In biology Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, origin, evolution, distribution, and taxonomy, phylogenetics is the study of evolutionary Evolution is the change in the inherited traits of a population of organisms through successive generations. After a population splits into smaller groups, these groups evolve independently and may eventually diversify into new species. Ultimately, life is descended from a common ancestory through a long series of these speciation events, relatedness among various groups of organisms In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole. An organism may either be unicellular (single-celled) or be composed of, as in humans, many trillions of cells grouped into (for example, species In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are often used, such as based on similarity of DNA or or populations), which is discovered through molecular sequencing data and morphological data matrices. The term phylogenetics is of Greek origin from the terms phyle/phylon (φυλή/φῦλον), meaning "tribe, race," and genetikos (γενετικός), meaning "relative to birth" from genesis (γένεσις, "birth"). Taxonomy Alpha taxonomy is the science of finding, describing and categorising organisms, thus leading to the recognition of proposed taxonomic groups, or taxa (singular: taxon), which may then be named, the classification, identification, and naming of organisms, has been richly informed by phylogenetics but remains methodologically and logically distinct.[1] The fields overlap however in the science of phylogenetic systematics – often called "cladism" or "cladistics" –, where only phylogenetic trees are used to delimit taxa A taxon is a group of (one or more) organisms, which a taxonomist adjudges to be a unit. Usually a taxon is given a name and a rank, although neither is a requirement. Defining what belongs or does not belong to such a taxonomic group is done by a taxonomist. It is not uncommon for one taxonomist to disagree with another on what exactly belongs to, which represent groups of lineage-connected individuals.[2] In biological systematics Biological systematics is the study of the diversification of life on the planet Earth, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees . Phylogenies have two components, branching order (showing group relationships) and branch length (showing amount of evolution) as a whole, phylogenetic analyses have become essential in researching the evolutionary tree of life Charles Darwin believed that phylogeny, the ascent of all species through time, was expressible as a metaphor he termed the Tree of Life. The modern development of this idea is called the Phylogenetic tree.

Contents

Construction of a phylogenetic tree

Evolution is regarded as a branching process, whereby populations are altered over time and may speciate into separate branches, hybridize In biology and specifically genetics, hybrid has several meanings, all referring to the offspring of sexual reproduction together, or terminate by extinction In biology and ecology, extinction is the end of an organism or group of taxa. The moment of extinction is generally considered to be the death of the last individual of that species . Because a species' potential range may be very large, determining this moment is difficult, and is usually done retrospectively. This difficulty leads to phenomena. This may be visualized in a phylogenetic tree A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics. The taxa joined together in the tree are implied to have descended from a.

The problem posed by phylogenetics is that genetic Genetics , a broad discipline of biology, is the science of heredity, genes, DNA, mutation, etc., and their functions and aspects in living organisms. The fact that living things inherit traits from their parents has been used since prehistoric times to improve crop plants and animals through selective breeding. However, the modern science of data are only available for the present, and fossil Fossils are the preserved remains or traces of animals, plants, and other organisms from the remote past. The totality of fossils, both discovered and undiscovered, and their placement in fossiliferous (fossil-containing) rock formations and sedimentary layers (strata) is known as the fossil record. The study of fossils across geological time, how records (osteometric data) are sporadic and less reliable. Our knowledge of how evolution operates is used to reconstruct the full tree.[3] Thus, a phylogenetic tree is based on a hypothesis of the order in which evolutionary events are assumed to have occurred.

Cladistics Cladistics is a method of classifying species of organisms into groups called clades, which consist of 1) all the descendants of an ancestral organism and 2) the ancestor itself. For example, birds, dinosaurs, crocodiles, and all descendants of their most recent common ancestor form a clade. In the terms of biological systematics, a clade is a is the current method of choice to infer phylogenetic trees. The most commonly-used methods to infer phylogenies include parsimony Parsimony is the use of the simplest or most frugal route of explanation available. The word derives from Middle English parcimony, from Latin parsimonia, from parsus, past participle of parcere: to spare. It is a general principle that has applications from science to philosophy and all related fields, maximum likelihood Maximum likelihood estimation is a popular statistical method used for fitting a statistical model to data, and providing estimates for the model's parameters, and MCMC Markov chain Monte Carlo methods (which include random walk Monte Carlo methods), are a class of algorithms for sampling from probability distributions based on constructing a Markov chain that has the desired distribution as its equilibrium distribution. The state of the chain after a large number of steps is then used as a sample from the-based Bayesian inference Bayesian inference is statistical inference in which evidence or observations are used to update or to newly infer what is known about underlying parameters or hypotheses. The name "Bayesian" comes from the use of Bayes' theorem in the updating process. Bayes' theorem was introduced by Reverend Thomas Bayes. Phenetics In biology, phenetics, also known as taximetrics, is an attempt to classify organisms based on overall similarity, usually in morphology or other observable traits, regardless of their phylogeny or evolutionary relation. It is closely related to numerical taxonomy which is concerned with the use of numerical methods for taxonomic classification, popular in the mid-20th century but now largely obsolete, uses distance matrix In mathematics, a distance matrix is a matrix containing the distances, taken pairwise, of a set of points. It is therefore a symmetric N×N matrix containing non-negative reals as elements, given N points in Euclidean space. The number of pairs of points N×(N-1)/2 is the number of independent elements in the distance matrix-based methods to construct trees based on overall similarity, which is often assumed to approximate phylogenetic relationships. All methods depend upon an implicit or explicit mathematical model A mathematical model uses mathematical language to describe a system. The process of developing a mathematical model is termed mathematical modelling . Mathematical models are used not only in the natural sciences (such as physics, biology, earth science, meteorology) and engineering disciplines, but also in the social sciences (such as economics, describing the evolution of characters observed in the species included, and are usually used for molecular phylogeny Molecular phylogenetics, also known as molecular systematics, is the use of the structure of molecules to gain information on an organism's evolutionary relationships. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree, wherein the characters are aligned nucleotide Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides play central roles in metabolism. In that capacity, they serve as sources of chemical energy , participate in cellular signaling (cyclic guanosine monophosphate and cyclic adenosine monophosphate), and are incorporated into or amino acid Amino acids are molecules containing an amine group, a carboxylic acid group and a side chain that varies between different amino acids. These molecules contain the key elements of carbon, hydrogen, oxygen, and nitrogen. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula sequences.

Grouping of organisms

Phylogenetic groups, or taxa A taxon is a group of (one or more) organisms, which a taxonomist adjudges to be a unit. Usually a taxon is given a name and a rank, although neither is a requirement. Defining what belongs or does not belong to such a taxonomic group is done by a taxonomist. It is not uncommon for one taxonomist to disagree with another on what exactly belongs to, can be monophyletic In common cladistic usage, a monophyletic group is a taxon which forms a clade, meaning that it consists of an ancestor and all its descendants. The term is synonymous with the uncommon term holophyly. It is contrasted with the terms paraphyly, which is a taxon consisting of an ancestor and some of its descendants, and polyphyly, which is a taxon, paraphyletic A group of taxa is said to be paraphyletic if the group contains its last common ancestor but does not contain all the descendants of that ancestor. This term is used in both phylogenetics[note 1] and linguistics, or polyphyletic For example, the group consisting of warm-blooded animals is polyphyletic, because it contains both mammals and birds, but the most recent common ancestor of mammals and birds was cold-blooded. Warm-bloodedness evolved separately in the ancestors of mammals and the ancestors of birds, so it is not a true phylogenetic grouping.

There are some terms that describe the nature of a grouping in such trees. For instance, all birds and reptiles are believed to have descended from a single common ancestor, so this taxonomic grouping (yellow in the diagram below) is called monophyletic In common cladistic usage, a monophyletic group is a taxon which forms a clade, meaning that it consists of an ancestor and all its descendants. The term is synonymous with the uncommon term holophyly. It is contrasted with the terms paraphyly, which is a taxon consisting of an ancestor and some of its descendants, and polyphyly, which is a taxon. "Modern reptile" (cyan Cyan (pronounced /ˈsaɪæn/; from Greek: κύανoς , meaning "dark blue substance") may be used as the name of any of a number of colors in the blue/green range of the spectrum. In reference to the visible spectrum cyan is used to refer to the color obtained by mixing equal amounts of green and blue light or the removal of red from in the diagram) is a grouping that contains a common ancestor, but does not contain all descendants of that ancestor (birds are excluded). This is an example of a paraphyletic A group of taxa is said to be paraphyletic if the group contains its last common ancestor but does not contain all the descendants of that ancestor. This term is used in both phylogenetics[note 1] and linguistics group. A grouping such as warm-blooded In biology, a warm-blooded animal species is one whose members maintain thermal homeostasis; that is, they keep their body temperature at a roughly constant level, regardless of the ambient temperature. This involves the ability to cool down or produce more body heat. Warm-blooded animals mainly control their body temperature by regulating their animals would include only mammals and birds (red/orange in the diagram) and is called polyphyletic For example, the group consisting of warm-blooded animals is polyphyletic, because it contains both mammals and birds, but the most recent common ancestor of mammals and birds was cold-blooded. Warm-bloodedness evolved separately in the ancestors of mammals and the ancestors of birds, so it is not a true phylogenetic grouping because the members of this grouping do not include the most recent common ancestor.

Molecular phylogenetics

Main article: Molecular phylogenetics Molecular phylogenetics, also known as molecular systematics, is the use of the structure of molecules to gain information on an organism's evolutionary relationships. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree

The evolutionary connections between organisms are represented graphically through phylogenetic trees. Due to the fact that evolution takes place over long periods of time that cannot be observed directly, biologists must reconstruct phylogenies by inferring the evolutionary relationships among present-day organisms. Fossils can aid with the reconstruction of phylogenies; however, fossil records Fossils are the preserved remains or traces of animals, plants, and other organisms from the remote past. The totality of fossils, both discovered and undiscovered, and their placement in fossiliferous (fossil-containing) rock formations and sedimentary layers (strata) is known as the fossil record. The study of fossils across geological time, how are often too poor to be of good help. Therefore, biologists tend to be restricted with analysing present-day organisms to identify their evolutionary relationships. Phylogenetic relationships in the past were reconstructed by looking at phenotypes A phenotype is any observable characteristic or trait of an organism: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior . Phenotypes result from the expression of an organism's genes as well as the influence of environmental factors and the interactions between the two, often anatomical characteristics. Today, molecular data, which includes protein and DNA sequences, are used to construct phylogenetic trees.[4]

Ernst Haeckel's recapitulation theory

During the late 19th century, Ernst Haeckel Ernst Heinrich Philipp August Haeckel , also written von Haeckel, was an eminent German biologist, naturalist, philosopher, physician, professor and artist who discovered, described and named thousands of new species, mapped a genealogical tree relating all life forms, and coined many terms in biology, including phylum, phylogeny, ecology and the's recapitulation theory The theory of recapitulation, also called the biogenetic law or embryological parallelism and often expressed as "ontogeny recapitulates phylogeny" is a discredited biological hypothesis. First proposed by Étienne Serres in 1824–26 as what became known as the "Meckel-Serres Law", it attempted to provide a link between, or biogenetic law, was widely accepted. This theory was often expressed as "ontogeny Ontogeny (ontos present participle of 'to be', genesis 'creation') describes the origin and the development of an organism from the fertilized egg to its mature form. Ontogeny is studied in developmental biology, developmental psychology, developmental cognitive neuroscience, and developmental psychobiology. Ontogeny is that branch of life science recapitulates phylogeny", i.e. the development of an organism exactly mirrors the evolutionary development of the species. Haeckel's early version of this hypothesis [that the embryo mirrors adult evolutionary ancestors] has since been rejected, and the hypothesis amended as the embryo's development mirroring embryos of its evolutionary ancestors. He was accused by five professors of falsifying his images of embryos (See Ernst Haeckel Ernst Heinrich Philipp August Haeckel , also written von Haeckel, was an eminent German biologist, naturalist, philosopher, physician, professor and artist who discovered, described and named thousands of new species, mapped a genealogical tree relating all life forms, and coined many terms in biology, including phylum, phylogeny, ecology and the). Most modern biologists recognize numerous connections between ontogeny and phylogeny, explain them using evolutionary theory Evolutionary developmental biology is a field of biology that compares the developmental processes of different animals and plants in an attempt to determine the ancestral relationship between organisms and how developmental processes evolved. It addresses the origin and evolution of embryonic development; how modifications of development and, or view them as supporting evidence for that theory. Donald I. Williamson suggested that larvae and embryos represented adults in other taxa that have been transferred by hybridization (the larval transfer theory).[5][6] However, Williamson's views do not represent mainstream thought in molecular biology[7], and there is a significant body of evidence against the larval transfer theory.[8]

Gene transfer

In general, organisms can inherit genes in two ways: vertical gene transfer and horizontal gene transfer Horizontal gene transfer , also Lateral gene transfer (LGT), is any process in which an organism incorporates genetic material from another organism without being the offspring of that organism. By contrast, vertical transfer occurs when an organism receives genetic material from its ancestor, e.g. its parent or a species from which it evolved. Vertical gene transfer is the passage of genes from parent to offspring, and horizontal gene transfer or lateral gene transfer Horizontal gene transfer , also Lateral gene transfer (LGT), is any process in which an organism incorporates genetic material from another organism without being the offspring of that organism. By contrast, vertical transfer occurs when an organism receives genetic material from its ancestor, e.g. its parent or a species from which it evolved occurs when genes jump between unrelated organisms, a common phenomenon in prokaryotes The prokaryotes are a group of organisms that lack a cell nucleus (= karyon), or any other membrane-bound organelles. They differ from the eukaryotes, which have a cell nucleus. Most are unicellular, but a few prokaryotes such as myxobacteria have multicellular stages in their life cycles. The word prokaryote comes from the Greek πρό- (pro-) &.

Horizontal gene transfer has complicated the determination of phylogenies of organisms, and inconsistencies in phylogeny have been reported among specific groups of organisms depending on the genes used to construct evolutionary trees.

Carl Woese came up with the three-domain theory of life (eubacteria, archaea and eukaryotes) based on his discovery that the genes encoding ribosomal RNA Ribosomal ribonucleic acid is the central component of the ribosome, the protein manufacturing machinery of all living cells. The function of the rRNA is to provide a mechanism for decoding mRNA into amino acids and to interact with the tRNAs during translation by providing peptidyl transferase activity.The tRNA then brings the necessary amino are ancient and distributed over all lineages of life with little or no horizontal gene transfer. Therefore, rRNAs Ribonucleic acid is a biologically important type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA is very similar to DNA, but differs in a few important structural details: in the cell, RNA is usually single-stranded, while DNA is usually double- are commonly recommended as molecular clocks for reconstructing phylogenies.

This has been particularly useful for the phylogeny of microorganisms, to which the species concept does not apply and which are too morphologically simple to be classified based on phenotypic traits.

Taxon sampling and phylogenetic signal

Owing to the development of advanced sequencing techniques in molecular biology Molecular biology is the study of biology at a molecular level. The field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein, it has become feasible to gather large amounts of data (DNA or amino acid sequences) to infer phylogenetic hypotheses. For example, it is not rare to find studies with character matrices based on whole mitochondrial In cell biology, a mitochondrion is a membrane-enclosed organelle found in most eukaryotic cells. These organelles range from 0.5 to 10 micrometers (μm) in diameter. Mitochondria are sometimes described as "cellular power plants" because they generate most of the cell's supply of adenosine triphosphate (ATP), used as a source of genomes (~16,000 nucleotides, in many animals). However, it has been proposed that it is more important to increase the number of taxa in the matrix than to increase the number of characters, because the more taxa the more robust is the resulting phylogenetic tree [9] . This may be partly due to the breaking up of long branches Long branch attraction is a phenomenon in phylogenetic analyses (most commonly those employing maximum parsimony) when rapidly evolving lineages are inferred to be closely related, regardless of their true evolutionary relationships. For example, in DNA sequence-based analyses, the problem arises when sequences from two (or more) lineages evolve. It has been argued that this is an important reason to incorporate data from fossils into phylogenies where possible. Of course, phylogenetic data that include fossil taxa are generally based on morphology, rather than DNA data. Using simulations, Derrick Zwickl and David Hillis[10] found that increasing taxon sampling in phylogenetic inference has a positive effect on the accuracy of phylogenetic analyses.

Another important factor that affects the accuracy of tree reconstruction is whether the data analyzed actually contain a useful phylogenetic signal, a term that is used generally to denote whether related organisms tend to resemble each other with respect to their genetic material or phenotypic traits.[11] Ultimately, however, there is no way to measure whether a particular phylogenetic hypothesis is accurate or not, unless the "true" relationships among the taxa being examined are already known. The best result an empirical systematist can hope to attain is a tree with branches well-supported by the available evidence.

See also

Evolutionary biology portal Tarbosaurus at the Naturkundemuseum Münster in Münster, Germany

References

  1. ^ Edwards AWF, Cavalli-Sforza LL Phylogenetics is that branch of life science,which deals with the study of evolutionary relation among various groups of organisms,through molecular sequencing data. (1964). Systematics Assoc. Publ. No. 6: Phenetic and Phylogenetic Classification. ed. Reconstruction of evolutionary trees. pp. 67–76.
  2. ^ Speer, Vrian (1998). "UCMP Glossary: Phylogenetics". UC Berkeley. http://www.ucmp.berkeley.edu/glossary/glossary_1.html. Retrieved 2008-03-22.
  3. ^ Cavalli-Sforza LL, Edwards AWF (Sep., 1967). "Phylogenetic analysis: Models and estimation procedures". Evol. 21 (3): 550–570. doi:10.2307/2406616. http://links.jstor.org/sici?sici=0014-3820%28196709%2921%3A3%3C550%3APAMAEP%3E2.0.CO%3B2-I.
  4. ^ Pierce, Benjamin A. (2007-12-17). Genetics: A conceptual Approach (3rd ed.). W. H. Freeman. ISBN 978-0716-77928-5.
  5. ^ Williamson DI (2003-12-31). "xviii". The Origins of Larvae (2nd ed.). Springer. pp. 261. ISBN 978-1402-01514-4.
  6. ^ Williamson DI (2006). "Hybridization in the evolution of animal form and life-cycle". Zoological Journal of the Linnean Society 148: 585–602. doi:10.1111/j.1096-3642.2006.00236.x.
  7. ^ John Timmer, "Examining science on the fringes: vital, but generally wrong", ARS Technica, 9 November 2009
  8. ^ Michael W. Hart, and Richard K. Grosberg, "Caterpillars did not evolve from onychophorans by hybridogenesis", Proceedings of the National Academy of the Sciences, 30 October 2009 (doi: 10.1073/pnas.0910229106)
  9. ^ Wiens J (2006). "Missing data and the design of phylogenetic analyses". Journal of Biomedical Informatics 39: 34–42. doi:10.1016/j.jbi.2005.04.001.
  10. ^ Zwickl DJ, Hillis DM (2002). "Increased taxon sampling greatly reduces phylogenetic error". Systematic Biology 51 (4): 588–598. doi:10.1080/10635150290102339. PMID 12228001.
  11. ^ Blomberg SP, Garland T Jr, Ives AR (2003). "Testing for phylogenetic signal in comparative data: behavioral traits are more labile". Evolution 57 (4): 717–745. PMID 12778543. PDF

Further reading

External links

Basic topics in evolutionary biology
Evidence of common descent
Processes of evolution Adaptation · Macroevolution · Microevolution · Speciation
Population genetic mechanisms Genetic drift · Gene flow · Mutation · Natural selection
Evolutionary developmental biology (Evo-devo) concepts Canalisation · Modularity · Phenotypic plasticity
Evolution of Organs and biological processes Aging · Cellular · DNA · The Ear · The Eye · Flagella · Flight · Hair · Human intelligence · Modular · Muticellular · Sex
Taxa evolution Birds · Butterflies · Dinosaurs · Dolphins and whales · Fungi · Horses · Humans · Influenza · Insects · Lemur · Life · Molluscs · Plants · Sirenians (sea cows) · Spiders
Modes of speciation Anagenesis · Catagenesis · Cladogenesis
History of evolutionary thought Charles Darwin · On the Origin of Species · Modern evolutionary synthesis · Gene-centered view of evolution · Life (classification trees)
Other subfields Ecological genetics · Molecular evolution · Phylogenetics · Systematics
List of evolutionary biology topics · Timeline of evolution
Topics in phylogenetics
Relevant fields Computational phylogenetics · Molecular phylogeny · Cladistics
Basic concepts Phylogenetic tree · Phylogenetic network · Long branch attraction · Clade · Ghost lineage
Inference methods Maximum parsimony · Maximum likelihood · Neighbor-joining · UPGMA · Bayesian inference · Least squares
Current topics PhyloCode · DNA barcoding
-morphy Symplesiomorphy · Apomorphy · Plesiomorphy · Synapomorphy · Autapomorphy
-phyly Monophyly/Holophyly · Paraphyly · Polyphyly
List of evolutionary biology topics

Categories: Phylogenetics

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