Bayes: pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation. BMC Bioinformatics 26(8):268

Biology Department, Queens College, CUNY, Flushing, NY 11367-1597, USA.
BMC Bioinformatics (Impact Factor: 2.58). 02/2007; 8(1):268. DOI: 10.1186/1471-2105-8-268
Source: PubMed


Although testing for simultaneous divergence (vicariance) across different population-pairs that span the same barrier to gene flow is of central importance to evolutionary biology, researchers often equate the gene tree and population/species tree thereby ignoring stochastic coalescent variance in their conclusions of temporal incongruence. In contrast to other available phylogeographic software packages, msBayes is the only one that analyses data from multiple species/population pairs under a hierarchical model.
msBayes employs approximate Bayesian computation (ABC) under a hierarchical coalescent model to test for simultaneous divergence (TSD) in multiple co-distributed population-pairs. Simultaneous isolation is tested by estimating three hyper-parameters that characterize the degree of variability in divergence times across co-distributed population pairs while allowing for variation in various within population-pair demographic parameters (sub-parameters) that can affect the coalescent. msBayes is a software package consisting of several C and R programs that are run with a Perl "front-end".
The method reasonably distinguishes simultaneous isolation from temporal incongruence in the divergence of co-distributed population pairs, even with sparse sampling of individuals. Because the estimate step is decoupled from the simulation step, one can rapidly evaluate different ABC acceptance/rejection conditions and the choice of summary statistics. Given the complex and idiosyncratic nature of testing multi-species biogeographic hypotheses, we envision msBayes as a powerful and flexible tool for tackling a wide array of difficult research questions that use population genetic data from multiple co-distributed species. The msBayes pipeline is available for download at under an open source license (GNU Public License). The msBayes pipeline is comprised of several C and R programs that are run with a Perl "front-end" and runs on Linux, Mac OS-X, and most POSIX systems. Although the current implementation is for a single locus per species-pair, future implementations will allow analysis of multi-loci data per species pair.

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Available from: Michael Hickerson, Oct 02, 2015
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    • "After preliminary analyses, we removed the marker C-myc2 to avoid unrealistic results due the low number of gene copies and low variability. We performed the rejection step in msReject (Hickerson et al. 2007) with a tolerance of 0.0001 (0.01 for prior selection). Following Pelletier and Carstens (2014), we used three distinct measures of nucleotide diversity (within population one, within population two, and between populations) as observed summary statistics, which were calculated on a per locus basis in DnaSP 5.10 (Librado and Rozas 2009). "
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    ABSTRACT: The evolutionary history of Neotropical organisms has been often interpreted through broad-scale generalizations. The most accepted model of diversification for the Brazilian Atlantic forest (BAF) rely on putative historical stability of northern areas and massive past habitat replacement of its southern range. Here, we use the leaf frog Phyllomedusa distincta, endemic to the southern BAF, to better understand diversification patterns within this underexplored rainforest region. We used an integrative approach coupling fine-scale sampling and multilocus sequence data, with traditional and statistical phylogeographic (multilocus approximate Bayesian computation) methods to explore alternative hypotheses of diversification. We also employed species paleodistribution modeling to independently verify habitat stability upon a spatially explicit model. Our data support two divergent lineages with coherent geographic distribution that span throughout northern and southern ranges. Demographic estimates suggested the Southern lineage has experienced a recent population expansion, whereas the Northern lineage remained more stable. Hypothesis testing supports a scenario of ancient vicariance with recent population expansion. The paleodistribution model revealed habitat discontinuity during the Last Glacial Maximum (LGM) with one area of putative stability within the range of the Northern lineage. Evidence on genetic structure, demography, and paleodistribution of P. distincta support a historically heterogeneous landscape for the southern BAF, with both areas of forest stability and regions where forest occupation is probably recent. We also associate the southern end of the Cubatão shear zone with a phylogeographic break in the BAF. Taken together, our results argue for the idea of multiple mechanisms generating diversity in this biome and underscore the need of fine-scale data in revealing more detailed pictures.
    Organisms Diversity & Evolution 08/2015; DOI:10.1007/s13127-015-0228-4 · 2.89 Impact Factor
    • "Because of problems with the prior distributions used in some implementations of the hABC method (i.e. msbayes ; Hickerson et al. 2007; Huang et al. 2011) that cause a bias towards supporting clustered divergences (Oaks et al. 2013, 2014 "
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    Molecular Ecology 07/2015; 24(16). DOI:10.1111/mec.13305 · 6.49 Impact Factor
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    • "We automated this process using perl scripts (available online, see data accessibility section). For the rejection step, we used msReject (Hickerson et al. 2007) with a tolerance of 0.0001. We used three distinct measures of nucleotide diversity (within population one, within population two and between "
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    ABSTRACT: In this study we investigated the relative contribution of geographic barriers and Pleistocene refuges in the diversification of the Rhinella crucifer species complex, a group of endemic toads with a widespread distribution in the Brazilian Atlantic Forest (AF). We used intensive sampling and multilocus DNA sequence data to compare nucleotide diversity between refuge and non-refuge areas, investigate regional demographic patterns, estimate demographic parameters related to genetic breaks, and test refuge versus barrier scenarios of diversification using approximate Bayesian computation. We did not find higher levels of genetic diversity in putative refuge areas, either at regional or biome scale. Rather, the demographic history of the species complex supports regional differences with moderate population growth in the north and central regions, and stability in southern AF. Genetic breaks were dated to the Plio-Pleistocene; however, our analyses rejected the role of refuges in creating a northern and central divergence, supporting a recent colonization scenario at a smaller scale within the central AF. Overall our data rule out massive climatically driven fragmentation and large-scale recolonization events for populations across the biome. We confirmed the importance of geographic barriers in creating main divergences and underscored the importance of searching for cryptic discontinuities in the landscape. Comparison of our results with those of other AF taxa indicates organismal specific responses to moderate shifts in habitat and that multiple refuges may constitute a more realistic model for diversification of Atlantic Forest biota.This article is protected by copyright. All rights reserved.
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