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      The phylogeny of pholcid spiders: a critical evaluation of relationships suggested by molecular data (Araneae, Pholcidae)

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      1 , , 1 , 2 , 3 , 4
      ZooKeys
      Pensoft Publishers
      Biogeography, phylogeny, systematics, taxonomy

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          Abstract

          Abstract

          With almost 600 species, the latest molecular phylogeny of pholcid spiders ( Eberle et al. 2018, BMC Evolutionary Biology) more than triples the largest previously available molecular phylogeny of the family. At the level of genera, the coverage is high (86%, i.e., 75 of the 87 named genera), and at the level of subfamilies it is complete. The present paper is an effort to critically evaluate the implications of this phylogeny for pholcid systematics. The analyses largely support the division of Pholcidae into five subfamilies: Ninetinae , Arteminae , Modisiminae , Smeringopinae , and Pholcinae . Their compositions are largely unchanged except that Chisosa Huber, 2000 is moved from Ninetinae to Arteminae . The positions of Artema Walckenaer, 1837 and Priscula Simon, 1893 in this system remain dubious. Relationships among subfamilies remain weakly supported, except for the sister group relationship between Smeringopinae and Pholcinae . Several major clades within subfamilies are separated from each other along geographical boundaries; for example within Modisiminae a South American clade and a Central + North American + Caribbean clade, and within Smeringopinae a Sub-Saharan clade and a clade ranging from the Mediterranean to Central Asia. Central + North American + Caribbean clades in both Ninetinae and Modisiminae may originate from South American ancestors.

          Many taxonomic changes are suggested by the data, some of which are formally implemented herein. Two new genera result from the splitting of Calapnita Simon, 1892 and Panjange Deeleman-Reinhold & Deeleman, 1983, respectively: Nipisa Huber, gen. n.; and Apokayana Huber, gen. n. Nine new genera result from splitting of Pholcus : Cantikus Huber, gen. n.; Kelabita Huber, gen. n.; Kintaqa Huber, gen. n.; Muruta Huber, gen. n.; Meraha Huber, gen. n.; Paiwana Huber, gen. n.; Pribumia Huber, gen. n.; Teranga Huber, gen. n.; and Tissahamia Huber, gen. n. Two genera are newly synonymized: Platnicknia Özdikmen & Demir, 2009 is synonymized with Modisimus Simon, 1893; Sihala Huber, 2011 is synonymized with Pholcus Walckenaer, 1805. Pholcus agadir Huber, 2011 is moved to Micropholcus Deeleman-Reinhold & Prinsen, 1987, resulting in the new combination Micropholcus agadir (Huber, 2011).

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          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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            Is It Better to Add Taxa or Characters to a Difficult Phylogenetic Problem?

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              Troubleshooting Molecular Phylogenetic Analyses

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                Author and article information

                Contributors
                Journal
                Zookeys
                Zookeys
                ZooKeys
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2018
                10 October 2018
                : 789
                : 51-101
                Affiliations
                [1 ] Alexander Koenig Research Museum of Zoology, Adenauerallee 160, 53113 Bonn, Germany Alexander Koenig Research Museum of Zoology Bonn Germany
                [2 ] Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark University of Copenhagen Copenhagen Denmark
                [3 ] Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318 Oslo, Norway University of Oslo Oslo Norway
                [4 ] Current address: Department of Natural History, University Museum of Bergen, University of Bergen, PO Box 7800, NO-5020 Bergen, Norway University of Bergen Bergen Norway
                Author notes
                Corresponding author: Bernhard A. Huber ( b.huber@ 123456leibniz-zfmk.de )

                Academic editor: J. Miller

                Article
                10.3897/zookeys.789.22781
                6193417
                1433244a-24ef-4d0d-a90b-a8bd2b9097e4
                Bernhard A. Huber, Jonas Eberle, Dimitar Dimitrov

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 5 December 2017
                : 20 August 2018
                Categories
                Research Article
                Arachnida
                Araneae
                Pholcidae
                Molecular Systematics
                Phylogeny
                Systematics
                World

                Animal science & Zoology
                biogeography,phylogeny,systematics,taxonomy,animalia,araneae,pholcidae
                Animal science & Zoology
                biogeography, phylogeny, systematics, taxonomy, animalia, araneae, pholcidae

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