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      Macroevolution of arboreality in salamanders

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          Abstract

          Evolutionary theory predicts that selection in distinct microhabitats generates correlations between morphological and ecological traits, and may increase both phenotypic and taxonomic diversity. However, some microhabitats exert unique selective pressures that act as a restraining force on macroevolutionary patterns of diversification. In this study, we use phylogenetic comparative methods to investigate the evolutionary outcomes of inhabiting the arboreal microhabitat in salamanders. We find that arboreality has independently evolved at least five times in Caudata and has arisen primarily from terrestrial ancestors. However, the rate of transition from arboreality back to terrestriality is 24 times higher than the converse. This suggests that macroevolutionary trends in microhabitat use tend toward terrestriality over arboreality, which influences the extent to which use of the arboreal microhabitat proliferates. Morphologically, we find no evidence for an arboreal phenotype in overall body proportions or in foot shape, as variation in both traits overlaps broadly with species that utilize different microhabitats. However, both body shape and foot shape display reduced rates of phenotypic evolution in arboreal taxa, and evidence of morphological convergence among arboreal lineages is observed. Taken together, these patterns suggest that arboreality has played a unique role in the evolution of this family, providing neither an evolutionary opportunity, nor an evolutionary dead end.

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          Stochastic mapping of morphological characters.

          Many questions in evolutionary biology are best addressed by comparing traits in different species. Often such studies involve mapping characters on phylogenetic trees. Mapping characters on trees allows the nature, number, and timing of the transformations to be identified. The parsimony method is the only method available for mapping morphological characters on phylogenies. Although the parsimony method often makes reasonable reconstructions of the history of a character, it has a number of limitations. These limitations include the inability to consider more than a single change along a branch on a tree and the uncoupling of evolutionary time from amount of character change. We extended a method described by Nielsen (2002, Syst. Biol. 51:729-739) to the mapping of morphological characters under continuous-time Markov models and demonstrate here the utility of the method for mapping characters on trees and for identifying character correlation.
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            Phylogenetic Analysis of Covariance by Computer Simulation

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              SIMMAP: Stochastic character mapping of discrete traits on phylogenies

              Background Character mapping on phylogenies has played an important, if not critical role, in our understanding of molecular, morphological, and behavioral evolution. Until very recently we have relied on parsimony to infer character changes. Parsimony has a number of serious limitations that are drawbacks to our understanding. Recent statistical methods have been developed that free us from these limitations enabling us to overcome the problems of parsimony by accommodating uncertainty in evolutionary time, ancestral states, and the phylogeny. Results SIMMAP has been developed to implement stochastic character mapping that is useful to both molecular evolutionists, systematists, and bioinformaticians. Researchers can address questions about positive selection, patterns of amino acid substitution, character association, and patterns of morphological evolution. Conclusion Stochastic character mapping, as implemented in the SIMMAP software, enables users to address questions that require mapping characters onto phylogenies using a probabilistic approach that does not rely on parsimony. Analyses can be performed using a fully Bayesian approach that is not reliant on considering a single topology, set of substitution model parameters, or reconstruction of ancestral states. Uncertainty in these quantities is accommodated by using MCMC samples from their respective posterior distributions.
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                Author and article information

                Contributors
                erica.baken@gmail.com
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                26 May 2019
                June 2019
                : 9
                : 12 ( doiID: 10.1002/ece3.2019.9.issue-12 )
                : 7005-7016
                Affiliations
                [ 1 ] Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames Iowa
                Author notes
                [*] [* ] Correspondence

                Erica K. Baken, Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA.

                Email: erica.baken@ 123456gmail.com

                Author information
                https://orcid.org/0000-0003-2972-7900
                Article
                ECE35267
                10.1002/ece3.5267
                6662381
                31380029
                846962d5-62f0-4db3-906c-aa596f7cbed9
                © 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 12 March 2019
                : 25 April 2019
                : 28 April 2019
                Page count
                Figures: 5, Tables: 1, Pages: 12, Words: 8788
                Funding
                Funded by: U.S. National Science Foundation
                Award ID: DEB-1556379
                Funded by: California Academy of Science
                Funded by: Society of Systematic Biologists Graduate Student Research Award
                Categories
                Original Research
                Original Research
                Custom metadata
                2.0
                ece35267
                June 2019
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.6.6.2 mode:remove_FC converted:29.07.2019

                Evolutionary Biology
                amphibian,macroevolution,microhabitat,phylogenetic comparative methods
                Evolutionary Biology
                amphibian, macroevolution, microhabitat, phylogenetic comparative methods

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