46-584: See List of Atriplex species Atriplex ( / ˈ æ t r ɪ p l ɛ k s / ) is a plant genus of about 250 species, known by the common names of saltbush and orache ( / ˈ ɒ r ɪ tʃ , - ə tʃ / ; also spelled orach ). It belongs to the subfamily Chenopodioideae of the family Amaranthaceae s.l. . The genus is quite variable and widely distributed. It includes many desert and seashore plants and halophytes , as well as plants of moist environments. The generic name originated in Latin and
92-469: A phylogenetic tree —a diagram setting the hypothetical relationships between organisms and their evolutionary history. The tips of 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
138-728: 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
184-578: A characteristic leaf anatomy, known as kranz anatomy. The genus Atriplex was first formally described in 1753 by Carl Linnaeus in Species Plantarum . The genus name was used by Pliny for orach, or mountain spinach ( A. hortensis ). The genus evolved in Middle Miocene , the C 4 -photosynthesis pathway developed about 14.1–10.9 million years ago (mya), when the climate became increasingly dry. The genus diversified rapidly and spread over
230-499: 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 –
276-436: A few, scattered species, and the larger Atriplex clade, which is highly diverse and found around the world. After phylogenetic research, Kadereit et al. (2010) excluded Halimione as a distinct sister genus. The remaining Atriplex species were grouped into several clades. The following is a cladogram with estimated divergence times for the tribe Atripliceae. To infer the phylogeny, an ITS matrix composed of spacer ITS-1,
322-536: 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
368-407: A perianth, but are enclosed by 2 leaf-like bracteoles , have a short style and 2 stigmas . After flowering, the bracteoles sometimes enlarge, thicken or become appendaged, enclosing the fruit but without adhering to it. The chromosome base number is x = 9, except for Atriplex lanfrancoi , which is x=10. A few Atriplex species are C 3 -plants , but most species are C 4 -plants , with
414-693: 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
460-462: 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
506-631: 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
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#1733085295203552-594: 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,
598-592: 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
644-603: Is Atriplex hortensis . The name is derived from Ancient Greek ἀτράφαξυς ( atraphaxys ), "orach", itself a Pre-Greek substrate loanword. Atriplex is an extremely species-rich genus and comprises about 250-300 species, with new species still being discovered. An example includes Atriplex yeelirrie , formally described in 2015. Traditional taxonomy of Atripliceae based on morphological features has been controversial. Molecular studies have found that many genera are not true clades . One such study found that Atripliceae could be divided into two main clades, Archiatriplex , with
690-550: 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
736-413: Is a component of systematics that uses similarities and differences of 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
782-630: Is a list of Atriplex species accepted by the Plants of the World Online as at June 2022: Phylogenetic In biology , phylogenetics ( / ˌ f aɪ l oʊ dʒ ə ˈ n ɛ t ɪ k s , - l ə -/ ) 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
828-614: The 5.8S subunit, and spacer ITS-2 were amplified and sequenced for each specimen. Not all species in the genus Atriplex are presented in the cladogram (based on page 7 of ). This work suggested that the Americas were colonised by C4 Atriplex from Eurasia or Australia. Furthermore, that in the Americas Atriplex first appeared in South America, where two lineages underwent in situ diversification and evolved sympatrically. North America
874-545: 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
920-438: The ancestral line, and does not show the origin or "root" of the taxa in question or 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
966-414: 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
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#17330852952031012-445: The branches, rarely in opposite pairs, either sessile or on a petiole , and are sometimes deciduous. The leaf blade is variably shaped and may be entire, tooth or lobed. The flowers are borne in leaf axils or on the ends of branches, in spikes or spike-like panicles . The flowers are unisexual , some species monoecious , others dioecious . Male flowers have 3-5 perianth lobes and 3-5 stamens . Female flowers are usually lacking
1058-436: 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
1104-408: The clonal evolution of tumors and molecular chronology , predicting and showing how cell populations vary throughout 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:
1150-511: The continents. The C 4 Atriplex colonized North America probably from Eurasia during the Middle/Late Miocene, about 9.8–8.8 mya, and later spread to South America. Australia was colonized twice by two C 4 lineages, one from Eurasia or America about 9.8–7.8 mya, and one from Central Asia about 6.3–4.8 mya. The last lineage diversified rapidly, and became the ancestor of most Australian Atriplex species. The type species ( lectotype )
1196-400: 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,
1242-413: 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
1288-445: 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 is
1334-597: 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
1380-488: 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
1426-668: 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
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1472-447: 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 the same useful traits. The phylogenetic tree shows which species of fish have an origin of venom, and related fish they may contain
1518-434: 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
1564-475: 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
1610-618: 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
1656-528: 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
1702-510: 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
1748-418: 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
1794-543: 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
1840-410: 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
1886-481: 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
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1932-421: 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
1978-484: 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 the relationships between viruses e.g., all viruses are descendants of Virus A. HIV forensics uses phylogenetic analysis to track
2024-460: The types of aberrations that occur, the rates of mutation , the high heterogeneity (variability) of tumor cell subclones, and 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
2070-543: Was applied by Pliny the Elder to the edible oraches. The name saltbush derives from the fact that the plants retain salt in their leaves; they are able to grow in areas affected by soil salination . Species of plants in genus Atriplex are annual or perennial herbs, subshrubs , or shrubs. The plants are often covered with bladderlike hairs, that later collapse and form a silvery, scurfy or mealy surface, rarely with elongate trichomes . The leaves are arranged alternately along
2116-1054: Was then colonised by Atriplex from South America, then one lineage later moved back to South America. Atriplex pentandra Atriplex hystrix Atriplex clivicola Atriplex taltalensis Atriplex vallenarensis Atriplex peruviana Atriplex leuca Atriplex philippii Atriplex myriophylla Atriplex chapinii Atriplex chizae Atriplex frigida Atriplex ameghinoi Atriplex monevidensis Atriplex pamparum Atriplex serenana Atriplex leucophylla Atriplex watsonii Atriplex acanthocarpa Atriplex polycarpa Atriplex canescens Atriplex phyllostegia Atriplex obovata Atriplex powellii Atriplex parishii Atriplex hymenelytra Atriplex parryi Atriplex lentiformis Atriplex undulata Atriplex patagonica Atriplex lithophila Atriplex atacamensis Atriplex braunii Atriplex oreophila Atriplex retusa Atriplex rusbyi List of Atriplex species The following
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