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      Development and patterning of a highly versatile visual system in spiders

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          Abstract

          Visual systems provide a key interface between organisms and their surroundings, and have evolved in many forms to perform diverse functions across the animal kingdom. Spiders exhibit a range of visual abilities and ecologies, the diversity of which is underpinned by a highly versatile, modular visual system architecture. This typically includes eight eyes of two developmentally distinct types, but the number, size, location and function of the eyes can vary dramatically between lineages. Previous studies of visual system development in spiders have confirmed that many components of the retinal determination gene (RDG) network are conserved with other arthropods, but so far, comparative studies among spiders are lacking. We characterized visual system development in seven species of spiders representing a range of morphologies, visual ecologies and phylogenetic positions, to determine how these diverse configurations are formed, and how they might evolve. Combining transcriptomics, in situ hybridization, and selection analyses, we characterize the repertoires and expression of key RDGs in relation to adult morphology. We identify key molecular players, timepoints and developmental events that may contribute to adult diversity, in particular the molecular and developmental underpinnings of eye size, number, position and identity across spiders.

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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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              BEDTools: a flexible suite of utilities for comparing genomic features

              Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets. Availability and implementation: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools Contact: aaronquinlan@gmail.com; imh4y@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review and editing
                Role: InvestigationRole: MethodologyRole: ResourcesRole: Supervision
                Role: InvestigationRole: VisualizationRole: Writing – original draft
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: SupervisionRole: Validation
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: VisualizationRole: Writing – original draftRole: Writing – review and editing
                Role: InvestigationRole: Resources
                Role: InvestigationRole: ResourcesRole: VisualizationRole: Writing – review and editing
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: VisualizationRole: Writing – original draftRole: Writing – review and editing
                Role: InvestigationRole: Visualization
                Role: InvestigationRole: Visualization
                Role: Formal analysisRole: ResourcesRole: SoftwareRole: SupervisionRole: Validation
                Role: Data curationRole: Formal analysisRole: InvestigationRole: Writing – review and editing
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: Writing – original draftRole: Writing – review and editing
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: VisualizationRole: Writing – original draftRole: Writing – review and editing
                Journal
                Proc Biol Sci
                Proc Biol Sci
                RSPB
                royprsb
                Proceedings of the Royal Society B: Biological Sciences
                The Royal Society
                0962-8452
                1471-2954
                March 2025
                March 12, 2025
                March 12, 2025
                : 292
                : 2042
                : 20242069
                Affiliations
                [ 1 ]Oxford University Museum of Natural History, University of Oxford, Parks Road; , Oxford OX1 3PW, UK
                [ 2 ]Department of Biological and Biomedical Sciences, Oxford Brookes University, Gipsy Lane; , Oxford OX3 0BP, UK
                [ 3 ]Enara Bio, Science Park, Bellhouse Building Level 3, Sanders Rd, Littlemore; , Oxford OX4 4GA, UK
                [ 4 ]Department of Biosciences, Durham University, Stockton Road; , Durham DH1 3LE, UK
                [ 5 ]Zoologisches Institut und Museum, Universität Greifswald, Loitzer Strasse 26; , Greifswald 17489, Germany
                [ 6 ]Department of Developmental Biology, Universität zu Köln, Zuelpicher Strasse 47B; , Köln 50674, Germany
                [ 7 ]School of Biology, St Andrews University; , St Andrews KY16 9ST, UK
                [ 8 ]Leibniz Institute for Biodiversity and Evolution, Museum für Naturkunde, Invalidenstrasse 43; , Berlin 10115, Germany
                Author notes

                Electronic supplementary material is available online at https://doi.org/10.6084/m9.figshare.c.7702953.

                Author information
                https://orcid.org/0000-0002-0043-906X
                https://orcid.org/0000-0003-0196-5069
                Article
                rspb20242069
                10.1098/rspb.2024.2069
                11896711
                40068820
                c656313d-4895-486f-90fd-b55d7628a075
                © 2025 The Author(s).

                Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

                History
                : August 29, 2024
                : November 29, 2024
                : January 20, 2025
                Funding
                Funded by: Leverhulme Trust, FundRef http://dx.doi.org/10.13039/501100000275;
                Funded by: John Fell Fund, University of Oxford, FundRef http://dx.doi.org/10.13039/501100004789;
                Funded by: Paul Scherrer Institut, FundRef http://dx.doi.org/10.13039/501100004219;
                Funded by: Deutsche Forschungsgemeinschaft, FundRef http://dx.doi.org/10.13039/501100001659;
                Categories
                1001
                1001
                1001
                58
                70
                Development and Physiology
                Research Articles

                Life sciences
                eye development,spiders,evolutionary neurobiology,visual systems,retinal determination

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