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45-497: There are two taxa with the name Pogonophora : Pogonophora, an obsolete animal phylum, now treated as part of the family Siboglinidae Pogonophora (plant) , a genus in the Euphorbiaceae [REDACTED] Topics referred to by the same term This disambiguation page lists articles about taxa associated with the same name. If an internal link led you here, you may wish to change
90-441: A fossil can inform its phylogenetic position in addition to morphology. By allowing all aspects of tree reconstruction to occur simultaneously, the risk of biased results is decreased. This approach has been improved upon by pairing it with different models. One current method of molecular clock calibration is total evidence dating paired with the fossilized birth-death (FBD) model and a model of morphological evolution. The FBD model
135-421: A larger sample of the fossil record of clades to estimate calibration densities empirically. Studies have shown that increasing the number of fossil constraints increases the accuracy of divergence time estimation. Sometimes referred to as tip dating , tip calibration is a method of molecular clock calibration in which fossils are treated as taxa and placed on the tips of the tree. This is achieved by creating
180-483: A matrix that includes a molecular dataset for the extant taxa along with a morphological dataset for both the extinct and the extant taxa. Unlike node calibration, this method reconstructs the tree topology and places the fossils simultaneously. Molecular and morphological models work together simultaneously, allowing morphology to inform the placement of fossils. Tip calibration makes use of all relevant fossil taxa during clock calibration, rather than relying on only
225-467: A population will accumulate at a clock-rate that is equal to the rate of neutral mutations in an individual. To use molecular clocks to estimate divergence times, molecular clocks need to be "calibrated". This is because molecular data alone does not contain any information on absolute times. For viral phylogenetics and ancient DNA studies—two areas of evolutionary biology where it is possible to sample sequences over an evolutionary timescale—the dates of
270-604: A single divergence date can be estimated from fossils, with all other dates inferred from that. Other sets of species have abundant fossils available, allowing the hypothesis of constant divergence rates to be tested. DNA sequences experiencing low levels of negative selection showed divergence rates of 0.7–0.8% per Myr in bacteria, mammals, invertebrates, and plants. In the same study, genomic regions experiencing very high negative or purifying selection (encoding rRNA) were considerably slower (1% per 50 Myr). In addition to such variation in rate with genomic position, since
315-463: Is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged . The biomolecular data used for such calculations are usually nucleotide sequences for DNA , RNA , or amino acid sequences for proteins . The notion of the existence of a so-called "molecular clock" was first attributed to Émile Zuckerkandl and Linus Pauling who, in 1962, noticed that
360-475: Is called the cephalic lobe, which ranges from one to over 200 thin branchial ciliated tentacles , each with tiny side branches known as pinnules. Behind this is a glandular forepart, which helps to secrete the tube. The main part of the body is the trunk, which is greatly elongated and bears various annuli, papillae, and ciliary tracts. Posterior to the trunk is the short metamerically segmented opisthosoma , bearing external paired chaetae , which help to anchor
405-427: Is novel in that it allows for "sampled ancestors", which are fossil taxa that are the direct ancestor of a living taxon or lineage . This allows fossils to be placed on a branch above an extant organism, rather than being confined to the tips. Bayesian methods can provide more appropriate estimates of divergence times, especially if large datasets—such as those yielded by phylogenomics —are employed. Sometimes only
450-406: Is weakly supported. clade Frenulata Osedax Sclerolinum (clade Monilifera) clade Vestimentifera Like other tube worms, vestimentiferans are benthic marine creatures. Riftia pachyptila , a vestimentiferan, is known only from the hydrothermal vent systems. Vestimentiferan bodies are divided into four regions: the obturaculum, vestimentum, trunk, and opisthosome. The main trunk of
495-407: The most recent common ancestor of the species in question. Expansion dating has been used to show that molecular clock rates can be inflated at short timescales (< 1 MY) due to incomplete fixation of alleles, as discussed below This approach to tip calibration goes a step further by simultaneously estimating fossil placement, topology, and the evolutionary timescale. In this method, the age of
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#1732852403351540-485: The trophosome . One gram of trophosome tissue can contain one billion bacteria. The origin of this symbiotic relationship is not currently known. The bacteria appear to colonize the host animal larvae after they have settled on a surface, entering them through their skin. This method of entry, known as horizontal transmission, means that each organism may have different species of bacteria assisting in this symbiosis. However, these bacteria all play similar roles in sustaining
585-512: The 'strict' molecular clock hypothesis and Joseph Felsenstein 's many-rates model and are made possible through MCMC techniques that explore a weighted range of tree topologies and simultaneously estimate parameters of the chosen substitution model. It must be remembered that divergence dates inferred using a molecular clock are based on statistical inference and not on direct evidence . The molecular clock runs into particular challenges at very short and very long timescales. At long timescales,
630-590: The animal to the base of its tube. The body cavity has a separate compartment in each of the first three regions of the body and extends into the tentacles. The opisthosoma has a coelomic chamber in each of its 5 to 23 segments, separated by septa . The worms have a complex closed circulatory system and a well-developed nervous system , but as adults, siboglinids completely lack a mouth, gut, and anus. The family Siboglinidae has been difficult to place in an evolutionary context. After examination of genetic differences between annelids, Siboglinidae were placed within
675-411: The body bears wing-like extensions. Unlike other siboglinids that never have a digestive tract , they have one that they completely lose during metamorphosis . The obturaculum is the first anterior body part. It is possible that the obturaculum is actually an outgrowth of the vestimentum rather than a separate body segment which would distinguish it from other siboglinids. The vestimentum, from which
720-529: The difference between the cytochrome c of a bacterium and yeast, wheat, moth, tuna, pigeon, and horse ranges from 64% to 69%. Together with the work of Emile Zuckerkandl and Linus Pauling, the genetic equidistance result led directly to the formal postulation of the molecular clock hypothesis in the early 1960s. Similarly, Vincent Sarich and Allan Wilson in 1967 demonstrated that molecular differences among modern Primates in albumin proteins showed that approximately constant rates of change had occurred in all
765-474: The different populations. Instead, they represent alternative alleles that were both present as part of a polymorphism in the common ancestor. The inclusion of differences that have not yet become fixed leads to a potentially dramatic inflation of the apparent rate of the molecular clock at very short timescales. The molecular clock technique is an important tool in molecular systematics , macroevolution , and phylogenetic comparative methods . Estimation of
810-592: The early 1990s variation among taxa has proven fertile ground for research too, even over comparatively short periods of evolutionary time (for example mockingbirds ). Tube-nosed seabirds have molecular clocks that on average run at half speed of many other birds, possibly due to long generation times, and many turtles have a molecular clock running at one-eighth the speed it does in small mammals, or even slower. Effects of small population size are also likely to confound molecular clock analyses. Researchers such as Francisco J. Ayala have more fundamentally challenged
855-490: The former phyla Pogonophora and Vestimentifera (the giant tube worms ). The family is composed of around 100 species of vermiform creatures which live in thin tubes buried in sediment (Pogonophora) or in tubes attached to hard substratum (Vestimentifera) at ocean depths ranging from 100 to 10,000 m (300 to 32,800 ft). They can also be found in association with hydrothermal vents , methane seeps , sunken plant material, and whale carcasses . The first specimen
900-432: The genera along a continuum. Sclerolinum is a monogeneric clade (which may be called Monilifera) living on organic-rich remains. Frenulates live in organic-rich sediment habitats. Osedax is a monogeneric clade specialized in living on whale bones, although recent evidence shows them living on fish bones as well. One probable relationship between the four clades is shown in the cladogram below. The position of Osedax
945-523: The geological record can be used to calibrate a rate of molecular evolution in a manner similar to node calibration. However, instead of calibrating from the known age of a node, expansion calibration uses a two-epoch model of constant population size followed by population growth, with the time of transition between epochs being the parameter of interest for calibration. Expansion calibration works at shorter, intraspecific timescales in comparison to node calibration, because expansions can only be detected after
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#1732852403351990-531: The group's name is derived, is a wing-like body part with glands that secrete the tube. In a ventroanterior position in the vestimentum is the brain which is postulated to be simpler than relatives that maintain a gut in the adult form. The opisthosome is the anchoring rear body part. Their primary nutrition is derived from the sulfide-rich fluids emanating from the hydrothermal vents where they live. The sulfides are metabolized by symbiotic hydrogen sulfide- or methane-oxidizing bacteria living in an internal organ,
1035-498: The intermediate samples can be used to calibrate the molecular clock. However, most phylogenies require that the molecular clock be calibrated using independent evidence about dates, such as the fossil record. There are two general methods for calibrating the molecular clock using fossils: node calibration and tip calibration. Sometimes referred to as node dating, node calibration is a method for time-scaling phylogenetic trees by specifying time constraints for one or more nodes in
1080-403: The lineages they assessed. The basic logic of their analysis involved recognizing that if one species lineage had evolved more quickly than a sister species lineage since their common ancestor, then the molecular differences between an outgroup (more distantly related) species and the faster-evolving species should be larger (since more molecular changes would have accumulated on that lineage) than
1125-456: The link to point directly to the intended article. Retrieved from " https://en.wikipedia.org/w/index.php?title=Pogonophora&oldid=761005718 " Category : Taxonomy disambiguation pages Hidden categories: Short description is different from Wikidata All article disambiguation pages All disambiguation pages Siboglinidae Siboglinidae is a family of polychaete annelid worms whose members made up
1170-422: The main stem of vertebrate evolution earlier than either birds or mammals, the cytochrome c of both mammals and birds should be equally different from the cytochrome c of fish. Similarly, all vertebrate cytochrome c should be equally different from the yeast protein." For example, the difference between the cytochrome c of a carp and a frog, turtle, chicken, rabbit, and horse is a very constant 13% to 14%. Similarly,
1215-435: The minimum constraint in node calibration analyses. However, determining how much older the node is allowed to be is challenging. There are a number of strategies for deriving the maximum bound for the age of a clade including those based on birth-death models, fossil stratigraphic distribution analyses, or taphonomic controls. Alternatively, instead of a maximum and a minimum, a probability density can be used to represent
1260-574: The molecular clock hypothesis. According to Ayala's 1999 study, five factors combine to limit the application of molecular clock models: Molecular clock users have developed workaround solutions using a number of statistical approaches including maximum likelihood techniques and later Bayesian modeling . In particular, models that take into account rate variation across lineages have been proposed in order to obtain better estimates of divergence times. These models are called relaxed molecular clocks because they represent an intermediate position between
1305-537: The molecular differences between the outgroup species and the slower-evolving species. This method is known as the relative rate test . Sarich and Wilson's paper reported, for example, that human ( Homo sapiens ) and chimpanzee ( Pan troglodytes ) albumin immunological cross-reactions suggested they were about equally different from Ceboidea (New World Monkey) species (within experimental error). This meant that they had both accumulated approximately equal changes in albumin since their shared common ancestor. This pattern
1350-465: The most dominant organisms associated with the hydrothermal vents in the Pacific Ocean. Tubeworms anchor themselves to the substratum of the hydrocarbon seep by roots located at the basal portion of their bodies. Intact tubeworm roots have proven very difficult to obtain for study because they are extremely delicate, and often break off when a tubeworm is removed from hypothermal vent regions. How long
1395-415: The number of amino acid differences in hemoglobin between different lineages changes roughly linearly with time, as estimated from fossil evidence. They generalized this observation to assert that the rate of evolutionary change of any specified protein was approximately constant over time and over different lineages (known as the molecular clock hypothesis ). The genetic equidistance phenomenon
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1440-409: The oldest fossil of each clade. This method does not rely on the interpretation of negative evidence to infer maximum clade ages. Demographic changes in populations can be detected as fluctuations in historical coalescent effective population size from a sample of extant genetic variation in the population using coalescent theory. Ancient population expansions that are well documented and dated in
1485-548: The order Polychaeta by scientific consensus. The fossil record along with molecular clocks suggest the family has Mesozoic (250 – 66 Mya) or Cenozoic (66 Mya – recent) origins. However, some fossils of crystallized tubes are attributed to early Siboglinidae dating back to 500 Mya. The oldest definitive specimens referred to the family came from Early Jurassic ( Pliensbachian - Toarcian ) Figueroa Sulfide deposits from San Rafael Mountains , found to be similar to modern Ridgeia . This tubes, known as ‘Figueroa tubes’, along
1530-475: The population is then 1/N, since each copy of the gene is as good as any other. Every generation, each individual can have new mutations, so there are μ {\displaystyle \mu } N new neutral mutations in the population as a whole. That means that each generation, μ {\displaystyle \mu } new neutral mutations will become fixed. If most changes seen during molecular evolution are neutral, then fixations in
1575-618: The problem is saturation . When enough time has passed, many sites have undergone more than one change, but it is impossible to detect more than one. This means that the observed number of changes is no longer linear with time, but instead flattens out. Even at intermediate genetic distances, with phylogenetic data still sufficient to estimate topology, signal for the overall scale of the tree can be weak under complex likelihood models, leading to highly uncertain molecular clock estimates. At very short time scales, many differences between samples do not represent fixation of different sequences in
1620-432: The roots of the tube worms can grow is unknown, but roots have been recovered longer than 30 m. A single aggregation of tubeworms can contain thousands of individuals, and the roots produced by each tubeworm can become tangled with the roots of neighbouring tubeworms. These mats of roots are known as "ropes", and travel down the tubes of dead tubeworms, and run through holes in rocks. The diameter and wall thickness of
1665-562: The tree. Early methods of clock calibration only used a single fossil constraint (e.g. non-parametric rate smoothing), but newer methods (BEAST and r8s ) allow for the use of multiple fossils to calibrate molecular clocks. The oldest fossil of a clade is used to constrain the minimum possible age for the node representing the most recent common ancestor of the clade. However, due to incomplete fossil preservation and other factors, clades are typically older than their oldest fossils. In order to account for this, nodes are allowed to be older than
1710-486: The tubeworm roots do not appear to change with distance from the trunk portion of the tubeworm's body. Like the trunk portion of the body, the roots of the vestimentiferan tubeworms are composed of chitin crystallites, which support and protect the tubeworm from predation and environmental stresses. Tubeworms build the external chitin structure themselves by secreting chitin from specialized glands located in their body walls. Molecular clock The molecular clock
1755-413: The uncertainty about the age of the clade. These calibration densities can take the shape of standard probability densities (e.g. normal , lognormal , exponential , gamma ) that can be used to express the uncertainty associated with divergence time estimates. Determining the shape and parameters of the probability distribution is not trivial, but there are methods that use not only the oldest fossil but
1800-472: The vestimentiferans. Endosymbionts have a wide variety of metabolic genes, which may allow them to switch between autotrophic and heterotrophic methods of nutrient acquisition. When the host dies, the bacteria are released and return to the free-living population in the seawater. Discovery of the hydrothermal vents in the eastern Pacific Ocean was quickly followed by the discovery and description of new vestimentiferan tubeworm species. These tubeworms are one of
1845-474: The work of Motoo Kimura developed the neutral theory of molecular evolution , which predicted a molecular clock. Let there be N individuals, and to keep this calculation simple, let the individuals be haploid (i.e. have one copy of each gene). Let the rate of neutral mutations (i.e. mutations with no effect on fitness ) in a new individual be μ {\displaystyle \mu } . The probability that this new mutation will become fixed in
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1890-523: The ‘Troodos collared tubes’ ( Cyprus , Turonian ) were resolved among modern vestimentiferans. Molecular work aligning five genes has identified four distinct clades within Siboglinidae. The clades are Vestimentifera , Sclerolinum , Frenulata , and Osedax . Vestimentiferans live in vent and seep habitats. Separation of vestimentiferans into seep and deep-sea-dwelling clades is still debated due to some phylogenies based on sequencing data placing
1935-473: Was also found for all the primate comparisons they tested. When calibrated with the few well-documented fossil branch points (such as no Primate fossils of modern aspect found before the K-T boundary ), this led Sarich and Wilson to argue that the human-chimp divergence probably occurred only ~4–6 million years ago. The observation of a clock-like rate of molecular change was originally purely phenomenological . Later,
1980-497: Was dredged from the waters of Indonesia in 1900. These specimens were given to French zoologist Maurice Caullery , who studied them for nearly 50 years. Most siboglinids are less than 1 millimetre (0.04 in) in diameter, but 10–75 centimetres (3.9–29.5 in) in length. They inhabit tubular structures composed of chitin which are fixed to rocks or substrates. The tubes are often clustered together in large colonies. Their bodies are divided into four regions. The anterior end
2025-414: Was first noted in 1963 by Emanuel Margoliash , who wrote: "It appears that the number of residue differences between cytochrome c of any two species is mostly conditioned by the time elapsed since the lines of evolution leading to these two species originally diverged. If this is correct, the cytochrome c of all mammals should be equally different from the cytochrome c of all birds. Since fish diverges from
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