Species Tree Likelihood Computation Given SNP Data Using Ancestral Configurations
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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 -
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. -
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. -
Genetic Relationship Among Languages: an Overview Ghayeth Ersheidat1* and Hafsa Tahir2 1Department of Translation, Faculty of Arts, Yarmouk University, Irbid, Jordon
INTERNATIONAL JOURNAL OF LANGUAGE EDUCATION AND APPLIED LINGUISTICS (IJLEAL) ISSN: 2289-7208 e-ISSN: 2289-9294 VOL. 10, ISSUE 1, 17 – 27 DOI: https://doi.org/10.15282/ijleal.v10.3320 ORIGINAL ARTICLE Genetic Relationship among Languages: An Overview Ghayeth Ersheidat1* and Hafsa Tahir2 1Department of Translation, Faculty of Arts, Yarmouk University, Irbid, Jordon. 2Department of Biology, Faculty of Scence and Technology, Virtual University of Pakistan, Lahore, Pakistan. ARTICLE HISTORY ABSTRACT – This paper reviews the basic concepts of historical linguistics and the comparative Revised: 4 March 2020 techniques used by various linguists who studied Indo-European and American languages to Accepted: 9 March 2020 determine a shared ancestry among languages. This paper also evaluates the major concepts of historical linguistics and the well-grounded theories and classifications that have guided and KEYWORDS shaped the modern linguistic classification practices. For over one and a half century, historical Historical comparative-method linguists have been deducing the origins of different languages. Genetic classifications have been Historical linguistics proposed for languages from all parts of the world and thus far, 142 language-families have been Indo-European languages identified. Although all of these classification schemes are controversial in terms of their validity Language family and reliability but with the progress in the field of bioinformatics, the problems in linguistic Linguistic-tree Proto-language reconstruction have been greatly resolved. Therefore, the historical classification schemes that have been proposed earlier are being radically revised as further progress is made. It is suggested that, to develop further understanding of the typical pattern of language diversification and genetic classification of languages, more recent studies based on sophisticated bioinformatics and statistical techniques for linguistic data analysis should be reviewed. -
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). -
Theoretical Population Biology the Probability of Reciprocal Monophyly
Theoretical Population Biology 129 (2019) 133–147 Contents lists available at ScienceDirect Theoretical Population Biology journal homepage: www.elsevier.com/locate/tpb The probability of reciprocal monophyly of gene lineages in three and four species Rohan S. Mehta *, Noah A. Rosenberg Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA article info a b s t r a c t Article history: Reciprocal monophyly, a feature of a genealogy in which multiple groups of descendant lineages each Received 9 August 2017 consist of all of the descendants of their respective most recent common ancestors, has been an important Available online 3 May 2018 concept in studies of species delimitation, phylogeography, population history reconstruction, systemat- ics, and conservation. Computations involving the probability that reciprocal monophyly is observed in Keywords: a genealogy have played a key role in criteria for defining taxonomic groups and inferring divergence Coalescent times. The probability of reciprocal monophyly under a coalescent model of population divergence has Gene trees Monophyly been studied in detail for groups of gene lineages for pairs of species. Here, we extend this computation to Species trees generate corresponding probabilities for sets of gene lineages from three and four species. We study the effects of model parameters on the probability of reciprocal monophyly, finding that it is driven primarily by species tree height, with lesser but still substantial influences of internal branch lengths and sample sizes. We also provide an example application of our results to data from maize and teosinte. ' 2018 Elsevier Inc. All rights reserved. 1. Introduction a recursive formula for the probability of reciprocal monophyly for three species in a model in which the three species descend A set of gene lineages is monophyletic if all of the lineages are from a common ancestor via two sequential divergence events. -
4 the History of Linguistics
The History of Linguistics 81 4 The History of Linguistics LYLE CAMPBELL 1 Introduction Many “histories” of linguistics have been written over the last two hundred years, and since the 1970s linguistic historiography has become a specialized subfield, with conferences, professional organizations, and journals of its own. Works on the history of linguistics often had such goals as defending a particu- lar school of thought, promoting nationalism in various countries, or focuss- ing on a particular topic or subfield, for example on the history of phonetics. Histories of linguistics often copied from one another, uncritically repeating popular but inaccurate interpretations; they also tended to see the history of linguistics as continuous and cumulative, though more recently some scholars have stressed the discontinuities. Also, the history of linguistics has had to deal with the vastness of the subject matter. Early developments in linguistics were considered part of philosophy, rhetoric, logic, psychology, biology, pedagogy, poetics, and religion, making it difficult to separate the history of linguistics from intellectual history in general, and, as a consequence, work in the history of linguistics has contributed also to the general history of ideas. Still, scholars have often interpreted the past based on modern linguistic thought, distorting how matters were seen in their own time. It is not possible to understand developments in linguistics without taking into account their historical and cultural contexts. In this chapter I attempt to present an overview of the major developments in the history of linguistics, avoiding these difficulties as far as possible. 2 Grammatical Traditions A number of linguistic traditions arose in antiquity, most as responses to linguistic change and religious concerns. -
Basics for the Construction of Phylogenetic Trees
Article ID: WMC002563 ISSN 2046-1690 Basics for the Construction of Phylogenetic Trees Corresponding Author: Mr. B P Niranjan Reddy, Senior Research Fellow, School of Sciences in Biotechnology, Jiwaji University - India Submitting Author: Mr. B.P.Niranjan Reddy, Senior Research Fellow, School of Sciences in Biotechnology, Jiwaji University - India Article ID: WMC002563 Article Type: Review articles Submitted on:03-Dec-2011, 11:47:15 AM GMT Published on: 03-Dec-2011, 08:06:40 PM GMT Article URL: http://www.webmedcentral.com/article_view/2563 Subject Categories:BIOLOGY Keywords:Phylogenetic tree, Model selection, Bootstrapping, Phylogeny free software How to cite the article:Niranjan Reddy B P. Basics for the Construction of Phylogenetic Trees . WebmedCentral BIOLOGY 2011;2(12):WMC002563 Source(s) of Funding: None Competing Interests: None Additional Files: Links to some very useful web pages for phylogenet WebmedCentral > Review articles Page 1 of 11 WMC002563 Downloaded from http://www.webmedcentral.com on 05-Dec-2011, 05:19:58 AM Basics for the Construction of Phylogenetic Trees Author(s): Niranjan Reddy B P Abstract the genes into various classes like orthologs, paralogs, in- or out-paralogs, to understand the evolution of the new functions through duplications, horizontal gene transfers, gene conversion, recombination, and Phylogeny- A Diagram for Evolutionary Network-is co-evolution etc. (Hafner and Nadler, 1988; Nei, 2003; used to infer the phylogenetic relationships among the Pagel, 2000). Phylogenetic analysis provides a species or genes. The phylogenetic analysis including powerful tool for comparative genomics (Pagel, 2000). morphological, biological, and bionomic characters, Genome sequencing projects are providing valuable allozyme, RFLP data have been extensively used to sequence information that is widely used to infer the infer the evolutionary relationship among the species evolutionary relationship between different species or during the pre-genomic era.