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      Detecting Regular Sound Changes in Linguistics as Events of Concerted Evolution

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          Summary

          Background

          Concerted evolution is normally used to describe parallel changes at different sites in a genome, but it is also observed in languages where a specific phoneme changes to the same other phoneme in many words in the lexicon—a phenomenon known as regular sound change. We develop a general statistical model that can detect concerted changes in aligned sequence data and apply it to study regular sound changes in the Turkic language family.

          Results

          Linguistic evolution, unlike the genetic substitutional process, is dominated by events of concerted evolutionary change. Our model identified more than 70 historical events of regular sound change that occurred throughout the evolution of the Turkic language family, while simultaneously inferring a dated phylogenetic tree. Including regular sound changes yielded an approximately 4-fold improvement in the characterization of linguistic change over a simpler model of sporadic change, improved phylogenetic inference, and returned more reliable and plausible dates for events on the phylogenies. The historical timings of the concerted changes closely follow a Poisson process model, and the sound transition networks derived from our model mirror linguistic expectations.

          Conclusions

          We demonstrate that a model with no prior knowledge of complex concerted or regular changes can nevertheless infer the historical timings and genealogical placements of events of concerted change from the signals left in contemporary data. Our model can be applied wherever discrete elements—such as genes, words, cultural trends, technologies, or morphological traits—can change in parallel within an organism or other evolving group.

          Graphical Abstract

          Highlights

          • Linguistic evolution is dominated by events of concerted evolutionary change

          • Modeling concerted evolution improves phylogenetic inference and dating

          • Events of concerted change conform closely to a Poisson process

          • Our model can be applied to genes, languages, cultures, and technological change

          Abstract

          Concerted evolution refers to the same evolutionary change occurring at different sites in a genome. It also occurs in languages when the same sound change occurs in different words. Hruschka et al. report a statistical model that can detect concerted changes and show how it substantially improves our understanding of how languages evolve.

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          Most cited references27

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          Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo.

          We describe a Bayesian method for investigating correlated evolution of discrete binary traits on phylogenetic trees. The method fits a continuous-time Markov model to a pair of traits, seeking the best fitting models that describe their joint evolution on a phylogeny. We employ the methodology of reversible-jump (RJ) Markov chain Monte Carlo to search among the large number of possible models, some of which conform to independent evolution of the two traits, others to correlated evolution. The RJ Markov chain visits these models in proportion to their posterior probabilities, thereby directly estimating the support for the hypothesis of correlated evolution. In addition, the RJ Markov chain simultaneously estimates the posterior distributions of the rate parameters of the model of trait evolution. These posterior distributions can be used to test among alternative evolutionary scenarios to explain the observed data. All results are integrated over a sample of phylogenetic trees to account for phylogenetic uncertainty. We implement the method in a program called RJ Discrete and illustrate it by analyzing the question of whether mating system and advertisement of estrus by females have coevolved in the Old World monkeys and great apes.
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            Abundant gene conversion between arms of palindromes in human and ape Y chromosomes.

            Eight palindromes comprise one-quarter of the euchromatic DNA of the male-specific region of the human Y chromosome, the MSY. They contain many testis-specific genes and typically exhibit 99.97% intra-palindromic (arm-to-arm) sequence identity. This high degree of identity could be interpreted as evidence that the palindromes arose through duplication events that occurred about 100,000 years ago. Using comparative sequencing in great apes, we demonstrate here that at least six of these MSY palindromes predate the divergence of the human and chimpanzee lineages, which occurred about 5 million years ago. The arms of these palindromes must have subsequently engaged in gene conversion, driving the paired arms to evolve in concert. Indeed, analysis of MSY palindrome sequence variation in existing human populations provides evidence of recurrent arm-to-arm gene conversion in our species. We conclude that during recent evolution, an average of approximately 600 nucleotides per newborn male have undergone Y-Y gene conversion, which has had an important role in the evolution of multi-copy testis gene families in the MSY.
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              Concerted evolution: molecular mechanism and biological implications.

              D. Liao (1998)
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                Author and article information

                Contributors
                Journal
                Curr Biol
                Curr. Biol
                Current Biology
                Cell Press
                0960-9822
                1879-0445
                05 January 2015
                05 January 2015
                : 25
                : 1
                : 1-9
                Affiliations
                [1 ]School of Human Evolution and Social Change, Arizona State University, PO Box 872402, Tempe, AZ 85287-2402, USA
                [2 ]School of Biological Sciences, University of Reading, Reading RG6 6BX, UK
                [3 ]The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
                [4 ]Krasnow Institute for Advanced Study, George Mason University, Mail Stop 2A1, 4400 University Drive, Fairfax, VA 22030, USA
                [5 ]Ronin Institute, 127 Haddon Place, Montclair, NJ 07043, USA
                [6 ]T-2, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
                Author notes
                []Corresponding author m.pagel@ 123456reading.ac.uk
                [∗∗ ]Corresponding author tanmoy@ 123456santafe.edu
                Article
                S0960-9822(14)01373-6
                10.1016/j.cub.2014.10.064
                4291143
                25532895
                775ece72-3bcf-44d4-8372-1368f632a1f3
                © 2015 The Authors

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

                History
                : 25 June 2014
                : 19 September 2014
                : 23 October 2014
                Categories
                Article

                Life sciences
                Life sciences

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