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      Skin patterning and internal anatomy in a fossil moonfish from the Eocene Bolca Lagerstätte illuminate the ecology of ancient reef fish communities

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          Abstract

          Colour patterning in extant animals can be used as a reliable indicator of their biology and, in extant fish, can inform on feeding strategy. Fossil fish with preserved colour patterns may thus illuminate the evolution of fish behaviour and community structure, but are understudied. Here we report preserved melanin‐based integumentary colour patterning and internal anatomy of the fossil moonfish Mene rhombea (Menidae) from the Bolca Lagerstätte (Eocene (Ypresian), north‐east Italy). The melanosome‐based longitudinal stripes of M.  rhombea differ from the dorsal rows of black spots in its extant relative M.  maculata, suggesting that the ecology of moonfish has changed during the Cenozoic. Extant moonfish are coastal schooling fish that feed on benthic invertebrates, but the longitudinal stripes and stomach contents with fish remains in M.  rhombea suggest unstructured open marine ecologies and a piscivorous diet. The localized distribution of extant moonfish species in the Indo‐Pacific Ocean may reflect, at least in part, tectonically‐driven reorganization of global oceanographic patterns during the Cenozoic. It is likely that shifts in habitat and colour patterning genes promoted colour pattern evolution in the menid lineage.

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          ImageJ2: ImageJ for the next generation of scientific image data

          Background ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software’s ability to handle the requirements of modern science. Results We rewrote the entire ImageJ codebase, engineering a redesigned plugin mechanism intended to facilitate extensibility at every level, with the goal of creating a more powerful tool that continues to serve the existing community while addressing a wider range of scientific requirements. This next-generation ImageJ, called “ImageJ2” in places where the distinction matters, provides a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. Conclusions Scientific imaging benefits from open-source programs that advance new method development and deployment to a diverse audience. ImageJ has continuously evolved with this idea in mind; however, new and emerging scientific requirements have posed corresponding challenges for ImageJ’s development. The described improvements provide a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs. Future efforts will focus on implementing new algorithms in this framework and expanding collaborations with other popular scientific software suites. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1934-z) contains supplementary material, which is available to authorized users.
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            Bon-EV: an improved multiple testing procedure for controlling false discovery rates

            Background Stability of multiple testing procedures, defined as the standard deviation of total number of discoveries, can be used as an indicator of variability of multiple testing procedures. Improving stability of multiple testing procedures can help to increase the consistency of findings from replicated experiments. Benjamini-Hochberg’s and Storey’s q-value procedures are two commonly used multiple testing procedures for controlling false discoveries in genomic studies. Storey’s q-value procedure has higher power and lower stability than Benjamini-Hochberg’s procedure. To improve upon the stability of Storey’s q-value procedure and maintain its high power in genomic data analysis, we propose a new multiple testing procedure, named Bon-EV, to control false discovery rate (FDR) based on Bonferroni’s approach. Results Simulation studies show that our proposed Bon-EV procedure can maintain the high power of the Storey’s q-value procedure and also result in better FDR control and higher stability than Storey’s q-value procedure for samples of large size(30 in each group) and medium size (15 in each group) for either independent, somewhat correlated, or highly correlated test statistics. When sample size is small (5 in each group), our proposed Bon-EV procedure has performance between the Benjamini-Hochberg procedure and the Storey’s q-value procedure. Examples using RNA-Seq data show that the Bon-EV procedure has higher stability than the Storey’s q-value procedure while maintaining equivalent power, and higher power than the Benjamini-Hochberg’s procedure. Conclusions For medium or large sample sizes, the Bon-EV procedure has improved FDR control and stability compared with the Storey’s q-value procedure and improved power compared with the Benjamini-Hochberg procedure. The Bon-EV multiple testing procedure is available as the BonEV package in R for download at https://CRAN.R-project.org/package=BonEV. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1414-x) contains supplementary material, which is available to authorized users.
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              The colour of fossil feathers.

              Feathers are complex integumentary appendages of birds and some other theropod dinosaurs. They are frequently coloured and function in camouflage and display. Previous investigations have concluded that fossil feathers are preserved as carbonized traces composed of feather-degrading bacteria. Here, an investigation of a colour-banded feather from the Lower Cretaceous Crato Formation of Brazil revealed that the dark bands are preserved as elongate, oblate carbonaceous bodies 1-2 microm long, whereas the light bands retain only relief traces on the rock matrix. Energy dispersive X-ray analysis showed that the dark bands preserve a substantial amount of carbon, whereas the light bands show no carbon residue. Comparison of these oblate fossil bodies with the structure of black feathers from a living bird indicates that they are the eumelanin-containing melanosomes. We conclude that most fossil feathers are preserved as melanosomes, and that the distribution of these structures in fossil feathers can preserve the colour pattern in the original feather. The discovery of preserved melanosomes opens up the possibility of interpreting the colour of extinct birds and other dinosaurs.
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                Author and article information

                Contributors
                valentina.rossi@ucc.ie
                r.unitt@ucc.ie
                maria.mcnamara@ucc.ie
                roberto.zorzin@comune.verona.it
                giorgio.carnevale@unito.it
                Journal
                Palaeontology
                Palaeontology
                10.1111/(ISSN)1475-4983
                PALA
                Palaeontology
                John Wiley and Sons Inc. (Hoboken )
                0031-0239
                1475-4983
                24 May 2022
                May-Jun 2022
                : 65
                : 3 ( doiID: 10.1111/pala.v65.3 )
                : e12600
                Affiliations
                [ 1 ] ringgold 8795; School of Biological, Earth & Environmental Sciences University College Cork Cork T23 TK30 Ireland
                [ 2 ] Museo di Scienze Naturali dell’Alto Adige Bolzano 39100 Italy
                [ 3 ] ringgold 8795; Environmental Research Institute University College Cork Cork T23 XE10 Ireland
                [ 4 ] ringgold 87944; Sezione di Geologia e Paleontologia Museo Civico di Storia Naturale di Verona Lungadige Porta Vittoria 9 37129 Verona Italy
                [ 5 ] ringgold 9314; Dipartimento di Scienze della Terra Università degli Studi di Torino Via Valperga Caluso 35 10125 Torino Italy
                Author notes
                [*] [* ] Corresponding author

                Author information
                https://orcid.org/0000-0001-6269-5328
                https://orcid.org/0000-0002-7504-1451
                https://orcid.org/0000-0003-0968-4624
                https://orcid.org/0000-0002-3433-4127
                Article
                PALA12600
                10.1111/pala.12600
                9324815
                2d23979e-dd8c-4b16-83ac-71108cdf221c
                © 2022 The Authors. Palaeontology published by John Wiley & Sons Ltd on behalf of The Palaeontological Association

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                : 07 October 2021
                : 07 February 2022
                Page count
                Figures: 5, Tables: 0, Pages: 11, Words: 6096
                Funding
                Funded by: European Research Council Consolidator Grant
                Award ID: H2020‐ERC‐COG‐101003293
                Funded by: Borsa di studio SPI
                Funded by: Università degli Studi di Torino , doi 10.13039/501100006692;
                Award ID: ex‐60%
                Categories
                Original Article
                Original Articles
                Custom metadata
                2.0
                May/June 2022
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.1.7 mode:remove_FC converted:26.07.2022

                colour patterning,bolca lagerstätte,soft tissue preservation,melanosome,internal anatomy

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