Cover not available
Article published In:
Understanding language genealogy: Alternatives to the tree model
Edited by Siva Kalyan, Alexandre François and Harald Hammarström
[Journal of Historical Linguistics 9:1] 2019
► pp. 9–69

Detecting non-tree-like signal using multiple tree topologies

| University of Reading | Max Planck Institute for the Science of Human History

Recent applications of phylogenetic methods to historical linguistics have been criticized for assuming a tree structure in which ancestral languages differentiate and split up into daughter languages, while language evolution is inherently non-tree-like (François 2014; Blench 2015: 32–33). This article attempts to contribute to this debate by discussing the use of the multiple topologies method (Pagel & Meade 2006a) implemented in BayesPhylogenies (Pagel & Meade 2004). This method is applied to lexical datasets from four different language families: Austronesian (Gray, Drummond & Greenhill 2009), Sinitic (Ben Hamed & Wang 2006), Indo-European (Bouckaert et al. 2012), and Japonic (Lee & Hasegawa 2011). Evidence for multiple topologies is found in all families except, surprisingly, Austronesian. It is suggested that reticulation may arise from a number of processes, including dialect chain break-up, borrowing (both shortly after language splits and later on), incomplete lineage sorting, and characteristics of lexical datasets. It is shown that the multiple topologies method is a useful tool to study the dynamics of language evolution.

Keywords: Bayesian phylogenetic inference, Austronesian, Sinitic, Indo-European, Japonic, language contact, reticulation
Article outline
  • 1.Introduction
  • 2.Reticulation in language and culture
  • 3.Multiple tree topologies
  • 4.Results
    • 4.1Austronesian
    • 4.2Indo-European
    • 4.3Japonic
    • 4.4Sinitic
  • 5.Discussion
  • 6.Conclusion
  • Acknowledgements
  • Note
  • References
Published online: 2 July 2019
DOI logo
https://doi.org/10.1075/jhl.17009.ver
References
Algeo, John & Thomas Pyles
2005 The Origins and Development of the English Language (Sixth Edition). Boston: Wadsworth.Google Scholar
Atkinson, Quentin D. & Russell D. Gray
2005 Curious Parallels and Curious Connections: Phylogenetic Thinking in Biology and Historical Linguistics. Systematic Biology 54:4.513–526. DOI logoGoogle Scholar
Beekes, Robert S. P.
2011 Comparative Indo-European Linguistics: An Introduction (Second Edition). Amsterdam: John Benjamins. DOI logoGoogle Scholar
Ben Hamed, Mahé & Feng Wang
2006 Stuck in the Forest: Trees, Networks, and Chinese Dialects. Diachronica 23:1.29–60. DOI logoGoogle Scholar
Blench, Roger
2015 “New Mathematical Methods” in Linguistics Constitute the Greatest Intellectual Fraud in the Discipline Since Chomsky. Talk presented at the Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.
Bouchard-Côté, Alexandre, David Hall, Thomas L. Griffiths & Dan Klein
2013 Automated Reconstruction of Ancient Languages Using Probabilistic Models of Sound Change. Proceedings of the National Academy of Sciences 110:11.4224–4229. DOI logoGoogle Scholar
Bouckaert, Remco, Philippe Lemey, Michael Dunn, Simon J. Greenhill, Alexander V. Alekseyenko, Alexei J. Drummond, Russell D. Gray, Marc A. Suchard & Quentin D. Atkinson
2012 Mapping the Origins and Expansion of the Indo-European Language Family. Science 337:6097.957–960. DOI logoGoogle Scholar
Bowern, Claire & Quentin D. Atkinson
2012 Computational Phylogenetics and the Internal Structure of Pama-Nyungan. Language 88:4.817–845. DOI logoGoogle Scholar
Bowern, Claire, Patience Epps, Russell D. Gray, Jane Hill, Keith Hunley, Patrick McConvell & Jason Zentz
2011 Does Lateral Transmission Obscure Inheritance in Hunter-Gatherer Languages? PLOS ONE 6:9.e25195. DOI logoGoogle Scholar
Bowern, Claire & Bethwyn Evans
eds. 2014 The Routledge Handbook of Historical Linguistics. London: Routledge.Google Scholar
Bryant, David & Vincent Moulton
2004 Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks. Molecular Biology and Evolution 21:2.255–265. DOI logoGoogle Scholar
Chang, Will, Chundra Cathcart, David Hall & Andrew Garrett
2015 Ancestry-Constrained Phylogenetic Analysis Supports the Indo-European Steppe Hypothesis. Language 91:1.194–244. DOI logoGoogle Scholar
Chousou-Polydouri, Natalia, Joshua Birchall, Sérgio Meira, Zachary O’Hagan & Lev Michael
2016 A Test of Coding Procedures for Lexical Data with Tupí-Guaraní and Chapacuran Languages. Proceedings of the Leiden Workshop on Capturing Phylogenetic Algorithms for Linguistics ed. by Christian Bentz, Gerhard Jäger & Igor Yanovich. Tübingen: University of Tübingen. Available at [URL]
Collard, Mark, Stephen J. Shennan & Jamshid J. Tehrani
2006 Branching, Blending, and the Evolution of Cultural Similarities and Differences Among Human Populations. Evolution and Human Behavior 27:3.169–184. DOI logoGoogle Scholar
Croft, William
2008 Evolutionary Linguistics. Annual Review of Anthropology 371.219–234. DOI logoGoogle Scholar
Drummond, Alexei J. & Remco R. Bouckaert
2015 Bayesian Evolutionary Analysis with BEAST. Cambridge: Cambridge University Press. DOI logoGoogle Scholar
Dunn, Michael
2014 Language Phylogenies. In Claire Bowern & Bethwyn Evans, eds., 190–211. London: Routledge.Google Scholar
2014 Indo-European Lexical Cognate Data. Zenodo. Available at DOI logoGoogle Scholar
Dunn, Michael, Simon J. Greenhill, Stephen C. Levinson & Russell D. Gray
2011 Evolved Structure of Language Shows Lineage-Specific Trends in Word-Order Universals. Nature 4731.79–82. DOI logoGoogle Scholar
Dyen, Isidore, Joseph B. Kruskal & Paul Black
1992 An Indo-European Classification: A Lexicostatistical Experiment. Transactions of the American Philosophical Society 821.1–132. DOI logoGoogle Scholar
Edwards, Anthony W. F. & Luigi Luca Cavalli-Sforza
1964 Reconstruction of Evolutionary Trees. Phenetic and Phylogenetic Classification ed. by V. H. Heywood & J. McNeill, 67–76. London: Systematics Association.Google Scholar
Eska, Joseph F. & Don Ringe
2004 Recent Work in Computational Linguistic Phylogeny. Language 80:3.569–582. DOI logoGoogle Scholar
Forster, Peter & Colin Renfrew
eds. 2006 Phylogenetic Methods and the Prehistory of Languages. Cambridge: McDonald Institute Monographs.Google Scholar
François, Alexandre
2014 Trees, Waves, and Linkages: Models of Language Diversification. In Claire Bowern & Bethwyn Evans, eds., 161–189.Google Scholar
Kalyan, Siva & Alexandre François
2018 Freeing the Comparative Method from the Tree Model: A Framework for Historical Glottometry. In Ritsuko Kikusawa & Lawrence Reid (eds.), Let’s talk about trees: Genetic Relationships of Languages and Their Phylogenic Representation (Senri Ethnological Studies, 98). Ōsaka: National Museum of Ethnology. 59–89.Google Scholar
Galucio, Ana Vilacy, Sérgio Meira, Joshua Birchall, Denny Moore, Nilson Gabas Júnior, Sebastian Drude, Luciana Storto, Gessiane Picançio & Carmen Reis Rodrigues
2015 Genealogical Relations and Lexical Distances Within the Tupian Linguistic Family. Boletim do Museu Paraense Emílio Goeldi, Ciências Humanas 10:2.229–274. DOI logoGoogle Scholar
Geisler, Hans & Johann-Mattis List
2013 Do Languages Grow on Trees? The Tree Metaphor in the History of Linguistics. Classification and Evolution in Biology, Linguistics and the History of Science: Concepts – Methods – Visualization ed. by Heiner Fangerau, Hans Geisler, Thorsten Halling & William Martin, 111–124. Stuttgart: Franz Steiner Verlag.Google Scholar
Gray, Russell D., David Bryant & Simon J. Greenhill
2010 On the Shape and Fabric of Human History. Philosophical Transactions of the Royal Society B 365:1559.3923–3933. DOI logoGoogle Scholar
Gray, Russell D., Simon J. Greenhill & Robert M. Ross
2007 The Pleasures and Perils of Darwinizing Culture (With Phylogenies). Biological Theory 2:4.360–375. DOI logoGoogle Scholar
Gray, Russell D. & Fiona M. Jordan
2000 Language Trees Support the Express-Train Sequence of Austronesian Expansion. Nature 4051.1052–1055. DOI logoGoogle Scholar
Gray, Russell D., Alexei J. Drummond & Simon J. Greenhill
2009 Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement. Science 323:5913.479–483. DOI logoGoogle Scholar
Greenhill, Simon J., Thomas E. Currie & Russell D. Gray
2009 Does Horizontal Transmission Invalidate Cultural Phylogenies? Proceedings of the Royal Society B 2761.2299–2306. DOI logoGoogle Scholar
Grollemund, Rebecca, Simon Branford, Koen Bostoen, Andrew Meade, Chris Venditti & Mark Pagel
2015 Bantu Expansion Shows That Habitat Alters the Route and Pace of Human Dispersals. Proceedings of the National Academy of Sciences 112:43.13296–13301. DOI logoGoogle Scholar
Hammarström, Harald, Sebastian Bank, Robert Forkel & Martin Haspelmath
2017 Glottolog 3.1. Jena: Max Planck Institute for the Science of Human History.Google Scholar
Heggarty, Paul
2006 Interdisciplinary Indiscipline? Can Phylogenetic Methods Meaningfully be Applied to Language Data – And to Dating Language? In Peter Forster & Colin Renfrew, eds., 183–194.Google Scholar
Heggarty, Paul, Warren Maguire & April McMahon
2010 Splits or Waves? Trees or Webs? How Divergence Measures and Network Analysis Can Unravel Language Histories. Philosophical Transactions of the Royal Society B 365:1559.3829–3843. DOI logoGoogle Scholar
Holm, Hans J.
2007 The New Arboretum of Indo-European “Trees”: Can New Algorithms Reveal the Phylogeny and Even Prehistory of Indo-European? Journal of Quantitative Linguistics 14:2–3.167–214. DOI logoGoogle Scholar
Hruschka, Daniel J., Simon Branford, Eric D. Smith, Jon Wilkins, Andrew Meade, Mark Pagel & Tanmoy Bhattacharya
2015 Detecting Regular Sound Changes in Linguistics as Events of Concerted Evolution. Current Biology 25:1.1–9. DOI logoGoogle Scholar
Huelsenbeck, John P., Fredrik Ronquist, Rasmus Nielsen & Jonathan P. Bollback
2001 Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology. Science 294:5550.2310–2314. DOI logoGoogle Scholar
Huson, Daniel H. & David Bryant
2006 Application of Phylogenetic Networks in Evolutionary Studies. Molecular Biology and Evolution 23:2.254–267. DOI logoGoogle Scholar
Huson, Daniel H. & Celine Scornavacca
2010 A Survey of Combinatorial Methods for Phylogenetic Networks. Genome Biology and Evolution 31.23–35. DOI logoGoogle Scholar
2012 Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks. Systematic Biology 61:6.1061–1067. DOI logoGoogle Scholar
Jacques, Guillaume & Johann-Mattis List
This issue. Save the Trees: Why We Need Tree Models in Linguistic Reconstruction. Journal of Historical Linguistics 9:1. 128–167. DOI logo
Jaeger, Gerhard & Søren Wichmann
2016 Inferring the World Tree of Languages From Word Lists. The Evolution of Language: Proceedings of the 11th International Conference on the Evolution of Language (EvoLang XI) ed. by Séan G. Roberts, Christine Cuskley, Luke McCrohon, Lluis Barceló-Coblijn, Olga Feher & Tessa Verhoef. Available at [URL]
Kalyan, Siva & Alexandre François
2018 Freeing the Comparative Method from the tree model: A framework for Historical Glottometry. In Ritsuko Kikusawa & Lawrence Reid (eds), Let’s talk about trees: Genetic Relationships of Languages and Their Phylogenic Representation (Senri Ethnological Studies, 98). Ōsaka: National Museum of Ethnology. 59–89.Google Scholar
Kelly, Luke J. & Geoff K. Nicholls
2017 Lateral Transfer in Stochastic Dollo Models. The Annals of Applied Statistics 11:2.1146–1168. DOI logoGoogle Scholar
Koonin, Eugene V., Kira S. Makarova & L. Aravind
2001 Horizontal Gene Transfer in Prokaryotes: Quantification and Classification. Annual Review of Microbiology 55:1.709–742. DOI logoGoogle Scholar
Lee, Sean
2018 The Best Fitting Tree Model for Japonic Languages. Zenodo. Available at DOI logoGoogle Scholar
Lee, Sean & Toshikazu Hasegawa
2011 Bayesian Phylogenetic Analysis Supports an Agricultural Origin of Japonic Languages. Proceedings of the Royal Society B, 2781.3662–3669. DOI logoGoogle Scholar
2014 Oceanic Barriers Promote Language Diversification in the Japanese Islands. Journal of Evolutionary Biology 27:9.1905–1912. DOI logoGoogle Scholar
Levinson, Stephen C. & Russell D. Gray
2012 Tools from Evolutionary Biology Shed New Light on the Diversification of Languages. Trends in Cognitive Sciences 16:3.167–173. DOI logoGoogle Scholar
List, Johann-Mattis
2015 Network Perspectives on Chinese Dialect History: Chances and Challenges. Bulletin of Chinese Linguistics 8:1.27–47. DOI logoGoogle Scholar
2016 Beyond Cognacy: Historical Relations Between Words and Their Implication for Phylogenetic Reconstruction. Journal of Language Evolution 1:2.119–136. DOI logoGoogle Scholar
2017 Chinese Dialect Database. Jena: Max Planck Institute for the Science of Human History. Available at [URL]
List, Johann-Mattis, Shijulal Nelson-Sathi, Hans Geisler & William Martin
2013 Networks of Lexical Borrowing and Lateral Gene Transfer in Language and Genome Evolution. Bioessays 36:2.141–150. DOI logoGoogle Scholar
List, Johann-Mattis, Shijulal Nelson-Sathi, William Martin & Hans Geisler
2014 Using Phylogenetic Networks to Model Chinese Dialect History. Language Dynamics and Change, 4:2.222–252. DOI logoGoogle Scholar
List, Johann-Mattis, Jananan Sylvestre Pathmanathan, Philippe Lopez & Eric Bapteste
2016 Unity and Disunity in Evolutionary Sciences: Process-Based Analogies Open Common Research Avenues for Biology and Linguistics. Biology Direct 111.360–375. DOI logoGoogle Scholar
Macklin-Cordes, Jayden, & Erich Round
2015 High-Definition Phonotactics Reflect Linguistic Pasts. Proceedings of the 6th Conference on Quantitative Investigations in Theoretical Linguistics ed. by Johannes Wahle, Marisa Kollner, Harald Baayen, Gerhard Jäger & Tineke Baayen-Oudshoorn, 1–5. Tübingen: University of Tübingen.Google Scholar
Maddison, Wayne P.
1997 Gene Trees in Species Trees. Systematic Biology 46:3.523–536. DOI logoGoogle Scholar
Matthews, Luke J., Jamie J. Tehrani, Fiona M. Jordan, Mark Collard & Charles L. Nunn
2011 Testing for Divergent Transmission Histories Among Cultural Characters: A Study Using Bayesian Phylogenetic Methods and Iranian Tribal Textile Data. PLOS ONE 61.e14810. DOI logoGoogle Scholar
Meira, Sérgio, Joshua Birchall & Natalia Chousou-Polydouri
2015 A Character-Based Internal Classification of the Cariban Language Family. Paper presented at the 48th Annual Meeting of the Societas Linguistica Europaea, Leiden, The Netherlands, September 2–5, 2015.
Morrison, David A.
2016 Genealogies: Pedigrees and Phylogenies Are Reticulating Networks Not Just Divergent Trees. Evolutionary Biology 43:4.456–473. DOI logoGoogle Scholar
Nakhleh, Luay, Don Ringe & Tandy Warnow
2005 Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages. Language 81:2.382–420. DOI logoGoogle Scholar
Nelson-Sathi, Shijulal, Johann-Mattis List, Hans Geisler, Heiner Fangerau, Russell D. Gray, William Martin & Tal Dagan
2011 Networks Uncover Hidden Lexical Borrowing in Indo-European Language Evolution. Proceedings of the Royal Society B 278:1713.1794–1803. DOI logoGoogle Scholar
Norman, Jerry
1988 Chinese. Cambridge: Cambridge University Press.Google Scholar
Nunn, Charles L., Christian Arnold, Luke Matthews & Monique Borgerhoff Mulder
2010 Simulating Trait Evolution for Cross-Cultural Comparison. Philosophical Transactions of the Royal Society B 365:1559.3807–3819. DOI logoGoogle Scholar
Nunn, Charles L., Monique Borgerhoff Mulder & Sasha Langley
2006 Comparative Methods for Studying Cultural Trait Evolution: A Simulation Study. Cross-Cultural Research 40:2.177–209. DOI logoGoogle Scholar
Pagel, Mark
2009 Human Language as a Culturally Transmitted Replicator. Nature Reviews Genetics 101.405–415. DOI logoGoogle Scholar
Pagel, Mark, Quentin D. Atkinson & Andrew Meade
2007 Frequency of Word-Use Predicts Rates of Lexical Evolution Throughout Indo-European History. Nature 4491.717–721. DOI logoGoogle Scholar
Pagel, Mark & Andrew Meade
2004 A Phylogenetic Mixture Model for Detecting Pattern-Heterogeneity in Gene Sequence or Character-State Data. Systematic Biology 53:4.571–581. DOI logoGoogle Scholar
2006a Detecting Conflicting Phylogenetic Signal: A Mixture Model Approach with Multiple Tree Topologies. Paper presented at the New Zealand Phylogenetics Meeting, Kaikoura, New Zealand, February 12–17, 2006. Available at [URL]
2006b Estimating Rates of Lexical Replacement on Phylogenetic Trees of Languages. In Peter Forster & Colin Renfrew, eds., 173–182.Google Scholar
N.d. Draft Manual for BayesPhylogenies . Available at [URL]
Pereltsvaig, Asya & Martin W. Lewis
2015 The Indo-European Controversy: Facts and Fallacies in Historical Linguistics. Cambridge: Cambridge University Press. DOI logoGoogle Scholar
Robbeets, Martine
2015 Diachrony of Verb Morphology: Japanese and the Transeurasian Languages. Berlin: Walter de Gruyter. DOI logoGoogle Scholar
Rokas, Antonis & Sean B. Carroll
2006 Bushes in the Tree of Life. PLOS Biology 4:11.e352. DOI logoGoogle Scholar
Ronquist, Fredrik, Paul van der Mark & John P. Huelsenbeck
2009 Bayesian Phylogenetic Analysis Using MrBayes. The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing ed. by Marco Salemi, Philippe Lemey & Anne-Mieke Vandamme, 210–266. Cambridge: Cambridge University Press. DOI logoGoogle Scholar
Shibatani, Masayoshi
1990 The Languages of Japan. Cambridge: Cambridge University Press.Google Scholar
Swadesh, Morris
1952 Lexico-statistic Dating of Prehistoric Ethnic Contacts: With Special Reference for North American Indians and Eskimos. Proceedings of the American Philosophical Society 96:4.452–463.Google Scholar
1955 Towards Greater Accuracy in Lexicostatistic Dating. International Journal of American Linguistics 21:2.121–137. DOI logoGoogle Scholar
Tadmor, Uri
2009 Loanwords in the World’s Languages: Findings and Results. Loanwords in the World’s Languages: A Comparative Handbook ed. by Martin Haspelmath & Uri Tadmor, 55–75. Berlin: Walter de Gruyter. DOI logoGoogle Scholar
Tehrani, Jamshid & Mark Collard
2002 Investigating Cultural Evolution Through Biological Phylogenetic Analyses of Turkmen Textiles. Journal of Anthropological Archaeology 21:4.443–463. DOI logoGoogle Scholar
Verkerk, Annemarie
2014 The Evolutionary Dynamics of Motion Event Encoding. Radboud University Nijmegen PhD dissertation.Google Scholar
Wang, Feng
2004 BCD: Basic Words of Chinese Dialects. Available at [URL]
Wang, William S.-Y.
1997 Languages or Dialects? The CUHK Journal of Humanities 11.54–62.Google Scholar
Wang, William S.-Y. & James W. Minett
2005 Vertical and Horizontal Transmission in Language Evolution. Transactions of the Philological Society 103:2.121–146. DOI logoGoogle Scholar
Wichmann, Søren, Robert S. Walker, Taraka Rama & Eric W. Holman
2011 Correlates of Reticulation in Linguistic Phylogenies. Language Dynamics and Change 1:2.205–240. DOI logoGoogle Scholar
Widmer, Manuel, Sandra Auderset, Johanna Nichols, Paul Widmer & Balthasar Bickel
2017 NP Recursion Over Time: Evidence from Indo-European. Language 93:4.799–826. DOI logoGoogle Scholar
Willems, Matthieu, Etienne Lord, Louise Laforest, Gilbert Labelle, François-Joseph Lapointe, Anna Maria Di Sciullo & Vladimir Makarenkov
2016 Using Hybridization Networks to Retrace the Evolution of Indo-European Languages. BMC Evolutionary Biology 16:1.180. DOI logoGoogle Scholar
Xie, Wangang, Paul O. Lewis, Yu Fan, Lynn Kuo & Ming-Hui Chen
2010 Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection. Systematic Biology 60:2.150–160. DOI logoGoogle Scholar
Zhou, Kevin & Claire Bowern
2015 Quantifying Uncertainty in the Phylogenetics of Australian Numeral Systems. Proceedings of the Royal Society B 282:1815.20151278. DOI logoGoogle Scholar
Zhou, Zhenhe
1991 Migrations in Chinese History and Their Legacy on Chinese Dialects. Journal of Chinese Linguistics Monograph Series 31.29–49.Google Scholar
Cited by

Cited by 5 other publications

Guzmán Naranjo, Matías & Laura Becker
2022. Statistical bias control in typology. Linguistic Typology 26:3 ► pp. 605 ff. DOI logo
Leino, Unni, Kaj Syrjänen & Outi Vesakoski
2020. Linguistic Change and Biological Evolution. In The Philosophy and Science of Language, ► pp. 179 ff. DOI logo
Lukas, Dieter, Mary Towner & Monique Borgerhoff Mulder
2021. The potential to infer the historical pattern of cultural macroevolution. Philosophical Transactions of the Royal Society B: Biological Sciences 376:1828 DOI logo
Macklin-Cordes, Jayden L. & Erich R. Round
2022. Challenges of sampling and how phylogenetic comparative methods help: with a case study of the Pama-Nyungan laminal contrast. Linguistic Typology 26:3 ► pp. 533 ff. DOI logo
Syrjänen, Kaj, Luke Maurits, Unni Leino, Terhi Honkola, Jadranka Rota & Outi Vesakoski
2021. Crouching TIGER, hidden structure: Exploring the nature of linguistic data using TIGER values. Journal of Language Evolution 6:2 ► pp. 99 ff. DOI logo

This list is based on CrossRef data as of 26 september 2023. Please note that it may not be complete. Sources presented here have been supplied by the respective publishers. Any errors therein should be reported to them.