Genetic Classification and Language Contact Michael Noonan University of Wisconsin-Milwaukee 1
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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. -
Indo-European: History, Families & Origins
Indo-European: History, Families & Origins 1 Historical Linguistics Early observations pointed to language relatedness: The Sanscrit language, whatever by its antiquity, is of a wonderful structure; more perfect than the Greek, more copious than the Latin, and more exquisitely refined than either, yet bearing to both of them a stronger affinity, both in the roots of verbs and in the forms of grammar, than could possibly have been produced by accident; so strong indeed, that no philologer could examine them all three, without believing them to have sprung from some common source, which, perhaps, no longer exists .... Sir William Jones -- Presidential Discourse at the February 2, 1786 meeting of the Asiatic Society 2 Darwin & Historical Linguistics Darwin's On The Origin of Species published in 1859 German biologist Ernst Haeckel persuades his friend - philologist August Schleicher, to read it Schleicher (and generations of historical linguists) apply evolutionary principle to comparative/historical linguistics 3 Test The Methodology Ferdinand de Saussure (1857-1913) used the comparative method to predict that a certain group of sounds had to have existed in Indo-European 20 years later, when Hittite texts were discovered, Saussure's laryngeals were attested! 4 Indo-European Family 5 Indo-European Homeland 6 Family Branching 7 Earliest Attestation of IE Daughter Languages Anatolian 17th c. B.C.E Indo-Aryan (Sanskrit) 15th c. B.C.E Greek 13th c. B.C.E. Iranian (Avestan / Old Persian) 7th c. B.C.E / 6th c. B.C.E. Italic 6th c. B.C.E Tocharian 6th c. B.C.E Germanic 1st c. -
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. -
Indo-European Linguistics: an Introduction Indo-European Linguistics an Introduction
This page intentionally left blank Indo-European Linguistics The Indo-European language family comprises several hun- dred languages and dialects, including most of those spoken in Europe, and south, south-west and central Asia. Spoken by an estimated 3 billion people, it has the largest number of native speakers in the world today. This textbook provides an accessible introduction to the study of the Indo-European proto-language. It clearly sets out the methods for relating the languages to one another, presents an engaging discussion of the current debates and controversies concerning their clas- sification, and offers sample problems and suggestions for how to solve them. Complete with a comprehensive glossary, almost 100 tables in which language data and examples are clearly laid out, suggestions for further reading, discussion points and a range of exercises, this text will be an essential toolkit for all those studying historical linguistics, language typology and the Indo-European proto-language for the first time. james clackson is Senior Lecturer in the Faculty of Classics, University of Cambridge, and is Fellow and Direc- tor of Studies, Jesus College, University of Cambridge. His previous books include The Linguistic Relationship between Armenian and Greek (1994) and Indo-European Word For- mation (co-edited with Birgit Anette Olson, 2004). CAMBRIDGE TEXTBOOKS IN LINGUISTICS General editors: p. austin, j. bresnan, b. comrie, s. crain, w. dressler, c. ewen, r. lass, d. lightfoot, k. rice, i. roberts, s. romaine, n. v. smith Indo-European Linguistics An Introduction In this series: j. allwood, l.-g. anderson and o.¨ dahl Logic in Linguistics d. -
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. -
Languages of the World--Native America
REPOR TRESUMES ED 010 352 46 LANGUAGES OF THE WORLD-NATIVE AMERICA FASCICLE ONE. BY- VOEGELIN, C. F. VOEGELIN, FLORENCE N. INDIANA UNIV., BLOOMINGTON REPORT NUMBER NDEA-VI-63-5 PUB DATE JUN64 CONTRACT MC-SAE-9486 EDRS PRICENF-$0.27 HC-C6.20 155P. ANTHROPOLOGICAL LINGUISTICS, 6(6)/1-149, JUNE 1964 DESCRIPTORS- *AMERICAN INDIAN LANGUAGES, *LANGUAGES, BLOOMINGTON, INDIANA, ARCHIVES OF LANGUAGES OF THE WORLD THE NATIVE LANGUAGES AND DIALECTS OF THE NEW WORLD"ARE DISCUSSED.PROVIDED ARE COMPREHENSIVE LISTINGS AND DESCRIPTIONS OF THE LANGUAGES OF AMERICAN INDIANSNORTH OF MEXICO ANDOF THOSE ABORIGINAL TO LATIN AMERICA..(THIS REPOR4 IS PART OF A SEkIES, ED 010 350 TO ED 010 367.)(JK) $. DEPARTMENT OF HEALTH,EDUCATION nib Office ofEduc.442n MD WELNicitt weenment Lasbeenreproduced a l l e a l O exactly r o n o odianeting es receivromed f the Sabi donot rfrocestarity it. Pondsof viewor position raimentofficial opinions or pritcy. Offkce ofEducation rithrppologicalLinguistics Volume 6 Number 6 ,Tune 1964 LANGUAGES OF TEM'WORLD: NATIVE AMER/CAFASCICLEN. A Publication of this ARC IVES OF LANGUAGESor 111-E w oRLD Anthropology Doparignont Indiana, University ANTHROPOLOGICAL LINGUISTICS is designed primarily, butnot exclusively, for the immediate publication of data-oriented papers for which attestation is available in the form oftape recordings on deposit in the Archives of Languages of the World. This does not imply that contributors will bere- stricted to scholars working in the Archives at Indiana University; in fact,one motivation for the publication -
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 -
RJSSER ISSN 2707-9015 (ISSN-L) Research Journal of Social DOI: Sciences & Economics Review ______
Research Journal of Social Sciences & Economics Review Vol. 1, Issue 4, 2020 (October – December) ISSN 2707-9023 (online), ISSN 2707-9015 (Print) RJSSER ISSN 2707-9015 (ISSN-L) Research Journal of Social DOI: https://doi.org/10.36902/rjsser-vol1-iss4-2020(225-232) Sciences & Economics Review ____________________________________________________________________________________ Urdubic as a Lingua Franca in the Arab Countries of the Persian Gulf * Dr. Riaz Hussain, Head ** Dr. Muhamad Asif, Head *** Dr. Muhammad Din __________________________________________________________________________________ Abstract A new lingua franca, Urdubic, is emerging in the Arab countries of the Persian Gulf. Its linguistic composition is defined by the reduced and simplified forms of Arabic and Urdu. The paper examines linguistic, social, and historical aspects of its sociolinguistic make-up. Recurrent patterns of mutual migration between Arabs and Indians have played a pivotal role in the development of this lingua franca. Today, it appears to permeate the very homes of the Arabs. The examples of linguistic features (combinations of Urdu and Arabic) of the pidgin mentioned in the current study show that Urban Arabic is accepting foreign influences. This influx of foreign languages has alarmed those Arabs who want to preserve the purity of Arabic. How long Urdubic is going to survive amid Arabs’ efforts to save Arabic from such foreign influences? The paper concludes with speculations about the future of Urdubic. Keywords: Pidgins, creoles, Persian Gulf, Arabic, Urdu Introduction Change is an integral part of life. There are changes in human society that are noticed at the time of occurrences such as economic reforms and sudden political changes. But, there are finer changes regarding human linguistic behavior that may occur as a result of large-scale social, economic, and political changes and may be noticed only after years of latent development. -
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. -
Disharmonic Headedness in Early Indo-European
Disharmonic headedness in early Indo-European Innovative reconstruction: disharmonic headedness in early Indo-European Ryan Hearn Cornell University [email protected] June 19, 2018 DiGS 20 Disharmonic headedness in early Indo-European Overview Main goals Main goals 1. Define \parallel syntactic innovation" for the purposes of this paper I Establish parallel syntactic innovation as a reliable basis for syntactic reconstruction 2. Examine complementizer development across the early Indo-European (IE) languages I Reconstruct a left-headed CP domain for Proto-Indo-European (PIE) 3. Examine auxiliary construction development across the early IE languages, especially Tocharian and ancient Greek I Reconstruct a right-headed TP domain for PIE Disharmonic headedness in early Indo-European Parallel Syntactic Innovation Syntactic Reconstruction I Historically, syntactic reconstruction worked very similarly to phonological/morphological reconstruction I Set up correspondence sets of either exact phrases, or of general word order I Now, generative syntax greatly constrains the possible structures we generate I This allows us to go a step further, and reconstruct the structure underlying our word orders I So, not only can we reconstruct the phonological form of function words, but also the features of their functional heads Disharmonic headedness in early Indo-European Parallel Syntactic Innovation But, what if a given function word is not reconstructible for the proto-language? I What if the words that fill a functional role aren't cognate I Or, what