相关论文: Phylogenetic signal in phonotactics

Traditional linguistic theories have largely regard language as a formal system composed of rigid rules. However, their failures in processing real language, the recent successes in statistical natural language processing, and the findings…

The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…

Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…

Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…

We provide an introductory review of Bayesian data analytical methods, with a focus on applications for linguistics, psychology, psycholinguistics, and cognitive science. The empirically oriented researcher will benefit from making Bayesian…

In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…

The speech signal conveys information on different time scales from short time scale or segmental, associated to phonological and phonetic information to long time scale or supra segmental, associated to syllabic and prosodic information.…

Binary trait data record the presence or absence of distinguishing traits in individuals. We treat the problem of estimating ancestral trees with time depth from binary trait data. Simple analysis of such data is problematic. Each homology…

Using Phylogenetic Algebraic Geometry, we analyze computationally the phylogenetic tree of subfamilies of the Indo-European language family, using data of syntactic structures. The two main sources of syntactic data are the SSWL database…

The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of…

We have developed an alignment-free method that calculates phylogenetic distances using a maximum likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic…

Newberry et al. (Detecting evolutionary forces in language change, Nature 551, 2017) tackle an important but difficult problem in linguistics, the testing of selective theories of language change against a null model of drift. Having…

A number of signal processing and statistical methods can be used in analyzing either pieces of text or DNA sequences. These techniques can be used in a number of ways, such as determining authorship of documents, finding genes in DNA, and…

Basic vocabulary in many Sulawesi Austronesian languages includes forms resisting reconstruction to any proto-form with phonological patterns inconsistent with inherited roots, but whether this non-conforming vocabulary represents…

Phylogenetic methods typically rely on an appropriate model of how data evolved in order to infer an accurate phylogenetic tree. For molecular data, standard statistical methods have provided an effective strategy for extracting…

Phylogenies (ancestry trees) depict the evolutionary history of an evolving population. In evolutionary computing, a phylogeny can reveal how an evolutionary algorithm steers a population through a search space, illuminating the…

Cultural phylogenies, or "trees" of culture, are typically built using methods from biology that use similarities and differences in artifacts to infer the historical relationships between the populations that produced them. While these…

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…

The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…

Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in…