相关论文: Challenges of sampling and how phylogenetic compar…

Phylogenetic methods have broad potential in linguistics beyond tree inference. Here, we show how a phylogenetic approach opens the possibility of gaining historical insights from entirely new kinds of linguistic data--in this instance,…

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…

Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…

Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that…

Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…

I survey some recent approaches to studying change in the lexicon, particularly change in meaning across phylogenies. I briefly sketch an evolutionary approach to language change and point out some issues in recent approaches to studying…

Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

The majority of current phylogenetic comparative methods assume that the stochastic evolutionary process is homogeneous over the phylogeny or offer relaxations of this in rather limited and usually parameter expensive ways. Here we make a…

As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…

By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to…

Comparison and contrast are the basic means to unveil causation and learn which treatments work. To build good comparison groups, randomized experimentation is key, yet often infeasible. In such non-experimental settings, we illustrate and…

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…

Gene innovation is a key mechanism on the evolution and phenotypic diversity of life forms. There is a need for tools able to study gene innovation across an increasingly large number of genomic sequences to maximally capitalise our…

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…

Understanding which phenotypic traits are consistently correlated throughout evolution is a highly pertinent problem in modern evolutionary biology. Here, we propose a multivariate phylogenetic latent liability model for assessing the…

Phylogenetic comparative methods (PCMs) are widely used to study trait evolution. However, many evolutionary histories involve reticulate evolutionary scenarios, such as hybridization, that violate core assumptions of these methods. In this…

Correlations between two variables of a high-dimensional system can be indicative of an underlying interaction, but can also result from indirect effects. Inverse Ising inference is a method to distinguish one from the other. Essentially,…

Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…

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…

Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies…