Related papers: Phylogenetic signal in phonotactics
Recent research has shown that language and the socio-cognitive phenomena associated with it can be aptly modeled and visualized through networks of linguistic entities. However, most of the existing works on linguistic networks focus only…
The study of spoken languages comprises phonology, morphology, and grammar. The languages can be classified as root languages, inflectional languages, and stem languages. In addition, languages continually change over time and space by…
Phylogenetic comparative methods may fail to produce meaningful results when either the underlying model is inappropriate or the data contain insufficient information to inform the inference. The ability to measure the statistical power of…
We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…
Our native language influences the way we perceive speech sounds, affecting our ability to discriminate non-native sounds. We compare two ideas about the influence of the native language on speech perception: the Perceptual Assimilation…
The total-evidence approach to divergence-time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent…
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes…
Recent advances in analysis of subband amplitude envelopes of natural sounds have resulted in convincing synthesis, showing subband amplitudes to be a crucial component of perception. Probabilistic latent variable analysis is particularly…
This paper introduces PhyloLM, a method adapting phylogenetic algorithms to Large Language Models (LLMs) to explore whether and how they relate to each other and to predict their performance characteristics. Our method calculates a…
Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data becomes more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and…
In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species…
Genetic data are often used to infer demographic history and changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed…
Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino-acid usage at contacting sites. Because homologous proteins…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
Animal sounds can be recognised automatically by machine learning, and this has an important role to play in biodiversity monitoring. Yet despite increasingly impressive capabilities, bioacoustic species classifiers still exhibit imbalanced…
Recently there has been renewed interest in phylogenetic inference methods based on phylogenetic invariants, alongside the related Markov invariants. Broadly speaking, both these approaches give rise to polynomial functions of sequence site…
While many studies have previously conducted direct comparisons between results obtained from frequentist and Bayesian models, our research introduces a novel perspective by examining these models in the context of a small dataset…
The application of conventional phylogenetic techniques for inferring cultural history is problematic due to differences in the nature of information transmission in biological and cultural realms. In culture, units of transmission are not…
Computational historical linguistics seeks to systematically understand processes of sound change, including during periods at which little to no formal recording of language is attested. At the same time, few computational resources exist…