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77-554: 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

154-498: A model organism ). Free-living ciliates are usually the top heterotrophs and predators in microbial food webs, feeding on bacteria and smaller eukaryotes, present in a variety of ecosystems, although a few species are kleptoplastic . Others are parasitic of numerous animals. Ciliates have a basal position in the evolution of alveolates, together with a few species of heterotrophic flagellates with two cilia collectively known as colponemids . The remaining alveolates are grouped under

231-421: A big portion of the oxygen produced worldwide, and comprising much of the marine phytoplankton ; the brown algae , filamentous or 'truly' multicellular (with differentiated tissues) macroalgae that constitute the basis of many temperate and cold marine ecosystems, such as kelp forests ; and the golden algae , unicellular or colonial flagellates that are mostly present in freshwater habitats. Inside Gyrista,

308-449: A collection of amoebae, flagellates and amoeboflagellates with complex life cycles, among which are some slime molds ( acrasids ). The two clades Euglenozoa and Percolozoa are sister taxa, united under the name Discicristata , in reference to their mitochondrial cristae shaped like discs. The species Tsukubamonas globosa is a free-living flagellate whose precise position within Discoba

385-814: 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

462-427: 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

539-476: 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

616-601: A major cause of harmful algal blooms due to their toxicity; some live as symbionts of corals, allowing the creation of coral reefs. Dinoflagellates exhibit a diversity of cellular structures, such as complex eyelike ocelli, specialized vacuoles, bioluminescent organelles, and a wall surrounding the cell known as the theca . Rhizaria is a lineage of morphologically diverse organisms, composed almost entirely of unicellular heterotrophic amoebae, flagellates and amoeboflagellates, commonly with reticulose (net-like) or filose (thread-like) pseudopodia for feeding and locomotion. It

693-463: A more reticulate evolutionary history of the organisms sampled. Protists A protist ( / ˈ p r oʊ t ɪ s t / PROH -tist ) or protoctist is any eukaryotic organism that is not an animal , land plant , or fungus . Protists do not form a natural group, or clade , but are a polyphyletic grouping of several independent clades that evolved from the last eukaryotic common ancestor . Protists were historically regarded as

770-609: 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

847-536: 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,

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924-441: 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

1001-699: A separate taxonomic kingdom known as Protista or Protoctista . With the advent of phylogenetic analysis and electron microscopy studies, the use of Protista as a formal taxon was gradually abandoned. In modern classifications, protists are spread across several eukaryotic clades called supergroups , such as Archaeplastida ( photoautotrophs that includes land plants), SAR , Obazoa (which includes fungi and animals), Amoebozoa and Excavata . Protists represent an extremely large genetic and ecological diversity in all environments, including extreme habitats. Their diversity, larger than for all other eukaryotes, has only been discovered in recent decades through

1078-469: A small group (3 species) of freshwater or marine suspension-feeding bacterivorous flagellates with typical excavate appearance, closely resembling Jakobida and some metamonads but not phylogenetically close to either in most analyses. Diaphoretickes includes nearly all photosynthetic eukaryotes. Within this clade, the TSAR supergroup gathers a colossal diversity of protists. The most basal branching member of

1155-445: 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

1232-474: A variety of algae. In addition, two smaller groups, Haptista and Cryptista , also belong to Diaphoretickes. The Stramenopiles, also known as Heterokonta, are characterized by the presence of two cilia, one of which bears many short, straw-like hairs ( mastigonemes ). They include one clade of phototrophs and numerous clades of heterotrophs, present in virtually all habitats. Stramenopiles include two usually well-supported clades, Bigyra and Gyrista , although

1309-443: A very sparse fossil record; a possible oomycete has been described from Cretaceous amber . Oomycota comes from oo- ( Ancient Greek : ωόν , romanized :  ōon , lit.   'egg') and -mycete ( Ancient Greek : μύκητας , romanized :  mýkitas , lit.   'fungus'), referring to the large round oogonia , structures containing the female gametes, that are characteristic of

1386-420: A wide variety of animals – which act as secondary or intermediate host – but can undergo sexual reproduction only in the primary or definitive host (for example: felids such as domestic cats in this case). Some species, for example Plasmodium falciparum , have extremely complex life cycles that involve multiple forms of the organism, some of which reproduce sexually and others asexually. However, it

1463-565: Is paraphyletic , with some analyses placing the root of the eukaryote tree within Metamonada. Discoba includes three major groups: Jakobida , Euglenozoa and Percolozoa . Jakobida are a small group (~20 species) of free-living heterotrophic flagellates, with two cilia, that primarily eat bacteria through suspension feeding; most are aquatic aerobes, with some anaerobic species, found in marine, brackish or fresh water. They are best known for their bacterial-like mitochondrial genomes. Euglenozoa

1540-399: 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

1617-604: 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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1694-415: 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

1771-440: Is a rich (>2,000 species) group of flagellates with very different lifestyles, including: the free-living heterotrophic (both osmo- and phagotrophic) and photosynthetic euglenids (e.g., the euglenophytes , with chloroplasts originated from green algae); the free-living and parasitic kinetoplastids (such as the trypanosomes ); the deep-sea anaerobic symbiontids ; and the elusive diplonemids . Percolozoa (~150 species) are

1848-423: 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

1925-506: 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

2002-445: Is not yet settled, but is probably more closely related to Discicristata than to Jakobida. The metamonads (Metamonada) are a phylum of completely anaerobic or microaerophilic protozoa, primarily flagellates . Some are gut symbionts of animals such as termites , others are free-living, and others are parasitic. They include three main clades: Fornicata , Parabasalia and Preaxostyla . Fornicata (>140 species) encompasses

2079-500: Is termed protistology . Protists are a diverse group of eukaryotes (organisms whose cells possess a nucleus ) that are primarily single-celled and microscopic but exhibit a wide variety of shapes and life strategies. They have different life cycles , trophic levels , modes of locomotion , and cellular structures . Although most protists are unicellular , there is a considerable range of multicellularity amongst them; some form colonies or multicellular structures visible to

2156-539: 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

2233-402: Is unclear how frequently sexual reproduction causes genetic exchange between different strains of Plasmodium in nature and most populations of parasitic protists may be clonal lines that rarely exchange genes with other members of their species. The pathogenic parasitic protists of the genus Leishmania have been shown to be capable of a sexual cycle in the invertebrate vector, likened to

2310-698: 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

2387-408: Is widespread among multicellular eukaryotes, it seemed unlikely until recently, that sex could be a primordial and fundamental characteristic of eukaryotes. The main reason for this view was that sex appeared to be lacking in certain pathogenic protists whose ancestors branched off early from the eukaryotic family tree. However, several of these "early-branching" protists that were thought to predate

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2464-499: The bicosoecids , phagotrophic flagellates that consume bacteria, and the closely related Placidozoa , which consists of several groups of heterotrophic flagellates (e.g., the deep-sea halophilic Placididea ) as well as the intestinal commensals known as Opalinata (e.g., the human parasite Blastocystis , and the highly unusual opalinids , composed of giant cells with numerous nuclei and cilia, originally misclassified as ciliates). The alveolates (Alveolata) are characterized by

2541-716: The bigyromonads , a group of bacterivorous or eukaryovorous phagotrophs. A small group of heliozoan-like heterotrophic amoebae, Actinophryida , has an uncertain position, either within or as the sister taxon of Ochrophyta. The little studied phylum Bigyra is an assemblage of exclusively heterotrophic organisms, most of which are free-living. It includes the Labyrinthulomycetes , among which are single-celled amoeboid phagotrophs, mixotrophs, and fungus-like filamentous heterotrophs that create slime networks to move and absorb nutrients, as well as some parasites. Also included in Bigyra are

2618-547: The diplomonads , with two nuclei (e.g., Giardia , genus of well-known parasites of humans), and several smaller groups of free-living, commensal and parasitic protists (e.g., Carpediemonas , retortamonads ). Parabasalia (>460 species) is a varied group of anaerobic, mostly endobiotic organisms, ranging from small parasites (like Trichomonas vaginalis , another human pathogen) to giant intestinal symbionts with numerous flagella and nuclei found in wood-eating termites and cockroaches . Preaxostyla (~140 species) includes

2695-532: The heterotrophic protists, known as protozoa , were considered part of the animal kingdom , while the phototrophic ones, called algae , were studied as part of the plant kingdom . Even after the creation of a separate protist kingdom, some minuscule animals (the myxozoans ) and 'lower' fungi (namely the aphelids , rozellids and microsporidians , collectively known as Opisthosporidia ) were studied as protists, and some algae (particularly red and green algae ) remained classified as plants. According to

2772-431: The monophyly of Bigyra is being questioned. Branching outside both Bigyra and Gyrista is a single species of enigmatic heterotrophic flagellates, Platysulcus tardus . Much of the diversity of heterotrophic stramenopiles is still uncharacterized, known almost entirely from lineages of genetic sequences known as MASTs (MArine STramenopiles), of which only a few species have been described. The phylum Gyrista includes

2849-480: The sequencing of entire genomes and transcriptomes , and electron microscopy studies of the flagellar apparatus and cytoskeleton . New major lineages of protists and novel biodiversity continue to be discovered, resulting in dramatic changes to the eukaryotic tree of life. The newest classification systems of eukaryotes do not recognize the formal taxonomic ranks (kingdom, phylum, class, order...) and instead only recognize clades of related organisms, making

2926-561: 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)

3003-562: The TSAR clade is Telonemia , a small (7 species) phylum of obscure phagotrophic predatory flagellates, found in marine and freshwater environments. They share some cellular similarities with the remaining three clades: Rhizaria , Alveolata and Stramenopiles , collectively known as the SAR supergroup . Another highly diverse clade within Diaphoretickes is Archaeplastida , which houses land plants and

3080-472: The anaerobic and endobiotic oxymonads , with modified mitochondria , and two genera of free-living microaerophilic bacterivorous flagellates Trimastix and Paratrimastix , with typical excavate morphology. Two genera of anaerobic flagellates of recent description and unique cell architecture, Barthelona and Skoliomonas , are closely related to the Fornicata. The malawimonads (Malawimonadida) are

3157-501: The apicomplexans ( Apicomplexa ) are a large (>6,000 species) and highly specialized group of obligate parasites who have all secondarily lost their photosynthetic ability (e.g., Plasmodium falciparum , cause of malaria ). Their adult stages absorb nutrients from the host through the cell membrane, and they reproduce between hosts via sporozoites, which exhibit an organelle complex (the apicoplast ) evolved from non-photosynthetic chloroplasts. The other branch of Myzozoa contains

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3234-401: 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

3311-450: The botanical ( ICN ) and the zoological ( ICZN ) codes of nomenclature . Protists display a wide range of distinct morphologies that have been used to classify them for practical purposes, although most of these categories do not represent evolutionary cohesive lineages or clades and have instead evolved independently several times. The most recognizable types are: In general, protists are typical eukaryotic cells that follow

3388-449: 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

3465-399: The clade Myzozoa , whose common ancestor acquired chloroplasts through a secondary endosymbiosis from a red alga. One branch of Myzozoa contains the apicomplexans and their closest relatives, a small clade of flagellates known as Chrompodellida where phototrophic and heterotrophic flagellates, called chromerids and colpodellids respectively, are evolutionarily intermingled. In contrast,

3542-470: The classification more stable in the long term and easier to update. In this new cladistic scheme, the protists are divided into various branches informally named supergroups . Most photosynthetic eukaryotes fall under the Diaphoretickes clade, which contains the supergroups Archaeplastida (which includes plants) and TSAR (including Telonemia , Stramenopiles , Alveolata and Rhizaria ), as well as

3619-446: The common characteristic of a ventral groove in the cell used for suspension feeding , which is considered to be an ancestral trait present in the last eukaryotic common ancestor . The Excavata is composed of three clades: Discoba , Metamonada and Malawimonadida , each including 'typical excavates' that are free-living phagotrophic flagellates with the characteristic ventral groove. According to most phylogenetic analyses, this group

3696-499: The current consensus, the term 'protist' specifically excludes animals, embryophytes (land plants) —meaning that all algae fall under this category— and all fungi, although lower fungi are often studied by protistologists and mycologists alike. The names of some protists (called ambiregnal protists), because of their mixture of traits similar to both animals and plants or fungi (e.g. slime molds and flagellated algae like euglenids ), have been published under either or both of

3773-761: The dinoflagellates and their closest relatives, the perkinsids ( Perkinsozoa ), a small group (26 species) of aquatic intracellular parasites which have lost their photosynthetic ability similarly to apicomplexans. They reproduce through flagellated spores that infect dinoflagellates, molluscs and fish . In contrast, the dinoflagellates ( Dinoflagellata ) are a highly diversified (~4,500 species) group of aquatic algae that have mostly retained their chloroplasts, although many lineages have lost their own and instead either live as heterotrophs or reacquire new chloroplasts from other sources, including tertiary endosymbiosis and kleptoplasty . Most dinoflagellates are free-living and compose an important portion of phytoplankton, as well as

3850-451: The emergence of meiosis and sex (such as Giardia lamblia and Trichomonas vaginalis ) are now known to descend from ancestors capable of meiosis and meiotic recombination , because they have a set core of meiotic genes that are present in sexual eukaryotes. Most of these meiotic genes were likely present in the common ancestor of all eukaryotes , which was likely capable of facultative (non-obligate) sexual reproduction. This view

3927-449: 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

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4004-497: 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

4081-513: 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

4158-409: 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

4235-535: The meiosis undertaken in the trypanosomes. The species diversity of protists is severely underestimated by traditional methods that differentiate species based on morphological characteristics. The number of described protist species is very low (ranging from 26,000 to 74,400 as of 2012) in comparison to the diversity of plants, animals and fungi, which are historically and biologically well-known and studied. The predicted number of species also varies greatly, ranging from 1.4×10 to 1.6×10 , and in several groups

4312-403: The naked eye. The term 'protist' is defined as a paraphyletic group of all eukaryotes that are not animals , plants or fungi . Because of this definition by exclusion, protists encompass almost all of the broad spectrum of biological characteristics expected in eukaryotes. The distinction between protists and the other three eukaryotic kingdoms has been difficult to settle. Historically,

4389-860: The number of predicted species is arbitrarily doubled. Most of these predictions are highly subjective. Molecular techniques such as environmental DNA barcoding have revealed a vast diversity of undescribed protists that accounts for the majority of eukaryotic sequences or operational taxonomic units (OTUs), dwarfing those from plants, animals and fungi. As such, it is considered that protists dominate eukaryotic diversity. Stramenopiles Alveolata Rhizaria Telonemia Haptista Microhelida Cryptista Archaeplastida Provora Hemimastigophora Meteora sporadica Discoba Metamonada Ancyromonadida Malawimonadida CRuMs Amoebozoa Breviatea Apusomonadida Opisthokonta The evolutionary relationships of protists have been explained through molecular phylogenetics ,

4466-713: 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

4543-473: 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

4620-439: 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

4697-452: 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

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4774-442: The photosynthetic Ochrophyta or Heterokontophyta (>23,000 species), which contain chloroplasts originated from a red alga . Among these are many lineages of algae that encompass a wide range of structures and morphologies. The three most diverse ochrophyte classes are: the diatoms , unicellular or colonial organisms encased in silica cell walls ( frustules ) that exhibit widely different shapes and ornamentations, responsible for

4851-573: The phyla Cryptista and Haptista . The animals and fungi fall into the Amorphea supergroup, which contains the phylum Amoebozoa and several other protist lineages. Various groups of eukaryotes with primitive cell architecture are collectively known as the Excavata . Excavata is a group that encompasses diverse protists, mostly flagellates, ranging from aerobic and anaerobic predators to phototrophs and heterotrophs. The common name 'excavate' refers to

4928-539: The presence of cortical alveoli , cytoplasmic sacs underlying the cell membrane of unknown physiological function. Among them are three of the most well-known groups of protists: apicomplexans, dinoflagellates and ciliates. The ciliates ( Ciliophora ) are a highly diverse (>8,000 species) and probably the most thoroughly studied group of protists. They are mostly free-living microbes characterized by large cells covered in rows of cilia and containing two kinds of nuclei, micronucleus and macronucleus (e.g., Paramecium ,

5005-405: 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

5082-475: The remaining eukaryotes. Protists generally reproduce asexually under favorable environmental conditions, but tend to reproduce sexually under stressful conditions, such as starvation or heat shock. Oxidative stress , which leads to DNA damage , also appears to be an important factor in the induction of sex in protists. Eukaryotes emerged in evolution more than 1.5 billion years ago. The earliest eukaryotes were protists. Although sexual reproduction

5159-423: The same principles of physiology and biochemistry described for those cells within the "higher" eukaryotes (animals, fungi or plants): they are aerobic organisms that consume oxygen to produce energy through mitochondria , and those with chloroplasts perform carbon fixation through photosynthesis in chloroplasts . However, many have evolved a variety of unique physiological adaptations that do not appear in

5236-417: 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

5313-479: The sister clade to Ochrophyta are the predominantly osmotrophic and filamentous Pseudofungi (>1,200 species), which include three distinct lineages: the parasitic oomycetes or water moulds (e.g., Phytophthora infestans , the agent behind the Irish Potato Famine ), which encompass most of the pseudofungi species; the less diverse non-parasitic hyphochytrids that maintain a fungus-like lifestyle; and

5390-717: The study of environmental DNA and is still in the process of being fully described. They are present in all ecosystems as important components of the biogeochemical cycles and trophic webs . They exist abundantly and ubiquitously in a variety of forms that evolved multiple times independently, such as free-living algae , amoebae and slime moulds , or as important parasites . Together, they compose an amount of biomass that doubles that of animals. They exhibit varied types of nutrition (such as phototrophy , phagotrophy or osmotrophy ), sometimes combining them (in mixotrophy ). They present unique adaptations not present in multicellular animals, fungi or land plants. The study of protists

5467-410: 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

5544-411: 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

5621-529: 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

5698-404: 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

5775-436: 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

5852-580: Was further supported by a 2011 study on amoebae . Amoebae have been regarded as asexual organisms , but the study describes evidence that most amoeboid lineages are ancestrally sexual, and that the majority of asexual groups likely arose recently and independently. Even in the early 20th century, some researchers interpreted phenomena related to chromidia ( chromatin granules free in the cytoplasm ) in amoebae as sexual reproduction. Some commonly found protist pathogens such as Toxoplasma gondii are capable of infecting and undergoing asexual reproduction in

5929-480: Was the last supergroup to be described, because it lacks any defining characteristic and was discovered exclusively through molecular phylogenetics . Three major clades are included, namely the phyla Cercozoa , Endomyxa and Retaria . Retaria contains the most familiar rhizarians: forams and radiolarians , two groups of large free-living marine amoebae with pseudopodia supported by microtubules , many of which are macroscopic. The radiolarians (Radiolaria) are

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