Related papers: Tracing evolutionary links between species

The controversy concerning both the definition of the species and methods for inferring the boundaries and numbers of species has occupied biologists for centuries, and the debate itself has become known as the species problem. The modern…

Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map.…

Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and…

Biological data objects often have both of the following features: (i) they are functions rather than single numbers or vectors, and (ii) they are correlated due to phylogenetic relationships. In this paper we give a flexible statistical…

Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…

The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…

Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…

Many questions that we have about the history and dynamics of organisms have a geographical component: How many are there, and where do they live? How do they move and interbreed across the landscape? How were they moving a thousand years…

The origin of cellular life can be described in terms of the transition from inorganic matter: solids, liquids and gases, to the emergence of cooperative assemblies of organic matter, DNA and proteins,capable of replication and metabolism.…

We use a generalised version of the individual-based Tangled Nature model of evolutionary ecology to study the relationship between ecosystem structure and evolutionary history. Our evolved model ecosystems typically exhibit interaction…

The theory of evolution by natural selection cannot be used to evaluate the truth value of the following proposition: Through evolution, there exists at least one species that can adapt to any one given environment. To address this issue,…

Darwin's theory of evolution is considered to be one of the greatest scientific gems in modern science. It not only gives us a description of how living things evolve, but also shows how a population evolves through time and also, why only…

Reconstructing the evolutionary past of a family of genes is an important aspect of many genomic studies. To help with this, simple operations on a set of sequences called orthology relations may be employed. In addition to being…

Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons invoke evolutionary histories, as…

Evolution is the fundamental physical process that gives rise to biological phenomena. Yet it is widely treated as a subset of population genetics, and thus its scope is artificially limited. As a result, the key issues of how rapidly…

For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…

Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…

It is generally accepted that "diversity" is associated with success in evolutionary algorithms. However, diversity is a broad concept that can be measured and defined in a multitude of ways. To date, most evolutionary computation research…

It is often stated that there are no laws in biology, where everything is contingent and could have been otherwise, being solely the result of historical accidents. Furthermore, the customary introduction of fundamental biological entities…