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      Island- and lake-like parallel adaptive radiations replicated in rivers

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          Abstract

          <p class="first" id="d995437e232">Parallel adaptive radiations have arisen following the colonization of islands by lizards and lakes by fishes. In these classic examples, parallel adaptive radiation is a response to the ecological opportunities afforded by the colonization of novel ecosystems and similar adaptive landscapes that favour the evolution of similar suites of ecomorphs, despite independent evolutionary histories. Here, we demonstrate that parallel adaptive radiations of cichlid fishes arose in South American rivers. Speciation-assembled communities of pike cichlids ( <i>Crenicichla</i>) have independently diversified into similar suites of novel ecomorphs in the Uruguay and Paraná Rivers, including crevice feeders, periphyton grazers and molluscivores. There were bursts in phenotypic evolution associated with the colonization of each river and the subsequent expansion of morphospace following the evolution of the ecomorphs. These riverine clades demonstrate that characteristics emblematic of textbook parallel adaptive radiations of island- and lake-dwelling assemblages are feasible evolutionary outcomes even in labile ecosystems such as rivers. </p>

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          Convergence, adaptation, and constraint.

          Convergent evolution of similar phenotypic features in similar environmental contexts has long been taken as evidence of adaptation. Nonetheless, recent conceptual and empirical developments in many fields have led to a proliferation of ideas about the relationship between convergence and adaptation. Despite criticism from some systematically minded biologists, I reaffirm that convergence in taxa occupying similar selective environments often is the result of natural selection. However, convergent evolution of a trait in a particular environment can occur for reasons other than selection on that trait in that environment, and species can respond to similar selective pressures by evolving nonconvergent adaptations. For these reasons, studies of convergence should be coupled with other methods-such as direct measurements of selection or investigations of the functional correlates of trait evolution-to test hypotheses of adaptation. The independent acquisition of similar phenotypes by the same genetic or developmental pathway has been suggested as evidence of constraints on adaptation, a view widely repeated as genomic studies have documented phenotypic convergence resulting from change in the same genes, sometimes even by the same mutation. Contrary to some claims, convergence by changes in the same genes is not necessarily evidence of constraint, but rather suggests hypotheses that can test the relative roles of constraint and selection in directing phenotypic evolution. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.
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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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              treePL: divergence time estimation using penalized likelihood for large phylogenies.

              Ever larger phylogenies are being constructed due to the explosion of genetic data and development of high-performance phylogenetic reconstruction algorithms. However, most methods for calculating divergence times are limited to datasets that are orders of magnitude smaller than recently published large phylogenies. Here, we present an algorithm and implementation of a divergence time method using penalized likelihood that can handle datasets of thousands of taxa. We implement a method that combines the standard derivative-based optimization with a stochastic simulated annealing approach to overcome optimization challenges. We compare this approach with existing software including r8s, PATHd8 and BEAST. Source code, example files, binaries and documentation for treePL are available at https://github.com/blackrim/treePL.
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                Author and article information

                Journal
                Proceedings of the Royal Society B: Biological Sciences
                Proc. R. Soc. B
                The Royal Society
                0962-8452
                1471-2954
                January 03 2018
                January 10 2018
                January 03 2018
                January 10 2018
                : 285
                : 1870
                : 20171762
                Article
                10.1098/rspb.2017.1762
                5784188
                29298932
                bc82704a-c98f-4e06-b10c-d59581f4d662
                © 2018
                History

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