title: Detecting regular sound changes in linguistics as events of concerted evolution.
abstract: 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.
authors.affiliation: School of Human Evolution and Social Change, Arizona State University, PO Box 872402, Tempe, AZ 85287-2402, USA.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Hruschka
authors.affiliation: School of Biological Sciences, University of Reading, Reading RG6 6BX, UK.
authors.forename: Simon
authors.initials: S
authors.lastname: Branford
authors.affiliation: The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA; Krasnow Institute for Advanced Study, George Mason University, Mail Stop 2A1, 4400 University Drive, Fairfax, VA 22030, USA.
authors.forename: Eric D
authors.initials: ED
authors.lastname: Smith
authors.affiliation: The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA; Ronin Institute, 127 Haddon Place, Montclair, NJ 07043, USA.
authors.forename: Jon
authors.initials: J
authors.lastname: Wilkins
authors.affiliation: School of Biological Sciences, University of Reading, Reading RG6 6BX, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Meade
authors.affiliation: School of Biological Sciences, University of Reading, Reading RG6 6BX, UK; The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA. Electronic address: m.pagel@reading.ac.uk.
authors.forename: Mark
authors.initials: M
authors.lastname: Pagel
authors.affiliation: The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA; T-2, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. Electronic address: tanmoy@santafe.edu.
authors.forename: Tanmoy
authors.initials: T
authors.lastname: Bhattacharya
mesh_terms: D003468:Cultural Evolution; D006801:Humans; D015233:Models, Statistical; D010700:Phonetics; D010802:Phylogeny