Phylogenies in the context of Biological data visualization


Phylogenies in the context of Biological data visualization

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⭐ Core Definition: Phylogenies

A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time. In other words, it 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. In evolutionary biology, all life on Earth is theoretically part of a single phylogenetic tree, indicating common ancestry. Phylogenetics is the study of phylogenetic trees. The main challenge is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of species or taxa. Computational phylogenetics (also phylogeny inference) focuses on the algorithms involved in finding optimal phylogenetic tree in the phylogenetic landscape.

Phylogenetic trees may be rooted or unrooted. 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.

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👉 Phylogenies in the context of Biological data visualization

Biological data visualization is a branch of bioinformatics concerned with the application of computer graphics, scientific visualization, and information visualization to different areas of the life sciences. This includes visualization of sequences, genomes, alignments, phylogenies, macromolecular structures, systems biology, microscopy, and magnetic resonance imaging data. Software tools used for visualizing biological data range from simple, standalone programs to complex, integrated systems.

An emerging trend is the blurring of boundaries between the visualization of 3D structures at atomic resolution, the visualization of larger complexes by cryo-electron microscopy, and the visualization of the location of proteins and complexes within whole cells and tissues. There has also been an increase in the availability and importance of time-resolved data from systems biology, electron microscopy, and cell and tissue imaging.

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Phylogenies in the context of Synapomorphies

In phylogenetics, an apomorphy (or derived trait) is a novel character or character state that has evolved from its ancestral form (or plesiomorphy). A synapomorphy is an apomorphy shared by two or more taxa and is therefore hypothesized to have evolved in their most recent common ancestor.

In cladistics, synapomorphy implies homology.

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Phylogenies in the context of Autapomorphy

In phylogenetics, an autapomorphy is a distinctive feature, known as a derived trait, that is unique to a given taxon. That is, it is found only in one taxon, but not found in any others or outgroup taxa, not even those most closely related to the focal taxon (which may be a species, family or in general any clade). It can therefore be considered as an apomorphy in relation to a single taxon. The word autapomorphy, introduced in 1950 by German entomologist Willi Hennig, is derived from the Ancient Greek words αὐτός (autós), meaning "self"; ἀπό (apó), meaning "away from"; and μορφή (morphḗ), meaning "shape, form".

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Phylogenies in the context of Symplesiomorphy

In phylogenetics, a plesiomorphy ("near form") and symplesiomorphy are synonyms for an ancestral character shared by all members of a clade, which does not distinguish the clade from other clades.

Plesiomorphy, symplesiomorphy, apomorphy, and synapomorphy all mean a trait shared between species because they share an ancestral species.

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Phylogenies in the context of Asteriornis

Asteriornis ("Asteria's bird") is an extinct genus of bird from the Late Cretaceous of Belgium which is known from a single species, Asteriornis maastrichtensis. It was a small, long-legged bird that lived near the coastline and co-existed with more "primitive" types of birds such as Ichthyornis. Asteriornis is one of the oldest-known birds irrefutably belonging to the group Neornithes, which encompasses all modern birds, and is possibly closely related to birds of the extant superorder Galloanserae such as chickens and ducks. It possesses characteristics of both galliformes (chicken-like birds) and anseriformes (duck-like birds), indicating its position as a close relative of the last common ancestor for both groups.

Asteriornis may shed light on why Neornithes were the only dinosaurs to survive the Cretaceous–Paleogene extinction event. Its coexistence with non-neornithean birds such as Ichthyornis implies that competition was not a primary factor for the extinction of non-neornitheans, which resembled modern birds in most respects but died out with other non-avian dinosaurs. Small size, a terrestrial lifestyle, and a generalist diet have all been inferred as ecological advantages possessed by early neornithes, allowing them to survive and diversify in the wake of the extinction. Asteriornis fulfills these qualities, suggesting that such suspicions were justified. Asteriornis is also evidence against a different hypothesis stating that modern birds originated from southern continents. This was supported by biogeographic ancestral reconstructions using phylogenies and the discovery of Vegavis (a possible neornithean from Antarctica), but Asteriornis's presence in Europe suggests that modern birds may have been widespread in northern continents in their early evolution.

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