: combinations of alleles at different loci that reduce fitness. Evolutionary rescue: an increase in population growth resulting from adaptation to otherwise extinction-causing environmental stress from standing genetic variation, de novo mutation or gene flow. Genetic load: the relative difference in fitness between the theoretically fittest genotype and the average genotype in a population. Caused by deleterious alleles in the case of mutational load. Other types of load include segregation, drift, epistatic, and migration. Genetic rescue: an increase in population fitness (growth) owing to immigration of new alleles. Genetic restoration: an increase in genetic variation and relative, but not absolute, fitness owing to immigration of new alleles. Heterosis: elevated fitness of offspring from matings between genetically divergent individuals. Invasive hybridization: cross-breeding between invasive and native species. Outbreeding depression: reduced fitness of offspring from matings between genetically divergent individuals. Transgressive hybridization: the creation of hybrids with phenotypes more extreme than their parental lines.
Proceedings of The Royal Society B: Biological Sciences, Jul 11, 2012
To predict how climate change will influence populations, it is necessary to understand the mecha... more To predict how climate change will influence populations, it is necessary to understand the mechanisms, particularly microevolution and phenotypic plasticity, that allow populations to persist in novel environmental conditions. Although evidence for climate-induced phenotypic change in populations is widespread, evidence documenting that these phenotypic changes are due to microevolution is exceedingly rare. In this study, we use 32 years of genetic data (17 complete generations) to determine whether there has been a genetic change towards earlier migration timing in a population of pink salmon that shows phenotypic change; average migration time occurs nearly two weeks earlier than it did 40 years ago. Experimental genetic data support the hypothesis that there has been directional selection for earlier migration timing, resulting in a substantial decrease in the late-migrating phenotype (from more than 30% to less than 10% of the total abundance). From 1983 to 2011, there was a significant decrease-over threefold-in the frequency of a genetic marker for late-migration timing, but there were minimal changes in allele frequencies at other neutral loci. These results demonstrate that there has been rapid microevolution for earlier migration timing in this population. Circadian rhythm genes, however, did not show any evidence for selective changes from 1993 to 2009.
Advances in molecular biology offer promise to the study of demographic characteristics of rare o... more Advances in molecular biology offer promise to the study of demographic characteristics of rare or hard-to-capture species, because individuals can now be identified through noninvasive sampling such as fecal collection or hair snags. However, individual genotyping using such methods currently leads to a novel problem that we call a ''shadow effect,'' because some animals not captured previously are believed to be recaptures due to their DNA profile being an indistinguishable shadow of previously captured animals. We evaluate the impact of the shadow effect on the two methods most commonly used in applied population ecology to estimate the size of closed populations: Lincoln-Petersen and multiple-recapture estimators in program CAPTURE. We find that the shadow effect can cause a negative bias in the estimates of both the number of different animals and the number of different genotypes. Furthermore, with Lincoln-Petersen estimators, the shadow effect can cause estimated confidence intervals to decrease even as bias increases. Because the bias arises from heterogeneity in apparent ''capture'' probabilities for animals with genetic shadows vs. those without, a model in program CAPTURE that is robust to capture heterogeneity (M h-jackknife) does not underestimate the number of genotypes in the population and only slightly underestimates the total number of individuals. As the shadow effect increases, CAPTURE is better able to correctly identify heterogeneity in capture probability and to pick M h-jackknife , so that the higher levels of shadow effect have less bias than medium levels. The shadow effect will occur in all estimates of demographic rates (including survival) that use DNA sampling to determine individual identity, but it can be minimized by increasing the number of individual loci sampled.
The effective population sizes (N e) of six populations of the long-toed salamander (Ambystoma ma... more The effective population sizes (N e) of six populations of the long-toed salamander (Ambystoma macrodactylum) from Montana and Idaho, USA were estimated from allozyme data from samples collected in 1978, 1996 and 1997 using the temporal allele frequency method. Five of the six estimates ranged from 23 to 207 (mean = 123 ± ± ± ± 79); one estimate was indistinguishable from infinity. In order to infer the actual N e of salamander populations, we compared the frequency distribution of our observed N e estimates with distributions obtained from simulated populations of known N e. Our observed N e estimate distribution was consistent with distributions from simulated populations with N e values of 10, 25, and 50, suggesting an actual N e for each of the six salamander populations of less than 100. This N e estimate agrees with most other N e estimates for amphibians. We conclude by discussing the conservation implications of small N e values in amphibians in the context of increasing isolation of populations due to habitat fragmentation.
Pacific salmon are a keystone resource in Alaska, generating annual revenues of well over ~US$500... more Pacific salmon are a keystone resource in Alaska, generating annual revenues of well over ~US$500 million/yr. Due to their anadromous life history, adult spawners distribute amongst thousands of streams, posing a huge management challenge. Currently, spawners are enumerated at just a few streams because of reliance on human counters and, rarely, sonar. The ability to detect organisms by shed tissue (environmental DNA, eDNA) promises a more efficient counting method. However, although eDNA correlates generally with local fish abundances, we do not know if eDNA can accurately enumerate salmon. Here we show that daily, and near-daily, flow-corrected eDNA rate closely tracks daily numbers of returning sockeye and coho spawners and outmigrating sockeye smolts. eDNA thus promises accurate and efficient enumeration, but to deliver the most robust numbers will need higher-resolution stream-flow data, at-least-daily sampling, and a focus on species with simple life histories, since shedding rate varies amongst jacks, juveniles, and adults.
Snakes have recently been proposed as model organisms for addressing both evolutionary and ecolog... more Snakes have recently been proposed as model organisms for addressing both evolutionary and ecological questions. Because of their middle position in many food webs they may be useful indicators of trophic complexity and dynamics. However, reliable data on snake populations are rare due to the challenges of sampling these patchily distributed, cryptic, and often nocturnal species and also due to their underrepresentation in the ecological literature. Studying a diurnally active stream-associated population of garter snakes has allowed us to avoid some of these problems so that we could focus on issues of sampling design and its influence on resulting demographic models and estimates. From 1986 to 2001, we gathered data on a population of the Pacific coast aquatic garter snake (Thamnophis atratus) in northwestern California by conducting 3-5 surveys of the population annually. We derived estimates for sex-specific survival rates and time-dependent capture probabilities using population analysis software and examined the relationship between our calculated capture probabilities and variability in sampling effort. We also developed population size and density estimates and compared these estimates to simple count data (often used for wildlife population monitoring). Over the 16-yr period of our study, we marked 1730 snakes and had annual recapture rates ranging from 13% to 32%. The best approximating demographic model for our data demonstrated higher survival rates for females than males and showed low and annually variable capture probabilities for both. Annual population size estimates (converted to linear densities), ranged from 58 to 131 snakes/km. Mean annual field counts typically accounted for only 5-10% of the total population size estimated using capture-recapture models. We found no evidence for a changing population size throughout the study. We found a positive relationship between sampling effort and capture probabilities. We evaluate survey design options that would help us approach recommended levels of capture probabilities and thus increase the precision of our estimates, allowing derivation of more complex demographic models. Our results should be useful in the development of monitoring programs for snakes and other secretive wildlife species and provide target demographic rate values for restoration of related at-risk snake species.
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Papers by David Tallmon