A phylogenetic tree (also phylogeny or evolutionary tree) is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. All life on Earth is part of a single phylogenetic tree, indicating common ancestry.
In a rooted phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of those descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetics. Unrooted trees illustrate only the relatedness of the leaf nodes and do not require the ancestral root to be known or inferred.
The idea of a tree of life arose from ancient notions of a ladder-like progression from lower into higher forms of life (such as in the Great Chain of Being). Early representations of "branching" phylogenetic trees include a "paleontological chart" showing the geological relationships among plants and animals in the book Elementary Geology, by Edward Hitchcock (first edition: 1840).
Charles Darwin featured a diagrammatic evolutionary "tree" in his 1859 book On the Origin of Species. Over a century later, evolutionary biologists still use tree diagrams to depict evolution because such diagrams effectively convey the concept that speciation occurs through the adaptive and semirandom splitting of lineages.
The term phylogenetic, or phylogeny, derives from the two ancient greek words φῦλον (), meaning "race, lineage", and γένεσις (), meaning "origin, source".
A rooted phylogenetic tree (see two graphics at top) is a directed tree with a unique node — the root — corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves of the tree.
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This course covers various data analysis approaches associated with applications of DNA sequencing technologies, from genome sequencing to quantifying gene expression, transcription factor binding and
The presentation of tree growth and formation of wood anatomical structures, linked to the description of specific physical and mechanical properties, makes it possible to understand the different for
Identifier et comprendre les débats et problèmes centraux en philosophie de la biologie, notamment autour de l'évolution biologique et de l'émergence du vivant. Evaluer et comparer les arguments cruci
In biology, a species (: species) is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. It is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. Other ways of defining species include their karyotype, DNA sequence, morphology, behaviour, or ecological niche. In addition, paleontologists use the concept of the chronospecies since fossil reproduction cannot be examined.
In biology, phylogenetics (ˌfaɪloʊdʒəˈnɛtɪks,_-lə-) is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by phylogenetic inference methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology. The result of such an analysis is a phylogenetic tree—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms.
The eukaryotes constitute the domain of Eukaryota (juːˈkærioʊts,_-əts), organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms are eukaryotes. They constitute a major group of life forms, alongside the two groups of prokaryotes, the Bacteria and the Archaea. Eukaryotes represent a small minority of the number of organisms, but due to their generally much larger size, their collective global biomass is much larger than that of prokaryotes.
In this paper we consider two aspects of the inverse problem of how to construct merge trees realizing a given barcode. Much of our investigation exploits a recently discovered connection between the symmetric group and barcodes in general position, based ...
2024
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Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...
Glacier-fed streams are the cold, ultra-oligotrophic, and unstable streams that are fed by glacial meltwater. Despite these extreme conditions, they harbour a diverse and abundant microbial diversity that develops into biofilms, covering the boulders and s ...