On Bayesian approach to composite Pareto models.
Ontology highlight
ABSTRACT:
SUBMITTER: Abdul Majid MH
PROVIDER: S-EPMC8460011 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundLife-course epidemiology studies people's health over long periods, treating repeated measures of their experiences (usually risk factors) as predictors or causes of subsequent morbidity and mortality. Three hypotheses or models often guide the analyst in assessing these sequential risks: the accumulation model (all measurement occasions are equally important for predicting the outcome), the critical period model (only one occasion is important) and the sensitive periods model (a catch-all model for any other pattern of temporal dependence).MethodsWe propose a Bayesian omnibus test of these three composite models, as well as post hoc decompositions that identify their best respective sub-models. We test the approach via simulations, before presenting an empirical example that relates five sequential measurements of body weight to an RNAseq measure of colorectal-cancer disposition.ResultsThe approach correctly identifies the life-course model under which the data were simulated. Our empirical cohort study indicated with >90% probability that colorectal-cancer disposition reflected a sensitive process, with current weight being most important but prior body weight also playing a role.ConclusionsThe Bayesian methods we present allow precise inferences about the probability of life-course models given the data and are applicable in realistic scenarios involving causal analysis and missing data.
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Project description:BackgroundMarine allopatric speciation is an enigma because pelagic larval dispersal can potentially connect disjunct populations thereby preventing reproductive and morphological divergence. Here we present a new hierarchical approximate Bayesian computation model (HABC) that tests two hypotheses of marine allopatric speciation: 1.) "soft vicariance", where a speciation involves fragmentation of a large widespread ancestral species range that was previously connected by long distance gene flow; and 2.) peripatric colonization, where speciations in peripheral archipelagos emerge from sweepstakes colonizations from central source regions. The HABC approach analyzes all the phylogeographic datasets at once in order to make across taxon-pair inferences about biogeographic processes while explicitly allowing for uncertainty in the demographic differences within each taxon-pair. Our method uses comparative phylogeographic data that consists of single locus mtDNA sequences from multiple co-distributed taxa containing pairs of central and peripheral populations. We use the method on two comparative phylogeographic data sets consisting of cowrie gastropod endemics co-distributed in the Hawaiian (11 taxon-pairs) and Marquesan archipelagos (7 taxon-pairs).ResultsGiven the Marquesan data, we find strong evidence of simultaneous colonization across all seven cowrie gastropod endemics co-distributed in the Marquesas. In contrast, the lower sample sizes in the Hawaiian data lead to greater uncertainty associated with the Hawaiian estimates. Although, the hyper-parameter estimates point to soft vicariance in a subset of the 11 Hawaiian taxon-pairs, the hyper-prior and hyper-posterior are too similar to make a definitive conclusion. Both results are not inconsistent with what is known about the geologic history of the archipelagos. Simulations verify that our method can successfully distinguish these two histories across a wide range of conditions given sufficient sampling.ConclusionAlthough soft vicariance and colonization are likely to produce similar genetic patterns when a single taxon-pair is used, our hierarchical Bayesian model can potentially detect if either history is a dominant process across co-distributed taxon-pairs. As comparative phylogeographic datasets grow to include > 100 co-distributed taxon-pairs, the HABC approach will be well suited to dissect temporal patterns in community assembly and evolution, thereby providing a bridge linking comparative phylogeography with community ecology.
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