Phylogenetic inference for function-valued traits: speech sound evolution.

Phylogenetic models have recently been proposed for data that are best represented as a mathematical function (i.e. function valued). Such methods can be used to model the change over time in function-based descriptions of various data of interest to evolutionary biologists, including the sound of speech. This approach to phylogenetic inference and analysis is challenging, both in terms of modeling the phylogenetics of functions and in engaging with previously existing evidence for character-state change. Nevertheless, it is both a real and exciting prospect. Our approach could provide those interested in investigating a greater range of evolutionary processes with the ability to use statistical hypothesis-testing procedures and to create estimates of the states of function-valued characteristics (e.g. speech sounds) at earlier historical times.

[1]  VINCENT M. JANIK,et al.  Pitfalls in the categorization of behaviour: a comparison of dolphin whistle classification methods , 1999, Animal Behaviour.

[2]  T. F. Hansen,et al.  Phylogenies and the Comparative Method: A General Approach to Incorporating Phylogenetic Information into the Analysis of Interspecific Data , 1997, The American Naturalist.

[3]  M. Pagel,et al.  The comparative method in evolutionary biology , 1991 .

[4]  Fred L. Bookstein,et al.  5 – CAN BIOMETRICAL SHAPE BE A HOMOLOGOUS CHARACTER? , 1994 .

[5]  V. Gracco,et al.  Functional data analyses of lip motion. , 1996, The Journal of the Acoustical Society of America.

[6]  R. Gray,et al.  Language-tree divergence times support the Anatolian theory of Indo-European origin , 2003, Nature.

[7]  J C Lucero,et al.  Time normalization of voice signals using functional data analysis. , 2000, The Journal of the Acoustical Society of America.

[8]  P. Goloboff,et al.  Phylogenetic morphometrics (I): the use of landmark data in a phylogenetic framework , 2010, Cladistics : the international journal of the Willi Hennig Society.

[9]  F J Rohlf,et al.  COMPARATIVE METHODS FOR THE ANALYSIS OF CONTINUOUS VARIABLES: GEOMETRIC INTERPRETATIONS , 2001, Evolution; international journal of organic evolution.

[10]  John A. D. Aston,et al.  Linguistic pitch analysis using functional principal component mixed effect models , 2010 .

[11]  Mark Kirkpatrick,et al.  Up hill, down dale: quantitative genetics of curvaceous traits , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[12]  Simon J. Greenhill,et al.  Languages Evolve in Punctuational Bursts , 2008, Science.

[13]  Sound Change: Phonetics , 2006 .

[14]  Jorge C Lucero,et al.  Speech production variability in fricatives of children and adults: results of functional data analysis. , 2008, The Journal of the Acoustical Society of America.

[15]  Nick S. Jones,et al.  Evolutionary inference for function-valued traits: Gaussian process regression on phylogenies , 2010, Journal of The Royal Society Interface.

[16]  Bart de Boer,et al.  Self-organization in vowel systems , 2000, J. Phonetics.

[17]  W. S. Allen,et al.  Vox Latina: The Pronunciation of Classical Latin, W. Sidney Allen , 1991 .

[18]  Henry W. Altland,et al.  Applied Functional Data Analysis , 2003, Technometrics.

[19]  J. Felsenstein Phylogenies and quantitative characters , 1988 .

[20]  M. Kirkpatrick,et al.  A quantitative genetic model for growth, shape, reaction norms, and other infinite-dimensional characters , 1989, Journal of mathematical biology.

[21]  August Schleicher,et al.  Compendium Der Vergleichenden Grammatik Der Indogermanischen Sprachen , 2013 .

[22]  John Coleman,et al.  Acoustics of American English speech : a dynamic approach , 1993 .

[23]  S. Öhman Coarticulation in VCV Utterances: Spectrographic Measurements , 1966 .

[24]  Richard Gomulkiewicz,et al.  Hypothesis Testing in Comparative and Experimental Studies of Function-Valued Traits , 2008, Evolution; international journal of organic evolution.

[25]  W. S. Allen,et al.  Phonetics in ancient India , 1954 .

[26]  Hans-Georg Müller,et al.  Functional Data Analysis , 2016 .

[27]  P. Goloboff,et al.  Phylogenetic morphometrics (II): algorithms for landmark optimization , 2011, Cladistics : the international journal of the Willi Hennig Society.

[28]  Alex Acero,et al.  Spoken Language Processing: A Guide to Theory, Algorithm and System Development , 2001 .

[29]  David Abercrombie,et al.  Towards a history of phonetics , 1981 .

[30]  Ryuji Suzuki,et al.  Information entropy of humpback whale songs. , 1999, The Journal of the Acoustical Society of America.

[31]  Peter L. Tyack,et al.  Acoustic Communication Under the Sea , 1998 .

[32]  Tandy Warnow,et al.  Indo‐European and Computational Cladistics , 2002 .

[33]  Ben Maassen,et al.  Proceedings of the 10th Annual Conference of the International Speech Communication Association (Interspeech 2009) , 2009 .

[34]  Greg Kochanski,et al.  Connecting Intonation Labels to Mathematical Descriptions of Fundamental Frequency , 2007, Language and speech.

[35]  J. Felsenstein Phylogenies and the Comparative Method , 1985, The American Naturalist.

[36]  James Mallory,et al.  The Oxford Introduction to Proto-Indo-European and the Proto-Indo-European World , 2006 .

[37]  T. F. Hansen,et al.  TRANSLATING BETWEEN MICROEVOLUTIONARY PROCESS AND MACROEVOLUTIONARY PATTERNS: THE CORRELATION STRUCTURE OF INTERSPECIFIC DATA , 1996, Evolution; international journal of organic evolution.

[38]  F. Ferraty,et al.  The Oxford Handbook of Functional Data Analysis , 2011, Oxford Handbooks Online.

[39]  Alvin M. Liberman,et al.  The Grammars of Speech and Language. , 1970 .

[40]  W. S. Allen,et al.  Vox Graeca: The Pronunciation of Classical Greek , 1969 .

[41]  Richard A. Pimentcl,et al.  THE NATURE OF CLADISTIC DATA , 1987, Cladistics : the international journal of the Willi Hennig Society.

[42]  Norman MacLeod,et al.  Phylogenetic signals in morphometric data , 2000 .