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51-528: 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

102-505: A binary tree ), and an unrooted bifurcating tree takes the form of an unrooted binary tree , a free tree with exactly three neighbors at each internal node. In contrast, a rooted multifurcating tree may have more than two children at some nodes and an unrooted multifurcating tree may have more than three neighbors at some nodes. Both rooted and unrooted trees can be either labeled or unlabeled. A labeled tree has specific values assigned to its leaves, while an unlabeled tree, sometimes called

153-540: A phylogenetic analysis of extant organisms and/or fossils . The last universal common ancestor (LUCA) is the most recent common ancestor of all current life on Earth, estimated to have lived some 3.5 to 3.8 billion years ago (in the Paleoarchean ). The project of a complete description of the phylogenetic relationships among all biological species is dubbed the " tree of life ". This involves inference of ages of divergence for all hypothesized clades ; for example,

204-461: A "first couple". It rather reflects the presence of a single individual with high reproductive success in the past, whose genetic contribution has become pervasive throughout the population over time. It is also incorrect to assume that the MRCA passed all, or indeed any, genetic information to every living person. Through sexual reproduction , an ancestor passes half of his or her genes to each descendant in

255-407: A clear outgroup. Another method is midpoint rooting, or a tree can also be rooted by using a non-stationary substitution model . Unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about ancestry. They do not require the ancestral root to be known or inferred. Unrooted trees can always be generated from rooted ones by simply omitting the root. By contrast, inferring

306-813: A combination of genes that come from different genomic sources (e.g., from mitochondrial or plastid vs. nuclear genomes), or genes that would be expected to evolve under different selective regimes, so that homoplasy (false homology ) would be unlikely to result from natural selection. When extinct species are included as terminal nodes in an analysis (rather than, for example, to constrain internal nodes), they are considered not to represent direct ancestors of any extant species. Extinct species do not typically contain high-quality DNA . The range of useful DNA materials has expanded with advances in extraction and sequencing technologies. Development of technologies able to infer sequences from smaller fragments, or from spatial patterns of DNA degradation products, would further expand

357-427: A function of the number of tips. For 10 tips, there are more than 34 × 10 6 {\displaystyle 34\times 10^{6}} possible bifurcating trees, and the number of multifurcating trees rises faster, with ca. 7 times as many of the latter as of the former. A dendrogram is a general name for a tree, whether phylogenetic or not, and hence also for the diagrammatic representation of

408-504: A haplogroup is defined by the accumulation of mutations in STR sequences of the Y-Chromosome of that haplogroup only. Y-DNA network analysis of Y-STR haplotypes showing a non-star cluster indicates Y-STR variability due to multiple founding individuals. Analysis yielding a star cluster can be regarded as representing a population descended from a single ancestor. In this case the variability of

459-411: A matrix of genetic distances . The hierarchical clustering dendrogram would show a column of five nodes representing the initial data (here individual taxa), and the remaining nodes represent the clusters to which the data belong, with the arrows representing the distance (dissimilarity). The distance between merged clusters is monotone, increasing with the level of the merger: the height of each node in

510-471: A more reticulate evolutionary history of the organisms sampled. Most recent common ancestor In biology and genetic genealogy , the most recent common ancestor ( MRCA ), also known as the last common ancestor ( LCA ), of a set of organisms is the most recent individual from which all the organisms of the set are descended . The term is also used in reference to the ancestry of groups of genes ( haplotypes ) rather than organisms. The MRCA of

561-608: A more suitable metaphor than the tree . Indeed, phylogenetic corals are useful for portraying past and present life, and they have some advantages over trees ( anastomoses allowed, etc.). Phylogenetic trees composed with a nontrivial number of input sequences are constructed using computational phylogenetics methods. Distance-matrix methods such as neighbor-joining or UPGMA , which calculate genetic distance from multiple sequence alignments , are simplest to implement, but do not invoke an evolutionary model. Many sequence alignment methods such as ClustalW also create trees by using

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612-594: A non-genetic, mathematical model or computer simulation. In organisms using sexual reproduction , the matrilineal MRCA and patrilineal MRCA are the MRCAs of a given population considering only matrilineal and patrilineal descent, respectively. The MRCA of a population by definition cannot be older than either its matrilineal or its patrilineal MRCA. In the case of Homo sapiens , the matrilineal and patrilineal MRCA are also known as " Mitochondrial Eve " (mt-MRCA) and " Y-chromosomal Adam " (Y-MRCA) respectively. The age of

663-536: A number of different formats, all of which must represent the nested structure of a tree. They may or may not encode branch lengths and other features. Standardized formats are critical for distributing and sharing trees without relying on graphics output that is hard to import into existing software. Commonly used formats are Although phylogenetic trees produced on the basis of sequenced genes or genomic data in different species can provide evolutionary insight, these analyses have important limitations. Most importantly,

714-437: A phylogenetic tree. A cladogram only represents a branching pattern; i.e., its branch lengths do not represent time or relative amount of character change, and its internal nodes do not represent ancestors. A phylogram is a phylogenetic tree that has branch lengths proportional to the amount of character change. A chronogram is a phylogenetic tree that explicitly represents time through its branch lengths. A Dahlgrenogram

765-448: A set of individuals can sometimes be determined by referring to an established pedigree . However, in general, it is impossible to identify the exact MRCA of a large set of individuals, but an estimate of the time at which the MRCA lived can often be given. Such time to most recent common ancestor ( TMRCA ) estimates can be given based on DNA test results and established mutation rates as practiced in genetic genealogy, or by reference to

816-523: A single sex chromosome in the male individual and is passed on to male descendants without recombination. It can be used to trace patrilineal inheritance and to find the Y-chromosomal Adam , the most recent common ancestor of all humans via the Y-DNA pathway. Approximate dates for Mitochondrial Eve and Y-chromosomal Adam have been established by researchers using genealogical DNA tests . Mitochondrial Eve

867-444: A tree shape, defines a topology only. Some sequence-based trees built from a small genomic locus, such as Phylotree, feature internal nodes labeled with inferred ancestral haplotypes. The number of possible trees for a given number of leaf nodes depends on the specific type of tree, but there are always more labeled than unlabeled trees, more multifurcating than bifurcating trees, and more rooted than unrooted trees. The last distinction

918-481: Is a diagram representing a tree . This diagrammatic representation is frequently used in different contexts: The name dendrogram derives from the two ancient greek words δένδρον ( déndron ), meaning "tree", and γράμμα ( grámma ), meaning "drawing, mathematical figure". For a clustering example, suppose that five taxa ( a {\displaystyle a} to e {\displaystyle e} ) have been clustered by UPGMA based on

969-602: Is a diagram representing a cross section of a phylogenetic tree. A phylogenetic network is not strictly speaking a tree, but rather a more general graph , or a directed acyclic graph in the case of rooted networks. They are used to overcome some of the limitations inherent to trees. A spindle diagram, or bubble diagram, is often called a romerogram, after its popularisation by the American palaeontologist Alfred Romer . It represents taxonomic diversity (horizontal width) against geological time (vertical axis) in order to reflect

1020-629: Is estimated to have lived about 200,000 years ago. A paper published in March 2013 determined that, with 95% confidence and that provided there are no systematic errors in the study's data, Y-chromosomal Adam lived between 237,000 and 581,000 years ago. The MRCA of all humans alive today would, therefore, need to have lived more recently than either. It is more complicated to infer human ancestry via autosomal chromosomes . Although an autosomal chromosome contains genes that are passed down from parents to children via independent assortment from only one of

1071-506: Is most true of genetic material that is subject to lateral gene transfer and recombination , where different haplotype blocks can have different histories. In these types of analysis, the output tree of a phylogenetic analysis of a single gene is an estimate of the gene's phylogeny (i.e. a gene tree) and not the phylogeny of the taxa (i.e. species tree) from which these characters were sampled, though ideally, both should be very close. For this reason, serious phylogenetic studies generally use

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1122-566: Is nearly immune to sexual mixing, unlike the nuclear DNA whose chromosomes are shuffled and recombined in Mendelian inheritance . Mitochondrial DNA, therefore, can be used to trace matrilineal inheritance and to find the Mitochondrial Eve (also known as the African Eve ), the most recent common ancestor of all humans via the mitochondrial DNA pathway. Likewise, Y chromosome is present as

1173-537: Is the most biologically relevant; it arises because there are many places on an unrooted tree to put the root. For bifurcating labeled trees, the total number of rooted trees is: For bifurcating labeled trees, the total number of unrooted trees is: Among labeled bifurcating trees, the number of unrooted trees with n {\displaystyle n} leaves is equal to the number of rooted trees with n − 1 {\displaystyle n-1} leaves. The number of rooted trees grows quickly as

1224-542: The European Neolithic . The age of the MRCA of all living humans is unknown. It is necessarily younger than the age of either the matrilinear or the patrilinear MRCA, both of which have an estimated age of between roughly 100,000 and 200,000 years ago. A study by mathematicians Joseph T. Chang, Douglas Rohde and Steve Olson used a theoretical model to calculate that the MRCA may have lived remarkably recently, possibly as recently as 2,000 years ago. It concludes that

1275-503: The Y-STR sequence, also called the microsatellite variation, can be regarded as a measure of the time passed since the ancestor founded this particular population. The descendants of Genghis Khan or one of his ancestors represents a famous star cluster that can be dated back to the time of Genghis Khan. TMRCA calculations are considered critical evidence when attempting to determine migration dates of various populations as they spread around

1326-403: The last universal common ancestor (human– bacteria ). It is also possible to consider the ancestry of individual genes (or groups of genes, haplotypes ) instead of an organism as a whole. Coalescent theory describes a stochastic model of how the ancestry of such genetic markers maps to the history of a population. Unlike organisms, a gene is passed down from a generation of organisms to

1377-470: The Americas. European colonization of the Americas and Australia was found by Chang to be too recent to have had a substantial impact on the age of the MRCA. In fact, if the Americas and Australia had never been discovered by Europeans, the MRCA would only be about 2.3% further back in the past than it is. Note that the age of the MRCA of a population does not correspond to a population bottleneck , let alone

1428-600: The MRCA of all Carnivora ( cats , dogs , etc) is estimated to have diverged some 42 million years ago ( Miacidae ). The concept of the last common ancestor from the perspective of human evolution is described for a popular audience in The Ancestor's Tale by Richard Dawkins (2004). Dawkins lists "concestors" of the human lineage in order of increasing age, including hominin (human– chimpanzee ), hominine (human– gorilla ), hominid (human– orangutan ), hominoid (human– gibbon ), and so on in 40 stages in total, down to

1479-573: The MRCA of all humans probably lived in East Asia, which would have given them key access to extremely isolated populations in Australia and the Americas. Possible locations for the MRCA include places such as the Chuckchi and Kamchatka Peninsulas that are close to Alaska, places such as Indonesia and Malaysia that are close to Australia or a place such as Taiwan or Japan that is more intermediate to Australia and

1530-543: The ancestry of a set of populations. In this case, populations are defined by the accumulation of mutations on the mtDNA, and special trees are created for the mutations and the order in which they occurred in each population. The tree is formed through the testing of a large number of individuals all over the world for the presence or lack of a certain set of mutations. Once this is done it is possible to determine how many mutations separate one population from another. The number of mutations, together with estimated mutation rate of

1581-529: 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

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1632-402: The extant population. The identical ancestors point is a point in the past more remote than the MRCA at which time there are no longer organisms which are ancestral to some but not all of the modern population. Due to pedigree collapse , modern individuals may still exhibit clustering, due to vastly different contributions from each of ancestral population. Dendrogram A dendrogram

1683-472: The genealogical MRCA (most recent common ancestor by any line of descent) of all living humans cannot be traced genetically because the DNA of the great majority of ancestors is completely lost after a few hundred years. It is therefore computed based on non-genetic, mathematical models and computer simulations. Since Mitochondrial Eve and Y-chromosomal Adam are traced by single genes via a single ancestral parent line,

1734-526: The human MRCA is unknown. It is no greater than the age of either the Y-MRCA or the mt-MRCA, estimated at around 200,000 years. Unlike in pedigrees of individual humans or domesticated lineages where historical parentage is known, in the inference of relationships among species or higher groups of taxa ( systematics or phylogenetics ), ancestors are not directly observable or recognizable. They are inferences based on patterns of relationship among taxa inferred in

1785-429: The mtDNA in the regions tested, allows scientists to determine the approximate time to MRCA ( TMRCA ) which indicates time passed since the populations last shared the same set of mutations or belonged to the same haplogroup . In the case of Y-Chromosomal DNA, TMRCA is arrived at in a different way. Y-DNA haplogroups are defined by single-nucleotide polymorphism in various regions of the Y-DNA. The time to MRCA within

1836-445: The next generation either as perfect replicas of itself or as slightly mutated descendant genes . While organisms have ancestry graphs and progeny graphs via sexual reproduction , a gene has a single chain of ancestors and a tree of descendants. An organism produced by sexual cross-fertilization ( allogamy ) has at least two ancestors (its immediate parents), but a gene always has one ancestor per generation. Mitochondrial DNA (mtDNA)

1887-431: The next generation; in the absence of pedigree collapse , after just 32 generations the contribution of a single ancestor would be on the order of 2 , a number proportional to less than a single basepair within the human genome . The MRCA is the most recent common ancestor shared by all individuals in the population under consideration. This MRCA may well have contemporaries who are also ancestral to some but not all of

1938-407: The observed divergence is due to migration as evidenced by the archaeological record. However, if the date of genetic divergence occurs at a different time than the archaeological record, then scientists will have to look at alternate archaeological evidence to explain the genetic divergence. The issue is best illustrated in the debate surrounding the demic diffusion versus cultural diffusion during

1989-436: The optimal tree using many of these techniques is NP-hard , so heuristic search and optimization methods are used in combination with tree-scoring functions to identify a reasonably good tree that fits the data. Tree-building methods can be assessed on the basis of several criteria: Tree-building techniques have also gained the attention of mathematicians. Trees can also be built using T-theory . Trees can be encoded in

2040-402: The parent of all other nodes in the tree. The root is therefore a node of degree 2, while other internal nodes have a minimum degree of 3 (where "degree" here refers to the total number of incoming and outgoing edges). The most common method for rooting trees is the use of an uncontroversial outgroup —close enough to allow inference from trait data or molecular sequencing, but far enough to be

2091-405: The range of DNA considered useful. Phylogenetic trees can also be inferred from a range of other data types, including morphology, the presence or absence of particular types of genes, insertion and deletion events – and any other observation thought to contain an evolutionary signal. Phylogenetic networks are used when bifurcating trees are not suitable, due to these complications which suggest

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2142-473: 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

2193-573: The root of an unrooted tree requires some means of identifying ancestry. This is normally done by including an outgroup in the input data so that the root is necessarily between the outgroup and the rest of the taxa in the tree, or by introducing additional assumptions about the relative rates of evolution on each branch, such as an application of the molecular clock hypothesis . Both rooted and unrooted trees can be either bifurcating or multifurcating. A rooted bifurcating tree has exactly two descendants arising from each interior node (that is, it forms

2244-416: The simpler algorithms (i.e. those based on distance) of tree construction. Maximum parsimony is another simple method of estimating phylogenetic trees, but implies an implicit model of evolution (i.e. parsimony). More advanced methods use the optimality criterion of maximum likelihood , often within a Bayesian framework , and apply an explicit model of evolution to phylogenetic tree estimation. Identifying

2295-437: The time to these genetic MRCAs will necessarily be greater than that for the genealogical MRCA. This is because single genes will coalesce more slowly than tracing of conventional human genealogy via both parents. The latter considers only individual humans, without taking into account whether any gene from the computed MRCA actually survives in every single person in the current population. Mitochondrial DNA can be used to trace

2346-411: The tree before hybridisation takes place, and conserved sequences . Also, there are problems in basing an analysis on a single type of character, such as a single gene or protein or only on morphological analysis, because such trees constructed from another unrelated data source often differ from the first, and therefore great care is needed in inferring phylogenetic relationships among species. This

2397-526: The trees that they generate are not necessarily correct – they do not necessarily accurately represent the evolutionary history of the included taxa. As with any scientific result, they are subject to falsification by further study (e.g., gathering of additional data, analyzing the existing data with improved methods). The data on which they are based may be noisy ; the analysis can be confounded by genetic recombination , horizontal gene transfer , hybridisation between species that were not nearest neighbors on

2448-420: The two ancient greek words φῦλον ( phûlon ), meaning "race, lineage", and γένεσις ( génesis ), 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. The root node does not have a parent node, but serves as

2499-652: The two parents, genetic recombination ( chromosomal crossover ) mixes genes from non-sister chromatids from both parents during meiosis , thus changing the genetic composition of the chromosome. Different types of MRCAs are estimated to have lived at different times in the past. These time to MRCA ( TMRCA ) estimates are also computed differently depending on the type of MRCA being considered. Patrilineal and matrilineal MRCAs (Mitochondrial Eve and Y-chromosomal Adam) are traced by single gene markers, thus their TMRCA are computed based on DNA test results and established mutation rates as practiced in genetic genealogy. The time to

2550-399: The variation of abundance of various taxa through time. A spindle diagram is not an evolutionary tree: the taxonomic spindles obscure the actual relationships of the parent taxon to the daughter taxon and have the disadvantage of involving the paraphyly of the parental group. This type of diagram is no longer used in the form originally proposed. Darwin also mentioned that the coral may be

2601-446: The world. For example, if a mutation is deemed to have occurred 30,000 years ago, then this mutation should be found amongst all populations that diverged after this date. If archeological evidence indicates cultural spread and formation of regionally isolated populations then this must be reflected in the isolation of subsequent genetic mutations in this region. If genetic divergence and regional divergence coincide it can be concluded that

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