96-538: The alveolates (meaning "pitted like a honeycomb") are a group of protists , considered a major clade and superphylum within Eukarya . They are currently grouped with the stramenopiles and Rhizaria among the protists with tubulocristate mitochondria into the SAR supergroup . The most notable shared characteristic is the presence of cortical (near the surface) alveoli (sacs) . These are flattened vesicles (sacs) arranged as
192-477: A mitosome , the circular mitochondrial genomes of Acavomonas and Babesia microti , and Toxoplasma ' s highly fragmented mitochondrial genome, consisting of 21 sequence blocks which recombine to produce longer segments. The relationship of apicomplexa, dinoflagellates and ciliates had been suggested during the 1980s, and this was confirmed in the early 1990s by comparisons of ribosomal RNA sequences, most notably by Gajadhar et al . Cavalier-Smith introduced
288-498: 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
384-404: A plastid . Chromerids, apicomplexans, and peridinin dinoflagellates have retained this organelle . Going one step even further back, the chromerids, the peridinin dinoflagellates and the heterokont algae have been argued to possess a monophyletic plastid lineage in common, i.e. acquired their plastids from a red alga , and so it seems likely that the common ancestor of alveolates and heterokonts
480-728: A bacterial genome over three types of outbreak contact networks—homogeneous, super-spreading, and chain-like. They summarized the resulting phylogenies with five metrics describing tree shape. Figures 2 and 3 illustrate the distributions of these metrics across the three types of outbreaks, revealing clear differences in tree topology depending on the underlying host contact network. Super-spreader networks give rise to phylogenies with higher Colless imbalance, longer ladder patterns, lower Δw, and deeper trees than those from homogeneous contact networks. Trees from chain-like networks are less variable, deeper, more imbalanced, and narrower than those from other networks. Scatter plots can be used to visualize
576-421: 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,
672-449: 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
768-499: A disproof of a previously widely accepted theory. During the late 19th century, Ernst Haeckel 's recapitulation theory , or "biogenetic fundamental law", was widely popular. It was often expressed as " ontogeny recapitulates phylogeny", i.e. the development of a single organism during its lifetime, from germ to adult, successively mirrors the adult stages of successive ancestors of the species to which it belongs. But this theory has long been rejected. Instead, ontogeny evolves –
864-523: A diverse group (>1,000 living species) of amoebae, often bearing delicate and intricate siliceous skeletons. The forams (Foraminifera) are also diverse (>6,700 living species), and most of them are encased in multichambered tests constructed from calcium carbonate or agglutinated mineral particles. Both groups have a rich fossil record, with tens of thousands of described fossil species. Phylogenetic In biology , phylogenetics ( / ˌ f aɪ l oʊ dʒ ə ˈ n ɛ t ɪ k s , - l ə -/ )
960-536: A language as an evolutionary system. The evolution of human language closely corresponds with human's biological evolution which allows phylogenetic methods to be applied. The concept of a "tree" serves as an efficient way to represent relationships between languages and language splits. It also serves as a way of testing hypotheses about the connections and ages of language families. For example, relationships among languages can be shown by using cognates as characters. The phylogenetic tree of Indo-European languages shows
1056-664: A layer just under the membrane and supporting it, typically contributing to a flexible pellicle (thin skin). In armored dinoflagellates they may contain stiff plates. Alveolates have mitochondria with tubular cristae ( invaginations ), and cells often have pore-like intrusions through the cell surface. The group contains free-living and parasitic organisms, predatory flagellates , and photosynthetic organisms. Almost all sequenced mitochondrial genomes of ciliates and apicomplexa are linear. The mitochondria almost all carry mtDNA of their own but with greatly reduced genome sizes. Exceptions are Cryptosporidium which are left with only
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#17328518941251152-601: 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
1248-474: A model alveolate, having been genetically studied in great depth over the longest period of any alveolate lineage. They are unusual among eukaryotes in that reproduction involves a micronucleus and a macronucleus . Their reproduction is easily studied in the lab, and made them a model eukaryote historically. Being entirely predatory and lacking any remnant plastid, their development as a phylum illustrates how predation and autotrophy are in dynamic balance and that
1344-417: A phylogenetic tree can be living taxa or fossils , which represent the present time or "end" of an evolutionary lineage, respectively. A phylogenetic diagram can be rooted or unrooted. A rooted tree diagram indicates the hypothetical common ancestor of the tree. An unrooted tree diagram (a network) makes no assumption about the ancestral line, and does not show the origin or "root" of the taxa in question or
1440-693: A shared evolutionary history. There are debates if increasing the number of taxa sampled improves phylogenetic accuracy more than increasing the number of genes sampled per taxon. Differences in each method's sampling impact the number of nucleotide sites utilized in a sequence alignment, which may contribute to disagreements. For example, phylogenetic trees constructed utilizing a more significant number of total nucleotides are generally more accurate, as supported by phylogenetic trees' bootstrapping replicability from random sampling. The graphic presented in Taxon Sampling, Bioinformatics, and Phylogenomics , compares
1536-462: A significant source of error within phylogenetic analysis occurs due to inadequate taxon samples. Accuracy may be improved by increasing the number of genetic samples within its monophyletic group. Conversely, increasing sampling from outgroups extraneous to the target stratified population may decrease accuracy. Long branch attraction is an attributed theory for this occurrence, where nonrelated branches are incorrectly classified together, insinuating
1632-631: A single tree with true claim. The same process can be applied to texts and manuscripts. In Paleography , the study of historical writings and manuscripts, texts were replicated by scribes who copied from their source and alterations - i.e., 'mutations' - occurred when the scribe did not precisely copy the source. Phylogenetics has been applied to archaeological artefacts such as the early hominin hand-axes, late Palaeolithic figurines, Neolithic stone arrowheads, Bronze Age ceramics, and historical-period houses. Bayesian methods have also been employed by archaeologists in an attempt to quantify uncertainty in
1728-469: 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
1824-594: A small group of taxa to represent the evolutionary history of its broader population. This process is also known as stratified sampling or clade-based sampling. The practice occurs given limited resources to compare and analyze every species within a target population. Based on the representative group selected, the construction and accuracy of phylogenetic trees vary, which impacts derived phylogenetic inferences. Unavailable datasets, such as an organism's incomplete DNA and protein amino acid sequences in genomic databases, directly restrict taxonomic sampling. Consequently,
1920-592: A species to uncover either a higher abundance of important bioactive compounds (e.g., species of Taxus for taxol) or natural variants of known pharmaceuticals (e.g., species of Catharanthus for different forms of vincristine or vinblastine). Phylogenetic analysis has also been applied to biodiversity studies within the fungi family. Phylogenetic analysis helps understand the evolutionary history of various groups of organisms, identify relationships between different species, and predict future evolutionary changes. Emerging imagery systems and new analysis techniques allow for
2016-587: A taxon now split because each has a distinctive organization or ultrastructural identity . The Acavomonidia are closer to the dinoflagellate/perkinsid group than the Colponemidia are. As such, the informal term "colponemids", as it stands currently, covers two non-sister groups within Alveolata: the Acavomonidia and the Colponemidia. The Apicomplexa and dinoflagellates may be more closely related to each other than to
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#17328518941252112-474: 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
2208-420: 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
2304-565: 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
2400-550: Is "tree shape." These approaches, while computationally intensive, have the potential to provide valuable insights into pathogen transmission dynamics. The structure of the host contact network significantly impacts the dynamics of outbreaks, and management strategies rely on understanding these transmission patterns. Pathogen genomes spreading through different contact network structures, such as chains, homogeneous networks, or networks with super-spreaders, accumulate mutations in distinct patterns, resulting in noticeable differences in
2496-440: 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
2592-407: 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 a separate taxonomic kingdom known as Protista or Protoctista . With the advent of phylogenetic analysis and electron microscopy studies,
2688-445: 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
2784-500: 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
2880-437: Is the identification, naming, and classification of organisms. Compared to systemization, classification emphasizes whether a species has characteristics of a taxonomic group. The Linnaean classification system developed in the 1700s by Carolus Linnaeus is the foundation for modern classification methods. Linnaean classification relies on an organism's phenotype or physical characteristics to group and organize species. With
2976-444: Is the study of the evolutionary history of life using genetics, which is known as phylogenetic inference . It establishes the relationship between organisms with the empirical data and observed heritable traits of DNA sequences, protein amino acid sequences, and morphology . The results are a phylogenetic tree —a diagram setting the hypothetical relationships between organisms and their evolutionary history. The tips of
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3072-402: 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
3168-408: 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
3264-765: The Cercozoa . The ellobiopsids are of uncertain relation within the alveolates. Silberman et al 2004 establish that the Thalassomyces genus of ellobiopsids are alveolates using phylogenetic analysis, however as of 2016 no more certainty exists on their place. In 2017, Thomas Cavalier-Smith described the phylogeny of the Alveolata as follows: Heterotrichea Karyorelictea Desmata Spirotrichia Colponemea Acavomonadea Apicomonada Sporozoa Dinoflagellata Perkinsea Alveolata Cavalier-Smith 1991 [Alveolatobiontes] The development of plastids among
3360-499: 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
3456-716: 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
3552-547: 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
3648-572: The ellobiopsids . In 2001, direct amplification of the rRNA gene in marine picoplankton samples revealed the presence of two novel alveolate lineages, called group I and II. Group I has no cultivated relatives, while group II is related to the dinoflagellate parasite Amoebophrya , which was classified until now in the Syndiniales dinoflagellate order. Some studies suggested the haplosporids , mostly parasites of marine invertebrates, might belong here, but they lack alveoli and are now placed among
3744-532: 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
3840-431: 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
3936-480: 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
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4032-485: The Chromerida and the heterokont algae acquired their plastids from a red alga with evidence of a common origin of this organelle in all these four clades. A Bayesian estimate places the evolution of the alveolate group at ~ 850 million years ago . The Alveolata consist of Myzozoa , Ciliates , and Colponemids. In other words, the term Myzozoa, meaning "to siphon the contents from prey", may be applied informally to
4128-545: The German Phylogenie , introduced by Haeckel in 1866, and the Darwinian approach to classification became known as the "phyletic" approach. It can be traced back to Aristotle , who wrote in his Posterior Analytics , "We may assume the superiority ceteris paribus [other things being equal] of the demonstration which derives from fewer postulates or hypotheses." The modern concept of phylogenetics evolved primarily as
4224-517: 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
4320-645: The absence of genetic recombination . Phylogenetics can also aid in drug design and discovery. Phylogenetics allows scientists to organize species and can show which species are likely to have inherited particular traits that are medically useful, such as producing biologically active compounds - those that have effects on the human body. For example, in drug discovery, venom -producing animals are particularly useful. Venoms from these animals produce several important drugs, e.g., ACE inhibitors and Prialt ( Ziconotide ). To find new venoms, scientists turn to phylogenetics to screen for closely related species that may have
4416-466: The alveolates is intriguing. Cavalier-Smith proposed the alveolates developed from a chloroplast-containing ancestor, which also gave rise to the Chromista (the chromalveolate hypothesis). Other researchers have speculated that the alveolates originally lacked plastids and possibly the dinoflagellates and Apicomplexa acquired them separately. However, it now appears that the alveolates, the dinoflagellates,
4512-472: 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
4608-501: 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
4704-402: The balance can swing one way or other at the point of origin of a new phylum from mixotrophic ancestors, causing one ability to be lost. Few algae have been studied for epigenetics . Those for which epigenetic data are available include some algal alveolates. Protist A protist ( / ˈ p r oʊ t ɪ s t / PROH -tist ) or protoctist is any eukaryotic organism that
4800-414: The basis of a computational classifier used to analyze real-world outbreaks. Computational predictions of transmission dynamics for each outbreak often align with known epidemiological data. Different transmission networks result in quantitatively different tree shapes. To determine whether tree shapes captured information about underlying disease transmission patterns, researchers simulated the evolution of
4896-436: The basis that apicomplexans possess a plastid surrounded by four membranes, and that peridinin dinoflagellates possess a plastid surrounded by three membranes, Petersen et al. have been unable to rule out that the shared stramenopile-alveolate plastid could have been recycled multiple times in the alveolate phylum, the source being stramenopile-alveolate donors, through the mechanism of ingestion and endosymbiosis . Ciliates are
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#17328518941254992-450: 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
5088-436: The branching pattern and "degree of difference" to find a compromise between them. Usual methods of phylogenetic inference involve computational approaches implementing the optimality criteria and methods of parsimony , maximum likelihood (ML), and MCMC -based Bayesian inference . All these depend upon an implicit or explicit mathematical model describing the evolution of characters observed. Phenetics , popular in
5184-460: The characteristics of species to interpret their evolutionary relationships and origins. Phylogenetics focuses on whether the characteristics of a species reinforce a phylogenetic inference that it diverged from the most recent common ancestor of a taxonomic group. In the field of cancer research, phylogenetics can be used to study the clonal evolution of tumors and molecular chronology , predicting and showing how cell populations vary throughout
5280-619: The ciliates. Both have plastids , and most share a bundle or cone of microtubules at the top of the cell. In apicomplexans this forms part of a complex used to enter host cells, while in some colorless dinoflagellates it forms a peduncle used to ingest prey. Various other genera are closely related to these two groups, mostly flagellates with a similar apical structure. These include free-living members in Oxyrrhis and Colponema , and parasites in Perkinsus , Parvilucifera , Rastrimonas and
5376-399: 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,
5472-470: 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
5568-430: The common ancestor of the subset of alveolates that are neither ciliates nor colponemids. Predation upon algae is an important driver in alveolate evolution, as it can provide sources for endosymbiosis of novel plastids. The term Myzozoa is therefore a handy concept for tracking the history of the alveolate phylum. The ancestors of the alveolate group may have been photosynthetic. The ancestral alveolate probably possessed
5664-446: 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
5760-400: The correctness of phylogenetic trees generated using fewer taxa and more sites per taxon on the x-axis to more taxa and fewer sites per taxon on the y-axis. With fewer taxa, more genes are sampled amongst the taxonomic group; in comparison, with more taxa added to the taxonomic sampling group, fewer genes are sampled. Each method has the same total number of nucleotide sites sampled. Furthermore,
5856-499: 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
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#17328518941255952-413: The data distribution. They may be used to quickly identify differences or similarities in the transmission data. Phylogenetic tools and representations (trees and networks) can also be applied to philology , the study of the evolution of oral languages and written text and manuscripts, such as in the field of quantitative comparative linguistics . Computational phylogenetics can be used to investigate
6048-761: 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
6144-426: The direction of inferred evolutionary transformations. In addition to their use for inferring phylogenetic patterns among taxa, phylogenetic analyses are often employed to represent relationships among genes or individual organisms. Such uses have become central to understanding biodiversity , evolution, ecology , and genomes . Phylogenetics is a component of systematics that uses similarities and differences of
6240-597: The discovery of more genetic relationships in biodiverse fields, which can aid in conservation efforts by identifying rare species that could benefit ecosystems globally. Whole-genome sequence data from outbreaks or epidemics of infectious diseases can provide important insights into transmission dynamics and inform public health strategies. Traditionally, studies have combined genomic and epidemiological data to reconstruct transmission events. However, recent research has explored deducing transmission patterns solely from genomic data using phylodynamics , which involves analyzing
6336-488: The dotted line represents a 1:1 accuracy between the two sampling methods. As seen in the graphic, most of the plotted points are located below the dotted line, which indicates gravitation toward increased accuracy when sampling fewer taxa with more sites per taxon. The research performed utilizes four different phylogenetic tree construction models to verify the theory; neighbor-joining (NJ), minimum evolution (ME), unweighted maximum parsimony (MP), and maximum likelihood (ML). In
6432-668: The emergence of biochemistry , organism classifications are now usually based on phylogenetic data, and many systematists contend that only monophyletic taxa should be recognized as named groups. The degree to which classification depends on inferred evolutionary history differs depending on the school of taxonomy: phenetics ignores phylogenetic speculation altogether, trying to represent the similarity between organisms instead; cladistics (phylogenetic systematics) tries to reflect phylogeny in its classifications by only recognizing groups based on shared, derived characters ( synapomorphies ); evolutionary taxonomy tries to take into account both
6528-451: 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
6624-432: The formal name Alveolata in 1991, although at the time he considered the grouping to be a paraphyletic assemblage. Many biologists prefer the use of the colloquial name 'alveolate'. Alveolata include around nine major and minor groups. They are diverse in form, and are known to be related by various ultrastructural and genetic similarities: The Acavomonidia and Colponemidia were previously grouped together as colponemids,
6720-475: The majority of models, sampling fewer taxon with more sites per taxon demonstrated higher accuracy. Generally, with the alignment of a relatively equal number of total nucleotide sites, sampling more genes per taxon has higher bootstrapping replicability than sampling more taxa. However, unbalanced datasets within genomic databases make increasing the gene comparison per taxon in uncommonly sampled organisms increasingly difficult. The term "phylogeny" derives from
6816-535: 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
6912-618: The mid-20th century but now largely obsolete, used distance matrix -based methods to construct trees based on overall similarity in morphology or similar observable traits (i.e. in the phenotype or the overall similarity of DNA , not the DNA sequence ), which was often assumed to approximate phylogenetic relationships. Prior to 1950, phylogenetic inferences were generally presented as narrative scenarios. Such methods are often ambiguous and lack explicit criteria for evaluating alternative hypotheses. In phylogenetic analysis, taxon sampling selects
7008-403: 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,
7104-860: 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 ,
7200-442: 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
7296-573: 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
7392-528: The phylogenetic history of a species cannot be read directly from its ontogeny, as Haeckel thought would be possible, but characters from ontogeny can be (and have been) used as data for phylogenetic analyses; the more closely related two species are, the more apomorphies their embryos share. One use of phylogenetic analysis involves the pharmacological examination of closely related groups of organisms. Advances in cladistics analysis through faster computer programs and improved molecular techniques have increased
7488-510: The precision of phylogenetic determination, allowing for the identification of species with pharmacological potential. Historically, phylogenetic screens for pharmacological purposes were used in a basic manner, such as studying the Apocynaceae family of plants, which includes alkaloid-producing species like Catharanthus , known for producing vincristine , an antileukemia drug. Modern techniques now enable researchers to study close relatives of
7584-539: 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 ,
7680-415: The progression of the disease and during treatment, using whole genome sequencing techniques. The evolutionary processes behind cancer progression are quite different from those in most species and are important to phylogenetic inference; these differences manifest in several areas: the types of aberrations that occur, the rates of mutation , the high heterogeneity (variability) of tumor cell subclones, and
7776-418: The properties of pathogen phylogenies. Phylodynamics uses theoretical models to compare predicted branch lengths with actual branch lengths in phylogenies to infer transmission patterns. Additionally, coalescent theory , which describes probability distributions on trees based on population size, has been adapted for epidemiological purposes. Another source of information within phylogenies that has been explored
7872-543: The relationship between two variables in pathogen transmission analysis, such as the number of infected individuals and the time since infection. These plots can help identify trends and patterns, such as whether the spread of the pathogen is increasing or decreasing over time, and can highlight potential transmission routes or super-spreader events. Box plots displaying the range, median, quartiles, and potential outliers datasets can also be valuable for analyzing pathogen transmission data, helping to identify important features in
7968-410: The relationships between several of the languages in a timeline, as well as the similarity between words and word order. There are three types of criticisms about using phylogenetics in philology, the first arguing that languages and species are different entities, therefore you can not use the same methods to study both. The second being how phylogenetic methods are being applied to linguistic data. And
8064-575: The relationships between viruses e.g., all viruses are descendants of Virus A. HIV forensics uses phylogenetic analysis to track the differences in HIV genes and determine the relatedness of two samples. Phylogenetic analysis has been used in criminal trials to exonerate or hold individuals. HIV forensics does have its limitations, i.e., it cannot be the sole proof of transmission between individuals and phylogenetic analysis which shows transmission relatedness does not indicate direction of transmission. Taxonomy
8160-475: 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
8256-423: 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
8352-485: The same useful traits. The phylogenetic tree shows which species of fish have an origin of venom, and related fish they may contain the trait. Using this approach in studying venomous fish, biologists are able to identify the fish species that may be venomous. Biologist have used this approach in many species such as snakes and lizards. In forensic science , phylogenetic tools are useful to assess DNA evidence for court cases. The simple phylogenetic tree of viruses A-E shows
8448-481: The shape of phylogenetic trees, as illustrated in Fig. 1. Researchers have analyzed the structural characteristics of phylogenetic trees generated from simulated bacterial genome evolution across multiple types of contact networks. By examining simple topological properties of these trees, researchers can classify them into chain-like, homogeneous, or super-spreading dynamics, revealing transmission patterns. These properties form
8544-479: 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
8640-717: 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
8736-421: The third, discusses the types of data that is being used to construct the trees. Bayesian phylogenetic methods, which are sensitive to how treelike the data is, allow for the reconstruction of relationships among languages, locally and globally. The main two reasons for the use of Bayesian phylogenetics are that (1) diverse scenarios can be included in calculations and (2) the output is a sample of trees and not
8832-550: 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
8928-458: Was also photosynthetic. In one school of thought the common ancestor of the dinoflagellates , apicomplexans , Colpodella , Chromerida , and Voromonas was a myzocytotic predator with two heterodynamic flagella , micropores , trichocysts , rhoptries , micronemes , a polar ring and a coiled open sided conoid . While the common ancestor of alveolates may also have possessed some of these characteristics, it has been argued that Myzocytosis
9024-580: 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
9120-411: Was not one of these characteristics, as ciliates ingest prey by a different mechanism. An ongoing debate concerns the number of membranes surrounding the plastid across apicomplexans and certain dinoflagellates, and the origin of these membranes. This ultrastructural character can be used to group organisms and if the character is in common, it can imply that phyla had a common photosynthetic ancestor. On
9216-480: 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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