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59-489: Hesperornithiformes Sharpe , 1899 Hesperornithes is an extinct and highly specialized group of aquatic avialans closely related to the ancestors of modern birds . They inhabited both marine and freshwater habitats in the Northern Hemisphere, and include genera such as Hesperornis , Parahesperornis , Baptornis , Enaliornis , and Potamornis , all strong-swimming, predatory divers. Many of

118-469: 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

177-495: A King's Scholarship. He then moved to Loughborough Grammar School . He returned to London at the age of sixteen and worked as a clerk with W. H. Smith & Sons. He already took an interest in ornithology and was interested in writing a monograph on the kingfishers. After two years, in 1865, he joined the company of the bookseller Bernard Quaritch and had an opportunity to examine ornithological books and began to work in earnest on his monograph, purchasing specimens of kingfishers from

236-728: 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

295-499: 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  –

354-536: 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

413-632: A meagre income. At nineteen, in 1867, he became a librarian at the Zoological Society of London on the recommendation of Osbert Salvin and Philip Sclater and he completed his Monograph of the Kingfishers (1868–71) during this period. The book was produced in parts with 121 illustrations. He then began to collaborate with Henry Dresser on A History of the Birds of Europe but this had to be abandoned because of his new appointment. On

472-700: 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

531-462: 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

590-631: 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

649-594: 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,

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708-592: 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

767-550: 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

826-413: 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

885-423: Is known about this group rests on analyses of single species, as few provide sufficiently complete fossils for analysis. Although some of the smaller and more basal species, like those belonging to the subgroups Enaliornithidae and Brodavidae , might have been able to fly, the larger hesperornithids like Hesperornis and Baptornis had only vestigial wings. As in the case of modern foot-propelled diving birds,

944-664: The Late Cretaceous of North America. Small hesperornithean bones are known from the freshwater deposits of the Late Cretaceous of the Judith River Group as well as the Hell Creek and Lance Formations , and in several Eurasian sites. These species were about the size of a cormorant or a loon. The clade Hesperornithes was originally named as a subclass of Aves by Furbringer in 1888. However, it

1003-889: The Paleognathae (based on perceived similarities in the bony palate ). These similarities, however, as the more recently determined fact that the osteons of their bones – at least in Hesperornis – were arranged in a pattern similar to that in Neognathae , are today considered to be due to convergent evolution . In 2015, a species-level phylogenetic analysis found the following relationships among hesperornitheans. Pasquiaornis Enaliornis AMNH 5101 FMNH 395 Baptornis advenus Brodavis varneri Brodavis baileyi Fumicollis hoffmani Parahesperornis alexi Hesperornis [REDACTED] [REDACTED] Richard Bowdler Sharpe Richard

1062-558: 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

1121-777: The Zoological Society of London. A gold medal was awarded to him in 1891 by the Emperor of Austria. As of 2019, in the online list of world birds maintained by Frank Gill and David Donsker on behalf of the International Ornithologists' Union , Sharpe is credited with formally describing and coining the Latin names of 233 species of bird as well as 201 subspecies . He is also credited with introducing 45 genera . Many species and subspecies of birds have been named after him including: A genus Sharpia

1180-438: 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

1239-414: 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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1298-436: 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

1357-408: 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:

1416-400: 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,

1475-413: 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

1534-598: The death of George Robert Gray in 1872 he joined the British Museum as a Senior Assistant in the Department of Zoology, taking charge of the bird collection. On 3 December 1867 he married Emily Eliza, daughter of J. W. Burrows of Cookham. He named a subspecies of the common paradise kingfisher ( Tanysiptera galatea emiliae ) after his wife in 1871. They had ten daughters and many of them contributed to his books (and of other authors too) by hand colouring

1593-448: 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

1652-597: 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

1711-488: 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

1770-668: 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

1829-490: The femur and metatarsus of these animals were short, whereas the tibia was long. The legs were also set far back on the body, as in loons , grebes or penguins . Hesperornithids must have been powerful swimmers and divers but extremely ungainly on the land, and probably spent little time ashore except to nest. They were rather long-bodied, and measured about 6 feet (180 cm) long. Some researchers think that on land they had to slide on their bellies and push with their legs;

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1888-529: The front, thus allowing the lower teeth to disengage. Currently, the hesperornitheans are recognized as a very specialized lineage that is not ancestral to modern birds. Still, their relationship is close enough that they probably diverged from the ancestors of modern birds as late as the earliest Cretaceous . The earliest known hesperornithean is the Early Cretaceous Enaliornis . The majority of hesperornithean species are known from

1947-647: The hip and knee joints were shaped such that these species could not move them dorsoventrally, and in a resting position the feet projected sideways from the body, which would have prevented them from walking upright. The anatomy of their toes suggests that hesperornitheans had lobes of skin for propulsion underwater similar to grebes , rather than being webbed. The dense bones of these animals decreased their buoyancy, making diving easier. However, morphometric comparison with modern diving birds suggests that hesperornitheans share more similarities with diving ducks and cormorants rather than with loons or grebes . The snout

2006-447: 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

2065-434: 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

2124-762: The industrialist and amateur ornithologist Henry Seebohm , Colonel John Biddulph , C. B. Rickett, F. W. Styan , Alfred Russel Wallace , George Ernest Shelley , Philip Sclater and the bird illustrator John Gould . Sharpe founded the British Ornithologists' Club in 1892 and edited its bulletin. He wrote thirteen and a half of the 27 volumes of the Catalogue of the Birds in the British Museum (1874–1898). His handsome Birds of Paradise , published in two large volumes (over 21 inches x 14 inches) in 1891 and 1898, presented these colourful birds to

2183-415: The latter name. Clarke also defined the more inclusive group Hesperornithidae as all hesperornitheans closer to Hesperornis than to Baptornis . Hesperornitheans were originally combined with Ichthyornis in the paraphyletic group " Odontornithes " by Othniel Charles Marsh , in 1873. In 1875, they were separated as Odontolcae . The group was often considered to be related to loons and grebes, or to

2242-568: The lithograph plates. One daughter, Emily Mary , worked in the entomology department of the Natural History Museum between 1905 and 1925. He became Assistant Keeper in 1895, a position he held until his death from pneumonia in 1909. He died at his home in Chiswick. In 1911 a £100 civil pension was granted to his wife and daughters Emily Mary, Ada Lavinia and Eva Augusta. As curator of the bird collections, Sharpe's main work

2301-475: 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

2360-621: 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

2419-407: The name "Bowdler" at birth, but all adopted it later in life. The eldest daughter, Emily Mary Bowdler Sharpe , was a biologist and author in her own right, and also worked at the British Museum. The other nine daughters (Ada Lavinia, Eva Augusta, Lilian Bertha, Dora Louise, Lena Violet, Daisy Madeline, Sylvia Rosamund, Hilda Marion, and Aimee Marjorie) all worked as colourists on his works. Sharpe

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2478-528: 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

2537-516: 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

2596-418: 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

2655-543: 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

2714-410: 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

2773-484: 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

2832-482: The species most specialized for swimming were completely flightless. The largest known hesperornithean, Canadaga arctica , may have reached a maximum adult length of 2.2 metres (7.2 ft). Hesperornitheans were the only Mesozoic avialans to colonize the oceans. They were wiped out in the Cretaceous–Paleogene extinction event , along with enantiornitheans and all other non-avian dinosaurs. Most of what

2891-421: 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

2950-640: The top, with Ernst Hartert and several others having to restrain him and prevent him from jumping off. A regular at the Savage and Whitefriars Club, he and his wife threw a party in February 1888 with 120 guests and entertainment that included humorous sketches, songs, recitals and music. Sharpe was awarded an honorary LL.D. by the University of Aberdeen. He was fellow of the Linnean Society and

3009-484: 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

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3068-460: 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

3127-624: The world: as Sharpe wrote in his preface, "a great number of the species are here figured for the first time". Sharpe was nominated at the International Ornithological Congress at Paris in 1900 to preside over the London Congress in 1905. Sharpe was noted as a genial and humorous person. Richard Meinertzhagen and his brother were introduced to the bird collections by him. He was fond of children, having ten daughters himself. None of them were given

3186-510: Was also known for his practical jokes and pranks. When Eugene Oates was working on the Fauna of British India , he found the notes lying on a table and filled up a stray statement on the call of a white wagtail (ssp. lugens ) which went into print ( The note of this species is a prolonged "Pooh." ). On one occasion, Sharpe ascended the Eiffel tower with friends but became hysterical on reaching

3245-701: Was born in London, the first son of Thomas Bowdler Sharpe. His grandfather, Reverend Lancelot Sharpe was Rector of All Hallows Staining . His father was a publisher on Skinner Street and was best known for being the publisher of Sharpe's London Magazine , an illustrated periodical (weekly but monthly from 1847). His care from the age of six was under an aunt, Magdalen Wallace, widow of the headmaster at Grammar School in Sevenoaks and went to school in Brighton. At nine he studied at The King's School, Peterborough receiving

3304-503: Was erected but is now considered to be synonymous with Ploceus . 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

3363-406: Was generally ignored in the scientific literature in favor of the order-level name Hesperornithiformes , coined one year later. In 2004, Clarke became the first to define the hesperornithean group in terms of phylogenetics . Clarke defined Hesperornithes as all species closer to Hesperornis regalis than to modern birds, and regarded Hesperornithiformes as a junior synonym, though she did not define

3422-415: Was in classifying and cataloguing the collections. He also played a major role in acquiring private collections by persuading wealthy collectors and travellers to contribute to the museum. In 1872 the museum had 35,000 bird specimens; the collection had grown to half a million specimens by the time of his death. These included the bequests of Allan Octavian Hume , Osbert Salvin and Frederick DuCane Godman ,

3481-418: Was long, and tipped with a slightly hooked beak. Behind the beak, the jaws were filled with a series of simple, sharp teeth which were set into a longitudinal groove. These probably helped to seize fish , like the serrated beak of mergansers . Unlike modern birds, they retained a joint between the lower jaw bones. It is believed that this allowed them to rotate the back portion of the mandible independently of

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