Tutorial on computational linguistic phylogeny

Linguistics and Language Compass

Volumn 2, Issue 5, 2008, Pages 760-820

  Nichols, Johanna ^a   Warnow, Tandy ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 65349085831     PISSN: None     EISSN: 1749818X     Source Type: Journal    
DOI: 10.1111/j.1749-818X.2008.00082.x     Document Type: Article

References (116)

1. Alpher, Barry, and David Nash. 1999. Lexical replacement and cognate equilibrium in Australia. Australian Journal of Linguistics 19.4-56.
2. Anthony, David W. 2007. The horse, the wheel, and language: How Bronze age riders from the Eurasian steppes shaped the modern world. Princeton, NJ: Princeton University Press.
3. Atkiinson, Quentin, and Russell Gray. 2006. How old is the Indo-European language family? Illumination or more moths to the flame? Phylogenetic methods and the prehistory of languages, ed. by Peter Forster and Colin Renfrew, 91-110. Cambridge, UK: MacDonald Institute Press, University of Cambridge.
4. Bandelt, Hans-Jurgen, Peter Forster, and A. Röhl. 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16.37-48.
5. Barbançon, François, Tandy Warnow, Steven N. Evans, Donald A. Ringe, Jr, and Luay Nakhleh. forthcoming. An experimental study comparing linguistic phylogenetic reconstruction methods. Proceedings of a conference on Language and Genes, University of California, Santa Barbara, September 2006. http://www.cs.utexas.edu/users/tandy/ nanterre-talk.ppt.
6. Bastin, Yvonne. 1983. Classification lexicostatistique des langues bantoues (214 releves). Bulletin des Séances de l'Académie royale des sciences d'outre-mer 27.173-99.
7. Bastin, Yvonne, A. Coupez and M. Mann. 1999. Continuity and divergence in the Bantu languages: Perspectives from a lexicostatistical study. Tervuren, Belgium: Musée royal d'Afrique Centrale.
8. Blust, Robert A. 1978. Eastern Malayo-Polynesian: A subgrouping argument. Second international conference on Austronesian linguistics: proceedings (Pacific Linguistics C-61), 181-234. Canberra, Australia: Research School of Pacific Studies, Australian National University.
9. Blust, Robert A. 1985. The Austronesian homeland: A linguistic perspective. Asian Perspectives 26.45-67.
10. Blust, Robert A. 1994. The Austronesian settlement of mainland Southeast Asia. Papers from the Second Annual Meeting of the Southeast Asian Linguistics Society, ed. by Karen L. Adams and Thomas John Hudak, 25-83. Tempe, AZ: Program for Southeast Asian Studies, Arizona State University.
11. Blust, Robert A. 1995. The prehistory of the Austronesian speaking people: A view from language. Journal of World Prehistory 9.453-510.
12. Blust, Robert A. 2000. Why lexicostatistics doesn't work: The 'universal constant' hypothesis and the Austronesian languages. Time depth in historical linguistics, Vol. 2, ed. by Colin Renfrew, April McMahon and Larry Trask, 311-31. Cambridge, UK: The McDonald Institute for Archaeological Research.
13. Bradley, David. 1994. East and Southeast Asia. Atlas of the world's language, ed. by Christopher Moseley and R. E. Asher, 159-92. London, UK: Routledge.
14. Brown, Cecil H., Eric W. Holman, Søren Wichmann, and Viveka Vilupillai. forthcoming 2008. Automated classification of the world's languages: A description of the method and preliminary results. Sprachtypologie und Universalienforschung.
15. Bryant, David, and Vincent Moulton. 2002. NeighborNet: An agglomerative method for the construction of planar phylogenetic networks. Proceedings of the 2nd International Workshop on Algorithms in Bioinformatics (WABI'02), Rome (2002), Lecture Notes in Computer Science (LNCS #2452), ed. by Roderic Guigó and Daniel Gusfield, 375-91. London, UK: Springer-Verlag.
16. Bryant, David, and Vincent Moulton. 2004. NeighborNet: An agglomerative algorithm for the construction of phylogenetic networks. Molecular Biology and Evolution 21(2).255-65.
17. Bryant, David, Flavia Filimon, and Russell Gray. 2005. Untangling our past: Languages, trees, splits, and networks. The evolution of cultural diversity: A phylogenetic approach, ed. by Ruth Mace, Clare J. Holden and Stephen Shennan, 67-83. London, UK: University College London Press.
18. Cysouw, Michael, Søren Wichmann, and David Kamholz. 2006. A critique of the separation base method for genealogical subgrouping, with data from Mixe-Zoquean. Journal of Quantitative Linguistics 13.225-64.
19. Darden, Bill J. 2001. On the question of the Anatolian origin of Indo-Hittite. Greater Anatolia and The Indo-Hittite language family, ed. by Robert Drews, 184-228. Washington, DC: Institute for the Study of Man.
20. Donohue, Mark, and Simon Musgrave. 2007. Typology and the linguistic macrohistory of Island Melanesia. Oceanic Linguistics 46.348-87.
21. Donohue, Mark, and Søren Wichmann. 2008. Typology, areality, and relatedness. Oceanic Linguistics 48.223-32.
22. Dunn, Michael, Angela Terrill, Ger P. Reesink, Robert A. Foley, and Stephen C. Levinson. 2005. Structural phylogenetics and the reconstruction of ancient language history. Science 309.2072-5.
23. Dunn, Michael, Robert A. Foley, Stephen C. Levinson, Ger P. Reesink, and Angela Terrill. 2007. Statistical reasoning in the evaluation of typological diversity in Island Melanesia. Oceanic Linguistics 46.388-403.
24. Dyen, Isidore, Joseph B. Kruskal and Paul Black. 1992. An Indoeuropean classification: A lexicostatistical experiment. Transactions of the American Philosophical Society 82, pt. 5. Philadelphia, PA: American Philosophical Society.
25. Embleton, Sheila. 1986. Statistics in historical linguistics. Bochum, Germany: Brockmeyer.
26. Erdem, Esra, Vladimir Lifschitz, Luay Nakhleh, and Donald A. Ringe, Jr. 2003. Reconstructing the evolutionary history of Indo-European languages using answer set programming. Proceedings of the 5th International Symposium on Practical Aspects of Declarative Languages (PADL 03), 13-14 January 2003, pp. 160-76.
27. Erdõs, Peter L., Michael A. Steel, Laszlo Székély, and Tandy Warnow. 1999a. A few logs suffice to build almost all trees - I. Random Structures and Algorithms, 14.153-84. (Also appears as DIMACS Technical Report 97-71.)
28. Erdõs, Peter L., Michael A. Steel, Laszlo Székély, and Tandy Warnow. 1999b. A few logs suffice to build almost all trees - II. Theoretical Computer Science 221(1-2).77-118.
29. Eska, Joseph F., and Donald A. Ringe, Jr. 2004. Recent work in computational linguistic phylogeny. Language 80.569-82.
30. Evans, Steven N., Donald A. Ringe, Jr, and Tandy Warnow. 2006. Inference of divergence times as a statistical inverse problem. Phylogenetic methods and the prehistory of languages, ed. by Peter Forster, and Colin Renfrew, 119-29. Cambridge, UK: McDonald Institute for Archaeological Research, University of Cambridge.
31. Evans, Steven N., and Tandy Warnow. 2005. Unidentifiable divergence times in rates-across-sites models. IEEE/ACM Transactions on Computational Biology and Bioinformatics 1.130-4. Field, Fredric W. 2002. Linguistic borrowing in bilingual contexts. Amsterdam, The Netherlands/Philadelphia, PA: Benjamins.
32. Foley, William A. 2007. Language change and diffusion in the Sepik region, PNG. MS, University of Sydney.
33. Forster, Peter, and Alfred Toth. 2003. Toward a phylogenetic chronology of ancient Gaulish, Celtic, and Indo-European. Proceedings of the National Academy of Sciences, USA 100.9079-84.
34. Foulds, L. R., and Ronald L. Graham. 1982. The Steiner problem in phylogeny is NP-complete. Advances in Applied Mathematics 3.43-9.
35. Goddard, Ives. 1996. The west-to-east cline in Algonquian dialectology. Actes du Vingtcinquième Congrès des algonquinistes, ed. by William Cowan, 187-211. Ottawa, Canada: Carleton University.
36. Goloboff, Pablo, Steven Farris, and Kevin Nixon. 2003. T.N.T: Tree analysis using new technology, version 1.0. Program and documentation. .
37. Grace, George W. 1996. Regularity of change in what? The comparative method reviewed, ed. by Mark Durie and Malcolm Ross, 156-79. New York, NY/Oxford, UK: Oxford University Press.
38. Gray, Russell D., and Fiona M. Jordan. 2000. Language trees support the express-train sequence of Austronesian expansion. Nature 405.1052-5.
39. Gray, Russell D., and Quentin D. Atkinson. 2003. Language-tree divergence times support the Anatolian theory of Indo-European origins. Nature 426.435-9.
40. Gray, Russell D., Simon Greenhill, and Robert Blust. 2007. Computational phylogenetic methods and Austronesian subgrouping. Presented at International Congress of Historical Linguists, Montreal.
41. Greenhill, S. J., and R. D., Gray 2005. Testing population dispersal hypotheses: Pacific settlement, phylogenetic trees, and Austronesian languages. The evolution of cultural diversity: Phylogenetic approaches, ed. by R. Mace, C. Holden and S. Shennan, 31-52. London, UK: UCL Press.
42. Greenhill, Simon J., Robert A. Blust, and Russell D. Gray. 2003-2008. Austronesian Basic Vocabulary Database .
43. Guthrie, Malcolm. 1967-71. Comparative Bantu (4 vols.). Farnborough, UK: Gregg. Haas, Mary R. 1949. The position of Apalachee in the Muskogean family. International Journal of American Linguistics 15.121-7.
44. Guthrie, Malcolm. 1979. Southeastern languages. The languages of native America, ed. by Lyle Campbell and Marianne Mithun, 299-326. Austin, TX: University of Texas Press.
45. Haspelmath, Martin, and Uri Tadmor. n.d. Loanword Typology
46. Haspelmath, Martin, Matthew S. Dryer, David Gil, and Bernard Comrie (eds) 2005. World Atlas of Language Structures. Oxford, UK: Oxford University Press.
47. Hinnebusch, Thomas J. 1996. Skewing in lexicostatistic tables as an indicator of contact. Paper presented at the Round Table on Bantu Historical Linguistics, Université Lumière 2, Lyon, France, 30 May-1 June 1996.
48. Holden, Clare J. 2002. Bantu language trees reflect the spread of farming across Sub-Saharan Africa: A maximum-parsimony analysis. Proceedings of the Royal Society of London Series B 269.793-9.
49. Holden, Clare J., A. Meade, and M. Pagel. 2005. Comparison of maximum parsimony and Bayesian Bantu language trees. The evolution of cultural diversity: A phylogenetic approach, ed. by R. Mace, C. J. Holden, and S. Shennan, 53-65. London, UK: University College London Press.
50. Holden, Clare J., and Russell Gray. 2006. Rapid radiation, borrowing, and dialect continua in the Bantu languages. Phylogenetic methods and the prehistory of languages, ed. by Peter Forster and Colin Renfrew, 19-31. Cambridge, UK: MacDonald Institute Press, University of Cambridge.
51. Holland, B., and V. Moulton 2003. Consensus networks: A method for visualizing incompatibilities in collections of trees. Workshop on algorithms for bioinfomatics, ed. by G. Benson and R. Page. Lecture Notes in Computer Science, Vol. 2812, 165-76. Berlin, Germany: Springer.
52. Holm, Hans J. 2000. Genealogy of the main Indo-European branches applying the separation base method. Journal of Quantitative Linguistics 7.73-95.
53. Holm, Hans J. 2003. The proportionality trap. Or: What is wrong with lexicostatistical subgrouping? Indogermanische Forschungen 108.38-46.
54. 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 14.167-214.
55. Huelsenbeck, John and Fredrik Ronquist, 2001. MrBayes: Bayesian inference of phylogeny, Bioinformatics 17.754-5.
56. Huson, Daniel. 1998. SplitsTree: A program for analyzing and visualizing evolutionary data. Bioinformatics 14(1).68-73.
57. Huson, D., and D. Bryant 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 32.254-67.
58. Ives, John W. 2003. Alberta, Athapaskans, and Apachean origins. Archaeology in Alberta: A view from the new millennium, ed. by J. W. Brink and J. F. Dormaar. Medicine Hat, Alberta: Archaeological Society of Alberta.
59. Janhunen, Juha. 2001. Indo-Uralic and Ural-Altaic: On the diachronic implications of areal typology. Early contacts between Uralic and Indo-European: Linguistic and archaeological considerations, ed. by Christian Carpelan, Asko Parpola and Petteri Koskikallio, 207-20. Helsinki, Finland: Suomalais-Ugrilainen Seura.
60. Kaufman, Terrence, and John Justeson. 2004. Epi-Olmec. The encyclopedia of the world's ancient languages, ed. by R. D. Woodard, 1071-111. Cambridge, UK: Cambridge University Press.
61. Kessler, Brett. 2001. The significance of word lists. Stanford, CA: CSLI.
62. Kim, Junhyong, and Tandy Warnow. 1999. Tutorial on Phylogenetic Tree Estimation. Intelligent Systems for Molecular Biology, Heidelberg 1999 .
63. Kirch, Patrick V. 1997. The Lapita peoples: Ancestors of the oceanic world. Cambridge, MA: Blackwell.
64. Kirch, Patrick V. 2000. On the road of the winds: An archaeological history of the Pacific islands before European contact. Berkeley, CA: University of California Press.
65. Lees, Robert B. 1953. The basis of glottochronology. Language 29.113-27.
66. Lohr, Marisa. 1999. Methods for the genetic classification of languages. PhD dissertation, University of Cambridge.
67. Lynch, John. 1999. Linguistic change in southern Melanesia: Linguistic aberrancy and genetic distance. Archaeology and languages, ed. by Roger Blench and Matthew Spriggs, 149-59. London, UK: Routledge.
68. Mallory, J. P. 1989. In search of the Indo-Europeans: Language, archaeology, and myth. New York, NY: Thames & Hudson.
69. Marten, Lutz. 2006. Bantu classification, Bantu trees, and phylogenetic methods. Phylogenetic methods and the prehistory of languages, ed. by Peter Forster and Colin Renfrew, 43-56. Cambridge, UK: MacDonald Institute Press, University of Cambridge.
70. Matisoff, James. 2000. On the uselessness of glottochronology for the subgrouping of Tibeto-Burman. Time depth in historical linguistics, ed. by Colin Renfrew, April McMahon and Larry Trask, 333-72. Cambridge, UK: The McDonald Institute for Archaeological Research. McMahon, April, and Robert McMahon. 2005. Language classification by numbers. Oxford, UK: Oxford University Press.
71. McMahon, April, Paul Heggarty, Robert McMahon, and Natalia Slaska. 2005. Swadesh sublists and the benefits of borrowing: An Andean case study. Transactions of the Philological Society 103.147-70.
72. Michener, C. D., and Robert R. Sokal. 1957. A quantitative approach to a problem in classification. Evolution 11.130-62.
73. Minett, James W., and William S-Y. Wang. 2003. On detecting borrowing: distance-based and character-based approaches. Diachronica 20.289-330.
74. Moret, B. M. E., U. Roshan, and T. Warnow. 2002. Sequence length requirements for phylogenetic methods. Proceedings of the 2nd International Workshop on Algorithms in Bioinformatics (WABI'02), Rome (2002), Lecture Notes in Computer Science (LNCS #2452), ed. by Roderic Guigó and Daniel Gusfield, 343-56. London, UK: Springer-Verlag.
75. Nakhleh, Luay 2005. Phylogenetic networks, PhD dissertation. The University of Texas at Austin.
76. Nakhleh, Luay, Katherine St. John, Usman Roshan, Jerry Sun, and Tandy Warnow. 2001. Designing fast converging phylogenetic methods. 9th Int'l Conf. on Intelligent Systems for Molecular Biology (ISMB 2001), Copenhagen, in Bioinformatics 17(suppl. 1).S190-8.
77. Nakhleh, Luay, Donald A. Ringe, Jr, and Tandy Warnow. 2005a. Perfect phylogenetic networks: A new methodology for reconstructing the evolutionary history of natural languages. Language 81.382-420.
78. Nakhleh, Luay, Tandy, Warnow, Donald A., Ringe, Jr, and Steven N. Evans. 2005b. A comparison of phylogenetic reconstruction methods on an IE dataset. Transactions of the Philological Society 103.171-92.
79. Nash, David. 2002. Historical linguistic geography of southeast Western Australia. Language in native title, ed. by John Henderson and David Nash, 205-30. Canberra, Australia: AIATSIS Native Title Research Unit, Aboriginal Studies Press.
80. Naylor, Gavin, and Fred Kraus. 1995. The relationship between s and m and the retention index. Systematic Biology 44(4).559-62.
81. Nicholls, Geoff, and Russell Gray. 2008. Dated ancestral trees from binary trait data and their application to the diversification of languages. Journal of the Royal Statistical Society Series B: Statistical Methodology 70.545-66.
82. Nichols, Johanna. 1992. Linguistic diversity in space and time. Chicago, IL: University of Chicago Press.
83. Nichols, Johanna. 1997. Modeling ancient population structures and movement in linguistics. Annual Review of Anthropology 26.359-84.
84. Nichols, Johanna. 2006. Quasi-cognates and lexical type shifts: Rigorous distance measures for long-range comparison. Phylogenetic methods and the prehistory of languages, ed. by Peter Forster and Colin Renfrew, 57-65. Cambridge, UK: MacDonald Institute Press, University of Cambridge.
85. Nichols, Johanna. 2007. Language dispersal from the Black Sea region. The black sea flood question: Changes in coastline, climate, and human settlement, ed. by Valentina Yahko-Holmbach, Allan S. Gilbert, Nicolae Panin and Pavel M. Dolukhanov, 775-96. Dordrecht, The Netherlands: Kluwer.
86. Nichols, Lynn, and Johanna Nichols. 2007. Lexical derivational properties resist diffusion. Presented at Workshop on Language contact and morphosyntactic variation and change, 7th biennial meeting, Association for Linguistic Typology, Paris.
87. Pagel, Mark, Quentin Atkinson, and Andrew Meade. 2007. Frequency of word use predicts rates of lexical evolution throughout Indo-European history. Nature 449.717-21.
88. Pawley, Andrew K., and Malcolm D. Ross. 1993. Austronesian historical linguistics and culture history. Annual Review of Anthropology 22.425-59.
89. Rannala, Bruce, John P. Huelsenbeck, Ziheng Yang, and Rasmus Nielsen. 1998. Taxon sampling and the accuracy of large phylogenies. Systematic Biology 47.702-10.
90. Renfrew, Colin. 1987. Archaeology and language: The puzzle of Indo-European origins. Cambridge, UK: Cambridge University Press.
91. Rexová, KateRina, Daniel Frynta, and J. Zrzavý. 2003. Cladistic analysis of languages: Indo-European classification based on lexicostatistical data. Cladistics 19.120-7.
92. Rexová, KateRina, Yvonne Bastin, and Daniel Frynta. 2006. Cladistic analysis of Bantu languages: A new tree based on combined lexical and grammatical data. Naturwissenschaften 93(4).189-94.
93. Ringe, Donald A., Jr, Tandy Warnow and Ann Taylor. 2002. Indo-European and computational cladistics. Transactions of the Philological Society 100.59-129.
94. Robinson, D. F. and L. R. Foulds. 1981. Comparison of phylogenetic trees. Mathematical Biosciences 53.131-47.
95. Ross, Malcolm D. 1988. Proto Oceanic and the Austronesian languages of western Melanesia. Canberra, Australia: Australian National University.
96. Ross, Malcolm D. 1995. Comparative Austronesian dictionary: An introduction to Austronesian studies. Trends in linguistics, 10, ed. by Darrell Tryon. Vol. 1, 27-42. Berlin, Germany/New York, NY: Mouton de Gruyter.
97. Ross, Malcolm D. 1996. Contact-induced change and the comparative method: Cases from Papua New Guinea. The comparative method reviewed, ed. by Mark Durie and Malcolm D. Ross, 180-217. New York, NY: Oxford University Press.
98. Ross, Malcolm D. 1997. Social networks and kinds of speech-community event. Archaeology and language I: Theoretical and methodological orientations, ed. by Roger Blench and Matthew Spriggs, 209-61. London, UK/New York, NY: Routledge.
99. Ross, Malcolm D. 2002. Final words: Research themes in the history and typology of western Austronesian languages. The history and typology of Western Austronesian voice systems, ed. by Fay Wouk and Malcolm Ross, 451-74. Canberra, Australia: Pacific Linguistics.
100. Ross, Malcolm D., and Åshild Naess. 2007. An Oceanic origin for Äiwoo, the language of the Reef Islands? Oceanic Linguistics 46(2).456-98.
101. Saitou, Naryua, and Masatoshi Nei. 1987. The neighbor-joining method: A new method, for reconstructing phylogenetic trees. Molecular Biology and Evolution 4.406-25.
102. Saunders, Arpiar. 2005. Linguistic phylogenetics of the Austronesian family: A performance review of methods adapted from biology. BA thesis, Swarthmore College. .
103. Serva, Maurizio, and Filippo Petroni. 2008. Indo-European languages tree by Levenshtein distance. Europhysics Letters 81.68005-9.
104. Steel, Michael A. 1992. The complexity of reconstructing trees from qualitative characters and subtrees. Journal of Classification 9.91-116.
105. Swadesh, Morris. 1952. Lexicostatistic dating of prehistoric ethnic contacts. Proceedings of the American Philosophical Society 96.452-63.
106. Swadesh, Morris. 1955. Toward greater accuracy in lexicostatistic dating. International Journal of American Linguistics 21.121-37.
107. Swofford, David, 1996. PAUP*: Phylogenetic analysis using parsimony (and other methods), version 4.0. Sunderland, MA: Sinauer Assoc.
108. Thomason, Sarah G. 2001. Language contact. Washington, DC: Georgetown University Press.
109. Thomason, Sarah G., and Terrence Kaufman. 1988. Language contact, creolization, and genetic linguistics. Berkeley, CA: University of California Press.
110. Wang, William S-Y, and James W. Minett. 2005. Vertical and horizontal transmission in language evolution. Transactions of the Philological Society 103(2).121-46.
111. Warnow, Tandy, Bernard M. E. Moret, and Katherine St. John. 2001. Absolute convergence: True trees from short sequences. Proceedings of 12th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 01), Washington, DC, USA, 186-95. Philadelphia, PA: Society for Industrial and Applied Mathematics.
112. Warnow, Tandy, Steven N. Evans, Donald A. Ringe, Jr, and Luay Nakhleh. 2006. A stochastic model of language evolution that incorporates homoplasy and borrowing. Phylogenetic methods and the prehistory of languages, ed. by Peter Forster and Colin Renfrew, 75-87. Cambridge, UK: MacDonald Institute Press, University of Cambridge.
113. Waterman, Michael S., Temple Smith, M. Singh, and W. A. Beyer. 1977. Additive evolutionary trees. J. Theoretical Biology 64, 199-213.
114. Wichmann, Søren. 1995. The relationship among the Mixe-Zoquean languages of Mexico. Salt Lake City, UT: University of Utah Press.
115. Wichmann, Søren, and Arpiar Saunders. 2007. How to use typological databases in historical linguistic research. Diachronica 24.373-404.
116. Zobel, Erik. 2002. The position of Chamorro and Palauan in the Austronesian family tree: Evidence from verb morphosyntax. The history and typology of Western Austronesian voice systems (Pacific Linguistics; 518), ed. by Fay Wouk and Malcolm Ross, 405-34. Canberra, Australia: Australian National University.