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      Beak shape and nest material use in birds

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          Abstract

          The evolution of behaviour can both influence, and be influenced by, morphology. Recent advances in methods and data availability have facilitated broad-scale investigations of physical form and behavioural function in many contexts, but the relationship between animal morphology and object manipulation—particularly objects used in construction—remains largely unknown. Here, we employ a new global database of nest materials used by 5924 species of birds together with phylogenetically informed random forest models to evaluate the link between beak shape and these nest-building materials. We find that beak morphology, together with species diet and access to materials, can predict nest-material use above chance and with high accuracy (68–97%). Much of this relationship, however, is driven by phylogenetic signal and sampling biases. We therefore conclude that while variation in nest material use is linked with that of beak shape across bird species, these correlations are modulated by the ecological context and evolutionary history of these species.

          This article is part of the theme issue ‘The evolutionary ecology of nests: a cross-taxon approach’.

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          Random Forests

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            APE: Analyses of Phylogenetics and Evolution in R language.

            Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.
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              BEAST: Bayesian evolutionary analysis by sampling trees

              Background The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. Results BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at under the GNU LGPL license. Conclusion BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Writing – review & editing
                Role: Data curationRole: Writing – review & editing
                Role: SupervisionRole: Writing – review & editing
                Role: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Writing – original draftRole: Writing – review & editing
                Journal
                Philos Trans R Soc Lond B Biol Sci
                Philos Trans R Soc Lond B Biol Sci
                RSTB
                royptb
                Philosophical Transactions of the Royal Society B: Biological Sciences
                The Royal Society
                0962-8436
                1471-2970
                August 28, 2023
                July 10, 2023
                July 10, 2023
                : 378
                : 1884 , Theme issue ‘The evolutionary ecology of nests: a cross-taxon approach’ compiled and edited by Mark C. Mainwaring, Mary Caswell Stoddard, Iain Barber, D. Charles Deeming and Mark E. Hauber
                : 20220147
                Affiliations
                [ 1 ] School of Earth Sciences, University of Bristol, , Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
                [ 2 ] Department of Anthropology, Durham University, , Dawson Building, South Road, Durham DH1 3LE, UK
                [ 3 ] School of Biology, University of St Andrews, , Harold Mitchell Building, St Andrews KY16 9TJ, UK
                Author notes

                One contribution of 20 to a theme issue ‘ The evolutionary ecology of nests: a cross-taxon approach’.

                [ † ]

                Formerly Kevin N. Laland.

                Electronic supplementary material is available online at https://doi.org/10.6084/m9.figshare.c.6677602.

                Author information
                http://orcid.org/0000-0002-8259-1275
                http://orcid.org/0000-0001-8939-8016
                http://orcid.org/0000-0001-7978-7966
                Article
                rstb20220147
                10.1098/rstb.2022.0147
                10331908
                37427471
                e8f3d52f-ac6e-4ec2-b033-f744222f1a87
                © 2023 The Authors.

                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
                : December 16, 2022
                : March 6, 2023
                Funding
                Funded by: Biotechnology and Biological Sciences Research Council, http://dx.doi.org/10.13039/501100000268;
                Award ID: BB/S01019X/1
                Funded by: John Templeton Foundation, http://dx.doi.org/10.13039/100000925;
                Award ID: 60501
                Funded by: H2020 European Research Council, http://dx.doi.org/10.13039/100010663;
                Award ID: 788203
                Categories
                1001
                70
                Articles
                Research Articles
                Custom metadata
                August 28, 2023

                Philosophy of science
                object manipulation,form-function coevolution,bird nests,morphology,construction,behaviour

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