Related papers: Tracing evolutionary links between species
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…
Darwin's hypothesis that all extant life forms are descendants of a last common ancestor cell and diversification of life forms results from gradual mutation plus natural selection represents a mainstream view that has influenced biology…
The grand challenges in biology today are being shaped by powerful high-throughput technologies that have revealed the genomes of many organisms, global expression patterns of genes and detailed information about variation within…
The rich and varied ways that genetic material can be passed between species has motivated extensive research into the theory of phylogenetic networks. Features that align with biological processes, or with desirable mathematical…
Evolutionary relationships between species are usually represented in phylogenies, i.e. evolutionary trees, which are a type of networks. The terminal nodes of these trees represent species, which are made of individuals and populations…
A hierarchical structure describing the inter-relationships of species has long been a fundamental concept in systematic biology, from Linnean classification through to the more recent quest for a 'Tree of Life.' In this paper we use an…
Rapid developments in genetics and biology have led to phylogenetic methods becoming an important direction in the study of cancer and viral evolution. Although our understanding of gene biology and biochemistry has increased and is…
Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and…
Gene gains and losses have shaped the gene repertoire of species since the universal last common ancestor to species today. Genes in extant species were gained at different historical times via de novo creation of new genes, duplication of…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
The classification of life should be based upon the fundamental mechanism in the evolution of life. We found that the global relationships among species should be circular phylogeny, which is quite different from the common sense based upon…
Darwin claims in the {\em Origin} that similarity is evidence for common ancestry, but that adaptive similarities are "almost valueless" as evidence. This claim seems reasonable for some adaptive similarities but not for others. Here we…
Culture evolves, not just in the trivial sense that cultures change over time, but also in the strong sense that such change is governed by Darwinian principles. Both biological and cultural evolution are essentially cumulative selection…
Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the…
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…
Phylogeny can be inferred using two sources of data from an organism: morphological data and molecular data. Historically, phylogenies were usually inferred using morphological characters, but some morphological features may not necessarily…
Our understanding of the evolutionary process has gone a long way since the publication, 150 years ago, of "On the origin of species" by Charles R. Darwin. The XXth Century witnessed great efforts to embrace replication, mutation, and…
Phylogenetics is a widely used concept in evolutionary biology. It is the reconstruction of evolutionary history by building trees that represent branching patterns and sequences. These trees represent shared history, and it is our…
Many people are familiar with the physico-chemical properties of gene sequences. In this paper I present a mathematical perspective: how do mathematical principles such as information theory, coding theory, and combinatorics influence the…