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      Neotropical ant parasitoids (Hymenoptera: Eucharitidae): interpreting taxonomy, phylogeny and divergent morphologies

      1 , 2 , 1

      Systematic Entomology

      Wiley

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          Missing data and the design of phylogenetic analyses.

           John Wiens (2006)
          Concerns about the deleterious effects of missing data may often determine which characters and taxa are included in phylogenetic analyses. For example, researchers may exclude taxa lacking data for some genes or exclude a gene lacking data in some taxa. Yet, there may be very little evidence to support these decisions. In this paper, I review the effects of missing data on phylogenetic analyses. Recent simulations suggest that highly incomplete taxa can be accurately placed in phylogenies, as long as many characters have been sampled overall. Furthermore, adding incomplete taxa can dramatically improve results in some cases by subdividing misleading long branches. Adding characters with missing data can also improve accuracy, although there is a risk of long-branch attraction in some cases. Consideration of how missing data does (or does not) affect phylogenetic analyses may allow researchers to design studies that can reconstruct large phylogenies quickly, economically, and accurately.
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            Is Open Access

            Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

            The presence of rogue taxa (rogues) in a set of trees can frequently have a negative impact on the results of a bootstrap analysis (e.g., the overall support in consensus trees). We introduce an efficient graph-based algorithm for rogue taxon identification as well as an interactive webservice implementing this algorithm. Compared with our previous method, the new algorithm is up to 4 orders of magnitude faster, while returning qualitatively identical results. Because of this significant improvement in scalability, the new algorithm can now identify substantially more complex and compute-intensive rogue taxon constellations. On a large and diverse collection of real-world data sets, we show that our method yields better supported reduced/pruned consensus trees than any competing rogue taxon identification method. Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116 334 taxa each. For simulated data sets, we show that when removing/pruning rogue taxa with our method from a tree set, we consistently obtain bootstrap consensus trees as well as maximum-likelihood trees that are topologically closer to the respective true trees.
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              Inferring Evolutionary Process from Phylogenetic Tree Shape

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                Author and article information

                Journal
                Systematic Entomology
                Syst Entomol
                Wiley
                0307-6970
                1365-3113
                October 31 2019
                April 2020
                December 16 2019
                April 2020
                : 45
                : 2
                : 464-480
                Affiliations
                [1 ]Department of EntomologyUniversity of California, Riverside Riverside CA U.S.A.
                [2 ]Department of Entomology, National Museum of Natural HistorySmithsonian Institution Washington DC U.S.A.
                Article
                10.1111/syen.12407
                © 2020

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