Figure 1. Subtypes of homology in molecular biology

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Figure 1. Subtypes of homology in molecular biology Figure 1. Subtypes of homology in molecular biology. Three processes, speciation, duplication, and lateral transfer underly the three basic types of homology in molecular evolution. The processes are illustrated in (A), the resulting relations are illustrated in (B). From: Beyond cognacy: historical relations between words and their implication for phylogenetic reconstruction Journal of Language Evolution. 2016;1(2):119-136. doi:10.1093/jole/lzw006 Journal of Language Evolution | © The Author 2016. Published by Oxford University Press. All rights reserved. for permissions, please e-mail: journals.permissions@oup.com

Figure 2. Complex historical relations between reflexes of Proto-Indo-European *(s)ker- ‘cut off’. From: Beyond cognacy: historical relations between words and their implication for phylogenetic reconstruction Journal of Language Evolution. 2016;1(2):119-136. doi:10.1093/jole/lzw006 Journal of Language Evolution | © The Author 2016. Published by Oxford University Press. All rights reserved. for permissions, please e-mail: journals.permissions@oup.com

Figure 3. Degrees of cognacy in Indo-European language history: the development of words meaning ‘to give’ from Proto-Indo-European via Latin to Italian and French (A), and the development of words meaning ‘sun’ in from Proto-Indo-European to Italian, French, Swedish, and German (B). From: Beyond cognacy: historical relations between words and their implication for phylogenetic reconstruction Journal of Language Evolution. 2016;1(2):119-136. doi:10.1093/jole/lzw006 Journal of Language Evolution | © The Author 2016. Published by Oxford University Press. All rights reserved. for permissions, please e-mail: journals.permissions@oup.com

Figure 4. The different dimensions of the linguistic sign: (A) Shows the classical model after Saussure (1916). (B) Shows an extended sign model in which the language, the system in which a sign is used was added as a third component. From: Beyond cognacy: historical relations between words and their implication for phylogenetic reconstruction Journal of Language Evolution. 2016;1(2):119-136. doi:10.1093/jole/lzw006 Journal of Language Evolution | © The Author 2016. Published by Oxford University Press. All rights reserved. for permissions, please e-mail: journals.permissions@oup.com

Figure 5. From gain–loss models to weighted directed character-state transitions: (A) Shows a strict approach in which four partially related compound words (as show at the bottom of D) are modeled as four different characters. (B) Shows the consequences of a lumping approach when partially cognate words are treated as fully cognate in binary presence–absence models. (C) Shows weighted directed character–state transitions, based on known transition tendencies displayed at the top of (D), with arrows indicating directions and edge width indicating the relative strength of transition tendencies. From: Beyond cognacy: historical relations between words and their implication for phylogenetic reconstruction Journal of Language Evolution. 2016;1(2):119-136. doi:10.1093/jole/lzw006 Journal of Language Evolution | © The Author 2016. Published by Oxford University Press. All rights reserved. for permissions, please e-mail: journals.permissions@oup.com

Figure 6. Comparing multistate models for lexical change Figure 6. Comparing multistate models for lexical change. The figure shows how the evolution of the four words for ‘moon’ is inferred within a parsimony framework. On top, the etymological structure of the words is displayed, and unique colors are assigned to refer to the morpheme structure in the remainder of the figure (A). On the left, the penalties for character transitions (step matrices) are shown for the FITCH (B), the SANKOFF (C), and the DWST model (D). For SANKOFF and DWST, example calculations for transition penalties are displayed on the right (see also the main text). For each model, all trees with optimal weight are displayed. Dashed edges in the trees indicate a transition involving a change. Numbers on dashed lines denote the weight, as derived from the corresponding matrix of transition penalties on the left. From: Beyond cognacy: historical relations between words and their implication for phylogenetic reconstruction Journal of Language Evolution. 2016;1(2):119-136. doi:10.1093/jole/lzw006 Journal of Language Evolution | © The Author 2016. Published by Oxford University Press. All rights reserved. for permissions, please e-mail: journals.permissions@oup.com

Figure 7. One of four optimal scenarios for the development of words for ‘moon’ along the Arbre reference phylogeny. From: Beyond cognacy: historical relations between words and their implication for phylogenetic reconstruction Journal of Language Evolution. 2016;1(2):119-136. doi:10.1093/jole/lzw006 Journal of Language Evolution | © The Author 2016. Published by Oxford University Press. All rights reserved. for permissions, please e-mail: journals.permissions@oup.com