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      Golden Orbweavers Ignore Biological Rules: Phylogenomic and Comparative Analyses Unravel a Complex Evolution of Sexual Size Dimorphism

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          Abstract

          Instances of sexual size dimorphism (SSD) provide the context for rigorous tests of biological rules of size evolution, such as Cope’s rule (phyletic size increase), Rensch’s rule (allometric patterns of male and female size), as well as male and female body size optima. In certain spider groups, such as the golden orbweavers (Nephilidae), extreme female-biased SSD (eSSD, female:male body length \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\ge$\end{document} 2) is the norm. Nephilid genera construct webs of exaggerated proportions, which can be aerial, arboricolous, or intermediate (hybrid). First, we established the backbone phylogeny of Nephilidae using 367 anchored hybrid enrichment markers, then combined these data with classical markers for a reference species-level phylogeny. Second, we used the phylogeny to test Cope and Rensch’s rules, sex specific size optima, and the coevolution of web size, type, and features with female and male body size and their ratio, SSD. Male, but not female, size increases significantly over time, and refutes Cope’s rule. Allometric analyses reject the converse, Rensch’s rule. Male and female body sizes are uncorrelated. Female size evolution is random, but males evolve toward an optimum size (3.2–4.9 mm). Overall, female body size correlates positively with absolute web size. However, intermediate sized females build the largest webs (of the hybrid type), giant female Nephila and Trichonephila build smaller webs (of the aerial type), and the smallest females build the smallest webs (of the arboricolous type). We propose taxonomic changes based on the criteria of clade age, monophyly and exclusivity, classification information content, and diagnosability. Spider families, as currently defined, tend to be between 37 million years old and 98 million years old, and Nephilidae is estimated at 133 Ma (97–146), thus deserving family status. We, therefore, resurrect the family Nephilidae Simon 1894 that contains Clitaetra Simon 1889, the Cretaceous Geratonephila Poinar and Buckley (2012), Herennia Thorell 1877, Indoetra Kuntner 2006, new rank, Nephila Leach 1815, Nephilengys L. Koch 1872, Nephilingis Kuntner 2013, Palaeonephila Wunderlich 2004 from Tertiary Baltic amber, and Trichonephila Dahl 1911, new rank. We propose the new clade Orbipurae to contain Araneidae Clerck 1757, Phonognathidae Simon 1894, new rank, and Nephilidae. Nephilid female gigantism is a phylogenetically ancient phenotype (over 100 Ma), as is eSSD, though their magnitudes vary by lineage.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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              phytools: an R package for phylogenetic comparative biology (and other things)

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                Author and article information

                Contributors
                Role: Associate Editor
                Journal
                Syst Biol
                Syst. Biol
                sysbio
                Systematic Biology
                Oxford University Press
                1063-5157
                1076-836X
                July 2019
                04 December 2018
                04 December 2018
                : 68
                : 4
                : 555-572
                Affiliations
                [1 ]Evolutionary Zoology Laboratory, Department of Organisms and Ecosystems Research, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia
                [2 ]Evolutionary Zoology Laboratory, Biological Institute ZRC SAZU, Novi trg 2, SI-1001 Ljubljana, Slovenia
                [3 ]Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution, NW, Washington, DC 20560-0105, USA
                [4 ]Centre for Behavioural Ecology and Evolution, College of Life Sciences, Hubei University, 368 Youyi Road, Wuhan, Hubei 430062, China
                [5 ]Department of Entomology, Plant Pathology, & Nematology, University of Idaho, 875 Perimeter Dr. MS 2329, Moscow, ID 83844-2329, USA
                [6 ]Department of Life Sciences, National Chung Hsing University, No.145 Xingda Rd., South Dist., Taichung City 402, Taiwan
                [7 ]Division of Animal Evolutionary Biology, Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
                [8 ]Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL 32306-4295, USA
                [9 ]Department of Scientific Computing, Florida State University, 400 Dirac Science Library, Tallahassee, FL 32306-4120, USA
                [10 ]Department of Biology, University of Vermont, 316 Marsh Life Science Building, 109 Carrigan Drive, Burlington, VT 05405-0086, USA
                [11 ]Department of Entomology and Nematology, University of California Davis, 1 Shields Drive, Davis, CA 95616, USA
                Author notes
                Correspondence to be sent to: Evolutionary Zoology Laboratory, Department of Organisms and Ecosystems Research, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia; E-mail: matjaz.kuntner@ 123456nib.si .
                Article
                syy082
                10.1093/sysbio/syy082
                6568015
                30517732
                711c0c2b-9ef1-4012-b51e-968649b5fe7d
                © The Author(s) 2018. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contactjournals.permissions@ 123456oup.com

                History
                : 5 July 2018
                : 20 November 2018
                : 26 November 2018
                Page count
                Pages: 18
                Funding
                Funded by: Slovenian Research Agency 10.13039/501100004329
                Award ID: J1-6729
                Award ID: P1-0236
                Award ID: BI-US/17-18-011
                Funded by: National Science Foundation 10.13039/100000001
                Award ID: DEB-0841610
                Funded by: Doctoral Dissertation Improvement
                Award ID: DEB-1311494
                Funded by: Auburn University Department of Biological Sciences and College of Sciences and Mathematics
                Funded by: Auburn University Cellular and Molecular Biosciences Peaks of Excellence Research Fellowship
                Categories
                Regular Articles

                Animal science & Zoology
                body size evolution,female gigantism,web asymmetry,cope’s rule,rensch’s rule,nephilidae,phonognathidae,orbipurae

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