16
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      Early origin of viviparity and multiple reversions to oviparity in squamate reptiles.

      Ecology Letters
      Animals, Biological Evolution, Lizards, physiology, Oviparity, Snakes, Viviparity, Nonmammalian

      Read this article at

      ScienceOpenPublisherPubMed
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Viviparity has putatively evolved 115 times in squamates (lizards and snakes), out of only ~ 140 origins in vertebrates, and is apparently related to colder climates and other factors such as body size. Viviparity apparently evolves from oviparity via egg-retention, and such taxa may thus still have the machinery to produce thick-shelled eggs. Parity mode is also associated with variable diversification rates in some groups. We reconstruct ancestral parity modes accounting for state-dependent diversification in a large-scale phylogenetic analysis, and find strong support for an early origin of viviparity at the base of Squamata, and a complex pattern of subsequent transitions. Viviparous lineages have higher rates of speciation and extinction, and greater species turnover through time. Viviparity is associated with lower environmental and body temperatures in lizards and amphisbaenians, but not female mass. These results suggest that parity mode is a labile trait that shifts frequently in response to ecological conditions. © 2013 John Wiley & Sons Ltd/CNRS.

          Related collections

          Most cited references50

          • Record: found
          • Abstract: found
          • Article: not found

          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.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach

            Rates of molecular evolution vary widely between lineages, but quantification of how rates change has proven difficult. Recently proposed estimation procedures have mainly adopted highly parametric approaches that model rate evolution explicitly. In this study, a semiparametric smoothing method is developed using penalized likelihood. A saturated model in which every lineage has a separate rate is combined with a roughness penalty that discourages rates from varying too much across a phylogeny. A data-driven cross-validation criterion is then used to determine an optimal level of smoothing. This criterion is based on an estimate of the average prediction error associated with pruning lineages from the tree. The methods are applied to three data sets of six genes across a sample of land plants. Optimally smoothed estimates of absolute rates entailed 2- to 10-fold variation across lineages.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              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.
                Bookmark

                Author and article information

                Journal
                23953272
                10.1111/ele.12168

                Chemistry
                Animals,Biological Evolution,Lizards,physiology,Oviparity,Snakes,Viviparity, Nonmammalian
                Chemistry
                Animals, Biological Evolution, Lizards, physiology, Oviparity, Snakes, Viviparity, Nonmammalian

                Comments

                Comment on this article