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109-578: Charles Darwin described it as "the most remarkable reef in the West Indies " in 1842. In addition to its barrier reef, it also boasts three distinct Caribbean atolls : Turneffe Atoll , Glover's Reef and Lighthouse Reef . Lighthouse Reef is the most easterly diving area in Belize, it is home to the Great Blue Hole , made famous by Jacques Cousteau in 1970; Turneffe Atoll lies directly to

218-442: A common ancestor is now generally accepted and considered a fundamental scientific concept. In a joint publication with Alfred Russel Wallace , he introduced his scientific theory that this branching pattern of evolution resulted from a process he called natural selection , in which the struggle for existence has a similar effect to the artificial selection involved in selective breeding . Darwin has been described as one of

327-451: A genealogical branching of a single evolutionary tree , in which "It is absurd to talk of one animal being higher than another", thereby discarding Lamarck's idea of independent lineages progressing to higher forms. While developing this intensive study of transmutation, Darwin became mired in more work. Still rewriting his Journal , he took on editing and publishing the expert reports on his collections, and with Henslow's help obtained

436-469: 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

545-562: A 230-page "Essay", to be expanded with his research results if he died prematurely. In November, the anonymously published sensational best-seller Vestiges of the Natural History of Creation brought wide interest in transmutation. Darwin scorned its amateurish geology and zoology, but carefully reviewed his own arguments. Controversy erupted, and it continued to sell well despite contemptuous dismissal by scientists. Darwin completed his third geological book in 1846. He now renewed

654-513: A 48 percent reduction in live coral cover across the Belize reef system. Usually, it is hard to distinguish whether the reason for coral bleaching is human activities or natural reasons such as storms or bacterial fluctuations. In the case of the Belize Barrier Reef, many factors which make the distinction difficult do not apply. Human population in this area is much more sparse than the corresponding areas near other coral reefs, so

763-845: A Bachelor of Arts degree as the first step towards becoming an Anglican country parson . Darwin was unqualified for Cambridge's Tripos exams and was required instead to join the ordinary degree course. He preferred riding and shooting to studying. During the first few months of Darwin's enrolment at Christ's College, his second cousin William Darwin Fox was still studying there. Fox impressed him with his butterfly collection, introducing Darwin to entomology and influencing him to pursue beetle collecting. He did this zealously and had some of his finds published in James Francis Stephens ' Illustrations of British entomology (1829–1932). Through Fox, Darwin became

872-673: A Treasury grant of £1,000 to sponsor this multi-volume Zoology of the Voyage of H.M.S. Beagle , a sum equivalent to about £115,000 in 2021. He stretched the funding to include his planned books on geology, and agreed to unrealistic dates with the publisher. As the Victorian era began, Darwin pressed on with writing his Journal , and in August 1837 began correcting printer's proofs . As Darwin worked under pressure, his health suffered. On 20 September, he had "an uncomfortable palpitation of

981-728: 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

1090-591: A beginning to each crop of species". Darwin's book The Structure and Distribution of Coral Reefs on his theory of atoll formation was published in May 1842 after more than three years of work, and he then wrote his first "pencil sketch" of his theory of natural selection. To escape the pressures of London, the family moved to rural Down House in Kent in September. On 11 January 1844, Darwin mentioned his theorising to

1199-547: A book on geology. When they reached Brazil, Darwin was delighted by the tropical forest , but detested the sight of slavery there , and disputed this issue with FitzRoy. The survey continued to the south in Patagonia . They stopped at Bahía Blanca , and in cliffs near Punta Alta Darwin made a major find of fossil bones of huge extinct mammals beside modern seashells, indicating recent extinction with no signs of change in climate or catastrophe. He found bony plates like

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1308-718: A break and went "geologising" in Scotland. He visited Glen Roy in glorious weather to see the parallel "roads" cut into the hillsides at three heights. He later published his view that these were marine-raised beaches, but then had to accept that they were shorelines of a proglacial lake . Fully recuperated, he returned to Shrewsbury in July 1838. Used to jotting down daily notes on animal breeding, he scrawled rambling thoughts about marriage, career and prospects on two scraps of paper, one with columns headed "Marry" and "Not Marry" . Advantages under "Marry" included "constant companion and

1417-471: A calm spell. On their first stop ashore at St Jago in Cape Verde, Darwin found that a white band high in the volcanic rock cliffs included seashells. FitzRoy had given him the first volume of Charles Lyell 's Principles of Geology , which set out uniformitarian concepts of land slowly rising or falling over immense periods, and Darwin saw things Lyell's way, theorising and thinking of writing

1526-562: A close friend and follower of botany professor John Stevens Henslow . He met other leading parson-naturalists who saw scientific work as religious natural theology , becoming known to these dons as "the man who walks with Henslow". When his own exams drew near, Darwin applied himself to his studies and was delighted by the language and logic of William Paley 's Evidences of Christianity (1795). In his final examination in January 1831, Darwin did well, coming tenth out of 178 candidates for

1635-412: A copy of his journal for his family. He had some expertise in geology, beetle collecting and dissecting marine invertebrates, but in all other areas, was a novice and ably collected specimens for expert appraisal. Despite suffering badly from seasickness, Darwin wrote copious notes while on board the ship. Most of his zoology notes are about marine invertebrates, starting with plankton collected during

1744-499: 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  –

1853-596: A fascination and expertise in marine invertebrates, dating back to his student days with Grant, by dissecting and classifying the barnacles he had collected on the voyage, enjoying observing beautiful structures and thinking about comparisons with allied structures. In 1847, Hooker read the "Essay" and sent notes that provided Darwin with the calm critical feedback that he needed, but would not commit himself and questioned Darwin's opposition to continuing acts of creation . In an attempt to improve his chronic ill health, Darwin went in 1849 to Dr. James Gully 's Malvern spa and

1962-529: A fortnight mapping strata in Wales. After leaving Sedgwick in Wales, Darwin spent a few days with student friends at Barmouth . He returned home on 29 August to find a letter from Henslow proposing him as a suitable (if unfinished) naturalist for a self-funded supernumerary place on HMS  Beagle with captain Robert FitzRoy , a position for a gentleman rather than "a mere collector". The ship

2071-532: A freed black slave who had accompanied Charles Waterton in the South American rainforest . In Darwin's second year at the university, he joined the Plinian Society , a student natural-history group featuring lively debates in which radical democratic students with materialistic views challenged orthodox religious concepts of science. He assisted Robert Edmond Grant 's investigations of

2180-473: A friend in old age ... better than a dog anyhow", against points such as "less money for books" and "terrible loss of time". Having decided in favour of marriage, he discussed it with his father, then went to visit his cousin Emma on 29 July. At this time he did not get around to proposing, but against his father's advice, he mentioned his ideas on transmutation. He married Emma on 29 January 1839 and they were

2289-530: A giant capybara . The armour fragments were actually from Glyptodon , a huge armadillo-like creature, as Darwin had initially thought. These extinct creatures were related to living species in South America. In mid-December, Darwin took lodgings in Cambridge to arrange expert classification of his collections, and prepare his own research for publication. Questions of how to combine his diary into

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2398-556: A giant version of the armour on local armadillos . From a jaw and tooth he identified the gigantic Megatherium , then from Cuvier's description thought the armour was from this animal. The finds were shipped to England, and scientists found the fossils of great interest. In Patagonia, Darwin came to wrongly believe the territory was devoid of reptiles. On rides with gauchos into the interior to explore geology and collect more fossils, Darwin gained social, political and anthropological insights into both native and colonial people at

2507-506: A great name among the Naturalists of Europe". On 2 October 1836, Beagle anchored at Falmouth , Cornwall. Darwin promptly made the long coach journey to Shrewsbury to visit his home and see relatives. He then hurried to Cambridge to see Henslow, who advised him on finding available naturalists to catalogue Darwin's animal collections and to take on the botanical specimens. Darwin's father organised investments, enabling his son to be

2616-536: 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

2725-515: A minor role to natural selection, and it was not until the emergence of the modern evolutionary synthesis from the 1930s to the 1950s that a broad consensus developed in which natural selection was the basic mechanism of evolution. Darwin's scientific discovery is the unifying theory of the life sciences , explaining the diversity of life . Darwin was born in Shrewsbury , Shropshire, on 12 February 1809, at his family's home, The Mount . He

2834-539: A programmer of laws. Darwin stayed with his freethinking brother Erasmus, part of this Whig circle and a close friend of the writer Harriet Martineau , who promoted the Malthusianism that underpinned the controversial Whig Poor Law reforms to stop welfare from causing overpopulation and more poverty. As a Unitarian, she welcomed the radical implications of transmutation of species , promoted by Grant and younger surgeons influenced by Geoffroy . Transmutation

2943-591: A sand beach. He theorised that as the land rose, oceanic islands sank, and coral reefs round them grew to form atolls . On the geologically new Galápagos Islands , Darwin looked for evidence attaching wildlife to an older "centre of creation", and found mockingbirds allied to those in Chile but differing from island to island. He heard that slight variations in the shape of tortoise shells showed which island they came from, but failed to collect them, even after eating tortoises taken on board as food. In Australia,

3052-517: A self-funded gentleman scientist , and an excited Darwin went around the London institutions being fêted and seeking experts to describe the collections. British zoologists at the time had a huge backlog of work, due to natural history collecting being encouraged throughout the British Empire, and there was a danger of specimens just being left in storage. Charles Lyell eagerly met Darwin for

3161-579: A series of books, and in his final book, The Formation of Vegetable Mould, through the Actions of Worms (1881), he examined earthworms and their effect on soil. Darwin published his theory of evolution with compelling evidence in his 1859 book On the Origin of Species . By the 1870s, the scientific community and a majority of the educated public had accepted evolution as a fact . However, many initially favoured competing explanations that gave only

3270-700: 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

3379-462: 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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3488-719: A similarity between farmers picking the best stock in selective breeding, and a Malthusian Nature selecting from chance variants so that "every part of newly acquired structure is fully practical and perfected", thinking this comparison "a beautiful part of my theory". He later called his theory natural selection , an analogy with what he termed the "artificial selection" of selective breeding. On 11 November, he returned to Maer and proposed to Emma, once more telling her his ideas. She accepted, then in exchanges of loving letters she showed how she valued his openness in sharing their differences, while expressing her strong Unitarian beliefs and concerns that his honest doubts might separate them in

3597-631: 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

3706-594: 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,

3815-592: 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

3924-468: A time of revolution, and learnt that two types of rhea had separate but overlapping territories. Further south, he saw stepped plains of shingle and seashells as raised beaches at a series of elevations. He read Lyell's second volume and accepted its view of "centres of creation" of species, but his discoveries and theorising challenged Lyell's ideas of smooth continuity and of extinction of species. Three Fuegians on board, who had been seized during

4033-550: 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

4142-413: 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

4251-526: Is claimed by scientists that over 40% of Belize's coral reef has been damaged since 1998. The Belize Barrier Reef has been affected by mass-bleaching events. The first mass bleaching occurred in 1995, with an estimated mortality of 10 percent of coral colonies, according to a report by the Coastal Zone Management Institute in Belize. A second mass-bleaching event occurred, when Hurricane Mitch struck in 1998. Biologists observed

4360-471: Is known as a Malthusian catastrophe . Darwin was well-prepared to compare this to Augustin de Candolle 's "warring of the species" of plants and the struggle for existence among wildlife, explaining how numbers of a species kept roughly stable. As species always breed beyond available resources, favourable variations would make organisms better at surviving and passing the variations on to their offspring, while unfavourable variations would be lost. He wrote that

4469-686: The Linnean Society of London . Darwin's work established evolutionary descent with modification as the dominant scientific explanation of natural diversification. In 1871, he examined human evolution and sexual selection in The Descent of Man, and Selection in Relation to Sex , followed by The Expression of the Emotions in Man and Animals (1872). His research on plants was published in

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4578-554: The Narrative were resolved at the end of the month when FitzRoy accepted Broderip's advice to make it a separate volume, and Darwin began work on his Journal and Remarks . Darwin's first paper showed that the South American landmass was slowly rising, and with Lyell's enthusiastic backing he read it to the Geological Society of London on 4 January 1837. On the same day, he presented his mammal and bird specimens to

4687-602: The Royal Society 's Royal Medal, and it made his reputation as a biologist . Upon the conclusion of his research, Darwin declared "I hate a barnacle as no man ever did before." In 1854, he became a Fellow of the Linnean Society of London , gaining postal access to its library. He began a major reassessment of his theory of species, and in November realised that divergence in the character of descendants could be explained by them becoming adapted to "diversified places in

4796-942: The Zoological Society . The ornithologist John Gould soon announced that the Galápagos birds that Darwin had thought a mixture of blackbirds , " gros-beaks " and finches , were, in fact, twelve separate species of finches . On 17 February, Darwin was elected to the Council of the Geological Society, and Lyell's presidential address presented Owen's findings on Darwin's fossils, stressing geographical continuity of species as supporting his uniformitarian ideas. Early in March, Darwin moved to London to be near this work, joining Lyell's social circle of scientists and experts such as Charles Babbage , who described God as

4905-521: The first Beagle voyage then given Christian education in England, were returning with a missionary. Darwin found them friendly and civilised, yet at Tierra del Fuego he met "miserable, degraded savages", as different as wild from domesticated animals. He remained convinced that, despite this diversity, all humans were interrelated with a shared origin and potential for improvement towards civilisation. Unlike his scientist friends, he now thought there

5014-519: The marsupial rat-kangaroo and the platypus seemed so unusual that Darwin thought it was almost as though two distinct Creators had been at work. He found the Aborigines "good-humoured & pleasant", their numbers depleted by European settlement. FitzRoy investigated how the atolls of the Cocos (Keeling) Islands had formed, and the survey supported Darwin's theorising. FitzRoy began writing

5123-598: The ordinary degree. Darwin had to stay at Cambridge until June 1831. He studied Paley's Natural Theology or Evidences of the Existence and Attributes of the Deity (first published in 1802), which made an argument for divine design in nature , explaining adaptation as God acting through laws of nature . He read John Herschel 's new book, Preliminary Discourse on the Study of Natural Philosophy (1831), which described

5232-596: The "final cause of all this wedging, must be to sort out proper structure, & adapt it to changes", so that "One may say there is a force like a hundred thousand wedges trying force into every kind of adapted structure into the gaps of in the economy of nature, or rather forming gaps by thrusting out weaker ones." This would result in the formation of new species. As he later wrote in his Autobiography : In October 1838, that is, fifteen months after I had begun my systematic enquiry, I happened to read for amusement Malthus on Population, and being well prepared to appreciate

5341-558: 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

5450-618: The Wedgwoods were adopting Anglicanism . Robert Darwin, a freethinker , had baby Charles baptised in November 1809 in the Anglican St Chad's Church, Shrewsbury , but Charles and his siblings attended the local Unitarian Church with their mother. The eight-year-old Charles already had a taste for natural history and collecting when he joined the day school run by its preacher in 1817. That July, his mother died. From September 1818, he joined his older brother Erasmus in attending

5559-459: The afterlife. While he was house-hunting in London, bouts of illness continued and Emma wrote urging him to get some rest, almost prophetically remarking "So don't be ill any more my dear Charley till I can be with you to nurse you." He found what they called "Macaw Cottage" (because of its gaudy interiors) in Gower Street , then moved his "museum" in over Christmas. On 24 January 1839, Darwin

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5668-506: The anatomy and life cycle of marine invertebrates in the Firth of Forth , and on 27 March 1827 presented at the Plinian his own discovery that black spores found in oyster shells were the eggs of a skate leech . One day, Grant praised Lamarck 's evolutionary ideas . Darwin was astonished by Grant's audacity, but had recently read similar ideas in his grandfather Erasmus' journals. Darwin

5777-438: 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

5886-414: 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

5995-521: The bleaching event itself. With continuous bleaching, the coral reef will have little to no chance of recovery. Cave dive sites: Charles Darwin Charles Robert Darwin ( / ˈ d ɑːr w ɪ n / DAR -win ; 12 February 1809 – 19 April 1882) was an English naturalist , geologist , and biologist , widely known for his contributions to evolutionary biology . His proposition that all species of life have descended from

6104-437: The botanist Joseph Dalton Hooker , writing with melodramatic humour "it is like confessing a murder". Hooker replied, "There may, in my opinion, have been a series of productions on different spots, & also a gradual change of species. I shall be delighted to hear how you think that this change may have taken place, as no presently conceived opinions satisfy me on the subject." By July, Darwin had expanded his "sketch" into

6213-436: 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

6322-408: 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:

6431-400: 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,

6540-413: 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

6649-448: 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

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6758-597: 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

6867-488: 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

6976-542: The duties of Secretary of the Geological Society. After initially declining the work, he accepted the post in March 1838. Despite the grind of writing and editing the Beagle reports, Darwin made remarkable progress on transmutation, taking every opportunity to question expert naturalists and, unconventionally, people with practical experience in selective breeding such as farmers and pigeon fanciers . Over time, his research drew on information from his relatives and children,

7085-456: The east of Belize City and is the nearest of the atolls to that city. These different reefs provide diverse scuba diving opportunities that include walls, pinnacles and reef flats that are located throughout an enormous area of sea. The Belize Barrier Reef is home to a large diversity of plants and animals: With 90% of the reef still needing to be researched, it is estimated that only 10% of all species have been discovered. A large portion of

7194-459: The economy of nature". Phylogenetics 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

7303-668: 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

7412-713: The family butler, neighbours, colonists and former shipmates. He included mankind in his speculations from the outset, and on seeing an orangutan in the zoo on 28 March 1838 noted its childlike behaviour. The strain took a toll, and by June he was being laid up for days on end with stomach problems, headaches and heart symptoms. For the rest of his life, he was repeatedly incapacitated with episodes of stomach pains, vomiting, severe boils , palpitations, trembling and other symptoms, particularly during times of stress, such as attending meetings or making social visits. The cause of Darwin's illness remained unknown, and attempts at treatment had only ephemeral success. On 23 June, he took

7521-588: The first country in the world to completely ban bottom trawling in December 2010. In December 2015, Belize banned offshore oil drilling within 1 km of the Barrier Reef. Despite these protective measures, the reef remains under threat from oceanic pollution as well as uncontrolled tourism, shipping, and fishing. Other threats include hurricanes, along with global warming and the resulting increase in ocean temperatures, which causes coral bleaching . It

7630-597: The first time on 29 October and soon introduced him to the up-and-coming anatomist Richard Owen , who had the facilities of the Royal College of Surgeons to work on the fossil bones collected by Darwin. Owen's surprising results included other gigantic extinct ground sloths as well as the Megatherium Darwin had identified, a near complete skeleton of the unknown Scelidotherium and a hippopotamus -sized rodent -like skull named Toxodon resembling

7739-582: The heart", so his doctors urged him to "knock off all work" and live in the country for a few weeks. After visiting Shrewsbury, he joined his Wedgwood relatives at Maer Hall , Staffordshire, but found them too eager for tales of his travels to give him much rest. His charming, intelligent, and cultured cousin Emma Wedgwood , nine months older than Darwin, was nursing his invalid aunt. His uncle Josiah pointed out an area of ground where cinders had disappeared under loam and suggested that this might have been

7848-472: The highest aim of natural philosophy as understanding such laws through inductive reasoning based on observation, and Alexander von Humboldt 's Personal Narrative of scientific travels in 1799–1804. Inspired with "a burning zeal" to contribute, Darwin planned to visit Tenerife with some classmates after graduation to study natural history in the tropics. In preparation, he joined Adam Sedgwick 's geology course, then on 4 August travelled with him to spend

7957-426: The human activity and pollution are much lower compared to other coral reefs and the Belize reef system is in a much more enclosed area. When coral bleaching occurs, a large part of the coral dies, and the remaining part of the ecosystem begins the process of repairing the damage. But the chances of recovery are low, as corals that are bleached become much more vulnerable to disease. Disease often kills more corals than

8066-447: 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

8175-434: 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

8284-475: 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

8393-621: 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

8502-538: The most influential figures in human history and was honoured by burial in Westminster Abbey . Darwin's early interest in nature led him to neglect his medical education at the University of Edinburgh ; instead, he helped to investigate marine invertebrates . His studies at the University of Cambridge 's Christ's College from 1828 to 1831 encouraged his passion for natural science . However, it

8611-503: The nearby Anglican Shrewsbury School as a boarder . Darwin spent the summer of 1825 as an apprentice doctor, helping his father treat the poor of Shropshire, before going to the well-regarded University of Edinburgh Medical School with his brother Erasmus in October 1825. Darwin found lectures dull and surgery distressing, so he neglected his studies. He learned taxidermy in around 40 daily hour-long sessions from John Edmonstone ,

8720-433: The official Narrative of the Beagle voyages, and after reading Darwin's diary, he proposed incorporating it into the account. Darwin's Journal was eventually rewritten as a separate third volume, on geology and natural history. In Cape Town , South Africa, Darwin and FitzRoy met John Herschel, who had recently written to Lyell praising his uniformitarianism as opening bold speculation on "that mystery of mysteries,

8829-496: The origin of species". Without telling Darwin, extracts from his letters to Henslow had been read to scientific societies, printed as a pamphlet for private distribution among members of the Cambridge Philosophical Society , and reported in magazines, including The Athenaeum . Darwin first heard of this at Cape Town, and at Ascension Island read of Sedgwick's prediction that Darwin "will have

8938-522: The parents of ten children, seven of whom survived to adulthood. Continuing his research in London, Darwin's wide reading now included the sixth edition of Malthus 's An Essay on the Principle of Population . On 28 September 1838, he noted its assertion that human "population, when unchecked, goes on doubling itself every twenty-five years, or increases in a geometrical ratio", a geometric progression so that population soon exceeds food supply in what

9047-528: 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

9156-573: The possibility that "one species does change into another" to explain the geographical distribution of living species such as the rheas, and extinct ones such as the strange extinct mammal Macrauchenia , which resembled a giant guanaco , a llama relative. Around mid-July, he recorded in his "B" notebook his thoughts on lifespan and variation across generations – explaining the variations he had observed in Galápagos tortoises , mockingbirds, and rheas. He sketched branching descent, and then

9265-516: 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

9374-418: 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

9483-587: The reef is protected by the Belize Barrier Reef Reserve System, which includes seven marine reserves , 450 cayes , and three atolls . It totals 960 square kilometres (370 sq mi) in area, including: In 1996 the reserve system was designated a World Heritage Site due to its vulnerability and the fact that it contains the most important and significant natural habitats for in-situ conservation of biological diversity (according to criteria VII, IX, and X). Belize became

9592-543: 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

9701-410: 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

9810-520: The replacement of extinct species by others" as "a natural in contradistinction to a miraculous process". When organising his notes as the ship sailed home, Darwin wrote that, if his growing suspicions about the mockingbirds, the tortoises and the Falkland Islands fox were correct, "such facts undermine the stability of Species", then cautiously added "would" before "undermine". He later wrote that such facts "seemed to me to throw some light on

9919-484: 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

10028-408: The struggle for existence which everywhere goes on from long-continued observation of the habits of animals and plants, it at once struck me that under these circumstances favourable variations would tend to be preserved, and unfavourable ones to be destroyed. The result of this would be the formation of new species. Here, then, I had at last got a theory by which to work... By mid-December, Darwin saw

10137-409: The systematics of the taxa. He wrote his first examination of the species in 1846, but did not formally describe it until 1854. FitzRoy's long delayed Narrative was published in May 1839. Darwin's Journal and Remarks got good reviews as the third volume, and on 15 August it was published on its own. Early in 1842, Darwin wrote about his ideas to Charles Lyell, who noted that his ally "denies seeing

10246-421: 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

10355-484: 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

10464-460: 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

10573-420: The voyage began on 27 December 1831; it lasted almost five years. As FitzRoy had intended, Darwin spent most of that time on land investigating geology and making natural history collections, while HMS Beagle surveyed and charted coasts. He kept careful notes of his observations and theoretical speculations, and at intervals during the voyage his specimens were sent to Cambridge together with letters including

10682-421: The voyage, Darwin began detailed investigations and, in 1838, devised his theory of natural selection. Although he discussed his ideas with several naturalists, he needed time for extensive research, and his geological work had priority. He was writing up his theory in 1858 when Alfred Russel Wallace sent him an essay that described the same idea, prompting the immediate joint submission of both their theories to

10791-403: The work of earthworms , inspiring "a new & important theory" on their role in soil formation , which Darwin presented at the Geological Society on 1 November 1837. His Journal was printed and ready for publication by the end of February 1838, as was the first volume of the Narrative , but FitzRoy was still working hard to finish his own volume. William Whewell pushed Darwin to take on

10900-707: Was elected a Fellow of the Royal Society (FRS). On 29 January, Darwin and Emma Wedgwood were married at Maer in an Anglican ceremony arranged to suit the Unitarians, then immediately caught the train to London and their new home. Darwin now had the framework of his theory of natural selection "by which to work", as his "prime hobby". His research included extensive experimental selective breeding of plants and animals, finding evidence that species were not fixed and investigating many detailed ideas to refine and substantiate his theory. For fifteen years this work

11009-418: Was a " wren " was in the finch group . Darwin had not labelled the finches by island, but from the notes of others on the ship, including FitzRoy, he allocated species to islands. The two rheas were distinct species, and on 14 March Darwin announced how their distribution changed going southwards. By mid-March 1837, barely six months after his return to England, Darwin was speculating in his Red Notebook on

11118-472: Was anathema to Anglicans defending social order, but reputable scientists openly discussed the subject, and there was wide interest in John Herschel's letter praising Lyell's approach as a way to find a natural cause of the origin of new species. Gould met Darwin and told him that the Galápagos mockingbirds from different islands were separate species, not just varieties, and what Darwin had thought

11227-418: Was his five-year voyage on HMS  Beagle from 1831 to 1836 that truly established Darwin as an eminent geologist. The observations and theories he developed during his voyage supported Charles Lyell 's concept of gradual geological change . Publication of his journal of the voyage made Darwin famous as a popular author. Puzzled by the geographical distribution of wildlife and fossils he collected on

11336-425: Was in the background to his main occupation of writing on geology and publishing expert reports on the Beagle collections, in particular, the barnacles . The impetus of Darwin's barnacle research came from a collection of a barnacle colony from Chile in 1835, which he dubbed Mr. Arthrobalanus . His confusion over the relationship of this species ( Cryptophialus minutus ) to other barnacles caused him to fixate on

11445-504: Was no unbridgeable gap between humans and animals. A year on, the mission had been abandoned. The Fuegian they had named Jemmy Button lived like the other natives, had a wife, and had no wish to return to England. Darwin experienced an earthquake in Chile in 1835 and saw signs that the land had just been raised, including mussel -beds stranded above high tide. High in the Andes he saw seashells, and several fossil trees that had grown on

11554-577: Was rather bored by Robert Jameson 's natural-history course, which covered geology – including the debate between neptunism and plutonism . He learned the classification of plants and assisted with work on the collections of the University Museum , one of the largest museums in Europe at the time. Darwin's neglect of medical studies annoyed his father, who sent him to Christ's College, Cambridge , in January 1828, to study for

11663-574: Was surprised to find some benefit from hydrotherapy . Then, in 1851, his treasured daughter Annie fell ill, reawakening his fears that his illness might be hereditary. She died the same year after a long series of crises. In eight years of work on barnacles, Darwin's theory helped him to find " homologies " showing that slightly changed body parts served different functions to meet new conditions, and in some genera he found minute males parasitic on hermaphrodites , showing an intermediate stage in evolution of distinct sexes . In 1853, it earned him

11772-482: Was the fifth of six children of wealthy society doctor and financier Robert Darwin and Susannah Darwin (née Wedgwood). His grandfathers Erasmus Darwin and Josiah Wedgwood were both prominent abolitionists . Erasmus Darwin had praised general concepts of evolution and common descent in his Zoonomia (1794), a poetic fantasy of gradual creation including undeveloped ideas anticipating concepts his grandson expanded. Both families were largely Unitarian , though

11881-446: Was to leave in four weeks on an expedition to chart the coastline of South America. Robert Darwin objected to his son's planned two-year voyage, regarding it as a waste of time, but was persuaded by his brother-in-law, Josiah Wedgwood II , to agree to (and fund) his son's participation. Darwin took care to remain in a private capacity to retain control over his collection, intending it for a major scientific institution. After delays,

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