Hypoxia (environmental)

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Hypoxia_(environmental)

Hypoxia refers to low oxygen conditions. Normally, 20.9% of the gas in the atmosphere is oxygen. The partial pressure of oxygen in the atmosphere is 20.9% of the total barometric pressure. In water, oxygen levels are much lower, approximately 1%, and fluctuate locally depending on the presence of photosynthetic organisms and relative distance to the surface (if there is more oxygen in the air, it will diffuse across the partial pressure gradient).

Atmospheric hypoxia

Atmospheric hypoxia occurs naturally at high altitudes. Total atmospheric pressure decreases as altitude increases, causing a lower partial pressure of oxygen which is defined as hypobaric hypoxia. Oxygen remains at 20.9% of the total gas mixture, differing from hypoxic hypoxia, where the percentage of oxygen in the air (or blood) is decreased. This is common in the sealed burrows of some subterranean animals, such as blesmols. Atmospheric hypoxia is also the basis of altitude training which is a standard part of training for elite athletes. Several companies mimic hypoxia using normobaric artificial atmosphere.

Aquatic hypoxia

Oxygen depletion is a phenomenon that occurs in aquatic environments as dissolved oxygen (DO; molecular oxygen dissolved in the water) becomes reduced in concentration to a point where it becomes detrimental to aquatic organisms living in the system. Dissolved oxygen is typically expressed as a percentage of the oxygen that would dissolve in the water at the prevailing temperature and salinity (both of which affect the solubility of oxygen in water; see oxygen saturation and underwater). An aquatic system lacking dissolved oxygen (0% saturation) is termed anaerobic, reducing, or anoxic; a system with low concentration—in the range between 1 and 30% saturation—is called hypoxic or dysoxic. Most fish cannot live below 30% saturation. Hypoxia leads to impaired reproduction of remaining fish via endocrine disruption. A "healthy" aquatic environment should seldom experience less than 80%. The exaerobic zone is found at the boundary of anoxic and hypoxic zones. 

Hypoxia can occur throughout the water column and also at high altitudes as well as near sediments on the bottom. It usually extends throughout 20-50% of the water column, but depending on the water depth and location of pycnoclines (rapid changes in water density with depth). It can occur in 10-80% of the water column. For example, in a 10-meter water column, it can reach up to 2 meters below the surface. In a 20-meter water column, it can extend up to 8 meters below the surface.

Causes of hypoxia

Decline of oxygen saturation to anoxia, measured during the night in Kiel Fjord, Germany. Depth = 5 m

Oxygen depletion can result from a number of natural factors, but is most often a concern as a consequence of pollution and eutrophication in which plant nutrients enter a river, lake, or ocean, and phytoplankton blooms are encouraged. While phytoplankton, through photosynthesis, will raise DO saturation during daylight hours, the dense population of a bloom reduces DO saturation during the night by respiration. When phytoplankton cells die, they sink towards the bottom and are decomposed by bacteria, a process that further reduces DO in the water column. If oxygen depletion progresses to hypoxia, fish kills can occur and invertebrates like worms and clams on the bottom may be killed as well.

Still frame from an underwater video of the sea floor. The floor is covered with crabs, fish, and clams apparently dead or dying from oxygen depletion.

 

Hypoxia may also occur in the absence of pollutants. In estuaries, for example, because freshwater flowing from a river into the sea is less dense than salt water, stratification in the water column can result. Vertical mixing between the water bodies is therefore reduced, restricting the supply of oxygen from the surface waters to the more saline bottom waters. The oxygen concentration in the bottom layer may then become low enough for hypoxia to occur. Areas particularly prone to this include shallow waters of semi-enclosed water bodies such as the Waddenzee or the Gulf of Mexico, where land run-off is substantial. In these areas a so-called "dead zone" can be created. Low dissolved oxygen conditions are often seasonal, as is the case in Hood Canal and areas of Puget Sound, in Washington State. The World Resources Institute has identified 375 hypoxic coastal zones around the world, concentrated in coastal areas in Western Europe, the Eastern and Southern coasts of the US, and East Asia, particularly in Japan.

Jubilee photo from Mobile Bay

Hypoxia may also be the explanation for periodic phenomena such as the Mobile Bay jubilee, where aquatic life suddenly rushes to the shallows, perhaps trying to escape oxygen-depleted water. Recent widespread shellfish kills near the coasts of Oregon and Washington are also blamed on cyclic dead zone ecology.

Phytoplankton breakdown

Scientists have determined that high concentrations of minerals dumped into bodies of water causes significant growth of phytoplankton blooms. As these blooms are broken down by bacteria, such as Phanerochaete chrysosprium, oxygen is depleted by the enzymes of these organisms.

Breakdown of lignin

Tetrapyrrol ring, the active site of Ligninperoxidase enzyme

 

Phytoplankton are mostly made up of lignin and cellulose, which are broken down by enzymes present in organisms such as P. chrysosprium, known as white-rot. The breakdown of cellulose does not deplete oxygen concentration in water, but the breakdown of lignin does. This breakdown of lignin includes an oxidative mechanism, and requires the presence of dissolved oxygen to take place by enzymes like ligninperoxidase. Other fungi such as brown-rot, soft-rot, and blue stain fungi also are necessary in lignin transformation. As this oxidation takes place, CO₂ is formed in its place.

Active site of tetrapyrrol ring binding oxygen

 

Oxyferroheme is converted to Ferri-LiP with the addition of veratric alcohol, and gives off diatomic oxygen radical.

 

This is the breakdown of a confieryl alcohol by a hydrogen ion to make propanol and ortho-methoxyphenol.

 

Ligninperoxidase (LiP) serves as the most import enzyme because it is best at breaking down lignin in these organisms. LiP disrupts C-C bonds and C-O bonds within Lignin's three-dimensional structure, causing it to break down. LiP consists of ten alpha helices, two Ca²⁺ structural ions, as well as a heme group called a tetrapyrrol ring. Oxygen serves an important role in the catalytic cycle of LiP to form a double bond on the Fe²⁺ ion in the tetrapyrrol ring. Without the presence of diatomic oxygen in the water, this breakdown cannot take place because Ferrin-LiP will not be reduced into Oxyferroheme. Oxygen gas is used to reduce Ferrin-LiP into Oxyferroheme-LiP. Oxyferroheme and veratric alcohol combine to create oxygen radical and Ferri-LiP, which can now be used to degrade lignin. Oxygen radicals cannot be used in the environment, and are harmful in high presence in the environment.

Once Ferri-LiP is present in the ligninperoxidase, it can be used to break down lignin molecules by removing one phenylpropane group at a time through either the LRET mechanism or the mediator mechanism. The LRET mechanism (long range electron transfer mechanism) transfers an electron from the tetrapyrrol ring onto a molecule of phenylpropane in a lignin. This electron moves onto a C-C or C-O bond to break one phenylpropane molecule from the lignin, breaking it down by removing one phenylpropane at a time.

In the mediator mechanism, LiP enzyme is activated by the addition of hydrogen peroxide to make LiP radical, and a mediator such as veratric alcohol is added and activated creating veratric alcohol radical. Veratric alcohol radical transfers one electron to activate the phenylpropane on lignin, and the electron dismantles a C-C or C-O bond to release one phenylpropane from the lignin. As the size of a lignin molecule increases, the more difficult it is to break these C-C or C-O bonds. Three types of phenyl propane rings include coniferyl alcohol, sinapyl alcohol, and-coumaryl alcohol.

LiP has a very low MolDock score, meaning there is little energy required to form this enzyme and stabilize it to carry out reactions. LiP has a MolDock score of -156.03 kcal/mol. This is energetically favorable due to its negative free energy requirements, and therefore this reaction catalyzed by LiP is likely to take place spontaneously. Breakdown of propanol and phenols occur naturally in the environment because they are both water-soluble.

Environmental factors

The breakdown of phytoplankton in the environment depends on the presence of oxygen, and once oxygen is no longer in the bodies of water, ligninperoxidases cannot continue to break down the lignin. When oxygen is not present in the water, the breakdown of phytoplankton changes from 10.7 days to a total of 160 days for this to take place.

The rate of phytoplankton breakdown can be represented using this equation: 

${\displaystyle G(t)=G(0)e^{-kt}}$

In this equation, G(t) is the amount of particulate organic carbon (POC) overall at a given time, t. G(0) is the concentration of POC before breakdown takes place. k is a rate constant in year-1, and t is time in years. For most POC of phytoplankton, the k is around 12.8 years-1, or about 28 days for nearly 96% of carbon to be broken down in these systems. Whereas for anoxic systems, POC breakdown takes 125 days, over four times longer. It takes approximately 1 mg of Oxygen to break down 1 mg of POC in the environment, and therefore, hypoxia takes place quickly as oxygen is used up quickly to digest POC. About 9% of POC in phytoplankton can be broken down in a single day at 18 °C, therefore it takes about eleven days to completely break down a full phytoplankton.

After POC is broken down, this particulate matter can be turned into other dissolved organic carbon, such as carbon dioxide, bicarbonate ions, and carbonate. As much as 30% of phytoplankton can be broken down into dissolved organic carbon. When this particulate organic carbon interacts with 350 nm ultraviolet light, dissolved organic carbon is formed, removing even more oxygen from the environment in the forms of carbon dioxide, bicarbonate ions, and carbonate. Dissolved inorganic carbon is made at a rate of 2.3-6.5 mg/(m^3)day.

As phytoplankton breakdown, free phosphorus and nitrogen become available in the environment, which also fosters hypoxic conditions. As the breakdown of these phytoplankton takes place, the more phosphorus turns into phosphates, and nitrogens turn into nitrates. This depletes the oxygen even more so in the environment, further creating hypoxic zones in higher quantities. As more minerals such as phosphorus and nitrogen are displaced into these aquatic systems, the growth of phytoplankton greatly increases, and after their death, hypoxic zones are formed.

Solutions

To combat hypoxia, it is essential to reduce the amount of land-derived nutrients reaching rivers in runoff. This can be done by improving sewage treatment and by reducing the amount of fertilizers leaching into the rivers. Alternately, this can be done by restoring natural environments along a river; marshes are particularly effective in reducing the amount of phosphorus and nitrogen (nutrients) in water. Other natural habitat-based solutions include restoration of shellfish populations, such as oysters. Oyster reefs remove nitrogen from the water column and filter out suspended solids, subsequently reducing the likelihood or extent of harmful algal blooms or anoxic conditions. Foundational work toward the idea of improving marine water quality through shellfish cultivation was conducted by Odd Lindahl et al., using mussels in Sweden. More involved than single-species shellfish cultivation, integrated multi-trophic aquaculture mimics natural marine ecosystems, relying on polyculture to improve marine water quality. 

Graphs of oxygen and salinity levels at Kiel Fjord in September 1998.

Technological solutions are also possible, such as that used in the redeveloped Salford Docks area of the Manchester Ship Canal in England, where years of runoff from sewers and roads had accumulated in the slow running waters. In 2001 a compressed air injection system was introduced, which raised the oxygen levels in the water by up to 300%. The resulting improvement in water quality led to an increase in the number of invertebrate species, such as freshwater shrimp, to more than 30. Spawning and growth rates of fish species such as roach and perch also increased to such an extent that they are now amongst the highest in England.

In a very short time the oxygen saturation can drop to zero when offshore blowing winds drive surface water out and anoxic depth water rises up. At the same time a decline in temperature and a rise in salinity is observed (from the longterm ecological observatory in the seas at Kiel Fjord, Germany). New approaches of long-term monitoring of oxygen regime in the ocean observe online the behavior of fish and zooplankton, which changes drastically under reduced oxygen saturations (ecoSCOPE) and already at very low levels of water pollution.

Exaptation (updated)

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Exaptation

Exaptation and the related term co-option describe a shift in the function of a trait during evolution. For example, a trait can evolve because it served one particular function, but subsequently it may come to serve another. Exaptations are common in both anatomy and behaviour. Bird feathers are a classic example: initially they may have evolved for temperature regulation, but later were adapted for flight. Interest in exaptation relates to both the process and products of evolution: the process that creates complex traits and the products (functions, anatomical structures, biochemicals, etc.) that may be imperfectly developed. Exaptation was proposed by Stephen Jay Gould and Elisabeth Vrba as a replacement for what they considered to be a teleologically loaded term 'pre-adaptation'.

History and definitions

Charles Darwin

The idea that the function of a trait might shift during its evolutionary history originated with Charles Darwin (Darwin 1859). For many years the phenomenon was labeled "preadaptation", but since this term suggests teleology in biology, appearing to conflict with natural selection, it has been replaced by the term exaptation.

The idea had been explored by several scholars when in 1982 Stephen Jay Gould and Elisabeth Vrba introduced the term "exaptation". However, this definition had two categories with different implications for the role of adaptation.

(1) A character, previously shaped by natural selection for a particular function (an adaptation), is coopted for a new use—cooptation. (2) A character whose origin cannot be ascribed to the direct action of natural selection (a nonaptation), is coopted for a current use—cooptation. (Gould and Vrba 1982, Table 1)

The definitions are silent as to whether exaptations had been shaped by natural selection after cooption, although Gould and Vrba cite examples (e.g., feathers) of traits shaped after cooption. Note that the selection pressure upon a trait is likely to change if it is (especially, primarily or solely) used for a new purpose, potentially initiating a different evolutionary trajectory.

To avoid these ambiguities, Buss et al. (1998) suggested the term "co-opted adaptation", which is limited to traits that evolved after cooption. However, the commonly used terms of "exaptation" and "cooption" are ambiguous in this regard. 

Preadaptation

In some circumstances, the "pre-" in preadaptation can be interpreted as applying, for non-teleological reasons, prior to the adaptation itself, creating a meaning for the term that is distinct from exaptation. For example, future environments (say, hotter or drier ones), may resemble those already encountered by a population at one of its current spatial or temporal margins. This is not actual foresight, but rather the luck of having adapted to a climate which later becomes more prominent. Cryptic genetic variation may have the most strongly deleterious mutations purged from it, leaving an increased chance of useful adaptations, but this represents selection acting on current genomes with consequences for the future, rather than foresight.

Function may not always come before form: developed structures could change or alter the primary functions they were intended for due to some structural or historical cause.

Examples

Bird feathers of various colors

Exaptations include the co-option of feathers, which initially evolved for heat regulation, for display, and later for use in bird flight. Another example is the lungs of many basal fish, which evolved into the lungs of terrestrial vertebrates but also underwent exaptation to become the gas bladder, a buoyancy control organ, in derived fish. A third is the repurposing of two of the three bones in the reptilian jaw to become the malleus and incus of the mammalian ear, leaving the mammalian jaw with just one hinge.

A behavioural example pertains to subdominant wolves licking the mouths of lead wolves as a sign of submissiveness. (Similarly, dogs, which are wolves who through a long process were domesticated, lick the faces of their human owners.) This trait can be explained as an exaptation of wolf pups licking the faces of adults to encourage them to regurgitate food.

Arthropods provide the earliest identifiable fossils of land animals, from about 419 million years ago in the Late Silurian, and terrestrial tracks from about 450 million years ago appear to have been made by arthropods. Arthropods were well pre-adapted to colonize land, because their existing jointed exoskeletons provided support against gravity and mechanical components that could interact to provide levers, columns and other means of locomotion that did not depend on submergence in water.

Metabolism can be considered an important part of exaptation. As one of the oldest biological systems and being central to life on the Earth, studies have shown that metabolism may be able to use exaptation in order to be fit, given some new set of conditions or environment. Studies have shown that up to 44 carbon sources are viable for metabolism to successfully take place and that any one adaptation in these specific metabolic systems is due to multiple exaptations. Taking this perspective, exaptations are important in the origination of adaptations in general. A recent example comes from Richard Lenski's E. coli long-term evolution experiment, in which aerobic growth on citrate arose in one of twelve populations after 31,000 generations of evolution. Genomic analysis by Blount and colleagues showed that this novel trait was due to a gene duplication that caused oxic expression of a citrate transporter gene that is normally only expressed under anoxic conditions, thus exapting it for aerobic use. Metabolic systems have the potential to innovate without adaptive origins. 

Gould and Brosius took the concept of exaptation to the genetic level. It is possible to look at a retroposon, originally thought to be simply junk DNA, and deduce that it may have gotten a new function to be termed as an exaptation. Given an emergency situation in the past, a species may have used junk DNA for a useful purpose in order to evolve and be able to survive. This may have occurred with mammalian ancestors when confronted with a large mass extinction about 250 million years ago and substantial increase in the level of oxygen in Earth's atmosphere. More than 100 loci have been found to be conserved only among mammalian genomes and are thought to have essential roles in the generation of features such as the placenta, diaphragm, mammary glands, neocortex, and auditory ossicles. It is believed that as a result of exaptation, or making previously "useless" DNA into DNA that could be used in order to increase survival chance, mammals were able to generate new brain structures as well as behavior to better survive the mass extinction and adapt to new environments. Similarly, viruses and their components have been repeatedly exapted for host functions. The functions of exapted viruses typically involve either defense from other viruses or cellular competitors or transfer of nucleic acids between cells, or storage functions. Koonin and Krupovic suggested that virus exaptation can reach different depths, from recruitment of a fully functional virus to exploitation of defective, partially degraded viruses, to utilization of individual virus proteins.

Adaptation and exaptation cycle

It was speculated by Gould and Vrba in one of the first papers written about exaptation, that when an exaptation arises, it may not be perfectly suited for its new role and may therefore develop new adaptations to promote its use in a better manner. In other words, the beginning of developing a particular trait starts out with a primary adaptation toward a fit or specific role, followed by a primary exaptation (a new role is derived using the existing feature but may not be perfect for it), which in turn leads to the development of a secondary adaptation (the feature is improved by natural selection for better performance), promoting further development of an exaptation, and so forth.

Once again, feathers are an important example, in that they may have first been adapted for thermoregulation and with time became useful for catching insects, and therefore served as a new feature for another benefit. For instance, large contour feathers with specific arrangements arose as an adaptation for catching insects more successfully, which eventually led to flight, since the larger feathers served better for that purpose.

Implications

Evolution of complex traits

One of the challenges to Darwin's theory of evolution was explaining how complex structures could evolve gradually, given that their incipient forms may have been inadequate to serve any function. As George Jackson Mivart (a critic of Darwin) pointed out, 5 percent of a bird wing would not be functional. The incipient form of complex traits would not have survived long enough to evolve to a useful form.

As Darwin elaborated in the last edition of The Origin of Species, many complex traits evolved from earlier traits that had served different functions. By trapping air, primitive wings would have enabled birds to efficiently regulate their temperature, in part, by lifting up their feathers when too warm. Individual animals with more of this functionality would more successfully survive and reproduce, resulting in the proliferation and intensification of the trait.

Eventually, feathers became sufficiently large to enable some individuals to glide. These individuals would in turn more successfully survive and reproduce, resulting in the spread of this trait because it served a second and still more beneficial function: that of locomotion. Hence, the evolution of bird wings can be explained by a shifting in function from the regulation of temperature to flight.

Jury-rigged design

Darwin explained how the traits of living organisms are well-designed for their environment, but he also recognized that many traits are imperfectly designed. They appear to have been made from available material, that is, jury-rigged. Understanding exaptations may suggest hypotheses regarding subtleties in the adaptation. For instance, that feathers evolved initially for thermal regulation may help to explain some of their features unrelated to flight (Buss et al., 1998). However, this is readily explained by the fact that they serve a dual purpose.

Some of the chemical pathways for physical pain and pain from social exclusion overlap.^[26] The physical pain system may have been co-opted to motivate social animals to respond to threats to their inclusion in the group.

Evolution of technology

Exaptation has received increasing attention in innovation and management studies inspired by evolutionary dynamics, where it has been proposed as a mechanism that drives the serendipitous expansion of technologies and products in new domains.

Heteroplasmy

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Heteroplasmy

Heteroplasmy is the presence of more than one type of organellar genome (mitochondrial DNA or plastid DNA) within a cell or individual. It is an important factor in considering the severity of mitochondrial diseases. Because most eukaryotic cells contain many hundreds of mitochondria with hundreds of copies of mitochondrial DNA, it is common for mutations to affect only some mitochondria, leaving most unaffected.

Although detrimental scenarios are well-studied, heteroplasmy can also be beneficial. For example, centenarians show a higher than average degree of heteroplasmy.

Microheteroplasmy is present in most individuals. This refers to hundreds of independent mutations in one organism, with each mutation found in about 1–2% of all mitochondrial genomes.

 

 

Types of heteroplasmy

In order for heteroplasmy to occur, organelles must contain a genome and, in turn, a genotype. In animals, mitochondria are the only organelles that contain their own genomes, so these organisms will only have mitochondrial heteroplasmy. In contrast, photosynthetic plants contain mitochondria and chloroplasts, each of which contains plastid genomes. Therefore, plant heteroplasmy occurs in two dimensions.

Organelle inheritance patterns

In 1909, while studying chloroplast genomes, Erwin Baur made the first observations about organelle inheritance patterns. Organelle genome inheritance differs from nuclear genome, and this is illustrated by four violations of Mendel's laws.

1. During asexual reproduction, nuclear genes never segregate during cellular divisions. This is to ensure that each daughter cell gets a copy of every gene. However, organelle genes in heteroplasmic cells can segregate because they each have several copies of their genome. This may result in daughter cells with differential proportions of organelle genotypes.
2. Mendel states that nuclear alleles always segregate during meiosis. However, organelle alleles may or may not do this.
3. Nuclear genes are inherited from a combination of alleles from both parents, making inheritance biparental. Conversely, organelle inheritance is uniparental, meaning the genes are all inherited from one parent.
4. It is also unlikely for organelle alleles to segregate independently, like nuclear alleles do, because plastid genes are usually on a single chromosome and recombination is limited by uniparental inheritance.

There is a wide variety of mitochondrial DNA genotypes in the maternal pool, which is represented by the bottle. The two genotypes in this maternal pool are represented by blue and yellow. When generated, each oocyte receives a small subsampling of mitochondrial DNA molecules in differing proportions. This is represented by the conveyor belt with oocytes, each one unique, as they are produced.

 

Vegetative segregation

Vegetative segregation, the random partitioning of cytoplasm, is a distinguishable characteristic of organelle heredity. During cell division, the organelles are divided equally, providing each daughter cell with a random selection of plasmid genotypes.

Uniparental inheritance

Uniparental inheritance refers to the fact that, in most organisms, many offspring inherit organelle genes from only one parent. However, this is not a general law. Many organisms that have the ability to differentiate maternal and paternal sexes will produce offspring with a mixture of maternal, paternal, and biparental mitochondrial DNA.

Mitochondrial bottleneck

Entities undergoing uniparental inheritance and with little to no recombination may be expected to be subject to Muller's ratchet, the inexorable accumulation of deleterious mutations until functionality is lost. Animal populations of mitochondria avoid this buildup through a developmental process known as the mtDNA bottleneck. The bottleneck exploits stochastic processes in the cell to increase in the cell-to-cell variability in mutant load as an organism develops: a single egg cell with some proportion of mutant mtDNA thus produces an embryo where different cells have different mutant loads. Cell-level selection may then act to remove those cells with more mutant mtDNA, leading to a stabilisation or reduction in mutant load between generations. The mechanism underlying the bottleneck is debated, with a recent mathematical and experimental metastudy providing evidence for a combination of random partitioning of mtDNAs at cell divisions and random turnover of mtDNA molecules within the cell.

The mitochondrial bottleneck concept refers to the classic evolutionary term, which is used to explain an event that reduces and specifies a population. It was developed to describe why mitochondrial DNA in an embryo might be drastically different from that of its mother. When a large population of DNA is subsampled, each sample population will receive a slightly different proportion of mitochondrial genotypes. Consequently, when paired with a high degree of replication, a rare or mutated allele can begin to proportionally dominate. In theory, this makes possible a single-generation shift of overall mitochondrial genotype.

Selection

Although it is not well characterized, selection can occur for organelle genomes in heteroplasmic cells. Intracellular ("within cells") selection occurs within individual cells. It refers to the selective segregation of certain genotypes in mitochondrial DNA that allows the favoured genotype to thrive. Intercellular ("between cells") selection occurs on a larger scale, and refers to the preferential growth of cells that have greater numbers of a certain mitochondrial genotype. Selective differences can occur between naturally occurring, non-pathological mtDNA types when mixed in cells, and may depend on tissue type, age, and genetic distance. Selective differences between naturally occurring mtDNA types may pose challenges for gene therapies.

In mitochondrial DNA, there is evidence for potent germline purifying selection, as well as purifying selection during embryogenesis. Additionally, there is a dose-dependent decrease in reproduction ability for females that have mutations in mitochondrial DNA. This demonstrates another selection mechanism to prevent the evolutionary preservation of harmful mutations.

Reduced recombination

It is very rare for organelle genes from different lineages to recombine. These genomes are usually inherited uniparentally, which does not provide a recombination opportunity. If they are inherited biparentally, it is unlikely that the organelles from the parents will fuse, meaning they will not share genomes. 

However, it is possible for organelle genes from the same lineage to recombine. Intramolecular and intermolecular recombination can cause inversions and repeats in chloroplast DNA, and can produce subgenomic circles in mitochondrial DNA.

Mitochondrial mutations in disease

Mutations in mitochondrial DNA are usually single nucleotide substitutions, single base insertions, or deletions.

Because each cell contains thousands of mitochondria, nearly all organisms house low levels of mitochondrial variants, conferring some degree of heteroplasmy. Although a single mutational event might be rare in its generation, repeated mitotic segregation and clonal expansion can enable it to dominate the mitochondrial DNA pool over time. When this occurs, it is known as reaching threshold, and it usually results in physiological consequences.

Severity and time to presentation

Symptoms of severe heteroplasmic mitochondrial disorders do not usually appear until adulthood. Many cell divisions and a great deal of time are required for a cell to accumulate enough mutant mitochondria to cause symptoms. An example of this phenomenon is Leber optic atrophy. Generally, individuals with this condition do not experience vision difficulties until they have reached adulthood. Another example is MERRF syndrome (or Myoclonic Epilepsy with Ragged Red Fibers). In MELAS, heteroplasmy explains the variation in severity of the disease among siblings. 

Screening

Preimplantation genetic screening (PGS) can be used to quantitate the risk of a child of being affected by a mitochondrial disease. In most cases, a muscle mutation level of approximately 18% or less confers a 95% risk reduction.

Sequence illustrating heteroplasmy genotype of 16169 C/T in Nicholas II of Russia.

 

Notable cases

One notable example of an otherwise healthy individual whose heteroplasmy was discovered incidentally is Nicholas II of Russia, whose heteroplasmy (and that of his brother) served to convince Russian authorities of the authenticity of his remains.

Vestigiality

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Vestigiality

 

In humans the vermiform appendix is a vestigial structure; it has lost much of its ancestral function.

Vestigiality is the retention during the process of sexual reproduction of genetically determined structures or attributes that have lost some or all of their ancestral function in a given species. Assessment of the vestigiality must generally rely on comparison with homologous features in related species. The emergence of vestigiality occurs by normal evolutionary processes, typically by loss of function of a feature that is no longer subject to positive selection pressures when it loses its value in a changing environment. The feature may be selected against more urgently when its function becomes definitively harmful, but if the lack of the feature provides no advantage, and its presence provides no disadvantage, the feature may not be phased out by natural selection and persist across species. 

Examples of vestigial structures are the loss of functional wings in island-dwelling birds; the human appendix and vomeronasal organ; and the hindlimbs of the snake and whale.

Overview

The Darwin-tubercle (left) is a vestigial form of the ear tip (right) in the mammalian ancestors of humans—here shown in a crab-eating macaque.

Vestigial features may take various forms; for example, they may be patterns of behavior, anatomical structures, or biochemical processes. Like most other physical features, however functional, vestigial features in a given species may successively appear, develop, and persist or disappear at various stages within the life cycle of the organism, ranging from early embryonic development to late adulthood. 

Vestigial hindlegs (spurs) in a boa constrictor

 

Vestigiality, biologically speaking, refers to organisms retaining organs that have seemingly lost their original function. The issue is controversial and not without dispute; nonetheless, vestigial organs are common evolutionary knowledge. In addition, the term vestigiality is useful in referring to many genetically determined features, either morphological, behavioral, or physiological; in any such context, however, it need not follow that a vestigial feature must be completely useless. A classic example at the level of gross anatomy is the human vermiform appendix—though vestigial in the sense of retaining no significant digestive function, the appendix still has immunological roles and is useful in maintaining gut flora.

Similar concepts apply at the molecular level—some nucleic acid sequences in eukaryotic genomes have no known biological function; some of them may be "junk DNA", but it is a difficult matter to demonstrate that a particular sequence in a particular region of a given genome is truly nonfunctional. The simple fact that it is noncoding DNA does not establish that it is functionless. Furthermore, even if an extant DNA sequence is functionless, it does not follow that it has descended from an ancestral sequence of functional DNA. Logically such DNA would not be vestigial in the sense of being the vestige of a functional structure. In contrast pseudogenes have lost their protein-coding ability or are otherwise no longer expressed in the cell. Whether they have any extant function or not, they have lost their former function and in that sense, they do fit the definition of vestigiality.

Vestigial structures are often called vestigial organs, although many of them are not actually organs. Such vestigial structures typically are degenerate, atrophied, or rudimentary,^[3] and tend to be much more variable than homologous non-vestigial parts. Although structures commonly regarded "vestigial" may have lost some or all of the functional roles that they had played in ancestral organisms, such structures may retain lesser functions or may have become adapted to new roles in extant populations.

It is important to avoid confusion of the concept of vestigiality with that of exaptation. Both may occur together in the same example, depending on the relevant point of view. In exaptation, a structure originally used for one purpose is modified for a new one. For example, the wings of penguins would be exaptational in the sense of serving a substantial new purpose (underwater locomotion), but might still be regarded as vestigial in the sense of having lost the function of flight. In contrast Darwin argued that the wings of emus would be definitely vestigial, as they appear to have no major extant function; however, function is a matter of degree, so judgments on what is a "major" function are arbitrary; the emu does seem to use its wings as organs of balance in running. Similarly, the ostrich uses its wings in displays and temperature control, though they are undoubtedly vestigial as structures for flight.

Vestigial characters range from detrimental through neutral to favorable in terms of selection. Some may be of some limited utility to an organism but still degenerate over time if they do not confer a significant enough advantage in terms of fitness to avoid the effects of genetic drift or competing selective pressures. Vestigiality in its various forms presents many examples of evidence for biological evolution.

History

The blind mole rat (Spalax typhlus) has tiny eyes completely covered by a layer of skin.

Vestigial structures have been noticed since ancient times, and the reason for their existence was long speculated upon before Darwinian evolution provided a widely accepted explanation. In the 4th century BC, Aristotle was one of the earliest writers to comment, in his History of Animals, on the vestigial eyes of moles, calling them "stunted in development" due to the fact that moles can scarcely see. However, only in recent centuries have anatomical vestiges become a subject of serious study. In 1798, Étienne Geoffroy Saint-Hilaire noted on vestigial structures:

“

Whereas useless in this circumstance, these rudiments... have not been eliminated, because Nature never works by rapid jumps, and She always leaves vestiges of an organ, even though it is completely superfluous, if that organ plays an important role in the other species of the same family.

”

His colleague, Jean-Baptiste Lamarck, named a number of vestigial structures in his 1809 book Philosophie Zoologique. Lamarck noted "Olivier's Spalax, which lives underground like the mole, and is apparently exposed to daylight even less than the mole, has altogether lost the use of sight: so that it shows nothing more than vestiges of this organ."

Charles Darwin was familiar with the concept of vestigial structures, though the term for them did not yet exist. He listed a number of them in The Descent of Man, including the muscles of the ear, wisdom teeth, the appendix, the tail bone, body hair, and the semilunar fold in the corner of the eye. Darwin also noted, in On the Origin of Species, that a vestigial structure could be useless for its primary function, but still retain secondary anatomical roles: "An organ serving for two purposes, may become rudimentary or utterly aborted for one, even the more important purpose, and remain perfectly efficient for the other.... [A]n organ may become rudimentary for its proper purpose, and be used for a distinct object."

In the first edition of On the Origin of Species, Darwin briefly mentioned inheritance of acquired characters under the heading "Effects of Use and Disuse", expressing little doubt that use "strengthens and enlarges certain parts, and disuse diminishes them; and that such modifications are inherited". In later editions he expanded his thoughts on this, and in the final chapter of the 6th edition concluded that species have been modified "chiefly through the natural selection of numerous successive, slight, favorable variations; aided in an important manner by the inherited effects of the use and disuse of parts".

In 1893, Robert Wiedersheim published The Structure of Man, a book on human anatomy and its relevance to man's evolutionary history. The Structure of Man contained a list of 86 human organs that Wiedersheim described as, "Organs having become wholly or in part functionless, some appearing in the Embryo alone, others present during Life constantly or inconstantly. For the greater part Organs which may be rightly termed Vestigial." Since his time, the function of some of these structures have been discovered, while other anatomical vestiges have been unearthed, making the list primarily of interest as a record of the knowledge of human anatomy at the time. Later versions of Wiedersheim's list were expanded to as many as 180 human "vestigial organs". This is why the zoologist Horatio Newman said in a written statement read into evidence in the Scopes Trial that "There are, according to Wiedersheim, no less than 180 vestigial structures in the human body, sufficient to make of a man a veritable walking museum of antiquities."

Common descent and evolutionary theory

Vestigial structures are often homologous to structures that are functioning normally in other species. Therefore, vestigial structures can be considered the evidence for evolution, the process by which beneficial heritable traits arise in populations over an extended period of time. The existence of vestigial traits can be attributed to changes in the environment and behavior patterns of the organism in question. Through an examination of these various traits, it is clear that evolution had a hard role in the development of organisms. Every anatomical structure or behavior response has origins in which they were, at one time, useful. As time progressed, the ancient common ancestor organisms did as well. Evolving with time, natural selection played a huge role. More advantageous structures were selected, while others were not. With this expansion, some traits were left to the wayside. As the function of the trait is no longer beneficial for survival, the likelihood that future offspring will inherit the "normal" form of it decreases. In some cases, the structure becomes detrimental to the organism (for example the eyes of a mole can become infected). In many cases the structure is of no direct harm, yet all structures require extra energy in terms of development, maintenance, and weight, and are also a risk in terms of disease (e.g., infection, cancer), providing some selective pressure for the removal of parts that do not contribute to an organism's fitness. A structure that is not harmful will take longer to be 'phased out' than one that is. However, some vestigial structures may persist due to limitations in development, such that complete loss of the structure could not occur without major alterations of the organism's developmental pattern, and such alterations would likely produce numerous negative side-effects. The toes of many animals such as horses, which stand on a single toe, are still evident in a vestigial form and may become evident, although rarely, from time to time in individuals. 

The vestigial versions of the structure can be compared to the original version of the structure in other species in order to determine the homology of a vestigial structure. Homologous structures indicate common ancestry with those organisms that have a functional version of the structure. Douglas Futuyma has stated that vestigial structures make no sense without evolution, just as spelling and usage of many modern English words can only be explained by their Latin or Old Norse antecedents.

Vestigial traits can still be considered adaptations. This is because an adaptation is often defined as a trait that has been favored by natural selection. Adaptations, therefore, need not be adaptive, as long as they were at some point.

Examples

Non-human animals

Letter c in the picture indicates the undeveloped hind legs of a baleen whale.

 

Vestigial characters are present throughout the animal kingdom, and an almost endless list could be given. Darwin said that "it would be impossible to name one of the higher animals in which some part or other is not in a rudimentary condition."

The wings of ostriches, emus, and other flightless birds are vestigial; they are remnants of their flying ancestors' wings. The eyes of certain cavefish and salamanders are vestigial, as they no longer allow the organism to see, and are remnants of their ancestors' functional eyes. Animals that reproduce without sex (via asexual reproduction) generally lose their sexual traits, such as the ability to locate/recognize the opposite sex and copulation behavior.

Boas and pythons have vestigial pelvis remnants, which are externally visible as two small pelvic spurs on each side of the cloaca. These spurs are sometimes used in copulation, but are not essential, as no colubrid snake (the vast majority of species) possesses these remnants. Furthermore, in most snakes, the left lung is greatly reduced or absent. Amphisbaenians, which independently evolved limblessness, also retain vestiges of the pelvis as well as the pectoral girdle, and have lost their right lung.

Vestigial attachement clamps in various genera of protomicrocotylids. Accessory sclerites (black) are present in normal clamps but absent in simplified clamps. Lethacotyle (right) has no clamp at all.

 

A case of vestigial organs was described in polyopisthocotylean Monogeneans (parasitic flatworms). These parasites usually have a posterior attachment organ with several clamps, which are sclerotised organs attaching the worm to the gill of the host fish. These clamps are extremely important for the survival of the parasite. In the family Protomicrocotylidae, species have either normal clamps, simplified clamps, or no clamps at all (in the genus Lethacotyle). After a comparative study of the relative surface of clamps in more than 100 Monogeneans, this has been interpreted as an evolutionary sequence leading to the loss of clamps. Coincidentally, other attachment structures (lateral flaps, transverse striations) have evolved in protomicrocotylids. Therefore, clamps in protomicrocotylids were considered vestigial organs.

In the foregoing examples the vestigiality is generally the (sometimes incidental) result of adaptive evolution. However, there are many examples of vestigiality as the product of drastic mutation, and such vestigiality is usually harmful or counter-adaptive. One of the earliest documented examples was that of vestigial wings in Drosophila. Many examples in many other contexts have emerged since.

Humans

The muscles connected to the ears of a human do not develop enough to have the same mobility allowed to many animals.

Human vestigiality is related to human evolution, and includes a variety of characters occurring in the human species. Many examples of these are vestigial in other primates and related animals, whereas other examples are still highly developed. The human caecum is vestigial, as often is the case in omnivores, being reduced to a single chamber receiving the content of the ileum into the colon. The ancestral caecum would have been a large, blind diverticulum in which resistant plant material such as cellulose would have been fermented in preparation for absorption in the colon. Analogous organs in other animals similar to humans continue to perform similar functions. An alternative explanation would be the possibility that natural selection selects for larger appendices because smaller and thinner appendices would be more susceptible to inflammation and disease. The coccyx, or tailbone, though a vestige of the tail of some primate ancestors, is functional as an anchor for certain pelvic muscles including: the levator ani muscle and the largest gluteal muscle, the gluteus maximus.

Other structures that are vestigial include the plica semilunaris on the inside corner of the eye (a remnant of the nictitating membrane); and, as pictured, muscles in the ear and other parts of the body. Other organic structures (such as the occipitofrontalis muscle) have lost their original functions (keep the head from falling) but are still useful for other purposes (facial expression).

Humans also bear some vestigial behaviors and reflexes. The formation of goose bumps in humans under stress is a vestigial reflex; its function in human ancestors was to raise the body's hair, making the ancestor appear larger and scaring off predators. The arrector pili muscle, which is a band of smooth muscle that connects the hair follicle to connective tissue, contracts and creates the goosebumps on skin.

There are also vestigial molecular structures in humans, which are no longer in use but may indicate common ancestry with other species. One example of this is a gene that is functional in most other mammals and which produces L-gulonolactone oxidase, an enzyme that can make vitamin C. A documented mutation deactivated the gene in an ancestor of the modern infraorder of monkeys, and apes, and it now remains in their genomes, including the human genome, as a vestigial sequence called a pseudogene.

The shift in human diet towards soft and processed food over time caused a reduction in the number of powerful grinding teeth, especially the third molars or wisdom teeth, which were highly prone to impaction.

Plants and fungi

Plants also have vestigial parts, including functionless stipules and carpels, leaf reduction of Equisetum, paraphyses of Fungi. Well known examples are the reductions in floral display, leading to smaller and/or paler flowers, in plants that reproduce without outcrossing, for example via selfing or obligate clonal reproduction.

Atavism

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Atavism

 

Early embryos of various species display some ancestral features, like the tail on this human embryo. These features normally disappear in later development, but it may not happen if the animal has an atavism.

 

In biology, an atavism is a modification of a biological structure whereby an ancestral trait reappears after having been lost through evolutionary change in previous generations. Atavisms can occur in several ways; one of which is when genes for previously existing phenotypic features are preserved in DNA, and these become expressed through a mutation that either knocks out the overriding genes for the new traits or makes the old traits override the new one. A number of traits can vary as a result of shortening of the fetal development of a trait (neoteny) or by prolongation of the same. In such a case, a shift in the time a trait is allowed to develop before it is fixed can bring forth an ancestral phenotype. Atavisms are often seen as evidence of evolution.

In social sciences, atavism is the tendency of reversion. For example, people in the modern era reverting to the ways of thinking and acting of a former time. The word atavism is derived from the Latin atavus—a great-great-great-grandfather or, more generally, an ancestor. 

Biology

Evolutionarily traits that have disappeared phenotypically do not necessarily disappear from an organism's DNA. The gene sequence often remains, but is inactive. Such an unused gene may remain in the genome for many generations. As long as the gene remains intact, a fault in the genetic control suppressing the gene can lead to it being expressed again. Sometimes, the expression of dormant genes can be induced by artificial stimulation.

Atavisms have been observed in humans, such as with infants born with vestigial tails (called a "coccygeal process", "coccygeal projection", or "caudal appendage"). Atavism can also be seen in humans who possess large teeth, like those of other primates. In addition, a case of "snake heart", the presence of "coronary circulation and myocardial architecture [which resemble] those of the reptilian heart", has also been reported in medical literature. Atavism has also recently been induced in modern avian dinosaur (bird) foetuses to express dormant ancestral non-avian dinosaur features, including teeth.

Other examples of observed atavisms include:

• Hind limbs in cetaceans.
• Extra toes of the modern horse.
• Reappearance of limbs in limbless vertebrates.
• Re-evolution of sexuality from parthenogenesis in orbitid mites.
• Teeth in chickens.
• Dewclaws in dogs.
• Reappearance of prothoracic wings in insects.
• Reappearance of wings on wingless stick insects and earwigs.
• Atavistic muscles in several birds and mammals such as the beagle and the jerboa.
• Extra toes in guinea pigs.
• Reemergence of sexual reproduction in the flowering plant Hieracium pilosella and the Crotoniidae family of mites.
• Webbed feet in adult axolotls.
• Human tails (not pseudo-tails) and supernumerary nipples in humans (and other primates).
• Color blindness in humans.

Culture

Atavism is a term in Joseph Schumpeter's explanation of World War I in twentieth-century liberal Europe. He defends the liberal international relations theory that an international society built on commerce will avoid war because of war's destructiveness and comparative cost. His reason for World War I is termed "atavism", in which he asserts that senescent governments in Europe (those of the German Empire, Russian Empire, Ottoman Empire, and Austro-Hungarian Empire) pulled the liberal Europe into war, and that the liberal regimes of the other continental powers did not cause it. He used this idea to say that liberalism and commerce would continue to have a soothing effect in international relations, and that war would not arise between nations which are connected by commercial ties.

University of London professor Guy Standing has identified three distinct sub-groups of the precariat, one of which he refers to as "atavists", who long for what they see as a lost past.

Social Darwinism

During the interval between the acceptance of evolution in the mid-1800s and the rise of the modern understanding of genetics in the early 1900s, atavism was used to account for the reappearance in an individual of a trait after several generations of absence—often called a "throw-back". The idea that atavisms could be made to accumulate by selective breeding, or breeding back, led to breeds such as the Heck cattle. This had been bred from ancient landraces with selected primitive traits, in an attempt of "reviving" the aurochs, an extinct species of wild cattle. The same notions of atavisms were used by social Darwinists, who claimed that inferior races displayed atavistic traits, and represented more primitive traits than other races. Both atavisms and Ernst Haeckel's recapitulation theory are related evolutionary progress, as development towards greater complexity and superior ability.

In addition, the concept of atavism as part of an individualistic explanation of the causes of criminal deviance was popularised by the Italian criminologist Cesare Lombroso in the 1870s. He attempted to identify physical characteristics common to criminals and labeled those he found as atavistic, 'throw-back' traits that determined 'primitive' criminal behavior. His statistical evidence and the closely related idea of eugenics have long since been abandoned by the scientific community, but the concept that physical traits may affect the likelihood of criminal or unethical behavior in a person still has some scientific support.