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THE INDO-EUROPEAN FAMILY — the LINGUISTIC EVIDENCE by Brian D
THE INDO-EUROPEAN FAMILY — THE LINGUISTIC EVIDENCE by Brian D. Joseph, The Ohio State University 0. Introduction A stunning result of linguistic research in the 19th century was the recognition that some languages show correspondences of form that cannot be due to chance convergences, to borrowing among the languages involved, or to universal characteristics of human language, and that such correspondences therefore can only be the result of the languages in question having sprung from a common source language in the past. Such languages are said to be “related” (more specifically, “genetically related”, though “genetic” here does not have any connection to the term referring to a biological genetic relationship) and to belong to a “language family”. It can therefore be convenient to model such linguistic genetic relationships via a “family tree”, showing the genealogy of the languages claimed to be related. For example, in the model below, all the languages B through I in the tree are related as members of the same family; if they were not related, they would not all descend from the same original language A. In such a schema, A is the “proto-language”, the starting point for the family, and B, C, and D are “offspring” (often referred to as “daughter languages”); B, C, and D are thus “siblings” (often referred to as “sister languages”), and each represents a separate “branch” of the family tree. B and C, in turn, are starting points for other offspring languages, E, F, and G, and H and I, respectively. Thus B stands in the same relationship to E, F, and G as A does to B, C, and D. -
Math/C SC 5610 Computational Biology Lecture 12: Phylogenetics
Math/C SC 5610 Computational Biology Lecture 12: Phylogenetics Stephen Billups University of Colorado at Denver Math/C SC 5610Computational Biology – p.1/25 Announcements Project Guidelines and Ideas are posted. (proposal due March 8) CCB Seminar, Friday (Mar. 4) Speaker: Jack Horner, SAIC Title: Phylogenetic Methods for Characterizing the Signature of Stage I Ovarian Cancer in Serum Protein Mas Time: 11-12 (Followed by lunch) Place: Media Center, AU008 Math/C SC 5610Computational Biology – p.2/25 Outline Distance based methods for phylogenetics UPGMA WPGMA Neighbor-Joining Character based methods Maximum Likelihood Maximum Parsimony Math/C SC 5610Computational Biology – p.3/25 Review: Distance Based Clustering Methods Main Idea: Requires a distance matrix D, (defining distances between each pair of elements). Repeatedly group together closest elements. Different algorithms differ by how they treat distances between groups. UPGMA (unweighted pair group method with arithmetic mean). WPGMA (weighted pair group method with arithmetic mean). Math/C SC 5610Computational Biology – p.4/25 UPGMA 1. Initialize C to the n singleton clusters f1g; : : : ; fng. 2. Initialize dist(c; d) on C by defining dist(fig; fjg) = D(i; j): 3. Repeat n ¡ 1 times: (a) determine pair c; d of clusters in C such that dist(c; d) is minimal; define dmin = dist(c; d). (b) define new cluster e = c S d; update C = C ¡ fc; dg Sfeg. (c) define a node with label e and daughters c; d, where e has distance dmin=2 to its leaves. (d) define for all f 2 C with f 6= e, dist(c; f) + dist(d; f) dist(e; f) = dist(f; e) = : (avg. -
The Geography and History of *R-Loss in Southern Oceanic Languages Alexandre François
Where *R they all? The Geography and History of *R-loss in Southern Oceanic Languages Alexandre François To cite this version: Alexandre François. Where *R they all? The Geography and History of *R-loss in Southern Oceanic Languages. Oceanic Linguistics, University of Hawai’i Press, 2011, 50 (1), pp.140 - 197. 10.1353/ol.2011.0009. hal-01137686 HAL Id: hal-01137686 https://hal.archives-ouvertes.fr/hal-01137686 Submitted on 17 Oct 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Where *R they all? The Geography and History of *R-loss in Southern Oceanic Languages Alexandre François LANGUES ET CIVILISATIONS À TRADITION ORALE (CNRS), PARIS, AND AUSTRALIAN NATIONAL UNIVERSITY Some twenty years ago, Paul Geraghty offered a large-scale survey of the retention and loss of Proto-Oceanic *R across Eastern Oceanic languages, and concluded that *R was “lost in proportion to distance from Western Oceanic.” This paper aims at testing Geraghty’s hypothesis based on a larger body of data now available, with a primary focus on a tightly knit set of languages spoken in Vanuatu. By observing the dialectology of individual lexical items in this region, I show that the boundaries between languages retaining vs. -
Understanding the Processes Underpinning Patterns Of
Opinion Understanding the Processes Underpinning Patterns of Phylogenetic Regionalization 1,2, 3,4 1 Barnabas H. Daru, * Tammy L. Elliott, Daniel S. Park, and 5,6 T. Jonathan Davies A key step in understanding the distribution of biodiversity is the grouping of regions based on their shared elements. Historically, regionalization schemes have been largely species centric. Recently, there has been interest in incor- porating phylogenetic information into regionalization schemes. Phylogenetic regionalization can provide novel insights into the mechanisms that generate, distribute, and maintain biodiversity. We argue that four processes (dispersal limitation, extinction, speciation, and niche conservatism) underlie the forma- tion of species assemblages into phylogenetically distinct biogeographic units. We outline how it can be possible to distinguish among these processes, and identify centers of evolutionary radiation, museums of diversity, and extinction hotspots. We suggest that phylogenetic regionalization provides a rigorous and objective classification of regional diversity and enhances our knowledge of biodiversity patterns. Biogeographical Regionalization in a Phylogenetic Era 1 Department of Organismic and Biogeographical boundaries delineate the basic macrounits of diversity in biogeography, Evolutionary Biology, Harvard conservation, and macroecology. Their location and composition of species on either side of University, Cambridge, MA 02138, these boundaries can reflect the historical processes that have shaped the present-day USA th 2 Department of Plant Sciences, distribution of biodiversity [1]. During the early 19 century, de Candolle [2] created one of the University of Pretoria, Private Bag first global geographic regionalization schemes for plant diversity based on both ecological X20, Hatfield 0028, Pretoria, South and historical information. This was followed by Sclater [3], who defined six zoological regions Africa 3 Department of Biological Sciences, based on the global distribution of birds. -
A Little- Described Language of Solomon Islands
i Grammatical Relations and Syntactic Ergativity in Roviana: A little- described language of Solomon Islands A DISSERATION TO THE GRADUATE DIVISION OF THE UNIVERSITY OF HAWAI‘I AT MĀNOA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR IN PHILOSOPHY IN LINGUISTICS MAY 2020 by Peter Schuelke Dissertation Committee: William O’Grady, Chairperson Andrea Berez-Kroeker Robert Blust Bradley McDonnell Alexander Mawyer Keywords: Roviana, Ergativity, Language Documentation ii Acknowledgements I would like to start by thanking the Roviana language community for their support and friendship, I could not have done this without you. There are too many people to thank everyone individually, but there are a few people I must mention by name. Frank Tuke was my first Roviana friend and he eventually became my collaborator in linguistics. Glo Oxenham is my teacher and friend and she, along with her friends and family in Wellington NZ, have continually supported this work. I would like to also thank the whole Tuke family, the Tolavae community, Gizo community, Munda community, Rarumana community, and my friends in Honiara. Leana hola koa gamu doduru. I would like to thank my mentor Al Schutz who taught me about academic writing and was even the last proofreader of this very dissertation. Not only that, Al taught me so much about Pacific linguistics, descriptive linguistics, and friendship. I would like to thank my best friend Alex D. Smith. Alex has been my biggest supporter from the very beginning. He proofread my work and provided comments on everything from my writing sample to this dissertation. He is a brilliant linguist, a loyal friend, and courageous human being. -
Molecular Phylogenetics (Hannes Luz)
Tree: minimum but fully connected (no loop, one breaks) Molecular Phylogenetics (Hannes Luz) Contents: • Phylogenetic Trees, basic notions • A character based method: Maximum Parsimony • Trees from distances • Markov Models of Sequence Evolution, Maximum Likelihood Trees References for lectures • Joseph Felsenstein, Inferring Phylogenies, Sinauer Associates (2004) • Dan Graur, Weng-Hsiun Li, Fundamentals of Molecular Evolution, Sinauer Associates • D.W. Mount. Bioinformatics: Sequences and Genome analysis, 2001. • D.L. Swofford, G.J. Olsen, P.J.Waddell & D.M. Hillis, Phylogenetic Inference, in: D.M. Hillis (ed.), Molecular Systematics, 2 ed., Sunder- land Mass., 1996. • R. Durbin, S. Eddy, A. Krogh & G. Mitchison, Biological sequence analysis, Cambridge, 1998 References for lectures, cont’d • S. Rahmann, Spezielle Methoden und Anwendungen der Statistik in der Bioinformatik (http://www.molgen.mpg.de/~rahmann/afw-rahmann. pdf) • K. Schmid, A Phylogenetic Parsimony Method Considering Neigh- bored Gaps (Bachelor thesis, FU Berlin, 2007) • Martin Vingron, Hannes Luz, Jens Stoye, Lecture notes on ’Al- gorithms for Phylogenetic Reconstructions’, http://lectures.molgen. mpg.de/Algorithmische_Bioinformatik_WS0405/phylogeny_script.pdf Recommended reading/watching • Video streams of Arndt von Haeseler’s lectures held at the Otto Warburg Summer School on Evolutionary Genomics 2006 (http: //ows.molgen.mpg.de/2006/von_haeseler.shtml) • Dirk Metzler, Algorithmen und Modelle der Bioinformatik, http://www. cs.uni-frankfurt.de/~metzler/WS0708/skriptWS0708.pdf Software links • Felsenstein’s list of software packages: http://evolution.genetics.washington.edu/phylip/software.html • PHYLIP is Felsenstein’s free software package for inferring phyloge- nies, http://evolution.genetics.washington.edu/phylip.html • Webinterface for PHYLIP maintained at Institute Pasteur, http://bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html • Puzzle (Strimmer, v. -
Trees, Waves and Linkages: Models of Language Diversification Alexandre François
Trees, Waves and Linkages: Models of Language Diversification Alexandre François To cite this version: Alexandre François. Trees, Waves and Linkages: Models of Language Diversification. Bowern, Claire; Evans, Bethwyn. The Routledge Handbook of Historical Linguistics, Routledge, pp.161-189, 2014, 978-0-41552-789-7. 10.4324/9781315794013.ch6. halshs-00874726v2 HAL Id: halshs-00874726 https://halshs.archives-ouvertes.fr/halshs-00874726v2 Submitted on 19 Mar 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. The Routledge Handbook of Historical Linguistics Edited by Claire Bowern and Bethwyn Evans RH of Historical Linguistics BOOK.indb iii 3/26/2014 1:20:21 PM 6 Trees, waves and linkages Models of language diversifi cation Alexandre François 1 On the diversifi cation of languages 1.1 Language extinction, language emergence The number of languages spoken on the planet has oscillated up and down throughout the history of mankind.1 Different social factors operate in opposite ways, some resulting in the decrease of language diversity, others favouring the emergence of new languages. Thus, languages fade away and disappear when their speakers undergo some pressure towards abandoning their heritage language and replacing it in all contexts with a new language that is in some way more socially prominent (Simpson, this volume). -
The East Papuan Languages: a Preliminary Typological Appraisal
7KH(DVW3DSXDQ/DQJXDJHV$3UHOLPLQDU\7\SRORJLFDO 0LFKDHO'XQQ*HU35HHVLQN$QJHOD7HUULOO$SSUDLVDO Oceanic Linguistics, Volume 41, Number 1, June 2002, pp. 28-62 (Article) 3XEOLVKHGE\8QLYHUVLW\RI+DZDL L3UHVV DOI: 10.1353/ol.2002.0019 For additional information about this article http://muse.jhu.edu/journals/ol/summary/v041/41.1dunn.html Access provided by Max Planck Digital Library (18 Feb 2016 13:04 GMT) The East Papuan Languages: A Preliminary Typological Appraisal Michael Dunn max planck institute for psycholinguistics, nijmegen Ger Reesink university of leiden and max planck institute for psycholinguistics, nijmegen Angela Terrill australia national university This paper examines the Papuan languages of Island Melanesia, with a view to considering their typological similarities and differences. The East Papuan lan- guages are thought to be the descendants of the languages spoken by the original inhabitants of Island Melanesia, who arrived in the area up to 50,000 years ago. The Oceanic Austronesian languages are thought to have come into the area with the Lapita peoples 3,500 years ago. With this historical backdrop in view, our paper seeks to investigate the linguistic relationships between the scattered Papuan lan- guages of Island Melanesia. To do this, we survey various structural features, including syntactic patterns such as constituent order in clauses and noun phrases and other features of clause structure, paradigmatic structures of pronouns, and the structure of verbal morphology. In particular, we seek to discern similarities between the languages that might call for closer investigation, with a view to estab- lishing genetic relatedness between some or all of the languages. In addition, in examining structural relationships between languages, we aim to discover whether it is possible to distinguish between original Papuan elements and diffused Austro- nesian elements of these languages. -
5 Computational Methods and Tools Introductory Remarks by the Chapter Editor, Joris Van Zundert
5 Computational methods and tools Introductory remarks by the chapter editor, Joris van Zundert This chapter may well be the hardest in the book for those that are not all that computationally, mathematically, or especially graph-theoretically inclined. Textual scholars often take to text almost naturally but have a harder time grasping, let alone liking, mathematics. A scholar of history or texts may well go through decades of a career without encountering any maths beyond the basic schooling in arith- metic, algebra, and probability calculation that comes with general education. But, as digital techniques and computational methods progressed and developed, it tran- spired that this field of maths and digital computation had some bearing on textual scholarship too. Armin Hoenen, in section 5.1, introduces us to the early history of computational stemmatology, depicting its early beginnings in the 1950s and point- ing out some even earlier roots. The strong influence of phylogenetics and bioinfor- matics in the 1990s is recounted, and their most important concepts are introduced. At the same time, Hoenen warns us of the potential misunderstandings that may arise from the influx of these new methods into stemmatology. The historical over- view ends with current and new developments, among them the creation of artificial traditions for validation purposes, which is actually a venture with surprisingly old roots. Hoenen’s history shows how a branch of computational stemmatics was added to the field of textual scholarship. Basically, both textual and phylogenetic theory showed that computation could be applied to the problems of genealogy of both textual traditions and biological evolution. -
The Anâtaxis Phylogenetic Reconstruction Algorithm
U´ G` F´ Departement´ d’informatique Professeur Bastien Chopard Institut Suisse de Bioinformatique Dr Gabriel Bittar The Anataxisˆ phylogenetic reconstruction algorithm THESE` present´ ee´ a` la Faculte´ des sciences de l’Universite´ de Geneve` pour obtenir le grade de Docteur es` sciences, mention bioinformatique par Bernhard Pascal Sonderegger de Heiden (AR) These` No 3863 Geneve` Atelier d’impression de la Section de Physique 2007 FACULTE´ DES SCIENCES Doctorat es` Sciences mention bioinformatique These` de Monsieur Bernhard SONDEREGGER Intitulee:´ The Anataxisˆ phylogenetic reconstruction algorithm La faculte´ des sciences, sur le preavis´ de Messieurs B. CHOPARD, professeur ad- joint et directeur de these` (Departement´ d’ informatique), G. Bittar, Docteur et co- directeur de these` (Institut Suisse de Bioinformatique, Geneve,` Suisse), A. BAIROCH, professeur adjoint (Faculte´ de medecine,´ Section de medecine´ fon- dementale, Departement´ de biologie structurale et bioinformatique) et N. SALAMIN, docteur (Universite´ de Lausanne, Faculte´ de biologie et de mede- cine Departement´ d’ecologie´ et evolution,´ Lausanne, Suisse), autorise l’impression de la presente´ these,` sans exprimer d’opinion sur les propositions qui y sont enonc´ ees.´ Geneve,` le 26.06.2007 Th`ese-3863- Le Doyen, Pierre SPIERER Contents Contents i Remerciements 1 Preface 1 R´esum´een franc¸ais 5 Introduction a` la phylogen´ etique´ ....................... 5 L’algorithme Anataxisˆ ............................. 8 Calcul de dissimilitudes ............................ 11 Validation numerique´ .............................. 11 Implementation´ ................................. 12 Exemple biologique ............................... 13 Conclusion .................................... 14 1 An introduction to phylogenetics 17 1.1 Homology and homoplasy ........................ 18 1.1.1 Characters and their states .................... 18 1.1.2 Homology is a phylogenetic hypothesis ............ 20 1.1.3 Homoplasy, a pitfall in phylogenetics ............ -
Myth of the Caucasian Sprachbund: the Case of Ergativity
The myth of the Caucasian Sprachbund: The case of ergativity. Kevin Tuite, Université de Montréal and ANU Research Centre for Linguistic Typology Département d’anthropologie Université de Montréal Case postale 6128, Succursale centre-ville Montréal, Québec H3C 3J7, Canada [email protected] 1. Introduction. The study of linguistic areas, or “Sprachbünde”, owes a great deal to the important research of Murray B. Emeneau on the geographical distribution of linguistic features among the languages of India and its neighboring countries. In the introduction he wrote to a collection of his essays, Emeneau observes, with deserved pride, that his work has “introduced the Indian linguistic area … as a worthy partner of the Balkans or the Caucasus” (Emeneau, 1980). I hope that the distinguished Sankritist and Dravidologist will not take it amiss if I use a quotation from his writings to introduce a paper in which I will argue that the Caucasus, whatever it might be in geolinguistic terms, is not a Sprachbund like the Balkans or, for that matter, the Indian subcontinent. 1.1. Trubetzkoy on Sprachbünde. The term Sprachbund was introduced to the linguistic world seventy years ago (although it had appeared in a tract on cultural themes by Trubetzkoy five years earlier (Toman, 1995: 204)), on the occasion of the 1st International Congress of Linguists in April 1928. At a session devoted to the “Établissement et délimination des termes techniques”, the phonologist Nikolai Trubetzkoy proposed that, in order avoid “Missverständnisse und Fehler” in the classification of languages, a distinction be made between Sprachfamilien and Sprachbünde: Gruppen, bestehend aus Sprachen, die eine große Ähnlichkeit in syntaktischer Hinsicht; eine Ähnlichkeit in den Grundsätzen des morphologischen Baues aufweisen; und eine große Anzahl gemeinsamer Kulturwörter bieten, manchmal auch äussere Ähnlichkeit im Bestande der Lautsystem, — dabei aber keine systematischen Lautentsprechungen, Myth of the Caucasian Sprachbund (K. -
Phylogeography and Molecular Systematics of Species Complexes in the Genus Genetta (Carnivora, Viverridae)
Phylogeography and Molecular Systematics of Species Complexes in the Genus Genetta (Carnivora, Viverridae) Carlos Alberto Rodrigues Fernandes A thesis submitted to the School of Biosciences, Cardiff University, Cardiff for the degree of Doctor of Philosophy Cardiff University School of Biosciences 2004 UMI Number: U584656 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. Dissertation Publishing UMI U584656 Published by ProQuest LLC 2013. Copyright in the Dissertation held by the Author. Microform Edition © ProQuest LLC. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 I declare that I conducted the work in this thesis, that I have composed this thesis, that all quotations and sources of information have been acknowledged and that this work has not previously been accepted in an application for a degree. Carlos A. R. Fernandes Abstract The main aim of this study was to estimate phylogeographic patterns from mitochondrial DNA diversity and relate them with evolutionary structure in two species complexes of genets, Genetta genetta and Genetta “rubiginosa ”, which have fluid morphological variation. Both are widely distributed in sub-Saharan Africa but whereas G. “rubiginosa ” appears in both closed and open habitats, G. genetta is absent from the rainforest and occurs also in the Maghreb, southwest Europe, and Arabia.