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55-793: Huerteales is the botanical name for an order of flowering plants . It is one of the 17 orders that make up the large eudicot group known as the rosids in the APG III system of plant classification . Within the rosids, it is one of the orders in Malvidae , a group formerly known as eurosids II and now known informally as the malvids . This is true whether Malvidae is circumscribed broadly to include eight orders as in APG III, or more narrowly to include only four orders. Huerteales consists of four small families , Petenaeaceae , Gerrardinaceae , Tapisciaceae , and Dipentodontaceae . Petenaeaceae consists of

110-728: 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

165-409: A calyx tube and compound , rather than simple leaves. Tapiscia has a uniloculate ovary with a single ovule. Huertea has one locule containing two ovules, or two locules, each containing one ovule. Gerrardina , Dipentodon , and Perrottetia have two ovules in each locule. Tapiscia lacks the nectary disk that is characteristic of the order. Huertea lacks stipules. Until the first decade of

220-547: A careful check is needed to see which circumscription is being used (for example Fabaceae , Amygdaloideae , Taraxacum officinale ). Depending on rank , botanical names may be in one part ( genus and above), two parts (various situations below the rank of genus) or three parts (below the rank of species). The names of cultivated plants are not necessarily similar to the botanical names, since they may instead involve "unambiguous common names" of species or genera. Cultivated plant names may also have an extra component, bringing

275-499: 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  –

330-597: A formal name is to have a single name that is accepted and used worldwide for a particular plant or plant group. For example, the botanical name Bellis perennis denotes a plant species which is native to most of the countries of Europe and the Middle East , where it has accumulated various names in many languages. Later, the plant was introduced worldwide, bringing it into contact with more languages. English names for this plant species include: daisy, English daisy, and lawn daisy. The cultivar Bellis perennis 'Aucubifolia'

385-536: 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

440-457: A maximum of four parts: A botanical name in three parts, i.e., an infraspecific name (a name for a taxon below the rank of species) needs a "connecting term" to indicate rank. In the Calystegia example above, this is "subsp.", an abbreviation for subspecies . In botany there are many ranks below that of species (in zoology there is only one such rank, subspecies, so that this "connecting term"

495-417: 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

550-693: 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

605-462: 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

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660-476: A single genus and species Petenaea cordata from Southern Mexico, Guatemala and Belize. Gerrardinaceae consists of a single genus, Gerrardina . Tapisciaceae has two genera, Tapiscia and Huertea . Until 2006, Dipentodontaceae was treated as consisting of a single genus, Dipentodon . Since that time, some authors have included Perrottetia in Dipentodontaceae, even though no formal revision of

715-631: 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

770-594: 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,

825-592: 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

880-550: 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

935-480: Is a classification, not a formal botanical name. The botanical name is Saxifraga aizoon subf. surculosa Engl. & Irmsch. ( ICN Art 24: Ex 1). Generic, specific, and infraspecific botanical names are usually printed in italics . The example set by the ICN is to italicize all botanical names, including those above genus, though the ICN preface states: "The Code sets no binding standard in this respect, as typography

990-408: Is a golden-variegated horticultural selection of this species. The botanical name itself is fixed by a type , which is a particular specimen (or in some cases a group of specimens) of an organism to which the scientific name is formally attached. In other words, a type is an example that serves to anchor or centralize the defining features of that particular taxon. The usefulness of botanical names

1045-438: Is a matter of editorial style and tradition not of nomenclature". Most peer-reviewed scientific botanical publications do not italicize names above the rank of genus, and non-botanical scientific publications do not, which is in keeping with two of the three other kinds of scientific name : zoological and bacterial ( viral names above genus are italicized, a new policy adopted in the early 1990s). For botanical nomenclature,

1100-544: Is always given in single quotation marks. The cultivar, Group, or grex epithet may follow either the botanical name of the species, or the name of the genus only, or the unambiguous common name of the genus or species. The generic name, followed by a cultivar name, is often used when the parentage of a particular hybrid cultivar is not relevant in the context, or is uncertain. (specific to botany) (more general) Phylogenetic In biology , phylogenetics ( / ˌ f aɪ l oʊ dʒ ə ˈ n ɛ t ɪ k s , - l ə -/ )

1155-455: Is based on molecular phylogenetic analysis of DNA sequences . All of the Huerteales are woody plants . The leaves are alternate with toothed margins. The inflorescence is cymose , but sometimes nearly racemose or umbelliform . The bases of the calyx , corolla and stamens are fused to form a hypanthium which is in some cases very short. The ovary is unilocular , at least at

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1210-634: Is in the order Crossosomatales . For most of the twentieth century, Gerrardina and Dipentodon had usually been placed in Flacourtiaceae, a family that is now recognized by only a few taxonomists , and then only as a segregate of Salicaceae . Perrottetia , meanwhile, had usually been placed, with considerable doubt, in Celastraceae . Ever since Dipentodon was named in 1911, there had been occasional suggestions that it might be related to Tapiscia and Huertea . In 2001, Alexander Doweld established

1265-599: Is limited by the fact that taxonomic groups are not fixed in size; a taxon may have a varying circumscription , depending on the taxonomic system , thus, the group that a particular botanical name refers to can be quite small according to some people and quite big according to others. For example, the traditional view of the family Malvaceae has been expanded in some modern approaches to include what were formerly considered to be several closely related families. Some botanical names refer to groups that are very stable (for example Equisetaceae , Magnoliaceae ) while for other names

1320-459: Is not used in zoology). A name of a "subdivision of a genus" also needs a connecting term (in the Acacia example above, this is "subg.", an abbreviation for subgenus ). The connecting term is not part of the name itself. A taxon may be indicated by a listing in more than three parts: " Saxifraga aizoon var. aizoon subvar. brevifolia f. multicaulis subf. surculosa Engl. & Irmsch." but this

1375-437: 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

1430-444: 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

1485-420: The ICN prescribes a two-part name or binary name for any taxon below the rank of genus down to, and including, the rank of species. Taxa below the rank of species get a three part ( infraspecific name ). A binary name consists of the name of a genus and an epithet. In the case of cultivated plants, there is an additional epithet which is an often non-Latin part, not written in italics. For cultivars, it

1540-545: 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

1595-645: 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

1650-414: 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

1705-436: 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

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1760-460: 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

1815-400: 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,

1870-413: 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

1925-426: 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

1980-597: 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

2035-488: 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

2090-668: 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

2145-423: The family has been published as of 2008. Thus the order Huerteales consists of six genera. The largest genus, Perrottetia , contains about 15 of the approximate total of 25 species in the order. The Huerteales are shrubs or small trees found in most tropical or warm temperate regions. The flowers of Perrottetia have been studied in detail, but otherwise, all five of the genera are poorly known. The order

2200-576: The first phylogenetic study that included all of the genera of Huerteales. From one of their data matrices, they derived a well supported phylogeny for the order, as well as strongly supported relationships among the four orders of malvids. The phylogeny shown below is the one found by Worberg and co-authors. Monospecific genera are represented by species names. Sapindales Petenaea cordata Gerrardina Tapiscia sinensis Huertea Dipentodon sinicus Perrottetia Brassicales Malvales Botanical name The purpose of

2255-475: 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

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2310-618: 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

2365-525: The order Huerteales, defining it to consist of Tapiscia , Huertea , and Dipentodon . This grouping was later supported by molecular phylogenetic studies. In 2006, a study of DNA sequences showed that Perrottetia was misplaced in Celastrales and that it is sister to Dipentodon in Huerteales. Also in 2006, it was found that Gerrardina is a malvid, but its placement within this group remained uncertain. In 2009, Andreas Worberg and co-authors produced

2420-528: 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

2475-510: 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

2530-415: 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

2585-418: 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

2640-543: 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

2695-410: 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

2750-575: 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

2805-485: 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

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2860-481: 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

2915-421: 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

2970-470: The top, with one or two ovules per carpel . The number of carpels is variable. Other characters are generally found in Huerteales, but with the exceptions noted below. Gerrardina differs from the rest of Huerteales in that the stamens are opposite the petals , instead of being opposite the sepals . Dipentodon and Perrottetia are distinctive in that the calyx and corolla are not well differentiated, but resemble each other. Tapiscia and Huertea have

3025-688: The twenty-first century, the five genera of Huerteales had usually been placed into three unrelated families. Tapiscia and Huertea had long been known to be related. Most authors had placed them in Staphyleaceae and had placed that family in the order Sapindales . Armen Takhtajan established the family Tapisciaceae in 1987 and placed it in Sapindales, but this treatment was not followed by many others and it did not stand up to phylogenetic analysis. Since that time, Staphyleaceae has been recircumscribed . It no longer includes Tapiscia and Huertea and it

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