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Incorrect handling of calibration information in divergence time inference: an example from volcanic islands.

ABSTRACT: Divergence time studies rely on calibration information from several sources. The age of volcanic islands is one of the standard references to obtain chronological data to estimate the absolute times of lineage diversifications. This strategy assumes that cladogenesis is necessarily associated with island formation, and punctual calibrations are commonly used to date the splits of endemic island species. Here, we re-examined three studies that inferred divergence times for different Hawaiian lineages assuming fixed calibration points. We show that, by permitting probabilistic calibrations, some divergences are estimated to be significantly younger or older than the age of the island formation, thus yielding distinct ecological scenarios for the speciation process. The results highlight the importance of using calibration information correctly, as well as the possibility of incorporating volcanic island studies into a formal, biogeographical hypothesis-testing framework.

SUBMITTER: Mello B

PROVIDER: S-EPMC3399139 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature

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Incorrect handling of calibration information in divergence time inference: an example from volcanic islands.

Mello Beatriz B Schrago Carlos G CG

Ecology and evolution 20120301 3

Divergence time studies rely on calibration information from several sources. The age of volcanic islands is one of the standard references to obtain chronological data to estimate the absolute times of lineage diversifications. This strategy assumes that cladogenesis is necessarily associated with island formation, and punctual calibrations are commonly used to date the splits of endemic island species. Here, we re-examined three studies that inferred divergence times for different Hawaiian lin ...[more]

PMID: 22822429

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Project description:BackgroundRisk factors increase the incidence and severity of chronic disease. To examine future trends and develop policies addressing chronic diseases, it is important to capture the relationship between exposure and disease development, which is challenging given limited data.ObjectiveTo develop parsimonious risk factor models embeddable in chronic disease models, which are useful when longitudinal data are unavailable.DesignThe model structures encode relevant features of risk factors (e.g., time-varying, modifiable) and can be embedded in chronic disease models. Calibration captures time-varying exposures for the risk factor models using available cross-sectional data. We illustrate feasibility with the policy-relevant example of smoking in India.MethodsThe model is calibrated to the prevalence of male smoking in 12 Indian regions estimated from the 2009-2010 Indian Global Adult Tobacco Survey. Nelder-Mead searches (250,000 starting locations) identify distributions of starting, quitting, and restarting rates that minimize the difference between modeled and observed age-specific prevalence. We compare modeled life expectancies to estimates in the absence of time-varying risk exposures and consider gains from hypothetical smoking cessation programs delivered for 1 to 30 years.ResultsCalibration achieves concordance between modeled and observed outcomes. Probabilities of starting to smoke rise and fall with age, while quitting and restarting probabilities fall with age. Accounting for time-varying smoking exposures is important, as not doing so produces smaller estimates of life expectancy losses. Estimated impacts of smoking cessation programs delivered for different periods depend on the fact that people who have been induced to abstain from smoking longer are less likely to restart.ConclusionsThe approach described is feasible for important risk factors for numerous chronic diseases. Incorporating exposure-change rates can improve modeled estimates of chronic disease outcomes and of the long-term effects of interventions targeting risk factors.

Dataset Information

Incorrect handling of calibration information in divergence time inference: an example from volcanic islands.

Publications

Incorrect handling of calibration information in divergence time inference: an example from volcanic islands.

Similar Datasets

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