Divergent evolution or divergent selection is the accumulation of differences between closely related populations within a species, leading to speciation. Divergent evolution is typically exhibited when two populations become separated by a geographic barrier (such as in allopatric or peripatric speciation) and experience different selective pressures that drive adaptations to their new environment. After many generations and continual evolution, the populations become unable to interbreed with one another. The American naturalist J. T. Gulick (1832-1923) was the first to use the term "divergent evolution", with its use becoming widespread in modern evolutionary literature. Classic examples of divergence in nature are the adaptive radiation of the finches of the Galapagos or the coloration differences in populations of a species that live in different habitats such as with pocket mice and fence lizards.
The term can also be applied in molecular evolution, such as to proteins that derive from homologous genes. Both orthologous genes (resulting from a speciation event) and paralogous genes (resulting from gene duplication) can illustrate divergent evolution. Through gene duplication, it is possible for divergent evolution to occur between two genes within a species. Similarities between species that have diverged are due to their common origin, so such similarities are homologies. In contrast, convergent evolution arises when an adaptation has arisen independently, creating analogous structures such as the wings of birds and of insects.
The term divergent evolution is believed to have been first used by J. T. Gulick. Divergent evolution is commonly defined as what occurs when two groups of the same species evolve different traits within those groups in order to accommodate for differing environmental and social pressures. Various examples of such pressures can include predation, food supplies, and competition for mates. The tympanal ears of certain nocturnal insects are believed to be a result of needing the ultrasonic hearing that tympanal ears provide in order to hear predators in the dark. Non-nocturnal insects - that do not need to fear nocturnal predators - are often found to lack these tympanal ears.
Animals undergo divergent evolution for a number of reasons. Predators or their absence, changes in the environment, and the time at which certain animals are most active are chief among them.
A lack of predators – predatory birds and mammals - for cliff-side nest residing kittiwake caused that particular group of kittiwake to lose their ancestral mobbing behavior that had been exhibited up until that point for protecting young. The mobbing behavior normally displayed by the kittiwake is lost when the kittiwake take residence in this area with little threat from predators towards their young. The mobbing behavior was originally developed to protect ground-level nests containing young from various predators such as reptiles, mammals and other birds.
The cliff-side nesting area itself was similarly responsible for the kittiwakes losing their mobbing mentality – predatory mammals small enough to fit on the cliff edges along with the kittiwakes and their offspring would not be able to make the climb up while predatory birds would not be able to maneuver near the cliff face while also being afflicted by the weather conditions of the area.
Divergent evolution is always coupled with convergent evolution, as they are both similar and different in various facets such as whether something evolves, what evolves, and why it evolves. It is instructive to compare divergent evolution with both convergent and parallel evolution.
Convergent evolution is defined as a similar trait evolution that occurs in two otherwise different species of animal as a result of those two species living in similar environments with similar environmental pressures like predators and food supply. It differs from divergent evolution in that the species involved are different while the traits they obtain do not differ from each other. An example of convergent evolution is the development of horns in various species for sparring over mates, resources, and territory 
Parallel evolution is the development of a similar trait in species descending from the same ancestor. It is similar to divergent evolution in that the species descend from the same ancestor, but it differs in that the trait is the same while in divergent evolution the trait is not. An example of parallel evolution are certain arboreal frog species, 'flying' frogs, in both Old World families and New World families having developed the ability of gliding flight. They have "enlarged hands and feet, full webbing between all fingers and toes, lateral skin flaps on the arms and legs, and reduced weight per snout-vent length".
One of the most famous examples of divergent evolution is the case of Darwin's Finches. During Darwin’s travels to the Galápagos Islands he discovered several different species of finch that shared a common ancestor. They lived on varying diets and had beaks that differed in shape and size reflecting their diet. The change in beak shape and size was believed to be a result of the lengths the birds had to go to in order to support their change in diet. Some Galapagos finches have beaks that are larger and more powerful to crack nuts with. A different type allows the bird to use cactus spines to spear insects in the bark of trees.
Another good example of divergent evolution is the origin of the domestic dog and the modern wolf. Dogs and wolves both diverged from a common ancestor. To further support divergent evolution of dogs and wolves, genomic research was conducted to compare mitochondrial DNA to indicate the presence of shared ancestry. Taking 162 wolves from various parts of the world as well as 140 dogs of 60 different breeds, it is found that dogs and wolves have shared ancestry by how similar their DNA sequences are. Comparison of the physical characteristics reveal that dogs and wolves have similar body shape, skull size, and limb formation, further supporting their close genetic makeup and thus shared ancestry. An example of this would be how physically and behaviorally similar malamutes and huskies are to wolves. Huskies and malamutes have very similar body size and skull shape. Huskies and wolves share similar coat patterns as well as tolerance to cold. In the hypothetical situations, mutations and breeding events were simulated to show the progression of the wolf behavior over ten generations. The results concluded that even though the last generation of the wolves were more docile and less aggressive, the temperament of the wolves fluctuated greatly from one generation to the next.
In enzymology, a 2-dehydro-3-deoxy-phosphogluconate aldolase (EC 18.104.22.168), commonly known as KDPG aldolase, is an enzyme that catalyzes the chemical reaction
Hence, this enzyme primarily has one substrate, 2-dehydro-3-deoxy-D-gluconate 6-phosphate, and two products, pyruvate and D-glyceraldehyde 3-phosphate.
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. It is used in the Entner–Doudoroff pathway in prokaryotes, feeding into glycolysis. 2-dehydro-3-deoxy-phosphogluconate aldolase is one of the two enzymes distinguishing this pathway from the more commonly known Embden–Meyerhof–Parnas pathway. This enzyme also participates in following 3 metabolic pathways: pentose phosphate pathway, pentose and glucuronate interconversions, and arginine and proline metabolism.
In addition to the cleavage of 2-dehydro-3-deoxy-D-gluconate 6-phosphate, it is also found to naturally catalyze Schiff base formation between a lysine E-amino acid group and carbonyl compounds, decarboxylation of oxaloacetate, and exchange of solvent protons with the methyl hydrogen atoms of pyruvate.Catalytic triad
A catalytic triad is a set of three coordinated amino acids that can be found in the active site of some enzymes. Catalytic triads are most commonly found in hydrolase and transferase enzymes (e.g. proteases, amidases, esterases, acylases, lipases and β-lactamases). An Acid-Base-Nucleophile triad is a common motif for generating a nucleophilic residue for covalent catalysis. The residues form a charge-relay network to polarise and activate the nucleophile, which attacks the substrate, forming a covalent intermediate which is then hydrolysed to release the product and regenerate free enzyme. The nucleophile is most commonly a serine or cysteine amino acid, but occasionally threonine or even selenocysteine. The 3D structure of the enzyme brings together the triad residues in a precise orientation, even though they may be far apart in the sequence (primary structure).As well as divergent evolution of function (and even the triad's nucleophile), catalytic triads show some of the best examples of convergent evolution. Chemical constraints on catalysis have led to the same catalytic solution independently evolving in at least 23 separate superfamilies. Their mechanism of action is consequently one of the best studied in biochemistry.Chronospecies
A chronospecies is a species derived from a sequential development pattern which involves continual and uniform changes from an extinct ancestral form on an evolutionary scale. This sequence of alterations eventually produces a population which is physically, morphologically, and/or genetically distinct from the original ancestors. Throughout this change, there is only one species in the lineage at any point in time, as opposed to cases where divergent evolution produces contemporary species with a common ancestor. The related term paleospecies (or palaeospecies) indicates an extinct species only identified with fossil material. This identification relies on distinct similarities between the earlier fossil specimens and some proposed descendant, although the exact relationship to the later species is not always defined. In particular, the range of variation within all the early fossil specimens does not exceed the observed range which exists in the later species.
A paleosubspecies (or palaeosubspecies) identifies an extinct subspecies which evolved into the currently existing form. This connection with relatively recent variations, usually from the Late Pleistocene, often relies on the additional information available in subfossil material. Most of the current species have changed in size adapting to the climatic changes during the last ice age (see Bergmann's Rule).
The further identification of fossil specimens as part of a "chronospecies" relies on additional similarities which more strongly indicate a specific relationship with a known species. For example, relatively recent specimens – hundreds of thousands to a few million years old – with consistent variations (e.g. always smaller but with the same proportions) as a living species might represent the final step in a chronospecies. This possible identification of the immediate ancestor of the living taxon may also rely on stratigraphic information to establish the age of the specimens.
The concept of chronospecies is related to the phyletic gradualism model of evolution, and also relies on an extensive fossil record, since morphological changes accumulate over time and two very different organisms could be connected by a series of intermediaries.Convergent evolution
Convergent evolution is the independent evolution of similar features in species of different lineages. Convergent evolution creates analogous structures that have similar form or function but were not present in the last common ancestor of those groups. The cladistic term for the same phenomenon is homoplasy. The recurrent evolution of flight is a classic example, as flying insects, birds, pterosaurs, and bats have independently evolved the useful capacity of flight. Functionally similar features that have arisen through convergent evolution are analogous, whereas homologous structures or traits have a common origin but can have dissimilar functions. Bird, bat, and pterosaur wings are analogous structures, but their forelimbs are homologous, sharing an ancestral state despite serving different functions.
The opposite of convergence is divergent evolution, where related species evolve different traits. Convergent evolution is similar to parallel evolution, which occurs when two independent species evolve in the same direction and thus independently acquire similar characteristics; for instance, gliding frogs have evolved in parallel from multiple types of tree frog.
Many instances of convergent evolution are known in plants, including the repeated development of C4 photosynthesis, seed dispersal by fleshy fruits adapted to be eaten by animals, and carnivory.Euperipatoides kanangrensis
Euperipatoides kanangrensis is a species of velvet worm of the Peripatopsidae family, described in 1996 from specimens collected in Kanangra-Boyd National Park, New South Wales. It is endemic to Australia. The embryonic development of Euperipatoides kanangrensis has been described. This species is used as model organism for the last common ancestor of the Panarthropoda. It resembles fossil Cambrian lobopodians.Homology (biology)
In biology, homology is the existence of shared ancestry between a pair of structures, or genes, in different taxa. A common example of homologous structures is the forelimbs of vertebrates, where the wings of bats, the arms of primates, the front flippers of whales and the forelegs of dogs and horses are all derived from the same ancestral tetrapod structure. Evolutionary biology explains homologous structures adapted to different purposes as the result of descent with modification from a common ancestor. The term was first applied to biology in a non-evolutionary context by the anatomist Richard Owen in 1843. Homology was later explained by Charles Darwin's theory of evolution in 1859, but had been observed before this, from Aristotle onwards, and it was explicitly analysed by Pierre Belon in 1555.
In developmental biology, organs that developed in the embryo in the same manner and from similar origins, such as from matching primordia in successive segments of the same animal, are serially homologous. Examples include the legs of a centipede, the maxillary palp and labial palp of an insect, and the spinous processes of successive vertebrae in a vertebral column. Male and female reproductive organs are homologous if they develop from the same embryonic tissue, as do the ovaries and testicles of mammals including humans.
Sequence homology between protein or DNA sequences is similarly defined in terms of shared ancestry. Two segments of DNA can have shared ancestry because of either a speciation event (orthologs) or a duplication event (paralogs). Homology among proteins or DNA is inferred from their sequence similarity. Significant similarity is strong evidence that two sequences are related by divergent evolution from a common ancestor. Alignments of multiple sequences are used to discover the homologous regions.
Homology remains controversial in animal behaviour, but there is suggestive evidence that, for example, dominance hierarchies are homologous across the primates.J. T. Gulick
John Thomas Gulick (March 13, 1832 – April 14, 1923) was an American missionary and naturalist from Hawaii. He performed some of the first modern evolutionary studies, starting with a collection of Hawaiian land snails.Oaxaca Valley
The Central Valleys (Spanish: Valles Centrales) of Oaxaca, also simply known as the Oaxaca Valley, is a geographic region located within the modern-day state of Oaxaca in southern Mexico. In an administrative context, it has been defined as comprising the districts of Etla, Centro, Zaachila, Zimatlán, Ocotlán, Tlacolula and Ejutla. The valley, which is located within the Sierra Madre Mountains, is shaped like a distorted and almost upside-down “Y,” with each of its arms bearing specific names: the northwestern Etla arm, the central southern Valle Grande, and the Tlacolula arm to the east. The Oaxaca Valley was home to the Zapotec civilization, one of the earliest complex societies in Mesoamerica, and the later Mixtec culture. A number of important and well-known archaeological sites are found in the Oaxaca Valley, including Monte Alban, Mitla, San José Mogote and Yagul. Today, the capital of the state, Oaxaca City, is located in the central portion of the valley.Outline of genetics
The following outline is provided as an overview of and topical guide to genetics:
Genetics – science of genes, heredity, and variation in living organisms. Genetics deals with the molecular structure and function of genes, and gene behavior in context of a cell or organism (e.g. dominance and epigenetics), patterns of inheritance from parent to offspring, and gene distribution, variation and change in populations.PA clan of proteases
The PA clan (Proteases of mixed nucleophile, superfamily A) is the largest group of proteases with common ancestry as identified by structural homology. Members have a chymotrypsin-like fold and similar proteolysis mechanisms but can have identity of <10%. The clan contains both cysteine and serine proteases (different nucleophiles). PA clan proteases can be found in plants, animals, fungi, eubacteria, archaea and viruses.The common use of the catalytic triad for hydrolysis by multiple clans of proteases, including the PA clan, represents an example of convergent evolution. The differences in the catalytic triad within the PA clan is also an example of divergent evolution of active sites in enzymes.Paradox of the plankton
In aquatic biology, the paradox of the plankton describes the situation in which a limited range of resources supports an unexpectedly wide range of plankton species, apparently flouting the competitive exclusion principle which holds that when two species compete for the same resource, one will be driven to extinction.Parrotbill
The parrotbills are a group of peculiar birds native to East and Southeast Asia, though feral populations exist elsewhere. They are generally small, long-tailed birds which inhabit reedbeds and similar habitat. They feed mainly on seeds, e.g. of grasses, to which their bill, as the name implies, is well-adapted. Living in tropical to southern temperate climates, they are usually non-migratory.
The bearded reedling or "bearded tit", a Eurasian species long placed here, is more insectivorous by comparison, especially in summer. It also strikingly differs in morphology, and was time and again placed in a monotypic family Panuridae. DNA sequence data supports this.
As names like "bearded tit" imply, their general habitus and acrobatic habits resemble birds like the long-tailed tits. Together with these and others they were at some time placed in the titmouse family Paridae. Later studies found no justification to presume a close relationship between all these birds, and consequently the parrotbills and bearded reedling were removed from the tits and chickadees and placed into a distinct family, Paradoxornithidae. As names like Paradoxornis paradoxus - "puzzling, paradox bird" - suggest, their true relationships were very unclear, although by the latter 20th century they were generally seen as close to Timaliidae ("Old World babblers") and Sylviidae ("Old World warblers").
Since 1990 (Sibley & Ahlquist 1990), molecular data has been added to aid the efforts of discovering the parrotbills' true relationships. As Paradoxornis species are generally elusive and in many cases little-known birds, usually specimens of the bearded reedling which are far more easy to procure were used for the analyses. Often, the entire group was entirely left out of analyses, being small and seemingly insignificant in the large pattern of bird evolution (e.g. Barker et al. 2002, 2004). The bearded reedling tended to appear close to larks in phylogenies based on e.g. DNA-DNA hybridization (Sibley & Ahlquist 1990), or on mtDNA cytochrome b and nDNA c-myc exon 3, RAG-1 and myoglobin intron 2 sequence data (Ericson & Johansson 2003). Placement in a superfamily Sylvioidea which contained birds such as Sylviidae, Timaliidae and long-tailed tits - but not Paridae - was confirmed.
Cibois (2003a) analyzed mtDNA cytochrome b and 12S/16S rRNA sequences of some Sylvioidea, among them several species of Paradoxornis but not the bearded reedling. These formed a robust clade closer to the Sylvia typical warblers and some presumed "Old World babblers" such as Chrysomma sinense than to other birds. The puzzle was finally resolved by Alström et al. (2006), who studied mtDNA cytochrome b and nDNA myoglobin intron 2 sequences of a wider range of Sylvioidea: The bearded reedling was not a parrotbill at all, but forms a distinct lineage on its own, the relationships of which are not entirely resolved at present. The parrotbills' presence in the clade containing Sylvia, on the other hand, necessitates that the Paradoxornithidae are placed in synonymy of the Sylviidae. Cibois (2003b) even suggested that these themselves were to be merged with the remaining Timaliidae and the latter name to be adopted. This has hitherto not been followed and researchers remain equivocal as many taxa in Sylviidae and Timaliidae remain to be tested for their relationships. In any case, it is most likely that the typical warbler-parrotbill group is monophyletic and therefore agrees with the modern requirements for a taxon. Hence, whether to keep or to synonymize it is entirely a matter of philosophy, as the scientific facts would agree with either approach.
The interesting conclusion from an evolutionary point of view is that the morphologically both internally homogenous and compared to each other highly dissimilar typical warblers and parrotbills form the two extremes in the divergent evolution of the Sylviidae. This is underscored by looking at the closest living relatives of the parrotbills in the rearranged Sylviidae: The genus Chrysomma are non-specialized species altogether intermediate in habitus, habitat and habits between the typical warblers and the parrotbills. Presumably, the ancestral sylviids looked much like these birds. How dramatic the evolutionary changes wrought upon the parrotbills in their adaptation to feeding on grass caryopses and similar seeds were can be seen by comparing them with the typical fulvettas, which were formerly considered Timaliidae and united with the alcippes (Pasquet 2006). These look somewhat like drab fairy-wrens and have none of the parrotbills' adaptations to food and habitat. Yet it appears that the typical fulvettas' and parrotbills' common ancestor evolved into at least two parrotbill lineages independently (Cibois 2003a) & (Yeung et al. 2006). Only the wrentit, the only American sylviid, resembles the parrotbills much in habitus, though not in color pattern, and of course, as an insectivore, neither in bill shape.Patricia Babbitt
Patricia Clement Babbitt is a Professor and Principal Investigator (PI) in the School of Pharmacy at the University of California, San Francisco (UCSF). She was elected a fellow of the International Society for Computational Biology (ISCB) in 2018 for outstanding contributions to the fields of computational biology and bioinformatics. She is the Director of the UCSF Biological and Medical Informatics Graduate Program and serves on Advisory Boards for the UniProt Database, the Metacyc Metabolic Pathway Database, the HHMI Scientific Review Board, and as a Deputy Editor for PLoS Computational Biology.Pedodiversity
Pedodiversity is the variation of soil properties (usually characterised by soil classes) within an area.
Pedodiversity studies were first started by analyzing soil series–area relationships (Beckett and Bie, 1978). According to Guo et al. (2003) the term pedodiversity was developed by McBratney (1992) who discussed landscape preservation strategies based on pedodiversity. Recently, examinations of pedodiversity using indices commonly used to characterize bio-diversity have been made Ibáñez et al. (1995) first introduced ecological diversity indices as measures of pedodiversity. They include
Species richness, abundance, and Shannon index. Richness is the number of different soil types, which is the number of soil classes at particular level in a taxonomic system. Abundance is defined as the distribution of the number of soil individuals.
Just as biologists and ecologists talk about biodiversity, geologists on geodiversity, soil scientists can talk about pedodiversity. Pedodiversity has some overlap with biodiversity as soil contains organisms. Pedodiversity is a measure of soil variation, and pedodiversity is a function of soil formation.
Pedodiversity can be thought as a way to preserve, or even reconstruct, the soil cover. Just as biologists argue that organisms need to be maintained, soil scientists can argue that preserving soil will maintain organisms as well as other unique soil materials equally crucial in insuring our future wellbeing. In areas which have been degraded it will become important to reconstruct the variation. A quantitative knowledge of natural pedodiversity will ease the task of the person who attempts to rebuild quasi-natural soil systems.
Soil scientists have pragmatically adapted the concept of biodiversity and used diversity index such as Shannon index using taxa from well-accepted international soil classification systems.
Jonathan Phillips showed that in eastern North Carolina intrinsic variability within homogeneous landscape units is more important in determining the total pedodiversity of the study area than is the extrinsic variability associated with measurable differences in topography, parent material, and vegetation/land use.
In another study, they found that soils in Ouachita Mountains of Arkansas vary considerably within small more-or-less homogeneous areas, and richness–area analysis shows that the overall pattern of pedodiversity is dominated by local, intrinsic (within-plot) variability as opposed to between-plot variability. This is consistent with variation controlled mainly by individual trees and local lithological variations. Given the criteria used to distinguish among soil types, biomechanical as opposed to chemical and hydrological effects of trees are indicated. Results also suggest divergent evolution whereby the pedologic effects of trees are large and long-lived relative to the magnitude of the initial effects and lifespan of the plants.Guo et al. recently explored quantitative aspects of pedodiversity for the USA based on the State Soil Geographic database (STATSGO). They found that the West USDA-NRCS geographical region has the highest soil taxa richness, followed by the Northern Plains. The South Central region has the highest taxa evenness, while taxa evenness in the West region is the lowest. The West or the South Central regions have the highest overall soil diversity in the four highest taxonomic categories, while the West or Northern Plains regions have the highest diversity in the two lowest taxonomic levels. The high diversity index in the West region results from high taxa richness while the high diversity index in the South Central region results from an evenness of taxa. As the taxonomic level decreases, the pattern of taxa abundance approaches a lognormal distribution. One of the key findings of this research is that at lower levels of soil taxonomic divisions (especially the series level), soil taxa increase continuously with increasing area, indicating considerable soil endemism in the USA (and likely around the world), a key consideration in conservation and preservation
However conventional diversity measures, only measure the relative abundance of soil classes, and there is no information on the taxonomic similarity or differences between soil classes. New measures of pedodiversity, such as the mean soil taxonomic distance, which considers both information on the relative abundance and the taxonomic differences between soil classes have been developed and shown to be a better measure.
The diversity of soils and landforms has hardly received any attention although their spatial and temporal variation may produce important quantitative and qualitative changes in the landscape. It is only in the last few years that the term diversity has also caught the attention of scientists working on soils and other fields within the earth sciences which creates a forum and research projects on geodiversity. Measurements of diversity were introduced to pedology few years ago. The concept of pedodiversity is now widely accepted within the soil science community. Pedodiversity, as well as biodiversity, may be considered as a framework to analyze spatial patterns, being recognized as a novel pedometric tool. Pedodiversity is a measure of soil variation and also a function of soil formation and development or evolution. Pedodiversity is introduced to pedology to analyze soil spatial patterns, soil geography, and test the pedogenetic theories. Thus, pedodiversity is not only concerned with analysis of the pedotaxa number in a given area or region, but it should tackle also with the pedological structures, spatial pedotaxa and soilscapes structure.Periplaneta japanna
Periplaneta japanna is a subtropical field-dwelling cockroach endemic to southern Japan. The Japanese common name, ウルシゴキブリ, means urushi cockroach, or lacquer tree cockroach.
Nymphs and adults are a dark black, and typically live under stones and pieces of wood. Their ability to bore or live in rotting wood enables their spread via ocean currents.The species is found on several Japanese islands, distributed continuously from Japan’s southwestern Ryukyu Islands chain to the south of Kiyushu Island, and on Hachijō-jima Island.Nymph specimens from Hachijō-jima Island and Naha, Okinawa responded to photoperiodic stimulii quite differently during laboratory-induced diapause tests. This “might be regarded as the result of divergent evolution” between the parapatric populations.Product (chemistry)
Products are the species formed from chemical reactions. During a chemical reaction reactants are transformed into products after passing through a high energy transition state. This process results in the consumption of the reactants. It can be a spontaneous reaction or mediated by catalysts which lower the energy of the transition state, and by solvents which provide the chemical environment necessary for the reaction to take place. When represented in chemical equations products are by convention drawn on the right-hand side, even in the case of reversible reactions. The properties of products such as their energies help determine several characteristics of a chemical reaction such as whether the reaction is exergonic or endergonic. Additionally the properties of a product can make it easier to extract and purify following a chemical reaction, especially if the product has a different state of matter than the reactants. Reactants are molecular materials used to create chemical reactions. The atoms aren't created or destroyed. The materials are reactive and reactants are rearranging during a chemical reaction. Here is an example of reactants: CH4 + O2. A non-example is CO2 + H2O or "energy".
Much of chemistry research is focused on the synthesis and characterization of beneficial products, as well as the detection and removal of undesirable products. Synthetic chemists can be subdivided into research chemists who design new chemicals and pioneer new methods for synthesizing chemicals, as well as process chemists who scale up chemical production and make it safer, more environmentally sustainable, and more efficient. Other fields include natural product chemists who isolate products created by living organisms and then characterize and study these products.Protein superfamily
A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology). Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if no sequence similarity is evident. Sequence homology can then be deduced even if not apparent (due to low sequence similarity). Superfamilies typically contain several protein families which show sequence similarity within each family. The term protein clan is commonly used for protease and glycosyl hydrolases superfamilies based on the MEROPS and CAZy classification systems.Short interspersed nuclear element
Short interspersed nuclear elements (SINEs) are non-autonomous, non-coding transposable elements (TEs) that are about 100 to 700 base pairs in length. They are a class of retrotransposons, DNA elements that amplify themselves throughout eukaryotic genomes, often through RNA intermediates.
The internal regions of SINEs originate from tRNA and remain highly conserved, suggesting positive pressure to preserve structure and function of SINEs. While SINEs are present in many species of vertebrates and invertebrates, SINEs are often lineage specific, making them useful markers of divergent evolution between species. Copy number variation and mutations in the SINE sequence make it possible to construct phylogenies based on differences in SINEs between species. SINEs are also implicated in certain types of genetic disease in humans and other eukaryotes.
In essence, short interspersed nuclear elements are genetic parasites which have evolved very early in the history of eukaryotes to utilize protein machinery within the organism as well as to co-opt the machinery from similarly parasitic genomic elements. The simplicity of these elements make them incredibly successful at persisting and amplifying (through retrotransposition) within the genomes of eukaryotes. These “parasites” which have become ubiquitous in genomes can be very deleterious to organisms as discussed below. However, eukaryotes have been able to integrate short-interspersed nuclear elements into different signaling, metabolic and regulatory pathways and have become a great source of genetic variability. They seem to play a particularly important role in the regulation of gene expression and the creation of RNA genes as discussed in Sines and Gene-Regulation. This regulation extends to chromatin re-organization and the regulation of genomic architecture; furthermore, the different lineages, mutations, and activity among eukaryotes make short-interspersed nuclear elements an incredible useful tool in phylogenetic analysis.Vatteluttu script
The Vaṭṭeḻuttu, also spelled Vattezhutthu (literally "Round Script", Tamil: வட்டெழுத்து, vaṭṭeḻuttu, Tamil pronunciation: [ʋəʈːeɻʉt̪ːʉ]; Malayalam: വട്ടെഴുത്ത് vaṭṭeḻuttŭ) was an abugida writing system in southern India and Sri Lanka in the later half of the first millennium AD. Vatteluttu was the common script for writing various forms of the Tamil language in the region of the Pandyas and Cheras until the 9th century, after which it came to be replaced by the present-day Tamil script everywhere except in Kerala.It is known that the Tamil Script became current in the Chola and Pandya kingdoms by the 10th century. Southern Grantha (Pallava Grantha) script - formerly used writing Sanskrit in south India - evolved into modern Malayalam script in Kerala.Derived from the Tamil-Brahmi script, the Vatteluttu was developed in southern India and was extensively used for writing various forms of Tamil and Malayalam. The early cave inscriptions discovered from southern India, in Tamil-Brahmi script (Damili script), have supplied some of the connecting links between Brahmi script and Vatteluttu.Vatteluttu is attested from the 6th century AD.Vatteluttu was adopted by the Kodungallur Cheras (from 9th century) and their successor-states in Kerala. Kodungallur Chera epigraphs in Old Malayalam are composed mostly in Vatteluttu. After the Kodungallur Chera period (12th century) the Vatteluttu went on evolving and gradually developed into "Kolezhuttu" in Kerala. Use of Vatteluttu - albeit in a decadent form - continued among certain classes in Kerala, especially Muslims and Christians up to the 19th century Inhabitants of Kuccaveli, located north of Trincomalee, used the Vatteluttu between the 5th and 8th centuries AD, attested to on rock inscriptions found there.
|Patterns of evolution|