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《International Symposium》 Let's Talk About Trees National Museum
《International Symposium》 Let’s Talk about Trees National Museum of Ethnology, Osaka, Japan. February 10, 2013 Abstract [Austronesian Language Case Studies 2] Limitations of the tree model: A case study from North Vanuatu Siva KALYAN1 and Alexandre FRANÇOIS2 1. Northumbria University 2. CNRS/LACITO Since the beginnings of historical linguistics, the family tree has been the most widely accepted model for representing historical relations between languages. It is even being reinvigorated by current research in computational phylogenetics (e.g. Gray et al. 2009). While this sort of representation is certainly easy to grasp, and allows for a simple, attractive account of the development of a language family, the assumptions made by the tree model are applicable in only a small number of cases. The tree model is appropriate when a speaker population undergoes successive splits, with subsequent loss of contact among subgroups. For all other scenarios, it fails to provide an accurate representation of language history (cf. Durie & Ross 1996; Pawley 1999; Heggarty et al. 2010). In particular, it is unable to deal with dialect continua, as well as language families that develop out of dialect continua (for which Ross 1988 has proposed the term "linkage"). In such cases, the scopes of innovations (in other words, their isoglosses) are not nested, but rather they persistently intersect, so that any proposed tree representation is met with abundant counterexamples. Though Ross's initial observations about linkages concerned the languages of Western Melanesia, it is clear that linkages are found in many other areas as well (such as Fiji: cf. Geraghty 1983). In this presentation, we focus on the 17 languages of the Torres and Banks islands in Vanuatu, which form a linkage (Tryon 1996, François 2011), and attempt to develop adequate representations for it. -
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. -
Philological Sciences. Linguistics” / Journal of Language Relationship Issue 3 (2010)
Российский государственный гуманитарный университет Russian State University for the Humanities RGGU BULLETIN № 5/10 Scientific Journal Series “Philological Sciences. Linguistics” / Journal of Language Relationship Issue 3 (2010) Moscow 2010 ВЕСТНИК РГГУ № 5/10 Научный журнал Серия «Филологические науки. Языкознание» / «Вопросы языкового родства» Выпуск 3 (2010) Москва 2010 УДК 81(05) ББК 81я5 Главный редактор Е.И. Пивовар Заместитель главного редактора Д.П. Бак Ответственный секретарь Б.Г. Власов Главный художник В.В. Сурков Редакционный совет серии «Филологические науки. Языкознание» / «Вопросы языкового родства» Председатель Вяч. Вс. Иванов (Москва – Лос-Анджелес) М. Е. Алексеев (Москва) В. Блажек (Брно) У. Бэкстер (Анн Арбор) В. Ф. Выдрин (Санкт-Петербург) М. Гелл-Манн (Санта Фе) А. Б. Долгопольский (Хайфа) Ф. Кортландт (Лейден) А. Лубоцкий (Лейден) Редакционная коллегия серии: В. А. Дыбо (главный редактор) Г. С. Старостин (заместитель главного редактора) Т. А. Михайлова (ответственный секретарь) К. В. Бабаев С. Г. Болотов А. В. Дыбо О. А. Мудрак В. Е. Чернов ISSN 1998-6769 © Российский государственный гуманитарный университет, 2010 УДК 81(05) ББК 81я5 Вопросы языкового родства: Международный научный журнал / Рос. гос. гуманитар. ун-т; Рос. Акад. наук. Ин-т языкознания; под ред. В. А. Дыбо. ― М., 2010. ― № 3. ― X + 176 с. ― (Вестник РГГУ: Научный журнал; Серия «Филологические науки. Языко- знание»; № 05/10). Journal of Language Relationship: International Scientific Periodical / Russian State Uni- versity for the Humanities; Russian Academy of Sciences. Institute of Linguistics; Ed. by V. A. Dybo. ― Moscow, 2010. ― Nº 3. ― X + 176 p. ― (RSUH Bulletin: Scientific Periodical; Linguistics Series; Nº 05/10). ISSN 1998-6769 http ://journal.nostratic.ru [email protected] Дополнительные знаки: С. -
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. -
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 -
UC Berkeley UC Berkeley Electronic Theses and Dissertations
UC Berkeley UC Berkeley Electronic Theses and Dissertations Title Iranian Dialectology and Dialectometry Permalink https://escholarship.org/uc/item/5pv6f9g9 Author Cathcart, Chundra Aroor Publication Date 2015 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California Iranian Dialectology and Dialectometry By Chundra Aroor Cathcart A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Linguistics in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Andrew J. Garrett, Chair Professor Gary B. Holland Professor Martin Schwartz Spring 2015 Abstract Studies in Iranian Dialectology and Dialectometry by Chundra Aroor Cathcart Doctor of Philosophy in Linguistics University of California, Berkeley Professor Andrew Garrett, Chair This dissertation investigates the forces at work in the formation of a tightly knit but ultimately non-genetic dialect group. The Iranian languages, a genetic sub-branch of the larger Indo-European language family, are a group whose development has been profoundly affected by millennia of internal contact. This work is concerned with aspects of the diversification and disparification (i.e., the development of different versus near-identical features across languages) of this group of languages, namely issues pertaining to the development of the so-called West Iranian group, whose status as a legitimate genetic subgroup has long remained unclear. To address the phenomena under study, I combine a traditional comparative-historical approach with existing quantitative methods as well as newly developed quantitative methods designed to deal with the sort of linguistic situation that Iranian typifies. The studies I undertake support the idea that West Iranian is not a genetic subgroup, as sometimes assumed; instead, similarities between West Iranian languages that give the impression of close genetic relatedness have come about due to interactions between contact and parallel driftlike tendencies. -
Tocharian Studies
Tocharian Studies Works 1 This book was kindly reviewed by Ronald Kim & Melanie Malzahn Václav Blažek Tocharian Studies Works 1 Edited by Michal Schwarz Masaryk University Brno 2011 IV This book was published under patronage of the Centre for the Interdiscipli- nar Research of Ancient Languages and Older Stages of Modern Languages (project code: MSM 0021622435) at Masaryk University in Brno and thanks to the grants GAAV No. IAA901640805 & MUNI/21/BLA/2011. All articles are reprinted with kind permission from following journals (in alphabetical order): Archív orientální Historische Sprachforschung Indogermanische Forschungen Journal of Indo-European Studies Lingua Posnaniensis Linguistica Baltica Linguistica Brunensia Tocharian and Indo-European Studies © 2011 Václav Blažek © 2011 Masarykova univerzita ISBN 978-80-210-7645-7 (online : pdf) ISBN 978-80-210-5600-8 (brožovaná vazba) ISBN 978-80-210-5599-5 (Box Set) DOI: 10.5817/CZ.MUNI.M210-5600-2011 V Content Preface (Melanie Malzahn) VIII Introduction and Plan of the Works of Václav Blažek X Chronological list of all Tocharian articles of Václav Blažek XII with editorial notes I. Etymology 1 Tocharian Linguistics During the Last 25 Years. Archív Ori- 2 entální 56 (1988), 77-81. Slavic-Tocharian Isoglosses I. Sl. *kъpъ : Toch. *kwip- 10 “shame”. Tocharian and Indo-European Studies 5 (1991), 123-128. Slavic-Tocharian Isoglosses II. Sl. *čьlnъ : Toch. *kolmo- 15 “ship”. Tocharian and Indo-European Studies 5 (1991), 129- 133. Slavic-Tocharian Isoglosses III. Linguistica Baltica 4 (1995), 19 233-238. Tocharian-Anatolian isoglosses (1-4). Tocharian and Indo-Eu- 25 ropean Studies 7 (1997), 229-233. It is possible to restore Tocharian A ku//// “nave, hub”? Tocha- 30 rian and Indo-European Studies 7 (1997), 234-235. -
Dissertation / Doctoral Thesis
DISSERTATION / DOCTORAL THESIS Titel der Dissertation /Title of the Doctoral Thesis „Kinship and Affinity in Indo-European: Universal, Inherited, Contact, and Area Specific Features of Indo-European Kinship Terms (with a Special Focus on the Iranian Branch)“ verfasst von / submitted by Veronika Milanova, MA angestrebter akademischer Grad / in partial fulfilment of the requirements for the degree of Doktorin der Philosophie (Dr.phil.) Wien, 2020 / Vienna 2020 Studienkennzahl lt. Studienblatt / UA 792 327 degree programme code as it appears on the student record sheet: Dissertationsgebiet lt. Studienblatt / Sprachwissenschaft field of study as it appears on the student record sheet: Betreut von / Supervisor: Univ.-Prof. Mag. Dr. Melanie Malzahn, Privatdoz. 2 Acknowledgements This dissertation is the fruit of almost six years of hard but absorbing work with ever-surprising results. The research has mostly been carried out at the University of Vienna. However, it also profited much from courses of the Leiden Summer School of Linguistics (2016), of the summer school “Roots of Europe” (2017, Copenhagen), Pavia International Summer School for Indo- European Linguistics (2017), and a research-study stay at Mondes Iranien et Indien (Paris 2019). It is not a simple task to give a full list of people to whom I should express my gratitude. I am greatly indebted to my supervisor, Professor Melanie Malzahn, for her invaluable advice and support, the right proportion of control and freedom of self-expression, endless patience and optimism throughout all these years. Further, this research would not be possible without the Doc- Stipendium of the Austrian Academy of Sciences (ÖAW) that gave me a great chance to concentrate on my work, take part in international conferences and summer schools. -
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.