Related papers: Extended Distance-based Phylogenetic Analyses Appl…
Large Language Models (LLMs) are accelerating scientific idea generation, but rigorously evaluating these numerous, often superficial, AI-generated propositions for novelty and factual accuracy is a critical bottleneck; manual verification…
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…
Aiming to advance research in the field of interpretability of deep learning models for tree species classification using TLS 3D point clouds we present insights in the classification abilities of YOLOv8 through a new framework which…
Time-calibrated species phylogenies are critical for addressing a wide range of questions in evolutionary biology, such as those that elucidate historical biogeography or uncover patterns of coevolution and diversification. Because…
Summary: Both theory and empirical evidence indicate that phylogenies (trees) of different genes (loci) do not display precisely matched topologies. This phylogenetic incongruence is attributed to the reticulated evolutionary history of…
Long-range migrations and the resulting admixtures between populations have been important forces shaping human genetic diversity. Most existing methods for detecting and reconstructing historical admixture events are based on allele…
Using 17 chemical elements as a proxy for stellar DNA, we present a full phylogenetic study of stars in the solar neighbourhood. This entails applying a clustering technique that is widely used in molecular biology to construct an…
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…
Phylogenetic methods have long been used in biology, and more recently have been extended to other fields - for example, linguistics and technology - to study evolutionary histories. Galaxies also have an evolutionary history, and fall…
Continuing improvements in computing hardware are poised to transform capabilities for in silico modeling of cross-scale phenomena underlying major open questions in evolutionary biology and artificial life, such as transitions in…
The construction of a dendogram on a set of individuals is a key component of a genomewide association study. However even with modern sequencing technologies the distances on the individuals required for the construction of such a…
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…
It was recently observed by de Vienne et al. that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on…
We propose a novel combination of methods that (i) portrays quantitative characteristics of a DNA sequence as an image, (ii) computes distances between these images, and (iii) uses these distances to output a map wherein each sequence is a…
Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a…
Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…
When conducting inter-species regression analyses, the phylogenetic relationships between the individual species need to be taken into account. In this paper, a procedure for conducting such analyses is proposed, which only requires the use…
A variant of microcephalin, MCPH1 gene, was introgressed about 37,000 years ago into Homo sapiens genetic pool from an archaic (Homo erectus) lineage and rose to exceptionally high frequency of around 70 percent worldwide today. It is…
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…
Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…