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.

To fully exploit the potential of computational phylogenetic methods for cognate data one needs to leverage specific (complex) models an machine learning-based techniques. However, both approaches require datasets that are substantially larger than the manually collected cognate data currently available. To the best of our knowledge, there exists no feasible approach to automatically generate larger cognate datasets. We substantiate this claim by automatically extracting datasets from BabelNet, a large multilingual encyclopedic dictionary. We demonstrate that phylogenetic inferences on the respective character matrices yield trees that are largely inconsistent with the established gold standard ground truth trees. We also discuss why we consider it as being unlikely to be able to extract more suitable character matrices from other multilingual resources. Phylogenetic data analysis approaches that require larger datasets can therefore not be applied to cognate data. Thus, it remains an open question how, and if these computational approaches can be applied in historical linguistics.

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.

Lexical resemblances among a group of languages indicate that the languages could be genetically related, i.e., they could have descended from a common ancestral language. However, such resemblances can arise by chance and, hence, need not always imply an underlying genetic relationship. Many tests of significance based on permutation of wordlists and word similarity measures appeared in the past to determine the statistical significance of such relationships. We demonstrate that although existing tests may work well for bilateral comparisons, i.e., on pairs of languages, they are either infeasible by design or are prone to yield false positives when applied to groups of languages or language families. To this end, inspired by molecular phylogenetics, we propose a likelihood ratio test to determine if given languages are related based on the proportion of invariant character sites in the aligned wordlists applied during tree inference. Further, we evaluate some language families and show that the proposed test solves the problem of false positives. Finally, we demonstrate that the test supports the existence of macro language families such as Nostratic and Macro-Mayan.