Computational phylogenetics has become an established tool in historical linguistics, with many language families now analyzed using likelihood-based inference. However, standard approaches rely on expert-annotated cognate sets, which are sparse, labor-intensive to produce, and limited to individual language families. This paper explores alternatives by comparing the established method to two fully automated methods that extract phylogenetic signal directly from lexical data. One uses automatic cognate clustering with unigram/concept features; the other applies multiple sequence alignment (MSA) derived from a pair-hidden Markov model. Both are evaluated against expert classifications from Glottolog and typological data from Grambank. Also, the intrinsic strengths of the phylogenetic signal in the characters are compared. Results show that MSA-based inference yields trees more consistent with linguistic classifications, better predicts typological variation, and provides a clearer phylogenetic signal, suggesting it as a promising, scalable alternative to traditional cognate-based methods. This opens new avenues for global-scale language phylogenies beyond expert annotation bottlenecks.

Working with cognate data involves handling synonyms, that is, multiple words that describe the same concept in a language. In the early days of language phylogenetics it was recommended to select one synonym only. However, as we show here, binary character matrices, which are used as input for computational methods, do allow for representing the entire dataset including all synonyms. Here we address the question how one can and if one should include all synonyms or whether it is preferable to select synonyms a priori. To this end, we perform maximum likelihood tree inferences with the widely used RAxML-NG tool and show that it yields plausible trees when all synonyms are used as input. Furthermore, we show that a priori synonym selection can yield topologically substantially different trees and we therefore advise against doing so. To represent cognate data including all synonyms, we introduce two types of character matrices beyond the standard binary ones: probabilistic binary and probabilistic multi-valued character matrices. We further show that it is dataset-dependent for which character matrix type the inferred RAxML-NG tree is topologically closest to the gold standard. We also make available a Python interface for generating all of the above character matrix types for cognate data provided in CLDF format.

Languages disfavor word forms containing sequences of similar or identical consonants, due to the biomechanical and cognitive difficulties posed by patterns of this sort. However, the specific evolutionary processes responsible for this phenomenon are not fully understood. Words containing sequences of identical consonants may be more likely to arise than those without; processes of word form mutation may be more likely to remove than create sequences of identical consonants in word forms; finally, words containing identical consonants may die out more frequently than those without. Phylogenetic analyses of the evolution of homologous word forms indicate that words with identical consonants arise less frequently than those without, and processes which mutate word forms are more likely to remove sequences of identical consonants than introduce them. However, words with identical consonants do not die out more frequently than those without. Further analyses reveal that forms with identical consonants are replaced in basic meaning functions more frequently than words without. Taken together, results suggest that the under representation of sequences of identical consonants is overwhelmingly a byproduct of constraints on word form coinage, though processes related to word usage also serve to ensure that such patterns are infrequent in more salient vocabulary items. These findings clarify previously unknown aspects of processes of lexical evolution and competition that take place during language change, optimizing communicative systems.