Related papers: Five Statistical Questions about the Tree of Life
The branching structure of biological evolution confers statistical dependencies on phenotypic trait values in related organisms. For this reason, comparative macroevolutionary studies usually begin with an inferred phylogeny that describes…
Stochastic branching processes are a classical model for describing random trees, which have applications in numerous fields including biology, physics, and natural language processing. In particular, they have recently been proposed to…
The marginal likelihood of a model is a key quantity for assessing the evidence provided by the data in support of a model. The marginal likelihood is the normalizing constant for the posterior density, obtained by integrating the product…
A central question in developmental biology is how size and position are determined. The genetic code carries instructions on how to control these properties in order to regulate the pattern and morphology of structures in the developing…
We propose a generic model of eco-systems, with a {\it hierarchical} food web structure. In our computer simulations we let the eco-system evolve continuously for so long that that we can monitor extinctions as well as speciations over…
Scientists world-wide are putting together massive efforts to understand how the biodiversity that we see on Earth evolved from single-cell organisms at the origin of life and this diversification process is represented through the Tree of…
A wide range of stochastic processes that model the growth and decline of populations exhibit a curious dichotomy: with certainty either the population goes extinct or its size tends to infinity. There is a elegant and classical theorem…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
For many taxa, the current high rates of extinction are likely to result in a significant loss of biodiversity. The evolutionary heritage of biodiversity is frequently quantified by a measure called phylogenetic diversity (PD). We predict…
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…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…
Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in expectation, is additive under a stochastic…
Divergence time estimation requires the reconciliation of two major sources of data. These are fossil and/or biogeographic evidence that give estimates of the absolute age of nodes (ancestors) and molecular estimates that give us estimates…
Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of…
We introduce a notion of finite sampling consistency for phylogenetic trees and show that the set of finitely sampling consistent and exchangeable distributions on n leaf phylogenetic trees is a polytope. We use this polytope to show that…
Human history leaves fingerprints in human languages. Little is known over language evolution and its study is of great importance. Here, we construct a simple stochastic model and compare its results to statistical data of real languages.…
Possibility to establish macroscopic phenomenological theory for biological systems, akin to the akin to the well-established framework of thermodynamics, is briefly reviewed. We introduce the concept of an evolutionary fluctuation-response…