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      Inverse dispersal patterns in a group of ant parasitoids (Hymenoptera: Eucharitidae: Oraseminae) and their ant hosts

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          SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

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            ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

            Motivation: The estimation of species phylogenies requires multiple loci, since different loci can have different trees due to incomplete lineage sorting, modeled by the multi-species coalescent model. We recently developed a coalescent-based method, ASTRAL, which is statistically consistent under the multi-species coalescent model and which is more accurate than other coalescent-based methods on the datasets we examined. ASTRAL runs in polynomial time, by constraining the search space using a set of allowed ‘bipartitions’. Despite the limitation to allowed bipartitions, ASTRAL is statistically consistent. Results: We present a new version of ASTRAL, which we call ASTRAL-II. We show that ASTRAL-II has substantial advantages over ASTRAL: it is faster, can analyze much larger datasets (up to 1000 species and 1000 genes) and has substantially better accuracy under some conditions. ASTRAL’s running time is O ( n 2 k | X | 2 ) , and ASTRAL-II’s running time is O ( n k | X | 2 ) , where n is the number of species, k is the number of loci and X is the set of allowed bipartitions for the search space. Availability and implementation: ASTRAL-II is available in open source at https://github.com/smirarab/ASTRAL and datasets used are available at http://www.cs.utexas.edu/~phylo/datasets/astral2/. Contact: smirarab@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
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              Model selection in historical biogeography reveals that founder-event speciation is a crucial process in Island Clades.

              Founder-event speciation, where a rare jump dispersal event founds a new genetically isolated lineage, has long been considered crucial by many historical biogeographers, but its importance is disputed within the vicariance school. Probabilistic modeling of geographic range evolution creates the potential to test different biogeographical models against data using standard statistical model choice procedures, as long as multiple models are available. I re-implement the Dispersal-Extinction-Cladogenesis (DEC) model of LAGRANGE in the R package BioGeoBEARS, and modify it to create a new model, DEC + J, which adds founder-event speciation, the importance of which is governed by a new free parameter, [Formula: see text]. The identifiability of DEC and DEC + J is tested on data sets simulated under a wide range of macroevolutionary models where geography evolves jointly with lineage birth/death events. The results confirm that DEC and DEC + J are identifiable even though these models ignore the fact that molecular phylogenies are missing many cladogenesis and extinction events. The simulations also indicate that DEC will have substantially increased errors in ancestral range estimation and parameter inference when the true model includes + J. DEC and DEC + J are compared on 13 empirical data sets drawn from studies of island clades. Likelihood-ratio tests indicate that all clades reject DEC, and AICc model weights show large to overwhelming support for DEC + J, for the first time verifying the importance of founder-event speciation in island clades via statistical model choice. Under DEC + J, ancestral nodes are usually estimated to have ranges occupying only one island, rather than the widespread ancestors often favored by DEC. These results indicate that the assumptions of historical biogeography models can have large impacts on inference and require testing and comparison with statistical methods. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
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                Author and article information

                Journal
                Systematic Entomology
                Syst Entomol
                Wiley
                0307-6970
                1365-3113
                June 27 2019
                January 2020
                June 09 2019
                January 2020
                : 45
                : 1
                : 1-19
                Affiliations
                [1 ]Department of EntomologyUniversity of California Riverside CA U.S.A.
                [2 ]Department of BiologyPennsylvania State University University Park PA U.S.A.
                [3 ]Department of Scientific ComputingFlorida State University, Dirac Science Library Tallahassee FL U.S.A.
                [4 ]Department of Biological ScienceFlorida State University Tallahassee FL U.S.A.
                Article
                10.1111/syen.12371
                © 2020

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