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

      1 , 2 , 3

      Ecology Letters

      Wiley

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          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.

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

           M. Sanderson (2002)
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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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              Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies.

              Species traits may influence rates of speciation and extinction, affecting both the patterns of diversification among lineages and the distribution of traits among species. Existing likelihood approaches for detecting differential diversification require complete phylogenies; that is, every extant species must be present in a well-resolved phylogeny. We developed 2 likelihood methods that can be used to infer the effect of a trait on speciation and extinction without complete phylogenetic information, generalizing the recent binary-state speciation and extinction method. Our approaches can be used where a phylogeny can be reasonably assumed to be a random sample of extant species or where all extant species are included but some are assigned only to terminal unresolved clades. We explored the effects of decreasing phylogenetic resolution on the ability of our approach to detect differential diversification within a Bayesian framework using simulated phylogenies. Differential diversification caused by an asymmetry in speciation rates was nearly as well detected with only 50% of extant species phylogenetically resolved as with complete phylogenetic knowledge. We demonstrate our unresolved clade method with an analysis of sexual dimorphism and diversification in shorebirds (Charadriiformes). Our methods allow for the direct estimation of the effect of a trait on speciation and extinction rates using incompletely resolved phylogenies.
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                Author and article information

                Journal
                Ecology Letters
                Ecol Lett
                Wiley
                1461023X
                January 2014
                January 2014
                August 19 2013
                : 17
                : 1
                : 13-21
                Affiliations
                [1 ]Department of Biological Sciences; The George Washington University; 2023 G St. NW Washington DC 20052 USA
                [2 ]Department of Biology; The Graduate School and University Center; The City University of New York; 365 5th Ave. New York NY 10016 USA
                [3 ]Department of Biology; The College of Staten Island; The City University of New York; 2800 Victory Blvd. Staten Island NY 10314 USA
                Article
                10.1111/ele.12168
                23953272
                © 2013
                Product
                Self URI (article page): http://doi.wiley.com/10.1111/ele.12168

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