Related papers: Detecting adaptive evolution in phylogenetic compa…

One of the most intriguing questions in evolution is how organisms exhibit suitable phenotypic variation to rapidly adapt in novel selective environments which is crucial for evolvability. Recent work showed that when selective environments…

Predicting the adaptation of populations to a changing environment is crucial to assess the impact of human activities on biodiversity. Many theoretical studies have tackled this issue by modeling the evolution of quantitative traits…

Many machine learning models have been proposed to classify phenotypes from gene expression data. In addition to their good performance, these models can potentially provide some understanding of phenotypes by extracting explanations for…

Evolutionary relationships between species are usually inferred through phylogenetic analysis, which provides phylogenetic trees computed from allelic profiles built by sequencing specific regions of the sequences and abstracting them to…

Populations of isogenic embryonic stem cells or clonal bacteria often exhibit extensive phenotypic heterogeneity which arises from stochastic intrinsic dynamics of cells. The internal state of the cell can be transmitted epigenetically in…

1) Micro-evolutionary predictions are complicated by ecological feedbacks like density dependence, while ecological predictions can be complicated by evolutionary change. A widely used approach in micro-evolution, quantitative genetics,…

We consider a transformed Ornstein-Uhlenbeck process model that can be a good candidate for modelling real-life processes characterized by a combination of time-reverting behaviour with heavy distribution tails. We begin with presenting the…

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…

Learning is a fundamental property of intelligent systems, observed across biological organisms and engineered systems. While modern intelligent systems typically rely on gradient descent for learning, the need for exact gradients and…

Principal component analysis is a widely-used method for the dimensionality reduction of a given data set in a high-dimensional Euclidean space. Here we define and analyze two analogues of principal component analysis in the setting of…

Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation…

Post-genomic research deals with challenging problems in screening genomes of organisms for particular functions or potential for being the targets of genetic engineering for desirable biological features. 'Phenotyping' of wild type and…

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…

All possible phenotypes are not equally accessible to evolving populations. In fact, only phenotypes of large size, i.e. those resulting from many different genotypes, are found in populations of sequences, presumably because they are…

Recognition of evolutionary units (species, populations) requires integrating several kinds of data such as genetic or phenotypic markers or spatial information, in order to get a comprehensive view concerning the differentiation of the…

One of the basic questions of phylogenomics is how gene function evolves, whether among species or inside gene families. In this chapter, we provide a brief overview of the problems associated with defining gene function in a manner which…

Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…

Phenology, the timing of cyclical plant life events such as leaf emergence and coloration, is crucial in the bio-climatic system. Climate change drives shifts in these phenological events, impacting ecosystems and the climate itself.…

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…

In this paper, the sensitivity analysis of a single scale model is employed in order to reduce the input dimensionality of the related multiscale model, in this way, improving the efficiency of its uncertainty estimation. The approach is…