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The phylogeographic history of the new world screwworm fly, inferred by approximate bayesian computation analysis.

ABSTRACT: Insect pest phylogeography might be shaped both by biogeographic events and by human influence. Here, we conducted an approximate Bayesian computation (ABC) analysis to investigate the phylogeography of the New World screwworm fly, Cochliomyia hominivorax, with the aim of understanding its population history and its order and time of divergence. Our ABC analysis supports that populations spread from North to South in the Americas, in at least two different moments. The first split occurred between the North/Central American and South American populations in the end of the Last Glacial Maximum (15,300-19,000 YBP). The second split occurred between the North and South Amazonian populations in the transition between the Pleistocene and the Holocene eras (9,100-11,000 YBP). The species also experienced population expansion. Phylogenetic analysis likewise suggests this north to south colonization and Maxent models suggest an increase in the number of suitable areas in South America from the past to present. We found that the phylogeographic patterns observed in C. hominivorax cannot be explained only by climatic oscillations and can be connected to host population histories. Interestingly we found these patterns are very coincident with general patterns of ancient human movements in the Americas, suggesting that humans might have played a crucial role in shaping the distribution and population structure of this insect pest. This work presents the first hypothesis test regarding the processes that shaped the current phylogeographic structure of C. hominivorax and represents an alternate perspective on investigating the problem of insect pests.

SUBMITTER: Fresia P

PROVIDER: S-EPMC3788763 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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The phylogeographic history of the new world screwworm fly, inferred by approximate bayesian computation analysis.

Fresia Pablo P Azeredo-Espin Ana Maria L AM Lyra Mariana L ML

PloS one 20131002 10

Insect pest phylogeography might be shaped both by biogeographic events and by human influence. Here, we conducted an approximate Bayesian computation (ABC) analysis to investigate the phylogeography of the New World screwworm fly, Cochliomyia hominivorax, with the aim of understanding its population history and its order and time of divergence. Our ABC analysis supports that populations spread from North to South in the Americas, in at least two different moments. The first split occurred betwe ...[more]

PMID: 24098436

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Project description:Admixture is a fundamental evolutionary process that has influenced genetic patterns in numerous species. Maximum-likelihood approaches based on allele frequencies and linkage-disequilibrium have been extensively used to infer admixture processes from genome-wide data sets, mostly in human populations. Nevertheless, complex admixture histories, beyond one or two pulses of admixture, remain methodologically challenging to reconstruct. We developed an Approximate Bayesian Computation (ABC) framework to reconstruct highly complex admixture histories from independent genetic markers. We built the software package MetHis to simulate independent SNPs or microsatellites in a two-way admixed population for scenarios with multiple admixture pulses, monotonically decreasing or increasing recurring admixture, or combinations of these scenarios. MetHis allows users to draw model-parameter values from prior distributions set by the user, and, for each simulation, MetHis can calculate numerous summary statistics describing genetic diversity patterns and moments of the distribution of individual admixture fractions. We coupled MetHis with existing machine-learning ABC algorithms and investigated the admixture history of admixed populations. Results showed that random forest ABC scenario-choice could accurately distinguish among most complex admixture scenarios, and errors were mainly found in regions of the parameter space where scenarios were highly nested, and, thus, biologically similar. We focused on African American and Barbadian populations as two study-cases. We found that neural network ABC posterior parameter estimation was accurate and reasonably conservative under complex admixture scenarios. For both admixed populations, we found that monotonically decreasing contributions over time, from Europe and Africa, explained the observed data more accurately than multiple admixture pulses. This approach will allow for reconstructing detailed admixture histories when maximum-likelihood methods are intractable.

Dataset Information

The phylogeographic history of the new world screwworm fly, inferred by approximate bayesian computation analysis.

Publications

The phylogeographic history of the new world screwworm fly, inferred by approximate bayesian computation analysis.

Similar Datasets

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