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34-561: The Oomycetes ( / ˌ oʊ . ə ˈ m aɪ s iː t s / ), or Oomycota , form a distinct phylogenetic lineage of fungus -like eukaryotic microorganisms within the Stramenopiles . They are filamentous and heterotrophic , and can reproduce both sexually and asexually . Sexual reproduction of an oospore is the result of contact between hyphae of male antheridia and female oogonia ; these spores can overwinter and are known as resting spores. Asexual reproduction involves

68-814: 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

102-427: 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

136-482: 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

170-609: 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

204-536: 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,

238-441: 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

272-445: 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

306-442: A very sparse fossil record; a possible oomycete has been described from Cretaceous amber . Oomycota comes from oo- ( ‹See Tfd› Greek : ωόν , translit.   ōon , lit.  "egg") and -mycete ( ‹See Tfd› Greek : μύκητας , translit.   mýkitas , lit.  "fungus"), referring to the large round oogonia , structures containing the female gametes, that are characteristic of

340-399: 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 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

374-609: 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

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408-415: Is a pathogen of mammals. The majority of the plant pathogenic species can be classified into four groups, although more exist. Phylogeny 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

442-423: 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

476-506: 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

510-539: 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

544-715: Is unique to the Kingdom Heterokonta. Spores of the few fungal groups which retain flagella (such as the Chytridiomycetes ) have only one whiplash flagellum. Oomycota and fungi have different metabolic pathways for synthesizing lysine and have a number of enzymes that differ. The ultrastructure is also different, with oomycota having tubular mitochondrial cristae and fungi having flattened cristae. In spite of this, many species of oomycetes are still described or listed as types of fungi and may sometimes be referred to as pseudo fungi, or lower fungi. Most of

578-565: 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 ( phûlon ), meaning "race, lineage", and γένεσις ( génesis ), meaning "origin, source". A rooted phylogenetic tree (see two graphics at top)

612-401: The biology of these organisms supports a relatively close relationship with some photosynthetic organisms, such as brown algae and diatoms . A common taxonomic classification based on these data, places the class Oomycota along with other classes such as Phaeophyceae (brown algae) within the phylum Heterokonta . This relationship is supported by a number of observed differences between

646-449: The characteristics of oomycetes and fungi. For instance, the cell walls of oomycetes are composed of cellulose rather than chitin and generally do not have septations . Also, in the vegetative state they have diploid nuclei, whereas fungi have haploid nuclei. Most oomycetes produce self-motile zoospores with two flagella . One flagellum has a "whiplash" morphology, and the other a branched "tinsel" morphology. The "tinsel" flagellum

680-449: 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

714-497: The formation of chlamydospores and sporangia , producing motile zoospores . Oomycetes occupy both saprophytic and pathogenic lifestyles, and include some of the most notorious pathogens of plants, causing devastating diseases such as late blight of potato and sudden oak death . One oomycete, the mycoparasite Pythium oligandrum , is used for biocontrol , attacking plant pathogenic fungi. The oomycetes are also often referred to as water molds (or water moulds ), although

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748-513: The group was arranged into six orders. However more recently this has been expanded considerably. Haptoglossales Eurychasmales Haliphthorales Olpidiopsidales Atkinsiellales Saprolegniales Leptomitales Rhipidiales Albuginales Peronosporales This group was originally classified among the fungi (the name "oomycota" means "egg fungus") and later treated as protists , based on general morphology and lifestyle. A cladistic analysis based on modern discoveries about

782-409: 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 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

816-713: The oomycetes produce two distinct types of spores. The main dispersive spores are asexual, self-motile spores called zoospores , which are capable of chemotaxis (movement toward or away from a chemical signal, such as those released by potential food sources) in surface water (including precipitation on plant surfaces). A few oomycetes produce aerial asexual spores that are distributed by wind. They also produce sexual spores, called oospores , that are translucent, double-walled, spherical structures used to survive adverse environmental conditions. Many oomycetes species are economically important, aggressive algae and plant pathogens . Some species can cause disease in fish , and at least one

850-473: The oomycetes. The name "water mold" refers to their earlier classification as fungi and their preference for conditions of high humidity and running surface water, which is characteristic for the basal taxa of the oomycetes. The oomycetes rarely have septa (see hypha ), and if they do, they are scarce, appearing at the bases of sporangia, and sometimes in older parts of the filaments. Some are unicellular, while others are filamentous and branching. Previously

884-439: 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

918-452: 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 a binary tree ), and an unrooted bifurcating tree takes

952-405: 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

986-417: 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

1020-410: 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 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

1054-411: 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

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1088-529: 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

1122-404: 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

1156-436: The water-preferring nature which led to that name is not true of most species, which are terrestrial pathogens. Oomycetes were originally grouped with fungi due to similarities in morphology and lifestyle. However, molecular and phylogenetic studies revealed significant differences between fungi and oomycetes which means the latter are now grouped with the stramenopiles (which include some types of algae ). The Oomycota have

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