Temporal Phylogenetic Networks and Logic Programming
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The Evolution of Language: Towards Gestural Hypotheses DIS/CONTINUITIES TORUŃ STUDIES IN LANGUAGE, LITERATURE AND CULTURE Edited by Mirosława Buchholtz Advisory Board Leszek Berezowski (Wrocław University) Annick Duperray (University of Provence) Dorota Guttfeld (Nicolaus Copernicus University) Grzegorz Koneczniak (Nicolaus Copernicus University) Piotr Skrzypczak (Nicolaus Copernicus University) Jordan Zlatev (Lund University) Vol. 20 DIS/CONTINUITIES Przemysław ywiczy ski / Sławomir Wacewicz TORUŃ STUDIES IN LANGUAGE, LITERATURE AND CULTURE Ż ń Edited by Mirosława Buchholtz Advisory Board Leszek Berezowski (Wrocław University) Annick Duperray (University of Provence) Dorota Guttfeld (Nicolaus Copernicus University) Grzegorz Koneczniak (Nicolaus Copernicus University) The Evolution of Language: Piotr Skrzypczak (Nicolaus Copernicus University) Jordan Zlatev (Lund University) Towards Gestural Hypotheses Vol. 20 Bibliographic Information published by the Deutsche Nationalbibliothek The Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data is available in the internet at http://dnb.d-nb.de. The translation, publication and editing of this book was financed by a grant from the Polish Ministry of Science and Higher Education of the Republic of Poland within the programme Uniwersalia 2.1 (ID: 347247, Reg. no. 21H 16 0049 84) as a part of the National Programme for the Development of the Humanities. This publication reflects the views only of the authors, and the Ministry cannot be held responsible for any use which may be made of the information contained therein. Translators: Marek Placi ski, Monika Boruta Supervision and proofreading: John Kearns Cover illustration: © ńMateusz Pawlik Printed by CPI books GmbH, Leck ISSN 2193-4207 ISBN 978-3-631-79022-9 (Print) E-ISBN 978-3-631-79393-0 (E-PDF) E-ISBN 978-3-631-79394-7 (EPUB) E-ISBN 978-3-631-79395-4 (MOBI) DOI 10.3726/b15805 Open Access: This work is licensed under a Creative Commons Attribution Non Commercial No Derivatives 4.0 unported license. -
Species Tree Likelihood Computation Given SNP Data Using Ancestral Configurations
Species Tree Likelihood Computation Given SNP Data Using Ancestral Configurations DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Hang Fan, M.S. Graduate Program in Statistics The Ohio State University 2013 Dissertation Committee: Professor Laura Kubatko, Advisor Professor Bryan Carstens Professor Radu Herbei 1 Copyright by Hang Fan 2013 2 Abstract Inferring species trees given genetic data has been a challenge in the field of phylogenetics because of the high intensity during computation. In the coalescent framework, this dissertation proposes an innovative method of estimating the likelihood of a species tree directly from Single Nucleotide Polymorphism (SNP) data with a certain nucleotide substitution model. This method uses the idea of Ancestral Configurations (Wu, 2011) to avoid the computation burden brought by the enumeration of coalescent histories. Importance sampling is used to in Monte Carlo integration to approximate the expectations in the computation, where the accuracy of the approximation is tested in different tree models. The SNP data is processed beforehand which vastly boosts the efficiency of the method. Gene tree sampling given the species tree under the coalescent model is employed to make the computation feasible for large trees. Further, the branch lengths on the species tree are optimized according to the computed species tree likelihood, which provides the likelihood of the species tree topology given the SNP data. For inference, this likelihood computation method is implemented in the stepwise addition algorithm to infer the maximum likelihood species tree in the tree space given the SNP data, and simulations are conduced to test the performance. -
EVOLUTIONARY INFERENCE: Some Basics of Phylogenetic Analyses
EVOLUTIONARY INFERENCE: Some basics of phylogenetic analyses. Ana Rojas Mendoza CNIO-Madrid-Spain. Alfonso Valencia’s lab. Aims of this talk: • 1.To introduce relevant concepts of evolution to practice phylogenetic inference from molecular data. • 2.To introduce some of the most useful methods and computer programmes to practice phylogenetic inference. • • 3.To show some examples I’ve worked in. SOME BASICS 11--ConceptsConcepts ofof MolecularMolecular EvolutionEvolution • Homology vs Analogy. • Homology vs similarity. • Ortologous vs Paralogous genes. • Species tree vs genes tree. • Molecular clock. • Allele mutation vs allele substitution. • Rates of allele substitution. • Neutral theory of evolution. SOME BASICS Owen’s definition of homology Richard Owen, 1843 • Homologue: the same organ under every variety of form and function (true or essential correspondence). •Analogy: superficial or misleading similarity. SOME BASICS 1.Concepts1.Concepts ofof MolecularMolecular EvolutionEvolution • Homology vs Analogy. • Homology vs similarity. • Ortologous vs Paralogous genes. • Species tree vs genes tree. • Molecular clock. • Allele mutation vs allele substitution. • Rates of allele substitution. • Neutral theory of evolution. SOME BASICS Similarity ≠ Homology • Similarity: mathematical concept . Homology: biological concept Common Ancestry!!! SOME BASICS 1.Concepts1.Concepts ofof MolecularMolecular EvolutionEvolution • Homology vs Analogy. • Homology vs similarity. • Ortologous vs Paralogous genes. • Species tree vs genes tree. • Molecular clock. -
The Probability of Monophyly of a Sample of Gene Lineages on a Species Tree
PAPER The probability of monophyly of a sample of gene COLLOQUIUM lineages on a species tree Rohan S. Mehtaa,1, David Bryantb, and Noah A. Rosenberga aDepartment of Biology, Stanford University, Stanford, CA 94305; and bDepartment of Mathematics and Statistics, University of Otago, Dunedin 9054, New Zealand Edited by John C. Avise, University of California, Irvine, CA, and approved April 18, 2016 (received for review February 5, 2016) Monophyletic groups—groups that consist of all of the descendants loci that are reciprocally monophyletic is informative about the of a most recent common ancestor—arise naturally as a conse- time since species divergence and can assist in representing the quence of descent processes that result in meaningful distinctions level of differentiation between groups (4, 18). between organisms. Aspects of monophyly are therefore central to Many empirical investigations of genealogical phenomena have fields that examine and use genealogical descent. In particular, stud- made use of conceptual and statistical properties of monophyly ies in conservation genetics, phylogeography, population genetics, (19). Comparisons of observed monophyly levels to model pre- species delimitation, and systematics can all make use of mathemat- dictions have been used to provide information about species di- ical predictions under evolutionary models about features of mono- vergence times (20, 21). Model-based monophyly computations phyly. One important calculation, the probability that a set of gene have been used alongside DNA sequence differences between and lineages is monophyletic under a two-species neutral coalescent within proposed clades to argue for the existence of the clades model, has been used in many studies. Here, we extend this calcu- (22), and tests involving reciprocal monophyly have been used to lation for a species tree model that contains arbitrarily many species. -
Outer and Inner Indo-Aryan, and Northern India As an Ancient Linguistic Area
Acta Orientalia 2016: 77, 71–132. Copyright © 2016 Printed in India – all rights reserved ACTA ORIENTALIA ISSN 0001-6483 Outer and Inner Indo-Aryan, and northern India as an ancient linguistic area Claus Peter Zoller University of Oslo Abstract The article presents a new approach to the old controversy concerning the veracity of a distinction between Outer and Inner Languages in Indo-Aryan. A number of arguments and data are presented which substantiate the reality of this distinction. This new approach combines this issue with a new interpretation of the history of Indo- Iranian and with the linguistic prehistory of northern India. Data are presented to show that prehistorical northern India was dominated by Munda/Austro-Asiatic languages. Keywords: Indo-Aryan, Indo-Iranian, Nuristani, Munda/Austro- Asiatic history and prehistory. Introduction This article gives a summary of the most important arguments contained in my forthcoming book on Outer and Inner languages before and after the arrival of Indo-Aryan in South Asia. The 72 Claus Peter Zoller traditional version of the hypothesis of Outer and Inner Indo-Aryan purports the idea that the Indo-Aryan Language immigration1 was not a singular event. Yet, even though it is known that the actual historical movements and processes in connection with this immigration were remarkably complex, the concerns of the hypothesis are not to reconstruct the details of these events but merely to show that the original non-singular immigrations have left revealing linguistic traces in the modern Indo-Aryan languages. Actually, this task is challenging enough, as the long-lasting controversy shows.2 Previous and present proponents of the hypothesis have tried to fix the difference between Outer and Inner Languages in terms of language geography (one graphical attempt as an example is shown below p. -
Origins of Human Language
Contents Volume 2 / 2016 Vol. Articles 2 FRANCESCO BENOZZO Origins of Human Language: 2016 Deductive Evidence for Speaking Australopithecus LOUIS-JACQUES DORAIS Wendat Ethnophilology: How a Canadian Indigenous Nation is Reviving its Language Philology JOHANNES STOBBE Written Aesthetic Experience. Philology as Recognition An International Journal MAHMOUD SALEM ELSHEIKH on the Evolution of Languages, Cultures and Texts The Arabic Sources of Rāzī’s Al-Manṣūrī fī ’ṭ-ṭibb MAURIZIO ASCARI Philology of Conceptualization: Geometry and the Secularization of the Early Modern Imagination KALEIGH JOY BANGOR Philological Investigations: Hannah Arendt’s Berichte on Eichmann in Jerusalem MIGUEL CASAS GÓMEZ From Philology to Linguistics: The Influence of Saussure in the Development of Semantics CARMEN VARO VARO Beyond the Opposites: Philological and Cognitive Aspects of Linguistic Polarization LORENZO MANTOVANI Philology and Toponymy. Commons, Place Names and Collective Memories in the Rural Landscape of Emilia Discussions ROMAIN JALABERT – FEDERICO TARRAGONI Philology Philologie et révolution Crossings SUMAN GUPTA Philology of the Contemporary World: On Storying the Financial Crisis Review Article EPHRAIM NISSAN Lexical Remarks Prompted by A Smyrneika Lexicon, a Trove for Contact Linguistics Reviews SUMAN GUPTA Philology and Global English Studies: Retracings (Maurizio Ascari) ALBERT DEROLEZ The Making and Meaning of the Liber Floridus: A Study of the Original Manuscript (Ephraim Nissan) MARC MICHAEL EPSTEIN (ED.) Skies of Parchment, Seas of Ink: Jewish Illuminated Manuscripts (Ephraim Nissan) Peter Lang Vol. 2/2016 CONSTANCE CLASSEN The Deepest Sense: A Cultural History of Touch (Ephraim Nissan) Contents Volume 2 / 2016 Vol. Articles 2 FRANCESCO BENOZZO Origins of Human Language: 2016 Deductive Evidence for Speaking Australopithecus LOUIS-JACQUES DORAIS Wendat Ethnophilology: How a Canadian Indigenous Nation is Reviving its Language Philology JOHANNES STOBBE Written Aesthetic Experience. -
The Shape of Phylogenetic Trees (Review Paper)
REVIEW PAPER: THE SHAPE OF PHYLOGENETIC TREESPACE KATHERINE ST. JOHN Abstract: Trees are a canonical structure for representing evolutionary histories. Many popular criteria used to infer optimal trees are computationally hard, and the number of possible tree shapes grows super-exponentially in the number of taxa. The underlying structure of the spaces of trees yields rich insights that can improve the search for optimal trees, both in accuracy and running time, and the analysis and visualization of results. We review the past work on analyzing and comparing trees by their shape as well as recent work that incorporates trees with weighted branch lengths. Keywords: tree metrics, treespace, maximum parsimony, maximum likelihood. Tree structures have long been used to represent the evolutionary histories of sets of species. For example, the tips of the trees represent extant species and the internal nodes represent speciation events. Despite its simplicity, the tree model captures much of the complexity of the underlying phenomena. However, the sheer number of possibilities forces many simply presented operations on trees to be computationally hard. For example, the maximum parsimony criteria (Farris, 1970; Fitch, 1971) that seeks the tree with the minimal number of changes across the edges is compu- tationally hard to compute exactly (Foulds and Graham, 1982). The addition of weights on the branches, to denote quantities such as amount of evolutionary change, the time, or the confidence on the existence of the branch, adds complexity to the model (Felsenstein, 1973, 1978). A pop- ular corresponding optimality criteria for weighted trees, the maximum likelihood criteria, is also computationally hard (Roch, 2006). -
Autochthonous Aryans? the Evidence from Old Indian and Iranian Texts
Michael Witzel Harvard University Autochthonous Aryans? The Evidence from Old Indian and Iranian Texts. INTRODUCTION §1. Terminology § 2. Texts § 3. Dates §4. Indo-Aryans in the RV §5. Irano-Aryans in the Avesta §6. The Indo-Iranians §7. An ''Aryan'' Race? §8. Immigration §9. Remembrance of immigration §10. Linguistic and cultural acculturation THE AUTOCHTHONOUS ARYAN THEORY § 11. The ''Aryan Invasion'' and the "Out of India" theories LANGUAGE §12. Vedic, Iranian and Indo-European §13. Absence of Indian influences in Indo-Iranian §14. Date of Indo-Aryan innovations §15. Absence of retroflexes in Iranian §16. Absence of 'Indian' words in Iranian §17. Indo-European words in Indo-Iranian; Indo-European archaisms vs. Indian innovations §18. Absence of Indian influence in Mitanni Indo-Aryan Summary: Linguistics CHRONOLOGY §19. Lack of agreement of the autochthonous theory with the historical evidence: dating of kings and teachers ARCHAEOLOGY __________________________________________ Electronic Journal of Vedic Studies 7-3 (EJVS) 2001(1-115) Autochthonous Aryans? 2 §20. Archaeology and texts §21. RV and the Indus civilization: horses and chariots §22. Absence of towns in the RV §23. Absence of wheat and rice in the RV §24. RV class society and the Indus civilization §25. The Sarasvatī and dating of the RV and the Bråhmaas §26. Harappan fire rituals? §27. Cultural continuity: pottery and the Indus script VEDIC TEXTS AND SCIENCE §28. The ''astronomical code of the RV'' §29. Astronomy: the equinoxes in ŚB §30. Astronomy: Jyotia Vedåga and the -
The Origins and the Evolution of Language Salikoko S. Mufwene
To appear in a shortened version in The Oxford Handbook of the History of Linguistics, ed. by Keith Allan. I’ll appreciate your comments on this one, because this project is going to grow into a bigger one. Please write to [email protected]. 6/10/2011. The Origins and the Evolution of Language Salikoko S. Mufwene University of Chicago Collegium de Lyon (2010-2011) 1. Introduction Although language evolution is perhaps more commonly used in linguistics than evolution of language, I stick in this essay to the latter term, which focuses more specifically on the phylogenetic emergence of language. The former, which has prompted some linguists such as Croft (2008) to speak of evolutionary linguistics,1 applies also to changes undergone by individual languages over the past 6,000 years of documentary history, including structural changes, language speciation, and language birth and death. There are certainly advantages, especially for uniformitarians, in using the broader term. For instance, one can argue that some of the same evolutionary mechanisms are involved in both the phylogenetic and the historical periods of evolution. These would include the assumption that natural selection driven by particular ecological pressures applies in both periods, and social norms emerge by the same 1 Interestingly, Hombert & Lenclud (in press) use the related French term linguistes évolutionnistes ‘evolutionary linguists’ with just the other rather specialized meaning, focusing on phylogenesis. French too makes a distinction between the more specific évolution du langage ‘evolution of language’ and the less specific évolution linguistique ‘linguistic/language evolution’. So, Croft’s term is just as non-specific as language evolution and évolution linguistique (used even by Saussure 1916). -
The Past in the Present
The Past in the Present THOMAS R. TRAUTMANN University of Michigan [email protected] Abstract: The theory-deadness of antiquity under the ideology of modernism, the theory-deadness of Asia under Eurocentrism, and the theory-deadness of the precolonial under post-colonial theory converge to hide the aliveness of ancient Indian phonological analysis in the present. This case study of the hiddenness of the past in the present leads to a consideration of how historians of the ancient world may act to illuminate the present. Faulkner has said, “The past is not dead, it is not even past.” The objective of this paper is to show, rigorously and through a par- ticular case, that the ancient past is essential to the understanding of the present, because the past lives in the present. If the argument succeeds it follows that the study of ancient history is not something that comes to an end at some date in the past, but has a continuing life in the present. It also follows that historians of the recent past cannot elucidate their field fully without the help of historians of the ancient past. It is not easy to demonstrate, because contemporary forces actively hide the continuing life of the past in the present. The hiddenness of this history is produced. There are, to be sure, areas of contemporary life whose pastness is not obscure. Everyday life contains abundant material contrivances and prac- tical routines that we know we owe to the ancestors. Learning from our parents how to button a button or tie a shoe, we set out upon a lifetime of performed routines that reenact techniques and use products of human inventiveness that we vaguely know we owe to some anonymous fore- bear, transmitted to us by an unbroken chain of teaching and performed iterations. -
Vocal Tract Influences on the Evolution of Speech and Language
Language & Communication 54 (2017) 9–20 Contents lists available at ScienceDirect Language & Communication journal homepage: www.elsevier.com/locate/langcom Language is not isolated from its wider environment: Vocal tract influences on the evolution of speech and language Dan Dediu a,b,*, Rick Janssen a, Scott R. Moisik a,c a Language and Genetics Department, Max Planck Institute for Psycholinguistics, Wundtlaan 1, Nijmegen, The Netherlands b Donders Institute for Brain, Cognition and Behaviour, Kapittelweg 29, Nijmegen, The Netherlands c Division of Linguistics and Multilingual Studies, Nanyang Technological University, 50 Nanyang Avenue, Singapore, Singapore article info abstract Article history: Language is not a purely cultural phenomenon somehow isolated from its wider envi- Available online 3 December 2016 ronment, and we may only understand its origins and evolution by seriously considering its embedding in this environment as well as its multimodal nature. By environment here Keywords: we understand other aspects of culture (such as communication technology, attitudes Biases towards language contact, etc.), of the physical environment (ultraviolet light incidence, air Language change humidity, etc.), and of the biological infrastructure for language and speech. We are spe- Linguistic diversity cifically concerned in this paper with the latter, in the form of the biases, constraints and Vocal tract Language evolution affordances that the anatomy and physiology of the vocal tract create on speech and language. In a nutshell, our argument is that (a) there is an under-appreciated amount of inter-individual variation in vocal tract (VT) anatomy and physiology, (b) variation that is non-randomly distributed across populations, and that (c) results in systematic differences in phonetics and phonology between languages. -
The Indo-Europeanization of the World from a Central Asian Homeland: New Approaches, Paradigms and Insights from Our Research Publications on Ancient India
Journal of Social Science Studies ISSN 2329-9150 2016, Vol. 3, No. 1 The Indo-Europeanization of the World from a Central Asian Homeland: New Approaches, Paradigms and Insights from Our Research Publications on Ancient India Sujay Rao Mandavilli (Corresponding author) Independent Scholar, India E-mail: [email protected] Received: August 3, 2015 Accepted: September 8, 2015 Published: September 10, 2015 doi:10.5296/jsss.v3i1.8278 URL: http://dx.doi.org/10.5296/jsss.v3i1.8278 Abstract In this paper, we bring together the concepts put forth in our previous papers and throw new light on how the Indo-Europeanization of the world may have happened from the conventional Central Asian homeland and explain the same using maps and diagrams. We also propose the ‘Ten modes of linguistic transformations associated with Human migrations.’ With this, the significance of the proposed term ‘Base Indo-European’ in lieu of the old term ‘Proto Indo-European’ will become abundantly clear to most readers. The approaches presented in this paper are somewhat superior to existing approaches, and as such are expected to replace them in the longer run. Detailed maps and notes demonstrating and explaining how linguistic transformations might have taken place in South Asia are available in this paper as understood from our previous research papers, and scholars from other parts of the world are invited to develop similar paradigms with regard to their home countries as far as the available data or evidence will allow them. This will help piece together a gigantic jig-saw puzzle, and lead to a revolution of sorts in the field, leading to a ripple-effect that will strongly impact several other related fields of study as well.